Do the creationist shuffle and twist!

Don’t you hate it when you get up in the morning and the first thing you read on the internet is the news that your entire career has been a waste of time, your whole field of study has collapsed, and you’re going to have to rethink your entire future? Happens to me all the time. But then, I read the creationist news, so I’ve become desensitized to the whole idea of intellectual catastrophes.

Today’s fresh demolition of the whole of evolutionary theory comes via Christian News, which reports on a paper in the journal Molecular Biology and Evolution which challenges the ape to human evolutionary theory. Wait, that’s a journal I read regularly. What did I miss?

Fresh findings in the field of genetics have directly challenged yet another key evolutionary hypothesis by showing that the differences between humans and apes cannot be easily accounted for under the theory of evolution.

A recent 12-page journal article, written by three scientists in Spain and published in Molecular Biology and Evolution, details the results of careful analysis of human and chimpanzee DNA. After comparing and contrasting thousands of orthologous genes from humans and chimps, the scientists found their final data to be very much at odds with evolutionary theory. [Oh, reeeally?] In fact, they even titled their article “Recombination Rates and Genomic Shuffling in Human and Chimpanzee—A New Twist in the Chromosomal Speciation Theory.”

I knocked over my bowl of oatmeal in my haste to track down this “groundbreaking genetic discovery,” and got the paper downloaded and read while I sipped my morning tea. Hey, it’s from Aurora Ruiz-Herrera‘s lab — I know her work. Good stuff. Nice to know she’s going to be winning the Nobel prize for toppling evolutionary theory, even if it means I’m going to have to find something new to study.

But there’s a little contradiction here. The creationist account continues:

Why are these findings seen as a “new twist” to the evolutionary theory? In short, because many scientists have claimed that genetic differences between humans and apes can be attributed to a process known as “genetic recombination,” [They do? News to me.] which is a phenomenon that generates slight genetic variation via meiosis. However, this new journal article seriously calls this proposition into question.

In their research, the three Spanish scientists scrutinized differences between human and chimp genes, expecting to find higher genetic recombination rates in these areas of dissimilarity [Are you sure about that, Christian News?]. Even though studies of human-chimp similarities have been conducted in years past, this particular research was unprecedented because the scientists took advantage of new, high-resolution genome maps.

Ultimately, the study results were contradictory to what evolutionists had theorized [Really?]. Not only were genetic recombination rates markedly low in areas of human-chimp DNA differences (“rearranged” chromosomes), but the rates were much higher in areas of genetic similarity (“collinear” chromosomes) [Correct.]. This is the reverse of what evolutionists had predicted. [Uh, what?]

“The analysis of the most recent human and chimpanzee recombination maps inferred from genome-wide single-nucleotide polymorphism data,” the scientists explained, “revealed that the standardized recombination rate was significantly lower in rearranged than in collinear chromosomes.” [Yes.]

Jeffrey Tomkins, a Ph.D. geneticist with the Institute for Creation Research (ICR), told the Christian News Network that these results were “totally backwards” from what evolutionists had predicted, since genetic recombination is “not occurring where it’s supposed to” under current evolutionary theory. [Now, you see, this is where I lose all respect for you, Mr Tomkins.]

The problem here is that while the creationists got the main result right, they tried to wedge it into a bungled, fallacious version of evolutionary theory. Ruiz-Herrera has refuted creationist evolution all right, but not the real science that the rest of us study. In fact, it goes the other way and uses detailed genomic maps to confirm a hypothesis about evolution.

You didn’t expect anything else, did you? This is the way it always turns out. Creationist makes claim, creationist interpretation is bullshit.

Let’s look at what the paper actually says. But first, a little background.

There are a number of common genetic changes that affect rates of recombination — inversions and translocations. These changes can suppress recombination.

For example, look at this pair of complementary chromosomes. One of them carries an inversion: that is, the chunk of DNA that carries the e, ro, and ca genes is flipped around on one strand, so that the sequence eroca on the white strand reads caroe on the black strand. This is not a problem for the organism. It still carries two copies of each of the genes, as it should, they’re just arranged in different ways on the two chromosomes.

This rearrangement does not inhibit pairing during meiosis, either. As you can see in the bottom illustration, the two chromosomes have to get all twisty and kama-sutraey to line up all the genes, but they can do it just fine. So meiosis, the process by which the organism produces gametes like sperm and egg, can work out with no problem. So this is a rearrangement that doesn’t affect viability or fertility in any significant way.

invxoa

With one exception. What if there is a crossover event, that is, an exchange of DNA strands, within the inversion? It can get ugly. In the diagram below, there has been a crossover or recombination event between the ro and ca genes. Try tracing the effects on each DNA strand with your finger — you’ll see that some of the strands are going to be really messed up.

invxob

Or just look below. The four DNA strands that result from this process are separated to make it clear what happens.

A crossover event involves two strands of DNA out of the total of four, so you still get two uninvolved bystanders, the two noncrossover products. They’re fine and will lead to two normal, healthy gametes with a full genetic complement.

The crossover strands are totally screwed up. One is now dicentric, having two centromeres — when they’re separated at cell division, it will be like a little tug-of-war. This is a gross abnormality in the chromosomes, and will be read as a problem that leads to suppression of division and cell death. The other crossover chromosome is acentric, no centromere at all, as well as being severely truncated and lacking most of the genes present on the chromosome. It will most likely be lost completely during cell division, leading to a genetic deficiency.

invxoc

The net result of all this finagling is an apparent suppression of crossovers in the progeny. The alleles present at the e, ro, and ca genes on each chromosome are locked in to each other and aren’t easily reshuffled around.

That’s all basic genetics. What does evolutionary theory think about inversions?

They are mechanisms that could reduce gene flow between two populations, one that carries the inversion and another that doesn’t. It’s a process that could contribute to genetic isolation between those populations, and could therefore be part of speciation.

I’m not making this up, and I’m not relying on esoteric knowledge to know this: the paper states it clearly in the opening paragraph!

More recently, a number of related studies have proposed an alternative explanation by which chromosomal rearrangements could reduce gene flow and potentially contribute to speciation by the suppression of recombination (Noor et al. 2001; Rieseberg 2001). According to this “suppressed recombination” model, chromosome rearrangements could have a minimal influence on fitness, but would suppress recombination leading to the reduction of gene flow across genomic regions and to the accumulation of incompatibilities.

That’s the part of evolutionary theory the scientists are addressing. It’s the idea that regions of DNA that differ, that lead to the differences between two related species, might also be accompanied by genetic changes like inversions that reduced gene flow between the founding populations. It’s a component of the speciation process that allowed novel polymorphisms to accumulate in one group without spreading to the other group.

Let me try to make this even simpler. The prediction of this hypothesis is that regions of DNA that contribute significantly to the differences between two species ought to also show higher frequencies of chromosomal rearrangements and lower frequencies of recombination. Master that one sentence and you’ll have the gist of this part of evolutionary theory.

So, in this paper, what did they find? They used high resolution genomic data to compare recombination rates in regions of the human and chimpanzee genome, predicting low recombination in those areas that are significantly different. Here’s the summary:

Overall, our data provide compelling evidence for the existence of low recombination rates within genomic regions that have been rearranged in the chromosomal evolution of human and chimpanzee.

Allow me to repeat what creationist geneticist Jeffrey Tomkins said.

Jeffrey Tomkins, a Ph.D. geneticist with the Institute for Creation Research (ICR), told the Christian News Network that these results were “totally backwards” from what evolutionists had predicted, since genetic recombination is “not occurring where it’s supposed to” under current evolutionary theory.

Huh. Did he not read that paragraph I quoted from the introduction, that clearly stated the expectation of evolutionary theory, and that the results fit that expectation?

Perhaps he skipped over the introduction, knowing it all already. So did he miss this statement in the results?

These data suggest that those chromosomes that have been maintained collinear during evolutionary history retained higher recombination rates than those that have been altered during evolution in each particular lineage.

That’s the flip side: collinear regions between chimp and human chromosomes retain a conserved arrangement, and have a higher recombination rate.

So he didn’t read or understand the introduction or the results. Did he comprehend this statement from the discussion?

Using this approach, we provide evidences of a reduction of recombination within genomic regions that have been implicated in the chromosomal evolution between human and chimpanzee.

I daresay Mr Tomkins failed to read the whole damned paper! Or stared at it with glazed eyes and struggled to find some imaginary objection he could use to distort it into a rejection of evolution.

I’m sorry to say that Dr Ruiz-Herrera will not be winning a Nobel prize for refuting evolution, but she has still made a useful and interesting contribution to the evidence for evolution.


Farré M, Micheletti D, Ruiz-Herrera A (2012) Recombination Rates and Genomic Shuffling in Human and Chimpanzee—A New Twist in the Chromosomal Speciation Theory. Mol Biol Evol 30(4):853-864.

Comments

  1. says

    Ruiz-Herrera has refuted creationist evolution all right, but not the real science that the rest of us study.

    Well, yeah, but they have immediate insight into Real Evolutionary Theory, just as they have immediate knowledge of True Design. They got the latter from God, the former from Satan (not directly, you infidels, but ultimately), its True Author.

    So they can just go on and attack the Real Evolutionary Theory and leave alone the strange version that scientists twist to fit Actual Design.

    Glen Davidson

  2. says

    Yet another example of the dangers of starting with a premise that MUST be correct and then attempting to find data that supports your premise rather than going where the data leads you.

  3. stanton says

    I daresay Mr Tomkins failed to read the whole damned paper! Or stared at it with glazed eyes and struggled to find some imaginary objection he could use to distort it into a rejection of evolution.

    Well, Creationists are notorious for their often deliberately poor reading comprehension skills.

  4. Lenard Lindstrom says

    Some confusion on my part, but in the bottom diagram doesn’t the sequence for the noncrossover black strand remain sr, ca, ro, e?

  5. amenhotepstein says

    Perhaps we can propose a blanket statement appended to the end of all peer-reviewed papers in evolution journals, something like this:

    “The results of this paper are in general agreement with the current theory of evolution by natural selection and do NOT, in any way, support creationist or intelligent design hypotheses.”

  6. omnicrom says

    Creationists read all scientific literature like they do the Bible, they can read anything to mean whatever they want it to mean.

  7. says

    This is the reverse of what evolutionists had predicted.

    Once again, the Creationists reveal that they’ve already accepted, even if not consciously, that science is a superior method of obtaining knowledge about the universe than, say, reading the Bible. If not, then the validity of various predictions wouldn’t matter a whit to them.

  8. says

    Don’t you hate it when you get up in the morning and the first thing you read on the internet is the news that your entire career has been a waste of time, your whole field of study has collapsed, and you’re going to have to rethink your entire future?

    Every single day! This is the story of architecture. Only I don’t need to read it on the internet.

    Sadly, I think that, as much as we are likely to win this game of science/rationality (goddist attempts aside), it will be meaningless in the larger social game. All this, too, will be tamed in the interests of the few and to further skew the social field. It’s a social game. Not about what is true or untrue. Science’s relevance is relative and determined by forces external to its practice. (Hell, societies have been wrought and collapsed in the absence of modern science). The science/religion spat is of little consequence.

    Goddists gaining traction in ‘Merika¹ will have little global impact. The US will only become less relevant as societies that do appreciate reality gain more traction. That being said, it is not where the real battle occurs: in the realm of global social dynamics. These move ahead independently of whether we share DNA with a chimp, or whether people do, or don’t, believe in imaginary gods.

    ¹ Though I do not think it all that consequential (on a global scale) that USAians shoot themselves in the foot (in terms of succumbing to religious dogma, rank superstition or moral bankruptcy), it would be sad to see the grand experiment fail.

  9. kevinalexander says

    So, if Tomkins is correct then the chimpanzee isn’t my cousin after all? That must mean that my uncle was the mailman.

  10. ibbica says

    OK so I haven’t been in a genetics class for some time now, but this post prompts me to ask: can you have multiple crossing-over locations per chromosome? And if so, would they all occur between the same pair of strands out of the four?
    Basically, I’m wondering if you always end up with two unchanged ‘parental’ strands… I mean, sure, that’s how it’s often shown in intro textbooks, but is that actually true? (Of course, if that’s too off-topic or complicated a thing to deal with in the comments section of a blog post, citations for further reading are welcome :) )

  11. Rich Woods says

    In short, because many scientists have claimed that genetic differences between humans and apes can be attributed to a process known as “genetic recombination,” [They do? News to me.]

    You’re forgetting to translate from the standard creationist counting system: one, two three, many.

  12. profpedant says

    I wonder if a little rearranging of the chromosomes of a horse or donkey would enable us to breed a consistently fertile mule…..

  13. timanthony says

    You called Mr. Tomkins a Mr. You have left him with no choice but to become very very offended offensive. You ignored his Ph.D. He is going to be angry, and then he’s gonna get MAD, and, and, then he’s gonna…

    you just wait, mister! I mean Professor! You’re really asking for it now!

  14. Amphiox says

    You’re forgetting to translate from the standard creationist counting system: one, two three, many.

    They have a three in their system?

  15. Amphiox says

    Though of course, when it comes to counting systems, two and only two numbers matter. Zero and 1.

  16. says

    even if it means I’m going to have to find something new to study.

    Nah, you’re fine. Your elitist government school will keep forcing the atheist religion of evolution onto unsuspecting students just like it has been all along, even after Darwin recanted his faith in it.

    /snark

  17. Azuma Hazuki says

    These guys are really narrowly-focused. In addition to being wrong, his blathering doesn’t matter because we’ve got two fucking ape chromosomes fused head to head in chromosome 2 with the telomeres in the middle and a rusted-out hulk of an inactive centromere way down one of the legs.

    Do these people just not know how to look at the big picture here or what? There should be some kind of penalty for people who keep doing shit like this…

  18. unclefrogy says

    I disagree theophontes it is part of the most important argument of all will we act in accordance with reality or delusion. We live in the world of reality which is described by science whether we admit it or not.
    it is not some side issue it is part of the central issue.
    All issues that work their way into the public discourse and policy have at there hart reality vs belief.
    Rational thought exemplified by the scientific understanding of evolution is just one answer to what we are, where we come from, what is reality and how does it really work.
    anything else is self-destructive.
    uncle frogy

  19. Hammer of dog says

    @Amphiox #20

    “Though of course, when it comes to counting systems, two and only two numbers matter. Zero and 1.”

    There are 10 types of people in the world, those who understand binary and those who don’t.

  20. mikeyb says

    This is just another albeit important messy empirical questions as to how evolution occurs, not if it has occurred. You could scan scientific journals every week and misunderstand and misconstrue papers to you hearts delight.

    Doesn’t mean a thing. I do think it is interesting though how common it is for scientists to find some new genetic, environmental, ecological etc, mechanism and trump it up as some new idea that is going to usher in an new Neo-darwinian synthesis, when time and time again it amounts to much ado about nothing in the overall scheme of basic evolutionary theory. One may call it the Steven J Gould effect.

  21. kantalope says

    Wait a darn minute. I could make a living out of reading and NOT understanding stuff. Ah man, all the time I’ve wasted trying to understand the stuff and not making a living. I’ve been doing it all backwards. ARGH!

  22. Rich Woods says

    @Amphiox #19:

    They have a three in their system?

    Admittedly some of them consider it a heresy.

    And I see Hammer of Dog has beaten me to your #10100.

  23. frankb says

    You’re forgetting to translate from the standard creationist counting system: one, two three, many.

    The trolls of discworld are much more sophisticated. They count one, two, many, lots.

  24. says

    I tried to quote that first paragraph of the paper with a link to your explanation here, but it told me I was a spambot. I took out the link but left the name of the blog; no luck. I took out all reference to Pharyngula: it still thinks I’m a spambot. Interesting!

    I try to tell creationists that strong evidence convinced rational people that evolution had occurred 200 years ago, before there was an explanation–even a theoretical one without a mechanism for inheritance–but they don’t listen.

  25. Trebuchet says

    Creationists lie! In other news, water is wet, lead is dense, and the sun rose in the east this morning.

  26. skaduskitai says

    @Amphiox:

    Ofcourse they have three in their counting system! The problem being that they can’t actually count to three as they think three equals one. That is probably what screws all their attempts at math.

  27. Rey Fox says

    A recent 12-page journal article, written by three scientists in Spain

    Woah woah guys, slow down!

  28. says

    @ unclefrogy

    Sorry, unclefroggy, I see I used the word “consequence” in my # 10 rather vaguely: “The science/religion spat is of little consequence.” I did not mean that as a general statement, but specifically in the context of socio-political power.

    Without trying to sound like a PZ-bot, I do think that he has the balance right in terms of his writings and efforts here on Pharyngula. Some might feel chagrined that he does not focus solely on science-blog writings such as this (whether or not to refute religious ignorance), but spends so much time on social justice and like issues. Science simply cannot function without social and political support, wereas society and its politics have always been able to function without overtly supporting, or endorsing, science. To be a driving force in society, science must fight for that position. It is not a given.

    We live in the world of reality which is described by science whether we admit it or not.

    Our primary milieu is social. Whether or not we utilise science to negotiate our way, is perhaps less important than you seem to think.

    Ken Ham (and others of like stripe. I do not know Mr Tomkins well enough to say, but he would appear to fit this category) has managed to do quite well for himself in the world. This in the absence of a coherent or relevant *real* world view. He has come to realise that he can cynically manipulate socio/political forces¹ to increase his social power – and enrich himself financially.

    For counter example, consider North Korea, a country that majority endorses science (insofar as it empowers Songon) and yet this fails to deliver to any but the military.

    ¹ In spite of being anti-reality, church groups reap major political concessions in vast swathes of the planet. Tax breaks for bullshit – this can only flow from the realm of politics. It is this politics that needs to be amended – not least for the sake of science.

  29. rq says

    There are 10 types of people in the world, those who understand binary and those who don’t.

    So I’m to understand that the person collecting animals for the ark was thinking in binary, and gathered five times less animals than god actually meant?

  30. chrislawson says

    theophontes, I think you missed the point of doublereed’s comment. What I took from it was that creationists incorrectly describe evidence for evolution as evidence against evolution and when challenged tend to fall back on a “well that’s my interpretation” argument. That is, doublereed was mocking creationist contortionism.

  31. unclefrogy says

    the mind might be more accurately said to live in a “social milieu”
    the body lives in the world described by science our behavior is effected by that social milieu but it lives and dies in the world of science regardless of the common beliefs shared by the group one belongs to. The outcomes of our decisions and actions are not determined by our beliefs or our desires but by reality.
    I see the conflict between belief and rational thought as expressed by science to be fundamental to the 21 century.
    Irrational belief and behavior is to be confronted where ever and when ever it is encountered.
    One of the things that I find appealing about this blog is it is not confined or constrained by any particular subject.
    uncle frogy

  32. DLC says

    I was half asleep when I read the title, and mindboggled it as “creation tits shuffle and twits. “

  33. says

    @ chrislawson

    That is, doublereed was mocking creationist contortionism.

    Oops, I missed the snark tags. (Sorry, doublereed, if I came across tetchy.) I still disagree though. I find creationists are very clear in their rejection of evolution. They do try and present an alternative hypothesis (well, such as it is): Goddidit! Mr Tomkins is precisely such a case in point. He is making specific claims against the current scientific position.

    (Yes I am aware of goddists who argue: “atheism/science/skeptisism… is just another belief system/ religion”. The example in the OP, however,is not of this type.)

    @ unclefrogy

    the mind might be more accurately said to live in a “social milieu”
    the body lives in the world described by science

    Not just “social milieu”. We are speaking rather of our true “evolutionary milieu”. We have been on top of the food chain for a while now. (Not as much as sharks, I’ll concede. They have remained, physically, in pretty much the same shape for some time. But their mental development never carried forward. Ours did. And this happened particularly in a social environment.)

    The outcomes of our decisions and actions are not determined by our beliefs or our desires but by reality.

    Yeah, but that reality is pretty tolerant even of the most aberrant ideas.

    Someone like Jim Bob Duggar (“fucker-for-christ“) makes a good living as a property agent. What does he care for science? He plays the social game with no small measure of success. This in spite of his disdain for reality, that reality (as you rightly say) his penis-weilding body occupies.

  34. says

    On the Christian News article that you reference, I noted and replied to a comment from Lucien.
    He did not reply. Perhaps you might.

    In fact, chimpanzee and gorilla chromosomes 12 represent a clear example because they share the same derivative form, whereas human chromosome 12 has maintained the ancestral state from the human–chimpanzee–gorilla ancestor
    My reply was:

    Are not ‘same derivative form’ and ‘ancestral state’ both assumptions based on the presumption that chimps, gorillas, and humans did in fact share a common ancestor? If they did NOT share a common ancestor, but DID share a common designer, these observations would be just as likely.

  35. Owen says

    @MikeyB:

    . I do think it is interesting though how common it is for scientists to find some new genetic, environmental, ecological etc, mechanism and trump it up as some new idea that is going to usher in an new Neo-darwinian synthesis, when time and time again it amounts to much ado about nothing in the overall scheme of basic evolutionary theory. One may call it the Steven J Gould effect.

    I think it’s more likely the “O hai! I can has funding?” effect…

  36. anteprepro says

    Are not ‘same derivative form’ and ‘ancestral state’ both assumptions based on the presumption that chimps, gorillas, and humans did in fact share a common ancestor? If they did NOT share a common ancestor, but DID share a common designer, these observations would be just as likely.

    How does a “common designer” make any fucking sense in this situation? Did apes, chimps, gorillas, and humans have a common designer that other animals didn’t? Was there a primate god designing these creatures while other gods added their trademarked genetic similarities to the arbitrary chunk of the animal kingdom that they were in charge of? No, a “common designer” doesn’t help to explain anything. Especially when your posited “common designer” is EVERY FUCKING THING’S COMMON DESIGNER. It doesn’t even properly handwave away the genetic similarities and dissimilarities that are utterly consistent with evolution and utterly nonsensical with cdesign proponentism.

  37. David Marjanović says

    can you have multiple crossing-over locations per chromosome?

    Yes.

    And if so, would they all occur between the same pair of strands out of the four?

    No, they’re random.

    If they did NOT share a common ancestor, but DID share a common designer, these observations would be just as likely.

    Why do you comment here when you haven’t read comment 22?

    I think it’s more likely the “O hai! I can has funding?” effect…

    Yeah, more specifically the “O hai! I can has impact factor?” effect.

  38. unclefrogy says

    this disconnect from reality we see so easily with these ridiculous anti evolution arguments just a good example of the disconnect that we as people are subject to.
    The negative effects may not be immediate like thinking you can fly and jumping of the roof but say using DDT did have long term effects which turned out to be very bad.
    You can almost pick any idea or area where we have choices and get away with ignoring reality you might not experience any intolerable negative effects that does not mean there are none or that they will not build up or accumulate damage some where else.
    we can even approach the social organization and function scientifically and try and determine what the effects of policy and actions for our long term survival.
    The conflict between belief and reality as here with anti-evolution is just one aspect of the disconnect. Another example is the belief that abstinence only sex education will reduce sexual behavior and reduce teen pregnancy.
    which doesn’t. or smoking tobacco is not dangerous.
    or reducing taxes will make the economy grow.
    or burning fossil fuel is not causing global warming.
    belief vs reality
    there is a big difference between rational analysis and self serving rationalization like we see here.with the god did it BS.
    That kind of thinking is of a piece it is the same people, the most amazing thing about it is it is accepted by so many as good.
    uncle frogy

  39. samharris says

    Tomkins has a real issue with competence. See for yourself:

    “The authors wrote, “The maximum likelihood time for accelerated growth was 5,115 years ago.” Old-earth proponents now have a new challenge: to explain why—after millions of years of hardly any genetic variation among modern humans—human genomic diversity exploded only within the last five thousand years?
    However, the same data conforms to and dramatically confirms biblical history. Since the author’s date represents the maximum time, the actual DNA diversification event probably occurred even sooner. ”

    http://www.icr.org/article/human-dna-variation-linked-biblical/