Rethinking FOXP2

Earlier studies have indicated that a gene called FOXP2, possibly involved in brain development, is extremely conserved in vertebrates, except for two notable mutations in humans. This finding suggested that this gene may in some way be involved in the evolution of language, and was thus dubbed by the popular press "the language" gene. See, for instance, this and this for some recent research on the geographic variation of this gene (and related genes) and its relation to types of languages humans use (e.g., tonal vs. non-tonal). Furthermore, a mutation in this gene in humans results in inability to form grammatically correct sentences.

This week, a new study shows that this gene is highly diverse in one group of mammals - the bats:

A new study, undertaken by a joint of team of British and Chinese scientists, has found that this gene shows unparalleled variation in echolocating bats. The results, appearing in a study published in the online, open-access journal PLoS ONE on September 19, report that FOXP2 sequence differences among bat lineages correspond well to contrasting forms of echolocation.

As Anne-Marie notes, this puts a monkey-wrench in the idea that FOXP2 is exclusively involved in language, but may be involved in vocalizations in general:

Said gene might have a new function (sensorimotor) besides the one originally attributed to it (verbal language).

Jonah Lehrer notes that the same mutation that in humans eliminates ability to use or comprehend correct grammar is also found in songbirds and the gene is expressed at high levels during the periods of intense song-learning. The story is obviously getting very interesting - does this gene have something to do with vocalizations? Or with communication? Or something totally third?

Looking forward to further responses by other blogs, hopefully Afarensis, John Hawks and Language Log?

The article on FOXP2 in bats was published yesterday on PLoS ONE so you can access it for free, read, donwload, use, reuse, rate, annotate and comment on.

This blog has (finally) gone to SEED

So, the day has finally arrived - the Big Move to SEED scienceblogs. Go check out the brand new front page and all the old and new bloggers there.

My new blog, a fusion of all three of my blogs, will be a new brand, with a new name - A Blog Around The Clock, reflecting my age and musical taste, my usual blogging frequency and the area of my scientific expertise, all in one title.

The Banner was designed by Carel Pieter Brest Van Kempen who also runs a delightful science/art blog Rigor Vitae.

The new URL is http://scienceblogs.com/clock/, the new Atom feed is http://scienceblogs.com/clock/atom.xml and the new RSS feed is http://scienceblogs.com/clock/index.xml.

Please change your bookmarks, blogrolls and newsfeeds to reflect this move.

As I said before, Circadiana and The Magic School Bus will be closed (but not deleted), while Science And Politics will slow down and will re-focus on local North Carolina topics, including local politics (which includes following the career of John Edwards), and perhaps an occasional post for my readers from the Balkans. If you are still interested in those topics, you are welcome to retain the bookmarks, blogrolls and newsfeeds for Science And Politics as well, but I will not be insulted if you do not, as my main blogging effort will be over there, on my new SB blog.

I encourage you to go and check all 24 newbies over on SEED - all wonderful bloggers you should read if you are interested in science. Let me introduce my new fraternity-mates to you:

Carl Zimmer, the NYTimes science/evolution reporter, is moving The Loom from here to here.

Matt Nisbett, an expert on political communication and writer of a monthly column for the Skeptical Inquirer Online is moving his blog Framing-Science from here to here.

My fellow North Carolinian, medblogger Abel PharmBoy, is moving Terra Sigillata from here to here.

James Hrynyshyn, another fellow North Carolinian, is moving Island Of Doubt from here to here.

My favourite cognitive psychology blogger Chris is moving Mixing Memory from here to here.

Philosopher of biology John Wilkins is moving Evolving Thoughts from here to here.

Mike The Mad Biologist is moving from here to here.

I thought that one of my favourite science bloggers George Wilkinson has quit blogging, but no, he is also moving Keat's Telescope from here to here.

Reveres, experts on Avian Flu, are moving Effect Measure from here to here.

Karmen is moving her beautiful Chaotic Utopia from here to here.

Sandra Porter is moving Discovering Biology In A Digital World from here to here.

Nick Anthis is moving The Scientific Activist from here to here.

Joseph is moving Corpus Callosum from here to here.

Jake Young, another one of several neuroscientists joining the team, is moving Pure Pedantry from here to here.

Shelley Batts, another neuroscientist, is moving Retrospectacle from here to here.

Evil Monkey is moving Neurotopia from here to here.

Mike Dunford is moving The Questionable Authority from here to here.

Mark Chu-Carroll is moving Good Math, Bad Math from here to here.

David Ng and Benjamin Cohen are moving from Science Creative Quarterly and Annals of Science to World's Fair.

The Cheerful Oncologist is moving from here to here.

Dr.Charles is moving the eponimous Examining Room from here to here.

Dr. X is moving Chemblog from here to here.

The rowdy bonobos from Dr. Joan Bushwell's Chimpanzee Refuge are moving from here to here.

Steinn, an astrophysicist, is moving Dynamics Of Cats from here to here.

Finally, Jonah Lerer is a SEED staffer, starting his own blog called The Frontal Cortex.

There were few surprises for me on this list. Two good blogfriends of mine (Revere and Mike the Mad Biologist) managed to keep me in the dark about their move until two days ago. On the other hand, two bloggers I thought were going to accept the invitation, are not on the list (yet?). Almost all of the others I knew about.

The SEED overlords intend to add more bloggers before the end of the year so keep an eye on SEED - that is where the SciBlogging action is going to be.

Technorati Tag: teaching-carnival

EduCarnivals

Carnival of Education #70 is up on The Education Wonks.

Carnival of Homeschooling #23 (the marine life edition) is up on PalmTree Pundit

Technorati Tag: teaching-carnival

Current Biological Diversity

BIO101 - Bora Zivkovic - Lecture 4, Part 3

In the first two parts of this lecture we tackled the Origin of Life and Biological Diversity and the mechanisms of the Evolution of Biological Diversity. Now, we'll take a look at what those mechanisms have produced so far - the current state of diversity on our planet.

The Three Domains

The organisms living on Earth today are broadly divided into three large domains: Bacteria, Archaea and Eukarya (Protista, Plants, Fungi and Animals). Our understanding of the relationship between the three domains is undergoing big changes right now. The old divisions have been based on morphological and biochemical differences, but recent genetic data are forcing us to rethink and revise the way we think about the three Domains.
It was thought before that Bacteria arose first, that Archaea evolved from a branch off of bacterial line, while the first Eukarya (protists) evolved through the process of endosymbiosis: small bacteria and archaea finding permanent homes within the cell of larger bacteria and forming organelles. It was thought that bacteria were always simple, that Archaea are somewhet more complex, and that Eukarya are the most complex.

Neither Bacteria nor Archaea possess any organelles or subcellular compartments. The chemistry of cell walls is strikingly different between the two groups. The genes of Archaea, like Eukaryia, have introns. Until recently, it was thought that bacterial genes have no introns, however remnants of bacterial introns have been recently discovered, suggesting that Bacteria used to have introns in the past but have secondarily lost them - becoming simpler over the 3.6 billions of evolution. The enzymes involved in transcription of DNA in Archaea are much more similar to the equivalent enzymes in Eukarya than those in Bacteria.

Molecular data, as well as what we know from evolutionary theory how population size affects the strength of natural selection, a new picture has emerged. The earliest Bacteria were simple, hugging the Left Wall of Complexity. While their population sizes were still small, Bacteria evolved greater and greater complexity, leaving the left wall somewhat, evolving more complex genomes, more complex mechanisms of DNA transcription (including introns), and perhaps even some organelles. Likewise, the Archaea split off of Bacteria (or perhaps they even appeared first) and evolved much greater complexity in parallel with the Bacteria. Eukarya also split off of Bacterial tree early on and evolved its own complexity. Thus there were three groups simultaneously evolving greater and greater complexity.
Then, Bacteria and Archaea grew up in population sizes. Instead of small pockets somewhere in the ocean, now bacteria and archaea occupied every spot on Earth in huge numbers. Large population size makes natural selection very strong. Greater complexity is not fit, thus it is selected against. Thus, the originally complex bacteria and archaea became simpler over time - they turned into lean, mean evolving machines that we see today - the dominant life forms on our planet throughout its history. They lost introns, they lost organelles, and lost many complicated enzymatic pathways, each species reducing its genome and strongly specializing for one particular niche.

On the other hand, Eukarya did not grow in numbers as much. The population sizes remained small, thus the selection against complexity was relaxed - the eukaryotes were free to evolve away from the Left Wall. They increased in complexity, engulfing other microorganisms that later became mitochondria and chloroplasts.

Thus, though we, for egocentric reasons, like to think of greater complexity as being better than being simple, the Big Story of the evolution of life on Earth is that of simplification. Natural selection harshly eliminated organisms that experimented with greater complexity - the Eukarya being the exception: an evolutionary accident that happened due to their existence in small, isolated populations in which selection against complexity is relaxed.

Bacteria

Bacteria are small, single-celled organisms with no internal structures or organelles. Bacteria may have cell walls on the surface of their cell membranes, and may have evolved cilia or flagella for locomotion. The DNA is usually organized in a single circular chromosome. Some bacteria congregate into collonies or chains, while in other species each cell lives on its own.

In the laboratory, bacteria can be easily separated into two major groups by the way their cell walls get stained by a particular stain into Gram positive (purple stain) and Gram negative (red stain) bacteria. By shape, bacteria are divided into cocci (spherical cells), bacilli (rod-like shapes) and spirilli (thread-like or worm-like cells).

Bacteria are capable of sensing their environment and responding to it - i.e., they are capable of exhibiting behavior. Bacteria are also capable of communicating with each other - for instance, they can sense how many of them are present in a particular place and they can all change their behavior once the poulation size reaches a sertain treshold - this kind of sensing is called quorum sensing.

Many bacteria are serious pathogens of plants and animals (including humans). Others are important decomposers of dead plants and animals, thus playing important roles in the ecology of the planet. Yet others are symbionts - living in mutualistic relationships with other organisms, e.g., with plants and animals.

The inside of out digestive tract provides a home for numerous microorganisms. The best way to think about out "intestinal flora" is in terms of an ecosystem. We acquire it at the moment of birth and build it up with the bacteria we get from the environment - mostly from our parents. The bacterial populations in the intestine go through stages of building an ecosystem, similarly to the secondary succession. If, due to disease or due to use of potent antibiotics, the balance of the ecosystem is disrupted, it may recover through phases akin to primary succession.

Experiments with completely internally sterile animals (mostly pigs and rabbits) demonstrated that we rely on our intestinal bacteria for some of our normal functions, e.g., digestion of some food components, including vitamins. In many ways, after millions of years of evolution, our internal bacteria have become an essential part of who we are, and there is now a push for sequencing the complete genome of our becterial flora and to include that information in the Human Genome. The composition of the bacterial ecosystem in out guts can affect the way we respond to disease, or even if we are going to get fat or not, thus there is much recent research on individual variation of the intestinal flora between human individuals, so-called "poo print" (yes, scientists do have a sense of humor).

Archaea

Archaea may have been the first life forms on the Earth. Today, they tend to occupy niches that no other organisms can. Thus, they are found living inside the rocks miles under the surface, they are found in extremely cold and extremely hot environments, in very salty, very acidic and very alkaline envrionments as well. The hot water of the Old Faithful geiser in Yellowstone national park are inhabited by a species of Archaea. They are difficult to study as they die in normal conditions in the laboratory - room temperature, neutral pH etc.

Deinococcus radiodurans is one famous Archean. It thrives inside nuclear reactors. Of course, our reactors are a very recent innovations, so the scientists were puzzled for a long time as to what natural environment selected these organisms to be able to survive in such a harsh environment. It turns out that dehydration (drying-out) has the same effects on the DNA as does radioactivity - fragmenting and tearing-up of pieces of the DNA molecule. Deinococcus evolved especially fast and accurate mechanisms for DNA repair. Bioengineering projects are underway to genetically engineer these Archaea in such a way that they can be used to clean up radioactive spills and digest nuclear waste.

Though some Archaea have been found to live inside our bodies, not a single one has, so far, been indentified as a pathogen. Only very recently (i.e., last few weeks) has it been shown that one archaean does have an effect on our health - not as a pathogen but as an enabler. It can migrate into roots of our teeth and set up colonies there. It then changes the environment in the tooth in such a way that it becomes conducive to the immigration and reproduction of a pathogenic bacterium than can then attack the tooth.

Protista

Protists are an artificial group of organisms - every eukaryote that cannot be classified as a plant, a fungus or an animal is placed in this category. Thus, the number of species of protists is very large and the diversity of shapes, sizes and types of metabolism is enormous.

Some protists are microscopic unicellular organisms, like the Silver Slipper (Paramecium), while others are multicellular and quite large (e.g, sea kelp). Some protists, e.g., cellular slime molds, have a single-celled and a multi-celled phase of their life-cycle.

Even some of the unicellular protists can be quite large - an Acetabularia ('mermaid's wineglass', see picture) cell is about 5 cm long, thus perfectly visible to the human eye. Most protists reproduce regularly by asexual processes, e.g., fission or budding, utilizing sexual reproduction (e.g., conjugation, which is gene-swapping) only in times of stress. Some protists are surrounded only by a plasma membrane, while some others form shells of silica (glass) around themselves. Some protists have flagella or cilia, while some others move by pseudopodia (false legs - ameboid movement).

Traditionally, protists have been artificially subdivided into three basic groups according to their metabolism: protists capable of photosynthesis (autotrophs) are called Algae, heterotrophs are called Protozoa, while the absorbers are Fungus-like protists. According to morphology, protists have been divided into about 15 phyla, grouped into six major groups. New molecular techniques are thoroughly changing the taxonomy and systematics of Protista. One group, the Green Algae, has recently been moved out of Protista and into the Kingdom Plantae. Another group, the Choanoflaggelata, has been moved to the Kingdom Animalia as they are most closely related to sponges.

Some protists are parasites that cause human diseases. Most well-known of those are Plasmodium (malaria), various species of Trypanosoma (sleeping sickness, leischmaniasis and Chagas Disease) and Giardia (Hiker's Diarrhea). Dinoflagellates live on the surface of the ocean and are almost as important for absorption of CO2 and production of O2 as are forests on land.

Plants

Plants are terrestrial, multicellular organisms capable of photosynthesis (though some species have secondarily moved back into the aquatic environment or lost the ability to photosynthetize). There are about 300,000 species of plants on Earth today. They are divided into two broad categories: non-vascular and vascular plants. Mosses, liverworths and some other smaller groups are non-vascular plants. All other plants are vascular, meaning that they possess systems of tubes and canals that are used to transports water and nutrients from root to stem and leaves, and from leaves back to the root. Those tubes and canals are called phloem and xylem.

Of the vascular plants, some reproduce by forming spores, while others produce seed. Seedless vascular plants that produce spores are, among others, ferns and horsetails. Seeds are produced by two large groups: Gymnosperms (e.g., conifers) and Angiosperms (flowering plants).

An important evolutionary trend in plants was a gradual reduction of the haploid portion of the life-cycle (gametophyte) and simultaneous rise to dominance of the diploid portion - the sporophyte. In mosses, for instance, almost all of the plant is haploid, except for the diploid spores developing at the very tip of the stem. In flowering plants, e.g., trees, almost all of the plant's cells are diploid (just like in us), while the flowers contain male and female gametes (pollen and egg).

Fungi

Fungi can be unicellular (e.g., some yeasts and molds) or multicellular (e.g, mushrooms). Molecular data show that fungi are more closely related to animals than plants. Fungi are heterotrophs that obtain nutrients from the soil by secreting enzymes into the substrate and absorbing the digested materials. They cannot photosynthetize. Fungi are composed of hyphae, which are thin long filaments. A mass of hyphae is called the mycelium which can build large structures like mushrooms. Spores are the means of reproduction and are formed by sexual or asexual processes.

Fungi tend to enter into symbiotic relationships with other organisms. Some of those relationships are parasitic, as in our own fungal diseases. Other relationships are mutualistic, e.g., lychens, mycorrhizae and endophytes. Lichens are a mutualistic association between a fungus and a photosynthesizer, usually a green algae. Mycorrhizae form mutualistic associations between the fungi and plant roots (e.g., alfalfa). Endophytes are plants that have fungi living inside them in intercellular spaces and may provide protection against herbivores by producing toxins.

Animals

Animals are multicellular heterotrophs (they do not photosynthetize). They exhibit embryonic development and mostly reproduce sexually. One of the important characteristics of animals is movement. While microorganisms (bacteria, archaea and small protists) can move, large organisms (large protists, plants and fungi) cannot - they are sessile (attached to the substrate). Animals are large organisms that are capable of active movement: swimming, crawling, walking, running, jumping or flying. While some animals are also sessile, at least one phase of their life-cycle (e.g., a larva) is capable of active movement.

Some of the major transitions in the evolution of animals are evolution of tissues, evolution of symmetry (first radial, later bilateral), evolution of pseudocoelom and coelom, the difference between Protostomes and Deuterostomes, and the evolution of segmentation.

There are about 37 phyla of animals. Animals can be divided into two sub-Kingdoms: Parazoans and Eumetazoans. Parazoans are choanoflagellates and sponges. They do not have tissues - their cells are randomly organized. A sponge can be pushed through a sieve and all cells get detached from each other during the process, yet they will reconnect and form an intact sponge afterwards. Sponges move by reorganization of the whole body - cells move over each other (pulling the silicate spicules along) and can move as much as 6mm per day. All other animals are Eumetazoans - their cells are organized within proper tissues.

Parazoans also have no body symmetry. Some phyla of animals (e.g, Cnidaria) have radial symmetry - they are called Radiata. Most phyla of animals - the Bilateria - have bilateral symmetry: the left and the right side of the body are mirror images of each other. In bilaterally symmetrical animals, there is early embryonic determination not juts of up-down axis, but also of front-back axis. Bilateral symmetry gives the animal direction - it moves in one direction, the sensory organs and the mouth tend to be in front, while excretion and reproduction are relegated to the back of the animal.

Early during development, the cells of the spherical embryo (gastrula) organize into layers. Some animals (Diploblasts) have only two layers: ectoderm on the outside and endoderm on the inside. Most animals (Triploblasts) have evolved a third layer in between - the mesoderm. Ectoderm gives rise to the skin and nervous system. Endoderm gives rise to the intestine and lungs, among else. Mesoderm gives rise to muscles and many other internal organs. Usually, Radiata are Diploblasts, while Bilateria are Triploblasts.

In more primitive animals, there is no internal body cavity (e.g., flatworms). In others, a cavity forms during the development between the endoderm and mesoderm - it is called pseudocoelom (e.g., nematodes). In most animals, a proper coelom develops between two layers of mesoderm. Our abdominal and chest cavities are parts of our coelom.

In most phyla of animals, the early embryo divides by spiral cleavage. The blastopore - an opening into the cavity of the blastula- eventually becomes the mouth. These animals are called Protostomes. Protostomes are further divided into two groups: in one group animals grow by adding body mass (e.g., annelids, molluscs and flatworms), while others grow by molting (e.g., nematodes and arthoropods).

In Echinodermata and Chordata, the embryo divides by radial cleavage. The blastopore becomes the anus. These animals are Deuterostomes.

Three large phyla of animals - Annelida, Arthropoda and Chordata evolved segmentation, using Hox genes to drive the development of each segment.

You will HAVE to read the three relevant animal chapters in the textbook to learn more about the following phyla: sponges, cnidarians, annelids, molluscs, arthropods and chordates.

Phylum Chordata is the one we are most interested in for egocentric reasons - because we are chordates. The phylum consists of some invertebrate groups and the Vertebrata (all other animal phyla are also Invertebrata). The invertebrate chordates are hemichordates (acorn worms), tunicates (Urochordata - sea squirts) and cephalochordates (e.g., the lancelet - Amphioxus, see picture). The larvae of invertebrate chordates are very similar to the larvae of echinoderms, both groups are also Deuterostomes, and recent molecular data confirm close relationship between chordates and echinoderms as well.

All chordates have, at least at some point during the development, a notochord. The early chordates were aquatic animals. Hagfish and lampreys are two of the most primitive groups of vertebrates. Before the molecular analysis was performed, these two groups were clumped into a single group of Jawless Fish (Agnatha), but have since been split into two separate classes.

'Fish' is the lay term for several different groups of aquatic vertebrates. The most important classes are cartilagenous fish (Chondrichthyes, e.g., sharks, rays and sturgeons), lobe-finned fish (Sarcopterygii, e.g., gars) and ray-finned fish (Actinopterygii - most fish that you can think of). The latter two of those are also sometimes lumped together and called the bony fish (Teleostei). Chrossopterygii, a once-prominent group of lobe-finned fish that survives today with only one living species (Coelacanth, or Latimeria), is the group that gave rise to ancient amphibians - the first vertebrates to invade the land (check out the Tiktaalik website for more information).

Amphibians are frogs, toads, salamanders and cecilians. At least one portion of the life-cycle - reproduction and early development - is dependent on water. They have legs for locomotion and lungs for respiration on land.

Reptilia are a large and diverse class of vertebrates. They include lizards, snakes, tuataras, turtles, tortoises and crocodilians. They have scaly skins that allows them to survive in arid environments. They have evolved an amniotic egg - an egg that contains nutrien-rich yolk and is contained within a leathery shell. Thus, reproduction and development are not dependent on water. Many reptiles live in deserts.

A now-extinct group of ancient reptiles (therapsyds) gave rise to mammals (class Mammalia) about 220 million years ago. The early mammals were quite large carnivores. However, during the 150 million year reign of the Dinosaurs (another extinct group of reptiles) mammals were constrained to a very small niche - that of nocturnal burrowing insectivores. Only after the demise of Dinosaurs (65 million years ago) could mammals embark on a fast evolutionary radiation that produced groups we know now.

Birds and mammals are endotherms - they can control (and keep constant) their body temperature by producing the heat in organs like muscles and liver. This is a metabolically expensive strategy that requires these animals to eat very frequently, but gives them speed and stamina and allows these animals to live in every part of the Earth, incuding polar regions. Other vertebrate classes are ectotherms - they gain their heat from the environment and, if they are cold, they are slow and sluggish.

As it is very difficult for large bodies to lose heat, large reptiles (like dinosaurs), once heated, can retain their body temperature for long periods of time - they are effectively warm-blooded. Some reptiles, notably pythons and iguanas, are capable of producing some of the heat internally. While they cannot keep a constant body temperature, they are capable of some degree of thermoregulation (e.g., becoming somewhat warmer than the external environment). By shivering their muscles, pythons raise their body temperature above ambient and use this heat to incubate their eggs.

There are about 4500 species of mammals, organized into 19 orders. The defining characteristics of mammals are milk ­producing glands and hair.

Monotremes (platypus and echidna) are egg-laying mammals. Their mammary glands are not completely evolved yet - the young lick the milk of off mothers hair.

Marsupials are the pouched mammals (e.g., kangaroo, koala, opossum). The immature newborn offspring crawls up into the pouch and lives inside it until they are large enough to fend for themselves.

Placental mammals (the remaining 17 orders) have a placenta that nourishes their embryos during development. The new molecular data, coupled with a number of exciting newly-discovered fossils, are changing our understanding of genealogical relationships between different orders of mammals, including our new knowledge about the evolution of whales, the relationship between elephants and hyraxes, between Carnivores and Pinnipedieans (seals, etc.) and between rodents and rabbits.

The most recent vertebrate class - the birds (Aves) - evolved out of a branch of Dinosaurs. There are 28 orders of bird in 166 families. Two primary characteristics distinguish birds from reptiles: feathers and flight skeleton. Their feathers are modified reptile scales. Feathers are obviously important for flight, but also insulate as birds are endotherms.

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 27, 28, 29, 30, 31, 32, 33 and 34.

Additional Readings:

New ideas about early evolution of life (http://scienceblogs.com/aetiology/2006/05/are_we_teaching_a_wrong_idea.php)

Previously in this series:

Biology and the Scientific Method
Cell Structure
Protein Synthesis: Transcription and Translation
Cell-Cell Interactions
Cell Division and DNA Replication
Cell Differentiation and Embryonic Development
Genotype and Phenotype
Evolution
Behavior
Ecology
Origin of Bioloigcal Diversity
Evolution of Biological Diversity

Technorati Tag: teaching-carnival

Evolution of Biological Diversity

BIO101 - Bora Zivkovic - Lecture 4, Part 2

In the previous segment of the lecture, we looked at the Origin of Life and the beginnings of the evolution of biological diversity. Now we move to explanations of the mechanisms by which diversity arises.

Although traits can be inherited by non-DNA ways, and DNA sequence does not neccessarily translate directly onto the traits, in the long term the differences between species tend to be recorded in the genome. Thus, differences between genomes of different species are most important differences between them. How do differences between genomes arise? There are six major (and some minor) ways this happens:

Mutations are small changes in the sequences of DNA. Some of the changes are just substitutions of one nucleotide with another, others are deletions, insertions and duplications of single nucleotides or small strings of nucleotides within a gene, or within a non-coding regulatory sequence. Such small changes may alter the function of the gene-product (protein) which may translate into changes in traits which may be selected for by natural or sexual selection.

Gene duplication occurs quite often due to errors in DNA replication during cell division, or due to errors in 'crossing-over' phase of meiosis. Instead of a single copy of a gene, the offspring have two copies of that same gene. As long as one copy remains unaltered and functions properly, the other gene is free to mutate (i.e., there will stabilizing selection on the first copy, and no selection for the preservation of the sequence of the second copy). The second gene may transiently become non-functional, but as it keep mutating it may beging coding for a completely novel protein which will start interacting with other molecules in the cell. If this new interaction confers increased fitness on the organism, this new gene sequence will become selected for and fine-tuned by natural (or sexual) selection for its new function.

Chromosome duplication may also occur due to errors in DNA replication during cell division. Instead of just one gene being duplicated, a large number of genes now exist in two copies, each pair of copies consisting of one copy that is preserved by stabilizing selection and another copy that is free to mutate and thus potentially evolve novel traits.

Genome duplication has occured many times, especially in plants. The whole genome doubles, i.e., all of the chromosomes are duplicated. The resulting state is called polyploidy. This provides a very large amount of genetic material for natural selection to tinker with and, over time, produce novel traits.

Rearrangement of segments of the DNA along the same chromosome, or between chromosomes, places different genes that were once far from each other into closer proximity. Thus, genes that were previously quite independent from each other may now be expressed together or may start influencing each other's expression. Thus, the genes become linked together (or unlinked from each other), restructuring the batteries of genes that work together in a common function. This may free some genes to evolve independently, while tying some genes together and thus constraining the direction in which development of traits may evolve.

Lateral transfer (sometimes called 'horizontal transfer') is an exchange of DNA sequences between individuals of the same species or of different species. While vertical transfer moves genes from parents to offspring, lateral transfer moves genes between unrelated individuals. Such transfer is very common in microorganisms. Some species of Bacteria, Archaea and Protista routinely engage in gene swapping, which results in increase of genetic diversity of the species and thus provides raw material for evolution to build new traits. Gene swapping between organisms of different species may transfer a complete function from one species to another. Sometimes viruses act as carriers of genes from one species to another. For instance, a virus may take a piece of a bacterial genome and later insert it into a genome of a plant or a mammal. Some key genes involved in the development of the placenta originated as bacterial genes inserted into early mammalian genomes via viruses.

One important thing to bear in mind is that evolution has to ensure the survival of the individual at all stages of its life-cycle, not just the adult. Thus, evolution of new traits can occur only if it does not disrupt the viability of eggs, larvae, immature adults and mature adults.

Another important thing to keep in mind is that traits arise through embryonic and post-embryonic development. Thus, evolution of traits is really evolution of development. Evolution of genomes, thus, is not evolution of random grab-bags of many genes, but evolution of complexes of genes involved in development of particular traits.

A product of a gene is a protein. A protein that is capable of binding to DNA and thus regulating the expression of other genes is called a transcription factor. When bound to a gene, a transcription factor may induce its expression, block its expression, or increase or decrease the rate of its expression. The patterns of gene expression are key to embryonic development and cell differentiation, so it is not surprising that transcription factors play a large role in evolution of new traits via development.

A novel pattern of gene expression may arise in two ways. First, by mutation of a transcription factor (so-called trans-factors), it changes which genes it affects and the way it affects them. Second, by mutations in regulatory regions (so-called cis-factors) of the target genes, the transcription factors may or may not bind to them, or a different transcription factor may bind to them, or the effect of the binding on transcription of the gene may change.

Most important genes in evolution of development are transcription factors. Often, they work in batteries (or complexes or toolkits), where one gene induces transcription of the second gene which in turn induces transcription of the third gene, and so on. Such batteries tend to be strongly preserved in many species of living organisms, though the genes that act as final targets of action of such complexes differ between species. Such complexes may determine what is up and what is down in an early embryo, or what is forward and what is bakward in an embryo. Such complexes are used over and over in evolution to produce protruding structures, like limbs. Another such complex has been used in 40 different groups of animals for the construction of 40 quite different types of eyes.

Possibly the most important such complex in animals is the complex of Hox genes that regulates segmentation. Most animals are segmented. While this is obvious in earthworms where all segments look alike, in many other animals segments are formed in the early embryo and each segment then develops unique structures on it. Thus, an insect will develop jaws and antennae on its head segment, wings and legs on its thoracic segment, and reproductive structures and stings on its abdominal segment. You will need to carefully read the handout "A Brief Overview of Hox Genes" (http://scienceblogs.com/pharyngula/2006/04/a_brief_overview_of_hox_genes.php) and be able to define Homeotic genes, Homeobox (DNA sequence), Homeodomain (protein structure) and Hox genes. Interestingly, non-segmented Cnidarians (corals and jellyfish) do not have true Hox genes, though they do have scatterings of Hox-like genes, which may be evolutionary precusors of true Hox genes.

Thus, evolution of diversity can be thought of in terms of changes in the way developmental toolkits are applied in each species. The same toolkits are used over and over for development of similar traits. The sequences of the genes within the toolkits will vary somewhat between species, and the sequences of genes that are final targets of action of toolkits will vary much more.

Thus, with quite a limited number of genetic toolkits, nature can develop a myriad different forms, from cabbages and sponges to honeybees and humans. This also explains why we do not need more than 30,000 genes to develop a human, as well as why our genome is about 99% identital to the chimpanzee genome. It is not the sequence of genes, but the combinatorics of the way the genes are turned on and off during the development that results in the final phenotype.

The common theme, then, is that evolution keeps tinkering with the same genetic toolkits over and over again. It is not neccessary to evolve thousands of completely new genes in order to have a new species spring up out of its ancestral species. A little tweak in developmental patterns of gene expression is all that is needed. The same genes may be expressed at a different place in the embryo in two different species (heterotopy), or may be expressed at a different time during development (heterochrony), or may result in expression of other final-target genes (heterotypy). Such changes account for most of the evolution of diversity of life on Earth.

Of course, such changes take a long time. It took about 3.6 billion years for life to evolve from the first primitive bacteria-like cells to the current diversity of millions of species of Bacteria, Archaea, Protista, Fungi, Plants and Animals. Our brains have never before needed to be able to comprehend such vastness of time. We do qute well with durations of seconds, minutes, hours and days. We are pretty good at mentally picturing the duration of weeks, months and years. A decade is probably the longest duration of time that our brains can correctly imagine. Already our perception of a century is distorted. Perception of a thousand years is impossible for human brains. Now try to imagine how long 10,000 years is? Any luck? Now try 100,000. How about 1.000,000 years? Add another zero and try comprehending 10.000,000 years. Multiply by ten again and try 100.000,000 years. Now try 1,000.000,000 years. Now try four times more - 4 billion years.

It is not surprising that some people, unable to comprehend 4 billion years, just plainly refuse to acknowledge that this amount of time actually passed and stick to a shorter, emotionally more pleasing yet incorrect number of about 6,000 years for the age of the Universe. Such people, of course, cannot believe that evolution actually happened, although mountains of evidence show us not just that it happened, but exactly how it happened. You can see exactly what happened when if you take your time and do this animation. You'll notice how the whole of human history is too short to be visible on a line representing billions of years. Given such enormous amount of time, the evolution of amazing diversity of life is not surprising. Actually, if such diversity did not arise - that would be a surprise.

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 24 and 27

Watch Animation:

http://www.johnkyrk.com/evolution.html

Handouts:

A Brief Overview of Hox Genes (http://scienceblogs.com/pharyngula/2006/04/a_brief_overview_of_hox_genes.php)
Bat Development (http://scienceblogs.com/pharyngula/2006/04/bat_development.php)
How To Make A Bat (http://scienceblogs.com/pharyngula/2006/04/how_to_make_a_bat.php)

Additional Readings:

Jellyfish Lack True Hox Genes (http://scienceblogs.com/pharyngula/2006/05/jellyfish_lack_true_hox_genes.php)

Previously in this series:

Biology and the Scientific Method
Cell Structure
Protein Synthesis: Transcription and Translation
Cell-Cell Interactions
Cell Division and DNA Replication
Cell Differentiation and Embryonic Development
Genotype and Phenotype
Evolution
Behavior
Ecology
Origin of Biological Diversity

Technorati Tag: teaching-carnival

Origin of Biological Diversity

BIO101 - Bora Zivkovic - Lecture 4, Part 1

Adaptation vs. Diversity

Biology is concerned with answering two Big Questions: how to explain the adaptation of organisms to their environments and how to explain the diversity of life on Earth.

Much of the course content so far engaged the question of the origin and evolution of adaptation, and much of the remainder of the course will also look at particular adaptations of humans and other vertebrates. This is the only lecture specifically targeting the question of diversity.

The way this material is usually taught is to go over long lists of organisms and tabulate their characters, how the members of one group are similar to each other and different from members of other groups. We, in our course, will try a different approach, i.e., not just describing, but also explaining diversity - how it comes about.

If you think about it, knowing what we learned so far about the way evolution works, the origin of adaptation and the origin of diversity are deeply intertwined: as local populations evolve adaptations to their current local environments, they become more and more different from each other until the species splits into two or more new species. Thus, evolution of adaptations to local conditions leads to proliferation of new species, thus to the increase in overall diversity of life on the planet.

Origin of Life

One can postulate four ways the life on Earth came about: a) it was created - poof! - out of nothing by an intelligent being, e.g., God; b) it was created - poof! - out of nothing by an intelligent being, e.g., space aliens, either on Earth or elsewhere, then brought to Earth; c) it spontaneously arose elsewhere in the Universe and was brought to Earth by comets and meteors; and d) it spontaneously arose out of chemical reactions in the ancient seas in the presence of the ancient atmosphere.

Science is incapable of addressing the first notion - being untestable and unfalsifiable (impossible to prove that it is wrong), it is properly outside of the realm of science and within the domain of religion.

The first three notions also just move the goalposts one step further - how did life (including God and/or Aliens) arise elsewhere in the Universe? Thus, scientists focus only on the one remaining testable hypothesis - the one about spontaneous and gradual generation of life out of non-life, a process called abiogenesis. The scientific study of abiogenesis cannot say and does not attempt to say, anything about existence of God or Aliens. It only attempts to figure out how life could have arisen on its own, sometime between 3 and 4 billion years ago.

All of life on Earth descends from a single common ancestor. It is quite possible that life initially arose multiple times, but as soon as one life form became established and competitive enough, all the other instances of spontaneous generation of life were outcompeted and did not leave progeny.

It is difficult to study the origin of life as molecules do not leave fossils. They do leave chemical traces, though, so we know a lot about the chemistry of the ancient oceans, soil and atmosphere. Thus, we know under what conditions and what available materials (and energy) life first arose. By replicating such conditions in the laboratory, we can study the details of how life might have evolved out of non-life.

The study of the origin of life is a lively and exciting area of biology, perhaps because so little has yet been settled with great certainty. There are a number of competing hypotheses promoted by various research groups. Those hypotheses can be classified into groups: RNA First, Protein First, RNA-Protein First and Bubbles First.

RNA is a molecule that can be replicated and thus can serve as the original hereditary material (DNA is too large and complex even for some of today's viruses, let alone for the first simple organisms). RNA is also capable of catalytic activity - promoting and speeding up reactions between other molecules, as well as replicating itself. Thus, RNA is the best candidate for the first molecule of life. Still, it is not capable of everything that life needs, so a few simple polypeptides (and those are really easy to synthetize in a flask mimicking the original Earth conditions) were probably involved from the very beginning. For those reactions to occur, they had to be separated from the remaining ocean - thus some kind of "cell membrane", like a soap bubble, was also neccessary for the origin and early evolution of life.

Those early "cells" competed against each other. Those that, through chemical evolution, managed to become good enough at remaining stable for a decent amount of time, capable of acquiring the energy from the environment, and capable of dividing into two "daughter cells" outcompeted the others - chemical evolution turned into biological evolution. As they changed through trial and error, some cells gradually got better at "living" and outcompeted all others. One best competitor of the early living world is the common ancestor of all of the subsequent life on Earth, including us.

Directionality of Evolution

There are two common misconceptions about evolution. First is the idea that evolution tends towards perfection. But, always remember that evolution favors individuals who are slightly better optimized to current local conditions than other individuals of the same species, i.e., what wins is the relative fitness, not absolute fitness (i.e., perfection). In other words, you have to be capable of surviving and reproducing in your current environment and be just a tad little bit better at it than your conspecifics - there is no need to be perfectly adapted.

The second common misconception about evolution is that it has a tendency to generate greater complexity. Originally, right after the initial origin of life on Earth, evolution did produce greater complexity, but only because there was no way to become any more simple than the first organisms already were. There is a "left wall" of complexity in the living world, i.e. there is a minimum complexity that is neccessary for something to be deemed alive.
Thus, initially, the only direction evolution could take was away from the left wall (red dot), i.e., becoming more complex. But once reasonable complex organisms evolved, they were not snuggled against the left wall any more (yellow dot). Adaptation to current local conditions can equally promote simplification as it does complexification of the organism in question. In other words, as populations evolve, the members of the populations are equally likely to become simpler than they are to become more complex.

Actually, as we know from the world of man-made machines, there is such a thing as being too complex (blue dot). Over-complicated machines break down much more easily and are more difficult to maintain and repair. Likewise, organisms of great complexity are often not as fit as their simpler relatives - their genomes are so large that the error rate is greater and cell division is more difficult. Cells can "go wild" and turn into cancer. Also, with so many interacting parts, it is more difficult for complicated organisms to evolve new adaptations as the development of the whole complex system has to change and adapt to such changes.

Thus, simplification is as often seen in evolution as is acquisition of greater complexity. Just think of parasites - they are all simplified versions of their free-living relatives - no need for eyes, other sensory organs or means of locomotion if one spends one's life attached to the lining of the host's intestine, sucking in nutrients and growing billions of eggs.

Measuring Diversity - Taxonomy and Systematics

People have always tried to classify living beings around them, by grouping them according to some man-made criteria, usually by the way they look, where they live, and how useful they may be to us. Only for the past 150 years we have understood that all organisms on our planet are geneologically related to each other, so we started classifying them according to the degree of relatedness - drawing family trees of Life.

Initially, classification was done according to anatomy and embryology of organisms. Such methods brought about the division of Life on Earth into six great Kingdoms: Bacteria, Archaea, Protista, Plants, Fungi and Animals. The first two are Prokaryotes (no nucleus), the latter four are Eukaryotes (cells have a nucleus).

The Kingdoms were, like Russian dolls, further subdividied into nested hierachies: each Kingdom was composed of a number of Phyla (Phylum = type). Each Phylum consists of Classes, those are made of Orders that are further subdivided into Families. Each family consists of Genera and each Genus is composed of the most closely related Species.

The proper name of each living organism on Earth is its binomial Latin name - capitalized name of the Genus and lower-case name of the species, both italicized, e.g., Homo sapiens, Canis familiaris, Equus caballus, Bos taurus (human, dog, horse and cow, respectively).

Lately, modern molecular genetic techniques have been applied to testing relationships between species, resulting in many changes in classification at lower levels of systematics (e.g,. species, genus, family, etc).

The knowledge gained from this approach also resulted in some big changes in the way we classify living organisms. Instead of six Kingdoms, we now divide life on Earth into three Domains: Bacteria, Archaea and Eukarya.

We are now aware that endosymbiosis (intercellular parasites, originally small bacterial cells entering and living inside larger bacterial cells) gave rise to organelles, like mitochondria and chloroplasts. We are now aware how much lateral (or horizontal) tranfer of genetic material is going on between species, i.e., the branching tree of life has many traversing connections between branches as well.

Cladistics is a relatively new method of classifying organisms, using multiple (often many) different genetic, morphological and other traits and building "trees" by calculating (using computer software) the probabilities of each two of the species being related to each other. Thus, "most likely" trees are plotted as cladograms which can further be tested and refined.

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 4 and 25

Previously in this series:

Biology and the Scientific Method
Cell Structure
Protein Synthesis: Transcription and Translation
Cell-Cell Interactions
Cell Division and DNA Replication
Cell Differentiation and Embryonic Development
Genotype and Phenotype
Evolution
Behavior
Ecology

Technorati Tag: teaching-carnival

New Garage for the Magic School Bus

I have started the engine, shifted into first gear, then second, and we're on our way on a two-day journey to our brand-new garage!

Yup, you may have heard about this already. Starting this Friday, this blog will fuse with my other two blogs (Science And Politics and Circadiana) and move to the ever-growing Scienceblogs.com, hosted by the SEED Magazine.

It does not work right now, but on Friday you will be able to access the new blog at this URL.

I'll give you the Feed once I get it, so you can all change your bookmarks, blogrolls and newsfeeds to the new address.

I may still post some lecture notes before Friday, but after the new blog begins, I will not post anything new here any more. The complete archives of this blog will remain here as there are some incoming links, but I will slowly, over the next few months, republish some of the best Magic School Bus posts over there. I hope you all move there with me - the new blog will be even better (and prettier) than this one.

Update: Due to technical problems, the new blogs will nost start tomorrow (Friday) but later, hopefully Monday of next week. I'll keep you posted.

Technorati Tag: teaching-carnival

Educarnivals

The 69th Edition of the Carnival of Education is up on Education in Texas
The 22nd edition of the Carnival of Homeschooling is up on Common Room.

Technorati Tag: teaching-carnival

Carnivals Ahoy!

Tangled Bank #54 is up on Science And Politics

Huge and beautiful 68th Carnival of Education is up on NYC Educator

Excellent 21st edition of Carnival of Homeschooling: The Map to A Progressive Dinner is up on Principled Discovery.

Organisms In Time and Space: Ecology

Ecology

BIO101 - Bora Zivkovic - Lecture 3 - Part 2

Ecology is the study of relationships of organisms with one another and their environment. Organisms are organized in populations, communities, ecosystems, biomes and the biosphere.

A population of organisms is a sum of all individuals of a single species living in one area at one time.

Individuals in a population can occupy space in three basic patterns: clumped spacing, random spacing and uniform spacing.

Metapopulations are collections of populations of the same species spread over a greater geographic area. There is some migration (ths gene-flow) between populations. Larger populations are sources and smaller populations are sinks of individuals within a metapopulation.

Population size is determined by four general factors: natality, mortality, immigration and emigration.

Natality depends on a number of factors: the proportion of the population that are at a reproductive age (as opposed to pre-reproductive and post-reproductive), proportion of the reproductively mature individuals that get to reproduce, sex-ratio of the reproductives, the mating system, the fertility of individuals (sometimes affected by parasites), the fecundity (number of offspring per female), the maturation rate (the amount of time needed for an individual to attaint sexual maturity), and longevity (amount of time an individual can live after reproducing).

Mortality is affected by bad weather, predation, parasitism and infectious diseases. It depends on the mortality of pre-reproductive stages (from eggs and embryos, through larva and juveniles), mortality of reproductive stages, and mortality of post-reproductive stages (often from disease or aging).

A population can, theoretically, grow exponentially indefinitely. However, in the real world, the growth is limited by the amount of space, food (energy) and predators. Thus, the population size often plateaus at an optimal number - the carrying capacity of that population.

Some organisms produce a large number of progeny, most of which do not make it to maturity. This is r-strategy. The population size of such species often fluctuates in boom-and-bust patterns.

Other organisms produce a small number of progeny and make a heavy investment into parenting and protecting each offspring, This is K-strategy. The population size of such species grows more slowly and tends to stabilize around the carrying capacity.

All populations show small year-to-year fluctuations of population sizes around the optimum number. Some species, however, exhibit regular oscillations in population sizes. Such oscillations often involve populations of two different species, usually a predator and its prey, the most famous example being that of the snowshoe hare and the lynx.

Correct prediction of future changes in a population size is essential for the assessment of the populations viability and for its protection.

A biological community is a collection of all individuals of all species in a particular area. Those species interact with each other in various ways, and have evolved adaptations to life in each others' presence.

Niche is a term that describes a life-role, or job-description, or one species' position in the community. An example may be a large herbivore, a nocturnal burrowing seed-eater, a seasonal fruit-eater, etc.

Within one community only one species can occupy any particular niche. If two species share some of their niche, they are in competition with each other. If two species occupy an identical niche, they cannot coexist - one of the species will be forced to move out or go extinct.

If two species compete for the same resource (food, territory, etc.), one will utilize the resource better than the other. Competitive exclusion is a process in which one species drives another species out of the community.

Complete exclusion is not inevitable. The competition between two species can be reduced by natural selection, i.e., one of the species will be forced to assume a slightly different niche. For instant, two species can geographically partition the territory, e.g., one living at higher altitude than the other on the same mountain-side. Two species can also temporally partition the niches, for instance one remaining active at night and the other becoming active during the day.

Predation is one of the most important interaction between species in a community. Predation often causes evolutionary arms-races between predators and prey. For instance, by killing the slowest zebras, lions select for greater speed in zebras. Greater speed in zebras selects for greater speed in lions.

The most interesting examples of evolutionary arms-races between pairs of enemies are those in which the prey is dangerous to the predator, often by being toxic or venomous. For example, garter snakes and tiger salamanders on the West coast are involved in one such arms-race. Prey - the salamander - secrete tetrodotoxin from its skin. This toxin paralyzes the snake. Locally, some snakes have evolved an ability to tolerate the toxin, but the side-effect of such evolution is that these snakes are slow and sluggish - themselves more vulnerable to predation by birds.

Ground squirrels (prey) in the Western deserts have evolved immunity to rattlesnake venom, so the rattlesnakes (predators) are becoming more venomous. Similarly, and in the same area, desert mice have evolved immunity to the toxin of their prey - the scorpions, resulting in increasing toxicity of the scorpion venom in that region (but not in areas where these two species do not overlap). A Death's-head sphynx moth steals honey from beehives and has evolved partial immunity to honey-bee venom.

Many plants have evolved thorns or toxic chemicals to ward off their enemies - the herbivores. Monarch butterflies are capable of feeding on milkweed despite this plant's toxic content. Moreover, the Monarchs store the noxious chemical they extracted from milkweed and that chemical makes the butterflies distasteful to their own predators.

The shape and color of the prey often evolves to protect from predation. Warning coloration, usually in very bright colors, informs the predators that the prey is dangerous. Aposomatic coloration is one commonly found kind of warning coloration - the black and yellow stripes on the bodies of many bees and wasps are almost a universal code for dangerous venomous stings.

Cryptic coloration, or camouflage, on the other hand, allows an animal to blend in with its surroundings. Many insect look like twigs, leaves or flowers, effectively hiding them from the eyes of predators. Some animals have evolved behavioral color-change, e.g., chameleons, some species of cuttlefish and the flounder.

Batesian mimicry is a phenomenon in which non-toxic species evolve to resemble a toxic species. Thus, some butterflies look very similar to Monarch butterflies and some defenseless flies and ants have aposomatic coloration.

Mullerian mimicry is a phenomenon in which two or more dangerous species evolve to look alike. This is "safety in numbers" strategy as a predator who tastes and spits out one of them, will learn to avoid all of them in the future.

Co-evolution does not occur only between enemies. It can also occur between species that positively affect each other. The best example is co-evolution of flowers and insect pollinators.

Symbiosis is a relationship between organisms that are not direct enemies (e.g,. predator and prey) to each other. Commensalism, mutualism and parasitism are forms of symbiosis.

In commensalism, one partner benefits, while the other one is not affected at all. For instance, birds building nests in a tree do not in any way affect the fitness of the tree.

Mutualism benefits both partners. The best known examples are lichens, mycorrhizae, and legumes. Birds that clean the skin or teeth of crocodiles, hippos or rhinos are protected by their hosts.

Parasitism is detrimental to one of the partners. Parasites that are too dangerous, i.e., those that kill their host, are not successful since they also die without leaving offspring. Thus, parasites evolve to be minimally harmful to their hosts. The same logic goes for infectious agents - the disease should help propagate the microorganism (e.g, by causing sneezing, diarrhea, etc.) without killing the host.

The organisms that make up ecosystems change over time as the physical and biological structure of the ecosystem changes. Right now, one of the effects of global warming is that some species migrate and others do not. Thus, old ecosystems break down and new ones are formed. The ecosystems are in a process of remodelling. During that process, many species are expected to go extinct.

When an ecosystem is disturbed to some extent, but not completely eradicated, the remodelling process that follows is called primary succession.

When an ecosystem is completely wiped out (e.g,. a volcanic eruption on an island), secondary succession occurs, with a predictable order in which species can recolonize the space. One species prepares the ground (quite literally) for the next one. The process may start with bacteria, lichens and molds, continuing with mosses, fungi, ferns and some insects, etc, finally ending with trees, birds and large mammals. The final structure of the ecosystem is quite stable over time - this is a mature ecosystem.

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 53-57.

Previously in this series:

Biology and the Scientific Method
Cell Structure
Protein Synthesis: Transcription and Translation
Cell-Cell Interactions
Cell Division and DNA Replication
Cell Differentiation and Embryonic Development
Genotype and Phenotype
Evolution
Behavior

Technorati Tag: teaching-carnival

Tangled Bank - last call for submissions

The next edition of Tangled Bank is fast approaching - it will appear on my other blog Science and Politics on Wednesday May 24th, very early in the morning. The deadline is 23rd at 8pm ET.

I have only eight entries so far - come on, people! Out of more than 400 science-related blogs, I get only eight posts?

Some carnivals have very strict entry policies - Carnival of Liberals is limited to the 10 best posts, and I And The Bird is limited to one post per blogger. Some carnivals actively encourage multiple submissions from each blogger, e.g., Teaching Carnival, Circus of the Spineless and Animalcules. Most other carnivals are ambiguous about the rules and it is up to each host to spell those out.

I am one of those hosts who likes big carnivals and encourages multiple entries. So, for this Tangled Bank send your best. If you send 15 entries, I'll pick 2 or 3 I like the best, but do not be afraid to send in multiple suggestions. Also, you can nominate someone else's post if you think it is really good and deserves a broader audience.

Send your entries to: Coturnix1 AT aol DOT com

What Creatures Do: Animal Behavior

BIO101 - Bora Zivkovic - Lecture 3 - Part 1

Imagine that you are a zebra, grazing in the savannah. Suddenly, you smell a lion. A moment later, you hear a lion approaching and, out of the corner of your eye, you see the lion running towards you.

What happens next? You start running away, of course. How does that happen? Your brain receieved information from your sensory organs, processed that information and made a decision to puruse a particular action. That decision is relayed to the muscles that do the actual running.

In short, that is behavior and it can be schematically depicted like this:

Environment---------> Sensor ----------> Integrator---------> Effector

Here, the change in the environment (appearance of a lion) is perceived by the sensors (eyes, nose, ears), processed by the effector (the brain) and results in the activity of the effectors (muscles).

But, it is usually not that simple. The flow chart, as depicted, may be accurate when describing behavior of a bacterium, a protist, a fungus or a plant. A molecule in the cell membrane of a bacterium may sense nutrients, toxins or light. This information is processed by the cell as a whole, and as a result, the cilia or flagella move the bacterium in an appropriate direction.

Specialized cells in the shoot-tips or root-tips may detect up and down, or the position of the Sun, and guide growth in an appropriate direction (shoots up, roots down). Sunflowers and some other plants track the position of the Sun throughout the day. Many plants open and close their flowers or leaves at particular times of day. Some flowers, e.g, Venus flytrap and some orchids, can move even faster in order to capture insects.

Pilobolus, a fungus (seen as fine white fuzz on manure), shoots its spores towards the Sun at a particular angle at a particular time of day. Those are all simple behaviors involving a single sensor, a single integrator and a single effector in a simple unidirectional flow of information.

Once we get to animals with central nervous systems, things get a little bit more complicated. There are often multiple sensors. In the zebra example, the changes in environment are detected by three separate sensors: for vision, audition and olfaction. Effectors are many muscles, working in a highly coordinated manner.

Sensors located in the muscles feed the information about their activity back to the integrator. Integrator feeds back to the sensors as well - raising the sensitivity of the sensory organs, including vision, hearing, smell and the tactile sense (touch), while reducing the sensitivity of other sensors, e.g., for pain. The subjective perception of the rate of passage of time slows down, allowing for more fine-grained sensation and faster decision-making by the integrator.

Furthermore, the integrator will stimulate secretion of the hormones which, in turn, may increase the ability of effectors (muscles) to do their work. Integrator will also raise the activity of other organ systems that are important in allowing muscles to perform at their maximal level, e.g., circulatory and respiratory systems that bring oxygen and energy to the muscles.

At the same time, the brain temporarily shuts down the activity of organ systems not neccessary for short-term survival, but which may take the valuable energy away from the muscles. Thus, the digestive, immune, excretory and reproductive systems are inhibited.

As the zebra runs away, the act of running results in subsequent changes in the environment, which are again detected by the sensors. The integrator makes decisions to suddenly sverve if the lion gets closer, or to buck and kick if the lion gets very close, or to stop and find the safest route back to the herd if the lion has abandoned the chase.

All the changes described in the zebra example above are elements of the stress response, which is an excellent example of a complex behavior. There are multiple sensors, multiple effectors, various modifications of the body's physiology, and several kinds of information feedbacks involved. Behavioral biology studies all aspects of it.

In addition, it is not just the activity itself, but also the propensity for such activity that is studied by behavioral biology. Probability of a behavior happening depends on the motivation, or the state of the effector. The state can be modified by hormones, hunger, tiredness, libido, general energy levels, etc. The effector (e.g, the brain) also possesses timing mechanims (clocks and celandars) which make some behaviors much more likely during the day or during the night, some more likely during spring or summer, others more likely during fall or winter.

What Is Behavior?

It is difficult to define behavior without resorting to just listing examples of various kinds of behaviors, but let's try to define it anyway: Behavior is a change in body's position, shape or color, or a change in potential for such change, in response to changes in the external or internal environment. Behavior is endogenously generated (i.e., if I move your arm - that is not your behavior, it's mine), purposive (meant to achieve a goal), and is an evolved adaptation that contributes to survival or reproduction, thus increases one's fitness (which is obvious in the case of the fleeing zebra).

How to study behavior?

The most informative and profitable way to study behavior is an integrative approach. This means that the behavior under study is approached at all levels of organization (from molecules to ecosystems) and from four different angles. The first angle is Mechanism, which denotes study of the physiology underlying behavior. Most of the analysis of the zebra's behavior described above focused on this aspect - the physiology of the sensory, neural, muscular and other systems and the way they work together to produce the behavior.

The second one is Ontogeny, the study of embryonic and post-embryonic development of the behavior - how does an individual acquire the behavior, how much is the behavior inherited vs. learned, at what time in one's life cycle can the behavior be learned or expressed, at what times of day or year are the behaviors most likely to be expressed, etc.

These first two angles - mechanism and ontogeny - are sometimes called Proximate Causes of behavior and are designed to ask and answer the "How" questions of behavior (how does it work, how does it develop). The next two are called Ultimate Causes of behavior and are designed to ask and answer the "Why" questions (why behave in such way).

History is the third approach. It studies the evolutionary history of a behavioral trait, usually by employing the comparative method, i.e., comparison of a number of related species, trying to discover if the behavior is common in all of them, in which case it is present due to the deep phylogenetic history, or of it most reliably varies with the type of environment the species lives in, suggesting that the behavior is a recent adaptation for a particular way of life. Finally, the fourth approach is Function. It tests the hypothesis that the behavior in question increases the animal's fitness, aids in survival and/or reproduction, and has evolved for that function - is it an adaptation.

Recently a fifth question has been added to this list. Animal cognition asks “Can animals think?” Here, careful use of some unusual (and quite controversial) methods, including anecdotes, introspection and anthropomorphism, aids in the development of testable hypotheses about the inner worlds of animals.

No other area of biology is as integrative as behavioral biology. It is possible for a biochemist to ignore ecology or for an ecologist to ignore biochemistry (though at the risk of performing irrelevant research), but a behavioral biologist cannot ignore any aspect of the biology of the species under study. This makes the study of behavior the glue that holds all of biology together. This makes behavioral biology difficult to do, as one needs to have strong background in many areas of biology, technical expertise in a broad range of laboratory and field techniques, and lots of time to follow up on the literature in a number of related fields.

Only a few - the best - behavioral biologists are capable of exploring every aspect of a behavior at all levels. Mostly, the problem is divided among a number of laboratories around the world, each researcher using a slightly different approach and different techniques. The laboratories then communicate with each other via formal channels - the publications in scientific journals - and via informal channels - conferences and personal communication. Thus, a big picture is slowly being built out of its smaller parts, each piece of research being informed by all other pieces of research.

Types of behaviors

Foraging behavior involves finding, catching, handling and ingesting food. It includes the formation and use of feeding territories, learning the hunting techniques, the physiology of hunger, as well as behavioral strategies for avoiding becoming prey.

Animal movement includes, most prominently, long-distance migration including the neural mechanisms of spatial orientation and navigation.

Communication is the ability of animals to communicate information to each other (within and betwen species) via several sensory channels (or modalities). Those modalities include vision (including infrared, ultraviolet and polarized light, as well as thermoreception), sound (including ultrasound, infrasound and substrate vibrations), chemical signals (smells, pheromones, taste), touch and electrical signals (as in electrical fish).

Reproductive behaviors encompass a broad range of behaviors. Mate-finding, male-male competition, mate-choice and courtship are behaviors involved in securing a mate. Mating behavior ensures fertilization. Nesting and parenting behaviors are meant to ensure the survival of the offspring.

Reproductive behaviors are important elements of evolutionary change. Many phenotypic traits are a result not of natural selection, but of sexual selection, where a trait is selected not by the physical environment but by potential mates. Traits favored by the individuals of the opposite sex tend to be more likely to be passed on to the next generation in that population. This leads to the evolution of exaggerated traits (e.g., the peacock's tail) and to differences between sexes (e.g., in many bird species the male is brightly colored while the female looks drab).

Mate choice can, potentially, be involved in sympatric speciation, if different individuals in the population favor different traits in their mates, so the gene flow between the two groups gets progressively smaller with each generation. This kind of mating is called assortative mating (as opposed to random mating, where each individual is equally likely to mate with each individual of the opposite sex).

The most common types of mating systems are monogamy, polygyny, and polyandry. A good example of polygyny is the elephant seal in which only one male (after defeating all the other males in one-on-one fights) mates with all the females in his territory.

Polyandry is found only a little less often - one female mates with multiple males over the course of a breeding season, resulting in her offspring being of mixed paternity (i.e., different eggs were fertilized by different males). This has been studied mostly in frogs.

Monogamy is the rarest form of mating strategy in the animal kingdom. A distinction is made between social monogamy and sexual monogamy. Many animals that form breeding pairs, including most species of birds, are engaged in social monogamy - the male and the female build the nest together, mate and raise the chicks together. However, DNA fingerprinting has shown that a small proportion of the eggs is invariably fertilized by a different male - a fleshy neighbor who may not be a good "husband" and "father", but whose size, bright colors or powerful song indicate other genetic qualities. Thus, some of the progeny of the same female will be fleshy sons, some will be "good husband" sons and some will be daughters - the female is hedging her bets about the production of grandoffspring.

Humans are not officially classified as monogamous animals - though human polygamy (both polygyny and polyandry) tends to be in the form of serial monogamy, i.e., sticking monogamously with one partner for a particular length of time, then changing the partner. Social norms have strongly opposed, but did not eradicate human non-monogamy. Increased life-span, invention of reliable contraception, and economic independence of women are making it more and more difficult to supress the non-monogamous tendencies in humans, as seen from statistics for divorce (around 50%), re-marrying, and cheating (around 60% of both men and women) that have held quite steady over the past 50 years or so.

Social behaviors involve relationships between individuals of the same species. Some animals tend to live alone, each individual defending a territory, and a male and a female meeting only briefly during the mating season. Other animals tend to live in smaller or larger groups. Some animals change their social structure seasonally - for instance, European quail live in coveys (10-12 birds) during the winter), in huge flocks during spring and fall migrations, and in breeding pairs during summer.

Within groups, there is often a hierarchy of individuals - the so-called "pecking order". The social hirearchy is established through aggression, often in form of ritualized displays. In many species, the ritualized aggressive behaviors are so-called "fixed-action patterns", i.e., a strongly heritable order of particular movements. Mating behaviors are also often fixed-action patterns.

In some species, the mating fixed-action patterns are also used for aggressive encounters. In some cases, when a male mounts another male utlizing a typical mating pattern, this is actually a display of social dominance. However, in other species, a male mounting a male is actually homosexual behavior, evolved not to determine social hirearchy, but quite the opposite, to increase social coherence within the group ("making friends"). In pygmy chimps (bonobos), everyone in a troup mates with everyone else in the troup, regardles of gender. This makes the troup socially cohesive (which helps in group's defense if attacked by another troup).

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapter 52.

Previously in this series:

Biology and the Scientific Method
Cell Structure
Protein Synthesis: Transcription and Translation
Cell-Cell Interactions
Cell Division and DNA Replication
Cell Differentiation and Embryonic Development
Genotype and Phenotype
Evolution


Technorati Tag: teaching-carnival

You can help educational programs

DonorsChoose is a nifty website that collects in one place many educational programs and initiatives. If you are a teacher you can pick one or more of those to support, or you can add one of your own. If you are a teacher who needs something, this is the place to ask for it. If you are a blogger, you can challenge your readers to donate to the program of your choosing. Donations are easy to do.

I am not a public school teacher so I cannot register, but I am a blogger and I want you to donate to the programs that you like the best, perhaps one of the science teaching programs, or, perhaps one of the North Carolina programs (click all images to enlarge).


My local favourite - and I cannot see if it is listed on there - is Destiny, a Science Bus that travels around the North Carolina schools and gives students (and teachers) hands-on experience with modern techniques in biology, linked to the real world (e.g., solving crimes) and with a heavy emphasis on evolution. The kids, for instance, get real samples of real DNA from several real species of fish, run real gels and construct real phylogenies of those fish species. Destiny was featured this morning on WUNC, as part of their high school series (I do not see a transcript or podcast there yet).

Destiny has some corporate sponsors, and is affiliated with the Biology Department at UNC, so I do not know if individual donations are necessary or even accepted. But I like the program nevertheless - if you are a high school teacher (or parent or administrator), try to get the bus to come to your school. You can send your money to some other cause, some science teacher in a poor community who needs a microscope or a computer for his classroom.


My big favourite, which is not local, is Project Exploration. This project is the brainchild of paleontologist Paul Sereno and his wife, historian and educator Gabrielle Lyons.

If you do not know who Paul Sereno is, you are probably not interested in dinosaurs at all, as he is the #1 Big Star of Dinosaur Paleontology. Among else, he has discovered Carcharodontosaurus saharicus, one of the largest dinosaur carnivores - the African version of T.rex. Jobaria tiguidensis is the best preserved skeleton of a long-necked dinosaur. Sarcosuchus imperator, better known as Supercroc was big enough crocodile to hunt and eat dinosaurs. He has also discovered Eoraptor lunensis and Herrerasaurus ischigualastensis, two of the oldest dino fossils belonging to some of the earliest dinosaurs. Deltadromeus agilis, discovered by Gabrielle Lyons, was one of the fastest dinosaurs ever.

I had a good fortune to see Sereno give a talk and briefly to introduce myself to him, at the 2000 meeting of the Society for Integrative and Comparative Biology in Chicago. My brother knows him much better, as he and Gabrielle knew each other from grad school. Thanks to their friendship I got, over the years, a bunch of informational materials from the Project Exploration, as well as some really cool stuff, like some Sahara sand, a small plant fossil and several T-shirts that you cannot buy - they are not for sale. One day when I get out of financial problems, I will make it an annual ritual to donate to their program, devoted to bringing excitement about science to inner-city schoolchildren, particularly minorities and girls. In the meantime, I hope that you donate. They do not take any money from the government and depend on individual donations for their operation. You can donate your money, or alternatives (stocks, time, work), easily through their website.


I will place a button on my sidebar that looks like this:

That way, you can just click whenever, in the future, you wish to send them a few bucks.
Update: Tara reminds me that it may be important to show you their financial report, as well as the outcomes of their work:

Our programs are creating pipelines to future careers in science:

* Students participating in our field programs are graduating high school at an 18% higher rate than their peers.
* Students are pursuing science in college—25% of all students and 34% of our girls declare science as their major.
* The girls in our programs are pursuing science in college at five times the national average.

Technorati Tag: teaching-carnival

From Genes To Species: A Primer on Evolution

Evolution

BIO101 - Bora Zivkovic - Lecture 2 - Part 4

Imagine a small meadow. And imagine in that meadow ten insects. Also imagine that the ten insects are quite large and that the meadow has only so much flowers, food and space to sustain these ten individuals and not any more. Also imagine that the genomes of those ten insects are identical, except for one individual: that one has a mutation in one gene (due to an error in DNA replication, or due to crossing-over during meiosis). That mutation, during development led to the induction of the production of more mitochondria in each muscle cell.

Normally, that mutation is not obvious - the insect flitters from flower to flower just like anyone else. However, if the situation arises, the mutant individual is just a tiny little bit faster because the additional mitochondria in muscles allow it to switch from aerobic to anaerobic sources of energy later than in other individuals. Thus, the "normal" individuals can fly one yard in one second, while the mutant can fly one yard plus one inch in one second.

Now imagine that, over some time period, a bird comes by the meadow four times. Each time, the bird chases the insects and catches the one that is the closest to her. Which individual is, statistically speaking, least likely to get caught and eaten? The mutant, as the little extra speed may give it just enough edge in comparison to other individuals. This comparative "extra edge" is called increased fitness.

After four insects have been eaten, six remain - three males and three females. They pair up, mate, lay eggs and die. Each pair lays, let's say eight eggs, which all hatch, proceed normally through the larval development and become adults. This makes a total of 24 insects in a meadow that can support only ten individuals. At the same time, the bird has laid eggs, the eggs hatched and the hatchlings sometimes come to the meadow to hunt.

Let's look at the genetics of this population for a moment. Two pairs of "normal" insects produced a total of 16 offspring, all of them "normal". The offspring of one "normal" and one "mutant" each got one of the chromosomes from the mother, the other one from the father. All of them will have the mutation on one, and not on the other chromosome. Let's say that having a mutation on only one chromosome adds a half-inch to the yard-per-second flaying speed. The full mutant is homozygous for this mutation. The half mutant is heterozygous for this mutation. The heterozygous individuals are still relatively more fit than the "normals". As the hatchling birds hunt down the insects and cut down the population to ten individuals, the half-mutants are more likely to be present in the remaining population than the non-mutants.

Let's call the "normal" variant of the gene A and the "mutant" variant of the same gene a. A and a are alleles of the same gene.

In the next generation, some normals will breed with normals, producing normal offspring. Some half-mutants will mate with normals and produce a mix of normals and half-mutants. Some half-mutants will mate with some half-mutants and the resulting eight offspring will consist of 2 normals (AA), two mutants (aa), and four semi-mutants (Aa).

As the a allele confers relative fitness to its carriers, this allele will spread through the population over several generations and either completely eliminate allele A, or attain some stable balanced ratio in the population.

When one compares the genetic composition of this population over generations, one notices that it changes over time, from preponderance of A in the first generation, through a series of intermediate stages, to the preponderance of a in the last generation.

The change of genetic composition of a population over multiple generations is called evolution. That sentence is the most commonly used definition of evolution.

The process that favored one allele over the other, resulting in evolution of flight speed in these insects, is called natural selection.

The environment - the carrying capacity of the meadow plus the bird predators - was the selecting agent. The process that turns a genetic change (mutation) into a trait that can affect fitness of the whole organism is development. Thus, one can also define evolution as "change of development by ecology".

For evolution to proceed, the trait must vary in a population, one of the variants has to confer greater fitness than the other variants, there has to be a limit on the fecundity (how many offspring can survive in each generation) leading to differential rate of reproduction, and the trait has to be heritable, i.e., the offspring have to be more like parents in respect to that trait than like other individuals in the population. The inheritance is usually, though not always, conferred by the genome (the DNA sequence).

The example we used is quite unrealistic. Populations are much more likely to number in thousands or millions than just ten individuals. Thus, instead of a few generations, it may take thousands or millions of generations for a new allele to sweep through the population. In annually breeding organisms, this means thousands to millions of years. In slow-breeding animals, like elephants, it will take even longer. In fast reproducers, like bacteria, this may only take several months or years, as in evolution of antibiotic resistance in bacteria or evolution of pesticide resistance in agricultural pests.

Another way that the example was unrealistic was the assumption that all the individuals were genetically identical to each other except for that one mutation in that one gene. In reality, there will be variation (two or more alleles) in every gene, and new mutations show up all the time. Some mutations decrease fitness, some are neutral and some increase fitness. Some alleles affect fitness depending on which other alleles of other genes are present in the same individuals, or depending on the environment it finds itself in at a particular time, as in the norm of reaction phenomenon. Due to this, some combinations of alleles may tend to move from one generation to the next together.

Finally, in many organisms, genes can be transmitted horizontally - not from parent to offpspring but directly from one individual to another. This most often happens in bacteria, where individual bacteria may excahge bits and pieces of their DNA. Likewise, viruses are carriers of DNA sequences from one organism to another as well. Some of the sequences in our genome are of bacterial origin, transmitted some time in the past by viruses, and now fully integrated into our genome and even assuming an indispensible function. For instance, HERV genes are originally viral genes that are now parts of our genome and are neccessary for the development of the placenta.

Thus, in the real world, the situation is more complicated than in our example. Still, the proportions of various alleles of many genes are constantly changing - evolution occurs all the time.

Let's now assume that our insects live in a much larger area and that there are millions of them. The frequences of various alleles fluctuate all the time, and there is quite a lot of genetic variation contained in the population. Natural selection may work on preserving the average phenotype as its fitness is high and outliers at each end have lower fitness. This is called stabilizing selection.

As the climate slowly changes, or other aspects of the environment change, the relative frequences of alleles of various genes will track those changes. New conditions may, for instance select for larger body size. The largest individuals tend to leave most offspring, while the smallest individuals, on average, put the least of their genes into the next generation. The selection for large body size is an example of directed selection.

In some cases, selection may favor the extremes, but not the middle. Fast fliers may be selected for because they can escape the birds. The slowest fliers may be selected because they mostly walk or crawl and are thus not easily spotted by birds. They are also fit, but via a different strategy. The medium-speed fliers are selected against. This is an example of discruptive selection, forming two different morphs of the same species.

If those two morphs tend to, on average, be more likely to find each other and mate with each other within a morph than between two morphs, this may lead to splitting the species into two species - this is called sympatric speciation. As the gene flow between the two groups declines, more and more mutations/alleles will be found only in one morph and not the other. Those genes will also be under the influence of selection, and the selecting environment is different between crawlers and fliers. Soon enough, the individuals belonging to the two groups will not even recognize each other as belonging to the same species. Even if they recognize each other, they may not like each other ("mate-choice") enough to mate. Even if they mate, their eggs may not be fertile. Even if their eggs are fertile, the resulting offspring may not be fertile (hybrids, like mules for instance). If, for whatever reason, two related populations do not, will not or cannot interbreed, they have became separate species - speciation occured.

Imagine now that a small cohort of about ten individuals got blown away by wind from the mainland to a nearby island. The mainland population is huge. The island population is tiny. The ability of any mutation or any allele to spread fast through the population is much greater in a small group. The selective pressures are also different.

It may be better for the island insects to be small and for the mainland insects to be large, perhaps due to the types of flowers or kinds of predators that are present. The mainland insects may be selected for high flying speed because of bird predation. The island insects may not have any bird predators, but, those individuals who are the best fliers are most likely to be swept off the island by wind and drown in the ocean, never placing their genes into the next generation. Thus, they are selected not to fly, even to lose their wings.

If, after a number of generations, those two populations again get into contact - e.g., a land bridge gradually arises, or another cohort of mainland insects floats on a log onto the island, the two populations will not recognize each other as the same species (or not like each other enough to mate, or not having fertile eggs or offspring). Thus, they have also become reproductively isolated, thus, by definition, they have become two separate species. Speciation occured. This type of speciation, where a geographic barrier separates two parts of a population preventing gene flow between them is called allopatric speciation, and is much better documented and much less controversial than sympatric speciation.

Billions of such speciation events, meaning branching of species into two or more species, resulted in the evolution of all species of organisms on Earth from a single common ancestor (a very primitive bacterium) over a period of more than 3.5 billion years.


Read:
Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 13, 21, 22, 23 and 24.

Watch animation:
Evolution

Further readings:
Understanding Evolution
What is Evolution?
Introduction to Evolutionary Biology
Evolution FAQs
Index to Creationist Claims
Talk Design Articles
Talk Reason
Transitions

Previously in this series:
Biology and the Scientific Method
Cell Structure
Protein Synthesis: Transcription and Translation
Cell-Cell Interactions
Cell Division and DNA Replication
Cell Differentiation and Embryonic Development
Genotype and Phenotype

Technorati Tag: teaching-carnival

Carnivals

Carnival of Education #67 is up on a Education Wonks.

Animal-themed Carnival of Homeschooling #20 is up on Home Sweet Home.

From Genes To Traits: How Genotype Affects Phenotype

How Genotype Affects Phenotype

BIO101 - Bora Zivkovic - Lecture 2 - Part 3

One often hears news reports about discoveries of a "gene for X", e.g., gene for alcoholism, gene for homosexuality, gene for breast cancer, etc. This is an incorrect way of thinking about genes, as it implies a one-to-one mapping between genes and traits.

This misunderstanding stems from historical precedents. The very first genes were discovered decades ago with quite primitive technology. Thus, the only genes that could be discovered were those with large, dramatic effects on the traits. For instance, a small mutation (change in the sequence of nucleotides) in the gene that codes for RNA that codes for one of the four elements of the hemoglobin protein results in sickle-cell anemia. The red blood cells are, as a result, mishapen and the ability of red blood cells to carry sufficient oxygen to the cells is diminished.

Due to such dramatic effects of small mutations, it was believed at the time that each gene codes for a particular trait. Today, it is possible to measure miniscule effects of multiple genes and it is well understood that the "one gene/one trait" paradigm is largely incorrect. Most traits are affected by many genes, and most genes are involved in the development of multiple traits.
A genome is all the genetic information of an individual. Each cell in the body contains the complete genome. Genomes (i.e., DNA sequences) differ slightly between individuals of the same species, and a little bit more between genomes of closely related species, yet even more between distantly related species.

Exact DNA sequence of an individual is genotype. The collection of all observable and measurable traits of that individual is phenotype.

If every position and every function of every cell in our bodies was genetically determined, we would need trillions of genes to specify all that information. Yet, we have only about 30,000 genes. All of our genes are very similar to the equivalent genes of chimpanzees, yet we are obviously very different in anatomy, physiology and behavior from chimpanzees. Furthermore, we share many of the same genes with fish, insects and even plants, yet the differences in phenotypes are enormous.

Thus, it follows logically that the metaphor of the genome as a blueprint for building a body is wrong. It is not which genes you have, but how those genes interact with each other during development that makes you different from another individual of the same species, or from a salmon or a cabbage.

But, how do genes interact with each other? Genes code for proteins. Some proteins interact with other proteins. Some proteins regulate the transcription or replication of DNA. Other proteins are enzymes that modify other chemicals. Yet other proteins are structural, i.e., become parts of membranes and other structures.

A slight difference in the DNA sequence will have an effect on the sequence of RNA and the sequence of the resulting protein, affecting the primary, secondary and tertiary structure of that protein. The changes in 3D shape of the protein will affect its efficiency in performing its function.

For instance, if two proteins interact with each other, and in order to do so need to bind each other, and they bind because their shapes fit into each other like lock and key, then change of shape of one protein is going to alter the efficiency of binding of the two. Changes in shapes of both proteins can either slow down or speed up the reaction. Change of rate of that one reaction in the cell will have effects on some other reaction in the cell, including the way the cell reacts to the signals from the outside.

Thus genes, proteins, other chemicals inside the cell, intercellular interactions and the external environment ALL affect the trait. Most importantly, as the traits are built during development, it is the interactions between all these players at all levels of organizations during development that determine the final phenotype of the organism.
The importance of the environment can be seen from the phenomenon of the norm of reaction. The same genotype, when raised in different environments results in different phenotypes. Furthermore, different genotypes respond to the same environmental changes differently from each other. One genotype may produce a taller plant at higher elevation while a slightly different genotype may respond quite the opposite: producing a shorter plant at higher elevations.
So, if genes do not code for traits, and the genome is not a blueprint, what is the best way to think about the genome and the genotype/phenotype mapping? I have given you handouts (see below) with four different alternative metaphors, any one of which, I hope, will feel clear and memorable to each student. I will now give you a fifth such metaphor, one of my own:

Imagine that a cell is an airplane factory. It buys raw materials and sells finished airplains. How does it do so? The proteins are the factory workers. Some of them import the materials, others are involved in the sale of airplanes. Some guard the factory from thieves, while others cook and serve food in the factory cafeteria.

But the most important proteins of this cell are those that assemble the parts of airplanes. When they need a part, e.g., a propeller, they go to the storeroom (nucleus) and check the Catalogue Of Parts (the DNA), and press the button to place an order for a particular part. Other proteins (storeroom managers) go inside and find the correct part and send it to the assembly floor (endoplasmatic reticulum).

But, protein workers are themselves robots assembled out of parts right there in the same factory, and the instructions for their assembly are also in the Catalogue of Parts (DNA) in the nucleus.

Handouts:

How do you wear your genes? by Richard Dawkins.
An analogy for the genome by Richard Harter.
It's not just the genes, it's the links between them by Paul Myers
PZ Myers' Own Original, Cosmic, and Eccentric Analogy for How the Genome Works -OR- High Geekology by Paul Myers

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 17.3 and 21.

Previously in this series:

Biology and the Scientific Method
Cell Structure
Protein Synthesis: Transcription and Translation
Cell-Cell Interactions
Cell Division and DNA Replication
Cell Differentiation and Embryonic Development

Technorati Tag: teaching-carnival

From Two Cells To Many: Cell Differentiation and Embryonic Development

Cell Differentiation and Embryonic Development

BIO101 - Bora Zivkovic - Lecture 2 - Part 2

There are about 210 types of human cells, e.g., nerve cells, muscle cells, skin cells, blood cells, etc. Wikipedia has a nice comprehensive listing of all the types of human cells.

What makes one cell type different from the other cell types? After all, each cell in the body has exactly the same genome (the entire DNA sequence). How do different cells grow to look so different and to perform such different functions? And how do they get to be that way, out of homogenous (single cell type) early embryonic cells that are produced by cell division of the zygote (the fertilized egg)?
The difference between cell types is in the pattern of gene expression, i.e., which genes are turned on and which genes are turned off. Genes that code for enzymes involved in detoxification are transribed in lver cells, but there is not need for them to be expressed in muscle cells or neurons. Genes that code for proteins that are involved in muscle contraction need not be transcribed in white blood cells. The patterns of gene expression are specific to cell types and are directly resposible for the differences between morphologies and functions of different cells.
How do different cell types decide which genes to turn on or off? This is the result of processes occuring during embryonic development.

The zygote (fertilized egg) appears to be a sphere. It may look homogenous, i.e., with no up and down, left or right. However, this is not so. The point of entry of the sperm cell into the egg may provide polarity for the cell in some organisms. In others, mother may deposit mRNAs or proteins in one particular part of the egg cell. In yet others, the immediate environment of the egg (e.g., the uterine lining, or the surface of the soil) may define polarity of the cell.

When the zygote divides, first into 2, then 4, 8, 16 and more cells, some of those daughter cells are on one pole (e.g., containing maternal chemicals) and the others on the other pole (e.g., not containing maternal chemicals). Presence of chemicals (or other influences) starts altering the decisions as to which genes will be turned on or off.

As some of the genes in some of the cells turn on, they may code for proteins that slowly diffuse through the developing early embryo. Low, medium and high concentrations of those chemicals are found in diferent areas of the embryo depending on the distance from the cell that produces that chemical.

Other cells respond to the concentration of that chemical by turning particular genes on or off (in a manner similar to the effects of steroid hormones acting via nuclear receptors, described last week). Thus the position (location) of a cell in the early embryo largely determines what cell type it will become in the end of the process of the embryonic development.

The process of altering the pattern of gene expression and thus becoming a cell of a particular type is called cell differentiation.

The zygote is a totipotent cell - its daughter cells can become any cell type. As the development proceeds, some of the cells become pluripotent - they can become many, but not all cell types. Later on, the specificity narrows down further and a particular stem cell can turn into only a very limited number of cell types, e.g., a few types of blood cells, but not bone or brain cells or anything else. That is why embryonic stem cell research is much more promising than the adult stem cell research.
The mechanism by which diffusible chemicals synthesized by one embryonic cell induces differentiation of other cells in the embryo is called induction. Turning genes on and off allows the cells to produce proteins that are neccessary for the changes in the way those cells look and function. For instance, development of the retina induces the development of the lens and cornea of the eye. The substance secreted by the developing retina can only diffuse a short distance and affect the neighboring cells, which become other parts of the eye.

During embryonic development, some cells migrate. For instance, cells of the neural crest migrate throughout the embryo and, depending on their new "neighborhood" differentiate into pigment cells, cells of the adrenal medula, etc.

Finally, many aspects of the embryo are shaped by programmed cell death - apoptosis. For instance, early on in development our hands look like paddles or flippers. But, the cells of our fingers induce the cell death of the cells between the fingers. Similarly, we initially develop more brain cells than we need. Those brain cells that establish connections with other nerve cells, muscles, or glands, survive. Other brain cells die.

Sometimes just parts of cells die off. For instance, many more synapses are formed than needed between neurons and other neurons, muscles and glands. Those synapses that are used remain and get stronger, the other synapses detach, and the axons shrivel and die. Which brain cells and which of their synapses survive depends on their activity. Those that are involved in correct processing of sensory information or in coordinated motor activity are retained. Thus, both sensory and motor aspects of the nervous system need to be practiced and tested early on. That is why embryos move, for instance - testing their motor coordination. That is why sensory deprivation in the early childhood is detrimental to the proper development of the child.

The details of embryonic development and mechanisms of cell differentiation differ between plants, fungi, protists, and various invertebrate and vertebrate animals. We will look at some examples of those, as well as some important developmental genes (e.g., homeotic genes) in future handouts/discussions, and will revisit the human development later in the course.

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 18 and 19.

Previously in this series:

Biology and the Scientific Method
Cell Structure
Protein Synthesis: Transcription and Translation
Cell-Cell Interactions
Cell Division and DNA Replication

Technorati Tag: teaching-carnival

Tangled Bank - call for submissions

Next edition of Tangled Bank, the blog carnival covering science, nature, medicine, environment and the intersection between science and society, will be held on Wednesday, May 24th, on my other blog, Science And Politics. Send your entries by Tuesday, May 23th at 5pm (Eastern) to: Coturnix1 AT aol DOT com.

From One Cell To Two: Cell Division and DNA Replication

Cell Division and DNA Replication

BIO101 - Bora Zivkovic - Lecture 2 - Part 1

In the first lecture, we covered the way science works and especially how the scientific method applies to biology. Then, we looked at the structure of the cell, building a map of the cell - knowing what processes happen where in the cell, e.g., the production of energy-rich ATP molecules in the mitochondria.

In the third part of the lecture, we took a closer look at the way DNA code gets transcribed into RNA in the nucleus, and the RNA code translated into protein structure in the rough endoplasmatic reticulum. Finally, we looked at several different ways that cells communicate with each other and with the environment, thus modifying cell function.

All of that information will be important in this lecture, as we cover the ways cells divide, how cell-division, starting with a fertilized cell, builds an embryo, how genetic code (genotype) influences the observable and measurable traits (phenotype) and, finally, how do these processes affect the genetic composition of the populations of organisms of the same species - the process of evolution.

Mitosis

The only way to build a cell is by dividing an existing cell into two. As the genome (the complete sequence of the DNA) is an essential part of a cell, it is neccessary for the DNA to be duplicated prior to cell division.

In Eukaryotic cells, chromosomes are structures composed mostly of DNA and protein. DNA is a long double-stranded chain-like molecule. Some portions of the DNA are permanently coiled and covered with protective proteins to prevent DNA expression (transcription). Other parts can be unraveled so transcription can occur.

The number of chromosomes is different in different species. Human cells possess 23 pairs of chromosomes. Prior to cell division each chromosome replicates producing two identical sister chromosomes - each eventually landing in one of the daughter cells.

The process of DNA replication - the way all of the DNA code of the mother cell duplicates and one copy goes into each daughter cell - is the most important aspect of cell division. It is wonderfully described in your handout and depicted in the animation. Other cell organelles also divide and split into two daughter cells. Once the process of DNA replication is over, the new portion of the cell membrane gets built transecting the cell and dividing all the genetic material into two cellular compartments, leading the cell to split into two cells.
Meiosis

Meiosis is a special case of cell division. While mitosis results in division of all types of cells in the body, meiosis results in the formation of sex cells - the gametes: eggs and sperm. Mitosis is a one-step process: one cell divides into two. Meiosis is a two-step process: one cell divides into two, then each daughter immediately divides again into two, resulting in four grand-daughter cells.

Each cell in the body has two copies of the entire DNA - one copy received from the mother, the other from the father. Fertilization (fusion of an egg and a sperm) would double the chromosome number in each generation if the egg and sperm cells had the duplicate copy. Meiosis ensures that gametes have only one copy of the genome - a mix of maternal and paternal sequences. Such a cell is called a haploid cell.

Once the egg and a sperm fuse, the resulting zygote (fertilized egg) again contains double dose of the DNA and is called a diploid cell. Thus the resultant zygote inherits genetic material from both its father and its mother. All the cells in the body except for the gametes are diploid. Sexual reproduction produces offspring that are genetically different from either parent.

DNA Replication

DNA replication is a complex process of duplication of the DNA involving many enzymes. It is the first and the most important process in cell division. Please read the handout (BREAKFAST OF CHAMPIONS DOES REPLICATION by David Ng) to appreciate the complexity of the process, but you do not need to memorize any of the enzymes for the exams. Also, it will help your understanding of the process if you watch this animation.

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 11, 12 and 14.

Further reading:

THE CELL CYCLE: A UNIVERSAL CELLULAR DIVISION PROGRAM By David Secko

Previously in this series:

Biology and the Scientific Method
Cell Structure
Protein Synthesis: Transcription and Translation
Cell-Cell Interactions

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Tar Heel Tavern - Learning for a Lifetime

Welcome to The Tar Heel Tavern, the showcase of North Carolina blogging goodness. In keeping with the theme of this blog, as well as the timeliness of the edition coinciding with college graduations and (almost) end of the school year, the entries today all have something to do with learning, teaching or education. It is not a huge edition, but it is all high quality blogging. So, let's get started....

Erin of Poetic Acceptance wrote a post titled Learning. What about it? You will have to click and see for yourself.

Alex Wilson is a teacher and a student, and his instructors are some very famous people: Narcissism and the Wannabe Clarionite

Waterfall of A Sort of Notebook is a teacher, so of course I could pick out several posts and it was hard to narrow the search down to just one, so I decided to include three: The First Steps about the wish to go back to grad school, Three Today - is this a case of burnout or righteous indignation? And I Love My Students - go see why.

From Mel's Kitchen: Goodbye gallbladder, hello low-fat foods is a forced learning experience about healthy eating.

On SpiritBlog you can learn something, I bet, you did not know before: The Gift of the Night Blooming Cereus.

Anonymoses reminds us that they are learning everything about us: Mining the President BACK!

Finally, I started teaching again, and I am posting my lecture notes on my blog.

Next edition of The Tar Heel Tavern will be hosted by an old friend and a repeat offender on the TTHT hall of hosting fame - Ogre of Ogre's Politics and Views.

We have a couple of more hosts lined up, but we always need more, so please volunteer at: Coturnix1 AT aol DOT com.

Carnivalia

Teaching Carnival #9 is up at Adventures in Ethics and Science.

Carnival of Education #66 is up on HUNBlog.

Carnival of Homeschooling is up on Why Homeschool.

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Cell-Cell Interactions

BIO101 - Bora Zivkovic - Lecture 1 - Part 4

Cell-cell interactions

Cells do not exist in complete isolation. For a coordinated function of cells in a tissue, tissues in an organ, organs in a system and systems in the body, cells need to be able to communicate with each other. Each cell should be capable of sending chemical signals to other cells and of receiving chemical signals from oter cells, as well as signals (chemical or other) from its immediate environment.

Cell membrane is a double layer of molecules of fat. Some small chemical messengers are capable of passing through the membrane. Most ions and most molecules cannot pass through the membrane, thus the information between the inside and the outside of the cell is mediated by proteins embedded in the membrane.

Membrane proteins serve various functions. For instance, such proteins form tight junctions that serve to glue neighboring cells together and prevent passage of substances between the two cells. Other surface proteins are involved in cell-cell recognition, which is important for the immune response. Other membrane proteins serve functions in communication between the inside of the cell and the cell's immediate environment.

How does a cell send a signal?

A cell can communicate signals to other cells in various ways. Autocrine signaling is a way for a cell to alter its own extracellular environment, which in turn affects the way the cell functions. The cell secretes chemicals outside of its membrane and the presence of those chemicals on the outside modifies the behavior of that same cell. This process is important for growth.

Paracrine signaling is a way for a cell to affect the behavior of neighboring cells by secreting chemicals into the common intercellular space. This is an important process during embryonic development.

Endocrine signaling utilizes hormones. A cell secretes chemicals into the bloodstream. Those chemicals affect the behavior of distant target cells. We will go into more details of autocrine, paracrine and endocrine signaling later on, when we tackle the human endocrine system.

Direct signaling is a transfer of ions or small molecules from one cell to its neighbor through pores in the membrane. Those pores are built out of membrane proteins and are called gap junctions. This is the fastest mode of cell-cell communication and is found in places where extremely fast and well-coordinated activity of cells in needed. An example of this process can be found in the heart. The muscle cells in the heart communicate with each other via gap junctions which allows all heart cells to contract almost simultaneously.
Finally, synaptic signaling is found in the nervous system. It is a highly specific and localized type of paracrine signalling between two nerve cells or between a nerve cell and a muscle cell. We will go into details of synaptic signaling when we cover the human nervous system.

How does a cell receive a signal?

Some small molecules are capable of entering the cell through the plasma membrane. Nitrous oxide is one example. Upon entering the cell, it activates an enzyme.

Some small hormones also enter the cell directly, by passing through the membrane. Examples are steroid hormones, thyroid hormones and melatonin. Once inside the cell, they bind cytoplasmic or nuclear receptors. The hormone-receptors complex enters the nucleus and binds to a particular sequence on the DNA. Binding dislodges a protein that inhibits the expression of the gene at that segment, so the gene begins to be transcribed and translated. Thus, a new protein appears in the cell and assumes its normal function within it (or gets secreted). The action of nuclear receptors is slow, as it takes some hours for the whole process to occur. The effect is long-lasting (or even permanent) and changes the properties of the cell. This type of process is important in development, differentiation and maturation of cells, e.g., gametes (eggs and sperm cells).
There are three types of cell surface receptors: membrane enzymes, ion channels, and transmembrane receptors.
When a signaling chemical binds to the membrane enzyme protein on the outside of the cell, this triggers a change in the 3D conformation of that protein, which, in turn, triggers a chemical reaction on the inside of the cell.

When a signaling molecule binds to an ion channel on the outside of the cell, this triggers the change of the 3D conformation of the protein and the channel opens, allowing the ions to move in or out of the cell following their electrical gradients and thus altering the polarization of the cell membrane. Some ion channels respond to non-chemical stimuli in the same way, including changes in electrical charge or mechanical disturbance of the membrane.
G protein-linked receptors are seven-pass transmembrane proteins. This means that the polypeptide chain traverses the membrane seven times. When a chemical - a hormone or a pharmaceutical agent - binds to the receptor on the outside of the cell, this triggers a series of chemical reactions, including the movement and binding of the G-protein, transformation of GTP into GDP and activation of second messengers. Second messengers (e.g., cyclic AMP) start a cascade of enzymatic reactions leading to the cellular response. This signaling method is quite fast and, more importantly, it amplifies the signal. Binding of a single hormone molecule quickly results in thousands of molecules of second messengers acting on even more molecules of enzymes and so on. Thus, the response to a small stimulus can be very large. We will go into details of G-protein-mediated signaling when we tackle the endocrine and the sensory systems.
References:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapter 7.

Previously in this series:
Biology and the Scientific Method
Cell Structure
Protein Synthesis: Transcription and Translation

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Protein Synthesis: Transcription and Translation

BIO101 - Bora Zivkovic - Lecture 1 - Part 3

The DNA code

DNA is a long double-stranded molecule residing inside the nucleus of every cell. It is usually tightly coiled forming chromosomes in which it is protected by proteins.

Each of the two strands of the DNA molecule is a chain of smaller molecules. Each link in the chain is composed of one sugar molecule, one phosphate molecule and one nucleotide molecule. There are four types of nucleotides (or 'bases') in the DNA: adenine (A), thymine (T), guanine (G) and cytosine (C). The two strands of DNA are structured in such a way that an adenine on one strand is always attached to a thymine on the other strand, and the guanine of one strand is always bound to cytosine on the other strand. Thus, the two strands of the DNA molecule are mirror-images of each other.

The exact sequence of nucleotides on a DNA strand is the genetic code. The total genetic code of all of the DNA on all the chromosomes is the genome. Each cell in the body has exactly the same chromosomes and exactly the same genome (with some exceptions we will cover later).

A gene is a small portion of the genome - a sequence of nucleotides that is expressed together and codes for a single protein (polypeptide) molecule.

Cell uses the genes to synthetise proteins. This is a two-step process. The first step is transcription in which the sequence of one gene is replicated in an RNA molecule. The second step is translation in which the RNA molecule serves as a code for the formation of an amino-acid chain (a polypeptide).
Transcription

For a gene to be expressed, i.e., translated into RNA, that portion of the DNA has to be uncoiled and freed of the protective proteins. An enzyme, called DNA polymerase, reads the DNA code (the sequence of bases on one of the two strands of the DNA molecule) and builds a single-stranded chain of the RNA molecule. Again, where there is a G in DNA, there will be C in the RNA and vice versa. Instead of thymine, RNA has uracil (U). Wherever in the DNA strand there is an A, there will be a U in the RNA, and wherever there is a T on the DNA molecule, there will be an A in the RNA.

Once the whole gene (100s to 10,000s of bases in a row) is transcribed, the RNA molecule detaches. The RNA (called messenger RNA or mRNA) may be further modified by addition of more A bases at its tail, by addition of other small molecules to some of the nucleotides and by excision of some portions (introns) out of the chain. The removal of introns (the non-coding regions) and putting together the remaining segments - exons - into a single chain again, is called RNA splicing. RNA splicing allows for one gene to code for multiple related kinds of proteins, as alternative patterns of splicing may be controlled by various factors in the cell.

Unlike DNA, the mRNA molecule is capable of exiting the nucleus through the pores in the nuclear membrane. It enters the endoplasmatic reticulum and attaches itself to one of the membranes in the rough ER.
Translation

Three types of RNA are involved in the translation process: mRNA which carries the code for the gene, rRNA which aids in the formation of the ribosome, and tRNA which brings individual amino-acids to the ribosome. Translation is controlled by various enzymes that recognize specific nucleotide sequences.

The genetic code (nucleotide sequence of a gene) translates into a polypeptide (amino-acid sequence of a protein) in a 3-to-1 fashion. Three nuclotides in a row code for one amino-acid. There are a total of 20 amino-acids used to build all proteins in our bodies. Some amino-acids are coded by a single triplet code, or codon. Other amino-acids may be coded by several different RNA sequences. There is also a START sequence (coding for fMet) and a STOP sequence that does not code for any amino-acid. The genetic code is (almost) universal. Except for a few microorganisms, all of life uses the same genetic code.

When the ribosome is assembled around a molecule of mRNA, the translation begins with the reading of the first triplet. Small tRNA molecules bring in the individual amino-acids and attach them to the mRNA, as well as to each other, forming a chain of amino-acids. When a stop signal is reached, the entire complex disassociates. The ribosome, the mRNA, the tRNAs and the enzymes are then either degraded or re-used for another translational event.

Protein synthesis - post-translational modifications

Translation of the DNA/RNA code into a sequence of amino-acids is just the beginning of the process of protein synthesis.

The exact sequence of amino-acids in a polypeptide chain is the primary structure of the protein.

As different amino-acids are molecules of somewhat different shapes, sizes and electrical polarities, they react with each other. The attractive and repulsive forces between amino-acids cause the chain to fold in various ways. The three-dimensional shape of the polypeptide chain due to the chemical properties of its component amino-acids is called the secondary structure of the protein.

Enzymes called chaperonins further modify the three-dimensional structure of the protein by folding it in particular ways. The 3D structure of a protein is its most important property as the functionality of a protein depends on its shape - it can react with other molecules only if the two molecules fit into each other like a key and a lock. The 3D structure of the fully folded protein is its tertiary structure.

Prions, the causes of such diseases as Mad Cow Disease, Scabies and Kreutzfeld-Jacob disease, are proteins. The primary and secondary structure of the prion is almost identical to the normally expressed proteins in our brain cells, but the tertiary structure is different - they are folded into different shapes. When a prion enters a healthy brain cell, it is capable of denaturing (unwinding) the native protein and then reshaping it in the same shape as the prion. Thus one prion molecule makes two - those two go on and make four, those four make eight, and so on, until the whole brain is just one liquifiied spongy mass.

Another aspect of the tertiary structure of the protein is addition of small molecules to the chain. For instance, phosphate groups may be attached to the protein (giving it additional energy). Also, short chains of sugars are usually bound to the tail-end of the protein. These sugar chains serve as "ZIP-code tags" for the protein, informing carrier molecules exactly where in the cell this protein needs to be carried to (usually within vesicles that bud off the RER or the Golgi apparatus). The elements of the cytoskeleton are used as conduits ("elevators and escalators") to shuttle proteins to where in the cell they are needed.

Many proteins are composed of more than one polypeptide chain. For instance, hemoglobin is formed by binding together four subunits. Each subunit also has a heme molecule attached to it, and an ion of iron attached to the heme (this iron is where oxygen binds to hemogolobin). This larger, more complex structure of the protein is its quaternary structure.

See animations:
Transcription
Translation

References:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 3, 14 and 15.

Previously in this series:
Biology and the Scientific Method
Cell Structure

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Cell Structure

BIO 101 - Bora Zivkovic - Lecture 1 - Part 2

The Cell

All living organisms are composed of one or more cells - the cell is the unit of organization of Life.

Most cells are very small. Exceptions? Ostrich egg is the largest cell. Nerve cell in a leg of a giraffe may be as long as 3m, but is very thin.

Basic Structure of the Cell

A cell is a small packet or bag of liquid. The liquid is cytoplasm (or cytosol), which is essentially salty water with various organic molecules suspended in it.

The cytoplasm is contained within a cell membrane. Cell membrane is a phospholypid bilayer - this means that it is composed of two layers of tighly packed molecules of fat. Within the membrane, proteins are embedded into the bilipid layer and are more or less free to move around within the membrane. These proteins are important for the communication between the inside and outside of the cell.

You can see a good image here.

On the outside of the membrane, some cells may have additional structures. For instance, many bacterial and plant cells have thick cell walls that confer more rigidity to the cell as well as better defense against mechanical, chemical or biological insults.

Some cells also have hair-like cilia on the surface (e.g., a protist called Silver Slipper), or long whip-like flagella at one end (e.g., sperm cells). Both of these structures allow the cell to move utilizing its own energy.

Inside every cell, there is hereditary material - DNA. Exceptions? Red blood cells which have a membrane and cytoplasm, but no hereditary material.

Differences between prokaryotes and eukaryotes:

Prokaryotes (bacteria) have a cell membrane and cytoplasm and no other organelles.
Eukaryotes (plants, animals, fungi, protista) have a number of different cell organelles.

The nuclear material in Prokaryotes is a single, circular strand of DNA.
The nuclear material in Eukaryotes is organized in multiple chromosomes contained with a nucleus.

Cell Organelles

Eukaryotic cells have organelles. Organelles are subcellular structures that provide internal compartmentalization and other functions.

Nuclues is a large membrane-bound organelle. Its function is to sequester the DNA from the rest of the cell. The nuclear membrane (or nuclear envelope), which is also a phospholipid bilayer, selectively allows molecules to pass between the nucleus and cytoplasm. Inside the nucleus, DNA is organized in chromosomes. A chromosome is a tighly coiled and wound strand of DNA packaged with various proteins (e.g,. histones).

Smooth endoplasmic reticulum is a system of membranes and is involved in carbohydrate and lipid synthesis.

Rough endoplasmic reticulum is a system of membranes that possesses ribosomes. Proteins are synthesized in the rough ER.

Golgi apparatus stores and packages various molecules. When a molecule is needed elsewhere in the cell, a portion of the Golgi membrane closes off and forms a vesicle that can be transported around the cell.

Some eukaryotic organelles contain a little bit of their own DNA: the mitochondria and the chloroplasts. These two organelles used to be intercellular parasites, i.e., different species of bacteria that, over time, became an integral part of a cell.

Chloroplasts are found in plant cells. Photosynthesis is the process that occurs in them.

Mitochondria are found in all Eukaryotic cells. Breakdown of glucose begins in the cytoplasm and ends in the mitochondria, where the final products of the breakdown are ATP, water, CO2 and heat. This process requires oxygen - that is why we breath: to provide the oxygen for the mitochodria and to get rid of carbon dioxide produced in the mitochondria.

ATP (adenosine triphosphate) is the energy currency of the living world. Every cellular process that requires energy gets it from ATP. Thus, mitochondria are sometimes refered to as "factories of the cell".

The final portion of the process of glucose digestion (the Krebs cycle) is, like any process, not 100% efficient. Errors happen and not every atom of every glucose molecule ends up where it should: in ATP, water or CO2. The result of this inefficiency is production of heat and production of highly reactive small molecules called free radicals (e.g., hydrogen peroxyde, H2O2). Free radicals tend to quickly react with whatever molecule they first encounter upon leaving the mitochondria. Such reactions damage those molecules, be they proteins, lipids, sugars or nucleic acids. The intercellular damage caused by free radicals is one aspect of the process of aging.

Some animals - birds and mammals - have harnessed the heat production by the mitochondria to keep a stable internal temperature. The efficiency of the mitochondrial "machine" is held low under the control of hormones like thyroid hormones. As a result, there is a greater production of free radicals, so warm-blooded animals evolved particularly good mechanisms for neutralizing free radicals and for repairing the damage. If a person keeps a constant low temperature or constant low-grade fever, the first thing the physician will check is the function of the thyroid gland.

The cytoskeleton, composed of filaments and microtubules, anchors the organelles and gives a cell its shape. Microtubules move organelles, including vesicles, within a cell. They also move the membrane-embedded proteins around where they are needed.

References:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapter 5

Previously in this series:
Biology and the Scientific Method

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Biology and the Scientific Method

This is the summary of the first part of the first lecture in Introduction to Life Science (this is a science requirement for non-science majors at an accelerated adult education program at a community college). The summary is more than just a series of bulleted points to be memorized, but it also does not contain all the examples, details, anecdotes, jokes, veering off on tangents, answering students’ questions etc. nor does it contain all the graphics, including those drawn on the whiteboard over the course of the lecture.

BIO101 - Bora Zivkovic - Lecture 1, Part 1

Introduction to Biology and the Scientific Method

A. Biology and Life

Biology is the science that studies life. What is life?

Unlike non-living matter, living things exhibit the following properties:

Order: a hierarchical organization (a 'nested hierarchy’, like Russian dolls). This means that organisms are composed of organs that work together in a systematic manner, the organs are composed of tissues, tissues of cells, cells of organelles, organelles of molecules and molecules of atoms, with the entire organization built in a way that maximizes the internal order, survival and reproduction of the organism.

Crystals exhibit order, but it is not hierarchical, and does not give the crystal a maximal chance of survival and reproduction. In living organisms, the properties of higher levels of organization cannot, unlike in crystals, be explained by the elements at the lower level of organization. Interactions between lower-level elements result in emergent properties at higher levels. For instance, from the order of nucleotides in the DNA we cannot infer how the whole organism looks like or behaves because the sequence does not specify the rules of interactions between the genes, gene-products (proteins), cells during development, and organisms inside their environments.

Sensitivity: response to stimuli in the environment. Even the simplest organisms, like bacteria, are capable of sensing changes in the environment and responding to such changes - they may swim away from or towards areas with higher concentrations of nutrients, salt, oxygen, or levels of illumination. Such responses (e.g., swimming) are active. A seed or a spore, seemingly "dead", will actively respond to good growing conditions by germinating. A piece of dead matter may expand or even melt at high temperature, but that response is passive - due purely to the laws of physics.

Growth, Development and Reproduction: having a life-cycle. Crystals may grow, but the growth does not change the basic organization of the crystal. On the other hand, growth of an organism is accompanied by reorganization, cell division and cell differentiation. Each organism, at least during some parts of its life cycle, undergoes growth, developmental changes, and production of offspring. The results of reproduction - the offspring - are similar to the parent(s) due to the code inherited via a molecule, either DNA or RNA.

Regulation: All organisms have evolved well-orchestrated biochemical, physiological and behavioral mechanisms that regulate all the organism's functions, which include finding and ingesting nutrients, processing nutrients and supplying all cells with the end-products of such processing, sequestering and eliminating the by-products of nutrient use. Likewise, every organism has evolved elaborate mechanisms for absorbing, storing, converting, using and dissipating energy - this last criterion may be the most important criterion for testing if something is alive or not, e.g., if one discovers a potentially living form on another planet.

Homeostasis: maintaining relatively constant internal conditions. We will cover this in much detail when we start the unit on human anatomy and physiology.

We will study the details of all five of the above criteria in this course. During the first three lectures, we will look at general properties of living organisms at all levels, from molecules, organelles and cells, through tissues, organs, systems and organisms, to populations, species, communities and ecosystems. During the remainder of the course we will take a look at specific cases: bacteria, protista, fungi, plants and animals, as well as details of the functioning of the human body.

A. Scientific Method and Process

Deductive reasoning applies general principles to predict specific results. Inductive reasoning uses specific observations to construct general principles. Here is a brief description of the steps in the hypothetico-deductive method:

Scientists make observations of processes and events found in nature.

The observations lead to questions: what is this, how does it work, why does it work the way it does? This may necessitate further observations to be made.

The questions are then asked in a form that suggests a possible explanation (hypothesis) for the observations. Scientists try to come up with all possible explanations and pit them against each others as alternative hypotheses.

Using the available knowledge and understanding of the related phenomena, the scientist makes a best guess at which of the alternative hypotheses is most likely to be correct.

Experiments are designed in such a way that one or more hypotheses are tested. This means that the experiment is geared specifically towards rejecting one's favored hypothesis: it is directly testing if that hypothesis is wrong. If the results are positive, the favored hypothesis is not rejected, but the alternative hypotheses may be rejected. If the results are negative, the favored hypothesis is rejected and one or more of the alternative hypotheses are accepted and further directly tested.

Often, two experiments are conducted at the same time. In one experiment, all the variables are kept constant except one, while the other experiment is called the control experiment, and in that experiment, that variable is left unaltered. The results of the two experiments are compared to each other using statistical methods to determine if the tested variable (the one not kept constant) indeed has an effect on the outcome.

After performing a series of experiments, a paper is written that provides some background information, describes the experimental methods and results, provides the statistical analysis, and draws conclusions from the results. The paper is then submitted for peer review and published in a scientific journal. We will take a look at some real scientific papers later on in the course, so you can see the structure and form of it and be able to find and read such primary literature.

Once all but one alternative hypothesis has been rejected over a series of experiments, the one remaining hypothesis is further tested. The hypothesis, if correct, can be used to make predictions which can be directly tested in subsequent experiments. Predictions provide a way to test the validity of a hypothesis.

As more and more studies are done and the hypothesis gets stronger and stronger (as all possible alternatives get rejected), it grows in its predictive power and it may also grow in its ability to explain a broader range of phenomena. Once a hypothesis reaches the stage at which it is supported with large amounts of evidence after repeated testing, it becomes a theory.

A theory is a body of interconnected concepts most strongly supported by scientific reasoning and experimental evidence. It is a scientific term that is used to denote the scientific concepts that have stood the test of time and are best supported by experimental evidence.

This sense of the word "theory" - the scientific ideas with the greatest certainty that they are correct - is in contrast to the colloquial use of the term, which means almost opposite - lack of certainty (as in "it's my theory that Secretariat was the greatest American athlete of all times", or "it's just a theory - nothing you should trust on its face"). Purveyors of pseudoscience (for financial, religious or political reasons) like to utilize the difference between the two senses of the word, dishonestly implying that a scientific theory they don't like is uncertain when just the opposite is true.

The strongest theories are those that are supported by a wide variety of kinds of evidence. Theory of evolution is one of the best supported theories of all science not only because it is backed up by mountains of evidence (and no evidence against it), but also because the evidence comes from many different areas of science: paleontology (fossils), biogeography, ecology, mathematical modeling, population and quantitative genetics, comparative genomics, medicine, agricultural breeding, study of animal behavior, comparative anatomy, comparative physiology and comparative embryology.

The way disparate data from quite different areas of science, when put together, all strengthen a single theory, is called consilience. Recently, this word has been misused in popular literature (including a book of the same name) and press to mean quite the opposite – taking the methodology or findings from one discipline and applying it to a variety of other disciplines, e.g., taking the logic of evolution by natural selection and applying it to chemistry, pharmacology, psychology or computer science. That is a worthy endeavor, but it not a correct meaning of the term ‘consilience’.

Sometimes you will see (as opposed to the image on p.5 of your textbook) scientific method schematically depicted like this:

There are two reasons why the Biology textbook does not show a graph like this: a) it is not applicable to biology, and b) it is wrong.

It is wrong because it places “law” above the theory. Actually, the opposite is true – many laws (in physics, for instance) are elements of a greater theory and are parts of the evidence that the theory is correct. Laws are usually mathematical depictions of regular behavior of some aspect of nature. In other words, laws describe nature but do not explain it. Theories explain nature and are thus on the top of the hierarchy of scientific knowledge.

The model above is inapplicable to biology (it was probably drawn by a physicist) because there are no laws in biology. There are rules (like Bergmann-Allen Rule in ecology or Cope’s Rule in evolutionary biology), there are generalizations (e.g., Scaling), there are mathematical models (e.g., in population genetics) and there are Principles (e.g., the Principle of Natural Selection), but there are no laws. Biology deals with processes at much higher levels than does physics, where emergent properties of complex systems introduce a dose of unpredictability. All potential “laws” in biology have many exceptions, or have to be limited to a very small subset of processes, or to a small subset of organisms – they are not exception-less as laws of physics are.

Hypothetico-deductive method described above, while arguably the most powerful part of the scientific method, is not the only one. There is a continuum of scientific “methods” as depicted here (from Brandon 1996):

Collecting the information about all the species of birds and salamanders in the mountains of North Carolina is not a test of hypothesis and is not manipulative (and is not experimental) – yet it is certainly science (place a dot in the bottom right corner of the graph) – it provides important information about the natural world. If patterns emerge from such a survey and prompt new ideas about species distribution, this can then be tested in a more experimental fashion.

Human Genome Project is highly manipulative (and expensive!), yet it is not hypothesis-testing (place a dot in the bottom left corner). Nobody predicted that we would find anything but the four nucleotides known to make up DNA. We had no predictions as what the sequence will be and what would it all mean. Once the work was done, we could use the HGP as a tool for testing new hypotheses, e.g., how many genes do we have, how they are related to the genes of chimps, how diverse are particular gene sequences in human population as a whole, etc.

Paleontology is somewhere in the middle. It is somewhat manipulative (it takes hard work and a lot of people to do it) and it is somewhat hypothesis-testing (place a dot smack in the middle of the graph). Paleontologists do not dig randomly – they dig in particular places on the planet in particular layers of the sediment, looking for fossils of particular kinds of organisms. For instance, a group recently did an excavation in a particular bed of Late Silurian layer, looking specifically for a fossil of an early tetrapod, i.e., a transitional organism between fully aquatic and fully terrestrial mode of life. They discovered exactly that – a fossil named Tiktaalik whose fins were better suited for walking on land than that of fishes (like mudskippers, catfish and lungsfish), yet not completely evolved for land use as in amphibians.

Sometimes nature provides an experiment that tests a hypothesis (a dot in the top right corner). For instance, a biogeographical model of island succession was tested when the volcano Krakatoa erupted and eliminated all life from the island. The scientists went there and observed which organisms flew in from the mainland, in which order, and how the ecosystem passed through several stages until it reached its mature stage, thus confirming (and somewhat modifying) their hypotheses.

No matter how strongly a theory is supported by empirical evidence, it is always theoretically conceivable that one day, some data will come in that will force the scientists to modify or even eliminate the theory. Even if the scientists are 99.999999999999999999999999999999999% certain that the theory is true, it is philosophically incorrect to say that it is 100% true and to call it the Truth with the capital T. That is why scientists, when interviewed in the media, often sound uncertain and wishy-washy, while some quack or pseudoscientist pronounces his absolute certainty. Audience not educated in the scientific method is likely to swallow the pseudoscience bait, hook and sinker because we, as humans, crave certainty. It takes some scientific training to be able to fully embrace and even love uncertainty. That is why it is difficult for scientific knowledge to counteract financially, religiously and politically motivated assaults on it. However, nature does not care about what we like and wish for: the apples will continue to fall down, the continents will continue to move around the globe (causing earthquakes and volcanic eruptions) and the organisms will continue to evolve whether we like it or not, whether we believe in it or not.

References:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapter 1

Tiktaalik web page

Figure 1 from:
Earth Sciences 10, Lecture 1: Scientific Method by Greg Anderson

Figure 2 from:
Brandon, RN, Does biology have laws? The experimental evidence. PSA 1996, vol. 2, 444—457.


Technorati Tag: teaching-carnival

Why Kids Blog?

See what the teachers say about it.

Carnivals

Carnival of Education #65 is up on Education Wonks.

Carnival of Homeschooling #18 is up on The Thinking Mother.

Science and the classroom

From the lab to the classroom:

From Brainethics comes an interesting article (pdf) about a meeting between neuroscientists and teachers. Apparently, a lot of brain science used in pedagogy these days is bogus, yet new stuff either does not exist or is not well known or is not implemented.

Turning a classroom into a computer:

From David Warlcick: The World is Shrinking — and more
The Computer Just Got Bigger

Technorati Tag: teaching-carnival

EduBlogging of the week

Carnival of Education #64 is up on Education Wonks and Carnival of Homeschooling #17 is up on Common Room.

Not more scientists, but more science-literate citizens

James Oblinger, the new President of North Carolina State University (promoted from within after many years as the Dean of the School Of Agriculture And Life Sciences), has a good editorial in today's News and Observer:

Nurturing success in the sciences:

We've all heard the line from President Bush: We need more students to join the "nerd patrol." It's an overly simple solution for a complex problem that imperils the traditions of invention and innovation that America prides itself on.
---------snip----------
To prepare our students to be successful, high-quality education in science, technology, engineering and mathematics is critical. These so-called STEM disciplines are increasingly driving innovation, discovery and economic growth. Some estimates indicate that about one-third of all jobs in the United States require a science or technology competency. The U.S. Department of Commerce projects that science and engineering will be responsible for more than 70 percent of job growth between 2002 and 2012.

Undoubtedly, the focus on problem-solving and critical thinking found in the STEM disciplines serves us well in a variety of fields and in daily life. Basic scientific literacy is necessary to understand many of the complex issues of our day. A solid background in science and math is fundamental to informed participation in modern society and, further, to wise decisions based on sound public policy.
------snip-------------
Among other things, we discussed roadblocks to reasserting U.S. competitiveness, including a poll indicating that 70 percent of American parents believe their school-age children are getting the right amounts of science and math. These parents also, the poll suggests, don't believe the jobs of the future will require more proficiency in science and math.

Perception and reality are on a collision course.

I cannot find which poll he is refering to, but I can imagine that there were three answers: a) my child is getting about the right amount of math and science in school; b) too little math and science, or c) too much math and science. I bet that the percentage of respondents answering c) was not zero. Those would be some fundies, I assume, though their children may not be in public schools anyway. But 70% stating that what they get in US public schools is enough?

Perhaps the most basic and most important strategy is to attract more students to these disciplines. To adequately address the issue on a long-term basis, we must improve our outreach to students and support education in STEM disciplines from kindergarten through graduate school. We must help our children become more aware of career choices in these fields and make careers in them more accessible. And we have to seek ways that will ensure success for students when they come to these subjects and college majors.
-----------snip---------------
It is equally important that as we educate tomorrow's science and math teachers, we're prepared to support them throughout their careers by providing continuing education, mentoring opportunities and classroom support.

I bolded that last sentence.

I think what Oblinger is hinting at throughout the article, but an unprepared mind may not understand, is that arguing for stronger science education does not mean more science majors, or more science Masters, or more science PhDs, or more science professors, but instead more science-literate citizens, people who can understand science reporting, people who can find and evaluate scientific information in libraries and online, people who have been trained in the art of critical thinking, people who are well-educated and well-informed participants in the democracy.

(Cross-posted on Science And Politics)
Technorati Tag: teaching-carnival

Carnivalia

New editions of the Carnival of Education and Carnival of Homeschooling are up now.

On the other hand, what do you think about science blogging?

Technorati Tag: teaching-carnival

Education against politicized science

An interesting article just appeared on PLoS - Biology:
Scientific Illiteracy and the Partisan Takeover of Biology (PDF). Here are a couple of short excerpts - you have to go and read the rest:

-----------snip-------------
Though some see the growing influence of ideology over scientific issues as a threat to America's standing as global science leader, a leading analyst of public attitudes toward science sees it as an opportunity for increasing scientific literacy. “Even though the scientific community can feel besieged by this anti-science sentiment,” says Jon D. Miller, who directs the Center for Biomedical Communications at Northwestern University Medical School, “most people really haven't made up their mind about this issue and, in fact, really haven't even thought about it.” Rather than fretting about the cultural divide—or worse, doing nothing—Miller urges scientists to do their part to bridge the gap.
-----------snip-------------
Most people don't have a cognitive framework for understanding stem cells, Miller explains. “Science happens so fast now that most adults couldn't possibly have learned about stem cells when they were in school.” And without this underlying schema, most people aren't going to pay attention to stem cells or any other unfamiliar scientific term. “People tune out things that they think are scientific or complicated,” he says. “If you are science averse and think you couldn't possibly know any science, the minute you hear ‘cell,’ ‘stem cell,’ ‘nanotechnology,’ ‘atomic,’ ‘nuclear,’ you turn the off switch.”
-----------snip-------------
Since 1979, he says, the proportion of scientifically literate adults has doubled—to a paltry 17%. The rest are not savvy enough to understand the science section of The New York Times or other science media pitched at a similar level. As disgracefully low as the rate of adult scientific literacy in the United States may be, Miller found even lower rates in Canada, Europe, and Japan—a result he attributes primarily to lower university enrollments.
-----------snip-------------
To measure public acceptance of the concept of evolution, Miller has been asking adults if “human beings, as we know them, developed from earlier species of animals” since 1985. He and his colleagues purposefully avoid using the now politically charged word “evolution” in order to determine whether people accept the basics of evolutionary theory. Over the past 20 years, the proportion of Americans who reject this concept has declined (from 48% to 39%), as has the proportion who accept it (45% to 40%). Confusion, on the other hand, has increased considerably, with those expressing uncertainty increasing from 7% in 1985 to 21% in 2005.
-----------snip-------------
It's not that Americans are rejecting science per se, Miller maintains, but longstanding conflicts between personal religious beliefs and selected life-science issues has been exploited to an unprecedented degree by the right-wing fundamentalist faction of the Republican Party. In the 1990s, the state Republican platforms in Alaska, Iowa, Kansas, Oklahoma, Oregon, Missouri, and Texas all included demands for teaching creation science. Such platforms wouldn't pass muster in the election, Miller says, but in the activist-dominated primaries, they drive out moderate Republicans, making evolution a political litmus test. Come November, the Republican candidate represents a fundamentalist agenda without making it an explicit part of the campaign. Last year, Miller points out, former Senator John Danforth, a moderate Missouri Republican, wrote in a New York Times opinion piece that for the first time in American history a political party has become an arm of a religious organization. The United States is the only country in the world where a political party has taken a position on evolution.
-----------snip-------------
The era of nonpartisan science is gone, says Miller, who urges scientists and science educators to learn the rules of this new game and get behind moderate Republicans as well as Democrats to protect the practice and teaching of sound science. Given the partisan attack on evolution and stem-cell research, he thinks scientists need to learn more about how the political process works. They need to be willing to run for the school board, write $500 or even $5,000 checks to support moderate candidates, and defeat Christian right-wing candidates. “Scientists need to become involved in partisan politics and to oppose candidates who reject evolution or attack scientific research,” he says. “It takes time, money, and paying attention to the issues.”
-----------snip-------------
Clearly, increasing scientific literacy is a long-term challenge. The US pre-collegiate science and math education system is broken. US high-school student performance ranks behind every European and Asian country, according to the 2003 Trends in International Math and Science Study conducted by the National Center for Education Statistics. Given that over half of high-school graduates don't go on to get college degrees, that's something to be concerned about. But Miller takes heart from the fact that, unlike any other country in the world, the United States requires the 47% of kids who do go to college to take a year of science—a distinction that may help the United States recover its flagging scientific standing. College professors would do well to remember that today's undergraduates are apt to be functioning 40 to 50 years from now, he says. “It's the last chance to teach people who are going to become important leaders in the community, and we should take this opportunity seriously.”
-----------snip-------------
The limiting step in enhancing scientific literacy is not people's capacity for learning, Miller says, as much as it is interest. When Americans are diagnosed with cancer or some other life-threatening disease, “the vast number of these people go online and learn more science in the next 12 months than a typical undergraduate will ever learn. It is impressive how much people can learn with the proper motivation. We need to get people to be savvy about how to find the information and make sense of it.”

Miller urges scientists to take comfort in the fact that the majority of Americans are not anti-science, but simply don't know how exciting scientific discovery can be. “We must be cautious and not presume that our society feels strongly about what scientists do one way or another. There's a lot of work to be done for us to tell people what we do, why we do it, and why it's important,” he advises. Given the pace of biomedical discoveries in the 21st century, he adds, it's likely that more and more scientific issues will reach the public agenda. “We're going to be revisiting various versions of these questions again and again. But there's a large segment of Americans who still haven't made up their mind on these issues. We in the scientific community have to treat them seriously, talk to them, and make our arguments. This is a great opportunity for us.”
-----------snip-------------

Bolded text is what I thought was interesting to me. As I said, go read the whole thing. The PDF version also has some graphs and images.

(Cross-posted on Science And Politics)

Technorati Tag: teaching-carnival

Another win for academic freedom

I don't know who the current president of Meredith College is (the old guy was just leaving at the time my wife was there), but kudos to the faculty for standing up to her and to her sneaky D-Ho-type friends:

Meredith College faculty reject BB&T money:

The faculty at Meredith College in Raleigh struck a blow for academic freedom Friday, and in so doing, might've cost the college $420,000 from the BB&T Charitable Foundation. At issue: A grant from BB&T--$60,000 a year for seven years--for an honors program featuring, apparently at the bank's insistence, such right-wing texts as Ayn Rand's Atlas Shrugged and Frederick Hayek's The Road to Serfdom.

Read the whole thing for background and details.

A few years back, they decided to get rid of the Southern Baptist sponsorship. Their worries about loosing all that money were apparently unwarranted. Happy with that decision, many others pitched in. Last time I was on campus I saw the brand new science building.

As for the course, I hope that, whoever is teaching the course will use the Rand and Hayek's writing to teach the studnets the critical thinking skills. Those works are alluring and deceptive in their erzatz "sophistication", and can be used fruitfully to teach skills like: fact-checking, detecting logical fallacies, and exploring how dangerous putting such ideas to practice is.

(Cross-posted on Science And Politics)

Technorati Tag: teaching-carnival

Teaching Carnival

The April edition of the Teaching Carnival (higher ed) is up on A Delicate Boy.

Technorati Tag: teaching-carnival

Carnival of Education

Welcome to the 62nd edition of the Carnival of Education. For most of you, this blog may be new, but some of you may be familiar with my other two blogs, the science blog Circadiana and the general-purpose blog Science And Politics. The Magic School Bus is the latest addition to my blogging empire - the third leg of the Triple Crown!

I was wondering what theme to use this time and how to classify the entries. Then, as the posts kept coming in I realized how many of them were practically unclassifable. So I was going to invent some kind of Borges' Chinese Classification of Animals to break down the entries.

Then, yesterday morning, cleaning the house for Passover and pulling out the Haggadahs for tonight, I knew this would just had to be a Passover Edition, and the Ten Plagues are ideal page-breakers placing together vaguely related posts into small groups (click the thumbnails to enlarge images, even the one that at first sight looks just black). How is this carnival different from all the other carnivals?

So, here we go, drop of wine by drop of wine....

* Passover Plague #1: Blood - G-d transformed the water in the Nile River into a river of blood for 7 days, causing the death of fish and leaving the Egyptians with undrinkable water. (Exodus 7:14-25)

Chris Clarke is a science and nature writer who blogs on Creek Running North. His wife is a school teacher and Chris had some thoughts about teaching just Last night.

Sandra Porter keeps Discovering biology in a digital world every day. Euthanasia? Dead issue. Ethical issues in biotechnology: contrasting companies and classrooms.

Janet D. Stemwedel aka Dr. Free-Ride of Adventures in Ethics and Science has been on a roll recently, and produced a four-parter post:
Study suggests U.S. science teaching falls short on content
How to fix science education in the U.S
Not-entirely-random bullets on science teaching as I rush to class
How important is effective teaching to science professors anyway?

* Passover Plague #2: Frogs - G-d created a swarm of frogs that came up out of the Nile river and covered the land of Egypt, infesting Egyptian houses. (Exodus 8:1-25)

Ruchira Paul is an Accidental Blogger and she explores the schoolchildren stereotyping of the image of a "scientist" in What Is Wrong With This Picture?

Editor's Choice #1: Ms. Frizzle (of course the Carnival on The Magic School Bus has to have Ms. Frizzle on board!) has some cool recent anecdotes from the classroom: Kids.

Cameron of My Corner of the Universe asks the perennial question: Physics First?. How about separate courses in physics and chemistry and earth science and biology every year from 5th through 12th grade (the way I had it as a kid)?

* Passover Plague #3: Lice - G-d created a plague of lice from handfuls of dust which swarmed in the air and irritated the skin of the Egyptians and their animals. (Exodus 8:16-19)

Dean Dad confesses something every day and compiles his confessions on a blog. This post really hit a nerve with me, as I am a gen-X-er myself: Generation X Faculty (and Deans): A Response to which Palazzo of The Daily Transcript had his own response: Yet another note on academic life.

Editor's Choice #2: My neighbor David Warlick of 2 Cents Worth explores a new concept in a two-part post: Flat Classrooms and Flat Classrooms - Curious Students.

Brett from The DeHavilland Blog has assembled an impressive list - and added thoughful comments - on How can business make an impact.

* Passover Plague #4: Dog Flies - G-d created the plague of dog flies that bit the Egyptians and attached themselves to their eyelids, but the Hebrews were unaffected by them. (Exodus 8:20-32)

Scott Elliott of Get On the Bus (Which bus? The Magic School Bus?) muses on a recent report: It actually IS harder to get into college today!

Portable classrooms may cause health problems. NYC Educator has the scoop: Trailer Trash.

Marcia Adair wrote a heart-breaking story about growing up too young: Just Another Maniac Monday

* Passover Plague #5: Murrain - murrain means a cattle plague. This is a virus that affects cattle and eventually kills them. Most Egyptian cattle were affected by this plague but the Hebrew cattle were not. (Exodus 9:1-7)

Mr. Lawrence of Get Lost, Mr. Chips is taunted by a particularly "good hearted" student: Haze Me.

Blaming the Student? Don't do it, says D-Ed Reckoning.

Mamacita of Scheiss Weekly has great anecdotes about some colorful characters in her middle school: Both are moist, brown, and strong-smelling. . . . . and The Lazy Boy.

The Art of Getting By may shock you with A Shock To The System - on dealing with children with special needs.

* Passover Plague #6: Boils - G-d sent the plague of boils so that the Egyptians would have great difficulty standing or walking, plus it was very painful to endure. (Exodus 9:8-12)

A Teacher's Perspective thinks positive. And asks us all to think positive. At least for a week. Check the Reality check....

Polski3 is positive. Do you know what a "dam cup" is? Read High BP or a pencil to learn.

Why are male teachers under suspicion when they want to work with younger kids? EdWonk reports in Irrational Suspicion

What would a Carnival of Education be without a post on Testing…testing… . Try also the podcast from The reflective teacher.

* Passover Plague #7: Hail - G-d kept on upping the ante by creating the worst hailstorm ever seen in Egypt until that time. People and animals perished as a result, and the agricultural economy of Egypt was severely damaged. (Exodus 9:13-35)

Harvey and Laurie of Trivium Pursuit provide some good answers to the question: Why Homeschool?

Headmistress, zookeeper of the homeschooling Common Room finds some Hidden Costs of Public Schools.

SpunkyHomeSchool wrote some More on the cost of homeschooling

* Passover Plague #8: Locusts - G-d created a swarm of locusts that covered Egypt, infested Egyptian homes, and ate all the plants left over from the hailstorm. There were clouds of locusts that were so dense, they darkened the sky. (Exodus 10:13-14, 19)

Bill and Melinda Gates concluded that their grants are not working. Scholar's Notebook reports in The failed promise of small learning communities.

National School Boards Association Dislikes Mayoral Control and the Mayor strikes back. Dave of Friends of Dave has the report.

DL of TMH’s Bacon Bits thinks that obedience is a positive trait that needs to be instilled in our children. Or is it just good old discipline: Obedience: In Danger of Extinction?

* Passover Plague #9: Darkness - G-d created darkness over the land of Egypt; it was so dark, one could feel it. The Egyptians could not see anyone in this thick darkness nor leave their houses for 3 days. However, the houses of the Hebrews were filled with light. (Exodus 10:21-29)

Here's a whole series on education politics in Illinois (and other places). Lennie of EducationMatters.US! has some words about the Illinois Big Ed tactics: No Tax Pledge: Bad Public Policy. And from Extreme Wisdom, in a similar vein, The Mob That Whacked Jersey (Or is it Illinois?), from CrossBlogging.com - Univeral Preschool Still In Budget, and from Citizens for Reasonable And Fair Taxes comes The Cost of Remedial Education..

From The Rain of I Thought a Think, looks at the new collective bargaining report from Rick Hess and Martin West: Nitpicking Hess and West: The Hourly Pay Issue

Andrew of EduWonk has his own take on the same report in Casey Turns The Guns On His Own Lines Just Like At [Insert Very Obscure Battle Here]

* Passover Plague #10: Death of the Firstborn Son - The final plague that befell the Egyptians was the slaying of the firstborn son of every Egyptian family, including the firstborn son in the Pharaoh's family. This plague caused the greatest emotional outcry from the Egyptian people, and finally convinced the Pharaoh to let the Hebrews leave Egypt. (Exodus 12:29-36)

Rightwingprof of the Right Wing Nation wrote about The NCC On NCLB. If you know me, you know I disagree, but it is a thought-provoking piece so go and read it for yourself and make your own opinion.

John and Michele of AFT NCLB Blog discuss the first NCLB report. First, John: Where's the Research?. Michele responds: Michele's Response to "Where's the Research?".

Let's finish with Scott Elliott again...or he'll bust your kneecaps.

Also, do not miss the latest edition of Carnival of Homeschooling on Tami's Blog and check out the next edition of the Teaching Carnival, coming up on April 15th on A Delicate Boy...

Next week, the Carnival is going back home to The Education Wonks. The deadline for entries is April 18th, 9:00 PM (Pacific). The address is: owlshome [at] earthlink [dot] net

Carnival of Education

Carnival of Education #61 is up on The Education Wonks.

Next Week's Carnival will be hosted by me right here at The Magic School Bus. Please send contributions to: Coturnix1 AT aol DOT com. Send your entries by 5:00PM EST on Tuesday, April 11th. Include the title of your post, and its URL. Of course, I am hoping for a nice showing by science educators next week (hint, hint).

Technorati Tag: teaching-carnival

Teaching Biology Lab - Week 4

So, yesterday was the last, fourth meeting of the lab. We started out by going over their homework questions about the evolution of Vertebrates. I was quite happy that only one person in only one question confused development with evolution - something that I see, unfortunately, very often. The legs of the frog do not "evolve" out of the body once the tadpole starts losing its tail: the frog legs evolved out of meaty fins of its Crossopterygian ancestors. Also, knowing that one of the questions concerned Amphioxus, I made sure the previous week to say something about it. For most questions, the students were really 'on the ball' - it is nice to have a class without a single (at least openly) Creationist student.

The first excercise of the day was supposed to be electrophoresis - we were supposed to run a gel. However, Ward's (second time this term) did not deliver the supplies on Friday (they will come on Monday and I can use them next time), so, without the chemicals, we could not do the excercise. Instead, we did a DNA fingerprinting excercise on paper, using paternity testing as an example. They were given two DNA sequences each from Mother, Child, Potential Father #1 and Potential Father #2. They were to use the restriction enzyme (scissors) to cut the sequences after T of each CAT sequence. Then, they figured out the sizes of the fragments and we drew the gel on the whiteboard representing what they would see if they actually had those sequences in real life.

It was easy then to figure out who the father was. We also mentioned some other reasons to use DNA fingerprinting, e.g., in forensic analysis (and yes, O.J.Simpson trial was mentioned). The technique has also shown that, contrary to millenia of misconception, the birds are not that loyal to their partners as we thought. Even in bluebirds, the poetic paragons of loyalty, some of the eggs are fertilized by the nest mate, and other eggs are fertilized by a fleshy neighbor. As a bonus, I gave them this to read and they loved it.

Next, I split the students into groups of four. We took some water-fleas (Daphnia) and placed them on microscope slides. In each group, one student did the 'handling' of the animals and chemicals, the second student called out the heart-beats seen under the microscope, the third student jotted down a dash for each heart beat and calculated the beats-per-minute value, while the fourth student kept time. For each treatment the students swapped roles. Each animal was first measured in fresh pond water, serving as its own control. Then, a drop of a treatment was added and the heart-rate counted again. The four treatments were caffeine, epinephrine (adrenaline), glucose and alcohol. Before the excercise started, the students stated their hypotheses and their expectations.

I was really happy to see how consistent the numbers were between groups, suggesting that they did the job correctly. Surprisingly, all four chemicals (in all replicates) induced slowing of the heart rate. We used the discussion time to talk about the biochemistry and physiology of the four chemicals, the effects of dose (the U-shaped curves), the compensation (e.g., the "crash" following a caffeine "high"), etc. It was taken as given that Daphnia and humans share much of their physiology: from utilization of glucose for energy (and formation of ATP), to existence of receptors for epinephrine and caffeine. No need to push evolution too hard - the common ancestry was an unspoken given.

After they finished their student evaluations, it was time for the last excercise of the course, the one they were all excited about - the dissection of the fetal pig. We worked all together, finding organs one at the time. For each organ, I asked questions about its function and often added some more interesting information (including the positive feedback loop I forgot to mention two weeks before, concerning the urinary bladder - thank you readers for the heads-up on that!). I think they had a blast!

And that was it for this session. I have a month free. Then, in May and June I will be teaching both the lecture and the lab. It is always good when the two courses are taught simultaneously by the same instructor. That way, I can make the too reinforce each other and work together well.

Previously in this series:
Teaching Biology To Adults
Teaching Biology Lab - Week 1
Teaching Biology Lab - Week 2
Teaching Biology Lab - Week 3

Technorati Tag: teaching-carnival

When Should Schools Start in the morning?

This being the National Sleep Awareness Week and on the heels of the recent study on sleep of adolescents, it is not surprising that this issue is all over the media, including blogs, these days.

I have written about it recently several times. I present some science and some opinion here and add a little more science and much more opinion here.

You can look at media coverage here and listen to an excellent podcast linked here. Some basic underlying science is covered here.

All of this targets highschoolers. However, there is barely any mention of college students who are, chronobiologically, in the same age-group as high-school students, i.e., their sleep cycles are phase-delayed compared to both little kids and to adults.

In a way, this may be because there is not much adults can do about college students. They are supposeduly adults themselves and capable of taking care of themselves. Nobody forces (at least in theory) them to take 8am classes. Nobody forces them to spend nights parying either.

They are on their own, away from their parents' direct supervision, so nobody can tell them to remove TVs and electronic games out of their bedrooms. The college administrators cannot deal with this because it is an invasion of students' privacy (unless it is one of those nutty unaccredited pseudo-colleges).

Yet, college students are, from what I heard, in much worse shape than high schoolers. Both groups should sleep around 9 hours per day (adults over thirty are good with about 8 hours). High schoolers get on average 6.9 hours. College students are down to about five! The continuous insomnia of college students even has its own name in chronobiology: Student Lag (like jet-lag without travelling to cool places). Is there anything we, as a society, can do to alleviate student lag? Should we?

Technorati Tag: teaching-carnival

Carnival time

Carnival of Education is up on Right Wing Nation.

Tangled Bank is up on Island Of Doubt.

Carnival of Homeschooling is up on Why Homeschool.

Technorati Tag: teaching-carnival

Teaching Biology Lab - Week 3

This week we had a busy lab, which means I did not have time for much inpired talking like I did last time. We did some exercises together as a group, while some other exercises were set as stations arund the room and each student did them alone, at their own time.

First, the students used the staining technique they learned last week to find out what kinds of organisms live on their fingers. They saw bacteria from store-bought colonies last week. This week they saw their own cocci and baccili. They also saw quite a lot of molds (and I placed on other microscopes some ready-made slides of Aspergillus, Rhizopus and Pennicilium for them to compare).

Of course, their first reaction is "Yeeew!" and comparisons who had dirty fingers and who did not. This was a nice entry for me to talk about all the symbiotic microorganisms that live on our body, as well as those that live inside of our bodies, mainly in the digestive system. I told them about the initiative to make the Human Genome Project complete by adding the complete sequqnces of all the microorganisms that live inside of our bodies. Without them, we are only half-human. They have co-evolved with us for millions of years and have taken on a number of roles that we are incpabale of doing ourselves, from defense to absorption of some vitamins. Also, it is useful to think of the bacteria in our intestines as an ecosystem. If you get sick and take lots of antibiotics, the bacterial flora is wiped out. Just like an island after a volcanic eruption, there is an orderly succession process that follows. There are species that come first and pave the way for the introduction of other species etc. Over time, the ecosystem changes a number of times until it reaches the mature, balanced stage.

The second big exercise was an experiment that tested essentially two things: 1) which of the three possible catalysts (sand, MnO2 or catalase) is the best at breaking down hydrogen peroxyde into water and oxygen; and 2) what intercellular conditions need to be met for catalase to work properly. Each test tube was a model of a cell. Just like in Week One, when we moved a salt-lake into a rubber hose, this week we moved a cell into a glass test-tube. That way, we can control all the factors one at a time and eliminate the complexities of the real world.

Manganese Dioxide actually worked too well - I think the students put too much in the tube! Sand was pretty slow. Catalase worked great this time around (last time it sat outside the fridge for a couple of days and got stale because nobody told me it has arrived!).

Catalase worked well on room temperature in water at pH=7. It did not work at all at pH=3 and pH=10, which I connected to the mechanisms of pH control I talked about at length last week (when I was talking about homeostasis and rheostasis, I used calcium control and pH control as two examples of processes where the limits are so narrow, there is no daily rhythm at all). Hot water denatured catalase (which is an enzyme, thus a protein). In ice-cold water, there was no reaction at first, but as the water warmed up to room temperature we could observe the reaction (oxygen forming bubbles).

Then I explained in quite a lot of detail what happens in the mitochondria, i.e., starting with food being digested and broken down to glucose, glucose being broken down via glucolysis and Krebs cycles, the electron transfer cascade from one cytochrome to the next with the final recepient being oxygen, and the resulting production of ATP. AS no machine is 100% efficient, there is some wobble in this mechanism as well, resulting in production of free radicals, one of which is hydrogen peroxyde. Free radicals are implicated in cell damage and perhaps the process of aging. Catalase is the enzyme that neutralizes free radicals and protects the cell from damage.

As every machine that transforms one form of energy into another is less than 100% efficient, some of the energy gets lost, mostly in the form of heat. Heat generated by the mitochondria in this process is what warms up our bodies and keeps our core body temperature more or less constant. Hormones, like thyroxine, can modulate the efficiency of the electron transfer, thus modulate the amount of heat produced by the cells in out body, thus controlling thermoregulation.

In the second half of the lab, students went around the lab and got familiarized with various types of plants, including mosses and ferns. They worked as a team to identify tree species from small disks. They made slides from leaves of Zebrina (a terrestrial plant) and Elodea (an aquatic plant) and found stomata in the former but not in the latter, and we discussed how stomata work and why a submerged plant would not need to have them.

We got a Venus flytrap to close its leaves (trick: do not use a pencil or a needle - use the corner tip of a paper towel) and discusssed the mechanism by which the leaves close at such a high speed.

Finally, the students looked at a number of animal specimens laid out in jars (mostly filled with alcohol, only a few in formaldehyde). Their job was to identify at least the Phylum for each specimen, which was, in some cases quite hard. If they managed to do that, they should also have tried to go down the taxonomic levels and try to identify the Class, Order, Family, Genus and perhaps even species (that last one was possible in only a couple of specimens, e.g., flunder and snapping turtle). This is an exercise I like a lot because it gives me an opportunity to give little tidbits about various animals, to tell some cool stories (e.g., how it was discovered here in NC, at Greensboro College, that sponges actually move along the surface), and to dispell some myths that people tend to have about some kinds of animals. This also reinforces the evolutionary message of the course - all those things are related and we explored their exact relationships. Homework: a worksheet - answering ten questions about vertebrate evolution.

Previously in this series:
Teaching Biology To Adults
Teaching Biology Lab - Week 1
Teaching Biology Lab - Week 2

Technorati Tag: teaching-carnival

On Teaching Science

EducationWonks found an excellent article written by a student about science education in elementary schools and beyond:
Light a fire under students for math, science programs :

-------snip----------

Upon reviewing the major points of the bill, however, I failed to find a specific focus on improving science and mathematics education in grades K-6. The bill seems to be geared toward secondary school students - those in junior high and high school - and even college students.

However, interest in science truly begins at the elementary level. A key component of improving the number of American scientists and engineers is igniting interest at a young age and nurturing that interest throughout a child's education.

Educational television can help to interest a child in a subject. When I was young, I watched "Bill Nye the Science Guy" and "Magic School Bus," and I learned much from those shows that I remember and utilize today. High school science teachers often use "Bill Nye the Science Guy" in their classrooms because it is such an excellent resource.

Currently, educational television leans toward multicultural education. While multicultural education is indeed extremely important, a balance should exist. A greater number of fun and educational science shows should appear.

Even if children enjoy math and science when they are young, they may lose or ignore that interest in junior high because of the enormous peer pressure to be "cool." If educators could find a method to make science "cool" and socially acceptable, I believe that many more students would pursue the subject.

Teenagers tend to believe that scientists are social pariahs who are concerned only with their work. Adults should strive to dissuade them from this perception by demonstrating that scientists and engineers are indeed normal human beings.

In addition, illustrating the application of classroom learning to real-life situations would more fully engage a young teenager. Instead of simply learning formulas and doing simple labs, science teachers should demonstrate the widespread effects and applications of their subject. Some teachers are already adept at this, but some are not. Students need applications to which they can relate.

Recently, the government has focused on improving standardized test scores. While that is certainly a worthy pursuit, better test scores will not increase interest in math and science. Politicians and government officials should instead attempt to develop a true interest and involvement in science and math among young people.

Careers in science and math are certainly not ideal for everyone. We shouldn't attempt to force young people into such careers. However, students may miss out on something they truly enjoy if their science education comes solely from a textbook, which I'm sure many would consider quite dull. In order to increase the number of math, science and engineering majors in the United States, we first have to infuse students with an enthusiasm for the subject.

Yes, yes, yes...

(cross-posted on Science And Politics)

Technorati Tag: teaching-carnival

Carnivals

Carnival of Education #59 is up on The Education Wonks.

Carnival of Homeschooling is up on PHAT Mommy.

Technorati Tag: teaching-carnival

Teaching Biology Lab - Week 2

When teaching the lecture portion of the course, I naturally have to prepare the lectures in advance, and each lecture has to cover a particular topic. This makes biology somewhat fragmentary and I try to use various strategies to connect one lecture to another, one topic to another, one area of biology to another, and especially each area of biology to evolution, as it is the unifying principle of all biology. As I have written before, I often use diseases, especially my favourite (what - you don't have a favourite disease?) - malaria.

On the other hand, teaching the lab is a great opportunity to introduce mini-lectures that appear almost like streams of consciousness, touching on several different topics in succession, veering off on tangents, yet actually serving as unifiers - demonstrating how evolution, ecology, physiology, behavior, genetics etc. are all connected. Teaching adults makes this even easier because they do not expect me to be a Perfect Human Being, and are capable of laughing with me. I can also use more real-life examples and they are not squeamish to talk or hear about sex.

In my lab yesterday, I did something like that. But I had a great starting point - the jigsaw puzzle excercise that I have described before here (also here, and check a long discussion thread here). I kept talking on and on and on. Here is, roughly, what I said and what the students said:

"A-ha, I see what all of you are doing first - turning all the pieces right side up. You know that each piece has a dull grey side and a colorful side. You also know that the colorful side is much more informative than the grey side. The grey side gives you only the information about shape, and even that only as a mirror image, while the other side also gives you information about color and pattern. You knew to do this because this is not, for any of you, a new excercise. You've all done jigsaw puzzles when you were kids and now you are doing them again with your own kids. This, as far as solving puzzles, gives you experience and prior knowledge. If you think of science, this is an equavalent of 6 or 8 or 10 years of grad school. You have background knowledge, you have experience, and you have perfected the use of the puzzle-piece-flipping technique. It is like being really good at using a microsope, something that you learned last week and will again use later today.

So, what are you doing first? Looking at the pieces - that is observation. You still have absolutely no idea what the Big Picture is going to be, but you are looking for a good starting point, so you are soaking in all the information that you can glean from all the jumbled pieces on the table. So you are taking prior knowledge and using it to make sense of observed phenomena.

What are you doing next? You are trying to put some pieces together. Those are experiments. Every time you pick up two pieces and try to put them together you are testing a hypothesis - that the two pieces will fit. Most of the time your experiment fails at the first try, so you try again by rotating the pieces a little bit at a time and trying again. If it does not work, you drop the pieces and leave them for later, as obviously you need additional information. If it works, you publish your findings in a scientific journal and move on to the next hypothesis.

I see that different people have different approaches. Some look for edge pieces and try to put them together. Others are looking for any two pieces that may have shape, color and pattern similar enough that they may fit together, yet others are looking for key pieces - those with most interesting pieces of information, like an eye or a nose.

This is just like personal styles of different scientists. Some start with easily gleaned information - the edges - and systematically build on it, piece by piece. They know that this approach is slow and tedious, but will certainly, over time, build the whole picture. Others do something more risky - go for the most interesting information although it is difficult to study it or to place it in a broader context. They are more likely to fail, but if they get it right, the returns on the investment are enormous - they have figured out what the big picture is going to be without doing all the detailed boring work.

Does anyone already know what the big picture is going to be? No? Any hints and hunches so far? Perhaps a chicken over here, but you are not sure. So, this is still a hypothesis and not yet a theory. The same here with deer? OK.

Do you ever try to force a piece in its place although it does not fit and keep it there?

I do.

A-ha. But later, once you find the correct piece that fits there, will you stubbornly resist removing the right piece?

No, I'd replace it.

Good. That is just like scientists work. Sometimes you tentatively accept wrong data because they serve as place-holders - they help drive the future research. And although everyone is aware that the data are flawed, everyone tolerates it until better data come along.

We seem to be missing a piece!

What piece?

A corner piece. Actually, all corner pieces.

Good. It took you about 10 minutes to discover that. I guess there was nobody here who always starts a jigsaw puzzle by looking for corner pieces. Do you really need the corner pieces in order to figure out what the big picture is?

No, not really...

Correct, the key information is unlikely to be at the periphery. But, you are humans, so it drives you nuts that the corner pieces are missing, so here they are - you can have them.

But, those are not our corner pieces they are theirs!

That's fine. I made sure when I bought the puzzles that the pieces have exactly the same shapes. You can use the wrong corner pieces as place-holders. They fit by shape, although they do not fit by color and pattern. By putting them in, it can help you add a couple of more pieces together. But in the end, you will not be happy with semi-correct data and will put a lot of effort into solving that problem. Perhaps, as science is collaborative, international, and does not recognize borders, you can negotiate with the other group to exchange the corner pieces later on in order to get a more perfect picture. It is like sharing data or sending each other laboratory reagents, or publishing all your findings in reputable journals for all to see.

In the same vein, I could have ruined some pieces by removing the colorful top layer. You would have only shape to work with as there is no more color or pattern to it. You would still be able to fit it into the puzzle and although it may look ugly and incomplete, it would help you build the rest of the puzzle by adding more pieces to it, and it is unlikely to affect the Big Picture. This is equivalent of incomplete data. You can reconstruct a piece of history from an ancient manuscript although it is partially burned. You can reconstruct the evolutionary history of a particular group of organisms by working with an incomplete fossil record - after all, there are other puzzle-pieces supporting your theory, for instance the data from genetics, embryology, comparative anatomy and physiology, etc.

Any ideas yet what the big picture is going to be?

We are going to have a bird - not the chicken as we first thought, but more something like a duck, as well as a cat, we think...

We thought at first it was going to be a deer, then we thought for a while that it was going to be a squirrel, now we are back to deer.

OK, so you have changed your minds over time. How easy or hard was it for you to change your minds?

Easy.

Good. So, you did not have a great emotional need to stick to your first guess and, once new information came in - when you placed a number of new pieces, you adapted your thinking to fit the new information. How sure you are that it is going to be a deer? Or a cat and a duck?

Pretty sure.

100%? Do you think it is possible that you may change your mind again as you place more and more pieces.

Perhaps, but unlikely.

OK, so now you have moved from the hypothesis stage to the theory stage. You are quite confident that you have a correct solution for the whole puzzle, although you are still missing many, many pieces and some modifications of the theory are still possible without changing the main gist of things.

Ha! Now this was interesting! You just put together an eye piece together with a nose piece and both to a group of green grass edge pieces. This is a relatively small amount of work: just two pieces being put together and placed in the context of the whole theory, but it is huge in terms of information content. This is something you would publish in a major journal, like Science or Nature or Journal of American Medical Association. On the other hand all those green edge pieces, as many as you have already put together after a lot of tedious work, as important they are for building the whole picture, are just not that interesting - they say little about the Big Picture or if your theory is correct. That is kind of stuff you would publish in the American Journal of Green-Grass Jigsaw-Puzzle Research - a lower-tier journal for sure.

Putting together pieces that fit well with your theory is sometimes called "normal science". Putting in the pieces that result in your changing your mind on what the Big Picture is going to be is sometimes called a "paradigm shift". So, you work within a paradigm that it is a squirrel and keep looking for pieces that have squirrel-like properties and putting them in, until you run out of such pieces and it looks less and less likely that it is a squirrel. Then, you find a couple of pieces that persuade you that you were wrong and that the Big Picture is the deer. You have experienced a paradigm shift, and now you are going to do some normal science within the new paradigm - adding more and more pieces with the assumption that it is going to turn out to be a deer.

We have a paradigm shift right now! It is not an adult deer but a fawn!

Great. It is a pretty big change. Although a fawn is technically a deer, there is a difference that is important in the description of your theory. You are now going to call it the Fawn Theory instead of The Grand Theory of Deer. Sometimes theory changes a lot, sometimes a little. Even if you think that the piece that will fill this hole is going to be just grass, if it turns out that it also contains a little flower, this is change in the theory. It does not overturn the whole theory - it is still going to be a fawn, but it will be a change in details. It is like adding sexual selection and neutral selection to the natural selection - the theory of evolution is not overturned - it just gets more detail and sophistication.

How about now? Do you think there is a possibility that adding another few pieces can make you completely change your mind on what the Big Picture will be? No? You are completely sure that you are correct although so many pieces are still missing from the puzzle? You would place it at 100% now? Yes? OK. But you, if you were a scientist, would never say that out loud, because, technically, this may happen no matter how sure you are. In well-supported theories, like relativity, plate-tectonics or evolution, chances of overturning the whole theory are practically zero, but it is considered bad form, philosophically incorrect, to state that a theory is Truth with capital T. Every new piece of the puzzle just confirms that all of life on Earth evolved out of a single common ancestor. Every new piece confirms that natural selection is the major mechanism of evolutionary change. Not a single piece of new information is at odds with those notions and have not been for the past 150 years of thousands and thousands of scientists looking really hard.

O-o!

What happened?

It is not one fawn - we have two! It was kinda hidden in one of the corners so we missed it at first.

Great. So, you get to keep the original theory of the fawn and get to add a second fawn. It is like keeping natural selection but adding sexual selection into the theory, something that Darwin himself did a couple of decades after he published the Origin of Species.

OK, how much your understanding of the whole picture changed since you just started the puzzle? A lot? Well, the science changes the same way. Theory of evolution from 1860s is not the same as the theory of evolution in 1900s, or the theory of evolution of 1940s, or 1960s, or today. We cannot use Origin of Species as a textbook today because so many details are different. Darwin got many details wrong, and in cases in which he got things correctly, he did not have much supporting evidence - his puzzle was based on too few puzzle pieces which we now have. But what Darwin got right was the Big Picture. He said it was going to be a Duck and the Cat and we still agree that it is a Duck and a Cat, although we now also known which flowers are growing around them and that the cat is very young and grey and looks like it may be an Abyssinian and the duck is also very young - just a duckling really and it is yellow and really cute. Darwin was right, but our knowledge is much more complete.

Also, if I was going to be really mean to you I would have also removed all the edge pieces. That way, you can never finish your puzzles, just like the work of science is never finished - there are always more details to uncover and more hypotheses to be tested. Also, no scientific theory lives in isolation. If I left the edges out, you would be able to connect one whole puzzle to the next puzzle to the next puzzle. A century or two ago, it was easy to ditinsguish what was biology, what was astronomy, what was physics, or chemistry or geology. Today, we know so much, the borders between disciplines are blurred. We have physical chemistry connecting physics and chemistry, biochemistry spanning biology and chemistry, biophysics in-between biology and physics - it's all connected. Not to mention how much one field uses the techniques developed by another field or is based on the knowledge developed by another field.

Now quit doing the puzzle.

Grrroooaaaannn!

What? Why groaning? I bet if I asked you 15 minutes ago you would have had no problem quitting. You, just like all scientists, are kids at heart. At the beginning you may have wondered what on earth are we doing playing jigsaw puzzles in college, but now you really like doing it. Fine, you may continue and finish the puzzles. Happy? Just like scientists, more you know about something, more you want to know. It is so hard to get scientists to retire - many work until the day they die. There is always another experiment to do, another hypothesis to test, another piece of information to collect. More you know, more you realize how much more there is to know, and more you want to learn more. It is a positive feedback loop...wait, do you remember what a positive feedback loop is? You all have had lecture portion of the course at some point in your careers. Can anyone give me an example of a positive feedback loop from human physiology - the way the human body works?

When you cut yourself, the way the blood clots and makes a scar.

Excellent, that is a very good example. The cut makes a molecule act on another molecule which energizes another molecule and that molecule may recruit more copies of the first molecule so the whole process works faster and faster over time. Let's make a more general description of a positive feedback loop. A process A triggers a process B which, in turn, triggers process A again. Moreover, it multiplies over time as A may trigger 10 instances of process B which in turn trigger 10 instances of process A each, so very soon you have both processes happening thousands of places simultaneously. Does anyone know any other examples of positive feedback loops in the human body?

[expectant looks]

OK, here's one. Breast-feeding. You all have children so you should know this one. When a baby is hungry it latches onto the nipple. There are receptors in the nipple that sense that and send a signal to the brain - more specifically the part of the brain that you may remember from the lectures called the posterior pituitary gland - which secretes a hormone called oxytocin - no, not Oxycontin, that is what Limbaugh is taking. Oxytocin makes the milk glands eject milk. The baby gets the milk and is prompted to suckle on the nipple some more which releases more oxytocin which releases more milk which makes the baby suckle more etc etc the process reinforces itself until the baby is not hungry any more and quits eating. How about another example? Also has to do with babies?

[blank stares]

OK, giving birth is a positive feedback loop, too. When the baby is ready to be born it signals the mother, which makes the uterus contracts. At that moment you know the baby is coming that day and you get in the car and go to the hospital. That first contraction of the uterus pushes the baby down a little bit. That movement stretches the uterus a little which results in release of more, again, oxytocin, which makes uterus contract again, which pushes the baby a little bit more out, which stretches the uterus more, which tirggers release of more oxytocin, which makes the uterus contract again....over and over again, faster and faster, until the baby is completely out. Good, how about another example? It also has to do something with babies. Anyone? Come on - you all have children - you should all know this outside of biology class, just from real life!

[eyes glazed over]

OK, here it is. It is making babies. Sex is a positive feedback loop. Just like doing the puzzle, it is easy to stop at the beginning, and much harder farther along you go. More you do it, more you want to do it and faster you go, until the orgasm in the end.

[giggles]

All right. Right off the top of my head I cannot think of another example of a positive feedback loop in the human physiology. Those are really rare. Most of the events are negative feedback loops. Can anyone give me an example?

Walking. It is loosing and regaining balance. You lean forward and you catch yourself from falling by stepping out.

Good. That is a pretty good example. Pretty much every time something goes away from the optimum, there are mechanisms that bring it back to the optimum. Put more formally, an event A triggers an event B which supresses the event A. For instance, if a hormone surges, there will be mechanisms that inhibit further synthesis and release of that hormone.

This whole concept of negative feedbcak loops keeping everything in the body at an optimum is called homeostasis and it can be depicted like this:
Let's say you exercise or go out in the hot sun. Your body temperature rises. As a response, you start sweating, perhaps lower your metabolic rate, there are changes on the sub-cellular level that we will discuss next week, you wil also try to find a shade and drink something cold. Thus, there are biochemical, physiological and behavioral mechanisms that will drive your elevated body temperature back towards its normal level. Likewise, if you go out in the cold and your temperature starts dropping, your metabolism gets cranked up, you shiver, you put on more clothes, go inside, light up the fireplace and drink hot chocolate - again biochemical, physiological and behavioral mechanisms that will drive the temperature back up to the optimum level.

Now, all this is correct, but this graph is correct only if the X-axis spans time in the range of minutes, e.g., from 0 to 60 minutes for the whole length of the graph. How does it look like if the X-axis spans 24 hours? It looks more like this:
This does not mean that homeostatic mechanisms do not work very well - they do. It just shows that the optimal values - those defended by the homeostatic mechanisms - are not static. They are dynamic. They change predictably over the course of the day. For instance, your body temperature is lowest just before dawn and highest in late afternoon. On the other hand your cortisol levels in the blood are the highest early in the morning, preparing your body to wake up and seize the day! This controlled dynamic change in optimal values is called rheostasis. The daily rhythms are called circadian rhythms and there is a small area at the bottom of the brain which contains a few thousand brain cells that act as a clock, a circadian clock, which acts a relay - telling other parts of the brain and other parts of the body when - over the course of a single day - to raise and when to drop the optimal values of whatever processes they govern.

[Update: Here I spent some more time describing two functions that do not show rhythms - blood levels of Calcium are constant and blood pH is constant because the optimal values have an extremely narrow range. I talked about parathormone here, etc.]

Let's take a break now. Please break down the puzzles and put them in these boxes here. By the time we come back, the slides you prepared first thing this morning will be dry and we can stain the bacteria and look at them under the microscope. This is obviously not hypothesis-testing. You are just learning a technique - how to flip the puzzle-pieces right side up so you can make observation of shapes, colors and patterns of...bacteria. Once you know how to do it, you can go on and make your own further obeservations and make predictions and test hypotheses. We'll do that, too. You will press your thumbs on the agarose in these petri dishes that I poured this morning and next week we are going to see what kinds of critters live on your fingers.


Finally, at the end today, we are going to dissect owl pellets. By using the charts I give you, you will try to figure out which pellet comes from a Northwestern owl and which one from a Southeastern owl. Your homework will be to explain the results and the methodology you used to figure it out and then, next week, we will talk about this some more."

And that is what we did. Wow - what a roller-coaster. From philosophy and sociology of science (no need to critique Kuhn at that level of instruction), through various areas of physiology to circadian rhythms, just to be continued with some microbiology and ecology in the second half of the lab. This is so much fun!



More in this series:
Teaching Biology To Adults
Teaching Biology Lab - Week 1
Teaching Biology Lab - Week 2
Teaching Biology Lab - Week 3

Technorati Tag: teaching-carnival

Education-related carnivals

The latest edition of the Teaching Carnival is up on The Salt Box.

Carnival of Education - Issue #58 is up on Education Wonks.

Carnival of Unschooling - the third edition is up on Atypical Homeschool.net.

The latest edition of the Carnival of Homeschooling is currently on Common Room.

Technorati Tag: teaching-carnival

Teaching Molecular Biology to people who are afraid of it

Afraid of the dense terminology of molecular biology? Don't despair! David Ng came to the rescue with a clear, easy and beautiful cartoon guide to DNA replication, over on The Science Creative Quarterly.

I may use it next time I teach the lecture portion of the Intro Bio course (in May). I hope that transcription and translation will come soon - in time for that.

Technorati Tag: teaching-carnival

Teaching Biology Lab

Yesterday I had my first class of the semster of the BIO Lab at the community college. This is the first time with a new syllabus, containing some new excercises.

At the beginning, we took a look at some cartoons, as examples of Inductive and Abductive Arguments, or, in other words, as examples of the way scientists think and work, which I used to explain why scientists never state "this is the Truth", but always sound a little less decisive. I also used it to explain the scientific definition of "theory" as opposed to the common usage of the word. I went through several theories (gravity, relativity, plate tectonics, etc), and ended with the Theory of Evolution, which - I stated with the authority of the Instructor-Who-Knows - is one of the best supported theories of all science.

One of the cartoons, the one described here, is titled “Dick should not drink the coffee.”:

Frame one: three people sitting at a counter with coffee cups.
Frame one: the person on the left takes a sip of coffee.
Frame two: the person on the left drops the cup and looks sick and drops the cup, the person on the right takes a sip of coffee.
Frame three: The person on the left keels over, the person on the right looks sick and drops his cup.
Frame four: Person on the right keels over, the person in the middle looks curiously at the contents of his coffee cup.

The second cartoon, named "The fellow stole the purse", had three frames:
Frame one: A room with a table, a purse on the table and a clock on the wall showing 5 o'clock
Frame one: A guy passes by the table and notices the purse
Frame two: The guy looks left and right (pretty shiftily). The time is 5 o'clock.
Frame three: The room is empty, the guy is not seen, the purse is not on the table, the clock shows 5:05.

The third cartoon, "Spot chased a cat":
Frame one: A man is walking a dog on a leash through a pretty meadow. The sun is shining.
Frame one: A text bubble points to somebody outside of the frame saying"MEOW!"
Frame two: The man has a surprised look on his face. He appears to be falling. He has just let go of the leash. The dog is gone from the frame. Someone outside the frame is saying "ARF! ARF! ARF!"

The students really jumped on this, showing what alternative hypotheses were possible to explain what we saw in the cartoon, but that would point to the titles being inaccurate. For instance, in the first cartoon, we are not 100% sure that the liquid in the cups (all three, or any one of them) is really coffee. We also do not know whose name is Dick.

In the second cartoon, we do not actually see the fellow taking the purse, so it is possible that he did not take it. Five minutes is sufficient time for someone else to come by and ake it. Perhaps the time difference between the frames two and three is not five minutes but 12 hours and 5 minutes, or 24 hours and 5 minutes, or even years apart. Perhaps the guy picked up the purse because it is his, or belongs to someone he knows, or because he works there and will put it in the "Lost and Found" office.

Likewise, in the third cartoon, we do not know whose name is Spot: the dog, the man, the cat or someone else? Again, we are not sure if the time difference between the two frames is just seconds (the cartoonist convention) or much longer. Perhaps the time is even going in reverse! Perhaps the cat was chased by another dog, and the dog from the cartoon chased the other dog. Perhaps somebody or something else said "Meow" - a dog, a person, a squirrel, a machine... Perhaps it is a monster mutant giant cat from the sci-fi channel that chased and grabbed the dog!

I used the cartoons to emphasize a couple of points:

First, that seeing something happen is not neccessary for making correct conclusions. We never see the coffee, or the act of picking up the purse, or the cat. Likewise, in science, we can infer information about events that happened far away (as in billions of miles away deep in the cosmos), about events that are too small for us to observe (e.g., atoms and subatomic particles), and about events that happened in the past (e.g., burning of Rome, or Big Bang). Likewise, we need to use inference to figure out what happens at timescales that are too short (microseconds, e.g., events at the atomic scale, activity of a neuron, etc.), or too long (millions and billions of years, as in plate tectonics and evolution).

Second, that we use background knowledge (cartoon conventions, what substance is usually found in coffee cups, how do English-speaking people transcribe noises made by dogs and cats, how to read the time off the clockface, the fact that usually dogs chase cats and not the other way round, etc.) to inform our analysis.

Third, that although the alternative hypotheses may be correct, they are all less likely than the one stated in the title, because all the alternatives require either unusual events, or thinking up additional players - which got me to the rule of parsimony and how it is used in science.

Finally, if we do additional research of such situations in real life, we may be able to put a number to the probability that the title is accurate versus the probability that any alternative hypothesis is correct, ie., we can use statistics.

Once we were done with the cartoons, we did two related excercises, both involving solving a crime scene mystery. Although nobody witnessed the murder, we could figure out who the killer was because we could match the hair samples and blood samples to one of the suspects (and not to the other suspects or the victim). Both of those excercises come in easy-to-do kits from Ward's and take about two hours to do them both. All along, as we were doing these, I was going back to the cartoon excercise and reminded them of some of the prinicples, e.g., parsimony, the lack of necessity for actually observing an event in order to correctly infer what happened (a canard often invoked by creationists - "nobody observed evolution in action", which actually is not true, and even if it was it does not matter, as there is plenty of evidence to infer that evolution occured before and is occuring right now, at time-scales longer than what we can usually pay attention to), etc.

In the second portion of the lab, we did an experiment with brine shrimp (Artemia salina). Usually this is done with larval brine shrimp and the students count the numbers of shrimp under the microscope. However, years ago I realized that adult shrimp work just as well, are easier and quicker to count and easier to get (I do not need to hatch and raise them myself in advance of the class - I just buy a dollar worth of them and a quart of water in a local fish store, sufficient for 5-6 racing tubes).

This is an excercise in which nature is brought into the lab. As a salt lake, brimming with brine shrimp, evaporates in summer, many aspects of water quality change, e.g., temperature and pH. Brine shrimp detect the changes and swim towards the deeper recesses of the lake, somewhere in its center, where they mate, lay eggs and finally, once the lake is completely gone, die. The eggs can survive compete dehydration for quite a long time. When the first rains of fall appear, about half of the eggs hatch, counting on the lake re-establishing itself again. However, this may be a mistake - a sporadic mid-summer shower that does not fill the lake. Thus, about a third of eggs hatch after two cycles: dry-wet-dry-wet. Finally, the remaining 1/6th of the eggs requires three such cycles. This way, no matter what strange pattern of weather occurs in any given year, the shrimp are highly likely to repopulate the late in fall (or the little "Sea Monkey" containers you buy in toy stores - that is what this animal is).

The point of the excercise is to tease out the factors, one by one, and figure out what do the brine shrimp really cue onto - something that cannot be done in the lake itself (though the students wanted to go to a field trip right away, what with the 80 degrees weather outside!).

The students filled clear plastic tubes (about half-inch in diameter) with the shrimp and water, closing the tube with rubber stoppers on both side and trying not to have air bubbles remaining in the tubes. They attached each tube to a yard stick using clamps at 0 inch, 12 inch, 24 inch and 36 inch markers (the first and the last are very ends of the tube). The clamps were left loose so the brine shrimp could feely swim through the tubes, and the tubes were laid horizontally on the desks.

We let the tubes sit for a while to allow the shrimp to equalize their densities along each tube (it is hard, due to the cumbersome way of injecting the water+shrimp into the tubes by syringe, to get them equalized to begin with). Then, we left one tube as a control, in one we added some acid on one end, in one we added some base on one end, in one we covered one third of the tube with a Ziploc bag filled with very warm (but NOT boiling hot!) water, and on one we placed a Ziploc bag full of ice on top of one third of the tube. We gave the shrimp about 30-45 minutes to swim weherever they wanted, then screwed down the clamps (to prevent the animals from moving from one segment of the tube to the next) and counted the numbers of animals in each segment, writing the data on the whiteboard.

In advance of placing the treatments, the students stated their hypotheses - where are the shrimp going to swim? The data confirmed their expectations: the shrimp swam away from the heat (as the shallow water in summer would be), towards the cold (but remaining at the edges of the ice-bag, not under it - that was too cold even for the bottom of the middle of the lake!), away from acid and away from base (again, away from the edges where much more decomposition is likely to occur as the fish and other animals and plants start dying).

They correctly pointed out to the factors that may have affected their data (e.g., the placement of tubes in relation to the ceiling lights). Then I gave them a little spiel about the neccessity to repeat this a number of times and do the statistics in order to be confident about their findings. Repetition can also control for some of the other factors, by filling the tubes from the left in half of the cases and from the right in half of the cases, while always applying the treatment on the left end of the tube; by placing the tubes in different relations to the lights (or somehow manipulating the lighting conditions in the room to be more evenly spread), etc.

In addition to these treatments, we also did another test. Brine shrimp are diurnal migrants. During the day, they swim down towards the bottom (away from sunlight) - this is negative phototaxis, i.e., running away from light. During the night, they swim towards the surface, toward the moonlight - positive phototaxis.

The intensity of light tells them if it is day or night. The circadian clock tells them if it is time for negative or positive phototaxis. What we do not know is, if the swiming "up" and "down" is aided by gravity, or by the direction from which the light is coming. In other words, when they see light, and the clock tells them to swim towards the surface, do they swim towards the light no matter where it is, or do they swim "up", no matter where the light is?

By placing a tube in a horizontal position, we eliminated gravity as a factor. Placing one end of the tube directly under the ceiling light and covering the other end of the tube with a stack of pices of black screen (and just a couple of pieces of screen on the middle segment), we built a light gradient. The shrimp swam towards the dark, telling us that they new that it was daytime, and that they do not need informaiton about gravity for diurnal miration, but do direct phototaxis: swim towards the light wherever it may be.

More next week, as the course progresses...

Technorati Tag: teaching-carnival

Freshman Science Course

Rob the Dirty Liberal has some interesting and thought-provoking ideas about a college freshman science course - or how one can be designed: University Science Education: A New Approach. What do you think?

An attempt at communicating science to lay audience on a blog

Last night I wrote a long post on Circadiana about a new study linking Lithium, Circadian Clocks and Bipolar Disorder. I wrote that post while having fresh in my mind the recent discussions about the strategies that scientists can use to communicate their findings to the lay audience.

Thus, I tried to write that post, although it is about a paper that describes yet another little detail in the complexity of nitty-gritty details of the circadian clock, with lay audience in mind. This is what I tried to do, and you tell me if I succeeded or not, and if not, what I could have done better:

First, with the title and the first paragraph or two, I tried to hook the audience. People love diseases, so I put Bipolar Disorder right up front.

Then, I provided a little bit of historical background which also highlights some aspects of scientific method, specifically the differences in approach between the time when a new discipline just begins and later when the discipline is mature.

Next, I showed how two seemingly distant areas of research got connected to each other and briefly highlighted a couple of studies provoked by the realization of that connection.

Then, in order to be able to explain the new paper, I went all the way back to BIO101 and explained briefly how transcription and translation work. I covered only those aspects of it that are relevant to the main story, leaving much detail out. I tried to leave the specialized terminology out as well. Actually, those few terms that I used I tried to slyly slide in without drawing attention to the fact that those words are specialized scientific terms. First time I use a term, I use it in a colloquial manner (though correctly), and the second time I use it in a more conventional way, but with no fuss (and no italics or bold either). Do not scare people with language!

I then moved on to the description of the molecular mechanism of the mammalian circadian clock. Again, I only cover aspects of it that are essential for understanding the new research, leaving a lot of details out. I use the terminology I just explained in the preceeding paragraphs exactly in the way I used them there.

At the end of that portion of the post, I feel that the reader naturally comes to the correct question that needs to be asked (I am leading the reader there all along) and then show that the new paper addresses exactly that question. The paper itself is full of difficult detail. I omit all that and describe, in simplest possible terms, the main gist of the paper, and how it connects lithium to circadian clocks to Bipolar Disorder.

I placed a lot of pictures in the post that should help the reader visualize and understand what I am saying. I also provide links for people who want to learn more.

Let me know how YOU felt when reading that and if you think some aspects of the presentation can be improved and in what way.

Cross-posted on Science And Politics

Technorati Tag: teaching-carnival

Teaching Carnival - Science Edition

The sixth edition of the Teaching Carnival is up on Science And Politics.

technorati tag: teaching-carnival

Teaching Biology To Adults

I teach Biology at a community college, but not on the main campus. Instead, I teach at a satellite campus dedicated to adult education. Those are all accelerated courses, which means that classes meet for about three hours once a week, either in the evening or on Saturday, and the classes last five, eight or twelve weeks.

Biology lasts eight weeks, although I teach the Lab over four weeks, doubling the face-time each week - that way more gets done, students are happier, and if an experiment does not work out well, it is no big deal because it is not the only exercise of the day.

One of the problems that all of us on the satellite campus have to deal with is the requirement that our classes exactly mirror the classes taught on the main campus, using exactly the same syllabus. This means that material taught for a whole semester has to be completely covered in eight (or five or twelve) sittings.

We deal with it in creative ways, trying not to get our students' heads to explode, but it is not easy. Unfortunately, the main campus administration appears to be adamant about this, and the satellite campus administration appears to be too timid to even voice some protest, let alone do something about it.

The duration of the class is not the only problem. We also have a very different audience. While main campus has a number of majors, we offer only four, stuff like business and computers. Thus, my biology class, which is designed for biology majors, never has biology majors in it.

The age difference is another factor. My students are adults, with jobs and families, with life experience, with little money and even less time. Often they go to school because their employers ask them to do so (and pay for their tuition) if they want that promotion (or not to get laid-off). Main campus caters to the more traditional crowd of 20-year old kids whose only job is to go to school.

Another difference is in their educational background. My students got out of high school many years ago. If they had biology at all, they remember it as boring rote memorization of Krebs cycles, flower parts, human anatomy and classification of invertebrates, with no mention of evolution at all. They come to my classroom with fear. The current crop of high-school graduates has had much better science instruction and approaches biology with eager anticipation.

My main goal, something often thwarted by the requirements of the syllabus, is to show the students that biology is fun, that science is not a monolithic body of knowledge but a method and a process, that evolution is the only way to explain everything and anything in biology, and that the class is not as hard as they feared it would be.

As non-science majors they really do not need to know the details of the life cycles of ferns and mosses - the time taken up with that boring nitty-gritty detail would be better used in covering some Big Picture aspects of the course, for instance its relevance to daily life.

As I have written before, I like to use diseases as entry points into each lecture, as well as the glue that connects the disparate topics together (you will see how if you click on that link).

If I had the freedom to design my own course, I would start each topic with a discussion of an assigned article from the media, covering topics from AIDS to Mad Cow Disease, from Intelligent Design to environmental protection, from cloning to stem cell research, etc. This immediately makes the material relevant as these topics are hot and my students are quite likely to be interested in them.

This initial discussion would be a good way for me to gauge what misperceptions my students have. Then, I can lead the discussion in the direction I want it to go, that is, to the point where I say :"OK, now listen up, I will now explain in more detail the science underlying this topic". That would be the cue for them to sit back and pay attention, perhaps take notes, as I am about to lunge into a lecture on whatever the topic of the day is.

Actually, now that I think about it, that wouldn't be a bad method for teaching science majors either. What do you think?

technorati tag: teaching-carnival

Are you teaching in college AND you are a blogger?

I will be hosting the sixth edition of the Teaching Carnival on Science And Politics (my 'home' blog) on February 15th, 2006. Unlike Carnival of Education which covers all aspects of teaching at all levels, this one is focused on Higher Ed.

As a lot of science bloggers read my blogs and a certain proportion of them teach at the University level, I hope to strengthen the science section of the carnival next month. Hopefully some of my neighbors, the North Carolina bloggers, will see this post and contribute their posts, too. Also, posts about higher ed from students' perspective are welcome. English-language posts only, please.

There are a couple of different ways to submit your entries. The easiest, most direct way is to e-mail me the Permalink at:
Coturnix1 AT aol DOT com.
You'll get a thank-you note and thus be sure that I have received it.

You can also try to submit via the submission form at Blogcarnival.com, but I do not know who will receieve it and if it is guaranteed I will get it on time.

The best way to submit, the way favoured by the folks running this carnival, is to tag your posts with the teaching-carnival tag. If you do not know how to tag a post, you can go here for an explanation and the exact code.

I will, starting about tomorrow and ending about two hours before posting the carnival, search the del.icio.us tags, Technorati tags and Technorati search for posts written and tagged since the last edition went up on January 15th, 2006.

Also, feel free to recommend other bloggers' posts to me to the above e-mail address. You can check the previous editions of the Teaching Carnival in the archives on the sidebar of the carnival homepage.

I will move this post to the top every now and then as a reminder to all of you to write and submit a post dealing with college teaching!

technorati tag: teaching-carnival

Podcastercon2006 - the Teaching Session

Sorry for three days of absence from this blog. I needed some time to recuperate after the Podacstercon which I attended last Saturday. It was a marvelous experience. For more information check out the Podcastercon blog, the wiki, a nice article in News and Observer, the blog reports via Technorati tags, Technorati search and Google blogsearch and pictures on Flickr.

Kudos to Brian Russell for organizing an unconference and taking the concept to the maximum. All sessions were designed by participants by editing the wiki ahead of time. Some of the open sessions were designed on the spot! With at least half of the participants constantly online via their laptops, and two big screens in each of the two big classrooms, it was possible to make changes on the go and still be confident that all participants would be cognizant of the changes.

At one point someone asked "What are we supposed to do now?" and the next person answered "This is our conference. We'll do whatever we want. So, let's do something" That's the spirit! I did not see anyone uncomfortable with the free-flowing format. Everything that needed to happen happened and everyone was always in the loop.

The attendants, of course, are all used to the concept of swarming and connectivity and the order emerging out of chaos, so this worked perfectly for this kind of crowd. Still, if the conference gets bigger in the future (there were about 300 participants this time around, more than a third coming from out of state) and spreads over two days, perhaps a little bit more structure may be neccessary, but not too much more....

In the morning I attended The 411 - How to Podcast session. A little bit too non-linear and occasionally over my head (and I am a blogger, familiar with a lot of online stuff!), but I still managed to learn a lot or at least become familiar with some of the aspects of the process of making a podcast. Perhaps I should have gone to the Podcasting For Everyone open session in the afternoon - I heard it was better geared towards beginners (No, I do not regret attending the Podcasting and Traditional Media: Competition and Cooperation session - I have learned a lot about the radio business there).

First I need to chase down the tech-support guy to fix my sound card so I can do this. Then, guided by Brian's excellent Indy article, the book I got after the conference - Podcasting Hacks - also Podcasting For Dummies I just ordered, and the online tutorial Podcasting 101, I can get myself started on podcasting.

On a number of occasions in the past I've been frustrated when I wanted to include a paragraph or so from a source that is not available online (e.g., a book) in my blog posts. Mostly, I ignored it, sometimes I transcribed/retyped it, but in the future I plan to just read it into a microphone and embed an audio file into the post. How about a weekly podcast from James Dobson's childrearing books followed by my written commentary?

I met some extremely interesting people at the conference, as well as several bloggers I knew from before. We had dinner at Rathskeller and a beer at Fuse. It was a very valuable experience.

But the main reason I went to the Podcastercon was to attend the Education Session. It was worth it! David Warlick led the discussion. You can see his own comments, the workpage that was updated in real time during the session, and an excellent review by Teach42. There is so much material in all those places, there is no way I can summarize all of the session here, so just go and investigate by yourself.

What I want to do is record my lectures and have them available for students. I am teaching in March/April next time and I will definitely do this. But what was most interesting to me was the way this technology adapts to the psychology and sociology of today's students. As David stated in the beginning, today's students are extremely connected to each other. When they come into the classroom and are asked to switch off all of the electronic equipment (cell-phones, iPods, computers, etc.), we are cutting off their 'tentacles'. Now if I were a squid and someone cut off my tentacles I'd be very uncomfortable to say the least.

What the new technology does (and what freaks some people out) is that each student's work becomes public (not neccessarily to the wide world, but at least to other people within the school if the website is password-protected). In the past - and present - the only reader of the student's work is the teacher. In the future, all the work will be read, heard or seen by their peers. How is that going to shake the social organization of the classroom? Is that going to break down the traditional division into cliques of jocks, nerds, etc.? Is a popular jock going to be deflated when exposed to be a half-illiterate dummy, and a shy Goth girl in the corner becomes popular due to immense writing, speaking, acting or video-editing talents? Is the motivation going to rise for students to perform always their very best? I have asked similar questions regarding blogging in the classroom before. Is it going to have an effect like this?

That is why, I think, Fred Stuzman's work on The Facebook is so important (although it is a work on progress - he has done no stats yet, and I seriously doubt there is going to be a significant difference between # of friends that liberal and conservative students have, or the subtle changes in proportions of liberals and conservatives over time - it is only freshmen and only one semester so far, and a more longitudinal study is needed as I have stated before). What do you think?

Cross-posted on Science And Politics

Tags:teaching-carnival, podcastercon2006

Schools in Blogs, Blogs in schools

This is going to be long, but bear with me. I start with one specific course, than broaden the picture, muse a bit, meander somewhat, then ask some questions for which I would love some answers in the comments.

ColinMcEnroe's blogging class is over. They are supposed to turn in their final papers in hardcopy, but now that they are all bloggers in their own right, nothing comes more naturally to them than to post their papers on their blogs.

And they have written some fascinating things, some of which challenge the assumptions of old bloggers and professional blog-watchers. I strongly urge you to go and read their papers and post comments. Link to them - make them feel welcome into the blogosphere!

Let's start with Elin of Nileblog. She posted her paper in seven blogposts, well worth studying, as there are some surprising conclusions there:

The Rhetoric of Blogging (Part I) - Rhetoric
The Rhetoric of Blogging (Part II) - Science and Politics
The Rhetoric of Blogging (Part III) - Flu Wiki
The Rhetoric of Blogging (Part IV): Coffee Rhetoric Rhetoric
The Rhetoric of Blogging (Part V): Daily Kos
Rhetoric of Blogging (Part VI): Once more, with feeling
The Rhetoric of Blogging (Part VII): Closing thoughts on Nileblog

And yes, Nileblog will continue to exist in the future! Blogrolled!

Eric really took off with his blogging. He already has THREE blogspot blogs! One of which, this one, contains entirely the material of his blogging final paper about Links.

Shante also posted her paper on her blog: An exploration of the personal, and I hope she will continue blogging - she is a great writer.

Holly is a wonderful writer, but still nervous and shy about spilling everything out for everyone to read. She did, however, post her excellent paper on Creativity and Communication.

Jeff decided not to post the paper online, but appears that he will also continue with blogging. On the other hand, Dave of My Travels decided blogging is not for him and that's cool.

Screamin' Memey caught the blogging bug. That's the one to watch. No paper, though.... I believe that Semper Gumby was blogging even before the course started. It is an endless source of cool links to cool stuff.

Brett feels, perhaps of the whole class, most comfortable in the blogging medium - no qualms about posting the most personal stuff! But, where is the paper? Perpetual Perpetuity is on the roll! Also no paper.

Pangiuseppe decided mostly to comment on other people's blogs, but broke the silence to post this excellent final paper: Human Communication is Evolving in the Blogosphere.

Now, this guy's paper on 'metablognition' is of great interest to me, but it is not posted! Why? Has he moved to another blogging platform? Did this one also continue somewhere else? Both blogged regularly and then abruptly stopped. Strange...

Leon is running his own personal blog in Hungarian. But he did post his paper - RICHARD PRYOR AND SPEAKING THE TRUTH: On The Purpose and Voice of Personal Blogs - on his class blog.

I love this one! A blogger, blogging like a real pro, against blogging, but will consider continuing blogging, maybe, but probably not. Anyway, here's the term paper.

John of Jean DuBlog posted the results of his blogging ethics survey. Bill's Blither is an amazing blog. No paper, but who cares, this one stays on my blogroll.

Erin now feels free to blog on her own, now that the class is over and her paper is posted: Everyone's a Critic: Critical Thinking (or Lack Thereof) In the Blogosphere.

Something else happened in that class that is very interesting. Before the last class meeting, Colin had to warn them: "There's no crying in blog class!" And they sure cried. Dig through their blogs - especially the comments to posts in late December - to see for yourself. It is amazing how emotionally involved they got in this class. They all became fast friends. One is wondering why?

They believe this is because of a unique collection of fascinating individuals and the way they all clicked with each other. But is it really so unique? Or is it the fact they wrote their own and read each others' blogs that allowed them to get to know each other better than they would have if they just met on campus once a week for a semester? Does one's persona emerge on one's blog in ways that carefully managed image in real life cannot?

Now here's a thought: what if every class, from high school through grad school (with exception of humongous college freshman required classes that collect hundreds of students at a time), had a class blog and required students to keep their own blogs, write their assignments there, and post comments on each others' blogs? What would be good and bad consequences of such a practice if it became a norm?

Kids are already so used to being online. From AIM, XBoxLive and e-mail, through Facebook, Friendster and MySpace, to Xanga, AOL Blogs and LiveJournal, kids are definitely swimming through cyber-waters like fish.

Imagine starting in high school. Each teacher manages a class blog. Each student also runs a blog (perhaps on a platform that hides them from visitors outside of school). In each class, the class blog links to all the students and all the students link to the class blog and to each other. They are required to post their assignments on their blogs and to post links to those on the course blog. They are required to comment on each other's blogs and on the course blog.

We can assume that many students, just like the grad students in Colin's class, will also use their blogs to post stuff unrelated to class. Aware that teachers have access, they will probably heavily self-censor, but still, their true voice is likely to come out.

High school students come to school wearing a mask, an image they want to project. Freshmen in college do the same. But on their blogs, masks fall off. It is so hard to fake it online. See how Colin's students, at the very beginning of the course when they were still complete newbies, immediately lambasted XiaXue for being fake, and loved Coffee Rhetoric and Dooce for being genuine. The real persona eventually emerges.

If so many young students are uncomfortable being themselves in real life, but comfortable being themselves online, will their reading of each others' blogs help them get to know each other better, like each other better, become friends? Or is this going to be yet another tool to stir up trouble, gossip, form cliques and shun the outsiders?

Will a shy kid with great writing skills become popular? Will a popular jock be laughed at due to bad grammar and spelling? Would this be dangerous or wonderful for students' self-esteem?

How much would teachers have to learn how to monitor what is going on and interfere on behalf of victims? Would signs of depression, suicidal tendencies or aggressive intentions be detected earlier? How does one weigh pros and cons and thus organize the way this is all done?

How about college? There, each student would be a part of a number of blogging communities - one for each class they take. Will they care if they do not fit in with the engineering crowd but shine in a feminism class? How many blogging communities can one physically and mentally belong to before giving up on the whole thing?

How would mandatory blogging affect the level of reading and writing among the kids? If they know they are being read by classmates and teachers, will they try harder to write correctly? Will they become experts in detecting plagiarism on each other's posts, thus reducing its incidence overall?

Will discussions in comments sections raise the level and quality of thinking? We all know, as adults, how many heated discussions online end up with accusations of particular logical fallacies, e.g., ad hominem, red herring, slippery slope, etc. Will kids learn to recognize logical fallacies earlier if they are forced to comment on each others' blog early on in their careers? Will that positively affect the level of critical thinking? Will that prepare them better for their other college classes? Will that make them better citizens and better informed voters?

How would this affect the way teachers teach?

So, do you think it is possible to repeat the group cohesion effect of Colin's class in many other classes at difeferent ages and levels, no matter what the course subject is? Is that good or bad? Do benefits outweigh the risks? What other factors I am blind to? Comments are open.

Cross-posted on Science And Politics

Technorati tag: Teaching-Carnival

Teaching Evolution Successfully

The new article on PLoS, Evolution for Everyone: How to Increase Acceptance of, Interest in, and Knowledge about Evolution by David Sloan Wilson, describes a successful experiment of teaching evolution to a broad segment of the student population at Bighampton College (the paper looks nicer in PDF format).

Here are just a couple of snippets:

The main problem with accepting evolution involves implications, not facts. Threatening ideas are like other threats—the first impulse is to run away or attack them. Make the same ideas alluring, and our first impulse is to embrace them and make them our own. Neither impulse is very respectable scientifically. After all, scientists are supposed to accept ideas when they are true, regardless of their consequences. Nevertheless, the key to making evolution a subject that anyone can understand and everyone should want to understand is to focus first on the implications.

---------snip-----------

It might seem that boldly discussing subjects such as human infanticide (which the students quickly connect to the contemporary issue of abortion), along with other topics such as sex differences and homosexuality later in the course, is the ultimate in political incorrectness. However, I have taught this material for many years in prior courses without a single complaint, and the assessment of “Evolution for Everyone” demonstrates an overwhelmingly positive response across the religious and political spectrum.

---------snip-----------

The important point is that evolutionary theory can potentially explain the evolution of behaviors associated with morality and immorality. This is vastly different than the usual portrayal of evolution as a theory that explains immorality but leaves morality unaccounted for. The average student is well aware that immoral behaviors usually benefit the actor, that human groups have a disturbing tendency to confine moral conduct to their own members, and so on. When evolutionary theory is presented as a framework for understanding these patterns in all their complexity, including the good, the bad, the beautiful, and the ugly, it is perceived as a tool for understanding that can be used for positive ends, rather than as a threat.

You reaaly should read the whole thing, as it is informative, thought-provoking and almost exhilarating. No matter what prior education, strength of religious belief or political ideology the students (from a wide variety of majors) had prior to the course, they all had a positive experience, learned a lot, and understood both evolution in particular and scientific method in general much better than they did before the course.

Also, check out the course website for more information. One of the undergraduate students in the program finished his course project by having it published in Quarterly Review of Biology (pdf)!

I will definitely print this out and study it in detail in order to try to replicate it in the future.

Cross-posted on Science And Politics

Technorati tag: Teaching-Carnival

Dr.Love-of-Strange, or How I Learned To Love The Malaria...

There has been literally an explosion of new knowledge about malaria in the last ten years or so. It is an amazing disease. Looking at all the new findings coming out almost every week makes me salivate because of...teaching! Malaria is a fantastic case-study to keep mentioning over and over again throughout the course. Let me backtrack for a moment....

I teach general biology to adult non-science majors at a community college. It is a speed course, lasting only eight weeks. In eight meetings, one has to deliver an enormous amount of material to an audience that is terrified of science. Last time they had a science class was many years ago in high school. All they remember is that it was boring and hard.

At the time most of my students took biology in high school, the state syllabus was one of the most atrocious in the nation - much rote memorization of Latin words, be it human bones, parts of the flower, taxonomy of worms, or the steps in the Krebs cycle. Of course it was boring and hard - the old German style of teaching designed to instill discipline, not knowledge.

A few years ago, in response to Rep.Russell Capps' (R - Wake Co.) attempt to bring Creationism into NC classrooms, the state rewrote the science curriculum and it is now one of the best in the country - every unit in biology is taught within an evolutionary context. Teaching freshmen biology majors at State is a real pleasure now - those kids are excited and already knowledgable. But my adult students are not, and that makes them much more difficult to teach.

One of the problems of teaching introductory biology, at any level, is the way many units do not have an obvious relationship to "real life" of the students, especially the non-science majors. "Why should I learn this when it has no relevance to my life?' they ask.

The second problem is that biology is so big. The course is broken down into units, each unit introducing a different subdiscipline, e.g., genetics, evolution, behavior, anatomy, ecology, microbiology, etc. Taught like this, the units do not appear connected to each other. It feels like every week one starts on a completely different branch of science.

The solution to both problems is to find good case studies to use to introduce each topic. Hopefully, the case-study will be something "sexy", something that media writes about a lot, e.g., stem cell research, cloning, spotted owl habitat, global warming. I discovered that diseases are the best attention grabbers of all of such topic. By using cancer, AIDS, avian flu, SARS, etc. one can introduce any topic in biology and make it relevant to the student. Mad Cow Disease is a great way to get the students to pay attention before you lunge into the difficult lecture on protein synthesis (you start with prions, then work backwards).

The best examples are those diseases that can be used to span several topics. I found that Lyme disease and West Nile virus are really good for this - important discoveries on those were made by a whole range of researchers coming from very diffeerent angles, from genomics to ecology.

But by far the best is malaria. No matter what I talk about, I can smuggle malaria into it in one way or another. Genetics and genomics? Sure, this is the only disease in which all players' genomes have been sequenced (host - human, vector - mosquito, and parasite - Plasmodium). Population genetics? Sure. Blood physiology? Of course. Tertiary and quaternary structure of proteins? Just remember the sickle-cell anemia, which is also great for teaching about Mendelian inheritance. From protozoology and parasitology, through entomology and olfactory neurobiology, to immunology and evolution, one can always somehow bring malaria into the conversation. Hey, just this one story spans behavior, circadian clocks, evolutionary arms-races, melatonin, cellular endocrinology and insect olfaction (also see this, via this)!

And now there is more! Who would have thought that malaria had anything to do with taste and alcoholism?! I can already see how much fun teaching next spring will be.

Having malaria (or some such topic of your own choosing) coming up over and over again helps to unify various subdisciplines of biology in the minds of students. They see at least one example in which important knowledge has been accumulated by researchers in various fields. It is not just molecular biologists that can figure stuff out about diseases. Field ecologists can provide some key information - sometimes the most important piece of information from the point of view of prevention and treatment.

It also shows how deeply evolutionary thinking runs through all areas of biology. Practically all major advances in the study of malaria came through application of evolutionary theory to the disease. Just saying this is so may not be enough - demonstrating it, every week, on a topic they are inherently interested in, may help drive the point much harder.

Cross-posted on Science And Politics

Technorati tag: Teaching-Carnival

My first high-school teaching experience

Yesterday morning I went to Hillsborough and talked to two 10th grade classes about circadian clocks and sleep. That was quite an experience. I have just realized right there and then that this was the first time that I have ever set foot in an US high school.

I've had a PPT slideshow ready, but I suspected that a high school was not as technically well equipped as a University, so I changed my mind and did the whole thing just talking and drawing on the whiteboard (I was right about the AV - it did not work).

I was pleasantly surprised to see the kids genuinely interested and asking many good questions - both interrupting me throughout the lesson (THAT I liked a lot) and at the end. I was surprised at how many questions had something to do with alcohol. I was expecting questions related to sex.

Oh, and how did I get this gig in the first place? Well, of course, the science teacher reads both of my blogs... Thanks for the invitation and the experience.

Cross-posted on Science And Politics

Technorati tag: Teaching-Carnival

Using blogs in teaching

I teach biology to adults (non-science majors) at a local community college. For communication with students we are supposed to use the most cumbersome school website system ever designed. But who says that we cannot use blogs in teaching, too? This morning, I gave my students an assignment to write a paper. I did not give them any information on formatting. Instead, I told them to emulate the style and format of essays posted on Transitions, as well as to use that blog as a starting point, by following the links, for gathering information they need for their papers. We'll see how that works out.

Cross-posted on Science And Politics

Technorati tag: Teaching-Carnival

Teen Parenthood for the X-box generation

Earlier today Mrs.Coturnix and I took Coturnix Jr. and Coturnietta to the pediatrician (and the dentist - they are in the same building). While sitting in the waiting room we saw a strange scene. A father and a son (about 14-years old, I'd say) walked out of the office, the boy vigorously rocking a little baby, the father saying "It's great we have a car. Cars are good things".

I guess I made such a face that the receptionist started laughing: "It's a doll". A girl waiting in the same room offered an explanation that in middle school you get a doll for a couple of days and have to take care of it. The doll is computerized and cries "all the time" (her words spoken over a painful grimace).

The receptionist (quite young herself) mused that "in her day" the dolls were not so sophisticated so she and her friends just locked them up in the lockers. I asked for the name of the program and she said "Let me check", got up and in a few seconds came back with the answer: Baby Think It Over.

I looked at Mrs. Coturnix and said "I have to blog about this", so here is what I found:

Baby Think It Over is an educational program that is done in high schools (and recently in middle schools) to demonstrate to the adolescents what parenting really entails.

This paper describes research on the effectiveness of the method and provides background information on which the program is based.

Here you can see what the doll does and what the 'parent' is supposed to do.

This is a good essay by a student who's done it and here are a few more experiences.

See more.

Beats "abstinence-only" Xtian programs hands down, I'd say.

Update: If you did not bother clicking on the links, the program is designed not to teach kids to parent, but to show tham how HARD it is ....and it seems to be working! They want to party and sleep, not change diapers. Harsh reality kicks in.

Cross-posted on Science And Politics

Technorati tag: Teaching-Carnival

Teaching Blogging

Somewhat related to the whole ConvergeSouth experience. I've been pitching a blogging course to my school for a while now (not NCSU, but a community college where I teach). It's been slow and disheartening so far. Nobody knows what blogging is. Also, there is a rule that one needs to have an appropriate degree for a class. In the case of a blogging class, this would mean, or so they said, either journalism school or computer science.

Last night we had a faculty retreat and the main campus bigwigs showed up on our little satellite campus. The new Dean was there. He was talking, as a part of his top 5 things he wants to do, about completely re-doing the computer science curriculum, as well as pushing for more online and hybrid online/classroom) classes. I had only about 5-10 minutes, during a break, to corner him and to sell him these two points:

- Blogging class is important because it is the wave of the future and having such a course would prepare our students for the 21st century, as well as put the school on the map as a cutting-edge educational insitution. It would also be a hybrid class: first meeting in person to help students set up their own blogs, and the rest of the class online. I mentioned Colin McEnroe's blogging class up in Connecticut, as well as the position of North Carolina as the incubator of all new blogging ideas in the world, including the innovations by Greensboro News & Record that the whole world is watching.

- J-school graduates bring in the biases that make them most likely to misunderstand what blogging is all about, thus trying to teach a journalism class on computers instead of a blogging class. A computer scientist, likewise, would try to stick in too much technical stuff, and is likely to miss completely on the sociological, political and journalistic aspects of blogging. Thus, the proper background for teaching such a class is to be an experienced blogger, and I am one (using the fact that I was invited to ConvergeSouth - and I was, on purpose, wearing my ConvergeSouth T-shirt).

I talked fast. Ten minutes is not very much time (and I had to start with introducing myself and then chatting about Yugoslavia first). It worked. I am going to write up a proposal and it is likely to pass and I may start teaching it next year, perhaps as early as spring.

Cross-posted on Science And Politics

Technorati tag: Teaching-Carnival

Political Affiliation on Campus

The Facebook is an extremely popular social software on campuses around the country. According to Fred Stutzman, (hat tip: Paul Jones) 85% of incoming Freshmen at UNC - Chapel Hill had a facebook account on day one of class.

If you follow that link to Fred, you will see that he used the Search function of the Facebook to look at the breakdown of UNC students by political affiliation. Intrigued, I did the same thing for NCSU.

Here are the raw data:

Political Affiliation: Female / Male

Very Liberal: 244 / 264
Liberal : 1267 / 1122
Moderate: 1101 / 1491
Conservative: 1560 / 2312
Very Conservative: 119 / 320
Libertarian : 38 / 122
Apathetic : 94 / 309
Other : 152 / 509
-------------
Total 4575 / 6449

...and here is the graph:

The obvious difference is, as is expected, that the students at UNC report themselves to be more liberal than NCSU students. No surprises there. In both schools, guys are more conservative than girls - also no surprise. On both campuses, very few students choose the extreme options ("very liberal" or "very conservative").

What can we glean from these data? I say, not much. There is just too much information missing.

Sampling: What proportion of NCSU students have a profile on Facebook? Are the men or the women more likely to put up a profile? What is the sex-ratio of students at NCSU in the first place? Are people of a particular political ideology more or less likely to sign up on the facebook? Does that differ between the sexes (e.g., female libertarians are less likely to sign up than statistics would expect, but male libertarians are as likely as anyone else to sign up)?

It is not neccessary to choose any political affiliation when making a profile. What proportion of students have profiles with no political affiliation at all? Does that differ between males and females? Does that differ between people of different political ideologies?

Searching: What does the facebook search engine do? What proportion of hits tabulated above are alumni (graduated last year), grad students, faculty or staff? How many of the 'hits' are non-existent people? I have seen, when searching faculty, profiles of Albus Dumbledore, Rush Limbaugh, Andy Rooney and many other celebrities and fictional characters. Coach Herb Sendak is listed as a professor of philosophy!

Self-reporting: How accurate is the self-reporting? Are students choosing 'moderate', 'apathetic' or 'other' (or not to sign up at all) in order to not allienate their friends? Is the choice to avoid the tag "very" motivated by the same reasons? After all, the total number of friends is a currency of prestige on the facebook.

Meaning of labels: I think that people who reported being "very conservative" and "very liberal" can be believed on their word. The former are members of Young Republicans, GOP activists, and Christian fundamentalists. The latter are largely "Deaniacs", with some other Democratic activists, College Democrats, and Greens thrown in the mix, too.

What do the other labels mean? I did a little scan of the profiles listed as "other". Most people on facebook list membership of various virtual "clubs" or groups. I was expecting to find some Greens (the only major party that is not a choice on facebook) in this group. However, most of the "other" have listed membership in groups concerned with student life, popular culture, partying, drinking and sex - no politics. Shouldn't they picked "apathetic" instead? I have found some, among the "other" who are members of a variety of Republican, conservative, and Bush/Cheney clubs. Shouldn't these people self-report being "very conservative" instead?

How about Libertarians? It is a strong third party in North Carolina. Why were there four times more male than female self-reported libertarians? Is that the sex-ratio of the party membership in the state? Also, "libertarian" is a very inexact term. What does it really mean? I know some students who consider themselves libertarian, yet when poked with questions, reveal to be pure liberals. Do they know the meaning of labels?

What does "moderate" mean? If you considered yourself a moderate, you are likely not paying attention. I assume that the concept of moderation in everything, including politics, appeals to many. But, moderation in politics is a meaningless concept - it reveals lack of understanding, information and motivation. Most of the people who list themselves as moderate are, more honestly, apathetic. Some are perhaps liberals who think they are conservatives because of the way they were raised.

The biggest categories - liberals and conservatives - are probably even more or a grab-bag of apathetic, very liberal, very conservative, and libertarian students, many of whom are misguided about the proper meaning of the labels.

It is always a surprise for self-professed conservatives when they try to do various political quizzes online and find themselves to the Left of Marx. The meaning of terms has been obfuscated, often on purpose, by the two big political parties. Many core liberal values, especially those that most Americans hold the dearest, are erroneously believed to be conservative due to historical contingency that these values were held by the Republican Party some decades ago. Fiscal responsibility is a good example.

Many people vote GOP because they (correctly) equate modern GOP with conservatism and erroneosly think of themselves as conservatives. If given a qeustionnaire, they invariably turn out to be quite liberal. The Dems need to do something about this misperception, as it is a major source of drain of voters away from it.

A final note on the Facebook study: most college students do not care much about politics. They do not know enough. Their self-reported political affiliation is a pretty accurate break-down of what their parents think (not neccessarily correctly) is their political ideology.

On the other hand, college is supposed to be a place where one questions and leaves parents' beliefs. That is the place where one obtains information and facts, where one realizes that one has previously held erroenous ideas about history, economics, law, gender-relations, religion, science and politics. Thus, it is to be expected that college turns people into liberals, as the whole fabric of conservatism is based on erroneous and long-debunked notions about human nature, operation of complex systems (including economies) and everything else. It would be interesting to repeat the facebook search with divisions by year and see if recent alumni, grad students and seniors are more liberal than freshmen.

Update: Thoughts From Kansas did the analysis of the Facebook at KU.

Update 2: Fred Sutzman has more on the UNC use of Facebook, focusing on the freshman class. I initially got on the Facebook in order to see how many students are blogging (and Fred looks at that, too). A relatively small proportion of students put up a website on their profile. When they do, it is usually a Flickr (or some other photo) site. Some have websites made in class and not updated for two years. I found a few xanga, MSNSpaces, and a few LiveJournals, but not a single Blogger, not to mention more involved blogging platforms. Are the kids not blogging? Are they hiding their blogs/journals? I know of several students who have LiveJournals but do not provide links to them from their Facebook profiles - in other words their FB profile is their public face and their LJ is their private face, to be kept separate at all times and at all costs. When I go to bloggercons, I see grey hair everywhere. Are the kids going to take up blogging later, once they ar ea little older, smarter, better educated and have something to say beyond gossip?

Update 3: More thoughts: Someone with time and patience should look at political self-description of freshmen by major, and compare the numbers to that of the seniors in the same majors. Are conservatives drawn to business and liberals to sociology or does spending four years studying business turn one into a conservative and studying sociology makes one a liberal? Are geneticists and biochemists more conservative than ecologists and physiologists to begin with, or only after years of study? How do philosophers stack up against physicists? If college experience naturally turns one into a liberal, which majors are most successful (if any) at engendering that change? Do some majors turn kids into conservatives?

Cross-posted on Science And Politics

Technorati tag: Teaching-Carnival

Don't Know Much About History....

When I was in elementary school back in Belgrade (grades 1 through 8) I had the most horrible history teacher. She was an example that stereotype of "dumb blonde" is sometimes correct. She was hired, I assume, because she was the Barbie-doll trophy wife of the then mayor of Belgrade.

For four years I did not learn anything about history. I managed to get all 5s (equivalent of As) until the very end of eighth grade - almost evrybody in class did. And nobody learned anything.

In middle school (grades 9 through 12) I had, at first, a tough old history teacher. He called me up to the blackboard one day to ask me some questions. I did not really know much, I admit. He looked down at the big red class book and said something like this:

"I see you have all fives in every subject possible - language, math, geography, biology, physics, chemistry - what is so hard about history?"

I said:"Well, remembering all those millenia, centuries, years, dates, names of kings, emperors and military leaders".

He looked stunned: "B-b-b-but....what is left if you eliminate all those?"

Me: "Well, the interesting stuff - the story".

He mumbled something about the need to memorize facts anyway and gave me a (barely) passing grade. Still, from that moment on he liked me (and that was important one day a couple of years later when I got in trouble in school - he saved me). He had to follow the curriculum and he was too old and set in his way of thinking to ever be able to teach "the story", but I think he appreciated my sentiment.

The remaining three years of middle school (in Yugoslavia, the term "high school" is reserved for vocational education, e.g., two-year technical schools, reserved for those who did not manage to pass tough entry exams into the University - there is no such thing as college) I had a great history teacher. She obviously loved history. Although she had to teach the curriculum, which meant memorizing trivia, she managed to weave a story anyway. My problem was that, by that time, I was hopelessly unprepared - I had no background because I have not learned anything up till then. I got fevers several time trying to study history for her - it was hard work.

I so wish I had decent history education back then. I feel the gaps and holes in my history education every day, especially in long comment-threads on smart blogs. I spent a lot of time learning history of science (I took FOUR grad classes on this!). I am trying to make up by reading history books, but that is not the same.

I have recently finished "Marriage - a History" by Stephanie Coontz. Not just that it is a marvelously written story, as well as well documented piece of academic history, but I also learned so much from it about details of history that are completely un-related to marriage. Not to mention that the whole story is starting to make sense. I can now see how pieces join together to form a bigger jigsaw puzzle. I can see the relevance of history to today's world.

Why is history not taught that way from the very beginning? Also, are there any general history books out there that I may like and find useful in patching up the holes in my knowledge?

Cross-posted on Science And Politics

Technorati tag: Teaching-Carnival

Lefty and Righty excesses of pseudo-science

According to Michael Shermer there are:
- science
- borderlands science
- psuedoscience, and
- nonsense

Science is a methodology of figuring out, with as great confidence as possible, how the world works. Evolutionary theory is one of the biggest, strongest and best-supported bodies of all of science.

Borderland Science refers to first small steps in acquiring realistic knowledge about a not-well-understood aspect of the world. It aspires to become Science, but is often held back by various factors, e.g., difficulty in studying the phenomenon of interest, biases of the investigators, social biases against investigations of such phenomena, etc.

For instance, very little is known about hypnosis. It is a real phenomenon but very difficult to study. There is not much funding for it as there is a social bias against such research. Thus, it is still doing its first small pioneering steps and has not resulted in data that are good enough to place it in the realm of real Science.

Another example is Evolutionary Psychology - it is done by psychologists (thus real scientists) who understand biology very poorly, yet strive to make their research scientific. Their own biases make them go up wrong alleys and bark up wrong trees (I love adding up mixed matephors, sorry). Yet, they are asking real questions about real phenomena and it is expected that at some point evolutionary psychology (lowercase) will get its methodology straight and make enough advances to become real Science.

Pseudoscience is an attempt to sell out-of-ass beliefs as scientific by using hifallutin' terminology, perform meaningless calculations, draw elaborate charts etc. Examples are many (peruse past editions of the Skeptic's Circle for examples) and include astrology, biorhythms, pyramid force, Feng Shui, crystal balls, alternative medicine, Holocaust denial, Intelligent Design Creationism, and many, many others. The main goal, usually, is making a quick buck, although more sinister motivations are sometimes behind such ideas, i.e., these may serve as methods for making an unrespectable ideology (e.g., Nazism) respectable again, or there is political gain to be had.

Nonsense does not even pretend to be scientific, e.g., Old Earth Creationism.

The psuedoscientific ideas have cropped up, historically, both within the political Right and Left - and often completely detached from any ideology. The crucial difference between the two (today) is that the Lefty pseudoscience has no negative consequences for the broader society. Nobody is hurt if some Birkenstock Lefty performs chants and lights up incense during a spiritual night of camping out in the desert in Arizona.

Lefty pseudoscience was always marginal and marginalized by everyone on both the Left and the Right. No political party has ever pushed for astrology or biorhythms to be used in classrooms or in military planning.

However, attack on science, reason and rationality is the centerpiece of the Right-Wing strategy. The only way they can save their medieval notions about society, economics, religion, science, race, gender equality, etc. from being deposited forever in the trashbin of history is if they systematically brainwash every new generation into dogmatism, uncritical thinking and fearful obedience to their authority. They are in power now - White House, Congress, Supreme Court - and they are ramming anti-science and anti-reality ideas into school (and into media) as hard as they can.

Their strategy is to confuse everyone as to what is science, what is borderlands science, what is pseudoscience, what is nonsense, i.e., what are facts and what is opinion. They are pushing IDC in order to spread the seeds of that confusion. They sneer at the reality-based community. What they are trying to do is institute not just moral relativism, but also factual relativism - nobody knows what the truth is any more and nobody knows how to figure out what the truth is so the only recourse is to blindly believe one's leaders (while they steal your money and your labor).

Saying that pseudoscientific excesses of the Loony Left are equivalent to the pseudoscientific excesses of the Righteous Right is just an example of such factual (and moral) relativity. The former is silly, discredited, powerless and innocuous. The latter is serious, more and more mainstream and dangerous to the Enlightment and what it gave to the human civilization. The former is laughable. The latter is the key weapon of the Republican Party (at least the faction in power right now).

What about the notion that Academia is liberal, particularly in social sciences? True, and that is good. Let me try to explain why (though I have done it before).

Science changes and evolves and, by being self-correcting, gets closer and closer to the truth as time passes. For instance, current understanding of evolution is better than in 1960s, which in turn was better than the 1930s evolutionary theory, which was better than the theory as described in the Origin of Species, which was better than the ideas of Chambers or Lamarck.

Social sciences are "soft" so the self-correcting process takes longer and often incites more vigorous fights. Still, it does self-correct over time and the current state of psychology, sociology, anthropology, economics, etc. is much better than the 1960s social science, which was better than 1920s which was better than 1880s, which was better than 1670s....

What conservatives would like to see re-introduced into social science departments at the Universities is 1880s social science. This is equivalent to trying to re-introduce Lamarckism into biology departments.

The path towards greater accuracy within science is often not linear. There is often a pendulum motion between one extreme and the opposite extreme, one springing up as a reaction to the other, introducing its own excesses, then giving way to the opposite extreme.

"Nature" held sway for a while, then "nurture" took over as the dominant paradigm, nature again, nurture again....but today it is neither and both. We have arrived not at a grey compromise position somewhere in the middle between the two extremes, but at the more sophisticated understanding of the inheritance of behavioral traits.

Both "nature" and "nurture" are hierarchical positions. We have arrived at the current understanding when we ditched hierarchy in favor of a an interactionist system. This has happened in many areas of science, including evolutionary biology among others.

The same happened in political ideology. In 1930s, both conservative and liberal ideologies were hierarchical - the difference was who's on top (i.e., in control of economy). But today, conservative ideology still clings to hierarchy (it cannot change - it is BASED on hierarchy), while modern liberalism is an interactionist system.

Conservative childrearing philosophy (as explicated in e.g., James Dobson's manuals) leads to a hirerachical way of thinking about everything. It is very difficult for born-and-raised conservatives to comprehend non-hierarchical interactionist systems. That is why they do not understand what "free market" is all about, nor can they understand what modern liberalism is all about. They either assume it is the same as it was in the 1930s (thus calling us "commies"), or understand it has changed but do not understand how and instinctively recoil in fear when presented with something they are incapable of understanding (I have written many times and in great detail about various aspects of this so you can dig through the archives of the relevant category).

Back to liberal social science in academia. Excesses of conservatism in social sciences in the late 19th and early 20th century were replaced by excesses of liberal social sciences. Pendulum swung a few times, and each time there was self-correction and general improvement.

No, current state of social sciences is not perfect, but is immeasurably better than anything conservatives would like to put instead. Their social science has not evolved in almost a century - it is badly out of date. Most importantly, conservative social science is still hierarchical - implicitly or explicitly it is based on superiority of some groups (usually white rich Christian straight American males) over other groups.

Liberal social science has largely transcended hierarchical worldview and adopted interactionist thinking. With all its imperfections, it is the best we have at the moment, the closest to the true understanding of the reality. Conservatism has nothing to offer but return to an outmoded hierarchical way of thinking that can be used and abused in apologetics of various social inequities. Putting conservative social science back into the academia is just like hiring a Lamarckist in a biology department. A huge step backwards.

Hard sciences, social sciences, society and political ideology change and evolve over time. Invoking eugenics (which, btw, was apparently liked by conversatives, too, just ask Herr Adolf) or attacking 1960s or 1930s liberalism is exactly the same tactic that Creationists use when they attack the theory as described in the Origin instead of CURRENT evolutionary theory.

What happened in the past 30-40 years or so is that much of hard sciences, social sciences, society and liberal political ideology have moved from linear hierarchical thinking to non-linear interactionist thinking.

Liberals have embraced this change BECAUSE it eliminates some errors of historical liberalism (e.g,. of the 1930s or 1960s). Not all have changed, though. Lieberman is a dinosaur, and so are many others in the Democratic leadership. Some of the Feng-Shui liberals I criticized above are likewise stuck in the 1960s.

Embracing this change also helps liberalism form a unified, internally consistent ideology, in place of its usual issue-by-issue catalogue of stands.

However, conservatism CANNOT change and get modern and current because hierarchy is the ESSENCE of conservatism. Attempts to modernize weaken conservatism as it is forced to accept liberal views on individual issues (see Europe).

BushCo chose the opposite tactic - keep conservatism logically consistent and intact, thus, in the process, stopping the evolution of all political thought, of science and of society - keeping the status quo indefinitely. Systematic attack on science is a neccessary strategy, actually central strategy for that endeavor to succeed.

Conservatism is violently lashing out like a wounded beast feeling its own impending demise. It is still dangerous. If we are not careful it can kill us. If that happens, history stops, returns to 18th century norms, and persists in that state for a long time. We just have to win this fight, defeat this beast once for all, in order to save the Enlightement and allow the world to move on into the future.

Update (responses to critics):
Political theories