Evolution: the basics (by Dan Ryder)

If you look at human beings, it’s immediately obvious that there’s lots of variation. Much of that variation is accompanied by contributing genetic variation – on average, your DNA sequence differs from another person’s by about 0.1 percent (about 6 million letters of DNA).

Where did all this variation come from? From mutation, broadly construed. Whenever cells divide, copying errors can occur – from single-letter swaps, deletions, or insertions, to duplications of entire genes (or entire genomes – all the DNA!). Bits of DNA can be chopped out and moved around; in addition, viruses can insert their DNA sequences and sometimes these can stay put, like genetic squatters. All of these sorts of changes have been observed in the lab, and if any of them end up in sperm or egg cells, the resulting mutations are passed on to the next generation. A recent estimate for the single-letter mutations in humans suggests that you inherited about 30 of them from each of your parents! (That doesn’t include many of the other sorts of mutations, including e.g. gene duplications.) In other words: we’re all mutants.

A few of those mutations can have a large effect (sometimes good, but usually bad, causing a miscarriage), but most have a small or even zero effect. So variation accumulates – thus that 6 million letter difference that you have, on average, with someone else.

So far, young earth creationists agree.

Now, this variation is spread as evenly through the human population as all the sex allows. (Travel these days is making it more even.) But imagine that a group of people becomes isolated from the rest, so that nary a sperm makes it across the gap. What will happen? Well, both groups will continue to accumulate variation. But mutation is a random process; so the two groups will accumulate some different genetic variations. Maybe small differences that don’t matter at all, that are completely invisible – unless you sequence their DNA. Or maybe larger differences that still don’t matter, but that are visible (like racial differences).

Still, young earth creationists are nodding their heads.

Now what if those two groups stay isolated for, not thousands, but hundreds of thousands or millions of years. Those small differences will become larger, no? Like in Darwin’s finches, for example, or rock wallabies. Of course, there’s something else that can encourage change, and that’s natural selection. If one of the variants within a population has comparatively more offspring, that variant will become more common, and may even push out some other variants. For example, in a small population of brown bears that were isolated in arctic conditions, those with a light fur mutation would have been better off: precursors to the polar bear. This is a small but significant difference between the two groups. Other changes accumulated too, like skeletal and tooth changes, and we now have brown bears and polar bears as distinct species. (They can still interbreed in principle; they just tend not to because they don’t share a habitat any more.)

Still, John’s happy with all this. Because these changes are all within a “kind” – the human kind, the finch kind, the bear kind.

So where does he get off the boat? Actually, I have no idea. The longer the process goes on, the greater the variety that will be produced. He asks: how could mutation bring about large changes? I ask: how could it not bring about large changes!? It’s inevitable, given population separation and enough time. When the ball starts rolling down the hill, it keeps going unless you stop it. What stops it, John? (Maybe you’ll say: time, the young Earth. In which case the debate turns to the age of the Earth, and the impossible rate of evolution you’ll need to generate the observed variation within your “kinds”.)

How large a change is required for a change in a creationist “kind”? John is careful not to say. However, he is very clear that chimps and humans belong to different kinds. On the other hand, he thinks that all the rock wallabies belong to the same kind. Problem: the genetic distance between chimps and humans is the same as the genetic distance between the two most distantly related species of rock wallaby: 2%. If mutation and natural selection produced all the rock wallabies from a common ancestor, as John seems to accept, then how can he deny that it produced chimps and humans from a common ancestor too? For the wallabies, he accepts the mechanism (mutation and natural selection) and he accepts the common sense reasoning (the logic of common descent). But not in the chimp/human case, despite the fact that the mechanism would do the trick, the common sense reasoning applies, and the distance travelled would be the same.

Worse for him: the genetic distances within the kangaroo kind, the bear kind, the ape kind, the bird kind, and [gulp] the bacteria kind are much greater. And he indicates that they’re related by common descent too. (Though he won’t answer my direct questions to clarify that.) Well, if the range of genetic diversity within birds can be generated by common descent, so can the range of diversity within mammals. It’s roughly the same amount. John simply cannot have all the “kinds” he wants.

I’ve just shown that mutation and natural selection can produce large changes via common descent, and therefore changes in “kind”. Of course, John sees this problem. What he wants to say is this: God designed the “kinds” so that a certain amount of genetic variation was encouraged within them; they can mutate up to that point, but no further. (That’s ultimately what he means for the variation to be “built in” to the kind – see his finches point here.) The problem is there is absolutely no reason to suppose that mutation is restricted in this way. There’s nothing to stop the ball from rolling.

Worse for him, we know the ball didn’t stop rolling, because we have a record of the path it took in all the DNA sequences discussed in the “language analogy” thread, plus all the hundreds or thousands of similar DNA-based trees of descent that have been produced by biologists. These paths are consistent only with no-barrier mutation-based change. If there were barriers, they’d show up as separate, isolated trees of descent for each kind. But that simply isn’t what we find.

The mutation half of the evolution mechanism (by Dan Ryder)

The theory of evolution has two main planks: 1) organisms (and species) are related by common descent, and 2) variation is generated by mutation, natural selection, and chance (e.g. genetic drift). In a couple of places, John has now cast aspersions on mutation as a source of variation. Note that this doesn’t touch the first plank, common descent – that’s the one I’ve been pushing him on (e.g. here and here). No answers from him yet on that plank.

I’m happy to take up the topic of mutation, though.

First, in his “Trees and Kinds” post, John asserts without argument (and without defining his terms) that mutation can’t produce new kinds, because complex “information” always comes from intelligence. That’s demonstrably false on any reasonable interpretation of “information”. Karl Sims’ evolved virtual creatures in this cool movie and many other kinds of evolved artificial life (e.g. here and here) are clear counterexamples. In these examples, the programmer is like a designer who creates the first life, and then lets evolution do the rest. It’s clear that the increase in “information” as these creatures evolve comes not from the designer, but from the evolutionary mechanism. Indeed, the researchers involved often have little idea of how the creatures are even managing to do these things!

In the same post, John claims that biologists believe that mutation produces variation in organisms “by blind faith.” (The skunk complains of the rose’s stench.) Here are some powerful reasons why biologists accept mutation as the fundamental source of variation upon which natural selection acts:

a) Mutation-based evolution has been observed (despite John’s claim to the contrary):
• In Lenski’s meticulous experiment on E. coli, small populations (by bacterial standards) have been reproducing in controlled conditions (which limit evolution’s scope) for years, and Lenski’s team has tracked all the mutations. Some of these mutations have led to new capabilities, for instance the consumption of citrate in the presence of oxygen (a capability that is used to distinguish normal E. coli from Salmonella).
Kubinak et al. have observed viruses mutate to resist particular parts in mouse immune systems.
• Peter and Rosemary Grant observed mutation-based evolution occurring over the course of decades in Darwin’s finches. (More on finches in a moment.)
Castro-Nallar and colleagues have shown how, over the last hundred years alone, the HIV virus has mutated from a single type to hundreds. Many of these mutations are beneficial to the virus (though not to us!); for example, resistance to AZT.
• In the oral debate, John stated that antibiotic resistance in bacteria results only from genetic variation that is already present in the original population of bacteria. This is false – many novel mutations have been studied that lead to antibiotic resistance in various types of bacteria. See the review, Fitness effects of mutations in bacteria, or here (quote: “Spontaneous mutations, in particular, are pivotal in the emergence of novel resistances.”)
I could go on an on. But of course John won’t actually comment on any of those cases. He’ll just repeat his mantra, “But you haven’t shown me any evidence, yet, Dan! Where is it?” Maybe he thinks “evidence” means “bananas.” I’d have to agree with him that none of my posts contain bananas.

b) Mutation has been observed in the lab, of all sorts of different kinds (see my next post for some details). When we look at DNA sequences of modern related organisms (whether two human cousins or mice and bears) and compare them, we can work out the changes that would have led from a common ancestor’s DNA sequence to the sequences of those modern organisms. (Sometimes we even have the ancient DNA sequence, like with this polar bear.) Those transformations fit very nicely with the types of mutations we’ve observed in the lab.

We can even work out roughly how long the transformations must have taken, based on observed mutation rates. Then we can go to the fossil record, and see if that prediction matches. (See the amazing example of Foraminifera, in note 2 here.) Time and again, the genetic data fits with the fossil record. This is stunning evidence that mutation is the fundamental source of variation.

I should note that evolution acknowledges other sources of variation besides mutation, e.g. symbiosis (mitochondria and chloroplasts), sex, and recombination. (You might include here the insertion of viral genomes too, but I’m just counting that as a type of mutation.) Mutation doesn’t have to do all the work.

Finally, let me say something about John’s mistake about the finches, in his fifth paragraph here. He cites a Nature article (which is volume 442 by the way, not 445 as he states), claiming that it shows finch variations are not caused by mutations. He says “The genetic information for all finch beak shapes is built in and they can flip flop beak shape almost at will.”

First, flip-flopping is irrelevant – if the selection pressures reverse direction (as the Grants observed), so will beak shape. Evolution doesn’t have a “target”, though this is a popular misconception. Evolution is just about change whatever the direction.

Second, the study John cites does not show that beak shape variations are not caused by mutations. In fact, the article assumes that they are. What the article is showing is that there are separate mechanisms that determine different aspects of beak shape (e.g. length vs. width). This means that mutations can affect length and width independently, which makes it easier for finches to evolve new beak shapes. Of course, John would say: God designed that mechanism for easier evolvability; biologists would say that it’s a product of evolution – same old dispute. What’s not in dispute is that it’s mutation that causes the variation. (Indeed, Petren et al. work out the history of those genetic changes in “A phylogeny of Darwin’s Finches based on microsatellite DNA length variation”, Proc. R. Soc. Lond. B (1999) 266, 321-329.)

So-called “flood geology” (by Dan Ryder)

Sedimentary rock forms when layers of deposits (often in water, but also on land) gradually build up and are compressed into rock. Organisms become fossilized in some of these layers, and we can trace the gradual changes in the organisms on Earth by looking at those fossils, since newer ones are on top of older ones (unless there has been some geological upheaval). These patterns have allowed palaeontologists to construct family trees of life on Earth that are independently corroborated by the DNA analyses I discussed in my “language analogy” post.

Each type of fossil is found only in a restricted range of rock layers (strata) – sometimes a large range, sometimes a small range. For instance, you just don’t find the familiar mammals anywhere except the top layers. These regularities are so good that oil companies employ experts in the subject in order to identify layers, the better to find oil deposits.

All this suggested to early geologists that the Earth is very old indeed, and that there was a succession of different creatures throughout this extremely long history. But many geologists still wanted to hold on to the Biblically derived model that the Earth was only thousands of years old – they clung to the idea that all those layers were deposited by Noah’s Flood. That hope finally died with the advent of modern dating techniques, which demonstrate that these rocks go all the way back to roughly 4 billion years ago. Here is a partial list of those dating methods:

Amino acid racemization (L-to-D) (AAR), Argon40 to argon-39 chronometric, Astronomical polarity time scale (APTS), 10Be/9Be isotopic analysis, chronostratigraphy (requires chronometric methods as well), Coral reef annual layering, Dendochronology (tree-ring), Deuterium-hydrogen isotope analysis, Electron spin resonance (ESR), Fission track dating, Fluorine-uranium-nitrogen analysis (FUN), Geomagnetic (archaeomagnetic/paleomagnetic) reversal time scale (GTRS), Geomagnetic secular variation (around magnetic pole), Helium dating, Infrared-stimulated luminescence, Lutetium-176 to hafnium-176 geochronology, Meteorite cosmic-ray exposure, Milankovitch cycle astrochronology, Neon-21 to helium-3 dating, Obsidian hydration analysis (OHA), Ocean sediment core analysis, Optically stimulated luminescence (OSL), Oxygen-16/Oxygen18 stable isotope analysis, Polar ice-sheet core, Potassium-40 to argon-40 chronometric, radiocarbon dating, Radioluminescence (RL), Radon-222-lead-210-lead-206 chronometric, Rhenium-187-osmium-187 chronometric, Rubidium-87-strontium-87 chronometric, Samarium-147-neodymium-143 chronometric, Strontium87 to strontium-86 chronometric, Tephrochronology, Terrestrial rock cosmic-ray exposure, Thermoluminescence (TL), Thorium-232-lead-208 chronometric, Uranium-235-lead-207 chronometric, Uranium-238-uranium-234-thorium-230-radium-226-lead-206 chronometric (U-series) and Varve analysis.

Each method covers only a certain time range, from a few thousand years to billions of years. In each case, we take some natural process that changes with time, we measure its pattern of change today, and use that information to infer the dates of old things the process has affected. The marvellous thing is that we have so many completely different independent dating techniques that all agree where they overlap that we can be certain that we’re dating the rock layers correctly. Anyone who is not desperately hanging on to the inerrancy of Genesis will see that this is proof of an old Earth, and proof of the succession of organisms.

What can young earth creationists do with this evidence? They’re forced into contortions you wouldn’t believe:

1) They say that the strata were laid down from “settling” after Noah’s flood (except for the “creation week” layer at the very bottom). If you go to the McAbee fossil beds near Cache Creek (highly recommended!), you’ll find several hundred thousand micro-thin layers chock full of fossils (which geology dates to around 50 million years ago). After the rain stopped, the flood waters must have been as calm as a perfectly still aquarium for months or years to achieve that kind of settling! (But why the exactly similar layers?? I’ll tell you why: it’s a seasonal accumulation of debris, roughly one per year. But John can’t say that. And why are they now rock? Eons of compression, but John can’t say that either.)

2) They say that the settling occurred in such a way that each creature is found only within a certain range of layers across the globe. For example, hippopotami are always inexplicably found far above cockroaches with external ovipositors – I guess they were really, really heavy cockroaches! In the Grand Canyon, there are 2000 feet of sediment (containing marine organisms) before the first reptiles and plants appear. Were the reptiles treading water for months on end? (And the plants too?) Not only that, but the reptiles left tracks in the sediment (e.g. in the Hermit Shale layer). How did they manage to walk around on the bottom of the ocean, after having all been killed in the first 40 days of a violent global deluge, I wonder? And then other animals left more tracks on top of the layer above? and then the flood deposited thousands more feet of sediment? You can see why geologists laugh at so-called “flood geology.”

3) Moreover, they have to say that the many independent dating methods that make it *look* as though each layer is independently confirmed to be a certain age, and where these layers *appear* to follow a beautiful succession of dates, millions to billions of years old, are all wrong, in completely different ways for completely different reasons. That, I hope you can see, is utterly preposterous! All to save a literal interpretation of Genesis – there’s no independent confirmation of any of these crazy hypotheses.

The debate format

Just a reminder to everyone of the format: Mr. Mackay and I place our main points in posts (like this one) on the blog’s home page, and subsequent debate on that point (just between us) occurs in the comments. So make sure you click on the speech bubble at the top of each post, or the “replies” link at the bottom – that’s where most of the action is!

The language analogy (by Dan Ryder)

In this post, I will expand upon the language analogy I was able to present only briefly during the debate. The main message is this: the very same reasoning applies to both languages and the biological world to provide conclusive evidence for one thing being descended from another. If that reasoning is correct for languages (as everyone including the creationists admit), then it is correct for the biological world as well. By the same token, if a young-earth creationist decides to tilt at windmills and say that this reasoning is incorrect in order to deny the obvious fact of common descent in the biological world, then they are also forced to accept absurd claims about language, e.g. that French is not descended from Latin.

OK, here goes. During the Roman Empire, the territory covering Italy, France, and Spain all spoke Latin. There were local variations, but all these Latin speakers could understand one another. They had to, as there were extensive trade connections among them, requiring successful communication.

When the western Empire fell, however, these trade connections gradually disappeared. Communication was no longer important, and without this pressure to remain the same, the local variations increased in number and size. (Imagine if North Americans, Brits, and Aussies stopped communicating for a few hundred years!) Eventually, they diverged so much that the separate populations could no longer understand one another on the rare occasions they came into contact. They were not speaking Latin anymore; they were speaking its descendent languages: Italian, French, and Spanish. (This is the equivalent of descendent species in biology, which have become isolated and no longer “communicate” – or interbreed – with one another.)

Even if we knew none of this history, we could easily see that Italian, French, and Spanish have a common ancestor just by looking at their vocabulary, grammar, and sound. For example, “cat” is “gato”, “chat”, and “gato”; “tree” is “alberro”, “arbre” and “árbol”; and “tower” is “torre”, “tour”, and “torre”. The similarities are not coincidence: they indicate common ancestry. By contrast, the Swahili words for “cat”, “tree”, and “tower” are “paka”, “mti”, and “mnara”. This difference indicates that Swahili is much more distantly related, if it is related at all. Of course you have to look at the languages as a whole to be sure, and linguists have done just that – reconstructing the evolution of languages often without knowing the slightest thing about the people who spoke them.

In biological organisms, the things that change gradually are of course the genetic codes. These are even richer sources of information than languages – the human genome, for instance, is 3 billion letters long, about three times the length of the Encyclopedia Britannica. When we see that the chimp genome and the human genome are 98% similar, we (of course!) conclude that this isn’t a coincidence: they had a common ancestor. This is exactly the same reasoning as in the language case.

Linguists and biologists have both used this simple reasoning to build massive trees (or webs) of descent for most languages and for most organisms (in varying detail). They’ve been able to trace the geographic travels of both. They’ve been able to reconstruct both extinct languages and extinct genomes. They’ve been able to estimate the dates of these extinct languages and extinct organisms, based on rates of change measured today. They’ve been able to trace instances of “borrowing” terms (like the Swahili for “plow” is “plau”), and the biological equivalent (see Mackay’s “Family Trees” post & comments). In the biological case, this has all received ample confirmation in the fossil evidence. (In the language case, of course, the “fossil” evidence is ancient writing.)

Linguists know that common descent is a proven fact for languages. Biologists have even better evidence for common descent among organisms. Case closed – even we base our conclusions only on modern similarities and differences.

I’ve only lightly touched on this rich analogy, and I haven’t given any specific biological examples beyond the Meredith et al. paper I mentioned in my comment on Mackay’s “Family Trees” post. So I will gradually follow up on this and more in the comments, in the coming week and a half.

A challenge for John Mackay (by Dan Ryder)

Mr Mackay: In the debate, you responded to the argument described in my “debate summary” (below) by saying that science is not done by majority opinion, as though my argument was just: believe what the expert biologists say. That was not my argument. I was asking for an explanation for why, if you’re right that the biological evidence points towards separate origins, virtually all the experts (i.e. the biologists) disagree with you. Are they deluded? Or just stupid?

As I showed, the standard young-earth creationist response, which is to say the biologists are deluded by dogmatic atheism, is incorrect. (40% of biologists believe in God: data here.) For some inexplicable reason, you are still clinging to this myth in your posts so far (the last paragraph of “Family Trees”, and the last paragraph of your debate summary). You can’t do that.

My challenge to you is this: what is your new explanation for why biologists are supposedly misinterpreting the evidence so catastrophically? Are all those biologists simply stupid?

Mackay’s quote mining (by Dan Ryder)

John Mackay displays his lack of knowledge with the strings of quotations he presents below from evolutionary biologists. This is a popular practice in the young-earth creationist literature: quote some evolutionary biologist out of context so they sound like they’re disagreeing with evolution when they aren’t.

In his debate summary, he quotes Gould: “…our ability to classify both living and fossil species distinctly and using the same criteria, ‘fit splendidly with creationist tenets,’” as though Gould is saying that the variety of living and fossil creatures supports creationism. That’s not what he’s saying, as Gould himself complained in no uncertain terms, many years ago here. (Do you not check your sources at all, Mr. Mackay? This quote-mine was exposed back in 1984!) The quotation comes from p. 205 of The Panda’s Thumb, where the complete quote is: “This notion of species as ‘natural kinds’ fit splendidly with creationist tenets of a pre-Darwinian age.” First, he makes no mention of fossils at all – that’s just added in! Second, he is talking about what people used to think pre-Darwin. Third, he goes on to explain how evolutionary theory gives a much better account of what we find: a mix of stability and change throughout the fossil record.

What we don’t see are unchanging natural kinds, as they used to think – for example, there are hundreds of identified dinosaur species that we obviously don’t see today, and that are found only within a restricted range of strata in the fossil record: wikipedia’s list. Instead we see birds today, whose dinosaur ancestry (or at least cousinhood) is indicated by many different facts, including: skeletal similarity (vertebra, feet), similar lungs,and a collagen structure that is closest to modern birds. (For a basic summary of some of this information and more, see here.)

The next case of quote mining: Mackay quotes evolutionary biologist Thomas Kemp on the “sudden” appearance of “new taxa” in the fossil record, and a biology textbook to the same effect. “Sudden”, here, means on the order of hundreds of thousands of years, which already contradicts Mackay’s view that the earth is merely 10,000 years old. Second, the “new taxa” are often very similar indeed to related taxa: e.g. barosaurus and diplodocus (or other diplodocoids). If these are new “kinds”, using the meaningless creationist term, then a chihuahua is definitely a different kind from a great dane, and it’s game over for Mackay. (He has to maintain that all dogs are the same “kind”, or else he would have to admit that new kinds can come from old ones.)

In the quotations, Kemp and the textbook are discussing an issue within evolutionary biology concerning how rapid evolutionary change can be: when environmental change is rapid, evolutionary change can be too; when the environment is stable, so (typically) are species. If evolutionary change is caused by environmental selection, this is exactly what we would expect. These folks, who are staunch advocates of evolution, would be shocked to learn Mackay is misusing them as fake support for young-earth creationism.

Next case: In his new post (“Family Trees”), Mackay quote-mines an article from New Scientist in 2009 discussing the transfer of genetic material by methods other than reproduction. For instance, it has long been known that one bacterium can transfer short segments of DNA to another bacterium by connecting through a tube – a process known as “conjugation.” This is like the process whereby a language can borrow a term from another, rather than from its parent language(s): for example, we got “pajama” from Hindi-Urdu, not from the parent languages of Anglo-Saxon or medieval French. What this means is that, in bacteria and other single-celled creatures, common descent has a network or web shape rather than a tree shape. (This is also true, though to a much lesser extent, for multicellular creatures like us.)

When Mackay quotes these scientists as questioning the “tree of life”, they are merely suggesting that common descent takes the form of a web rather than a tree. They are not questioning common descent; rather they are displaying the incredible knowledge that we are acquiring about the details of common descent (just as we are about the common descent of languages using exactly the same methods). For example, Mackay quotes Eric Bapteste saying “We have no evidence at all that the tree of life is a reality” [rather than a web, I might add!], but conveniently leaves out Bapteste’s later comment: “The tree of life was useful. It helped us to understand that evolution was real.

I’ll have more to say about the language analogy in the post after my next one.