Wednesday, May 31, 2006

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, 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


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

Wednesday, May 24, 2006

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.

Sunday, May 21, 2006

Organisms In Time and Space: 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.


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

Technorati Tag: teaching-carnival

Tangled Bank - last call for submissions

The Tangled Bank

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

Saturday, May 20, 2006

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).


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

Technorati Tag: teaching-carnival

Wednesday, May 17, 2006

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:
Project Exploration
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


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.

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:

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

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


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

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

Monday, May 15, 2006

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.


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


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.


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

Sunday, May 14, 2006

Tangled Bank - call for submissions

The Tangled BankNext 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.


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 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.


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:


Previously in this series:

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

Technorati Tag: teaching-carnival

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.

Wednesday, May 10, 2006


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.

Technorati Tag: teaching-carnival

Monday, May 08, 2006

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.

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

Technorati Tag: teaching-carnival