If you’re looking for a meaty weekend read, look no further than Paul McBride’s thorough dismantling of Science and Human Origins
The creationists are howling. McBride’s evisceration, with Carl Zimmer’s detailed description of the evidence for chromosome fusion, all discrediting what they thought would be a hot new text on the scientific evidence for creation, has made them so furious that they’re even lashing out at me in email — I just linked to the evidence, so I imagine Zimmer and McBride must be seeing some entertaining spectacles in their inboxes. I do so love to see the creationists dancing in the flames of their own immolation.
I will say this, though: I did get one very polite email from a creationist, who told me that he was not a scientist, but that he’d read a couple of articles that sounded impressively sciencey to him, and asked if they didn’t represent a legitimate criticism of the chromosome fusion idea? And he very nicely sent along the two papers for me to read. Here they are:
Bergman J, Tomkins J (2011) The chromosome 2 fusion model of human evolution—part 1: re-evaluating the evidence. Journal of Creation 25(2):106-110.
Tomkins J, Bergman J (2011) The chromosome 2 fusion model of human evolution—part 1: re-evaluating the evidence. Journal of Creation 25(2):111-117.
Two things jumped out at me: it’s by batty Jerry Bergman, no credible source at all, and it’s published in the inbred in-house journal of the Institute for Creation Research. These are not legitimate science papers, although they do throw around enough science terms and techniques, and follow the form of a real science paper, to generate confusion in the mind of the naive reader. They’re beautiful examples of cargo cult science by creationists. Would you like to read them, or use them as bad examples? Here you go, download it for entertainment purposes only.
I read them anyway. I’m not going to bother with a detailed refutation, but I’ll give you the gist. The fundamental confusion in both papers is the nature of the evidence for an ancestral chromosome fusion, and a focus on irrelevant details that are not central to the argument.
The story is this. At some time after the separation of the human and chimpanzee lineages, two ancestral chromosomes, #12 and #13 in the chimpanzee, fused end-to-end to form a single chromosome, #2, in humans. Chimpanzee chromosome 13 forms the short arm (2p) and part of the long arm (2q) of human chromosome 2, while chimpanzee chromosome 12 forms most of the long arm (2q) of chromosome 2.
The primary evidence for this fusion is the comparative genetic content of these chromosomes. That is, most of the genes in chimpanzee chromosome 13 are found in human 2p, and most of the genes in chimpanzee chromosome 12 are in human 2q. The chromatin binding patterns line up, the sequence analysis confirms, and there have been some lovely FISH studies that show the correspondence.
What has since been done is that a prediction was made that there ought to be fragments of telomeres (the end caps of chromosomes) in the middle of chromosome 2, at the fusion site. Which has been examined. And the prediction has been confirmed.
Bergman and Tomkins ignore every single bit of that. Instead, what they do is focus on just the region of the fusion, and complain that it is a tangled mess and hard to interpret — that it is a degenerate telomeric region, rather than a complete and intact telomere, which is what they demand be present. This is an unrealistic expectation, given that every paper on the structure of the fusion region makes the point that it is degenerate.
An analogy: imagine a red Ford Mustang and a blue BMW X6 are in a head-on collision, and both have totally wrecked front ends, with bumpers and radiators and headlights interlocked and everything about their grilles in tangled confusion, and with bits and pieces torn loose and flung about. You’d be able to look at the crash and still tell by everything in and behind the engine compartment that Car #1 was a Mustang and Car #2 was an X6.
Bergman and Tomkins are the bewildered and incompetent investigators who ignore every other factor in the crash, look at a few particularly mangled bits of the wreckage, and declare that they can’t identify it, therefore…the two vehicles were assembled at the factory in this particular configuration, and no crash occurred. But they use lots of sciencey language to explain this at tendentious length, which is sufficient to convince non-scientists that the interpretation of an obvious historical event has been refuted. And that’s all they need to do to accomplish their goals: fling about unfounded fear, uncertainty, and doubt to win over the ignorant.
It’d be a goddamned telomere if it wasn’t degenerate–which is to say that it would be recognized (and treated) as properly the end of a chromosome, not a piece in the midst of the chromosome. That’s why it remains where it is, moron creationists!
So it’s the sort of telomere that could mark the fusion event, and these fucking idiots use that fact against the fusion event. They just try everything to try to smear evolution, never learning, never caring that their “evidence” is evidence for evolution. Admitting that fact is what they would never do.
Glen Davidson
I CLEARLY did not take enough biology in college, but let me see if I’m following you:
The evolutionary ancestor of humans and chimps diverged some point along the timeline, and one of the pieces of evidence for this divergence is the fact that there are a great deal of chromosomal similarities. Humans had two chromosomes turn into one, but we can still see the strong similarities. Someone, using this (and assuming more science information) used this theory to predict that we should be able to find telomere “wreckage” in the human chromosome, and that prediction turned out to be correct.
The creationists decided that because they failed to pass biology 202, and the chromosome just looks like a tangled mess to them (as it probably would to me, as well) that they these sciency people are just liars.
Is that anywhere near right?
So, do you plan to respond to that very polite creationist who admitted that he’s not a scientist? I fully realize that explaining every single flaw in creationist arguments is a nigh-infinite task, but for those who are (or at least seem to be) intellectually honest, learning the actual truth can be quite helpful.
Well, it’s kind of refreshing to see a “show me an intact telomere in the middle of a chromosome” line instead of all that “show me a transitional fossil” tediousness. Creationist arguments *do* evolve :)
This is a response to the polite creationist.
Neither Axe nor Gauger nor Luskin has engaged either Paul McBride or Carl Zimmer on their blogs (comments open), nor have they responded to criticism at the Amazon book review site (comments open) nor have they responded to Zimmer on his FaceBook page (comments open).
What they did, however, was to open up a FaceBook site for the “Biologic” Tute, limit comments to 100 words, erase Paul McBrides comments refuting their work and ban dissenting commenters. Why use social media if you’re going to moderate comments and invoke the Ban Hammer?
However, Thursday night’s dialog on their FaceBook creationist page was hilarious with Zimmer asking for a single reference only to get the reply “Buy my book.” Then after McBride provided the reference Zimmer was seeking the quote-mine was opened and Luskin’s lie revealed. Hilarity ensued followed by a round of Ban Hammering and comment deleting.
Academic freedom, viewpoint tolerance and teaching the controversy at its finest!
Somebody is going to have to do the thankless job of a line-by-line dismantling of these articles in response to the new technique of having more impressively sciencey-looking fake science.
I have a slightly related question: how are chromosomes numbered? Why is the human chromosome numbered #2, and why are the chimpanzee chromosomes numbered #12 and #13?
Ah, here’s my answer: “The consensus of the committee was that chromosomes should be numbered in order according to their pachytene length. Thus the numbering system of Shastry et al. (1960) which has been confirmed by Kurata et al. (1981) was accepted.” Retrospectively obvious, really.
Chromosomes are numbered according to their size so that the biggest is #1. Google human karyotype.
They apparently think that if they throw enough stuff around that sounds like science then the average person will consider evolution/creationism to be similar to competing religions. It’s hard to tell who is right just by looking at the facts alone. There’s just enough evidence on each side to mean that the only way to make a choice is to use faith to decide between them. Enough of the head; now open your heart.
This will probably work if your non-scientific audience is both eager to confirm what they already believe — and lazy.
Aaand i should have refreshed before posting
As is the norm, they also misrepresent they work they cite. Came across this at a discussion forum:
It is almost as if these people believe that nobody will ever double check their references.
I also note that I found it funny that Tomkins claimed in the online ‘pre-publication’ version of this amazing paper that Tomkins claims that evolutionists use BLASTn to do their analyses.
I’m no super scholar, but I have published a few phylogenetic papers, and not once did I ever use any type of BLAST to actually perform my analyses. To find available sequences to use in my dataset? Sure – but not to do an actual analysis.
I’ll just point out here that this degenerated telomere is a textbook example of one type of nonfunctional, “junk” DNA.
So this creationist “critique” of the evolutionary hypothesis of the fusion origin of human chromosome 2 relies on the existence of junk DNA, and creationists supposedly insist that junk DNA does not exist.
So they are in fact using a piece of general evidence FOR evolution and AGAINST design to try to dispute a specific evolutionary hypothesis upon which the broader theory of evolution does not, in fact, depend.
Even if their argument was right, what it actually does is FALSIFY creation/design theory in general, and SUPPORTS evolution theory, even if it might show that this one specific little chromosome fusion actually didn’t occur.
So, another spectacular own-goal from the creoIDiots. You’d think their net was already too full of balls to let another one in, but no….
I guess you realize that your response to the “polite creationist” will destroy his belief in a Special Creation for man and render his belief in Adam and Eve untenable, thereby destroying his belief in Genesis and the whole idea of Original Sin, not to mention any reasons he has to consider women to be responsible for the Fall, and to therefore treat them as second to man as God intended.
Further, having destroyed the notion of Original Sin, he will no longer have reason to believe that Jesus died on the Cross so that by believing in Him he can save himself from that Original Sin, and from all the other sins he commits by virtue of being human.
Not having the belief in Redemption he will no longer find it necessary to eat the flesh and drink the blood of his Savior and will fail to rise to the side of Jesus when he dies and instead will be relegated to Hell where he will be tortured for eternity in a pool of liquid fire.
God is, after all, just like a gangster’s protection racket, where you either pay up or suffer the consequences.
And that, PZ, I’m afraid, makes you a Reprobate, and sort of like Eliot Ness.
For my next feat, I predict that PZ will get an email from the Discovery Institute’s David Klinghoffer telling him how awful he is to rely on the review of the “hitherto obscure McBride” writing on a blog “no one before ever heard of.” By the end of it, I may be have been hoisted onto PZ’s shoulders which has been happening a lot lately.
Congratulations, Mr McBride, for your “thorough dismantling”.
No one before may have “ever heard of” your blog, but they do now, and for that you owe the DI a thank you.
They have learned that though you may have been quiet in the past, Still Monkeys run deep.
Klinghoffer is always pulling this stunt. A new book from the DI comes out, he whines and complains that the cowardly Darwinists are ignoring it. Eventually some among us get around to addressing their claims, they’re always found ludicrous, and then Klinghoffer complains that we didn’t take it seriously enough, that only a few critics came forward, that those critics aren’t the whole of biology.
It happened with Signature in the Cell. It happened with The Edge of Evolution. It happened with Explore Evolution. In every case, scientists eventually got around to critiquing them (there was no hurry, because these haven’t exactly been scientific blockbusters) and the criticisms get ignored.
And really, we’ve learned. We’ve been burned by this bogus nonsense coming out of the DI every goddamned time, and so there is no enthusiasm at all out of the anti-creationism community to take on any of it anymore.
Even way back when Icons of Evolution came out, a bunch of us got together out of a sense of duty to compile rebuttals to it, a project that only got partway done because we were all so bored with Jonathan Wells’ repetitious and unoriginal crap.
Klinghoffer’s hi-larious (I suspect unintentionally):
Only slightly OT:
My daughter just graduated high school and has focused on veterinary sciences, she will be starting at A&M next year.
I recently asked her how much evolution was taught in her biology classes. NONE, not one word.
It is only taught grudgingly in History classes. Brief mentions of Scopes, etc.
Thank You Texas !
I’d add to that list Larry Moran’s review of Wells’ The Myth of Junk DNA – when it was pointed out to Wells that there was a thorough and extensive review of his book Wells responded by saying “saturation bombing is extensive and thorough, too” and that “addressing it would be like trying to reason with a lynch mob”.
To be fair, as far as Science and Human Origins goes, two of the authors have begun giving some minor responses to my critique, albeit not in a forum where comments are allowed (at the Biologic Institute website). Curiously, Luskin has been the quiet one so far.
@ #21 scooterskutre says:
Since (as one savant put it) nothing in biology makes sense except in the light of evolution, I suggest you give your daughter a special graduation present: a set of books on the subject.
Darwin’s magnum opus, of course (be sure to get a reprint of the first edition); Dawkins, nearly any title (but I did find the Ancestors Tale compelling, and more approachable than the Selfish Gene); Coyne\, WEIT; Nick Lane, Life Ascending, for example. I’m sure other members of the pharyngulentsia can suggest other titles.
Buy them used from Amazon if money is at all an issue. Indeed, the hardbacks of these are likely OP by now.
The pussycats whose abscesses your daughter drains in later life and whose impacted anal sacs she expresses will thank you.
Question: Let’s say the common ancestor of chimps and humans had a chimp-like genome (just for the sake of the discussion). Fusion occurs and produces a mutant that we might call “the first hominid”. Who does the first hominid mate with? All the others around have a different, hence incompatible, arrangement of their chromosomes.
The answser is, of course, another mutant with the same restructured chromosomes. But it impresses me as unlikely that two chance mutants of the same type would turn up at the same time in the same place. Which is a bad objection since clearly the event took place.
Was there a single female, say, whose ova regularly resulted in fusion and the first pair was a pair of siblings? Or was this particular fusion rather common, just as chromosome 21 trisomy (Down syndrome) occurs quite frequently?
Or has some biologist already grokked the situation fully and I’m just sitting here wallowing in a slough of ignorance?
RFW – You’re assuming that individuals of the same species but with different karyotypes can’t interbreed. Reproductive success may be lower in these cases, but it can and does happen.
While there are loads of examples of karyotypic variation within species, I’ll just note that this includes cases within the primates.
sez rfw: “Question: Let’s say the common ancestor of chimps and humans had a chimp-like genome (just for the sake of the discussion). Fusion occurs and produces a mutant that we might call “the first hominid”. Who does the first hominid mate with? All the others around have a different, hence incompatible, arrangement of their chromosomes.”
The answer to your question is, that ‘first hominid’ mates with someone who is genetically compatible with them — and that genetically compatible partner could be someone with a different number of chromosomes. What really matters is not the number of chromosomes, but, rather, that the individual genes of Critter A line up properly with the individual genes of Critter B. A ‘chromosome’ is basically a way of packaging up a bundle of different genes; it’s likely that when two of Critter A’s chromosomes fuse, the packaged-up genes end up in a configuration which doesn’t line up properly with the genes of Critter B, but ‘likely’ isn’t ‘mandatory’. I don’t know, offhand, whether or not there are cases on record of successful mating between two critters where one critter is known to have a fused chromosome and the other isn’t… but I do know that there are a few species out there which have different ‘races’ with differing numbers of chromosomes, and these different ‘races’ remain interfertile.
no credible source at all, and it’s published in the inbred in-house journal of the Institute for Creation Research. These are not legitimate science papers
Well, is a paper that’s reviewed by one’s peers (if one’s peers are fellow wackaloons) “peer reviewed?” Or, as my friend the mad mathematician used to say, “I peer at a lot of this stuff when I review it…”
It is almost as if these people believe that nobody will ever double check their references.
Well, it worked in sunday school, didn’t it?
I’ll point out here, that chromosomal fusions are common and no big deal. Most domestic pigs have 38 chromosomes. A lot of wild pigs have 36. They are still the same species and still interfertile.
Other examples include such exotics as the horse and the mouse as well as the okapi.
The fact that humans have two less chromosomes than chimpanzees due to a chromosomal fusion is not surprising and poses no huge evolutionary problems. If pigs, mice, and horses can do it, so can we.
Mice generally have 2N=40 chromosomes.
Many populations are known that have chromosomal fusions and lower numbers.
On the island of Madeira, there are 6 populations of such. The lowest has multiple chromosomal fusions and 2N=22. To get that number requires 9 chromosomal fusions.
This all happened over a 500 year period, inasmuch as Madeira was uninhabited until recently. Chromosomal fusions are common and commonly seen.
RFW
We have a lot of normal books around the house, a couple of tree of life posters on the wall, watch a bunch of SCI channel, she is usually watching Animal Planet. We talk about science and evolution all the time, and we have a good time laughing about the stupid Christians and facepalming.
The only time she’s been exposed to religion is in public schools, usually a music or art class, but History as well. They manage to sneak it in everywhere. She doesn’t usually argue with them, but she’s been an ‘out’ atheist since Jr High. Not by our urging, her choice.
She’s studying to be an Agricultural Vet, not a pet doctor, and has been raising her own livestock animals since she was fifteen.
A&M is a great Ag school, but she’ll be knee deep in rednecks. She’s used to it.
Thanks for the explanations, people. My assumption that different karyotypes couldn’t breed (or at least have fertile offspring) was wrong.
I’ve learned something new today. Thanks again.
Biology question for PZ (or anyone else who understands this):
It seems that the change in chromosome count would be a pretty big thing when it comes to sexual compatibility, yet the mutation joining together simian chromosomes #12 and #13 to create human chromosome #2 must have happened in one egg or sperm cell in just one individual. Clearly that egg/sperm cell would have been compatible with gametes still containing the original number of chromosomes or it would have died off. How does that work? Was there a long period where many of our ancestors would be getting a different number of chromosomes from each parent but were still perfectly viable and healthy individuals? How would our genetics still function when there’s 23 and a half pairs of chromosomes present?
Hey richcon @ 33,
PZ touched on this a back in 2006 here: Luskin’s Ludicrous Genetics (he linked it a few days ago – my memory’s not that encyclopaedic!)
There’s also a more detailed treatment of “the fertility problem” by Dave Wisker here: The Rise of Human Chromosome 2
I’m not a biologist or biology student, so please let me know if I get anything wrong, but here’s a summary of my understanding:
An individual with chromosomes (a), (b), and a fused (a:b) still has two copies of each gene from chromosomes a & b, just packaged differently, so they function normally.
Their eggs or sperm could have various mixtures as enumerated by PZ:
(a) (b) a normal gamete : normal
(a:b) a gamete carrying the fusion, but with the normal complement of genes: normal
(a) (a:b) a gamete with an extra (a)—lethal
(a) a gamete with an no (b)—lethal
(b) (a:b) a gamete with an extra (b)—lethal
(b) a gamete with a no (a)—lethal
Wisker points out in part 3 of his series that biases in the way chromosomes are divided during meiosis, termed “meiotic drive,” can make some of these variations less likely than others. Experimentally, about 60% of the non-lethal gametes end up carrying the (a:b) fused form.
Obviously gametes without the fusion, (a) (b), can combine with gametes from the wider population to produce normal (a)(a) (b)(b) 48-chromosome offspring.
A gamete carrying the fusion can combine with a gamete from the wider population to produce a heterozygote like its mother/father: (a) (b) (a:b) with 47 chromosomes.
As noted above, this individual bearing one fusion still has the normal number of copies of each gene, and so functions normally.
As this fusion spreads through the population, eventually two individuals, each heterozygous for the fusion, may mate. If both contribute an (a:b)-carrying gamete, the resulting child will be homozygous, (a:b) (a:b), with 46 chromosomes like modern humans. As before, this individual still has two copies of every “a” and “b” gene, and so functions normally.
Note that all along the way, the 46 (a:b) (a:b), 47 (a) (b) (a:b), and 48 (a) (a) (b) (b) variants can all interbreed with one another, although the 47-chromosome heterozygotes are at a slight disadvantage (Wisker estimates the fertility impact at about 10%)
I hope that answers your question! If not, there’s a lot more detail in Wisker’s series.
dmgregory: Thanks for the explanation (and the link to PZ’s 2006 posting on it.) It makes sense that since all genes are still present on the merged chromosome and still active in essentially the same form that someone having this mutation would not have problems finding a viable mate. I was going to ask if there are living examples of species in the midst of a change of chromosome counts, but that’s before I followed PZ’s link on Robertsonian Transformations. 1 in 1000 humans already walking around with only 45 chromosomes due to another two being merged? And in very rare cases, 44? Boggles my mind. The only negative effects mentioned on that site are a slightly elevated risk (1%) of down syndrome and that a small minority of a (non-symmetrical) carrier’s egg or sperm are unviable leading to slightly more sex required to produce a baby, the poor souls. Maybe we are in the middle of a transition to 22 chromosome pairs?
I wonder: what sort of selective pressure would cause a merged Chromosome 2 to take hold across an entire species, and then the extinction of all non-merged 12-13 chromosome pairs? It seems to me that it can’t be the difference in fertility rates, because if that were strong enough to drive the older arrangement out of an entire species it would have been enough to prevent the merged chromosome from taking hold in the first place. Any ideas?
By the way, since that I have a pretty good understanding of evolution for a non-biologist and the fact that chromosome counts can change without messing up fertility seemed strange to me, why does it not surprise me at all that IDers have been using this very issue to declare Darwinian Evolution dead? :) (Then again, my reaction to being confused at something is to find someone who understands it and ask.)
Well, as a non-biologist, I take the attitude, given a list of possible biological mechanisms, the answer is yes to all somewhere in the world.
Thanks for the reply, richcon! I’m glad I could help. :)
As for how the mutation became fixed, Wisker tackles that in parts three and four of his series.
The basics:
Meiotic drive gives the fused version a slight edge over the unfused one when forming eggs or sperm, so it that helps it balance the minor fertility disadvantage. (10% fewer children, but they carry the fusion 60% of the time)
Then it’s mostly drift and the effects of small interbreeding populations (demes within a wider population, which exchange genes less often) that allow the fusion to drift to fixation, not unlike any other neutral or even slightly deleterious mutation that we find fixed in our genome today. Mammals like us tend to have small effective breeding populations, so there’s a significant component of chance to what ends up fixed in our genome.
Wisker estimates the probability of the fusion becoming fixed in the whole population as 4.5 to 10 percent. That might seem low, but we should positively expect a low value. If it were high, then we would expect our close relatives like gorillas and chimpanzees to have developed their own fixed fusions independently over the same time span.
Once again, I hope that helps! :) Thanks for asking questions! (You’re right, it’s definitely the best response to uncertainty)