Saturday, April 26, 2008

Mask of Biology II: Evolution

Evolution. Survival of the fittest. Darwin and natural selection of the most adaptive traits. If only it were so simple. This was what I once thought as well, despite being a biology major. It's an elegant and beautiful theory, but it's a theory in the same way that gravity's a theory. It has so many subtleties that are just now being explored. In the span of a single semester, I've had exposure to but only a fraction of evolution's complexity.

While I realize that few reading this might find this particular post interesting, I hope those that do can see my appreciation and awe of nature, and the humbleness it brings through my Mask of Biology. I don't know if my words will do any kind of justice to how I feel, but if it conveys even a little bit, I will count it a success.
1. Not always selection of the most adaptive
There is the tendency to think that the traits that are most adaptive and beneficial will always get passed on whereas detrimental traits will be eliminated. This is a rather gross over-simplification. Firstly, mutations are the ultimate source of variation. Most mutations are neutral, meaning that they don't impact the organism or its offspring at all. Some are harmful and some are beneficial.

Neutral mutations are passed on from generation to generation; over time, enough accumulate to make a difference in the genome (complete set of genes) of that organism. There are also varying degrees of detrimental and beneficial. The most detrimental (resulting in death before reproductive maturity) gets purged from the population rather quickly. Then there are some traits that are bad . . . but not so bad as to be worth eliminating. The opposite goes for beneficial traits. Some are so marginally beneficial that they might "accidentally" get lost. Sometimes really beneficial traits get "fixed" in the population, meaning that most individuals in that population will carry that trait.

This has been fairly straightforward so far. Now there's something called "linkage disequilibrium," another is called "positive selection sweep." In linkage disequilibrium (LD) it basically means that 2 traits are almost always seen together because they're physically very close to each other on chromosome. So if a mildly bad trait is next to a really good trait, chances are that you'll see both of them at the same time. Positive selection sweep is a means to detect whether or not positive selection (selection for a positive, aka beneficial, trait) has happened. Like LD, sometimes the trait being selected for is "so good" that it carries along bad traits with it as it "sweeps" across the genome.

Interestingly, it should also be worth noting that just because a trait's good, doesn't mean it'll reach fixation (again, where most individuals in the population carry the trait) on the first try. In fact, many/most such traits must arise independently several times before it can reach fixation. In a way, it's more or less the roll of a die.

2. Order matters
What evolves first and what evolves second matters. A good example is bat wings. 2 things must happen in the evolution of bat wings: elongation of finger bones and maintenance of skin webbing between the fingers. Both require evolution of different regulatory mechanisms, the question is, which came first?

In another paper, scientists "forced" bacteria to evolve from one state to another by making them adapt to a new food source and environment. So let's say the bacteria evolve from Species 1 to Species 2, and it required mutations A, B, C, and D. They went back and painstakingly made each mutation in different combinations (i.e. ABCD, ACDB, BCDA, etc) to see what happened. Surprisingly, they found that only a handful of combinations are able to evolve the bacteria from Species 1 to Species 2.

So back to the bat wings, just a sample of its complexity. The expression of the gene bmp4 increases bone growth, so it increases finger length. However, it also prevents interdigital webbing (skin between fingers). So another set of 2-3 genes are required to turn off bmp4 expression between the fingers. So again, which came first? Repression of bmp4 between fingers, or increase in bmp4 expression all around? No one knows.

3. Large vs. small mutations
There has been a debate between "large" mutations and "small" mutations. Large mutations are mutations that causes a sudden or significant change. For example, the alteration of 3 genes can change cells from growing cells to growing scales or feathers. Small mutations are mutations that on their own don't do much, but the sum product of them create large changes.

This is related to sudden change theories, like punctuated equilibrium or "hopeful monsters," to gradualism promoted by Darwin. There are clearly evidence of both throughout natural history. Sometimes you get a freaky mutation that just so happens to work, so it does. And other times small changes accumulate over many generations, and things gradually change from one thing to the other.

So even in the way things evolve there is no consensus.

4. Canalization
There are several concepts in evolution where diversity is somehow hidden or limited. This seems counterintuitive as generally evolution is thought of a driving force for change, for creating diversity, and not for maintaining the status quo. Why might this be? Well, for some things you really really don't want mutations to occur. For example, if a bad mutation occurred in the formation of the brain, that organism's brains will be scrambled. So you want brain formation to stay more or less the same throughout evolution. There are several biological mechanisms that prevent mutations or at least mask their effects from showing.

One is canalization, which is any genetic mechanism that reduces phenotypic diversity. Phenotype is what's actually expressed and seen. Again, genotype = what the genes actually say, and phenotype = what's actually seen. So a phenotype might be brown eyes when that person really has the genotype for brown and blue eyes.

Canalization acts kind of like a rug that hides things underneath it. What this means is that there's some genotype or genetic trait that acts like a rug. And it hides other genetic mutations under it, so the phenotypes for those mutations aren't seen. But, if conditions are just right, the rug can be pulled aside or shifted. And some of the phenotypes that were hidden under it can be seen.

5. Developmental System Drift
This is one of my favorite concepts. Basically you have a phenotype, but for that phenotype there are more than one genetic mechanisms that create it. At one point there may have only been one genotype for that phenotype, but over time, small mutations occur until eventually, you have 2+ different genotypes that still express the same phenotype.

I think I've used this analogy before. Let there be two genotypes "Shawn" and "Sean." Both are spelled differently but have the same pronunciation (aka, the same phenotype). Now, "Shawn" and "Sean" are considered two different species. So if they interbreed, the offspring would be an infertile or inviable hybrid. This is one way different species similar for a particular trait(s) speciate, or become different species from one another.

Developmental system drift (DSD) also allows the appearance of different phenotypes arising from a single one. For example, from "Shawn" you can get to "Shown" and from "Sean" you get to "Dean." Each only requires one "mutation" to get from something that's pronounced the same to two things that're different.

6. Genetic Constraint
There's a concept that there are simply limits on life. That there are only so many ways to develop along a path once it's been established. There are constraints on how things develop and constraints on what develops.

For example (and this will be a bad example) the evolution of legs favors even numbers. Once the evolutionary path to create legs has been established, legs will always be created in even numbers. This is a limit on what can develop. Then there are limits on how something develops. For example, the brain must develop in a certain way and a certain order. If it goes out of order, bad things happen. So nature constricts how a brain forms.

This leads to an interesting thought-experiment. If we were to back in time and restart the Cambrian explosion, would life on Earth today look the same? Or, if on another planet, conditions were exactly the same as they are here, would life look similar? This concept may not answer these questions. But what it does say is that, once a path has been laid out, there are only so many places it can go. So if life had favored a different set of beginning traits, things might've looked different.
So yeah, don't know how much of all the above people actually understand. But, if you got through it and even if you don't understand a word of it, I hope you might still be in awe of what the hell it could mean. Of course, this is nothing. "You ain't seen nothing yet" when it comes to evolution. We live in a world of constant change, and I think it's always good to see where things came from and how far they've come (or not).

Anyway, this is all the free-flowing biology for now. If you have any questions about evolution, or something biology, don't hesitate to ask. I may not know the answer (and many times I simply won't), but I think my B.S. in Biology affords enough knowledge to at least make a damn good guess. It's weird to be a graduate now. More on that later!

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