The mouse’s tale: or, Why I think evolution is true

The first, preliminary attempt to map the mouse genome was announced in December 2002. It provides startling evidence in support of the theory of evolution.

From the print edition of the Ottawa Citizen, Dec. 5, 2002:

The first glimpse inside the entire set of mouse genes shows that humans share 99 per cent of a mouse’s genes — all but 300 from a total package of 30,000 genes. …

The enormous similarity of mice and men … has already led to the discovery of 1,200 previously unknown human genes. If the human set of genes is our “book of life,” says the journal Nature, then the mouse genes form the “phrasebook” that helps us translate it. …

“This is akin to having two books written in two unknown languages, but with the same alphabet. When similarities are recognized between books, we start inferring relationships between languages, which helps decipher what are the words, punctuation marks, sentences, etc.,” [said Dr. Tom Hudson of McGill University]. …

Only now [in late 2002] is the whole set of mouse genes being unravelled and explained, by a team working on the problem since 2000. Today’s version is considered a draft, but it covers more than 95 per cent of the mouse’s DNA. …

A mouse has about 2.4 billion pieces of DNA compared with our 2.9 billion. Where it differs the most is in dozens of extra genes relating to its keen sense of smell. …

Francis Collins, who led the Human Genome Project, said that decoding the mouse’s genes “is like reading evolution’s lab notebook.”

The shared ancestors of humans and mice took separate paths in evolution 75 million years ago, he says. If there are pieces of DNA that remain the same after all those millions of years, these are almost certainly the ones we need to keep in order to survive.

“The text is not being allowed to get scrambled or garbled over time,” he said in a recent interview in Ottawa. “It is being maintained in a legible fashion through many, many, copyings.”

But let’s back up a step. Let’s consider two objections to Charles Darwin’s theory of evolution:  one scientific and the other theological.

First, the scientific objection. Darwin’s theory had at least one hugely significant gap. Darwin couldn’t explain how variation occurred from one generation to the next:

Darwin, being the kind of thinker he was, determined to get down to unassailable, rock-bottom, logical first principles, realized only too well that the theory of natural selection did not really satisfy unless an explanation of variation and heredity was added to it. How, in short, had the first primordial microbe spawned a second that was not exactly like it? …

Darwin broke his lance on variation. In his book [The Variation of Animals and Plants Under Domestication] he looked at it from every imaginable angle. He measured it, weighed it, tracked it, but he could not explain it. …

The answer to that enormous question of how it happened was locked up inside the cell and was destined to remain locked there until the next century.1

Evolution was still an open question — merely an attractive hypothesis — when Darwin died. Darwin’s successors — Mendel, de Vries, Watson, Crick, Franklin and others — supplied the elusive mechanism (genes, DNA) which had stumped him.

The objection was thus transformed into an outstanding confirmation of Darwin’s theory.

If the scientists were now satisfied, some Christians continued to be sceptical. This brings us to the theological objection. Actually, it is better described as an alternative explanation of the data.

Anyone can see that human beings look a lot like apes. And we now know that human beings and apes are genetically related:  indeed, there is a 98% correspondence between the genes of humans and those of chimpanzees. But does this data prove evolution to be true?

Some Christians offer a competing explanation. “It’s no surprise that there are points of correspondence from one species to the next”, they say. “Why should God continually reinvent the wheel? Why wouldn’t he use the same basic design for humans that he used for apes, while introducing the variations required to make us, us?” In that way, each species could be regarded as a separate act of creation, however great the similarities between them.

I am not trained in the sciences, so I held both of these possible interpretations in mind for some years. Sooner or later, data would emerge to settle the question, one way or the other.

The data emerged in December 2002. That’s why I still have the newspaper article in my files, four and a half years later. For me, the issue was resolved by this tale of the mouse genome.

Or perhaps I should say tail:

Mice and humans are so similar that we actually have the genes needed to make tails — except we don’t “express” those genes, or switch them on. …

The missing tails actually matter to medical research. Doctors want to know:  why don’t we look anything like mice if we share so many genes with them? The answer is that in any person’s body, at any time, some genes are at work and some are not.

Scientists used to talk about an “on-off switch” that tells genes when to work — for instance, growth genes that work in childhood but stop in a person’s teens.

But there are also different levels between fully active and fully “off”. Those growth genes, for instance, work fast in a fetus and newborn baby, then slow for a while, speed up in adolescence, then slow again and finally stop for good.

“The mouse sequence makes it easier to find the regions that control activity of genes — the ‘dimmer switches’,” says the Wellcome Trust.

In sum, human beings don’t look anything like mice, but 99% of a mouse’s genes are also present in human beings. Moreover, the genes we have in common include the gene for growing a tail:  but it doesn’t express itself in human beings because it is “switched off”.

For me, this datum decisively tips the scales in favour of the scientific explanation. I understand that God might use the same raw materials from one species to the next, instead of “reinventing the wheel”. But if human beings are a separate act of creation (not evolved from mice), why on earth would God provide us with a “tail” gene?

That’s why I think evolution is true.

~~~~~~~~~~~~~

1Maitland A. Edey and Donald C. Johanson, Blueprints: Solving the Mystery of Evolution, pp. 91-92.

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11 Comments (+add yours?)

  1. JewishAtheist
    Jun 15, 2007 @ 13:28:56

    How does belief in evolution affect your faith, if it does?

    Reply

  2. Knotwurth Mentioning
    Jun 15, 2007 @ 13:33:02

    We can ask why God would provide us with such a gene. To me, the more important question is still “where are all the species in between them and us?” For all that we can theorize on the way that it took place, the truth is there are still missing links. Theoretically, the evolutionary process would have happened one mutation at a time, generation-to-generation. If that was the case, should there not be some gradually increasing sense of species progression?

    The closest scientists get is pointing to skeletal remains of cavemen, that look somewhat like an ape-human build. But apparently, according to scientists that are a part of Creation Ministries International, this same skeletal subtype exists in many European countries. And if this is the only skeletal example, even that would seem flimsy. How can there exist any less than hundreds of thousands of transitional species between a mouse and a human, most of which would theoretically exist today since the mouse itself exists and the idea of natural selection says that the ones with the mutated, superior genes should be the ones surviving, not the predecessors.

    Until you can give me a better list than mouse-ape-human to demonstrate a clear progression through the animals, as far as I am concerned there is lacking evidence. Why did God give us a gene for a tail? Who knows. You yourself said that we cannot always know what God intends in your comments in “A Roman Catholic…”. But whatever the reason, the evolution counterargument doesn’t cut it, for me.

    Reply

  3. michael (a.k.a. snaars)
    Jun 15, 2007 @ 18:04:25

    I took a couple of biology courses just a few years ago. I was awestruck by the amount of evidence from cellular biology for common descent, and the variety of mechanisms for mutation and selection. There are probably thousands of examples akin to your mouse/human one – although, come to think of it, I don’t remember all of the examples having to do with genetics per se, but other molecular structures. I’m not a biologist, so I can’t remember the details, unfortunately. Nevertheless, the information is out there if you know where to dig.

    Incidentally, I think that if we look at the history and philosophy of science and criteria used for acceptance and/or rejection of scientific theories, these discoveries – the correlations between species on a cellular/molecular level, and the molecular-level mechanisms for mutation – weren’t absolutely necessary in order for evolution to be proved a better theory than creationism. I would have to do some research, but if I remember correctly, evolution was generally accepted among scientists during Darwin’s own lifetime. It was enough, for them, that Darwin had proved that evolution had occured – they how was still an open and highly interesting question, but didn’t have to be answered in order for evolution to be accepted as true. Descent with modification had been observed, and better fit the facts of biology and geology than creationism did. The evidence for evolution has been continuously mounting ever since.

    Reply

  4. addofio
    Jun 15, 2007 @ 21:50:42

    Three interesting and relevant snippets, one of which I just heard about today, on NPR.

    First, with regard to the puacity of intermediate forms. That to me is more than satisfactorily accounted for by the truly tiny proportion of dead critters that end up as fossils. It’s a bit of a miracle that we have enough fossils to piece together any kind of coherent story, in my opinion; that we do is strong evidence (in my mind) in favor of evolution, rather than the gaps being an argument against it.

    Second: there are intersting instances of gradual changes among intermediate forms among living species. One I remember from one of my college courses was a salamander found on the shores of Lake Michigan. There are a number of subspecies across the range, each of which freely interbreeds with the neighboring subspecies, But if you take one from the north-easternmost subspecies and another from the north-westernmost subsepcies (the extreme ends of their range), they can’t interbreed–they do not produce viable offspring. Such examples lead to interesting discussions about exactly what constitutes a species, and how species can be definitively identified. I never forgot this example, in part becasue it made me think that if we didn’t know exactly how all the different breeds of dogs had been produced, we probably wouldn’t consider (say) a chihuahua and a St. Bernard to be the same species, since they can’t mate and produce viable offspring under natural conditions.

    Third: For years–at least since my college days back in the late 60’s–scientists have known that only some small percentage of DNA constitutes what we know as genes. They used to assume that the rest was “junk DNA”–that it had no function, but was simply reproduced along with the genes as part of an evolutionary process playing out internally to the DNA. Dawkins based part of his argument in “The Selfish Gene” on the existence and uselessness of this “junk DNA”.

    Well, according to what I heard–and I didn’t listen to the entire show–turns out this stuff isn’t “junk” at all. Rather, it serves vital regulatory functions, telling the genes when and how much to turn on or off. They seem to think there’s more than one type of this stuff–one of which I think the guy called “epigenetic DNA”, so if you’re less lazy than I am, you might be able to find out more about it.

    I must confess to petty feelings of satisfaction and So There! about this. I hated Dawkins’ thesis in “The Selfish Gene” when I read it (required reading for a course), and I never believed that 90% or more of DNA had no function*. I figured that we just didn’t know what it did, and Ha! turns out I was right. And though this doesn’t entirely invalidate Dawkins’ argument re: selfish genes, it does undermine it because he based a fair amount of his argument on the existence of the then-designated junk DNA. Since I find Dawkins rather irritating, this gives me some unholy glee.

    *Back in the 60s people used to mindlessly repeat the claim that we only use 10% of our brain, which I never believed either. Nature tends to be rather parsimonious; organs unused tend to fade away through the evolutionary process. Turns out that also was a matter of confusing “we don’t know what it does” with “it doesn’t do anything”. Now we knowbetter, though we still don’t know all the deatils of what everything does.

    Reply

  5. Stephen
    Jun 16, 2007 @ 16:16:02

    • Jewish Atheist:
    How does belief in evolution affect your faith, if it does?

    Evangelicals (which is where I started out) commonly regard God as actively involved in the details of people’s day-to-day lives, and in world history generally. This is where the theory of evolution strikes its deepest blow to theology. There is no reason why the Creator should not utilize evolution as a mechanism to diversify species. But admittedly it is a very hands-off approach, allowing natural selection to determine (most) developments.

    Hence the position of the Deists, that God set creation in motion after which he ceased to pay any further attention to it. I hope and trust (without being able to prove it objectively) that the Deists are wrong. Nonetheless, in my view, divine interventions must be regarded as the exception rather than the rule.

    This is precisely what theistic evolution suggests to me: that God allows evolution to run its course most of the time, but intervenes at critical junctures in order to give effect to his purpose for creation. For example, I still regard the appearance of human consciousness as more than a merely evolutionary development — a topic that you and I have exchanged opinions on elsewhere.

    Reply

  6. Stephen
    Jun 16, 2007 @ 16:44:27

    • Knotwurth:
    Why did God give us a gene for a tail? Who knows. You yourself said that we cannot always know what God intends in your comments in “A Roman Catholic…”.

    Stephen (not me — my interlocutor) misunderstood my point when I quoted Romans 11:33ff., and it seems that you have misunderstood it too.

    Yes, Paul admits that he doesn’t know the full mind of God. In context, I quoted the text to say that I don’t know whether human beings are the final end of evolution — the ultimate objective God has for his creation. It would be arrogant of me to claim that I know God’s masterplan.

    But Romans 11:33ff. is not a “get out of jail free” card, that allows Christians to duck clear evidence from science, or necessary deductions from logic. I don’t mean to characterize your position that way — I don’t presume to know the contours of your theology. I’m only clarifying my earlier remarks on this subject.

    The “tail” gene is hard evidence against the notion that humans are a separate act of creation. At least so far as our bodies are concerned, we evidently arose from “lower” organisms. At least, that’s my conclusion. I concede that the issue doesn’t turn on a single piece of evidence. I find this particular example compelling, but of course others may legitimately bring in other evidence to support a different conclusion, as you have done.

    • Michael:
    There are probably thousands of examples akin to your mouse/human one — although, come to think of it, I don’t remember all of the examples having to do with genetics per se, but other molecular structures.

    I agree completely. No doubt the post places too much weight on a single piece of evidence. Even in my own experience, my acceptance of evolution didn’t really happen in an instant when I read this one newspaper article. But I do find it to be a compelling example, in the context of a broader case in favour of evolution.

    • Addofio:
    According to what I heard … [“junk” DNA] serves vital regulatory functions, telling the genes when and how much to turn on or off.

    In fact, it says precisely that in the newspaper article I quoted in this post, but I left that part out because it wasn’t on point:

    “The difference between mice and us comes down, surprisingly, to DNA once dismissed as ‘junk’.”

    The so-called “dimmer switches” are located in

    “the regions of our DNA that were once dismissed as ‘junk DNA,’ since scientists assumed anything that wasn’t a gene was useless.”

    I had the same reaction when I first heard the expression “junk DNA”. I thought it was arrogant of geneticists to talk that way (as if they already possessed a complete understanding of the genome!). And, like you, I presumed the “junk” DNA had a purpose that hadn’t been figured out yet.

    On the other hand, it’s clear that some sequences of amino acids are, in fact, useless or even harmful. Here I’m relying on one of the chapters in Matt Ridley’s book, Genome. A given sequence may be repeated hundreds of times in some individuals. In some cases, excessive repetition gives rise to a fatal disease. In other cases, the repetition may be harmless … but it is a “junk” sequence.

    Reply

  7. Jamie
    Jun 16, 2007 @ 19:33:26

    Michael (a.k.a. snaars):

    It was enough, for them, that Darwin had proved that evolution had occured – they how was still an open and highly interesting question, but didn’t have to be answered in order for evolution to be accepted as true. Descent with modification had been observed, and better fit the facts of biology and geology than creationism did.

    I get your point, but proving “descent with modification” doesn’t prove molecules-to-man evolution. I don’t think anyone could say that Darwin proved the latter. As for “descent with modification,” all creationists that I know of would accept this principle. So why do you pit “descent with modification” against creationism? The two are not antithetical.

    Addofio:

    It’s a bit of a miracle that we have enough fossils to piece together any kind of coherent story, in my opinion; that we do is strong evidence (in my mind) in favor of evolution, rather than the gaps being an argument against it.

    I don’t follow. Can you explain this?

    Stephen:

    You quote the following portion of the article, but apparently don’t quote what comes immediately after. I am curious to know what follows this sentence:

    Mice and humans are so similar that we actually have the genes needed to make tails — except we don’t “express” those genes, or switch them on. …

    Offhand, I don’t really know how I would respond to this, because there aren’t many details here. There could be a myriad of interpretations. Just a guess, but these genes aren’t at all related to the ones that produce the human tail bone, are they?

    As a side note, your article says our genetic material is 99% the same as that in mice. I find it funny that mice are more closely related to us (genetically) than chimps, who are supposedly are closest relatives. I think those similarity percentages are a little misleading on multiple levels.

    One more note: I know we’ve discussed this before, but it still seems a little odd to me that you cite Mendel as providing a mechanism for evolution. Seems the basic point of Mendel’s research is that new traits are not actually “new,” but were present in the genetic material all along. Doesn’t this support a creationist perspective, rather than an evolutionary perspective?

    Reply

  8. Stephen
    Jun 16, 2007 @ 21:23:02

    Michael:
    I forgot to respond to this point:

    If I remember correctly, evolution was generally accepted among scientists during Darwin’s own lifetime.

    Many scientists immediately found Darwin’s theory persuasive. But there remained significant opposition to it.

    Edey and Johanson (Blueprints) point to two specific objections. The first was based on variation, as discussed in the post. Fleeming Jenkin,

    with a barrage of statistics and mathematical logic … pointed out that a single variation introduced into a population of any respectable size would be swamped almost immediately.

    It took the science of genetics to put that objection to rest (further explanation below). The other objection concerned the age of the earth. Lord Kelvin put his considerable authority behind a relatively young earth: 100 million years old at most, and cool enough to support life only for the last 20 million years. That sounds like lots of time, but it wasn’t enough to allow for Darwin’s “gradualism” model of evolution to work.

    Failure to fathom variation was bad enough. [Lord Kelvin’s argument] was devastating. The geologists were in disarray. Even Huxley, Darwin’s public bulldog, who had staked his career on an almost obsessive defense of evolution, was put to ducking and dodging. … The outlook for evolution became grimmer. By 1900 there was a strong backlash against it. (p. 100)

    • Jamie:
    I am curious to know what follows this sentence “… except we don’t “express” those genes, or switch them on.”.

    The next sentence is the one I quoted to Addofio: “The difference between mice and us comes down, surprisingly, to DNA once dismissed as ‘junk’.” At this point the article begins to discuss the switching on, switching off, and dimming of genes.

    Just a guess, but these genes aren’t at all related to the ones that produce the human tail bone, are they?

    I don’t know. I’m taking the statement at face value: that here we have a specific sequence of amino acids which constitutes, in mice, the gene that causes a tail to grow. In human beings, the same gene is present but not expressed.

    As Michael points out, there are hundreds of similar correspondences. From the same newspaper article,

    “Ninety per cent of genes associated with disease are identical in human and mouse, supporting the use of mice as model organisms” for research on human health, says the Wellcome Trust.

    Obviously I’m trusting that the scientists’ findings are reliable. But really … these are the same scientists who are responsible for identifying the genetic origins of various diseases. Their science has been proven in practice — it isn’t merely hypothetical. If they say that a certain gene is a “tail” gene, I’m confident they’re right.

    I find it funny that mice are more closely related to us (genetically) than chimps, who are supposedly our closest relatives. I think those similarity percentages are a little misleading on multiple levels.

    Your confusion is understandable. It seems that the authors of the respective articles are comparing two different things. The chimp comparison concerns “letters”:

    If you select at random any “paragraph” in the chimp genome and compare it with the comparable “paragraph” in the human genome, you will find very few “letters” are different: on average, less than two in every hundred. We are, to a ninety-eight per cent approximation, chimpanzees, and they are, with ninety-eight per cent confidence limits, human beings.

    By “letters”, I think Ridley means a sequence of three pairs of amino acids. (I’m going by memory.) Anyway, the mouse comparison concerns genes: i.e., much longer sequences of amino acids, without checking to see if each “letter” is identical —

    Humans share 99 per cent of a mouse’s genes — all but 300 from a total package of 30,000 genes.

    As the article explains, the 99% correspondence produces two dissimilar looking animals because of the switching on and off and dimming of otherwise identical genes.

    It still seems a little odd to me that you cite Mendel as providing a mechanism for evolution. Seems the basic point of Mendel’s research is that new traits are not actually “new,” but were present in the genetic material all along.

    What Mendel demonstrated was the persistence of traits once they had appeared in the genetic material. See the Fleeming Jenkin quote, above. Jenkin argued that a new trait would be swamped. Mendel demonstrated that it wouldn’t, that once a trait is established in the gene pool, it never entirely vanishes.

    The actual source of variation was nailed down in large part via the experiments of Hugo de Vries (who coined the term “mutation”) and Hermann Muller (who exposed flies to radiation), among others. Muller reasoned,

    How could there be an alteration in a single gene and not in the one next to it, only a millionth of an inch away? And yet … that was what happened — only one trait, presumably controlled by one gene, was affected when a mutation took place. Clearly the mutating force was an extraordinarily small, extraordinarily precise, and extraordinarily penetrating one. (Blueprints, p. 172)

    Once a gene has mutated, the mutation has a chance of getting established in the gene pool. If it succeeds in getting established, then it will persist — that was the significance of Mendel’s experiments.

    Reply

  9. michael (a.k.a. snaars)
    Jun 17, 2007 @ 12:52:32

    Jamie:

    why do you pit “descent with modification” against creationism?

    I don’t. When Darwin was young, most scientists were literal, Biblical, young-earth creationists by default. Darwin’s observations caused a sensation because everyone recognized the implication that the Genesis creation and flood stories could not be literally true. God did not create the various plants, birds, sea creatures, etc. – each species according to its kind.

    So, I’m not pitting descent with modification against creationism. I’m just describing historical events and the understanding of creationism as it existed in Darwin’s day. Apart from the question of whether evolution is actually true, I don’t think the history is particularly controversial.

    Creationism comes in many flavors these days. I do understand that most creationists no longer deny that some sort of evolution has indeed occurred, if only in a limited way. But evolution was in direct opposition to the creationism of Darwin’s day.

    The recent changes in the creationist ‘hypothesis’ seem ad hoc. They are a response to the ever-mounting and undeniable confirmations of evolutionary theory that have come from every scientific quarter – not just biology.

    [the] article says our genetic material is 99% the same as that in mice. I find it funny that mice are more closely related to us (genetically) than chimps, who are supposedly are closest relatives. I think those similarity percentages are a little misleading on multiple levels.

    I found this confusing as well. You weren’t addressing me with this comment, but I did think of one possible explanation for the confusing figures, and I’d like to share it. The article says that “humans share 99 per cent of a mouse’s genes — all but 300 from a total package of 30,000 genes.” If the human and chimp genomes contain more genes than the mouse genome – two or three percent, say – then we could share 99% of our genes with mice, and still end up more closely related to chimps because of similarites in the ‘left-over’ material. I’m not saying this is true; I’m just suggesting it as one possible explanation.

    Reply

  10. michael (a.k.a. snaars)
    Jun 17, 2007 @ 13:00:53

    Stephen: Many scientists immediately found Darwin’s theory persuasive. But there remained significant opposition to it.

    Thanks, Stephen. I didn’t mean to oversimplify. Nevertheless, despite widespread initial opposition which never completely flagged, and despite some highly rational and well-thought-out objections, Darwin’s ideas did become generally accepted, and are nearly-universally accepted among serious, well-respected scientists today.

    Reply

  11. michael (a.k.a. snaars)
    Jun 17, 2007 @ 13:07:13

    I just noticed a mistake in my comment to Jamie, in the third/fourth line up from the bottom.

    I should have written: “… then we could share 99% of the mouse’s genes (NOT 99% of our own genes) and still end up more closely related to chimps because of similarites in the ‘left-over’ material.”

    Reply

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