SINEs and wonders

DNA comparison of humans and other primatesI’m currently reading – devouring would be a better word – Sean B. Carroll’s book The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. It’s a well-written, gripping and persuasive account of how DNA evidence is providing irrefutable confirmation for the key mechanisms of evolution: descent with modification and natural selection.

This is a revolution that has occurred mainly within the past twenty-five years. Carroll explains how, in 1982, our total knowledge of DNA sequences from all living species would have filled a book about the size of his own (i.e. fewer than a million characters). By 2006, this had increased 40,000-fold, so that the books required to hold all the DNA text we now possess could be stacked to more than twice the height of the Sears Tower, with the pile growing by more than 30 storeys per year. This DNA evidence is enabling biologists to see how natural selection has operated at the level of genes to create the vast diversity of life we see around us.

One of the most persuasive and fascinating points made by Carroll relates to the DNA evidence for common descent among humans, apes and monkeys. Large amounts of DNA within our genome is non-coding (or “junk”) DNA: DNA that has no apparent function in creating proteins within the organism. The significance of this non-coding DNA is that natural selection does not operate upon it: it just sits there without alteration, other than the occasional harmless mutation.

Occasionally, a DNA copying error leads to chunks of this non-coding DNA being inserted into the genome near genes. These can either be “long interspersed elements” (LINEs) or “short interspersed elements” (SINEs). As Carroll explains (p.99), “once a SINE or LINE is inserted, there is no active mechanism for removing it”. Equally, the odds of two identical SINEs or LINEs arising by chance are almost non-existent.

Hence SINEs and LINEs provide a perfect indicator of shared descent. If two species contain the same SINE or LINE within their DNA then this can only be explained by their sharing a common ancestor. SINEs therefore provide a means for biologists to trace species’ kinship “beyond any doubt” (p.99).

This then brings us to the image at the top of this post, which is taken from p.100 of Carroll’s book (click for larger version). This shows various sets of data from a study by a team led by Abdul-Halim Salem at the University of Utah, in which a thick gel has been used to separate DNA of different sizes. The presence of a SINE leads to the DNA in some species being longer than equivalent genes in other species which lack that SINE.

So the first set of data shows a SINE which is specific to humans. But the second shows a SINE that is shared by humans, chimps and bonobos – evidence of common descent for the three species. And the third shows a SINE that is shared by all apes but not shared by monkeys.

Analysis of more than 100 SINEs enabled the researchers to produce the family tree for humans, apes and monkeys shown below (from p.101):

Evolutionary tree of hominoids

All I can say is I find this entirely persuasive beyond all conceivable doubt (unless we regard it as conceivable that God would deliberately engineer human DNA so as to create a misleading impression of common descent with other primates). It’s also one of the most interesting glosses I have ever read on the first clause of Genesis 2:7.

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16 Responses to SINEs and wonders

  1. Bror Erickson says:

    “All I can say is I find this entirely persuasive beyond all conceivable doubt (unless we regard it as conceivable that God would deliberately engineer human DNA so as to create a misleading impression of common descent with other primates).”
    I suppose i have to read the book. But part of me wonders if this does at all settle the question. We share many larger organs that are much more visible, but that has never settled the argument for common decent. So I imagine that sharing a few SINEs or LINEs together may not persuade on either.
    On another note I went and watche “Expelled” this weekend and thought it was quite an entertaining introduction to the debate.

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  3. Ross Nixon says:

    I am surprised when I see evangelical Christians taken in by the fantasy of Common Descent.

    Back in the 1960s most Christians assumed (wrongly) that the sciences dealing with this were rigorous, and tried to accomodate them into their theology.

    “The Genesis Flood” and other young-earth creationist publications/web articles have long since shown that a “plain” interpretation of Genesis 1-11 is easily defended. (See http://crev.info for up to date commentary)

  4. Paul Landgraf says:

    ‘All I can say is I find this entirely persuasive beyond all conceivable doubt (unless we regard it as conceivable that God would deliberately engineer human DNA so as to create a misleading impression of common descent with other primates).’

    I have often thought of that last statement–its presuppositions and its ramifications.

    The way the world looks geologically, it seems to have been formed over millions of years. And the way Jesus looked (the vast majority of his days on this planet), he seemed to be just another normal human being.

    God certainly could have made it a bit easier for people to believe in him. But he didn’t; we have it all the way it is. The next question, therefore, is not a ‘why’ question, but a ‘what’ … what do we do with it?

  5. Rick Ritchie says:

    I have found similar arguments by Spencer Wells of the Genographic Project to be plausible. I can see how if you can establish a general rate of mutation and a measure of mutations between gene sequences in different animals, you have some case for common origin.

    But I would want to do some spot checking on the argument before I went with it altogether.

    The idea of “junk DNA” appears somewhat controversial. It’s also a bit unprovable, unless we can remove all the junk DNA and see a healthy creature result.

    From what I found online (Excuse the Google research!), there are reputable evolutionary biologists who have doubts as to whether junk DNA is truly junk. Some think it has regulatory functions. Some also believe it is affected by evolution. (The mechanism for getting removing bad sequences is called death. This happens if the changes in “junk DNA” in fact do affect survival value.)

    See here for a sample:
    http://www.the-scientist.com/article/display/22805/

    I won’t claim expertise in the field, and it is possible you know enough about it to know why the above arguments are false. But I am a bit skeptical, even if I don’t reject the case you make above.

    If the sequences of junk DNA do make a difference to survival, then natural selection would provide a non-random means for getting to the same result in different species, as other arrangements may just be plain unworkable.

  6. John H says:

    Rick: I knew I’d live to regret using the “J” word! I don’t claim any expertise on the subject, but I’m aware that there are continuing debates over what functionality “non-coding” DNA may have. However, I don’t think total non-functionality is essential to the argument regarding SINEs, and I remain persuaded by Carroll’s argument that the best explanation for shared SINEs among humans and other primates is common descent.

    For the full version of the article you linked, click here. Interesting read.

    Paul:

    The way the world looks geologically, it seems to have been formed over millions of years. And the way Jesus looked (the vast majority of his days on this planet), he seemed to be just another normal human being.

    But the point is that Jesus was a normal human being, truly human in all respects. He didn’t just “seem to be” human, and the fact that he was also truly God did not make the impression of his humanity misleading. By contrast, if young-earth and other creationist models are correct, then the broad scientific understandings of the age of the universe and development of life on earth are either (a) so fundamentally and systematically incorrect as to cast more doubt on the reliability of human knowledge than anything postmodernism has been able to throw at us; or (b) not merely incomplete (like an understanding of Jesus that sees him as truly human) but actually misleading.

    In fact, a better (though still imprecise) analogy with the incarnation would be this: Jesus was truly human, as he appeared, but by faith we know that he was not merely human – there was more going on than met the eye. In the same way, the universe and life are truly as they appear to human eyes and scientific investigation (in cosmology, astronomy, evolutionary biology and so on). However, by faith we know that they are not merely as science presents them. There is something else going on. Behind the mask of impersonal forces there are the purposes of a loving God who made all these things.

    As I’ve said before, I think Psalm 104 provides a biblical basis for this dual understanding – of seeing things that are incontrovertibly capable of scientific description in impersonal terms without reference to God (the cycle of night/day, the hunting behaviour of predators) as in fact being used by God to accomplish his purposes.

  7. Paul Landgraf says:

    I think it’s okay to cast some doubt on the reliability of human knowledge once in a while. 😉 Some people think that they have things pretty well figured out.

    I guess I don’t have a problem saying that the physical evidence God provides can sometimes be ‘misleading’. Jesus with the Canannite woman (Matt. 15.21ff) was quite misleading, giving the definite impression that he was not going to help her.

    One of my teachers was fond of saying how we work our way backwards through the creed, coming to faith by the work of the Holy Spirit, believing in Christ, and then receiving all that creation had to offer (the good and the bad) as gift. Or something like that.

    That’s probably way off the subject though. Thanks for all your comments. Some extreme clarity there!

  8. Josh S says:

    If the physical universe is largely made up of illusions, then why should I believe that the Resurrection wasn’t an illusion as well? If there’s a high likelihood that everything we see is an illusion, then we have no compelling reason to believe that the things the writers of the Bible saw and wrote about were real. “But the Bible is inerrant” is a facile answer–why do you believe the Bible is inerrant? Wouldn’t you have to a priori believe that the people who wrote the Bible actually saw and experienced the things they wrote about? Fact is, an illusory world and a trustworthy Bible are contradictory, since you can’t have God completely thwarting human powers of observation except when he’s allowing people to observe things they’re going to write down later.

  9. Rick Ritchie says:

    “I remain persuaded by Carroll’s argument that the best explanation for shared SINEs among humans and other primates is common descent.”

    It sounds more probable than what I mentioned, I’ll grant that. That is different from being beyond all conceivable doubt.

    Here is another thing to take into consideration:
    http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=34249

    There have been mechanisms found for such material to be transferred horizontally between species long after their most recent common ancestor. Granted these are more ancient species with smaller genomes. But the discussion of how evolutionary mechanisms work on such areas of code makes the picture more complex.

    Thanks for the link, though. I’ll enjoy looking at it. I’m fighting less against the theory than the certainty, as I think it’s early for that. Unless these kinds of factors are being considered in the argument already.

  10. John H says:

    Rick: I’m not saying that it is in some objective sense persuasive beyond all conceivable doubt, as in the manner of a mathematical proof. That in itself would be a profoundly unscientific statement!

    I meant exactly what I said: “I find this entirely persuasive…” It was a statement about my response to reading this, not an assertion that this objectively excludes all possibility of contrary findings.

    If you want a more nuanced and objective statement, it would be this: the study described by Carroll appears to provide very strong confirmation of what had already been the generally-accepted scientific position. And even if later study casts doubt on some or all of the assumptions of that particular study, it is highly unlikely that the fundamental conclusion of shared descent will be overturned (or even that these particular SINEs will be shown to be present for reasons other than shared descent). At the very least, the onus is firmly on those who would dispute that conclusion to present compelling evidence to the contrary, rather than acting as if the issues remained finely balanced.

    To put it another way, if you are fighting against premature certainty, then I am equally exercised by artificially-prolonged and quixotic uncertainty (or outright denial). (And I stress I don’t say that to characterise you or anyone else in this discussion – but if you want to know where some of my passion on this subject comes from, then that’s part of the answer.)

  11. joel hunter says:

    Kudos to you, John, for (a) reading the work of a molecular biologist and geneticist, and (b) following the evidence and argument where it leads. I have profited from Stephen Matheson’s blog for about a year now, and encourage all creationists, especially YECists, to allow this Christian biologist to guide you through the evidence (and consider his arguments against the assumptions and claims of the popular creationist organizations).

  12. John H says:

    Joel: I should point out, just to avoid confusion, that Carroll’s book didn’t change my mind as such. I had already come (back) round to common descent and to evolution as the means by which “the Lord God formed the man out of the dust of the ground”. But I had not seen evidence for common descent presented so clearly and persuasively as the example given in Carroll’s book – so you might say it blew the last cobwebs of hesitation or uncertainty from my mind. 🙂

    I’ve been reading SM Matheson’s blog since Josh recommended it recently. Some interesting material there, and I particularly identify with the point he makes in one of his posts that his aim as a Christian biologist is “to offer fellow Christians at least one other choice”. I can’t claim anything approaching his scientific knowledge and expertise, but I share that desire.

  13. rpg says:

    As a professional molecular cell biologist who also happens to be a christian, I’ll 2nd (3rd?) the recommendation to read and inwardly digest Steve’s weblog. He recently talked about ‘junk’ DNA, which I commend to you.

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  15. Kepler says:

    If the physical universe is largely made up of illusions, then why should I believe that the Resurrection wasn’t an illusion as well?

    Josh makes a very important point, here. Suggesting (as YECs) do that the world has only the appearance of age is problematic on two levels.

    First of all, the Psalmist states that, “The Heavens are telling the Glory of God, and Earth displays His handiwork.” The Psalmist does not say that the earth displayed (past tense) His handiwork until the the flood made everything look old. No, the current world (which has not changed significantly since ~800 B.C. when the Psalms were penned) in which we live largely appears as God made it.

    Secondly, the incarnation depends on us (or, at the very least, the generation who lived with Him) being able to perceive that Jesus was indeed the Son of God. Jesus was real flesh and blood in a real world. To suggest that the world is only “apparently” old is to suggest that we cannot trust our senses at all – which flies in the face of Psalm 19, and suggests that all of the eyewitness testimony to the resurrection is untrustworthy and therefore worthless.

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