The Loom

Homo floresiensis: Two Years Out

i-c554df96a4f21e670b7b9115e540b7ef-new hobbit.jpgTwo years ago this month, I was taken aback by some explosive news. A team of Indonesian and Australian scientists reported that they had discovered fossils of what they claimed was a new species of hominid. It lived on the island of Flores in Indonesia, it stood three feet tall, and it had a brain about the size of a chimp’s. Making the report particularly remarkable was the fact that this hominid, which the scientists dubbed Homo floresiensis, lived as recently as 18,000 years ago. I wrote up a post on the paper, and took note of some strong skepticism from some quarters. And since then, I’ve found myself devoting a number of posts to the new papers from the discoverers of Homo floresiensis, and the emerging responses from the skeptics–so many that I gave them their own category. Recently there’s been so much stuff coming out pro and con that I have had to skip a couple opportunities to blog on Homo floresiensis–mainly because I’ve been frantically deep in the first draft of my current book on a very different topic: Escherichia coli. (I assume Homo floresiensis carried Escherichia coli in its gut, but the overlap stops there.)

Fortunately the first draft is now done, so I can let my mind drift back from the microbial world, to Homo floresiensis. And it just so happens that a big new paper has come out today which is a good topic on which to blog.

This paper, published in the Anatomical Record, actually builds on a much shorter one that appeared a few months ago in Science. To keep the strands of this story from tangling up with each other, let me lay out a timeline. (If you feel I’ve left something important out, remind me in the comments and I may insert it below…)

October 2004: Homo floresiensis makes its debut. The bones include only one brain-case, dubbed LB1. Along with the bones are lots of stone tools, raising the question of whether a small-brained hominid could have made or used them. Flores is also home to dwarf elephants, which illustrate the fact that many mammals evolve to smaller sizes on islands. Perhaps Homo floresiensis evolved from a bigger hominid. The best candidate, according to the authors, is Homo erectus, which spread from Africa about 1.8 million years ago and existed in southeast Asia perhaps as late as 50,000 years ago. Homo erectus was tall, could make simple tools, and had a brain about two-thirds the size our own. One line of evidence that may support this claim is the presence of stone tools on Flores dating back 840,000 years ago. They might have been left by Homo erectus migrants, whose descendants later evolved to tiny proportions.

November 2004: Things get weird. A prominent Indonesian paleoanthropologist named Teuku Jacob gets hold of the Flores bones and studies them for himself. He tells the press that Homo floresiensis is not a separate species, but a human pygmy, perhaps with a birth defect called microcephaly that causes small brains. (This is a line of argument taken by other skeptics.) The discoverers of the fossils cry foul, and three months later, when the bones are returned, they complain that some bones have been permanently damaged.

March 2005: Homo floresiensis gets a brain scan. The fossil discoverers team up with Dean Falk, a hominid brain expert, to give the LB1 brain case a CT scan. They reconstruct its brain and compare it to the brain of a human microcephalic, from a skull kept at the American Museum of Natural History. They argue that the brain is significantly different from the microcephalic, and most resembles that of Homo erectus.

June 2005: The site where Homo floresiensis was found is sealed off from any further investigation, reportedly due to the conflicts among the rival scientists. (I have not heard if it has been opened since then.)

October 2005: More bones. The discoverers of Homo floresiensis publish descriptions of additional fossils. These bones, including material from the lower jaw, arms, and legs, show strong similarities to the original fossils. They lack a chin, they have long arms relative to their legs, their teeth have some odd double roots, and so on. What’s more, they come from several ages. The bones that the authors assign to Homo floresiensis now range from 97,000 to 12,000 years. If LB1′s small skull belonged to a human with a genetic disorder, then why would all of these other individuals show so many similarities? Robert Martin, a primatologist at the Field Museum in Chicago who has expressed skepticism about Homo floresiensis, says he’s writing up a critical paper.

October 2005: After more bones come more brains. A few days after the new fossil paper is published, a German team of scientists publishes a comparison of LB1 to skulls from a different sample of microcephalics. The scientists argue that the brains are quite similar. They point out that microcephalics are quite variable in the shape and size of their brains, and say it’s premature to rule out the possibility that LB1 was microcephalic too. Dean Falk and her colleagues come right back at the Germans, arguing that they tipped the brains at the wrong angle before comparing them. If all the brains are lined up at the same angle, they look less similar.

May 2006: More skeptics weigh in. After a long winter without more news to take in, Robert Martin publishes his first attack on Homo floresiensis, teaming up with experts in other relevant areas such as William Dobyns, an expert on microcephaly at the University of Chicago. They present evidence that the microcephalic Falk chose was a nineteenth-century child named Jakob Moegele. An adult would have been a better comparison. The scientists present a couple sketches which they claim are more similar to LB1. The scientists also argue that LB1 is too small to be the result of evolutionary dwarfing. If Homo floresiensis followed the same trend that other mammals have, it should have had a much bigger brain relative to its body. Falk and her colleagues responded by asking how they could judge sketches (as opposed to detailed scans). They also hinted that perhaps Homo floresiensis might have evolved from an older, smaller branch of hominids.

June 2006: The discoverers of Homo floresiensis now publish new details on the stone tools. They argue that the tools from 840,000 years ago and the more recent ones found alongside the fossils probably represent a continuous technology made by the same lineage of hominids. To say that a small-brained hominid could not make such impressive tools is an assumption cloaked as a conclusion.

June 2006: A new idea emerges: Homo floresiensis is a healthy human. Gary Richards of the University of California at Berkeley argues that humans could have settled on the island of Flores and rapidly evolved into pygmies with small brains. Many of the traits that seem to set Homo floresiensis apart are also found sprinkled among living humans–particularly among pygmies.

August 2006: Teuku Jacob and an international team of colleagues take on Homo floresiensis. Their criticisms come from many different directions. They complain, for example, that the discoverers compared the hominid to European individuals. The proper comparison is between Homo floresiensis to people from southeast Asia and the Pacific (Australomelanesians)–especially pygmy Australomelanesians. They would have discovered many traits from Homo floresiensis in modern humans that they claimed were not found in our species. Jacob’s team also presents evidence that LB1 had an asymmetrical face–which is sometimes seen in microcephaly. The original discoverers hit back, telling reporters that the asymmetry might have come after death, as the skull was squeezed under sediment.

October 2006: A second vote for Homo floresiensis. The Journal of Human Evolution publishes an analysis of the Flores bones from a different team of scientists from Australia. I was too busy to write this one up, so let me just quote from the abstract now:

“We explore the affinities of LB1 using cranial and postcranial metric and non-metric analyses. LB1 is compared to early Homo, two microcephalic humans, a ‘pygmoid’ excavated from another cave on Flores, H. sapiens (including African pygmies and Andaman Islanders), Australopithecus, and Paranthropus. Based on these comparisons, we conclude that it is unlikely that LB1 is a microcephalic human, and it cannot be attributed to any known species. Its attribution to a new species, Homo floresiensis, is supported.”

Today: The Anatomical Record publishes a 23-page report from Martin, Dobyns, and company (Anatomical Record (DOI: 10.1002/ar.a.20394). This is not a new paper, so much as the paper Martin et al probably wanted to publish in the first place, rather than the clipped “Technical Comment” that is all Science will allow for such matters. So it’s a mix of points raised before, more evidence marshalled in support of those points, and some new information as well. It’s a very detailed attack on Homo floresiensis, and I don’t know of anything coming down the pike that will be more substantial. So if the original discoverers decide to write a detailed rebuttal of all the recent papers that have come out, this is one I’d imagine they’d pay a lot of attention to.

One subject that is new is the matter of the tools. Martin et al argue that the tools from 18,000 years ago are not like any simple tool linked to Homo erectus. They are more sophisticated, and have only been associated before with Homo sapiens and Neanderthals. The preservation of the tools in the Liang Bua cave, where the fossils were found, suggests to the scientists modern humans coming back again and again to the cave after they arrived on Flores.

The paper also presents new information on microcephalics. The researchers scanned Jakob Moegele’s skull (the original, not the cast that Falk used) to generate an endocast of his brain. They then carried out some of the same statistical studies on the shape of the LB1 brain. They compared LB1 to Jakob, as well as to two microcephalics who lived to adulthood, and a range of hominids and apes. They conclude several important things from this study. One is that microcephalics cover a huge range of shapes. Jakob’s brain was very different from that of the adult microcephalics. But those adults had brains that in some ways resembled Homo floresiensis. “LB1 is not clearly distinct from all modern human microcephalics,” the authors write. (Martin et al cast doubt on the recent Journal of Human Evolution paper, pointing out that the two microcephalic skulls studied there were over two thousand years old. One probably died before adulthood.)

Martin et al also argue (like Richards) that the other odd traits of Homo floresiensis are not as odd as the original discoverers claimed. For example, the discoverers pointed out the massive teeth in LB1′s jaws. But teeth are like brains: they don’t follow quite the same path as a shrinking body. If you compare primate species, a primate with a smaller body has teeth that are not as proportionately small. And one of the microcephalics Martin et al studied turned out to have similarly big teeth as well.

As we come up on the second anniversary of the initial announcement of Homo floresiensis, we’re in a strange spot. Microcephaly turns out to be a very peculiar condition that makes it very hard to distinguish humans from a possible species of very small hominids. Many different genes can give rise to the same conditions, producing different shapes to the brain, as well as different changes to other parts of the body. Scientists actually have a lot to learn about microcephaly–for one thing, many studies rely on remains in museum collections, which almost never included anything below the skull. At this point it’s not even clear if discovering more tiny hominids on Flores would make the case for a separate species. Under some conditions, it might be possible that a small population of islanders had a high proportion of microcephaly-triggering genes floating about. But that may be moot if nobody’s actually digging in the Liang Bua cave.

Now, if Homo floresiensis is the result of evolutionary dwarfing, then perhaps the debate might be advanced a bit if someone could find hominid fossils on other islands around southeast Asia that have also followed the Homo floresiensis path. On the other hand, if Homo floresiensis descended from ancient small hominids, those hominids would have to have come to Flores from Africa, where the oldest hominids are found. That’s a long path, with plenty of opportunities for fossils to be formed along the way. Whether anyone finds them is another question. Finally, there have been rumors of DNA from Liang Bua, but no published reports. So there’s another avenue of hope. I have no idea when I will be writing the next Homo floresiensis post, but I can only hope it continues to be interesting.

Update: Here’s the new paper’s link.

Comments

  1. #1 BC
    October 9, 2006

    The Discovery Channel recently had a show on Homo Floresiensis. There was an Indonesian scientist on there (who was most likely Teuku Jacob; they were also discussing that he had taken the bones). I couldn’t help but be disgusted by him. He insulted other scientists. He also did a study in some of the nearby villages to find humans who were short. He found one man who was short (I don’t remember exactly how short – maybe 4’5″). The Indonesian scientist then declared this short man to be the descendent of Homo Floresiensis, and declared that Homo Floresiensis was, therefore, human. I just shook my head in disbelief at the horrible logic of it all. It was hard to believe that anyone took Teuku Jacob seriously after seeing that display of simplistic nonsense.

  2. #2 LK
    October 9, 2006

    What is obvious about Jacob’s claim is that he has not considered the hypothesis that the Homo sapiens population of Flores and other Indonesian islands have been under the same evolutionary pressures as previous hominids. Hence why the stature of the individuals of the islands is so short, they are in the process of getting short under the same selective pressures – a snapshot of theorectical evolution in action!!!

    Of course this negates the fact that modern humans or modern human microcephalics possess few of the anatomical similarities of the Homo floriesiensis individuals (particularly the unique morphology of the arms, legs and feet – a skeleton is a the sum of its parts and must be considered completely) leading some researchers to speculate that they are more gibbon in appearance.

    The sad story of Homo floriesiensis is a case of misguided scientific nationalism, bigotry and media charlatans versus rationalism and extensive peer reviewed scientific analysis. One day, a book will be published on the poor state of research into South East Asian human evolution and why Teuku Jacob is one the principal reason for its stagnation. Luckily there are many up and coming Indonesian scientists who are more open minded and not held back by memories of colonialism and 1960/70s style Indonesian patriotism.

  3. #3 drew hempel
    October 9, 2006

    Looks like it’s time to once again finally read “The Red Ape” by Professor Jeffrey Schwartz — reissued last year. Shame of all the “scientists” who haven’t read it yet!!

  4. #4 Steviepinhead
    October 10, 2006

    And shame on those who don’t read books like “The Red Ape” in the context of all the other information that’s out there–not only the overall phylogenetic tree-mapping software, but specific sequences shared among chimpanzees and humans, but not between orangutans and humans. Likewise the fossil data on human origins, which tend to confirm that our ancestors were more and more chimp-like in overall proportion of limbs, teeth morphology, skull shape, as one goes back in time.
    It remains possible, of course, that Schwartz is correct–that new fossil data will turn up in the Far East or that something major has been overlooked with regard to the DNA data. If so, science will correct itself.
    And, needless to say, Schwartz is absolutely correct to be faxcinated by these intriguing, intelligent, unique and threatened relatives of ours–and no one disputes that they are certainly within that small and precious group of the three or four extant species on the planet who are most closely related to us.
    Beyond that, it’s not clear how “shame” is a useful emotion to inject into whatever scientific debate there may be about our origins–no one is accusing anyone involved of fraud or other ethical violations: we just have the usual situation of healthy tension between the current mainstream view and edgier propositions.
    And, of course, then there’s the outer frayed fringe of the demented–Schwartz certainly isn’t in that bunch.
    But can you say the same, drew?

  5. #5 BC
    October 10, 2006

    I was thinking something similar about the “Red Ape” book. I’ve done genetic analysis on humans, chimps, gorillas, and other species, though I’m not sure that I have any Orangutan data. It seems like an interesting hypothesis to test (though, I’m honestly rather skeptical that Orangutans are closer to humans than chimps). I’d like to put it to the test, though, if only for the chance to refute or validate the idea. (Although, I’m sure this sort of thing has been done in the past, leading us to the current human-chimp clade acceptance.)

  6. #6 Joseph Urban
    October 10, 2006

    Does one have yet a publication date for the book on
    Escherichia coli? Publisher, isbn #???
    If one might want to preorder a copy… .

  7. #7 drew hempel
    October 10, 2006

    It seems that resorting to some sort of emotional appeal is the most effective means to grab the attention of science-cultists. This is of course my expertise as an official online crank — here’s more of my melees vis a vis recent ad hominems by those who enjoy “talking amongst themselves” about me online. Notice how I up the ante of scientific rigor while exposing sophmoric strategies to write me off as some sort of intellectual canard.

    http://www.fstdt.com/conspiracy/comments.asp?id=263

  8. #8 Mesk
    October 11, 2006

    I’ve done some analysis comparing DNA samples from human, chimp, gorilla and orang – and consistently saw a (((human, chimp), gorilla), orang) topology. There’s a clear consensus in the literature that DNA evidence pretty much unambiguously places orang as the outgroup to human, chimp and gorilla. I guess the orang genome will settle this question once and for all, but I think the evidence at this stage is very strongly against the notion that humans and orangs are sister taxa.

  9. #9 drew hempel
    October 11, 2006

    OK — so far no one has read “The Red Ape” who posts on this blog. That’s unfortunate because the “mainstream” position is well-known but clearly “the mainstream” position (in all its patent-obsessed glory) ignored the evidence and logic presented by Professor Schwartz. Already his analysis has been misrepresented in the replies to my promotion of his work on this blog entry. I would hope that science wannabes would be more curious, if not at least feel a sense of intellectual responsibility to consider an area of analysis increasingly pertinent to today’s forays into hominid origins.

    Of course I could say the same about Stan Gooch as well but that’s a bit off the beaten path of this blog post.

    Like an elementary teacher scolding his demented students, I, once again, deplore you to just read Schwartz’ book before all the “herd mentality” defense mechanisms kick in, as the responses have already demonstrated.

    Or choose to remain ignorant while the truth comes back to haunt us.

  10. #10 Steviepinhead
    October 11, 2006

    Drew the Hempster:

    Already his analysis has been misrepresented in the replies to my promotion of his work on this blog entry.

    Any evidence or specifics for this claim, Drew?

    HAS Schwartz looked at specific marker segments of DNA, or is he just critiquing phylogenetic software programs?

    Nobody’s saying the guy’s not a good scientist, or that he hasn’t intelligently argued his case, or that the orang-human connection isn’t a possibility (I’m a big orang fan), just that–on the basis of the totality of the evidence curently out there, the claim seems unlikely to work out in Schwartz’s favor.

    As Mesk suggest, the orang genome should clear up any reasonable doubt, one way or the other.

  11. #11 drew hempel
    October 11, 2006

    Sorry there’s no Schwartz cliff notes. I read one scholarly book a day. If you’re into Orang-stuff then…. But considering I was once again censored from a blog online — I’ve pretty much written off the internet as full of caddy posers not really focusing on learning.

    Too slow a learning curve online — too much self-censorship!

  12. #12 Steviepinhead
    October 11, 2006

    Ah, drew, content-free posting at its best.

    No one is asking for Cliff notes on Schwartz. Other people are well able to read (though, in your case, only with difficulty, it appears…).

    What has been requested is for you to back up your claims here with evidence. Citation. Scientific-sounding things like that…

    If you can’t or won’t do that, then we likely won’t be paying much attention to you. No need to ban–a simple filter will work just as well: ah, it’s that hemped-out drew fellow again, fine, then, no need to tarry, as the eyes skip lightly down to the next comment on the thread.

  13. #13 drew hempel
    October 12, 2006

    Unless Schwartz posts his book online I can’t help you! What you have posted — if you read Schwartz book — is proven wrong:

    Likewise the fossil data on human origins, which tend to confirm that our ancestors were more and more chimp-like in overall proportion of limbs, teeth morphology, skull shape, as one goes back in time.

    Now stop wasting my time and go read his book!

  14. #14 drew hempel
    October 12, 2006

    Here’s a little teaser for you all:

    from P. 236 of the 2005 edition of “The Red Ape” by Professor Jeffrey Schwartz:

    “But cranial and dental morphology does contribute to an understanding of evolutionary relationships — especially when it is backed up by an array of other, not-hard-tissue features. As we’ve seen, though, the most robust theories of large-bodied hominoid relationships — human-orang and chimp-gorilla — contradict the preferred molecular scheme of relatedness. Nonetheless, since the ‘molecular assumption’ grew out of a general agreement of molecular schemes of similarity with an arrangement of organisms based on the study of morphology, one should be able to question the interpretation of molecules or sequence data. Why, for instance, should molecular similarity always reflect recency of molecular change? Why, as is often concluded in morphological analyses, couldn’t similarity in molecule or DNA sequence reflect primitive retention (and, therefore, nonrelatedness), while difference indicates that a taxon changed relative to those that remained primitively similar?”

  15. #15 Steviepinhead
    October 12, 2006

    drew-lewr:
    Assuming your quotation from Schwartz is accurate, he has raised questions that would require the appropriate “answers”–convincing argumentation from solid, consistent evidence–which, at the moment, you at least fail (and, it is fair to presume in the meanwhile, he also fails) to provide.

    Do his primitive-retention arguments make sense in any similar scenario, not involving his pet humang-orang hypothesis.

    Schwartz may yet be shown to be right or wrong. But your arguments on his behalf fail to meaningfully advance that debate.

  16. #16 drew hempel
    October 12, 2006

    Carl Zimmer has emailed me with the request that I be nice so I’ll just simply point out (for the 3rd time) that if you read his book — a public document that anyone can read — you’ll find Professor Schwartz’ detailed evidence and analysis (that’s how books work).

  17. #17 windy
    October 13, 2006

    OK — so far no one has read “The Red Ape” who posts on this blog.

    I have, and the parts where he tries to discredit genetic comparisons showing humans to be closest to chimps are very childish and stupid and rely on antiquated data.

    Schwarz asks “..is the difference between 1.1% [human-African apes] and 2.4% [human-orangutan] statistically significant, especially considering that a DNA molecule may consist of 10 to 100 million nucleotides?”

    Why would comparing a lot of nucleotides make a small difference *less* significant? And what is this “DNA molecule”?

    “We should learn from the unexpected results that The International Chimpanzee Chromosome 22 Consortium achieved upon comparing human chromosome 21 with its apparent counterpart in the chimpanzee, chromosome 22: not only do these hominoids differ by 83 percent in their amino-acid sequences (this difference itself being unexpected, given previous claims of similarity), but this significant difference is generated from very similar DNA sequences (again pointing out that DNA is not the “blueprint” it’s touted as being).”

    So, gross errors (83 % difference in protein sequences??) and misleading claims. DNA is not the blueprint? What?? Where does he think the protein products come from?

    The whole section on DNA is crap like this. It’s a waste of time to analyse it any further.

  18. #18 Steviepinhead
    October 13, 2006

    Well, maybe I should also make an effort to conform to Carl’s request to drew–so no more “drooler” and “hemp” asides!

    The guy just frustrates me–and this has been one of his easier to follow (less incoherent and irrelevant) exchanges.

    What windy said!

  19. #19 drew hempel
    October 13, 2006

    That’s not an error on Schwartz part but an error on your part — here’s his take on Chromosome 21 newly confirmed:

    Title: Atypical mutational properties of human chromosome 21 suggested by comparative genome-scale analyses
    Author(s): Vieira A
    Source: CYTOGENETIC AND GENOME RESEARCH 115 (1): 30-34 2006
    Document Type: Article
    Language: English
    Cited References: 22 Times Cited: 0
    Abstract: Mutation of genetic material is a necessary component of evolutionary change. There is evidence for both intragenome and intergenome heterogeneity in terms of mutation frequencies. Reported comparisons of DNA sequence differences between human and chimpanzee (Pan troglodytes) suggest that human chromosome 21 may exhibit mutational hypervariability relative to the other autosomes. In the present study, further evidence is provided for such hypervariability based on large-scale analyses of amino acid composition of (translated) human genes and pseudogenes. A comparison of the variation in the above cases (i.e., DNA sequence differences and amino acid composition differences) yields similar ratios (1.2-1.4) for chromosome 21 relative to the other autosomes, e.g., human chromosome 22 – an autosome that is more typical in this respect and is of similar size to 21. Human chromosome 21 is also presented in this study as being atypical in terms of reported associations between mutation rates and GC content or CpG dinucleotides. In terms of GC distribution patterns, a comparison of NT_011512 and NT_011520 contigs revealed a lower heterogeneity for human chromosome 21 relative to 22. Possible hypermutability of chromosome 21 is further discussed in the context of GC patterns, reported long interspersed nuclear element content (LINE1s), and the implications of these parameters for chromatin structure.
    KeyWords Plus: DNA-SEQUENCE; EUKARYOTIC GENOMES; GENES; ISOCHORES; STABILITY; RATES; BIAS
    Addresses: Vieira A (reprint author), Simon Fraser Univ, Endocrine & Metabol Res Lab, Fac Sci Appl, K9625,8888 Univ Dr, Burnaby, BC V5A 1S6 Canada
    Simon Fraser Univ, Endocrine & Metabol Res Lab, Fac Sci Appl, Burnaby, BC V5A 1S6 Canada
    E-mail Addresses: avvieira@sfu.ca
    Publisher: KARGER, ALLSCHWILERSTRASSE 10, CH-4009 BASEL, SWITZERLAND
    Subject Category: CELL BIOLOGY; GENETICS & HEREDITY
    IDS Number: 086MY

    ISSN: 1424-8581

  20. #20 drew hempel
    October 13, 2006

    To state that Schwartz relies on antiquated data is to wrongly represent his book — Schwartz relies on the latest data. Also if you read his analysis of the mutation differences then you might deepen your sense of logic (an extra bonus to reading — increasing general critical thinking skills from the analysis of a particular issue: it’s “how” the nucleotides are compared that matters). Schwartz writes in extended analysis on how nucleotides are analyzed and that is obvious to anyone with the book in front of them (just pointing this out for those of you who don’t have such luxuries as the free time to go to a university library).

  21. #22 Steviepinhead
    October 13, 2006

    Here’s what the article reporting the 83% difference in the human-chimp chromosome 22 comparison said:

    Fujiyama’s team found differences that may be more important than the single-letter changes.

    “There is also an impressive number (68,000) of small to large stretches of DNA that have been either gained or lost (these are called ’insertions or deletions’, ’indels’ for short) in one species or the other,” the researchers wrote.

    “These differences are sufficient to generate changes in most of the proteins: Indeed, 83 percent of the 231 coding sequences, including functionally important genes, show differences at the amino-acid sequence level,” they added.

    “Our data suggest that indels within coding regions (genes) represent one of the major mechanisms generating protein diversity and shaping higher primate species.”

    Thus, when coding sequences were compared in terms of the amino-acid sequence differences generated (generated directly by the different DNA sequences, so Schwart’s no-DNA-blueprint remark still make any sense), greater differences were found–functional significance still unknown–that the researchers expected from the much smaller percentage divergences between the overall sequences.

    Does Schwartz give us any reason to expect that the greater–almost double–difference in the overall human-orang sequences should produce fewer protein-sequence differences than were found in the human-chimp comparisons?

    Didn’t think so.

  22. #23 Steviepinhead
    October 13, 2006

    Errata: the word “doesn’t” was omitted after the bolded “still” above. The word “that” in the phrase “that the researchers,” a bit later in the same sentence, should’ve been a “than.”

    Preview, Stevie, preview…

  23. #24 windy
    October 13, 2006

    That’s not an error on Schwartz part but an error on your part — here’s his take on Chromosome 21 newly confirmed:

    Too bad that Schwartz was talking about Chromosome 22.

    Let’s believe Schwartz and say that Chromosome 22 shows 83% amino acid sequence divergence – however, according to the article it’s just a typical, boring chromosome – and remember that the article above says that the hypervariable chromosome 21 is 1.2-1.4 times more divergent. According to this, human and chimp proteins coded by Chr21 would have a sequence divergence of 99.6-116.2 %. Hallelujah! I am convinced! :)

  24. #25 drew hempel
    October 15, 2006

    Too bad more lies on this thread: “comparing” 21 and 22 is not “talking about Chromosome 22: Schwartz: “comparing human chromosome 21 with its apparent counterpart in the chimpanzee, chromosome 22:”

    Now — PZ Meyers even censors his open threads! That dude must be really scared of the truth. Nanobiomotors is not evolution! haha Dawkins is a Freemasonic promoter of Platonic Buckyfullerenes for “synthetic ecology.”

    Dawkins should go work for Cargill, shilling the replacement of Earth’s Brain with silica-Soy DNA biochips.

    Science-Cult Sheep.

  25. #26 windy
    October 16, 2006

    “comparing” 21 and 22 is not “talking about Chromosome 22: Schwartz: “comparing human chromosome 21 with its apparent counterpart in the chimpanzee, chromosome 22:”

    Ah, you’re right, my bad. I got confused by your preposterous claim that Vieira’s article would in any way, shape or form “confirm” Schwartz’s nonsense.

    Please provide the name of any protein that differs in humans and chimps by 83% or more of its amino acid sequence, if you would like to defend Schwartz’s claim that this is the average divergence in one hominoid chromosome. In that case it should be easy to find such a protein in GenBank and provide the link.

  26. #27 drew hempel
    October 16, 2006

    Schwartz states “amino acid sequences” which is confirmed by the link I ALREADY GAVE — google has tons of links on it:

    Human, chimp DNA changes mapped – Science – MSNBC.com
    Fujiyama’s team compared chromosome 22 on three different chimpanzees to its … 83 percent of the 231 coding sequences, including functionally important …
    http://www.msnbc.msn.com/id/5067906/ – 46k

  27. #28 drew hempel
    October 16, 2006

    Meanwhile the evil primates kill their peaceful predecessors.

    ENN FULL STORY
    Haze Distresses Orangutans in Indonesian Reserve

    October 16, 2006 — By Achmad Sukarsono, Reuters

    JAKARTA– Haze from Indonesian forest fires has disturbed orangutans living in a natural reserve on Borneo island, a park official said on Monday, blaming deer hunters for intentionally torching protected areas.

    The fires have been burning for weeks, creating the smoke that has spread over much of Southeast Asia, triggering fears of a repeat of the months of choking haze in 1997-98 that cost the region billions in economic losses.

    Saut Manalu, a senior official at the Tanjung Puting national park where 6,000 orangutans live, told Reuters by telephone that animals are even more affected by the smoke than humans.

    “We can hear them scream late at night,” he said, adding fires had been found inside the reserve that occupies a large swathe of land in Central Kalimantan province on Indonesia’s side of Borneo island.

    “The fires are at the rim while the orangutans live deeper inside. We are focusing on how to put out the fires. If they go out of control, we will take care of the animals. We may need to evacuate them,” said the park official.

  28. #29 windy
    October 17, 2006

    Real science says:
    Fujiyama’s team compared chromosome 22 on three different chimpanzees to its … 83 percent of the 231 coding sequences, including functionally important genes, show differences at the amino-acid sequence level

    Schwartz says:
    these hominoids differ by 83 percent in their amino-acid sequences

    Notice the difference??? If someone says: “I have a list of words in American English and British English and 83% of the words show differences in spelling*”. Do you and Schwartz say “Oh, 83 % of the letters in each word are different! Wow!”

    (*Actually, pronunciation might be a better metaphor, although it’s a bit misleading too. But it would be fun if Schwartz wrote “Many words which are spelled the same, are pronounced very differently by different people, showing that writing is not the ‘blueprint’ it’s touted as being…”)

  29. #30 drew hempel
    October 17, 2006

    Your contention is one of “logical type” — detailed by Gregory Bateson in his book “Mind and Nature.” Schwartz is carrying a difference of information into a “difference of difference” without making an error in logic. This can be easily misunderstood. Schwartz has never stated that 83% of the codes (or letters) are different but he has stated that there is a difference in 83% of the sequences (or letter orders) as the order of codes.

    So when you claim that Shwartz states: “Oh, 83 % of the letters in each word are different” — that’s an error in logical type. Schwartz is just repeating the results of the study: ORDER of letters (not the letters themselves).

    That’s a higher level of logical type — not only is it still correct but it’s an important insight into the information.

    Schwartz is emphasizing the relation between an “amino-acid sequence level” and “coding sequences.”

    Schwartz translated the “coding sequences” into the next order of logical type as “amino-acid sequences.”

  30. #31 drew hempel
    October 17, 2006

    So again your analogy is inaccurate. Schwartz is talking about order of letters causing word changes. Schwartz is accurate. To claim the difference is one of pronunciation and not meaning is wrong, as explained below:

    may 24, 2004 Nature:

    The researchers report in Nature that many of the differences were within genes, the regions of DNA that code for proteins. 83% of the 231 genes compared had differences that affected the amino acid sequence of the protein they encoded.

  31. #32 Steviepinhead
    October 17, 2006

    Well, drew, we at least agree that the remaining wild orangutangs–and their habitats–are entitled to as much protection and deference as possible, whether they should be considered our first cousins or our second cousins.

    The “sequence” quotation remains somewhat elusive. Whether we are talking single-letter changes in the coding sequences or “indels,” we still don’t necessarily know the ultimate impact on the functionality of the protein. Some mutations will add or drop one of the amino acids, or swap two of the existing amino acids around within the length of the (resulting) protein. Some “spelling errors,” whether involving one letter or something more complex, may not cause any functional change whatsoever, because several different triplets redundantly code for each of the amino acids.

    Even if a different amino acid is called for at some point in the sequence of the protein, that change may or may not have much functional impact, depending upon whether the change causes some sort of significantly-different folding or other stuctural change, and upon where any such hypothetical changes fall along the length of the protein–say in a “structural backbone” area or in an “interactive area” (a technically incorrect term by which I mean to include a number of possible concepts, including the “lock” or “key” areas that may be brought into bear as the protein goes about its tasks).

    Cumulatively, there is no doubt that there must be some significant duplications, variations, and functional changes scattered throughout the orang and homo genomes, or they wouldn’t be orangs and we wouldn’t be saps. But rattling off a statistic like 83% greatly exaggerates the likelihood of any particular potentially-sequence altering change included within that percentage resulting in a dramatic functional change. Indeed! Were it otherwise, Schwartz’s argument for a closer orang-homo relationship falls apart ab initio.

    And we are still clueless–based at least on the information offered up in support of Schwartz’s hypothesis to this point–whether the orang-homo 83% differences on just this one chromosome set (however meaningful they do or don’t turn out to be for functionality) compare with a parallel chimp-homo comparison. I would expect/predict that we will see some comparisons where orangs differ less than chimps from homo, and vice versa, but that “overall,” chimps will still differ less from humans–in ways that are significant to the uniqueness of the three species, and to their cladistic relationships–than orangs and humans.

    Undoubtedly, and maybe this is a “weak” interpretation of Schwartz’s claims with which I might agree, there is a vast amount of complex knowledge about the precise comparative proteonomic and regulatory differences buried “under” the “overall” 1.5 to 3% genome-sequence differences that remains to be elucidated.

    So far, however, and however equally endearing, precious, and deserving of respect-protection-admiration orangs may be, my overview is that chimps, bonobos, and gorillas are somewhat more closely related to “us” than are orangs.

    That of course, says nothing about the health of evolution or the strength of the human-great ape connection as a whole. Nor does it says nothing about the relative “value” of orangs. Indeed, it may yet turn out that it would be more of a compliment–if such a value judgment makes any sense–to be orang-related, rather than homo-chimp-gorilla related.

  32. #33 windy
    October 17, 2006

    Schwartz is emphasizing the relation between an “amino-acid sequence level” and “coding sequences.”

    No, he was trying to downplay the relation. “DNA is not the blueprint”, remember?

  33. #34 drew hempel
    October 17, 2006

    Again — I urge you — stevepinhead — to read Schwartz’ 2005 edition of “the Red Ape” wherein you’ll fine lengthy analysis of what these sequence differences mean vis a vis human-chimp relations.

    He’s not at all running away from DNA analysis — in fact quite the opposite — Schwartz is scrutinizing in the larger context of evolution.

    In fact the 83% difference in code sequences amounted to a 20% STRUCTURAL change in proteins — but then to state “Even if a different amino acid is called for at some point in the sequence of the protein, that change may or may not have much functional impact,…”

    Such lack of information in DNA analysis is accounted for by the other sources of information which Schwartz analyzes.

    So why refuse to read his book? Scared?

    Back to the herd!

  34. #35 drew hempel
    October 17, 2006

    Stevepinhead you ask “Does Schwartz give us any reason to expect that the greater–almost double–difference in the overall human-orang sequences should produce fewer protein-sequence differences than were found in the human-chimp comparisons?”

    Then YOU ANSWER YOUR OWN QUESTION !! How convenient!

    That’s science? Try ideology!!

    Read Schwartz book.

  35. #36 drew hempel
    October 17, 2006

    Let us now enjoy the teaser again:

    Here’s a little teaser for you all:

    from P. 236 of the 2005 edition of “The Red Ape” by Professor Jeffrey Schwartz:

    “But cranial and dental morphology does contribute to an understanding of evolutionary relationships — especially when it is backed up by an array of other, not-hard-tissue features. As we’ve seen, though, the most robust theories of large-bodied hominoid relationships — human-orang and chimp-gorilla — contradict the preferred molecular scheme of relatedness. Nonetheless, since the ‘molecular assumption’ grew out of a general agreement of molecular schemes of similarity with an arrangement of organisms based on the study of morphology, one should be able to question the interpretation of molecules or sequence data. Why, for instance, should molecular similarity always reflect recency of molecular change? Why, as is often concluded in morphological analyses, couldn’t similarity in molecule or DNA sequence reflect primitive retention (and, therefore, nonrelatedness), while difference indicates that a taxon changed relative to those that remained primitively similar?”

  36. #37 windy
    October 17, 2006

    So why refuse to read his book? Scared?

    Since it’s a waste of money, that’s why.

    More silliness: He claims that mitochondrial DNA differences in Bornean and Sumatran orangs are greater than between humans and chimps. I checked the article and this claim is wrong.

  37. #38 Alan Kellogg
    October 18, 2006

    LB1 is neither an abnormal human, or a normal hobbit. LB1 is an abnormal hobbit.

  38. #39 drew hempel
    October 18, 2006

    Why not quote Schwartz as you did before so I can prove you wrong again. Thus far you have proven yourself incapable of following basic logic. You have made 3 incorrect claims about Schwartz so far so I’m not surprised that your claims are peetering out into vague hints at your own previous errors.

  39. #40 Carl Zimmer
    October 18, 2006

    Well, this comment thread is becoming more like a comment loop. I think everyone who has wanted to say something about The Red Ape has had his or her chance, several times over. It’s time to close the thread down.

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