The Questionable Authority

A new (mis)take on an old paper

When an anti-evolutionist attempts to publicly “explain” a scientific paper, it usually signals two things: you should read the paper for yourself, and you should not be surprised to find that the creationist “explanation” misrepresents what the paper really says. A new blog post by Paul Nelson is no exception. Nelson, descending from the (relative) intellectual heights of the Discovery Institute to join the crowd at Dembski’s Whine Cellar, tells his readers that scientists did not grasp the true point of a 1975 paper because they did not read it all the way through.

The paper in question is a relatively famous one – it’s a paper in Science by Mary-Claire King and Allan Wilson that compared the available measures of genetic difference between humans and chimps with what was known about the morphological, behavioral, and cultural differences between the two species. King and Wilson, in this paper, calculated that there was a 1% genetic difference between humans and chimps, and that this difference is not enough to account for how different the two species really are. Nelson claims that scientists focused on the first finding because it was reported early in the paper, and missed the second part because it came later, after us lazy lab boys had given up on reading. (Nelson apparently believes that scientists share his work ethic.)

But one cannot hold King and Wilson responsible for what lazy readers did with their powerful paper. The “one percent” message comes on the second page of the paper (p. 108). If being mostly chimp, genetically speaking anyway, is what matters to a reader, chances are he’ll do what Simon and Garfunkel sang about in “The Boxer” — “a man hears what he wants to hear, and disregards the rest” — and stop reading.

The real message of King and Wilson 1975 arrives later in the paper, where casual readers don’t bother to follow:

The molecular similarity between chimpanzees and humans is extraordinary because they differ far more than sibling species in anatomy and way of life. Although humans and chimpanzees are rather similar in the structure of the thorax and arms, they differ substantially not only in brain size but also in the anatomy of the pelvis, foot, and jaws, as well as in relative lengths of limbs and digits. Humans and chimpanzees also differ significantly in many other anatomical respects, to the extent that nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart. Associated with these anatomical differences there are, of course, major differences in posture…, mode of locomotion, methods of procuring food, and means of communication. Because of these major differences in anatomy and way of life, biologists place the two species not just in separate genera but in separate families. So it appears that methods of evaluating the chimpanzee-human difference yield quite different conclusions. (p. 113, footnote numbers omitted; emphasis added)

Strangely enough, there is another, shorter, passage that makes essentially the same point found elsewhere in the paper. Nelson didn’t quote this one – I had to read the paper to find it.

The intriguing result, documented in this article, is that all the biochemical methods agree in showing that the genetic difference between humans and the chimpanzee is probably too small to account for their substantial organismal differences.

That quote is found on page 107 of the paper. That’s the first page of the article, one page prior to the mention of 99% similarity.

Reality, as is so often the case, simply does not match Nelson’s assertions here. The truth of the matter is that the King and Wilson paper did not become a landmark simply because they reported on the genetic similarity between our species and our close cousins. As good scientists are prone to do, King and Wilson did not simply report on what they saw. They took what they saw and understood then – in 1975 – and used it to make predictions about what they (or others) would find later on.

In 1975, scientists had only a very limited number of methods available for measuring genetic distance. They could look at differences in the proteins produced by genes a couple of different ways. They could also very crudely assess the degree of similarity between the DNA of two species by examining differences in melting temperature. The methods that evolutionary geneticists and molecular ecologists normally use (and take for granted) today were still a decade or more away.

Using the tools available, King and Nelson found that most chimp proteins are virtually identical to their human counterparts, and that the DNA of chimps matched the DNA of humans very closely in melting temperature experiments. At the same time, we know that there are some rather substantial differences between humans and chimps – besides the obvious differences in language, cultural behaviors, and intelligence, there are also significant (and obvious) differences in bone structure and overall physical appearance. The differences that they found in the proteins isn’t enough, they believed, to explain the differences. That, in turn, lead them to make the following prediction (also found on the first page of the paper):

In order to explain how species which have such similar genes can differ so substantially in anatomy and way of life, we review evidence concerning the molecular basis of evolution at the organismal level. We suggest that evolutionary changes in anatomy and way of life are more often based on changes in the mechanisms controlling the expression of genes than on sequence changes in proteins. We therefore propose that regulatory mutations account for the major biological differences between humans and chimpanzees.

That prediction, by the way, seems to have been on the money. The more we learn about genomes, about the way genes work, and about the similarities and differences between us and the chimps, the more accurate the prediction appears.

A news story in this week’s Science (also cited by Nelson) points out that:

When King [yes, that's the same King that wrote the other paper] and the rest of the researchers in the Chimpanzee Sequencing and Analysis Consortium first detailed the genome of our closest relative in 2005, they simultaneously provided the best validation yet of the 1% figure and the most dramatic evidence of its limitations. The consortium researchers aligned 2.4 billion bases from each species and came up with a 1.23% difference. However, as the chimpanzee consortium noted, the figure reflects only base substitutions, not the many stretches of DNA that have been inserted or deleted in the genomes. The chimp consortium calculated that these “indels,” which can disrupt genes and cause serious diseases such as cystic fibrosis, alone accounted for about a 3% additional difference (Science, 2 September 2005, p. 1468).

Entire genes are also routinely and randomly duplicated or lost, further distinguishing humans from chimps. A team led by Matthew Hahn, who does computational genomics at Indiana University, Bloomington, has assessed gene gain and loss in the mouse, rat, dog, chimpanzee, and human genomes. In the December 2006 issue of PLoS ONE, Hahn and co-workers reported that human and chimpanzee gene copy numbers differ by a whopping 6.4%, concluding that “gene duplication and loss may have played a greater role than nucleotide substitution in the evolution of uniquely human phenotypes and certainly a greater role than has been widely appreciated.”

Nelson may claim this as evidence that macroevolution is an “open puzzle,” but I suspect that most of us are going to see it for what it is – both the vindication of a past prediction, and an indication that we’re on the right track for learning more about what makes humans human and chimps chimp.

Comments

  1. #1 great_ape
    July 2, 2007

    I think you transposed Nelson and Wilson a few times in your post. Probably want to fix that.

  2. #2 Ron Okimoto
    July 2, 2007

    King and Wilson not King and Nelson?

  3. #3 ken
    July 2, 2007

    Seeing as the DI folks are privy to the Perfect Context from which all answers emerge, it should be bloody easy to crank out their own papers with astonishing insights.

  4. #4 Mike Dunford
    July 2, 2007

    Fixed the Nelson-Wilson foul-up. Thanks to all who pointed it out.

  5. #5 steve s
    July 2, 2007

    Paul Nelson’s a nice enough guy, and more honest than several prominent IDers, but he’s got no brains for science.

  6. #6 Unsympathetic reader
    July 2, 2007

    Heck, I read that paper over almost two decades ago and still remember that they had more to say than human and chimps exhibited ~1% sequence divergence in expressed genes.

    The take-home message of the King & Wilson paper was that relative levels of morphological and genetic divergence over time aren’t necessarily linearly proportional. It was not that the measures in either area are completely unrelated. Their anticipation of the importance of regulatory mutations is quite noteworthy.

    (Note that Mary-Claire King was also did the work that helped find BRCA1)

  7. #7 sparc
    July 2, 2007

    The funny thing is that Nelson ultimately implies that King and Wilson did not read or did not comprehend their own paper.

  8. #8 demallien
    July 3, 2007

    There’s still a stray “King and Nelson” lurking in para 11…

  9. #9 Science Avenger
    July 3, 2007

    The funny thing is that Nelson ultimately implies that King and Wilson did not read or did not comprehend their own paper.

    Funny perhaps, but par for the course for IDers/creationists. Behe believes there are a lot of papers that support his IC concept. None of the authors of those papers agrees.

    Personally I’m proud of them for reviewing a relatively recent paper. They finally got out of the 60’s.

  10. #10 Stephen
    July 3, 2007

    It’s part of a bizarre and consistent pattern of projection, isn’t it:
    – purveyors of astrology, homeopathy etc accuse skeptics of being closed-minded and ignoring the evidence;
    – fundamentalists accuse atheists of distorting bible verses and taking them out of context;
    – creationists (or ID-ers, if you will) accuse scientists of misreading scientific papers.

    I suggest dubbing it the porcelain syndrome: it’s not a case of the pot calling the kettle black, but the pot calling the porcelain black.

  11. #11 Ichthyic
    July 3, 2007

    Paul Nelson’s a nice enough guy

    yeah, “nice” in a Sal Cordova kinda way.

    having him even mention a paper by Wilson is an insult in my book.

    Wilson pioneered many of the genetic techniques we use today, like the molecular method associated with mtDNA. He also had a huge hand in the development of PCR techniques.

    he was a staunch evolution defender, and seeing Paul try to spin some kind of IDiocy out of something in one of his papers makes me sick to my stomach.

    sorry, “nice” just don’t cut it if you offend by misuse every time you open your damn mouth.

    Paul is nothing more than a con-man in a cheap suit; he’s just better educated than Sal.

  12. #12 Paul Nelson
    July 3, 2007

    {Just found this in the junk filter.}

    [crossposted at Panda's Thumb]

    Hi Mike,

    You asked:

    could you take a couple of minutes to elaborate on exactly why you believe that human-chimp divergence is macroevolutionary rather than microevolutionary?

    Micro, macro, tomato, tomahto…”I am apt to suspect there enters somewhat of a dispute of words into this controversy” (Hume 1779).

    But seriously: my first introduction to King & Wilson 1975 was, IIRC, reading Gould’s Ontogeny and Phylogeny (1977) as a college student, which then sent me back to the original paper. Gould was so excited about King & Wilson 1975 that he used it to launch the book’s epilogue (and thanked King and Wilson in his acknowledgments for providing the launching point) about searching for evolutionary mechanisms to explain the “phenomena of saltation” (p. 409):

    Although the differences between humans and chimps may be quantitative only, the two species as adults do not look much alike and their adaptive differences are, to say the least, profound (no monkey, despite the common metaphor, will ever type — much less write — the Iliad). Yet King and Wilson (1975), reviewing evidence for the astoundingly small differences in structural genes between the two species, have found that the average human polypeptide is more than 99 percent identical with its counterpart in chimps….For 44 structural loci, the average genetic distance between chimps and humans is less than the average distance between sibling species barely, if at all, distinguishable in morphology — and far less than the distance between any measured pair of congeneric species.

    What, then, is at the root of our profound separation? King and Wilson argue convincingly that the decisive differences must involve the evolution of regulation….Of the nature of our regulatory differences, King and Wilson profess ignorance: “Most important for the future study of human evolution would be the demonstration of differences between apes and humans in the timing of gene expression during development of adaptively crucial organ systems such as the brain” (p. 114).

    I think King and Wilson 1975 was deeply prescient — a great paper, deservedly a classic. But the puzzle they posed is still unsolved today. Sorry, Toejam, but that’s the truth; don’t gripe to me, take it up with Massimo Pigliucci:

    http://life.bio.sunysb.edu/ee/pigliuccilab/Lectures_files/lecture-evonovelties.pdf

    See slides 11 and 18-20.

    Consider an anatomical character that, except under pathologic circumstances, is universally shared in Homo sapiens, our white sclera:

    http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=11322803&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum

    How did this character arise, and how was it fixed, in our common ancestry with chimps (who lack the character)? Various adaptive hypotheses exist about the communication function of white sclera. These however tend to be of the “it’s good to have that trait, so we have it” sort. Given that other primates have pigmented sclera, it is likely that the common ancestor of chimps and humans also had pigmented sclera. The character “white sclera” must then have evolved on the branch leading to Homo sapiens.

    How did that happen? Anybody?

    Doc Bill, you asked about “astonishment.” My conversations about King & Wilson 1975 have typically gone (roughly) like this [EA, evolution activist; PN, me]:

    EA: King & Wilson showed that we’re basically chimps. You know, the “third chimpanzee,” as Jared Diamond put it. 99 percent identical genetically.

    PN: Actually, the main point of their paper was to argue that significant evolutionary change must arise from mutations in “regulatory,” not structural, genes, and that how this happens, and what these loci are, is an open puzzle.

    EA: Say what?

    About like that. This conversation does not occur with evolutionary biologists of my acquaintance who have read King & Wilson 1975.

  13. #13 Albatrossity
    July 3, 2007

    I just got around to reading the NewsFocus article in the last issue of Science that set Nelson off on this quote-mining enterprise. Amusingly enough, the last paragraph (and particularly the last sentence) of this article, by Jon Cohen, puts it all in perspective.

    Could researchers combine all of what’s known and come up with a precise percentage difference between humans and chimpanzees? “I don’t think there’s any way to calculate a number,” says geneticist Svante Paabo, a chimp consortium member based at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “In the end, it’s a political and social and cultural thing about how we see our differences.”

    —-
    Yes, folks, it’s not really about the science, which is moving forward quite well. From the perspective of folks like Nelson, it’s about politics and culture, per usual. And he doesn’t seem to think that politics and culture are moving in the right direction at all…

  14. #14 Mark Duigon
    July 3, 2007

    I was going to comment about lazy scientists at least reading the abstract, which would of course contain the real message, but when I checked the paper I found there was no abstract (in that era Science did not use abstracts). However, the “real message” can be found in the short summary at the end of the paper, which would be read by those who might not read the entire paper.

  15. #15 Heleen
    July 4, 2007

    Paul Nelson writes this:
    Because of these major differences in anatomy and way of life, biologists place the two species not just in separate genera but in separate families.

    Isn’t that a bit old fashioned? Some 10 years out of date?

  16. #16 slpage
    July 8, 2007

    Paul asks re: the white sclera in humans but not chimps:
    How did that happen? Anybody?

    Well, Paul, you see, cells have this stuff called DNA that can change, or ‘mutate’. And some of these mutations can get passed on to offspring. Apparently, one of those mutations that caused a white sclera got passed on in an early population of humans and eventually became fixed in the entire population.

    Now surely the creationist will ask what survival benefit it had such that it would have been selected for. And the knowledgible biologist will explain that not all traits need to be beneficial for survival to be selected for, and some do not even need to be selected for, in order to become fixed in a population.

    Rhetoric, as Paul knows, works best on people that don’t get the implied questions…

  17. #17 Lars
    July 14, 2007

    Mike, you say that Nelson “misrepresents what the paper really says”. Yet I’m not clear on the difference between what you say about the paper and what Nelson says about it. The only clear difference I see is in the conclusions you draw in the last few lines of your post. So how is Nelson misrepresenting what the paper really says?

    I don’t even see a significant difference between having an “open puzzle,” and being “on the right track for learning more”, except that the latter tries to put an optimistic spin on the situation.

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