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The One Percent Myth, and the Open Puzzle of Macroevolution

Gather ’round the fire, children, and I’ll tell you the whole sad story.

Once upon a time, Mary-Claire King and the late Allan Wilson published a paper — that became a widely-cited classic — about the genetic similarity of chimps and humans. “Evolution at Two Levels in Humans and Chimpanzees,” Science 188 (1975):107-116 was, alas, cited far more for proving the genetic near-identity of chimps and humans than for its much more interesting, deeper and more disturbing message: no one really understands how macroevolution occurs.

In brief: King and Wilson compared the chimp vs. human amino acid sequences of several proteins (such as cytochrome c, hemoglobin, and myoglobin), and found the sequences either identical, or very nearly so. Their conclusion? “…the sequences of human and chimpanzee polypeptides examined to date are, on the average, more than 99 percent identical” (p. 108). And thus was born what Jon Cohen, in the latest issue of Science, calls “The Myth of 1%,” namely, that Homo sapiens and Pan troglodytes are “genetically 99% the same.” (See Jon Cohen, “Relative Differences: The Myth of 1%,” Science 316 [29 June 2007]:1836.)

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)

There must be more to macroevolution — e.g., the origin of chimpanzees and humans from a common ancestor — than site-by-site amino acid changes in proteins, which was largely the picture drawn in textbook neo-Darwinism at the time (1975). Chimp hemoglobin is pretty much human hemoglobin, and so on, yet it’s always the chimps behind the bars, gazing out, when one visits the zoo:

The contrasts between organismal and molecular evolution indicate that the two processes are to a large extent independent of each other. Is is possible, therefore, that species diversity results from molecular changes other than sequence differences in proteins? (p. 114)

What genetic changes have caused the manifold organismal differences between chimps and humans? After all, that’s really what we want evolution to explain.

King and Wilson speculated about “regulatory mutations,” which is where evolutionary biology finds itself today, 32 years later. Over to Cohen:

Yet it remains a daunting task to link genotype to phenotype. Many, if not most, of the 35 million base-pair changes, 5 million indels in each species, and 689 extra genes in humans may have no functional meaning. “To sort out the differences that matter from the ones that don’t is really difficult,” says David Haussler, a biomolecular engineer at UC Santa Cruz…(p. 1836)

Always read a paper through to the end.

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28 Responses to The One Percent Myth, and the Open Puzzle of Macroevolution

  1. 1

    Paul,
    Could you perhaps give some more detail on how:

    There must be more to macroevolution — e.g., the origin of chimpanzees and humans from a common ancestor — than site-by-site amino acid changes in proteins, which was largely the picture drawn in textbook neo-Darwinism at the time (1975).

    follows from what you’ve written or quoted?

    This seems to be your main point, but I’m not sure how its supported by your arguments.

  2. Paul,

    How about a debate between you and Behe on common descent?

    Why not?

  3. “the 35 million base-pair changes, 5 million indels in each species”

    So the 95% to 99% in DNA differences is actually correct statistically?

    Then the following comment in creationsafaris.com is not being fair to the Darwin Party? That is, they are not really lying.

    But still, they purposely and knowingly over-emphasize it so much to make the common descent theory appears plausible? And now that it has served its purpose, the 1% myth is to be discarded?

    http://creationsafaris.com/cre.....#20070630a

    …Gagneux says, “For many, many years, the 1% difference served us well” …“Us” refers to the members of the Darwin Party, the dogmatists who shamelessly lied to advance their agenda. They had a strategy to portray humans and chimpanzees as similar as possible, in order to make their myth of common descent seem more plausible. Now, 32 years later, they have come clean, without any remorse, only because the usefulness of that lie has run out, and needs to be replaced by new lies. They had a political, social and cultural agenda that, in many cases, worked for 32 years.

  4. Patrick,

    Think about it this way. Suppose I give you, and one of your friends, this instruction on a slip of paper:

    “Build me a photon detector.”

    You come back with a reflecting telescope, and your friend comes back with a charge-coupled device (CCD). Both are photon detectors, yet the devices are otherwise strikingly different in form and function. Thus the difference that makes a difference, in re the final product — telescope vs. CCD — was not contained in the instruction I gave you, but rather in how you responded to that instruction.

    Segue to chimps and humans. If individual proteins (and genes) are largely identical between Homo and Pan, the difference that makes a difference, at the organismal level — i.e., what makes a human vs a chimp — isn’t likely to be found in single amino acid changes in such proteins.

    Which is why King and Wilson speculated about “regulatory mutations” (see pp. 114-115 of their 1975 paper). Have you read the paper?

  5. I’m with Ou Krokodil. I’d like to see a debate on common descent.

  6. I’d like to hear more about alternatives to common descent.

    If universal common descent is wrong, then how did it happen?

  7. If universal common descent is wrong, then how did it happen?

    If universal common descent is wrong then universal common descent is wrong. Whether a testable alternative is available is not one whit relevant.

  8. Personally, I’ve grown sick of hearing the 1% myth touted as truth by Darwinists without qualifications.

    Humans apparently share a 50% DNA likeness to bananas. So what conclusions must we draw from that?

    This site published an article stating that the percentage was more like 94 than 99.

    HERE

    I’ve seen figures as low as 86% in some articles.

    James Perloff stated, “The claim of 98 percent is based on a process called DNA hybridization. I don’t want to get too technical, but it consists of splitting some human DNA into single strands. They found they could rather conformably make it form a double strand with chimp DNA. And they infer from that the 98-99 percent similarity. But let me say this — since men and chimps look so similar, it wouldn’t be surprising that the DNA, which dictates their physical appearance, would also turn out to be somewhat similar. I would expect human DNA to be more similar to chimp DNA than to whale DNA on the same ground that you would expect two software programs for word processing to be more similar than a spreadsheet application.”

    Let’s also remember that a 4% difference is about 120 million base pairs difference. Huge!

    Even if the 1% were true it would mean 30 million base pair differences.

    Supposing any number of years would allow for 30 – 120 million base pair transitions from chimp to human is still ludicrous in probabilistic terms.

  9. borne

    Humans apparently share a 50% DNA likeness to bananas. So what conclusions must we draw from that?

    You are what you eat!

  10. You are what you eat!

    LOL. You actually made me laugh Dave. :)

  11. You are what you eat!

    Which makes it nice that we share similar chemistry with plants and animals. We can’t eat dirt and rocks!

  12. Constructive criticism invited — Would the following be a fair illustration?

    Suppose we were to compare proteins (especially structural proteins) to Lego bricks and other Lego pieces. To say that the genes of two organisms have high similarity would be somewhat like saying two Lego construction kits included a highly similar set of Lego bricks and other Lego pieces to use for construction.

    Nevertheless, there can be nontrivial differences in how the similar sets of parts could be assembled.

    Consequently, in light of obvious differences (e.g. between chimps and humans), for King and Wilson to speculate about “regulatory mutations” is a way of considering the question of differences in how the similar parts are assembled.

    [Additional thought: As long as one thinks that "junk" DNA is just junk, this will encourage the tunnel vision in which questions of similarity and differences may ignore the possible impact of non-coding regions of DNA.]

  13. Just to point out – Behe actually agrees that the arguments against common descent are 100% correct — that is, when Darwinian evolution is being considered. Behe’s point is that when you stop assuming Darwinian evolution, there ceases to be a good reason (at least for him) to doubt common descent.

  14. johnnyb: Behe’s point is that when you stop assuming Darwinian evolution, there ceases to be a good reason (at least for him) to doubt common descent.

    Actually, Behe acknowledges several reasons that are unresolved issues that weigh against common descent. He says about his own position that, although he doesn’t have answers to these issues, he puts more weight on the presence of apparently accidental similarities of the kind that would be hard to explain as intentional.

    IIRC, one of the questions on his Amazon blog addresses this subject. But one has to go to the full blog, past the review responses.

  15. 15

    Paul,
    The paper was written in 1975, and subsequent to then people have actually sequenced the chimpanzee and human genomes and described many of the differences, and greatly expanded our knowledge of genetics. For instance Hox genes were discovered in 1983, and as you’re no doubt aware in these cases amino-acid changes do regulate the development of the organism. Genes involved during early development will not necessarily be being expressed in the adult organisms which the authors tested. I’m not sure that basing an argument on a then interesting but now redundant piece of work is necessarily useful.

    Notwithstanding that you’re absolutely right that regulatory non-coding RNAs are important and overlooked. I’m told they form a gap in our understanding as they are fiendishly difficult to study. On the other hand you could equally make the statement “there must be more to all evolution than site by site changes in proteins”, and every biologist would agree with you; the evolution of (non-coding) ribosomes has been studied extensively.

    To be honest, I don’t see that there can be any argument that on a physical level humans and chimps are pretty similar, and on a mental level humans are much more advanced as is consistent with having a much bigger skull and longer period of development. If you were to argue something about morality, then it’s not clear to me that a simple social behavior like “Do unto others as you would have them do unto you”, and “love your neighbor as you love yourself” (assuming chimps don’t have these) could not develop in 5 million years, given that we’ve seen much more complex herding behavior and fighting behavior develop in dogs in the last thousand-odd years.

    Without this first premise that “humans and chimps are inexplicably different”, I’m not sure that your argument holds water.

  16. Paul, is there a relationship between this and what PE Johnson has commented on re: GC Williams’s idea that DNA is not the information, it is only the medium?
    (Also, any links to the articles?)

  17. Behe’s argument for common ancestry: the “mistakes” or “useless features” arguments…”shared between two species which, as far as we can tell, has no particular function”.

    Isn’t that “junk” DNA argument?

    What else could it be? Vestigial organs? Are there any known vestigial organs shared by humans and chimps which absolutely do not have any function, and which exist with function in a common ancestor?

    From Behe – Questions about my new book?

    http://www.amazon.com/gp/blog/.....AQDPU73HPH

    …I have no solutions to the difficult problems pointed to by scientists who are skeptical of universal common descent: ORFan genes, nonstandard genetic codes, different routes of embryogenesis by similar organisms, and so on. Nonetheless, as I see it, if, rather than Darwinian evolution, one is talking about “intelligently designed” descent, then those problems, while still there, seem much less insuperable. I certainly agree that random, unintelligent processes could not account for them, but an intelligent agent may have ways around apparent difficulties. So in judging the likelihood of common descent, I discount problems that could be classified as “how did that get here?” Instead, I give much more weight to the “mistakes” or “useless features” arguments. If some peculiar feature is shared between two species which, as far as we can tell, has no particular function, and which in other contexts we would likely call a genetic accident, then I count that as rather strong evidence for common descent.

  18. Patrick Caldon

    “I don’t see that there can be any argument that on a physical level humans and chimps are pretty similar”

    I don’t what you are saying, when it is so clear that humans and chimps are very different.

    So different that 1% difference must be a myth.

    “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.”

  19. Davescot

    Humans apparently share a 50% DNA likeness to bananas. So what conclusions must we draw from that?

    You are what you eat!

    Humans are worms are 75% similar in DNA.

    Anyone eating worms here?

    I see…men eat chickens, chickens eat worms.

  20. 20

    MathhewTan,
    The papers comment notwithstanding, I suspect the way of life issue is the much bigger component in the classification of humans than anatomy.
    The “genomic contribution” to our way of life (for want of a better phrase) may be a lot simpler than we think.

  21. Patrick Caldron,

    You said

    “Without this first premise that “humans and chimps are inexplicably different”, I’m not sure that your argument holds water.”

    What argument does not hold water?

    Are you saying that chimps and humans are just a few regulatory changes away from each other and if we just wait a short time we will see chimps turn into a more intelligent species?

    Are you saying that the differences are really less than 1% and this number has not been a mis-representation over the years?

    Just what are you trying to propose or say?

  22. borne said, “This site published an article stating that the percentage was more like 94 than 99.

    HERE

    I’ve seen figures as low as 86% in some articles.”

    The link “HERE” is broken. Where is the article/site?
    NG says 96% at here.
    [Evan] “Eichler and his colleagues found that the human and chimp sequences differ by only 1.2 percent in terms of single-nucleotide changes to the genetic code. But 2.7 percent of the genetic difference between humans and chimps are duplications, in which segments of genetic code are copied many times in the genome.” So the 99% figure comes from counting single-nucleotide changes, but is not an accurate representation of the total difference between human and chimp DNA.

    It’s also interesting that they state “the scientists identified some 40 million differences among the three billion DNA molecules, or nucleotides, in each genome.
    The vast majority of those differences are not biologically significant [= "junk DNA"?], but researchers were able to identify a couple thousand differences that are potentially important to the evolution of the human lineage.”

  23. I posted the following as a reply at the Panda’s Thumb and The Questionable Authority (Mike Dunford’s blog), but apparently the post is trapped in a moderation que:

    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/.....elties.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/si.....d_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.

  24. 24

    Jerry,

    I believe Paul’s argument could be summarized as:

    1) there is a fundamental difference between humans and chimps; in some manner it is “macro”
    2) the coding genome part of the differences are inadequate to explain this “macro” difference
    3) there must therefore be a big “macro” difference in the non-coding regulatory portion of the genome
    4) (implicit) “neo-darwinism” needs to account for these great changes in the non-coding regulatory genome

    Given that it seems likely that the coding difference between humans and chimps amounts to a couple of hundred genes or thereabouts, in my view it would not be astonishing if the changes in the non-coding regulatory component were of similar magnitude (but take into account that the individual non-coding regulatory potions are smaller than individual genes; therefore it might be disproportionately more non-coding regulatory components, but only to the extent that non-coding components are smaller).
    To me it’s not at all clear from chimp anatomy or behavior that there is some “macro” difference between humans and chimps on a genomic level, whatever “macro” means; presumably “macro” means “so great as to require processes other than those described in a standard college-level text on evolution and genetics which would be produced from a common ancestor of about 5 million years ago”. This does not say that the changes might not be “decisive”, in the sense that a lot hangs off them, but my guess is that they are also small. Small events, small changes often have big consequences, so it might well be with our development.

    In summary point (1) of Paul’s argument is not clear to me. Perhaps if he were to define “macro” in a more detailed way it would be clearer.

    Note that this does not imply that chimps and humans are a few hundred changes away from each other; but rather that humans and the human-chimp common ancestor are a few hundred changes from each other.

    Also my name is spelled “Caldon” without an “r”, thanks.

  25. The other aspect to all this may be the fact the partion of gene and phenotype, though reasonable, is a bit of an approximation. The phenotype may carry quite a bit of information, thus appeals to genetic similarity are misleading.

    See: Genomes and Form: The Case for Teleomorphic Recursivity by one the finest evolutionary biologists on the planet, Richard Sternberg:

    The genotype-phenotype (genome-form) distinction is considered by many to be fundamental to modern evolutionary thinking. Indeed, the premises that: DNA solely constitutes the genotype; that the phenotype is a transient product of the genotype, with the latter not only describing, but also implementing the construction of the former; and that the constructed materials and systems of the cell have no impact on the genotype, have become dogmas. Yet a vast body of data from molecular genetics reveals that cellular systems, directly and indirectly, alter the genome. Some of these data are reviewed. Proteins can influence mutations along the chromosomes, heritably modify the information content of DNA sequences, and, in some instances, reorganize the germline or somatic genome via DNA engineering pathways. These data suggest that the constructed (proteins, chromatin arrays, and metabolic pathways) has an important role in shaping the descriptor. Insofar as it is biochemically possible for states adopted by cellular structures to be stabilized and eventually memorized by engineering chromosomes, semantic closure can be transcended-meaning can be transferred from the domain of form to the genome, and this presumably ongoing process is termed teleomorphic recursivity. Throughout the paper, I implicitly argue that the genome-form partition is strictly a formal one, with no deeply material basis.

  26. 26

    Paul,
    To my mind white sclera do not appear to be a “macro” (in the sense of fundamentally inexplicable) change. For instance we know that wild mustard, cabbage, cauliflower and broccoli (and lots of other vegetables) had a common ancestor less than a few thousand years ago. To my untutored eye the difference between “proto-human with white sclera” and “proto-human without white sclera” would seem to be a lot less than that between these various vegetables.

    If indeed the development of white sclera is positive evidence of intelligent design, why don’t you encourage the Discovery Institute to fund a precise study of the regulatory elements leading to white sclera. Perhaps this would be of general interest for the ID debate, but even if you’re wrong and there is a bog-standard evolutionary mechanism which leads to white sclera the study would probably give some insight into various developmental disorders of the eye, so whatever the result of the study the Discovery Institute could rest happy that it had bettered the lot of humanity.

    I understand you’re a fellow of the DI, and they have a bit of a budget. You should really take something like this up with them.

  27. Dave: “you are what you eat”
    Bananas! I guess we are all monkeys after all! ;-)
    ————
    lars:

    The 94% article is supposed to be at
    http://www.uncommondescent.com.....ps-not-985

    I found it through using the search box and ’94%’

    I could not re-find the article that stated 86% – sorry.

  28. Patrick Caldon,

    I apologize for misspelling your name.

    You said

    “Note that this does not imply that chimps and humans are a few hundred changes away from each other; but rather that humans and the human-chimp common ancestor are a few hundred changes from each other.”

    This essentially says the same thing. Double a few hundred and one has at most a few hundred more.

    But it implies that only a few hundred changes separate us from some species that didn’t make it and they would be essentially the same because a few hundred in the scheme of things is not very much. What do we have of this species that the chimp doesn’t and why and vice versa.

    Sean Carroll believes that the switches that control human development represent in the order of 60 million nucleotides or more and would take several thousand pages to write down. So a few hundred changes might represent what percentage of this? How long is the average switch? It would be a very small percentage. And with switches we are not talking changes in amino acid sequences where many may not change much but changes to switches are changes to the basic code laying out the human and chimp body.

    This seems quite small to come up with all the differences between the chimp and the human.

    I always wonder about switches since apparently they are layers upon layers upon layers of them turning on and turning off in very complicated sequences and how mutations would affect these sequences in any positive way especially with a species that does not reproduce that frequently.

    As the king said in the “King and I”, it is a “Puzzlement.”

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