Evolution IX: Speciation, Revisited

or, Quantizing Continua

One of the most common questions asked about how speciation works (not asked here, though, grumble grumble. Go ahead and comment, people!) is how it is possible for a new species to arise. After all, when the first member of a new species shows up, it has nothing to breed with, right?

The following material is flagged Green Level. It is intended to reflect material that the author believes to be a matter of consensus among experts in the field. This belief may be incorrect, however; and as the author is not an expert and does not have an expert fact-checking the article, errors may creep in.

All (or most, anyway) of us were taught that every living thing belongs to a species, such as H. sapiens, G. gorilla, or E. coli. Everything in the same species can breed with anything else in the same species (barring things like sex differences), and with nothing of a different species. Things within the same species are similar, things of different specie are just too different. If we were to draw a diagram of species, with each species represented by a circle and overlapping circles representing populations able to breed, it would look like this:

Except that this is a lie to children. It is an oversimplification, exchanging truth for comprehensibility.
It is a description of how things generally work, that omits important details for the sake of being easily understood.

If you were to look at a human being on all scales of resolution, from the anatomical to the cellular to the genetic to the quantum, no part of the human would be stamped with the words "Homo Sapiens". And there is no generation in the future where a hypothetical stamp would magically change to "Homo Successor", barring radical genetic engineering.

In fact, there is no magic date before which humanity, or what would eventually become it, was always H. florenseis and afterward was always H. sapiens. There is a generation before which nothing was H. sapiens, if we define H. sapiens as anything that would biologically compatible with the humans that exist today if somehow preserved, but that generation did not suddenly transition to H. sapiens. Rather, if we redefine H. sapiens as anything compatible with the first generation to be compatible with modern humans,  the generation before was H. sapiens, even if modern H. sapiens would not be compatible with it.

In short, the question stems from an artifact of the mental models we use. We see each creature as being stamped with one species, even though this only crudely approximates the underlying reality. And as such, we see species as something that can be broken cleanly into separate, quantized chunks, when in reality it looks something more like this:

(And please, don't ask me about different chromosome numbers. I don't quite understand how it works, but apparently chromosomes are, to a degree, arbitrary divisions within the genome and the place where one chromosome stops and another starts, if it even works that way, can be rearranged.)

<<Sex |Evolution| ... I got nothing. End of Topic so far!>>

Evolution VIII: Sex

No, not like that. You pervert. Well, sort of like that.

The following material is flagged Yellow Level. It contains material that is disputed by some experts but accepted by others. Caution is advised when deciding whether you personally choose to believe it.

One question when dealing with evolution is: why is sex necessary for reproduction? Why must so many creatures obtain a mate?
Read on.
Suppose that we have a species that does not require mates. In this species, genes are passed on directly to offspring, with no interference. As a result, any mutations are unable to spread through the population except by displacing all other lines.
Now, suppose there is a mutation in that species that allows it to replace parts of its offspring's genetic code with parts of that of another member of the species. This mutation cannot become universal, unless the rest of the population is wiped out. So what possible advantage could it have?
Simple. Remember that evolution works because mutations sometimes make survival more likely. So, an individual whose offspring are able to have mutations from other individuals has offspring better suited to the conditions in which those mutations are advantageous. In other words, while evolution may be a matter of "survival of the fittest", it is important to remember that adaptability is fitness.
So why would sex become necessary? Consider that the one (inherent) advantage of sex is that it allows for the spread of mutations rapidly through a population, with purely detrimental mutations being eliminated or outcompeted quickly. In an environment that changes rapidly (and thus requires quick mutations from generation to generation in order to survive), it is far easier to copy someone else's mutations than to mutate rapidly enough to survive. So, there is a selective pressure favoring sexual reproduction. If the environment changes quickly enough, organisms that use asexual reproduction die off, eventually leaving only those organisms that are incapable of "deciding" to reproduce sexually.
(Note that this logic does not apply to all situations, and as such sexual reproduction is not universal. Some bacteria only reproduce asexually, other bacteria reproduce asexually but can exchange genetic information, and for that matter some species of lizard retain sexual instincts despite not exchanging genetic information.)

<<Common Criticisms |Evolution|Speciation, Revisited; or Quantizing Continua>>

And now, administrative stuff. I have no idea what I want to do next in this Topic. So, if anyone who reads this despite understanding this stuff has any suggestions, please mention them.

Evolution: Part VII: Common Criticisms

And here I answer the standard arguments advanced against evolution. As I am currently busy with finals, I have brought in a co-lecturer to debate: Bob from the works of Jack T. Chick. Please give him a warm welcome.

The following material is flagged Green Level. It is intended to reflect material that the author believes to be a matter of consensus among experts in the field. This belief may be incorrect, however; and as the author is not an expert and does not have an expert fact-checking the article, errors may creep in.

Thank you. Now then, let's discuss evolution.
Yes. Let's.
So, do you really believe that you are descended from an ape?
Depends on your definitions, really.
But isn't that what your theory teaches?
Hardly. What evolution teaches is that all species are descended from common ancestors, and that some are more closely related than others. For any meaningful definition of "ape" for which humans are descended from apes, humans are apes.
But evolution is a racist theory in which some organisms were more evolved than others.
No. What you are referencing is an outdated idea called the ladder of being, which actually predates Darwin. The ladder of being is the idea that there is a hierarchy of living organisms, and that over time, they advance up the "ladder".
That's not to say, of course, that evolution has never been used to justify racist ideologies, but to be perfectly honest, the only ideas that haven't at some point or another are the ones that simply haven't been around long enough. Even the civil rights movement had its black supremacists. For the most part, the racist interpretations have been pretty thoroughly discredited.
All right. Let's try something else. How do you know this is where life originated? Were you there?
First of all, evolution has nothing at all to do with where or how life began, only with what happens once it has. Evolution doesn't care whether its replicators were created by an act of divine will, or originated when lightning struck the seas, or are illusions crafted by an insane god to venerate it. Evolution only cares that replicators exist, and they show heredity with variation.
Second, the "were you there" bit has its own share of problems. If you would follow a hypothetical for me, let's say you are a crime scene investigator. You are called in to investigate a death, and you find the decedent in his bathtub, with multiple stab wounds. In his kitchen is a bloodstained knife, matching the wounds, and in fact DNA analysis indicates that the blood is his. Fingerprints on the knife match those of one of his house-guests, and DNA analysis indicates that the blood under the decedent's fingernails is that of the house-guest, and the house-guest has injuries resembling fingernail gouges. What conclusions can you draw, despite not having been there at the time?
It's not the same thing. For one, there are no accounts from anyone who actually was there.
Okay, we'll modify the scenario. The house-guest claims that a wizard appeared in the house, killed the decedent, and magically transformed the fingerprints on the knife to those of said guest before animating the decedent as a zombie and commanding it to attack him. Said zombie scratched him, and then was ordered to lie down in the bathtub and return to death. The wizard then flew out the window, cackling. The other house-guests, all friends of the suspect, corroborate this, although they could have been coached.
All right. I'll admit that the theory of creation sounds a bit like magic to those without the faith to keep an open mind. But the situation isn't like that. Where's the prints, the wounds, and the blood?
First, we must consider that, in science, it is not sufficient to simply explain the existing data. We must also predict future information. So let us look at what evolution predicts.
Evolution predicts that when new fossils are discovered, they will, if sorted by age, show slow transitions from one form to another. Keep in mind, there will be no "crocoducks"; each form will be able to survive on its own. The closest thing there is to a "crocoduck" is the common ancestor shared by reptiles and birds. This general observation has been found.
But how do you know how old the fossils are? Isn't it circular reasoning to say that a fossil is a particular age because it was found in a particular layer, and that that layer is that age because it has those fossils in it?
That would be circular reasoning... if that were the actual reasoning. The way it actually works has to do with radioactive decay. A certain proportion of the matter in any organism, any stone, or any object on Earth, really, is radioactive. When a fossil forms, the minerals that replace the bone contain traces of radioactive material.
Now then, radioactive material decays according to a specific mathematical principle. For any unit of time, a certain proportion of the material transforms into another material, which will later transform into another material, and so on until it is no longer radioactive. This is called the decay chain. If the proportion, original composition, and decay chain are known (and each can be figured out: the proportion and decay chain by watching a sample of the original material decay, and the original composition by studying rocks in the area), it's easy to apply some simple algebra to figure out how long it's been since the fossil formed.
All right. Next prediction?
Second, evolution predicts that there will be vestigial components in an organism at all levels: vestigial organs, vestigial structures within functional organs, vestigial organelles within cells, vestigial DNA, and so forth.
Are you talking about the appendix, coccyx, and so forth? The appendix has bacteria in it, and the coccyx has muscle attachments. They are not vestigial!
So what function do they serve? A vestigial organ is one that serves no purpose or a purpose other than its original one, not one that is not integrated into the rest of the organism. The appendix is homologous to an organ in many other animals that assists in digesting cellulose, and the coccyx is quite obviously a now-nonfunctional tail. Both organs may be removed surgically without ill effect unrelated to the surgery itself, therefore they are vestigial.
Furthermore, there are a number of other items. The blind spot in the eye, noncoding sequences of DNA, the list goes on.
Okay. Next?
Third, evolution predicts that evidential common descent will be more recent between more similar species. That is, when a point of divergence between species (the time at which the species became separate) is found, it will be more recent if the divergence is between similar species, such as bonobos and humans, than if the divergence is between radically different species, such as lemurs and jellyfish.
Isn't this even worse circular reasoning? By assuming that a point of divergence exists, you presuppose your own conclusion!
Good point. Let me revise: the existence of surface similarities should imply the existence of deeper similarities. If two species are similar on the surface, they will have similarities that are not connected to their surface similarities. For instance, any two humans are members of the same species, and thus that implies that their non-coding DNA is more similar than that of either is to that of an orangutang. And the non-coding DNA of a human is more similar to that of an orangutang than to that of an earthworm, which is more similar than to a mushroom, which is more similar than that of a bacterium.
I see. I'll try a new tactic then: if all humans are no more than mere animals, there is no reason to act morally.
That's an old one. The first answer is basically, "So what?" Whether something is moral is no indicator of whether it is true, and vice versa. It is immoral that childhood cancer, methamphetamine addiction, torture, genocide, Ebola, and From Another Time Another Land exist, but they continue to do so anyway.
Are you saying-
Yes. I realize that's not exactly the strongest argument. A better one would be that being an animal may be no reason to act morally, but it's no reason to act immorally either. As I showed before, animals are able to act according to what some might call "morality", even if they are only compelled by their instincts.
But surely the morality that human beings should be held to is of a higher standard than that of beasts.
There are some who would disagree, but you do have something of a point. Unfortunately, it's irrelevant. It's entirely possible to have a morality that is of a higher standard than mere instinct, and there's quite a few ideas about morality that have nothing to do with any kind of supernatural creator. Kant, Mill, Rand, Nietzsche, and others have developed their own forms of morality that are utterly divorced from any idea of deity.
Do you seriously call those correct moralities? What of unnatural acts? What of blasphemy?
I didn't say that those were correct, merely that they were a higher standard than "beast morals". We could spend lifetimes discussing what the true morality, if one exists, is and not get anywhere. In fact, that's been done. In any case, this isn't the proper discussion for that.
Right. I have no chance of convincing you to abandon your heathen codes, and you have no chance of turning me from God's path.
Also, we're starting to run out of column-inches. So, until next semester, be seeing you.
Thanks for having me.

 <<Cooperation III: Kin Selection |Evolution| Sex>>

Evolution: Part VI: Cooperation III: Kin Selection

In a number of species, humans included, individuals will often aid others, at their own detriment, when there is no possibility of reciprocation. In extreme examples, this can even extend to total self-sacrifice. How can evolution possibly explain this?

The following material is flagged Green Level. It is intended to reflect material that the author believes to be a matter of consensus among experts in the field. This belief may be incorrect, however; and as the author is not an expert and does not have an expert fact-checking the article, errors may creep in.

It is time we moved beyond the idea of evolution as purely selfish. It is time we looked at it in terms of genes, and how they move through populations. What matters is not the survival of the self, but rather the survival of as much of the self's genome as possible. This is why reproduction happens: in order to preserve the genome.

So, let's look at a population. We will think of this population as a flock of birds. When a predator approaches, a bird has two options: it can sneak away, making its own survival more likely; or it can call out, letting the rest of the flock know a predator approaches but dooming itself. Why would a bird ever cry out?

From a perspective saying that evolution is purely selfish, this would never happen. But it happens all the same, so that must not be strictly true.

But remember: one of the core ideas that absolutely must be true for evolution to work is that descendants must share traits with ancestors, and vice versa. And likeliness to alert the flock at the expense of oneself is a trait. If this trait is inherited, than any given bird's offspring are more or less likely to have it, and whether this is "more" or "less" depends on the parent itself.

So let's look at the probabilities. The "cry out" gene is known to be possessed by this one bird. That bird's parents, offspring, and full siblings each have a one-half chance of having it. Grandparents, grandchildren, aunts, uncles, nephews, nieces, first cousins, and half-siblings have a one-fourth chance. Great-grandparents, great-grandchildren, great-aunts, great-uncles, great-nephews, great-nieces, half-aunts, half-uncles, half-nephews, half-nieces, first-half-cousins, second cousins, and first-cousins-once-removed (whew!) have a one-eighth chance. And so on through the entire flock.

Parenthetical Note:
Anyone familiar with the work of Gregor Mendel will realize that I am absolutely butchering it. For instance, these exact probabilities only work with genomes that have exactly one copy of each trait. If the trait is a dominant and this is a diploid species, as most birds are, the odds of any parent having at least one copy are slightly better than one in two. If it's a recessive, the odds of any parent having at least one rises to one in one. So these exact numbers work for some strange hypothetical haploid species where each individual has two parents, but not for birds or peas, and especially not for bacteria or potatoes. And for that matter, the statistics are leaving out mutations, because the odds of an individual's germ-line mutations affecting a specific gene are pretty small. As in 1 in 100,000, or thereabouts. But it's still pretty close to correct. It's a heck of a lot more accurate than the "electrons are particles whizzing very fast around a nucleus, like planets around a star" Lie To Children in chemistry, or the "centrifugal and Coriolis forces are illusions" one in physics, and those can still make useful predictions. So yeah.

Also, anyone familiar with Bayes' Theorem will notice that it's getting the same treatment. The listed probabilities don't take the background incidence of the trait into consideration. If something's universal, the odds of it being in a given member of the species go way up.

We now return you to your regularly scheduled Topic.

 So, the odds are pretty good that, if you take half of one bird's surviving parents, and half of its offspring, and half of its siblings, and a quarter of its slightly more distant relatives, and an eighth of its extended family, and so on, they add up to more than one bird. So, as far as the gene is concerned, there is more of it outside this bird than inside it, and sacrificing less than half of all existing copies leaves it better off than sacrificing more than half.

This leads to an interesting idea that has shown up in evolutionary thought that, oddly, itself keeps evolving, called group selection. Essentially, this is the idea that, just as individuals compete, so do groups of individuals. To put it in a human perspective: individuals compete, but so do their clans, tribes, nations, and treaty organizations, and cooperation between the individuals of a group leads to more effective functioning as a group. The idea was discredited in its earliest stages (since the death of all individuals leads to the extinction of the group), but the modern and widely-accepted gene-centric view reaches conclusions that are shockingly similar.

Nothing in here is to say, of course, that evolution, competition, and outright conflict never happen between relatives. But it does point to a "no one hits my brother but me" type of attitude between them: that is, they will still compete, but will stand together against an outside threat.

<<Cooperation II: Tit-For-Tat|Evolution|Common Criticisms>>

Evolution: Part V: Cooperation II: Tit-Fot-Tat

We have seen that sometimes, organisms cooperate because, for each one, it is better than the alternative. But this is not always the case. Sometimes, two organisms are placed in direct competition.

The following material is flagged Green Level. It is intended to reflect material that the author believes to be a matter of consensus among experts in the field. This belief may be incorrect, however; and as the author is not an expert and does not have an expert fact-checking the article, errors may creep in.

So, last time we looked at a population in which cooperation was an undeniable advantage. But what about most other forms of cooperation listed in the article last time? What about times when not cooperating is better for the individual than cooperating?

Let's look at how that works.

• All other things being equal, it is better for the individual if they do not cooperate.
• All other things being equal, it is better for the individual if others cooperate with them.
• All other things being equal, it is better for the individual if all individuals cooperate than no individuals cooperate.
• If it is possible for individuals to meet more than once, it is better for each for all to cooperate twice than for each to cooperate once and be cooperated with once.

That's right, those of you who were following the game theory Topic. This is the Prisoner's Dilemma. And, if you recall, we have already shown that, in the case where the Prisoner's Dilemma is repeated and no player knows when the final iteration will be, it is to the advantage of each player to cooperate until their opponent fails to cooperate, and then respond in kind.

So what about when each player knows when the game will end?  Well, the behavior described there is consistent with what is observed in nature. If two organisms are cooperating, they will tend to break off their cooperation as soon as one is likely to have been mortally injured.

So, if a population is full of sociopathic individuals, how does this arise? Let's look at how the Tit-For-Tat strategy handles such a population.
In the first generation, Tit-For-Tat plays cooperate on the first turn, and defect on each turn afterward. Thus, Tit-For-Tat is at a marginal disadvantage. But, the selective pressure against a trait at a disadvantage is proportional to how much of a disadvantage it is. Which, in this case, is "not that much", so there's a decent chance that Tit-For-Tat makes it into the next generation.
In the second generation, it is possible for two individuals playing Tit-For-Tat to meet. In this case, these individuals will play cooperate on one another, and react to other individuals as described above. But since each is meeting an individual playing cooperate, the selective pressure is lessened.
In other words, the selective pressure against Tit-For-Tat is inversely proportional to (a strictly-increasing function of) the number of individuals already playing Tit-For-Tat.

<<Cooperation I: Bootstrapped Cooperation|Evolution|Cooperation III: Kin Selection>>

Evolution: Part IV: Cooperation I: Bootstrapped Cooperation

So, if evolution means that only the fittest survive; that passing on one's genes is impossible unless those genes make one claw one's way to the top of the heap, why is it that living things can work together? Why is it that a cell can have multiple parts (each descended from a separate living thing) that work together instead of tearing itself apart that way? Why do wolves work together to bring down their prey, instead of each going it alone and letting its competitors for food and mates get skewered by moose? Why is it that humans have an instinct to help one another in times of need, instead of (Objectivists and other sociopaths aside) saying "Screw you, I got mine"?
This is something of a complex question with multiple answers, each completely true and therefore none the complete truth.

The following material is flagged Green Level. It is intended to reflect material that the author believes to be a matter of consensus among experts in the field. This belief may be incorrect, however; and as the author is not an expert and does not have an expert fact-checking the article, errors may creep in.

 First, let us consider a simple organism. Let us consider the simplest of organisms, a single cell. Each of these cells can either photosynthesize and eat nutrients (say, sulfates) that bubble up from a volcanic vent far below.
So, all of these cells are coexisting happily. Well, not really. There's a limited amount of light, and a limited amount of nutrients, so the cells are competing for these resources, and frequently a cell is outcompeted and starves to death. (Not to mention that, lacking nervous systems, it isn't exactly easy for a cell to be happy anyway.)
Now, let us suppose that the area covered by the cells increases.
So, it seems as though nothing would happen here, right?
Not quite.
In the future, suppose that the descendants of these cells are neighbors. In the interface between the areas occupied by the two strains, interactions between the cells show up. Sometimes, the two strains fight one another. Sometimes, they ignore one another.
And, once in a great while, they cooperate. Sometimes, the two cells will grow together, starting to share resources. Sometimes, the cells will join, sharing resources so that when one does poorly, the other covers its needs.
Of course, in the environment described, the joined-cell pair must still compete with single cells. Its resource requirements are twice those of a single cell, but so is its resource production.
Usually, anyway. Suppose that the environment is not constant. Sometimes, a cloudy day means that there is less light. Sometimes, changes in the volcanic vent's output change the nutrients available. So, sometimes the ratio of light to nutrients changes. Sometimes, light-specialized cells outcompete nutrient-specialized cells. Sometimes, the opposite happens. But which is the joined-cell pair?
Both, obviously. In a completely dark area, the pair will do half as well as a nutrient-focused cell, and in nutrient-less water, the pair will do half as well as a light-focused cell. But, in each case, it will do infinitely better than a cell focused on what is absent. So, the cell pair is better able to handle changing environments. So, with the changing environment, eventually the cell-pairs outcompete the single cells.
We can even apply this (we can apply it better, in fact) using the assumption that in the beginning, each cell is able to handle both resources. In any population of cells, there will be mutations. In this case, some of the mutants are better able to handle one resource than the general population. So, sometimes one mutant will join to a mutant able to handle a different resource better than itself. And remember, each cell pair must compete with single cells.
Now, suppose that there is a limit on "safe resource absorption". There is a certain level at which more or better resource absorption "crowds out" some other mechanism. For instance, suppose that each type of resource-absorber takes up a certain amount of space in the cell, and a better absorber takes more space in the cell. In a normal cell, one absorber eventually collides with another, so past a certain point, the cell must "decide" between not increasing its efficiency or making itself more vulnerable to changes in its environment.
A cell-pair, though, need not make that decision. Since there are two cells, each can specialize in a different resource.

(Now, on to blog stuff. Unless I get comments telling me to continue evolution, next week it's back to game theory. Depending on what you tell me I ought to be doing, I'll be alternating between Topics each week.)

<<Speciation|Evolution|Cooperation II: Tit-For-Tat>> 

Evolution: Part III: Speciation

How does a situation arise such that one organism would be unable to breed with another? How could this possibly be an evolutionary advantage?

The following material is flagged Green Level. It is intended to reflect material that the author believes to be a matter of consensus among experts in the field. This belief may be incorrect, however; and as the author is not an expert and does not have an expert fact-checking the article, errors may creep in.

As with the previous example, let us say that we are looking at a population of bears in a cold place.
Now, let us suppose that the bears somehow split into two populations. Maybe the ice floes they live on are broken and begin drifting apart farther than the bears can swim. After millions of millions of generations, the bears build up a large number of mutations. Now, suppose that one mutation in one population is incompatible with another mutation in the other population. If those two mutations occur in the same individual, that individual will die off.
Contrary to how it may appear, this is not a disadvantage. As was mentioned above, a trait does not have to be beneficial in all situations in order to be beneficial; it only must be beneficial in the current situation. Similarly, it does not have to avoid being harmful in all situations in order to be harmless; it only must be harmless in the current situation. And the inability to breed with an individual one could not otherwise breed with is not a harmful trait. If the trait is beneficial (or even just allowed to spread over a few thousand more generations or so), the bears on the two floes will be separate species.

<<Irreducible Complexity|Evolution|Cooperation I: Bootstrapped Cooperation>>

Evolution: Part II: Irreducible Complexity

And Part II of the Evolution Topic. A system can arise in which each part is reliant on every other part, and the removal of one part causes the destruction of the whole. What use is half an eye? What use is blood that does not clot?

The following material is flagged Green Level. It is intended to reflect material that the author believes to be a matter of consensus among experts in the field. This belief may be incorrect, however; and as the author is not an expert and does not have an expert fact-checking the article, errors may creep in.

Let us assume that we have a population with mutants. Continuing from the last example, let's say we have bears, some of which have coats better able to trap heat. Then, let us say that this mutation becomes universal; in the last example, all of the bears become better able to trap heat.
Now, let us assume that a second mutation shows up. This mutation repurposes the protein responsible for fur that grants resistance to cold so that when expressed in fur, it will still have its original purpose, but when expressed in blood, it will grant further cold resistance by the same amount. (Yes, I know that this specific for-instance has an incredibly low chance of actually making any kind of biological sense. But we're discussing hypothetical abstractions anyway, and it gets the point across.) So, the two mutations spread through the population at about the same rate, right?
Wrong. Remember that the second mutation works by repurposing the first. In bears that do not have heat-trapping fur, the mutation for cold-resisting blood will, at best, do nothing. At worst, it will repurpose some other protein, and do something very interesting to the bear's internal biochemistry. So, the cold-resisting-blood mutation can at best spread through the population at the same rate as one with a neutral effect, and at worst cannot spread beyond the subset of the population that has the heat-trapping-fur mutation. In other words, the mutation is of no beneficial effect without the one it modifies.
Next, suppose that, once the cold-resisting-blood mutation has become universal (and of course, the heat-trapping-fur mutation with it), a mutation happens in the heat-trapping-fur gene that causes it to function better, but only if the cold-resisting-blood gene is also present. (And at this point, the specific examples start approaching impossibility, but again: for-instances, hypothetical abstractions, gets the point across, et cetera.) Since the cold-resisting-blood gene is universal, the heat-trapping-fur-mark-2 mutation has no drawbacks. Since a heat-trapping-fur gene still exists (and can still be adapted for the purposes for which the cold-resisting-blood gene uses it), the system still works. And so, we have a system that is stable as it is, but which will fall apart if any component is removed.

<<The Basics|Evolution|Speciation>>

Topic: Evolution

The Theory of Evolution by Natural Selection is the fundamental theory of biology, in much the same way that the atomic theory is the fundamental theory of chemistry. Unfortunately, there's a lot of misunderstanding about evolution, so I thought I'd clear it up a little.

1. The Basics 
2. Irreducible Complexity 
3. Speciation 
4. Cooperation I: Bootstrapped Cooperation
5. Cooperation II: Tit-For-Tat 
6. Cooperation III: Kin Selection 
7. Common Criticisms 
8. Sex 

Evolution: Part I: The Basics

Sorry for reposting old material, but I finally got to the point in the game theory Topic where I could do the bit on the evolution of cooperation (thus making evolution its own Topic), and I figured I ought to break up the first evolution post and make it a bit less wall-of-text-y. Game theory will return in four weeks unless I see something shiny and deserving of its own Topic.

The following material is flagged Green Level. It is intended to reflect material that the author believes to be a matter of consensus among experts in the field. This belief may be incorrect, however; and as the author is not an expert and does not have an expert fact-checking the article, errors may creep in.

First, let me explain what the theory of evolution actually says, since this is the most common point of disagreement. There are things (such as living beings, although a semi-controversial application of the theory called memetics posits that this can be expanded to include abstract information as well, and a type of robot called a von Neumann machine that constructs copies of itself would also count) that can "copy" themselves, which we will call replicators. Sometimes, when a replicator makes a copy of itself, it makes a small mistake, called a mutation. Sometimes, this mutation has no effect beyond possibly changing the effects of future mutations, such as a mutation in a set of "junk DNA" or in the comments of a piece of code. Sometimes, the mutation is neither harmful nor helpful, such as a change removing a vestigial organ. Sometimes, the mutation is harmful, such as a vertebrate forming without a DNA sequence coding for brain tissue. But sometimes, once in a great while, the mutation is actually useful, such as increasing how well the organism can process food.
Now, suppose that our mutant is in a place where its mutation is useful. Suppose that we're talking about a bear in a cold region that has fur better able to trap heat, or the like. That bear is going to find it a little bit easier to not freeze to death, and as such will have a slightly better chance of leaving copies of itself in the next generation of bears.
(As an aside, it is important to point out that a beneficial mutation is one that is beneficial in that specific environment. A bear with heat-trapping fur is at a disadvantage if taken to a place hot enough that water boils quickly, just as a heat-repelling one is at a disadvantage if taken to a place cold enough that all water is frozen. This will be important later on, when we talk about speciation. It will also be on the test, so I do hope you are taking notes.)
Now then, we have a bear in generation X with a 0.1% better ability to handle cold environments. This bear has a copy in generation X+1. Now, let us look at what that copy can do. Since it is a copy of the original bear, it also shares that 0.1% better ability. And if that bear manages to put copies in generation X+2, they will also share the improved ability to handle the cold, and so on. And eventually, those small chances add up. If in generation X+2 this improved ability saves one of the mutant bears, that means that there will be more of the bears with this ability in generation X+3. And this continues for a while.
But there is another factor: cold is not the only threat to the bears. Hunger is also a problem. Eventually, the bears hit a limit on the number that their food supply can support. With this limit in place, and the steadily growing number of bears able to handle cold, eventually the entire population of bears becomes able to handle the cold.
(Note that simple probability indicates that eventually, the bears with the higher survival rate would displace the bears with the lower survival rate, even if there were no population cap. This takes even longer, though.)

<<First in topic!|Evolution|Irreducible Complexity>>

Prediction regarding the UK

I had a realization about the riots in the UK.

The following material is flagged Violet Level.The author has seen something that gave him reason to retract the beliefs contained within, and only retains the posting for archival purposes.

It goes a bit like this: You know how they used to say that the revolution would not be televised? Well, in this age, that's about as far as you can get from the truth. The revolution will be televised. The revolution will be tweeted, blogged, radioed, and pamphlet-ed to within an inch of its life. The revolution will do this to itself, because the revolution must go viral to survive.

Do you remember what I said about evolution a while ago? As a refresher, there's a semi-controversial application of the theory called memetics. Memetics deals with the evolution of ideas, specifically ideas called memes that transmit themselves from one mind to another. In order to transmit themselves more effectively, some memes form structures called memeplexes (such as religions or political philosophies) in which each meme contributes to the survival and spread of others.

(It occurs to me that I need to write a post on the evolution of cooperation. Next time, maybe.)

So what does this have to do with television? Simple. Television, and other forms of mass media, are designed to transmit an idea from one person to a large number of people. Mass media allow memes and memeplexes to spread through a population much faster than simple word of mouth can carry them. So if one person has an idea, and that idea can be expressed in words or as an image or as a recording, that idea will start to spread faster once the meme hits a mass-media outlet.

And in the age of blogs, Twitter, and Facebook, everyone with an Internet connection is potentially a mass-media outlet.

And here's where the riots in the UK get into the post (warning: this is going to sound a bit Marxist, and the events described are a bit of an oversimplification). Once upon a time, there was a land called Egypt. The ruling parties of Egypt lived well, but the poor suffered and the middle-class was rapidly shrinking. Someone who was involved in a service operating in Egypt that allowed people to communicate got the idea of sparking some protests, just to see what would happen.

And happen things did! People started protesting the rulers. The rulers cracked down on these protests. This caused the protesters to begin protesting harder, and more people joined the protests. In time, the voice of the people was clearly organized against the rulers. The people of another land called the United States began to place pressure on their own ruler to assist the people of Egypt, and eventually managed it. In time, even the Egyptian army joined with the people, and the ruler was overthrown. The Egyptians began to draw up a new way of organizing their land, but there was some doubt as to whether or not the army could be trusted.

At the end of all this, things began to happen in yet another land called Great Britain. Britain had long had systems in place by which the poor were fed and the middle class protected, but ever since the reign of a leader named Thatcher these systems were being dismantled for the benefit of the rich. As the system by which the poor and the middle class could improve their stations was dismantled, riots began to break out. In response, the British judges began to place harsh sentences upon the rioters; the British government, like many governments, being heavily influenced by the rich.

Now, let us look at what is happening from a memetic standpoint.

One person working at Facebook, in the interest of SCIENCE!, distributed a meme, which we will call A. A, under specific conditions, led to revolts, creating a meme (B) in the minds of the rulers that caused them to crack down on the protests. However, the increased opposition led to the spread of A, and the increased spread of A strengthened B. This formed a simple pseudo-memeplex, in that memes held in different minds reinforced one another. In time, A grew to the point that it triggered a realization that it was the Voice of the People. Of course, this realization (C) itself became a meme. From that point, C exerted popularity pressure on various people's minds until the revolution succeeded (naturally eliminating B and making A temporarily irrelevant).

Of course, the success of the revolution was noticed by others, leading to a new meme (D) holding that revolution was possible. D is capable of forming memeplexes with any meme similar to A, and thus acts as a carrier for A and similar memes.

Then, some meme similar to A (possibly even A itself) landed in the mind of someone in Britain...

The whole point of this (and the prediction): The UK is going to be the next Egypt.

Link and cite: http://rationalwiki.org/wiki/Meme

On Evolution

More than once I have found myself arguing with creationists about the theory of evolution, so I will explain things here.

The following material is flagged Green Level. It is intended to reflect material that the author believes to be a matter of consensus among experts in the field. This belief may be incorrect, however; and as the author is not an expert and does not have an expert fact-checking the article, errors may creep in.

The Basics
First, let me explain what the theory of evolution actually says, since this is the most common point of disagreement. There are things (such as living beings, although a semi-controversial application of the theory called memetics posits that this can be expanded to include abstract information as well, and a type of robot called a von Neumann machine that constructs copies of itself would also count) that can "copy" themselves, which we will call replicators. Sometimes, when a replicator makes a copy of itself, it makes a small mistake, called a mutation. Sometimes, this mutation has no effect beyond possibly changing the effects of future mutations, such as a mutation in a set of "junk DNA" or in the comments of a piece of code. Sometimes, the mutation is neither harmful nor helpful, such as a change removing a vestigial organ. Sometimes, the mutation is harmful, such as a vertebrate forming without a DNA sequence coding for brain tissue. But sometimes, once in a great while, the mutation is actually useful, such as increasing how well the organism can process food.
Now, suppose that our mutant is in a place where its mutation is useful. Suppose that we're talking about a bear in a cold region that has fur better able to trap heat, or the like. That bear is going to find it a little bit easier to not freeze to death, and as such will have a slightly better chance of leaving copies of itself in the next generation of bears.
(As an aside, it is important to point out that a beneficial mutation is one that is beneficial in that specific environment. A bear with heat-trapping fur is at a disadvantage if taken to a place hot enough that water boils quickly, just as a heat-repelling one is at a disadvantage if taken to a place cold enough that all water is frozen. This will be important later on, when we talk about speciation. It will also be on the test, so I do hope you are taking notes.)
Now then, we have a bear in generation X with a 0.1% better ability to handle cold environments. This bear has a copy in generation X+1. Now, let us look at what that copy can do. Since it is a copy of the original bear, it also shares that 0.1% better ability. And if that bear manages to put copies in generation X+2, they will also share the improved ability to handle the cold, and so on. And eventually, those small chances add up. If in generation X+2 this improved ability saves one of the mutant bears, that means that there will be more of the bears with this ability in generation X+3. And this continues for a while.
But there is another factor: cold is not the only threat to the bears. Hunger is also a problem. Eventually, the bears hit a limit on the number that their food supply can support. With this limit in place, and the steadily growing number of bears able to handle cold, eventually the entire population of bears becomes able to handle the cold.
(Note that simple probability indicates that eventually, the bears with the higher survival rate would displace the bears with the lower survival rate, even if there were no population cap. This takes even longer, though.)


Irreducible Complexity
Now, let us assume that a second mutation shows up. This mutation repurposes the protein responsible for fur that grants resistance to cold so that when expressed in fur, it will still have its original purpose, but when expressed in blood, it will grant further cold resistance by the same amount. (Yes, I know that this specific for-instance has an incredibly low chance of actually making any kind of biological sense. But we're discussing hypothetical abstractions anyway, and it gets the point across.) So, the two mutations spread through the population at about the same rate, right?
Wrong. Remember that the second mutation works by repurposing the first. In bears that do not have heat-trapping fur, the mutation for cold-resisting blood will, at best, do nothing. At worst, it will repurpose some other protein, and do something very interesting to the bear's internal biochemistry. So, the cold-resisting-blood mutation can at best spread through the population at the same rate as one with a neutral effect, and at worst cannot spread beyond the subset of the population that has the heat-trapping-fur mutation. In other words, the mutation is of no beneficial effect without the one it modifies.
Next, suppose that, once the cold-resisting-blood mutation has become universal (and of course, the heat-trapping-fur mutation with it), a mutation happens in the heat-trapping-fur gene that causes it to function better, but only if the cold-resisting-blood gene is also present. (And at this point, the specific examples start approaching impossibility, but again: for-instances, hypothetical abstractions, gets the point across, et cetera.) Since the cold-resisting-blood gene is universal, the heat-trapping-fur-mark-2 mutation has no drawbacks. Since a heat-trapping-fur gene still exists (and can still be adapted for the purposes for which the cold-resisting-blood gene uses it), the system still works. And so, we have a system that is stable as it is, but which will fall apart if any component is removed.


Speciation
Now, let us suppose that the bears somehow split into two populations. Maybe the ice floes they live on are broken and begin drifting apart farther than the bears can swim. After millions of millions of generations, the bears build up a large number of mutations. Now, suppose that one mutation in one population is incompatible with another mutation in the other population. If those two mutations occur in the same individual, that individual will die off.
Contrary to how it may appear, this is not a disadvantage. As was mentioned above, a trait does not have to be beneficial in all situations in order to be beneficial; it only must be beneficial in the current situation. Similarly, it does not have to avoid being harmful in all situations in order to be harmless; it only must be harmless in the current situation. And the inability to breed with an individual one could not otherwise breed with is not a harmful trait. If the trait is beneficial (or even just allowed to spread over a few thousand more generations or so), the bears on the two floes will be separate species.


This will be continued later, after I have received some feedback on it. For now, this should cover the basics.

EDIT: I realized that I need to cover some more material, such as the evolution of cooperation. This will be discussed later.