Evolution

I think that there’s a great deal of misinformation about current scientific understanding of how evolution works, and thus I’ve decided to write an article on this topic. It is tailored as much as I can to this audience. I apologize if some of it is too simplistic, but one is never clear as to what level one ought to write for. This article is quite long (about 2000 words). Also, while I’m going to start by discussing Darwin, molecular biologists today are neither Darwinist or even neo-Darwinist, as that would have been understood several decades ago.

Darwin’s ‘Origin of the Species’ was a book substantially about different species of birds, finches specifically, that lived in the Galapagos islands. The central observation was that while all of the birds were clearly finches, as lived on the mainland, on these islands they had radiated into a variety of sub-populations, each specialized to a particular ecological niche. For instance, there were finches with bigger beaks, so they could crack tougher nuts; there were finches specialized for grains, for hunting insects, for fishing, et cetera. Two important concepts are presented here; natural selection, and ecological niches. Neither of these give most people, even die-hard Christians, much trouble (neither of these is evolution, either; that requires mutation, which I’ll address later).

Natural selection is a pretty easy one to understand. If the primary food available is nuts that are hard to crack, birds with bigger beaks will clearly get more to eat, have more young, etc. Their young will inherit their bigger beaks, and will also learn from their parents that nuts are an ideal food source; thus, both natural and social inheritance will reinforce this subspecies of finch’s predilection for eating nuts. These bigger beaks aren’t a mutation; they’re just natural variation within a population.

Ecological niches are also pretty easy to understand. Once there are birds specialized for eating nuts, birds that aren’t specialized for eating nuts have even less reason to go after them; they’re hard to eat, and they’re already being eaten by somebody else, anyway. They thus find something else to eat, and specialize in that the same way that the nut-eating birds specialized in eating nuts.

So far, nothing I’ve talked about is evolution, really, although it all contributes to it. This has all been ways of creating communities specialized in preserving –existing- sets of alleles (alternate versions of genes). In order to have evolution, you need two things; the sub-species have to stop breeding with each-other for an extended period, and you have to have mutation.

This cessation of interbreeding can be because of geographic distance or barriers, it can be because of essentially social reasons (Darwin’s finches are mostly capable of interbreeding – they just don’t), and it can be because it doesn’t really physically work. For instance, Great Danes and Chihuahuas are both dogs in species, and there was no evolution at work in producing the two; just breeding programs. However, the two aren’t really capable of interbreeding any more. This doesn’t make them different species; it does mean that if one of them started to pick up mutations, they wouldn’t be transmitted to the other.

As I’ve said, I don’t think that most of the above is controversial to most Christians. It’s all stuff that’s pretty intuitive, and which if you think about, you can see happening all around you. Where I think folks have problems is with the idea of random mutation producing improvements. Here, I’m going to have to digress into some background on how biology works; note that I’m going to ignore the issue of the origin of life, since that happened a long enough time ago that it’s not really possible to make scientific statements about it with existing data (that’s one of the reasons scientists are so interested in seeing if we can find life on other planets inside the solar system).

Genetic material is coded into DNA. DNA is made up of a large number of repetitions (base-pairs) of only four different bases (A,T,G, and C for short). We refer to them as base-pairs (or bp) because DNA, as everyone has probably seen in pictures, is composed of two strands, with one strand being a mirror image of the other (A always is paired with T, G with C, and visa-versa). Humans have about 4 billion bp in their genome; almost all of this is non-coding (more about this later). Most animal species, from flies to humans, have about 20,000 genes, give or take a factor of two. A gene has two important parts; a promoter, which is a set of instructions as to when it ought to be turned on or off, and a coding sequence, which encodes what protein ought to be made by it. On average, the coding sequence of a gene is about 1000 bp long, although they can be much smaller or much larger. (For interest’s sake, if you work it out, this means that there is only about 10 megabytes of code needed to specify a human … pretty efficient coding ! )

When a gene is turned on (according to its promoter), a protein called a transcriptase makes an RNA copy of it. RNA is a lot like DNA, and uses pretty much the same code, with two important differences: (1) All of the non-coding stuff gets edited out, and (2) It’s small and not attached to the rest of the DNA. This last means that it can be exported from the nucleus to the machinery that turns it into protein. Each protein has a different function; some act as messengers, some act as structure, some act as transcription factors (which control when other genes are turned on), some act as scaffolding for the assembly of more complicated structures, et cetera. So far, none of this really has anything directly to do with evolution, either; it’s just how all organisms from yeast to people work.

Also, there are a great many mechanisms in place to prevent mutation from happening. For instance, during DNA replication (when you’re making a new cell), there is a mild tendency to make copying errors. However, there is a way to tell which is the old and which is the new DNA, and various proteins move along the strands checking to see that the new DNA matches the old DNA. If there’s a mismatch, it assumes that the old DNA is more likely to be correct. The same sort of thing happens with, for instance, radiation induced damage. This sort of damage doesn’t usually turn one base-pair into another; it turns a base into something unrecognizable. Proteins can recognize damaged bases, and replace them with a base that properly matches the presumably intact base on the opposite strand.

All of these systems can make mistakes, of course, and so mutations can slip through. This happens very rarely; odds are that the set of chromosomes you pass onto your children will have at most four or five de-novo mutations. Out of four billion bases, that’s pretty good. Also, since 99% of your DNA isn’t in a gene, odds are pretty good that that’s not going to be anyplace coding, anyway. So, due to defects in mismatch repair, or in replication, or what have you, a very small number mutations slip through in each generation ( a common type of error is when copying regions with low complexity – repeats of the same set of bases over and over again, for instance). Mutations of this sort can make slight changes in protein structure, or in how it is turned on or off. Since you’ve already got a perfectly functional genome, you’d think this would almost always be bad for you, right? Well, you’d be right if this was all there was to it. However, as it turns out, most complex organisms are, if you’ll pardon the expression, designed to evolve.

Here we get back to all that junk DNA. About 5-10% of it is old virus integration sites, another 5% or so is structural, involved in scaffold attachment, or wrapping around histone cores. However, most of it is a particular kind of repetitive element, and the degraded remains of it. There exists in most species a type of element (in human, the most common are called LINE1 and ALU) that exists to do nothing but make copies of itself and stick them back into the genome. Sometimes, however, it’ll ‘reverse transcribe’ other things as well – such as the RNA produced by the functional genes around it. Thus, you can get copies of functional genes stuck back into the genome (the repetitive elements tend to be less picky about proofreading, too, so they frequently start out with mutations). These copies are important because it doesn’t matter if you mutate them. If you mutate them and they don’t do anything useful, as is usually the case, then no harm done – you’ve still got the original. The mutated copy slowly degrades away into unrecognizability. If you mutate it and it does something new and cool, then you’ve got a selective advantage in keeping it, and so it persists, as a slightly modified duplicate. In fact, in humans, almost all genes look like this; there are very few genes that don’t have a host of closely related genes which have obviously diverged from each-other. Almost every gene in a human can also be found in yeast; yeast has one version, where humans have many specialized copies (there are actually a couple of important pathways that first appear in worms, actually – but since worms, there’s almost nothing new).

Creation of more novel genes is facilitated by the fact that even individual genes – or proteins – tend to be made up of a set of different functional modules. These modules are also not immediately adjacent to each-other in the DNA, but are broken up into different ‘exons’, separated by sections of junk DNA. When the RNA is processed, these are assembled into one non-stop coding RNA, but they didn’t start that way. This means that in this process of reverse transcription, or during ordinary recombination, you can wind up with these modules being swapped around so that a new set of them are adjacent to each-other. Once again, since these are probably in a duplicate copy, no harm done – if its useless, it’ll mutate away. If it’s good for something, there’s a natural selection reason to preserve it.

Further, there are a whole host of other molecular mechanisms that we’re just beginning to understand that make evolution work better, and in fact serve no other real purpose. A couple of examples; it appears that there’s a mechanism to preserve old RNA, even through a couple of generations, so that if a new mutation turns out not to work well, the older version can be reverse transcribed back in to replace it. Next, there’s a category of genes called Heat Shock Proteins (for historical reasons). These are chaperones, which exist to preserve the conformation of other proteins. Thus, mutations in other proteins are hidden, because the heat shock protein keeps them masked. However, under extreme environmental stress these fall away, to reveal all of the previously hidden mutations. There was a very dramatic article on this a few years ago, in which they showed how radically different the progeny of a fly appeared in which these were removed; some had limbs twice as long, some had their eyes on stalks, some had extra body segments. Flies are less rigidly controlled than higher animals, but here’s the point; you never would have thought that the offspring of one animal could look so different. The difference was that the mutations that had previously been hidden by heat shock proteins had been revealed.

So: duplicate copies in which mutations are unimportant unless useful, modular construction of proteins so you can mix and match parts, specialized proteins to hide mutations until there’s environmental stress, an ‘archiving’ mechanism to store older versions of genes. All of this is just the tip of the iceberg; there’s research pointing to even more explicit mechanisms to enhance the rate of mutation in direct response to the environment, in a manner similar to how antibodies are generated. We don’t just evolve; we’re designed for it (or evolved for it).

As I am completely intimidated by your intelligence and am all but completely ignorant on the subject, I will instead post this rebuttle from a well known and much bemoaned as devoid of "real" science website-

http://www.answersingenesis.org/tj/v14/i2/junk_dna.asp

Good to see you again James

It's not actually a rebuttal (sp?) - so far as I can tell, she's acknowledging that the repetitive elements are useful for generating mutations, and claiming that this is how you got rapid diversification of species after the Flood.

An interesting speculation, although from the point of view of arguing strict creationism, it rather seems to be shooting yourself in the foot.

Yeah, I know, but I remembered reading (and not understanding) this article before, and its kinda the same subject.

Expand that conclusion? I'll have to read tommorow, the sandman is overtaking me.

Well, there's no difference, mechanistically, between increasing diversity within a species, and creating new species. Once you've admitted that there's an easy mechanism for doing one, you've pretty much admitted that there's an easy method for the other. Species are an artificial division; once you've got a lot of diversity within one, all you have to have to create another is for two pools to stop breeding with each-other for a long time. How long ago do you think mice and rats split?

BTW - something I thought was very funny in her article. Paraphrasing: "Those darned slippery evolutionists - if the data contradicts their hypothesis, they just change their hypothesis." Um ... yeah - that's how science works. It is a strength, not a weakness, to be able to change your mind in the face of new data.

For the record, though, aside from her editorial comments, I don't much object to her line of reasoning, given her premises, although I don't agree with several of her premises. I even agree with several of her statements about suspect methodologies. However, oddly enough, the main point of arguable disagreement I have with her is, in my opinion, she thinks mutation is happening too fast. She's wanting diversity to have arisen in only a few thousand years; I don't think that's enough time, by several orders of magnitude.

Hey, James. Why do you say this? Just curious as I hear it an awful lot from both Evolutionists and OEC's. Would you mind expanding on your doubt a bit (say...in a 1000 words or less )?

There are a lot of answers to this, but the answer most apropos to the discussion I've made is this:

We've measured the mutation rate between generations: it's tiny. Any given gene is likely to have a mutation in it only once in several hundred generations, based on mutations rates that are directly measurable today. A thousand years is only fifty generations; that's not enough time to, on average, have one mutation per gene, let alone the full diversity of allelic variation we see in the world around us. And even that assumes that your one mutation is going to do anything (the system's substantially redundant; on average a mutation is neither good or bad, but does nothing at all).

- James

James,

Clearly you have a dizzying intellect.

I appreciate the time you spent to produce a reasoned support for evolution. Few do that. I do have a question or two though. If macro-evolution is true, and according to your statements, I gather that you believe it is, then how does one account for the Cambrian Explosion?

Secondly, are we designed to evolve? At least that's what I hear you saying and if so, what about the genetic research (yeah, I'll have to go look it up...at least I heard about it) that points all humans (well, at least a good cross-section) to a common mother (Eve in Biblical accounts)? How does that jive with evolutionary theory.

I'm not well educated on this subject, but it is certainly one I like to think about and argue.

Funny - never thought of the Cambrian Explosion as a problem for evolution before.

There are several answers to this: first appearance of hard body parts, availability of a wide variety of niches, it wasn't -that- short a period, and, possibly, new genetic tools.

First appearance of hard body parts: there could have been a wider variety of creatures beforehand, but if they didn't have anything fossilizable, we wouldn't know.

Availability of a wide variety of niches: hard body parts are extremely useful. Their appearance means that the founder strain that evolved them could probably out-compete things in just about every other available ecological niche. Means that any mutation they got would be good for -something-; thus, rapid diversification. For example: if a modern mouse gets a mutation that makes him bigger, it's a bad mutation; he's going to try to compete with rats, which are already so much better at being rats that the mouse is out of luck. If rats didn't exist, it'd be a useful mutation, because he'd be moving into a new niche.

The Cambrian is tens of millions of years. Not actually too short a time to have all sorts of evolution.

Lastly, all of the genetic tools to allow rapid evolution must have appeared -some- time. Maybe it was then. If so, this is a huge competitive advantage, which, once again, would allow rapid diversification into different niches.

All of this is hand-waving, of course: there's no real way of knowing why exactly the Cambrian Explosion happened. The point of the above is to show that there are all sorts of hypotheses consistent with macro-evolution that account for it. Some of them may even be right !

I'll get to the second question in a later post.

- James

Maybe I have misunderstood the Cambrian Explosion, or maybe it has been misrepresented to me. The way I understand it, many complex, multicellular organisms appear in a very small portion of strata near the beginning of the Cambrian period. This follows only simple, single cell organisms in the strata layers below this. The layers are too close together and the multi-celled life appears much to quickly for the gradual evolution of these organisms to occur.

However, to buy into this, one must also buy into much of the school of flood geology, some of which I find to be somewhat questionable.

Given the caveat that I haven't personally seen or analyzed the raw data on this, I think that the most likely explanation for the cambrian explosion is that it was the start of things with hard body parts; things before that basically didn't fossilize (or did so with such rarity that we really don't have representative samples.) Thus, not such a big change, really.

There are several periods in the geological record, actually, in which there's rapid extinction/appearance of new forms. Some of these might have been environmental catastrophes, but a lot of them, I suspect, are the result of new "super life-forms" that could out-compete every other niche. Trilobytes out competed everything else (probably) in the late Cambrian, and became the dominant life-form on earth ... to be replaced by more specialized creatures later in the paleozoic. More recently, of course, people have driven most of the large animals on earth extinct (no sense in feeling guilty about it; we mostly did it 10,000 years ago, with the invention of the folsom point, the nuclear weapon of the paleolithic).

Where I'm going here is that the rapid appearance of new life forms in the early Cambrian was probably just such an event; hard body parts was such an advantage that these took over niches previously occupied by soft-bodied (and thus non-fossilizable) creatures.

- James

There is definitely hard evidence now, from molecular biology, that we are designed to evolve. Not only are there mechanisms that speed up evolution and predispose to preserving positive mutations, there are specific mechanisms to cause us to evolve faster under pressure.

The common mother is misleading. Where this comes from is a method of trying to date divergence points in evolution by trying to calculate how long it would have taken one individual to have generated all of the mutations one sees in sampling of populations from different places; thus, the method -assumes- a single parent, and then calculates when that individual would have existed.

However, from correlation between this sort of method and dating found in the geological record, it's a relatively accurate method of finding the timing on when a species first arose (with, presumably, a small number of geographically isolated individuals). This produced the somewhat surprising result that the species is substantially more recent than a lot of people thought (~200,000 years old). This largely means that the multi-regional hypothesis has got to be wrong (ie, this means that genetically modern humans arose in africa and exterminated all other proto-humans on the planet, rather than interbreeding with them.)

Also - this sort of study has shown that Neanderthals almost certainly weren't our ancestors. We're no more related to them than we are to Chimps. Just another almost-human species which we drove extinct when we proved smarter than they were (or faster breeding, or whatever).

- James

Hey, didn't I see something about that on the Discovery Channel.

Thanks James, you've made me realize my incredible ignorance on this topic. So, as much as I might like to argue these points more, I cannot with any validity. And, as much as I might like to research this (and believe me, I want to), I have more pressing matters at this time. So maybe I'll get back to you on all this and for now I must take your word on it.

Interesting stuff. But you are wrong on Darwin. hew had no idea the finces were different. Other naturalists noticed in drawing and then came up with that idea. Darwin wasn't a schooled naturalist, but rather studied theology. I got that from the book "A History of Nearly Everything" By Bill Bryson. Great book everyone should read it.