Ardipithecus: We Meet At Last

By Carl Zimmer | October 1, 2009 10:30 am

ardi recon440Meet Ardipithecus.

This introduction has been a long time coming. Some 4.4 million years ago, a hominid now known as Ardipithecus ramidus lived in what were then forests in Ethiopia. Fifteen years ago, Tim White of Berkeley and a team of Ethiopian and American scientists published the first account of Ardipithecus, which they had just discovered. But it was just a preliminary report, and White promised more details later, once he and his colleagues had carefully prepared and analyzed all the fossils they had unearthed. “Later,” it turned out, meant 15 years.

I’ve mentioned before how unfashionable this slow-cooked style of science can be. But sometimes, it’s the only way to do things right. Getting clues about HIV by observing sick chimpanzees in the wild takes years.  And so does reconstructing a fossil–particularly one as delicate as Ardipithecus happened to be. Today, the journal Science has handed many of its pages over to White and his colleagues, who have filled them with lots of details about Ardipithecus, plus a couple excellent articles by writer Ann Gibbons. Ardipithecus has gone from being an enigmatic collection of bones to a new touchstone for our early hominid ancestors.

To appreciate the importance of this new look of Ardipithecus, you have to step back into the history of hunting for hominid fossils. In the early 1970s, Tim White was part of a research team that found described what was, at the time, the oldest hominid known: a 3.2 million year old fossil of Australopithecus afarensis. What made their the discovery particularly spectacular was that they found it included a fair amount of a single A. afarensis individual, whom they which was named Lucy.

Combined with other A. afarensis fossils, paleonthropologists got a pretty decent picture of what hominids looked like. Lucy was a chimpanzee-sized ape with a brain that was only a little bigger than a chimp’s. She still had long arms and curving hands and other traits hinting that she could still climb in trees. But she also had feet with stiff, forward-facing toes, an adaptation for walking on the ground.

So things stood for about 20 years. But then, with the discovery of Ardipithecus and a few other hominid fossils, the record of our ancestry got pushed back millions of years. The oldest fossil that’s been identified as a hominid, Sahelanthropus tschadensis, dates back between 6 and 7 million years old. But scientists have only found pieces of the Sahelanthropus skull. Another species, Orrorin tugenensis, is 6 million years old; it’s represented by little more than a leg bone.

Scientists have learned a lot from these pre-Lucy hominid fossils, but before now they weren’t able to make very detailed reconstructions of these creatures. Only about halfway along the journey from the first hominids to us did hominids come into full-bodied focus.

ardi cover220

At first, Ardipithecus ramidus was yet another scrappy pre-Lucy fossil. The first report offered details about part of a 4.4 million-year-old jaw bone–a remarkable jaw bone, but just a jaw bone nonetheless. Soon after, White’s team found more fossil bones, from the hominid’s hand, skull, pelvis, feet, and on and on–110 pieces all told. But finding these pieces was just the start of the team’s labors. They picked away at the bits of rocks surrounding the fragile bits of fossils. They used a computer to manipulate CT-scans of the fossils to figure out how crushed fragments had originally fit together as a skull or a pelvis.

All this happened in strict secrecy. Some of us science writers knew a little about what the scientists were up to, but we could only guess when they’d finally finish working on the fossil. Sometimes when I’d speak to White, I’d inquire, and he’d politely say he wasn’t done yet.

Looking at the papers out today in Science, you can see that they’ve been very busy. I won’t even try to offer an all-encompassing account of their new results. In many cases, it wouldn’t actually be worth the effort, because these papers are just the first salvo in what will be a fascinating debate about how our ancestors evolved. I was speaking to University of Wisconsin paleoanthropologist John Hawks yesterday on another subject, and he was giddy about the papers’ imminent publication. “Tomorrow’s Christmas!” he said. (His young son overheard him on the phone and got very excited and confused. I had to give Hawks a few minutes  to explain the nature of metaphor. Not sure how well that went over.)

For now, I’ll point out a few of the results on Ardipithecus that are particularly intriguing.

Nice Guys With Little Teeth

Those of you reading this post that have a Y chromosome have canine teeth that are about the same size as those of my XX readers. The same rule applies to the teeth of some other primate species. But in still other species, the males have much bigger canines than the females. The difference corresponds fairly well to the kind of social lives these primates have. Big canines are a sign of intense competition between males. Canine teeth in some primate species get honed into sharp daggers that males can use as weapons in battles for territory and for the opportunity to mate with females.

Men have stubby canines, which many scientists take as a sign that the competition between males became less intense in our hominid lineage. That was likely due to a shift in family life. Male chimpanzees compete with each other to mate with females, but they don’t help with the kids when they’re born. Humans form long-term bonds, with fathers helping mothers by, for example, getting more food for the kids to eat. There’s still male-male competition in our lineage, but it’s a lot less intense than in other species.

White and his colleagues  found so many teeth of different Ardipithecus individuals that they could compare male and female canines with some confidence. The male teeth turn out to be surprisingly blunted. This result suggests that hominids shifted away from a typical ape social structure early in our ancestry. If this was a result of males forming long-term bonds with females and helping raise young, this shift was able to occur while hominids were still living a very ape-like life. Ardipithecus existed about 2 million years before the oldest evidence of stone tools, suggesting that technology was not the trigger for the evolution of nice hominid guys.

Walking, Of A Sort; And Climbing, Of A Sort

C. Owen Lovejoy of Kent State University spearheaded the studies on how Ardipithecus moved. He and his colleagues argue that its pelvis could support its upper body during bipedal walking. It wasn’t a fabulous walker, and was probably a terrible runner. Nevertheless, it had some of the same anchors for muscles that we have on our pelvis, and which chimpanzees and other apes lack. Its pelvis was, in other words, a mosaic. Lucy, we now can see, represents a later step in the journey towards out own walking-adapted anatomy.ardipithecus side view440

Ardipithecus‘s feet were mosaics too. The four little toes were adapted for walking on the ground. Yet the big toe was still opposable, much like our thumbs. This sort of big toe helped Ardipithecus move through the trees much more adeptly than Lucy.

But Ardipithecus could not climb through trees as well as, say, chimpanzees. Chimpanzees have lots of adaptations in their arms and shoulders to let them hang from branches and climb vertically up trees with incredible speed. Ardipithecus had hands were not stiffened enough to let them move like chimpanzees. Ardipithecus probably moved carefully through the trees, using its hands and feet all at once to grip branches.

Just a Reminder: We Didn’t Evolve From Chimpanzees

Chimpanzees may be our closest living relatives, but that doesn’t mean that our common ancestor with them looked precisely like a chimp. In fact, a lot of what makes a chimpanzee a chimpanzee evolved after our two lineages split roughly 7 million years ago. Ardipithecus offers strong evidence for the newness of chimps.

Only after our ancestors branched off from chimpanzees, Lovejoy and his colleagues argue, did chimpanzee arms evolve the right shape for swinging through trees. Chimpanzee arms are also adapted for knuckle-walking, while Ardipithecus didn’t have the right anatomy to lean comfortably on their hands. Chimpanzees also have peculiar adaptations in their feet that make them particularly adept in trees. For example, they’re missing a bone found in monkeys and humans, which helps to stiffen our feet. The lack of this bone makes chimpanzee feet even more flexible in trees, but it also makes them worse at walking on the ground. Ardipithecus had that same foot bone we have. This pattern suggests that chimpanzees lost the bone after their split with our ancestors, becoming even better at tree-climbing.

Chimpanzees do still tell us certain things about our ancestry. Our ancestors had chimp-sized brains. They were hairy like chimps and other apes. And like chimps, they didn’t wear jewelry or play the trumpet.

But then again, humans turn out to be a good stand-in for the ancestors of chimpanzees in some ways–now that Ardipithecus has clambered finally into view.

[Reconstructions: Copyright 2009, J.H. Matternes. Cover: Copyright 2008 T.H. White]

CATEGORIZED UNDER: Evolution, The Tangled Bank

Comments (127)

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  1. Thanks for this excellent write-up, Carl. I’m sure there will be a lot more to discuss, especially given the amount of material being released today! Now if we could only get some more complete material from Sahelanthropus and Orrorin…

  2. NewEnglandBob

    Fascinating. When more information comes, we want your interpretation.

  3. Thanks for the highlight reel, Carl. And what a fine illustration by J.H. Matternes. Mad skillz!

  4. “In fact, a lot of what makes a chimpanzee a chimpanzee evolved after our two lineages split roughly 7 million years ago.”

    Don’t molecular clocks place the divergence more recently? Ardipithecus ramidus still postdates the divergence, but I thought it was likely that Sahelanthropus tchadensis predated it.

    I’m confused by some assertions that, where Ar. ramidus and Pan differ, the last common human-chimpanzee ancestor must have been more like Ar. ramidus. Isn’t it equivocal until we find better material for members of the human-chimpanzee stem group (e.g., Sahelanthropus)?

    Carl: Note the word “roughly.” This 2008 review surveys a lot of earlier studies and gets no more precise than 4 to 8 million years ago.

    As for Saheanthropus, it’s still generally considered to be closer to us than to other living apes, so its age of 6-7 million years would raise some questions about the younger molecular clock estimates for the chimp-human split. But who knows how things may change once someone finds a Sahelanthropus skeleton beyond the skull?

    As for inferring the common ancestor of humans and chimps, it’s not just Ardipithecus that’s being considered here. Monkeys and gibbons, for example, lack a lot of special adaptations for climbing in trees found in chimpanzees. So do living humans. There might be two ways of interpreting this pattern. One is that the common ancestor of chimps and humans evolved to be a very agile tree-climber, and then humans later became ground-walking bipeds that lost that special anatomy. The other is that the common ancestor of chimpanzees and humans never had all that fancy anatomy to begin with. Now we have Ardipithecus, which was clearly a tree climber, but without the chimp’s fancy anatomy–instead, it had a more gibbon or monkey-like anatomy. So the simplest explanation is that chimpanzees got fancy on their own. [Warning: "fancy" may not actually appear in your physical anthropology textbook. "Derived" does just as well. ; ) ]

  5. Chimpanzees do still tell us certain things about our ancestry. Our ancestors had chimp-sized brains. They were hairy like chimps and other apes.

    Carl – How do we know that creatures like Ardipithecus were hairy? Is there any robust information on when the transition to modern hairlessness occurred?

  6. John Grehan

    I have not seen the Science articles yet, but I will be interested to see if they present any evidence that Ardipithecus belonged to a human-chimpanzee clade.

    The skeletal reconstruction indicates that Ardipithecus did not have an African ape type of torus across the glabella.

  7. Arturo

    I don’t know about you, but when I saw that drawing of “Ardi” I thought:
    “THEY FOUND BIGFOOT AT LAST!!” ….. but it lived 4.4 MYA.

  8. “Now we have Ardipithecus, which was clearly a tree climber, but without the chimp’s fancy anatomy–instead, it had a more gibbon or monkey-like anatomy. So the simplest explanation is that chimpanzees got fancy on their own.”

    Do orangutans and gorillas have this tree-climbing fancery?

    Also, aren’t the environments of Pan and Ardipithecus rather different? Couldn’t Pan be adapted to deep rainforest while Ardipithecus was adapted to woodland? (Although I guess some chimpanzees live in woodland as well.)

  9. David B. Benson

    Dave S (9) — The relative hairlessness of H. sapiens is the result of neotony. Neotony produces other characteristics; with enough good fossils the onset of neotony can be established. I don’t know when it occurred, but I suggest it is soley a genus Homo trait and maybe not even all the various (now-extinct) species. My reasoning is that control of fire had to come first.

  10. Carl Buell

    Great article Carl, thanks, and it’s wonderful that Jay Matternes is still turning out magnificent work.

  11. Joey Panto

    Ayn Rand’s voice is channeled from beyond to refute a creationist who thinks Ardipithecus disproves Darwin.

  12. Ross Macfarlane

    Are gorillas (and orangs) missing the same footbone as chimps?

  13. Can someone tell me, if Ardi – or Saleanthropus – and Pan have evolved in two distinct lines for these millions of years, why are humans studying chimps, and not vice versa? Did Pan get sent to the penalty box?

  14. Mark from Cleveland

    For years I have thought it was almost certain that the human linage became basically monogamous very early on. After watching a Bonobo at a zoo for hours that had a baby that was around a month old who could cling to her mothers coat with her four “hands” it seemed to me that the second something like that evolved to the point they could walk they would have had to be monogamous since that same mother would then have a much more difficult time caring for the baby, particularly if she was now in the open walking around. It seems to me monogamy always would have to predate walking.

  15. miko

    Mark: Humans aren’t monogamous (obviously, right?). True monogamy does exist in many animal lineages and has evolved multiple times.

    [Carl: There's a wide range of mating systems in mamals from strict monogamy to serial monogamy to mild polygyny to harems. Our species isn't strictly monogamous, but more to that end of the spectrum than a lot of other species.]

  16. Mark from Cleveland


    We are monogamous enough that the vast majority of our childern can count on the support of 2 parents, and those that can’t ussually still have a support system that extends beyond its mother, and that is all that counts. If mom is walking around and the only practical way to bring her kid with her is to have to tie up the use of at least one of her arms carring the child, or have the child walking with her, she and the child is a significantly more tempting target for a preditor then, say, a chimp or bonobo would be. If that tempting target can rely on a mate to bring food back to where ever she and the child are it is a whole lot less likely one of them ends up as someone elses dinner.

  17. Mark from Cleveland

    PS, in spending several hours watching that bonobo and her child, the child, as far as I could tell, had virtually no impact on her movement, so much so I literally did not even realize she was carrying a kid until at least 15 minutes into watching her do things like collect food (it was feeding time) and clambing back to her perch to eat. A human would kill to be able to all but Velcro her kid to her belly and then go about grocery shopping or climbing a tree. The only time the bonobo child effected the movement of the mom was when she took time to nurse it.

    Give that bonobo kid feet and suddenly it slows his mom down in her ability to gather food and climb back up to her perch because she has this kid that is like a sack of rocks she has to lug around..

  18. ShaunOTD

    Joseph #24
    “why are humans studying chimps, and not vice versa?”

    Who says they aren’t? More seriously though, because our ancestors filled ecological niches that favoured the selection of mutations for larger brain size & greater intelligence, compared with the ancestors of modern chimps. Intelligence is really no different from any of the other traits that differ between us and them.

  19. I’ve linked to your excellent article from Wikipedia’s Ardipithecus article.

  20. Michael Heath

    Here’s a press release by Dr. Lovejoy’s school quoting him. He’s claiming that Ardi is a homind, but that man didn’t evolve from apes.

    I sent an email to Dr. Lovejoy and the contact on this PR release containing the following:

    Regarding your press release here: [see above link], which is titled, “Man Did Not Evolve From Apes Says Leading Anthropologist”.

    How can your press release claim that man did not evolve from apes when in fact we were and still remain in the superfamily, Hominoidea, whose nickname is ‘apes’? I.e., we were and remain apes, as are gorillas, as are chimpanzees. Your own press release defines Ardi as a hominid, which is a family within the super-family of apes. Therefore your own press release contradicts your assertions unless you’re now proposing that hominids should not be classified in the superfamily Hominoidea.

    You have lots of science students, scientists, and others very befuddled.

    The ‘befuddled’ part is based on some comments I read at PZ Myer’s blog.

  21. Sili

    Are big canines the ancestral trait? And if yes, then why did we lose them? I can the see the mechanism for growing them in the first place, but it’s not obvious to me why they’d go away just because they’d been made redundant.

    That missing bone in chimp feet, is that one of Shubin’s “lossa little blobs”? (“One bone, two bones, lossa little blobs, digits”)

    [Carl: The bone is the os peroneum. It's definitely a little blob. Picture here. As for big canines, they were likely favored in our ape ancestors when they were having intense competition between the males. Once that competition lessened, according to this hypothesis, mutations that led to smaller canines in males did not reduce their reproductive success.]

  22. amphiox

    “why are humans studying chimps, and not vice versa?”

    And why are chimps so much better at climbing trees, and not vice versa?

    And it is self-evident that chimps are studying humans. When chimpanzees are documented snatching human infants to kill and eat, how do you think they learned to do that, if not by watching people, studying them, and discovering when and where the opportunities are available? When chimpanzee troops learn to avoid neighboring human villages, how did they learn that, if not by studying humans? When chimpanzees learn to exploit food drops left by researchers, how did they manage that, if not by studying humans and learning the patterns of the places and times?

  23. #30 & #35:

    Thanks for responding! I accept intelligence as one of many possible traits humans could have developed as a result of mutations. I also know many species adapt to humans. although the adaptation #35 attributes is very recent in the genetic time line. I guess I’m asking what compelled Ardi or some ancestor to push out from the jungle, and could it have been war with Pan? I know these questions rehash other work, but this Ardi article prompts wild speculation.

    I’ve also thought of violence in humans as social, not innate, because chimps are also sociable and deploy violence for certain social ends. But, now, in the wake of Ardi – and Carl’s essay – if both humans and Pan evolved in parallel lines with possible interactions, I don’t know what to make of that argument. I’m sorry for the naivete. I’m a natural science knuckle-dragger, but not, by God, a creationist! Publications like this do cause thought-provoking speculation, so even science buffs shouldn’t be so snarky.

  24. The facts are awesome. They are not only just inconsistent with a chimpanzee like common ancestor for a human-chimp clade, but more to the point, they in fact flatly deny any possibility of such a clade in the first place. One would have to completely discredit the science of paleontology in order to accommodate the Ardi data with a human-chimp grouping rather than with the alternative human-pongid (containing African apes and orangutans) sister grouping (1). In blatant violation of the premises of the science of paleontology, the human-chimp grouping requires one to favor a scheme that requires more than a dozen convergent events at the expanse of a scheme that requires none. Furthermore, one must also favor a scheme that has no identifiable ancestors among the numerous middle Miocene apes versus one that has them perfectly. All these absurd insults to paleontology would have been tolerable if the sole evidence for the human-chimp grouping, the interpretation of sequence similarity by the molecular clock hypothesis, is actually based on solid contradiction-free science. But alas, this is anything but the case. The molecular clock hypothesis has so many contradictions (hardly a secret) that it would be a dead or falsified theory in any other branch of science.

    1. Huang, S. Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers . Available from Nature Precedings (2009)

  25. Sven DiMilo

    Why don’t anthropologists just do cladistics like everybody else? Code the data and see what the algorithms suggest!

  26. As a Kent State Graduate Student, I can tell you that this announcement has been huge. Thanks for mentioning us, Carl!

    @Michael Heath

    I’m interested to hear his response, but I’m guessing Lovejoy did not write that release. In fact, I first heard about this finding on our website under the title “Man Did Not Evolve From Apes Says Leading Anthropologist”

  27. David B. Benson

    Joseph Steinberg (40) — I know of no evidence for group violence or war before agriculture. There is evidence of murder before that, see

    R. Dale Guthrie
    The Meaning of Paleolithic Art
    Univ. Chicago Press

  28. Zachary

    That’s a tautology though. Until humanity organized itself into large groups, there were no violent clashes between large groupings of humans.

  29. Drosera

    Shi Huang @41,

    First paragraph from his reference:

    “Interpretations of molecular data by the modern evolution theory are often sharply inconsistent
    with paleontological results. This is to be expected since the theory is only true for microevolution and yet fossil records are mostly about macroevolution.”

    Creationist or other kind of crackpot?

  30. johnk

    Is war innate?
    Is violence innate?

    As I see it, these may be impossible questions to answer. A wide range of human behaviors, most notably language, likely evolved by-way-of simultaneous biological and cultural evolution, one change depending on the other. At the endpoint, it’s impossible to say the trait is “biological” or “cultural”.

  31. I’d like to see a more detailed description of how one can conclude that chimp features evolved from a LCA that was more like Ardi than the other way around. For example, chimps knuckle-walk and Ardi didn’t. But gorillas also knuckle-walk. Another: chimps may be better aborealists than Ardi, but orangutans are more aboreal than chimps. I just think this could use some more fleshing out to us nonexperts.

    Somewhat tangential, but I think the idea that pre-agricultural hunter-gatherers were nonviolent towards outgroups to be wishful thinking. First of all, historical era hunter-gatherers were quite violent to other hunter-gatherers, and it seems unlikely that such an important trait was an agricultural invention borrowed by hunter-gatherers. More fundamentally, violence would effectively decide resource disputes. Except for rare periods of decimated populations or newly-discovered continents, resource constraints were a matter of life and death.

  32. David B. Benson

    Zachary (50) — Certainly not. Presumably early hunter-gathers lived, as now, in clans of about 20–40 as part of a “company” which met annually or semi-annually. Each company consisted of around 7–12 clans. But no evidence of interclan warefare much less intercompany warefare.

    Brian Schmidt (53) — I repeat, there is no evidence of group clashes, just murders. Guthrie’s book makes it clear that on several occasions in the evidence, groups murdered an individual; impossible to determine whether in or out group. I doubt that group clashes occurred very often as neither side could afford to take casualties. Hunting was too dangerous to suffer even further losess and there is evidence of prey turning on hunters as well as attacks by lions.

    Unplanned encounters between even clans must have been quite rare. On the Mammoth Steppe it seems that each clan would need an area about 100 kilmeters on a side; rather low population density.

  33. Drosera@51:

    The contradiction/discordance between the fossil record and molecular interpretation by the modern evolution theory has only two POSSIBLE and mutually exclusive explanations. 1. The fossil record is incomplete or bad. 2. The modern evolution theory is incomplete or bad. Now to say the fossil record is incomplete or bad is self defeating for the theory because the theory’s claim to ligitimacy is because it is (at least partly) consistent with the fossil record. That is to say that time of divergence as inferred from fossil records is roughly correlated with that infered by the molecualar clock or the mordern evolution theory (neutral theory plus Darwinism). So if the fossil records is incomplete or bad, you would not have any evidence for the theory in the first place. To blame the fossil record is for the theory to commit suicide. Therefore, this leaves logically the only other possible explaination the correct one. Better still, I have indeed come up with a more complete theory that grants the fossil record to be mostly complete and good and is completely in harmony with it. From the perspective of a disinterested truth seeker, the only criterion for truth is internal coherence without a single contradiction. Name calling is not science but religion. If you care about truth at all, try come up with a jsut single contradiction to my thoery and I will shut up for good. Or come with a single reason as to why anysane human being should be satisfied with a contradiction laden theory at the expanse of a contradiction-free one.

  34. Carl, Thanks for your openness in allowing the airing of a not-yet-mainstraim SCIENTIFIC view. Ironically, a magazine named SCIENCE could be so afraid of a single person’s view to allow it appear on its website. Totally understanble though from a human nature perspective. No one wants to be made a fool. But truth dose not care. I am sure would be delighted to be more on the right track (my view is first aired at its website) than its major competitor. Perhaps it already knew better than Science in denying the possibility of the huge Ardi story in its publications (my speculation).

    Below are some specific discussions on the flagship paper by White et al. Tim D. White, Berhane Asfaw, Yonas Beyene, Yohannes Haile-Selassie, C. Owen Lovejoy, Gen Suwa, and Giday WoldeGabriel (2 October 2009) Ardipithecus ramidus and the Paleobiology of Early Hominids. Science 326: 75-86.

    White et al: “we have learned that Ar. ramidus was a denizen of woodland with small patches of forest, and probably was more omnivorous than chimpanzees (ripe fruit specialists) and likely fed both in trees and on the ground.”

    Middle Miocene apes are already divided into two groups with one living in woodlands. As Stringer and Andrews write in their 2005 book: “Group one has robust jaws, enlarged molar teeth with thick enamel, and some buttressing of the face to accommodate chewing stresses caused by the large teeth and a hard fruit diet. They lived in seasonal woodland to open forest environments and were adapted to some extent to ground living.” They, I suggest, were the ancestors of humans and later developed bipedalism. To some authors, walking on two legs may arose more likely from a terrestrial form of locomotion on all fours (with on twos occasionally) rather than arboreal climbing and suspension. Ardi supports this perfectly. “The other group inhabited wetter, less seasonal forests and lived in trees employing a form of locomotion that involves some degree of suspension from overhead branches. Their jaws were more lightly built and their teeth not enlarged, so that their diet must have been soft fruits.” They are obviously the best candidates for the ancestors of pongids.

    White et al : “Ar. ramidus thus indicates that the last common ancestors of humans and African apes were not chimpanzee-like.”

    Indeed, Rama/siva is not chimpanzee like but Dryopithecus is. To accommodate the Ardi data with the human-chimp grouping would require the absurd notion that none of the two major groups of Miocene apes could qualify as ancestors to the MRCA of the human-chimp clade. One (rama/siva) is too human like (no suspension) and the other (dryopithecus) is too chimp/gorilla/pongo like (yes suspension). Any sane human not biased by the molecular clock based (mis)grouping of human and chimp could see the plain obvious from the fossil record that human and chimpanzee already have separate ape ancestors during early/middle Miocene.

    White et al: “Overall, Ar. ramidus demonstrates that the last common ancestors of humans and African apes were morphologically far more primitive than anticipated, exhibiting numerous characters reminiscent of Middle and Early Miocene hominoids.”

    Indeed. They have said it better than I can. They just did not make the most logical and straightforward deduction of what they said. That deduction is simply that Ardi was a descendant of one of the two major groups of Miocene apes, while African apes were descended from the other group. The real last common ancestors of humans and African apes lived in Early rather than Late Miocene.

    White et al: “Despite the demise of Ramapithecus as a putative hominid ancestor, at least one Eurasian Miocene ape, Ouranopithecus, has been suggested as being phyletically related to later African hominids (57), whereas another, Dryopithecus, is often considered an alternative sister taxon of the hominid and African ape clade (58). Ardipithecus effectively falsifies both hypotheses.”

    Yes, indeed. But that does not help these authors. What Miocene ancestor apes can they now offer us? None whatsoever. They are completely quiet on this key question. On the other hand, Ardi did not falsify but rather strongly supports the hypothesis that Dryopithecus was the ancestor of a pongid clade containing African apes and orangutans.

    White et al: “The new perspective that Ar. ramidus offers on hominoid postcranial evolution strongly suggests that Dryopithecus acquired forelimb adaptations to suspensory behaviors independently from African apes. …. An additional implication of Ar. ramidus stems from its demonstration that remarkable functional and structural similarities in the postcrania of Pongo and the African apes have evolved in parallel, as have those of Pan and Gorilla. Until now, a myriad of characters shared among the extant African apes were presumed to have been present also in ancestral hominids (because they were presumed to have been the ancestral state) (60). However, it now appears that many of these putative shared primitive characteristics have evolved independently.”

    Indeed, too many to be true. Let us here enumerate the absurdly high number of convergent events that must occur in order to accommodate Ardi with the human-chimp grouping, in contrast to zero such events for the human-pongid grouping. First, there are 4 independent inventions of suspensory behaviors in Dryopithecus, orangutan, gorilla, and chimpanzee. Note that suspension behaviors is a qualitative or macroevolutionary or epigenetic invention rather than quantitative or microevo. Life history as well as logical reasoning shows that quantitative features or microevolution are more likely to undergo convergent evolution, such as enamel thickness, body size or height. Second, other qualitative features shared by African apes that are unlikely to be convergent but must be required to be: 2 inventions of knuckle walking, foot structures lost twice (White et al: “Many of the foot’s primary adaptations to fulcrumation are probable retentions from the gorilla/chimpanzee/human last common ancestor (GLCA), but these have been eliminated in apes, presumably for vertical climbing.”), 2 inventions of rigid wrists, and 2 inventions of African ape hip structures. There are likely more but this incomplete list (a total of 14 convergent events and all for qualitative features) is far more than enough to show the extreme absurdity of the human-chimp grouping, especially in comparison with the conversion-free grouping of humans and pongids. As Pelbeam said: “They are hard to believe.” And well, that is because they are fiction.

    White et al: “In effect, there is now no a priori reason to presume that human-chimpanzee split times are especially recent, and the fossil evidence is now fully compatible with older chimpanzee-human divergence dates [7 to 10 Ma (12, 69)] than those currently in vogue (70).”

    This fossil date cannot possibly be reconciled with the molecular clock dating which typically is 5 Ma. This is sufficient to falsify the validity of the molecular clock and in turn its deductions, which include the human-chimpanzee grouping. The authors forgot that if they can freely allow themselves to doubt the molecular clock dating, they should be consistent and complete, which means “in effect, there is now no a priori reason to presume that there is a human-chimpanzee clade to the exclusion of other great apes.”

  35. Drosera

    Shi Huang @56 said,

    “Any sane human not biased by the molecular clock based (mis)grouping of human and chimp could see the plain obvious from the fossil record that human and chimpanzee already have separate ape ancestors during early/middle Miocene.”

    I see what your problem is, Shi Huang. You conflate molecular clock estimates with molecular phylogeny. Molecular phylogeny methods don’t require the molecular clock hypothesis. Maybe you should read up on them.

    At least you’re not a creationist, I’ll take that back.

  36. Torbjörn Larsson, OM

    This is really awesome!

    As for Saheanthropus, it’s still generally considered to be closer to us than to other living apes,

    In fact, IIRC browsing the Science articles, they place Sahelanthropus (~ 6 Ma) and Orrorin (~ 6 Ma) after the split and among the lines over A. kadabba (5.8 – 5.2 Ma) to A. ramidus (4.4 Ma).

    Not only that, but IIRC some paper hypothesized that Sahelanthropus and Orrorin actually belonged to Ardipithecus. Well, at least it’s the most parsimonious species and/or lineage grouping.

    I’d like to see a more detailed description of how one can conclude that chimp features evolved from a LCA that was more like Ardi than the other way around. For example, chimps knuckle-walk and Ardi didn’t. But gorillas also knuckle-walk.

    First, the papers themselves point out the apelike features of the hands (non knuckle-walking) and back (6 lumbars, curved as in apes and humans (4-5 lumbars), not straight as a chimpanzee), as well as the lower femur (strong hind muscles for climbing) and foot (the small bone that chimpanzee’s lack).

    Second, just a few weeks back there was a paper that gathered data on a lot of ape species, tested which features were correlated with knuckle-walking (most that have been so associated weren’t actually correlated) and concluded that knuckle-walking in chimpanzee and gorilla evolved independently. It’s easy enough to google.

    Among other things they employ very different mechanics. IIRC, chimpanzee hands flexes during knuckle-walk and are protected against over-flexing by locking protrusions. Gorilla hands are straight during knuckle-walk, using the load bearing “pillar mode” of elephant legs.

    Also, while they split earlier, don’t orangutans employ knuckle-walk too? I’ll bet the mechanism is yet different.

  37. Torbjörn Larsson, OM

    some paper hypothesized that Sahelanthropus and Orrorin actually belonged to Ardipithecus

    I should note that it was based on characters. Sahelanthropus teeth are close to A. kadabba by way of longer canines, but different from Pan by way of thickness of enamel. Similarly Orrorin leg bone groups with the australopithecines/ardipithecines.

  38. Torbjörn Larsson, OM

    D’oh! “lower femur” – lower pelvis.

  39. Why is the discussion always between chimps and humans? Orangs are more intelligent than chimps and we share a type C viral gene with them that other apes don’t have. How do they fit in the ancestor picture?

  40. Drosera

    Please don’t call orangutans ‘orangs’. Orang means ‘man’ or ‘person’, as you will notice when you travel to Sumatra or Borneo and ask the local people where you can see ‘orangs’.

  41. Drosera@58: “I see what your problem is, Shi Huang. You conflate molecular clock estimates with molecular phylogeny. Molecular phylogeny methods don’t require the molecular clock hypothesis. Maybe you should read up on them.”

    You seem to be saying that even if the molecular clock hypothesis is false, the existing molecular phylogeny methods would still produce the correct phylogeny. This position of yours is in fact commonly shared by many but is incorrect. There are several different ways to refute it.

    1. Let us here be clear and on the same page about what the molecular clock hypothesis is. The hypothesis is originally that (1) different species have ROUGHLY similar mutation rates per year; (2) a deduction of (1) is that time of divergence roughly correlates with genetic distance. This clock hypothesis in turn provoked the neutral theory and is by far the best ‘evidence’ for the neutral theory (by Kimura’s own admission), the only theory of molecular evolution.

    There is a common misconception about what it means when a molecular clock holds or does not hold. When a typical evolutionist say that molecular clock does not hold in a specific case, he is saying it based on some statistical test of relative rate. In such statistical tests, very small rate variations are interpreted to mean that the molecular clock does not hold (never mind that such test is based on false assumptions about macroevolution being no different from microevolution). But this in no way nullified any of the original two meanings of the molecular clock hypothesis. The original concept is a rough clock that allows some, say 20%, variation in rate. But in the practical uses in building phylogeny by an evolutionist, the clock can only allow a very small, say 5%, variation. So when a method is said not to require the molecular clock, it means a clock with only very small variation in rate. But the original concept of the clock, ie, genetic distance correlates with time of divergence, is absolutely a given for any existing methods. Indeed, these methods require a much stronger version of the clock hypothesis that genetic distance ALWAYS correlates with time of divergence.

    Here is a simple way of nullifying the existing methods and phylogenies produced by these methods. These methods require that the original concept of the clock to be 100% true (i.e., genetic distance ALWAYS correlates with time of divergence). But it is not (evidence for this is too numerous to mention). Thus, these methods cannot produce 100% correct phylogenies. So, the existing ape-human phylogeny has a chance to be wrong (And indeed it is, as now shown by both the Ardi data and the MGD based molecular phylogeny). But our standard of science is that we cannot and should not allow a phylogeny to have any chance to be untrue, no matter how small a chance.

    2. Any theory or method that can give the correct phylogeny should and must give the correct dating. This is because nature is a coherent whole rather than disconnected. A theory that only explains less than 100% of the domain of nature for which it is relevant is by definition incomplete or false. Now, before we have a theory that do account for 100%, it is human nature to allow ourselves a self-serving/deceiving position by saying that nature/biology is so complicated that we do not expect a biological theory to account for everything. But now that we have the MGD hypothesis that actually claims for the first time ever among all existing evolution theories to have not a single exception, we can no longer defend the modern evolution theory by saying that it is the best we humans can do. The MGD hypothesis produces both the correct phylogeny as well as correct dating that are in complete concordance with the fossil record.

    3. As far as I know, the neutral theory is the only one we got for explaining molecular evolution or is the foundation for molecular phylogeny. By saying that the molecular clock hypothesis and in turn the neutral theory is dispensable for building molecular phylogeny, you have depleted any theoretical foundation for it. That is logically unsound. Indeed, the original molecular clock hypothesis as I defined above is absolutely essential for building molecular phylogeny by the existing methods.

    4. If the assumptions are false, the methods are automatically false. The assumptions of the existing molecular phylogeny methods that are false and never seriously thought over or debated include the following. 1). No maximum cap on sequence divergence no matter how long evolution has been going on. Two humans can differ in sequence to the same extent as two bacteria given long enough time. 2). all genes or sequences that can be identified as orthologs are equally informative in phylogeny. Fast evolving genes that have reached maximum divergence are not distinguished from slow evolving ones. And evidence for the existence of these two classes of genes are ignored or overlooked. The failure to use only informative genes (ie, slow evolving) in all existing statistical methods effectively nullifies these methods, accounting for why their results are often false or inconsistent with the fossil record. 3) The original molecular clock hypothesis says that genetic distance sometimes correlates with time of divergence (because exceptions are common). But the assumption in existing phylogeny methods is that genetic distance always correlates with time of divergence.

    Statistical methods can only be as good as the assumptions underlying these methods. When all the major assumptions are false as explained above, the methods are automatically worthless regardless how many sophisticated math they may contain or in turn how scientific they may seem. The same also applies to cladistics used by morphologists.

    5. The molecular clock hypothesis and the neutral theory should never have been invented in the first place for macroevolution because it is a completely incorrect interpretation of the genetic equidistance result of Margoliash in 1963. The MGD hypothesis is the only explanation in 46 years for the overlap feature of the equidistance result.

    For those experts interested in an opposition party’s view on the existing molecular evolution methods, below are some specific rebuttal of the common methods described by two leading experts in their book, Nei and Kumar, (2000) Molecular evolution and phylogenetics.
    (also see Yang, (2006) Computational molecular evolution.)

    Nei/Kumar: “In phylogenetic inference, a certain optimization principle such as the maximum likelihood or the minimum evolution principle is often used for choosing the most likely topology. The theoretical basis of this procedure is not well understood.. At present, the methodology of phylogenetic reconstruction is quite controversial. ”

    So, in other words, we have no real understanding of why the existing methods should work. No theory exists that predicts that these methods should give the right phylogeny. In contrast, the new understanding (maximum cap on genetic distance and the distinction between fast and slow evolving genes, which are not at all taken into account by the existing methods) necessarily predicts that the existing methods should not be able to produce a phylogeny of all life forms that are 100% correct or of even a limited set of life forms with 100% certainty. Logic demands that if a phylogeny is not 100% certain, it is worthless. 99% certain can still be 100% wrong.

    Nei/Kumar: “Molecular phylogenetics is still a young scientific discipline, and it is important to realize that every statistical method has some strengths and some weakness, and none of the methods is almighty. One cannot reject a method simply because it did not work in a particular study or a particular computer simulation.”

    This is typical self-serving/deceiving. No one granted the evolutionists such a low standard of science except themselves. A method that has weakness or contradiction/exception is effectively no different from a false method, by definition. Thus all existing methods are false and should be rejected. A method that is 100% free of contradiction/exception is what we should aim for. I have now offered the slow clock method and its theoretical foundation the MGD hypothesis as the best candidate for a completely correct method of molecular phylogeny. The difference between Truth and falsehood is not quantitative but qualitative. When a method/theory has been found to have one contradiction, there is no reason whatsoever why a second one cannot be found later, in turn 3rd, in turn 4th, …and all the way to infinity. This is why a true theory/method should not have/allow a single contradiction within its domain of relevance.

    Nei/Kumar: “Unlike the case in physics, the predictive power of a model in biology is quite low. It seems to us that if the prediction (e.g., a phylogenetic tree reconstructed) of a model is correct 80% of the cases, it is a good model at least at the present time.”

    This low standard is nonscientific and meaningless. So, the present human-ape phylogeny may or may not belong to the 80% of cases where the method happens to give the correct phylogeny. In other words, it could be completely false. If it is not 100% certain, which it is not by the own admission of the molecular evolutionists, why should any palentologists try to interpret the fossil record assuming the existing human-ape molecular phylogeny to be 100% certain. Fossil record should be interpreted based on its own methodology and principle if it wants be viewed as a science at all. If its results contradict a molecular phylogeny, so be it especially when that phylogeny is only 80% certain. If we trust nature is a coherent whole, which by all account it is, we should have confidence that when both fossils and molecules are interpreted by the right methods and theory with 100% certainty, they should be found to be completely in harmony with each other. Indeed, the interpretation of DNA data by the MGD hypothesis and the slow clock method is in complete concordance with the hominoid fossil record when such record is interpreted by the standard methodology/premises of paleontology, which has proven to be largely correct since its interpretation has produced the initial evidence for the molecular approach in the first place. In short, fossil record should be used as independent evidence for molecular phylogeny, which was the case in the 1960s when the two branches first met. To be independent and scientific, fossils must be interpreted in a blind fashion without any concern about molecules.

    I am astonished to read as reported in Science that someone could say that the Ardi data would be boring if it turned out to support our expectations about the human-chimp ancestor. If a factual observation is uncovered that does not support the expectation/prediction of my theory, I would not call that fact interesting. I would be extremely upset and would just say the inevitable that my theory is wrong. If a factual observation does support the expectation/prediction of my theory, I would be extremely delighted and would call it extremely exciting rather than boring. The typical attitude of evolutionists towards unexpected new facts is extremely disturbing and non-scientific and makes a joke of testing their theory. Their theory stands no matter what the evidence say. To them, a new fact can only be either interesting or boring but can never be falsifying. But in truth, a new fact can only be either supporting or falsifying.

    Nei/Kumar: “What is then the theoretical basis of the LS (least square) method for estimating the correct topology? At this moment, we do not have a good answer to this question. We can simply argue that a topology of which the estimated branch lengths are closest to the observed ones should be a good topology.”

    The LS method is one of the common methods that do not require the narrowly defined molecular clock. But it is still based on the concept of the general molecular clock hypothesis that genetic distance is correlated with time of divergence. While no one can justify why the method should work (never mind how reckless a behavior on the part of molecular evolutionists in using it in the first place in the absence of justification), it is easy for me to justify why it should never work. The proven reality of maximum genetic distance and of the difference between slow and fast evolving genes effectively nullifies all existing methods of molecular phylogeny. Contrary to what most believe, a topology of which the estimated branch lengths are closest to the observed ones should NOT necessarily be a good topology. The observed DNA distance between human and chimp is much shorter than between human and orangutan, but the true topology shows human to be equidistant to chimp and orangutan. The observed distance between human and orangutan is similar to that between chimp and orangutan (when no distinction made between slow and fast evolving genes), but human is more distant to orangutan than chimp is in slow evolving genes. The existing theory/methods have no idea about this fact but the MGD does.

    Sorry this is a little too long for this forum but I thougt it is heathy for sciene to have a meaningful debate, especially when the existing opposition to the modern evolution theory knows very little science and cares only about God rather than a true law of evolution.

  42. Torbjörn Larsson: Orangutans walk on their fists (the proximal phalanges), not on their knuckles proper, so presumably the behavior is analogous rather than homologous.

    Drosera: “Orang” means “person” in Bahasa Indonesia, but in English it means “orangutan”.

  43. Drosera

    Shi Huang,

    You say “Logic demands that if a phylogeny is not 100% certain, it is worthless. 99% certain can still be 100% wrong.”

    If you don’t understand that a phylogeny, which is an attempted reconstruction of a long series of historical contingencies, can never be 100% certain, then you don’t understand the very basics of the discipline. You also seem to think that fossils allow for a perfect reconstruction of the underlying phylogeny, and that with 100% certainty, which should be good news to paleontologists. If only it were true.

    I will not attempt to point out all the misconceptions in your comment, but instead refer you to some recent textbooks that should be an educational experience for you:

    Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme. 2009. The Phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press.

    Guillome Lecointre. 2007. The tree of life: a phylogenetic classification. Belknap Press of Harvard University Press

    Joseph Felsenstein. 2003. Inferring phylogenies. Sinauer Asssociates.

  44. Drosera

    If you don’t understand that a phylogeny

    should be:

    If you don’t understand that an inferred phylogeny

  45. If nothing in phylogeny is 100% certain, then nothing can be falsified by facts. That is not science but phylosophy or religion. It is time to turn evolution study from a branch of phylosophy or religion into science. By the way I do claim that the hominoid phylogeny produced by my slow clock method is 100% certain. This makes it very easy to falsify it, just go look for one single contradiction.

    You say “which is an attempted reconstruction of a long series of historical contingencies.”
    This is an assumption and grants the Darwian theory of random accidents to be true. But we dont know that to be true. Perhaps it is not at all accidents for major events. Before we know that for sure, to assume we know one way or the other is simply non-scientific. We dont know if God exists or not. To assume we know one way or another is not science but religion. Atheism is just another branch of religion. At this point, a true scientist can only hold the postion of a disinterested truth seeker and let the facts and laws speak for themselves. If no God explains the facts the best, then no God it is. If God is absolutely essential for a contradiction free law of evolution, then God it is. The ultimate criterion for truth is not God or no God but is internal coherence of the whole story without a single contradiction.

    To have a meaningful debate in science, it is important to get to specifics. To generally label my view to be misconceptions without being specific does not help your case. For a start, try convince people that the existing methods does not absoluately require the molecular clock concept that genetic distance always correlate with time of divergence. On the other hand, it is totally understandable for you to consider my view false, just like the Sun-centered theory is viewed false by all except one 500 hundred years ago.

  46. Drosera

    Shi Huang,

    You don’t have a theory, you just have an obscure piece of numerology that you call the slow clock method. It is not science.

    From your last comment it is more than obvious that you have no idea what science is about. Are you familiar with the term ‘methodological naturalism’?

    Enough said. I wish you good luck with developing your theory of miraculous interventions. And congratulations with your top score on John Baez’s Crackpot Index!

  47. I have always felt myself to be too normal or average in everything I do to be a genius and I admire those crazy genius in art and science. If a scientist has never been called crazy/insane/crackpot in his life, he could be a very good scientist but never the very top. Your comment immediately reminds me this quote: “Your theory is crazy, but it’s not crazy enough to be true.” Thank you for giving me a top score on the crackpot index. I take it to mean that my theory is crazy enough.

    Of course I am familiar with ‘methodological naturalism’. But why should any sane person abide by it is beyond me. It rules out any possibility of resolving the ultimate question of mankind by the scientific method. That is a depressing prospect for science and humanity. I refuse to accept that, especially when that is simply a man made rule based more on fighting religion than for the sake and love of truth/science.

    My theory mentions no God. Its unmatched value is that it explains facts that no other theories can. Just to give one example. Try explain the overlap feature of the genetic equidistance result of Margoliash in 1963 with whatever theory you know. ‘Methodological naturalism’ is irrelevant if it does not help us solve puzzles. The genetic equidistance result is the number one puzzle in molecular evolution that has remained unsolved for 46 years until now by my crazy theory. Until you or your team of Darwinists have something sensible to say about this puzzle to compete with my theory, it is time for you to leave the court.

  48. Drosera

    I had a look at your article “The Genetic Equidistance Result of Molecular Evolution is Independent of Mutation Rates.”

    The extent of your ignorance is easily demonstrated by the following quote from your article:

    “The molecular distance between two different fungi can be just as great as that between fungi and humans, which is completely unexpected from Neo-Darwinism and would indeed be shocking to anyone with a Neo-Darwinian mindset.”

    For a ‘Neo-Darwinist’ this is not ‘completely unexpected’ or ‘shocking’ in the least. It just shows that you know nothing about fungal diversity.

    You go on to say: “Such exceptions are obviously inconvenient to the widely publicized theory [of Evolution] and hence rarely made known outside the small circle of molecular evolution specialists.”

    The conspiracy assumption is perhaps the key symptom for crackpottery.

    As for your ‘inexplicable’ equidistance result, this is just a saturation effect of random mutations. Think about it like this. Suppose you have three tables. On each table there are 600 dice, all showing sixes. Now, on tabel one you randomly select one of the dice every second, you roll it and put it back without changing the result. On table two you do the same, but once every five seconds. On table three you also do the same, but once every ten seconds. In this way you have a primitive model of an evolving gene in three different lineages with different mutation rates. The essential thing that you should try to understand is the following: if you continue this process long enough, the number of differences between the three sets of dice will be roughly equal. In other words, on each table there will be approximately 100 ones, 100 twos, 100 threes, etc. So in the end the sets of dice become equidistant to their ancestors and thus to each other, in spite of different mutation rates.

    You write in the article: “New ideas are needed to explain the genetic equidistance result that must grant different mutation rates to different species and must be independently testable.”

    No, it is just basic probability theory. You see, there is really no need for an evil conspiracy of Neo-Darwinists to explain why people are not impressed by your papers.

  49. Drosera@78

    You obviously know little about the history of the molecular evolution field to appreciate how shocking the molecular data was 46 years ago to NeoDarwinists. Here I show it to you with the own words of NeoDarwinists who was around at that time.

    Leigh Van Valen, 1974. J. Mol. Evo. 3:89-101. “This is especially true for the most remarkable result in molecular evolution, the approximately constant evolutionary rate of homologous proteins.” Note here that Van Valen misrepresented the equidistance result by the constant mutation rate interpretation. The real ‘most remarkable result’ here is the equidistance result rather than its tautological interpretation the constant mutation rate. The quote here is meant to illustrate that I am not the first to call the equidistance result the most remarkable.

    Nei and Sudhir Kumar, 2000, Molecular evolution and phylogenetics, page 188,
    “The constant rate of evolution was unthinkable for classical evolutionists, who had studied the evolution of morphological characters.” Pay attention to the word ‘unthinkable’.

    King JL, Jukes TH: Non-Darwinian evolution. Science 1964, 164:788-798. Just for what sake these authors would call molecular evolution non-darwinian (in the title of their article) if it is not completely unexpected from Darwinism?

    I never used the word conspiracy. You give it to me in order to mold me into a stereotype of crackpot. More likely it is a combination of human nature, carelessness, stupidity, etc that culminated in the messy situation we have today. Whatever the reason, it is simply a fact that 99.9% of biologists (based on my rough survey) have no idea that there is actually a most remarkable result in molecular evolution, let alone the equidistance result. I myself belong to that group just a few years ago and re-discovered the result independently. It shocked me.

    From the beginning, the equidistance result was carelessly interpreted by a tautology, the constant mutation rate. Your interpretation is a nice try for the fact that it is not in line with the mainstream. Welcome to the club of crackpot! But unfortunately you are not crazy enough. Try understand the equidistance result fully before explaining it. Here is the full story of equidistance. For a hypothetical protein conserved in say human, frog, fish and yeast, we have first the numerical feature of the result. Thus, human and frog are equidistant to fish with say 20% non-identity. And further, human, frog, and fish are equidistant to yeast with say 50% non-identity. Next, we have the overlap feature. Thus, the residue positions differing between frog and fish are mostly also different between human and fish. And, the residue position differing between human and yeast are mostly also different between fish and yeast or between frog and yeast. Now, the molecular clock idea explained the numerical feature but not the overlap feature. Your job now is to explain both features with whatever crackpot theory you can come up with (you obviously have not done that in your last comment). A crackpot theory is at least better than no theory. And no theory (or more accurately no correct theory) for the equidistance result is the situation I faced when I came up with the MGD hypothesis.

    I could care less if the mainstream today are not impressed by my papers. It took 100 years for the heliocentric theory to start impress people. No conspiracy needs to be invoked. Pure human nature. When truth collides with self interest, self interest takes priority for most people. as simple as that.

  50. Drosera

    “Just for what sake these authors would call molecular evolution non-darwinian (in the title of their article) if it is not completely unexpected from Darwinism?”

    For the simple reason that certain mutations do not influence fitness; they are neutral. That has to do with the specific details of the heriditary mechanism, which were of course unknown to Darwin. This is not the same thing as saying that it was unexpected. I am sure these authors would not say that all molecular evolution is non-darwinian. That would really be completely unexpected.

    “I never used the word conspiracy.”

    You clearly implied it. Read again what you wrote (“Such exceptions are obviously inconvenient to the widely publicized theory and hence rarely made known outside the small circle of molecular evolution specialists.”) I find it typical that you think you can accuse some of the most brilliant people on this planet of carelessness and stupidity.

    My interpretation, which contaoins nothing new, is entirely in line with the mainstream, since it is a well-known phenomenon that is a consequence of basic probability theory (google the words phylogeny saturation). Your ‘theory’ only seems to work to you because you compare very distantly related organisms, where you can expect the saturation effect even in slowly evolving genes. For more closely related organisms the equidistant result could be due to a molecular clock. It is not either or (The real situation is of course further complicated by the fact that not all mutations are neutral.) It is just another sign of the crackpot that he will not correct his mistakes even after these have been explained to him. Why am I not surprised?

    You say: ” It took 100 years for the heliocentric theory to start impress people.”

    “40 points for comparing yourself to Galileo, suggesting that a modern-day Inquisition is hard at work on your case, and so on.” [from John Baez's Crackpot Index]

  51. The fact that the overlap feature of the equidistance result was overlooked for 46 years suggests what? The exact opposite of carelessness and stupidity?

    Your interpretation is completely new because Margoliash interpreted his equidistance result by assuming a constant mutation rate and never said a word about saturation. And his interpretation is the mainstream view. Whereas you assumed different mutation rate and invoked saturation (cite me one paper where the result is interpreted in your way and I would be shocked). Plus you did not explain the overlap feature. Probability theory predicts few overlap. Now go back to my post and try come up with a real explanation (you dice analogy is bad and you should just deal with real life cases, like cytochrome c in human/fish/frog/yeast).

    Do you think there is any chance for the existing Darwinian theory to be completely wrong for macroevo while being true for microevo? If no, how come not a single contradiction for micro while numerous ones for macroevo? If yes, the person who would come up with a replacement would automatically qualify as a crackpot, by your or Baez’s definition. Dont you know that there is no real difference between a genius and a crackpot to a non-informed person like you. Both have non-mainstream and seemingly crazy views. The only difference is that the genius is proven correct some years later while the crackpot wrong. Science would not be self-correcting and progressing without these crackpots. Granted that only 1 out of a million or more crackpots would turn out to be for real. But if everyone is so fearful of being labelled crackpot by people like you/Baez, we would never see scientific revolutions again. There is no reason why such revolutions should see its last 150 years ago.

    But I dont mind to have people like you to safeguard the existing paradigm. I dont answer to you but to truth. Truth always originates from a single person. And that person’s standard for truth is not by consensus and he could not care less what people like you may think. That standard is simply not a single contradiction. Anyone who views a contradiction laden theory correct is dumb and worse than a crackpot, because such a theory is by definition false. Until I hear an evolutionist claim no contradiction for the modern evolution theory, which I have not and no one has, that theory is incomplete or false by their own twisted way of admission.

    So here is an advice to you. Instead of using the stupid and meaningless Baez’s index (which just shows how low a competency level you are at), try the real thing and pick out a single contradiction to my theory to prove to the world including me I am the biggest crackpot. It is pathetic that a person who has no trouble with a theory that no one dares to claim no contradiction and hence can never be proven true has no shame of freely calling others crackpots. If a crackpot is someone who views falsehood as truth, you are the perfect one by definition.

  52. Drosera: “You clearly implied it. Read again what you wrote (”Such exceptions are obviously inconvenient to the widely publicized theory and hence rarely made known outside the small circle of molecular evolution specialists.”) I find it typical that you think you can accuse some of the most brilliant people on this planet of carelessness and stupidity.”

    What I wrote does not necessarily imply conspiracy. You are overzealous to mold me into a stereotype. What I wrote described a factual reality perfectly explainable by human nature alone. It is a reality that there are inconvenient exceptions to the Darwin theory. It is also a reality that evolutionists do not talk about or publicize exceptions. In Jerry Conye’s or Richard Dawkins’ latest books, do you see s a single exception to the theory mentioned? I did not. Furthermore the reality of human nature is that we do not like to contradict ourselves. If we want to sell a story, we don’t normally undercut it by revealing its weakness. The motto of the Western society is not guilty until proven. We dont offer evidence against our own story. With all these reality, only a logically impaired overzealous person could read conspiracy from what I wrote.

  53. Drosera

    Shi Huang said,

    “Do you think there is any chance for the existing Darwinian theory to be completely wrong for macroevo while being true for microevo? If no, how come not a single contradiction for micro while numerous ones for macroevo?”

    That is another of your blind spots. A contradiction is not the same thing as failing to predict the outcome of a random process correctly. The science of meteorology is not completely wrong, in spite of the fact that we can’t predict next month’s weather with 100% certainty. And of course there is no difference between micro- and macro-evolution. If you can climb a ladder with 10 steps, you can also climb one with 100 steps, it just takes more time.

    “Dont you know that there is no real difference between a genius and a crackpot to a non-informed person like you.”

    A genius doesn’t make elementary mistakes that even a ‘non-informed person’ can spot. The Crackpot Index is a tongue-in-cheek method to distinguish between a genius and a crackpot. If you are indeed a genius then I suggest that you should first learn how not to come across as a crackpot. Stick to the facts and present these as clearly as possible; show why these facts could be a problem to established theory, and present you explanation. All the time, avoid obfuscations, irrelevancies, and undue attacks on the ‘establishment’. You have to convince the establishment, so it is really not wise to start by accusing them of stupidity and carelessness.

    But I have better things to do than trying to educate you. I’ve already made an attempt, and it’s getting tiresome. As I said, my dice example was just a primitive model, to get across the idea of saturation, nothing more. I also explained that the saturation effect and the molecular clock hypothesis are not mutually exclusive. In one of my first posts I pointed out to you that phylogeny reconstruction does not require a molecular clock. These things should have given you food for thought, but it appears that you are already saturated with your own preconceptions.

    Let me ask you a question: what is your explanation for ‘macro evolution’, if the current theory of random mutations and natural selection is so terribly wrong? Let me guess, is it Intelligent Design?

  54. Alan

    I just watched the Discovery channel show on Ardy and have now read this article. I have no educational background in the relevant areas and am confused by the following: It appears that based upon the conclusion that Ardy was bi-pedal but not a knuckle-walker that the above author and others conclude that chimpanzees and humans evolved from our common ancestor on separate branches. What is it that we have established scientifically that precludes the chimpanzee pre-dating Ardy and presenting us with a broad lineage of: common ancestor to chimpanzee to Ardy to Lucy to homosapien?

  55. KarlPopper

    “And the winner is, in the fifth round by a logical knockout(and inflamed sessile glands :-) …”Big Country” Drosera!” Props to Shi for not tapping out after encountering an immovable logical object. Shi Huang, I would drop down to crusier or perhaps bantam-weight, to be sure, and I suspect you will do fine.

    Finding this very special flame-war between Shi and Drosera arising out of such an unlikely topic, was an absolute and pernicious delight, and so much more fun and edifying than the comment section fisti-cuffs on Youtube or the Huffington Post. More than three word sentences, no cursing, correct spelling if poor syntax and a flurry of probability theory jabs (pun intended). Playing the dozens with the philosophy of science! Love it! Love it! I want to go back to grad school and listen to my PhiloSci prof better, damn it! Someone could affirm a consequent right in front of me and I wouldn’t know it anymore…Been selling out and working for the man too long, I guess.

    Seriously, good stuff Drosera. You got a little Chihuahua on us for a bit there but it’s all good bro/girl. Shi, I give perfunctory props for to you for tenacity if nothing else (for not tapping out) but sorry girl/bro, when someone has to write that much to get across a point of logic/argument, pretty quick, it starts to look like sleight of word and not strength of argument. Remember, forest for the trees, dude, forest for the trees, dude! I gave you the language barrier doubts too but I had to read Drosera’s replies to clearly understand the mechanics of your arguments/position. Love you guys though! Props and Peace Out.

  56. For a person used to contradiction as a way of thought, his low ability in logic or in coherent thought or argument would manifest in almost everything he says. I have repeatedly exposed your incoherence in this forum and I may have time to do a few more below. But I don’t have time to go on with you forever. Until one knows how to think coherently without contradicting oneself, he is incapable of distinguishing falsehood and truth. That is why the standard of no contradiction is so critical. Without it, we cannot even have a meaningful debate, let alone to discover truth. That standard is what mathematicians use and there is no reason why biologists should be made an exception. As I already corrected your error before, to say that randomness/accidents are way of life in biology cannot be used as an excuse because the basis for that saying, ie, Darwinism, has not been proven correct, has already been proven wrong (if one contradiction is enough), and hence can never be proven correct (by the standard of no contradiction). Darwinism is in practice no different from a false/incomplete theory. More precisely, Darwinism is true for microevolution but false for macroevolution.

    You say “That is another of your blind spots. A contradiction is not the same thing as failing to predict the outcome of a random process correctly”
    Who ever said it is? A typical straw man attack. Again, you have a habit of misrepresentation, typical of evolutionists like Dawkins or Jerry Coyne. When I talk about contradiction, I am referring to things that fall definitely within the domain of relevance for the predictive power of the theory. We are talking about a scientific claim by the theory that has definite predictions. If your theory does not and cannot give definite testable predictions, you don’t have a scientific theory. The science of meteorology never claimed that it can predict next month’s weather with 100% certainty. Thus, its failure to do so is not a contradiction. It never predicts it and so it does not get credit for it one way or another. (By the same reason, Darwinism never predicts creation of human being and so it cannot/should not get credit for the appearance of human one way or the other) Why am I not surprised that you could use such a stupid and meaningless example to illustrate contradiction? Contrast this example with the molecular clock. To explain the equidistance of human and frog to the simpler outgroup fish, the clock claims human and frog (or all life forms for that matter) have similar mutation rates. This claim is either true or false, and has testable predictions. Indeed, if it is a scientific claim, it must give testable predictions. One such prediction is that octopus and cockle should be equidistant to human the outgroup, or more generally, the equidistance to the outgroup should be independent of the complexity nature of the outgroup. But this prediction is easily proven false (octopus is closer to human than cockle is). (And your crackpot theory of saturation gets falsified here too) Therefore, to use the clock concept to explain the equidistance to a simpler outgroup is wrong or falsified because it is contradicted by the non-equidistance to a more complex outgroup. Where in this example has randomness any relevance?

    There is of course a difference between micro and macro evolution besides just time. If you can build a one story house with a cheap type of brick that can barely withstand the weight of a one story house, which is what you should use from the point of view of least expanse or economics, you cannot with more time build a 100 story house with the same brick. If you can climb a ladder with 10 steps, you cannot with more time climb a ladder with 10000 steps to reach a height of above say 5000 meters, because you will faint and fall to death from low oxygen. The point is that time is not at all the only difference between micro and macro-evolution as you or the mainstream think it is.

    Faced with an overzealous person eager to ridicule a challenger with whatever means possible, the best and only thing the challenger can do is to ignore it. Trying to behave in ways just in order not to be called a crackpot is futile and a complete waste of time.

    You are mistaken about the establishment. You can be a perfect nice guy but if your theory is not in line with the establishment, you will not be accepted. As Planck said it the best, a new theory does not convert the minds of the old or established. It just waits for them to die out. I am sure I am young/healthy enough to outlast most of the establishment. In the meantime, another young scientist may uncover a novel result that is best explained by the new theory. For his own sake or his self-interest, the young guy goes out all the way to publicize his data, indirectly benefiting the new theory. As time goes, more young scientists like that would emerge. That is, FYI, how a new revolution theory become accepted as repeatedly shown by history. That is how Copernicus’ theory became accepted 100 years after his death thanks to the new findings and the bravery of Galileo and Kepler. Galileo did not risk his life for the sake of Copernicus but for his own findings. That is the beauty of nature or human nature: even if everyone works for his own self interest at the expanse of truth, a true theory will still evolve from benefiting only the self interest of the inventor in the beginning into benefiting the self interests of a few young people, and eventually of all mankind. The establishment will ignore/suppress the new theory to protect its self-interest. But with time they will disappear. To the big picture, they are really harmless. Truth is for forever and a delay of a few generations is nothing. On the other hand, young people with a novel result and without a reputation or stake in anything yet will for his own interest to promote his result, and in turn indirectly also promoting the new theory which explains his result. Even as we speak here, new results inexplicable to the old theory but perfectly predicted by my new theory are emerging constantly. The Ardi data is one. For another one, see my comment on the Cell website on a recent paper in Cell “Protein sectors, evolutionary units of three dimensional structure (2009, 138: 774-786).

    It may be a depressing prospect for most people to have to wait a long time to receive reward or recognition for one’s hard work. But the pleasure of finding truth and the certain knowledge of the immortality nature of truth is of sufficient reward already to the inventor of truth, a pleasure only the foremost inventors can really appreciate, for which most people can never really understand. One simply cannot experience such pleasure second hand.

    Your advice to genius is a joke. A genius makes all sorts of elementary mistakes in everything except his invention that made his name. A genius is too busy with important stuff to learn how not to come across a crackpot, especially when he knows he will surely be labeled as one by some fraction of the population no matter how well he has learned or behaved. You are the perfect case in point. I never implied conspiracy and yet you can misread me to fit your preconceptions. For someone who does not follow the rule of no contradiction, he could call black white at will. You also remind me of a quote by Peter Atkins, what’s wrong with arrogance if you are right. Relative to truth, human feelings are irrelevant. Truth does not care if it hurts some people’s feelings.

    You said: “phylogeny reconstruction does not require a molecular clock”
    I challenged you in my previous post to say this: phylogeny reconstruction does not require the molecular clock concept that genetic distance always correlates with time of divergence. Why don’t you say it? Is the reality of sometimes no correlation between genetic distance and time of divergence taken into account in the common methods of phylogeny? Is it taken into account in the LS method? Why don’t you also say that all the assumptions of these methods are 100% correct? (because if they are not, those methods are jokes) List what these assumptions are if you don’t agree with the ones that I listed before. I have claimed elsewhere that no statement or rule or assumption in evolution is 100% true. You can give me one if you don’t agree. As far as I know, the only 100% correct rule is the inverse relationship between genetic diversity and epigenetic complexity. If you cannot falsify this rule with a single contradiction, then you must accept all of its deductions, including its number one deduction that macro and micro-evo is totally different.

    My explanation for macro-evolution is already in my published papers or preprints. It is an increase in epigenetic complexity and a decrease in genetic diversity as measured by point mutations. Let me ask you this, what is the cause of gravity? Newton thought it is God. Why don’t you atheists attack his three laws of motion then? What created the first life? Darwin thought it is God. Why you atheists follow his theory like he is your God then? (Oh, I forgot, contradiction is a way of life for you atheists.) So, whether God or not, a law is a law. In my case, my law is the inverse relationship between genetic diversity and epigenetic complexity. I could believe in God and yet you atheists would still have to accept my law, so long you don’t have a better law that can explain nature without contradiction. By the way, ID people don’t like to see a law of evolution without contradiction, because such a law excludes the God of Bible who can perform arbitrary miracles in violation of any law.

  57. Drosera

    Shi Huang,

    You have no theory. You have some misunderstood/mangled/ill-digested observations (equidistance), you have not the faintest idea of the role of chance in the evolutionary process, and you have a vague claim (‘the inverse relationship between genetic diversity and epigenetic complexity’) that you pulled out of your posterior end. This does not amount to a theory by any standard.

    You also display a total ignorance of the meaning of simplifying assumptions in science.

    The depth of your foolishness is further revealed when you suggest that people like me think that Darwin is a god. I can do very well without such a notion, thank you very much. That you can’t is your problem, not mine. All you are doing is raising the level of your crackpot index. It goes up and up.

  58. Drosera

    KarlPopper @86,

    I didn’t realize people were watching our little skirmish. Grab some more popcorn.

    Alan @85 asked,

    “What is it that we have established scientifically that precludes the chimpanzee pre-dating Ardy and presenting us with a broad lineage of: common ancestor to chimpanzee to Ardy to Lucy to homosapien?”

    A general principle is that when you have two very distinct extant species (like chimpanzees and humans), you don’t assume that one is an ancestor of the other. That is because it is very unlikely that all the differences between chimpanzees and humans are caused by changes in the human line only, while the chimps remained the same. It is far more plausible that there was a common ancestor that looked neither like a chimp nor like a human being. Since Ardipithecus is very old, it is not unreasonable to assume that it looked in many ways similar to that common ancestor. But in spite of what some people here think, we can’t be 100% certain about this, one way or the other.

  59. Drosera @86
    To end our little skirmish with you shouting a few empty slogans suits me just perfect. Good luck.

  60. Drosera: “It is far more plausible that there was a common ancestor that looked neither like a chimp nor like a human being. ”

    If that was the consensus view after 150 years of Darwinism but just before the Ardi finding, we would call Darwinism science. Expectation/prediction based on it actually gets confirmed for once.

  61. KarlPopper

    The Jiffy-Pop is on the stove…check out similar rants by the distinguished gentleman on Amazon where he review’s Coyne’s book and spawns a similar flame chain there. I read only the counter-points after a while.

    The banter took me back to grad school and reminded me of how much I enjoyed my PhiloSci courses and how much it influenced my admiration for the scientific method (and critical thinking). Little did I know that the symposium I took on hermeneutics was literally taking an irretrievable bite of the apple from the tree of secular knowledge… ;-) . The upside was that after 22 years I realized I was naked and should at least wear a fig leaf to class.

    All those years ago, my grad training was in Social Psychology with a concentration in theory and method. At department functions and grad parties, several, but not nearly all, pastoral counseling students in theology grad programs, would give me the stink eye when I mentioned my area of study. By choosing to be a psychologist, I was automatically a secular atheist competing with them for lost souls, whether I actually wanted to or not. No amount of explaining that I was researching and studying group behavior would assuage them that I wasn’t studying to become a counselor, clinician or personality theorist. Didn’t matter what explanation really, scientist or psychologist. Equaling damning to that audience at that time.

  62. Drosera

    Bye, Shi Huang. Come back when you can actually measure epigenetic complexity.


    It seems you can put away the Jelly-Pop. So you’re a shrink, huh? I’ll have to watch my tongue, then. Just want to let you know that I never wanted to sleep with my mother, or murder my father ;)

    And souls don’t exist, of course.

  63. Drosera

    I wrote: “It is far more plausible that there was a common ancestor that looked neither like a chimp nor like a human being. ”

    Maybe I should add one more thing. By a careful cladistic analysis it is often possible to infer which characters* one could expect to find in a common ancestor (this has to do with things called plesiomorphic and apomorphic character states). So here we have another piece of evidence to support the Theory of Evolution. For example, if all apes (chimpanzees, orangutans, gorillas, etc.) were knuckle-walkers, then such an analysis would suggest that the chimp-human common ancestor would probably be knuckle-walking (chimp-like in this respect). On the other hand, since it appears that there are different types of knuckle-walking, it may actually not be correct to regard this as a single character-state.

    *More accurately: character states.

  64. Drosera

    By the way, the same kind of analysis will predict that the last common ancestor of chimpanzees and humans had a hairy body. To some extent this justifies depicting Ardipithecus as being furry.

  65. Drosera

    KarlPopper @92,

    I had a look at the discussion over at Amazon that you mentioned. If I had seen this before, I would not have been so patient with our learned friend Shi Huang. The most hilarious thing that I noticed was that SH not only thinks that he has defeated neodarwinism, but that he also claims to have proved the Riemann Hypothesis (probably the most notorious unsolved problem in mathematics; it is one of the Millennium problems of the Clay Mathematics Institute. The person who solves it can pick up $1000,000)

    Just for fun, and since I am interested in mathematics, I looked up SH’s paper, titled: ‘Modeling the creative process of the mind by prime numbers and a simple proof of the Riemann Hypothesis.’

    Well, fun it was indeed. Here is a 32 page paper on one of the deepest problems in mathematics, and it doesn’t contain a single equation! It is even more obvious crackpottery than his biological stuff.

    I don’t have the time to do the calculation, but it would not surprise me if SH’s Crackpot Index would turn out to be a world record. He is surely the genius among crackpots! But you don’t have to feel pity for him, because he will soon be a millionaire…

  66. Just for fun, I looked up the crackpot index. Interesting enough, the feature that has the highest index score is the last: “50 points for claiming you have a revolutionary theory but giving no concrete testable predictions.” Obviously I should get a minus 50 for this one and Darwinism gets a positive 50, since one has to be stupid to fail to see which theory has more predictive power. (hint, Darwinism is pretty much irrelevant for 99% of DNA evolution we observe) Predictions and explaining as many detailed facts as possible is the only criterion I have come to know on my own observation since a few years ago to be the only real meaningful standard for crackpotery. The modern evolution theory of macroevolution is pretty high on this one, just like ID and numerous others.

  67. Drosera

    “50 points for claiming you have a revolutionary theory but giving no concrete testable predictions.”

    Let’s see.

    You claim that you have a revolutionary theory. – check
    You don’t really have a coherent theory, so it’s indeed just a claim. – check
    If you make predictions (such as?), then these can’t possibly follow from your ‘theory’, because you don’t have a theory. Therefore you don’t give concrete testable predictions based on your theory. -check

    Yes, these 50 points are fully deserved.

  68. Feel free to call black white. BTW, we should add 500 points for a theory that allows/has exceptions/contradictions or whose inventor/supporters never dare to even claim no contradictions. Let’s goodbye one more time.

  69. Drosera

    I give you 50 bonus points for basing an hypothesis on purely imaginary ‘observations’ and then claiming that the hypothesis explains these observations. This one is not in the official index, but I feel generous today.

    Goodbye, and don’t let the door hit you in the back.

  70. Megan

    Ardi is the bestt

  71. Debby Smith

    Why not compare Ardipithecus to Orangutans instead of Chimps?

  72. kristina

    why do all of you guys beleve this this is garbage!

  73. Gurleen(Kristina's Friend)

    Ya!! U have to be stupid:) And crazy to believe this how do scinetists know this maybe these bones are from an ape that used to look like a human, doesn’t meaaaaaaaan its a human duh!! im 12 and im evensmarter that most of you HAHAHAHAHA!!!

  74. Lula

    Why is there so much hoo ha over such a very small detail. Darwin was essentially right in the idea that natural selection will push evolution in a divergent or convergent manner. Plate tectonics, changes in climate and natural disaster have all affected species development. As we uncover more information, the big idea can be refined and further understood.
    Hands and feet. These seem to be the big issue….oh, and God. Well, either we have no idea what God is, as I seem to remember reading somewhere that he made us in his image….so what is all the fighting about. I believe that all mammals evolved from a tiny tree shrew with an apposable thumb. Not a fig leaf in sight. This is our most distant relative. One day, we may well know the closest common ancestor which will probably be rather different to what we imagine today with our current knowledge. So get over the chimpanzee thing. Darwin was working on the best information he had at the time and was bright enough to make the initial mental leap.
    What interests me much more is how Ardis’ foot became Lucys’ foot. How did an apposable thumb become the big toe. Interestingly, it remains a weak link in our bipedalism to this day with a high incidence of hallux abducto varus/valgus where the first metatarsal deviates medially towards the apposable position.

  75. I still remain unsure that the human race does not have severeal links to past generations. The high incidencew of hallux abducto valgus and varus indicates that this bipedal adaptation is more recent than the Lucy skeleton. For the foot to develop a sturdy first toe that became the main structure of propulsion and for the the musculature and and tendons to have changed that much in such little ecvolutionary history seems quick and unbelievable.that it happened in less than one million years between Ardi and Lucy I have read many of the papers around Lucy and Ardi but none of them seem to explain the rapid evolution of a seemingly vital structure in the identification of hominids. I still believe there are more than one species that took the same pair bondng, exclusive path to success. This would explain why some modern feet still favour weight bearing on the second and third metatarsal head.

  76. don johanson

    Dear Carl, enjoyed your post on Ardi. I just wanted to point out an error in your post.

    I invited Tim White to work on the Hadar hominid collection, including the Lucy skeleton. He was not a member of the team that FOUND the skeleton.

  77. John Jackson

    Huang Shi@71

    Oh Huang-jin Shi-zi! So many interesting ideas, but so much over-optimism for them!
    At the end of ‘1.’:
    “But our standard of science is that we cannot and should not allow a phylogeny to have any chance to be untrue, no matter how small a chance.” That clashes with the principle that theories should be preferred based simply on their power to predict/explain. If we insist that no theory could ever have the possibility of being untrue/disproved, we’d never even temporarily be happy with a theory.

    Start of 2:
    “2. Any theory or method that can give the correct phylogeny should and must give the correct dating.” I don’t know why you say that. However what you say next sounds promising…
    “This is because nature is a coherent whole rather than disconnected.” But what you say next is wrong…
    “A theory that only explains less than 100% of the domain of nature for which it is relevant is by definition incomplete or false” ..because theories can be useful if they merely predict/explain some things. It’s when they predict the wrong thing that they get into trouble – but you say they need merely fail to explain/predict everything! That’s far too strict!
    Later you say:
    “4. If the assumptions are false, the methods are automatically false” Although I consider people who forge their own detailed philosophies and theories are more valuable than those who just follow the crowd and never construct daring theories, I think your Philos. of Sci. is generating huge problems for you. The methods you refer to in 4 could be fine, and indeed the conclusions might conceivable also be “right”, even though assumptions and/or methods were wrong. You tend to coin valuable insightful statements that are ruined by being inaccurately stated, and being subsequently overladen. This goes beyond possible inaccuracy in the language.

    For example, in your definition of MGD on your blog:

    “1) The reality of maximum genetic distance/diversity (MGD):
    For any gene with a biological function, certain mutations that destruct the function will not be tolerated by the organism while those neutral or beneficial ones will.”
    Sort of, but actually mutations that destroy the utility of the gene, or much of it, may well be tolerated. Other aspects of the creature may be used. And look at sickle-cell anaemia. Each subsequent statement also cannot bear the weight further steps in your argument place on it. For example, the claim that more complex creatures have greater need for genes to stay unmutated. Unfortunately more complex creatures also have more spare or overlapping systems to help out a suboptimal allele.

    Perhaps you can check your steps & statements, and weed out those that have too great a chance of being false.

  78. Your matter of fact style is refreshing and scientific, uncommon in a lay forum. Some of your views are understandable and may even be correct in some context but not necessarily correct in general or in the context of the MGD hypothesis or from the perspective of a professional. I will engage in an exchange so long it is about pure science of some depth. Below is a response to your points in order.

    People often stretch their theory way beyond its real scope and power. They refuse to be satisfied with settling for a 100% correct theory in a small domain of relevance and always want to push their theory into a larger domain while sacrificing 100% certainty, and feel more important and influential as a result. Totally understandable. But, there is no such thing as a 99% correct theory. The reality is of course that people will always use their micro theory to explain macro reality in a mistaken way as long as we don’t yet have a 100% correct macro theory. It is okay to do that before we have a macro theory and it is even constructive to do as it just exposes the problems of the micro theory and hastens the end of it in the macro domain and the birth of a true macro theory. But once we do have a 100% correct macro theory, it would be foolish to stick with the micro theory or the stupid faith in the existence of a 99% correct theory.

    In this day and age, few theories do not explain some things or are not 100% true in some small domain of nature. But it is foolish to call a theory correct in domains where it fails to explain a contradiction. In evolution, the last thing people do is to define where the theory should work and where should not. Instead of saying we have a microevo theory that is 100% correct, we prefer to say that we have an evolution theory that we are not 100% certain (because of contradictions in the macro domain). But don’t bother to look for a replacement that is 100% certain because evolution is such that we can never be 100% certain. Well, this classic self-serving may fool themselves and some people but not all people can be fooled in such a stupid way.

    A method is flawed if its assumptions are wrong. The results of a flawed method are meaningless regardless whether they happen to be consistent with reality or not. If you are not a professional scientist, you may not appreciate what I just wrote. But that is where I will leave it. I never intended to communicate scientific details, except the common sense axiom involved, directly with non-professionals as it is not the most productive use of my time. That is why I wrote papers not books. Evolution as I know it is much more complex. I don’t expect lay people or even scientists not in the field to have any role in studing/understanding it one way or the other. The true theory should be resolved among a small number of professionals. The lay people can then just trust the experts and learn as second hand knowledge. How many lay people really understand relativity? Why should evolution be simpler than relativity when the brain for understanding relativity is a product of evolution? It was a bad start for Darwin’s book to target a lay audience. A science that is so simple that a lay person could feel and talk in forums like he knows all about it can hardly be called science.

    Building complex and robust machine may have more ways than just one. To have backups or overlapping systems is one way of doing it, the most stupid and awkward way. Instead of a single engine in a small plane, a more complex large plane may have 4 engines with 2 of them as backups. But is that the nature’s way for using DNA to build complex life? Do we have an extra heart or brain or any organ as pure backups? We don’t. If we don’t do it at the phenotype level, do we do it at the genotype level? Mostly not. Our gene numbers are much smaller than any one had predicted because complexity is not linked to an increase in gene numbers or in back up genes. Nature is smarter and does it by combinations of genes and by inventing novel and complex ways of using the same set of genes. And by giving extra functions to an existing gene. We create music not by inventing more notes, and the ways of using the existing notes are already infinite.

    To add back up or overlap system is not really an increase in complexity. A four engine plane and a one engine plane has the same level of complexity as far as the engine is concerned. To have a back up brain, we still need to have a complex brain in the first place. For that to happen, disorder and random mutation must be suppressed. Who can imagine a brain capable of infinite order like mathematics could tolerate a level of disorder/randomness in its building blocks like that of a flu virus or any simple virus like early life forms at the beginning of evolution?

    The backup way is also not sound for DNA based lives because, in my thinking, it increases the size of the genome and hence the target size for mutations. The backup copy is not expressed or functional in normal situations and therefore not maintained by natural selection and can easily lose its function due to accumulation of mutations. Thus, it is safe to predict that most paralogs of a gene in a complex organism have unique functions and are not just backups (plenty of data for this). Your claim of complex organisms have more backups is simply wishful thinking and not supported by facts. Don’t we have a lot of single mutation diseases in humans?

    For both genotypes and phenotypes, nature follows the rule of use it or lose it. Backups may have been invented once but would simply be lost due to disuse. Which is more effective in advancing complexity: to decrease mutations or to use backups? All facts of nature say the first. It is simply a reality that a theory based on that notion explains all facts whereas any theory that ignores it meets with countless contradictions.

    On the statement “For any gene with a biological function, certain mutations that destruct the function will not be tolerated by the organism while those neutral or beneficial ones will.” It is about a general major pattern. Special cases can happen that has special explanations, which still does not violate in principle the main pattern. One can easily argue that the sickle cell mutation is a good version in the fight against malaria.

    Yours is a common mistake in the evolution field that has infected the lay public. It is to ignore the main pattern and use whatever trivial pattern/facts to suit our theory and to invalidate the main pattern when our theory does not predict it. Given the infinite amount of data/facts of nature, any stupid theory can find some factual support, if the goal is not to account for the major patterns or is not to explain all without contradiction. The advance with time in complexity is the dominant pattern in evolution that is so obvious that it is hardly worth stating. (The best ancient Chinese thinkers from 5000-7000 years ago had always placed man above all else in nature and as equal in status to the creative power of nature namely yang/heaven and yin/earth as written in I-ching, which has been the foundation for the most long lasting civilization as well as the world view of the largest population on Earth. Ancients have much better intuitive sense than moderns simply because their focus is less distracted by trivial things or man-made artifacts, and intuition is the foundation of science.) But since our theory does not predict that, we ignore it and cite trivial cases of randomness to support no direction towards complexity. Or we use trivial and much less common cases of complexity loss like loss of limbs in snakes as evidence for no direction towards higher complexity. Or we cite abundant cases of no change in complexity during microevolution. But all these merely indicate that in addition to complexity increase, there is also another trend for stability or no change. One cannot use a single mechanism to explain two opposite major trends, which is what we are doing.

    We ignore the order/beauty/complexity of our big brain, and cite examples of imagined imperfections in some organs as evidence for the imperfections of nature or evolution. We ignore the general perfection of the human body and cite examples of rare diseases to fault the power of nature/evolution. In every case, the main pattern says that nature/evolution is all good, order, and beauty. The existence of disorder, randomness, and ugliness are all trivial and minor patterns. It is simply nonsensical to focus on the minor patterns and to turn blind to the main patterns. We should not explain the trivial at the expanse of the main but that has become a habitual behavior to most followers of evolution, another simple indication that we are not on the right path in understanding the main pattern.

  79. Barbara Meikle

    Why won’t the White team allow any other paleoanthropologists to view the actual fossils. Why so secretive?

  80. SLPage

    Let’s see…

    Shi has claims of a conspiracy of evolutionary ‘specialists’ to keep things quiet.. Claims ot have disproven some well-supported concept… Quotes Leigh VanValen’s 1974 paper…. claims sane people will agree with him. – looks like somebody has been reading Walter ReMine…

  81. If you are a scientist, may I suggest you deal with the specific facts and reasons discussed in my papers. For a start, try defend the existing interpretation of the genetic equidistance result against my interpretation.

  82. Some well supported concept? Like what? Name one and I will give you facts to show how it is incomplete or only true in microevolution but false in macroevolution.

  83. Rich

    Why, oh why do all comment sections devolve into Ad Hominem attacks of two blow-hards with nothing better to do than to piss on each others’ legs.

  84. Kim

    You know this article is most interesting. It’s fascinating to see that this animal looks so much like us. It’s hard not to think that we may come from them. But I know we did not as there were not enough fossils record to back up this claim.

    This led me to be so glad that I am vegan. The reason is — it is hard to say what is the difference between cow and pig or dog and cat. We decide that dogs or cats are so lovable so we spare their lives and make them our friends. While we eat the cows and pigs where many scientific reports saying that pigs are smarter than dogs.

    Likewise, it is hard to say what is the difference between us human beings and the Chimps.

  85. Peter OLalor

    A while ago I found on MSN science a report of a complete fossilized skeleton found in Europe that proved humans did not evolve from apes. It seems to have disappeared from the WWW
    I’m not referencing Ardipithecus.

    In addition another report suggested a split in the evolutionary tree that made Europeans their own species.

    Can anyone concur?

    Thank you

  86. Good post, Ardi is certainly exciting. And imagine waiting 17 years to publish! Science probably didn’t have a website when they started!

  87. I like that blog layout . How do you make it!? It is very sweet.


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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.


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