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Alien viruses from outer space and the great Archaeopteryx forgery


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The 'London specimen' of Archaeopteryx (in this case, a cast), now the holotype of A. lithographica. Image by H. Raab, from wikipedia.

ResearchBlogging.org

Today I want to talk about something completely different. During the 1980s astronomer Sir Fred Hoyle proposed (with his colleagues Chandra Wickramasinghe, Lee Spetner and R. S. Watkins) that the London Archaeopteryx specimen [shown here: image by H. Raab] was a forgery, made by pressing chicken feathers into plaster laid about the skeleton of the small predatory dinosaur Compsognathus.

This much is well known; also well known is Hoyle et al.’s claim that the specimen was originally acquired by Richard Owen “as a known fraud, with the intent of trapping Darwin and Huxley into claiming it in support of the evolutionary theory” (Hoyle & Wickramasinghe 1986, p. 112). As Gould (1987) argued, Hoyle and Wickramasinghe’s idea that Owen was a creationist and that it would have been to his advantage to discredit Archaeopteryx is a gross and thoroughly naïve misunderstanding of just about every aspect of Victorian palaeontology and sociopolitics, let alone Owen’s personal motivations and philosophy. Hoyle and Wickramasinghe seemed not to credit or even realise how Owen sunk time, effort, work and money into the reality of Archaeopteryx, nor what impact the unveiling of involvement in a hypothetical forgery would have on Owen’s personal reputation, or on that of the British Museum.

Perhaps not as well known as it should be is that Hoyle et al.’s ideas were published in the British Journal of Photography. I have no wish to cast aspersions, or to say anything negative about that venue, but it certainly cannot be considered a normal outlet for scientific results and I somehow doubt that it meets (or met) the standards of peer-review or any conditions usual for scientific results. The bulk of what Hoyle and Wickramasinghe had to say went into a book, Archaeopteryx The Primordial Bird: A Case of Fossil Forgery (Hoyle & Wickramasinghe 1986). They explained how Lee Spetner (a physicist based in Rehovot, Israel) had initially proposed the forgery idea in correspondence, and how R. S. Watkins both photographed the specimen on behalf of the group, and suggested British Journal of Photography as a publication venue.

This rather unfair cartoon of Fred Hoyle is credited to 'Paul S' and appeared in Moreton (1988).

We know from published articles, footnotes in papers, and Hoyle and Wickramasinghe’s book that a few ‘formal’ meetings were held between Hoyle et al. and research and curation staff at London’s Natural History Museum (at the time known as the British Museum (Natural History)). I wonder how friendly these meetings were (minutes do survive). Numerous to-ings and fro-ings in the scientific press were published, most appearing rightly critical of the Hoyle et al. idea, and some being very critical of Hoyle himself (e.g., Charig 1985, Williams 1985, Benton 1987, Connor 1987, Moreton 1988).

The museum’s Alan Charig and colleagues published an authoritative response in Science* (Charig et al. 1986). Stating at the outset that they “reject this forgery hypothesis unequivocally” (p. 623), they refuted in detail all of the evidence alleged to support the claim. They pointed to the many methodological and philosophical problems inherent to it, and showed time and again how the supposedly suspicious details raised by Hoyle and Wickramasinghe couldn’t be taken as evidence of forgery, but were instead genuine geological features or artefacts resulting from decades of preparation (Charig et al. 1986).

* Why Science and not Nature? Hmm.

The ‘Archaeopteryx is a forgery’ idea remains popular among creationists and others on the lunatic fringe, but even they fail to appreciate the bizarre logic behind Hoyle and Wickramasinghe’s argument. As explained in their book, Hoyle & Wickramasinghe (1986) sought to show that Archaeopteryx was a forgery because it proved an obstacle to their idea that dinosaurs and other Mesozoic vertebrates had been transmogrified by viral and/or bacterial storms that had rained down on the Cretaceous world from outer space, grafting new genetic information onto the animals and causing them to change into the birds and mammals of the Cenozoic (Hoyle & Wickramasinghe 1986). In other words, they were seriously proposing this sort of thing…

[‘Transmogrification event caused by incorporation of alien bacteria’ should really say ‘Transmogrification event caused by incorporation of alien VIRUSES’. My bad, sorry.]

As a pre-Cenozoic bird, Archaeopteryx did not fit and had to be explained away (Hoyle and Wickramasinghe were generally unaware of other pre-Cenozoic birds, and ignored Mesozoic mammals entirely). Had this entertaining scenario been presented to the public at the same time as the ‘Archaeopteryx is a forgery’ claim, it is doubtful if it would have been taken as seriously as it was in some circles.

Part of this text is adapted from the biography of Alan Charig that Richard Moody and I published a few years ago (Moody & Naish 2010). I’ve been saying for ages that I wanted to bring the true weirdness of Hoyle and Wickramasinghe’s evolutionary model to the fore, and what better way than to do it than with cartoons.

PS – this article was not intended as a full critique or evaluation of the ‘forged Archaeopteryx’ claim. I don’t feel the need to address this because it’s a total non-starter: there are now more than ten archaeopterygid specimens (most of which have nothing whatsoever to do with Victorian sociopolitics), and – even without the feathers – the skeletal anatomy of Archaeopteryx demonstrates an affinity with Cenozoic birds (Hoyle et al. very wrongly assumed that Archaeopteryx was skeletally identical to Compsognathus), as do a huge number of other Mesozoic maniraptoran fossils (many of which are feathered).

For previous Tet Zoo articles relevant to Archaeopteryx and some of the other issues touched on here, see…

Refs – -

Benton, M. J. 1987. Why Archaeopteryx is not a fake but suffers from too much publicity. Geology Today 3, 118-121.

Charig, A. J. 1985. Is Archaeopteryx a forgery? Biologist 32 (3), 122-123.

CHARIG, A., GREENAWAY, F., MILNER, A., WALKER, C., & WHYBROW, P. (1986). Archaeopteryx Is Not a Forgery Science, 232 (4750), 622-626 DOI: 10.1126/science.232.4750.622

Connor, S. 1987. Riddle of missing rock resurrects Archaeopteryx controversy. New Scientist 115 (1573), 27.

Gould, S. J. 1987. The fossil fraud that never was. New Scientist 113 (1553), 32-36.

Hoyle, F. & Wickramasinghe, C. 1986. Archaeopteryx The Primordial Bird: A Case of Fossil Forgery. Christopher Davies, Swansea.

Moody, R. T. J. & Naish, D. 2010. Alan Jack Charig (1927-1997): an overview of his academic accomplishments and role in the world of fossil reptile research. In Moody, R. T. J., Buffetaut, E., Naish, D. & Martill, D. M. (eds) Dinosaurs and Other Extinct Saurians: A Historical Perspective. Geological Society, London, Special Publications 343, pp. 89-109.

Moreton, S. 1988. Is Archaeopteryx the only old, cracked fossil? Geology Today 4 (3), 83-84.

Williams, N. 1985. Fraudulent feathers? Nature 314, 210.

Darren Naish About the Author: Darren Naish is a science writer, technical editor and palaeozoologist (affiliated with the University of Southampton, UK). He mostly works on Cretaceous dinosaurs and pterosaurs but has an avid interest in all things tetrapod. His publications can be downloaded at darrennaish.wordpress.com. He has been blogging at Tetrapod Zoology since 2006. Check out the Tet Zoo podcast at tetzoo.com!

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The views expressed are those of the author and are not necessarily those of Scientific American.





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  1. 1. Dartian 9:05 am 03/27/2012

    Darren:
    I somehow doubt that it meets (or met) the standards of peer-review or any conditions usual for scientific results

    Considering that British Journal of Photography is a magazine, not a peer-reviewed academic journal, that’s a pretty safe assumption.

    viral and/or bacterial storms that had rained down on the Cretaceous world from outer space

    Also on the post-Cretaceous world, causing (among other things) the Spanish influenza epidemic in the early 20th century.

    Seriously, this stuff is crackpottery on a truly epic scale. The Dunning-Kruger effect should have been called the Hoyle-Wikramasinghe effect instead.

    Link to this
  2. 2. David Marjanović 9:39 am 03/27/2012

    ZOMFG interstellar clouds (or was it comet tails) have low refractory index!!1! They totes consist of bacteria!!!1!eleventyone!!

    Why Science and not Nature? Hmm.

    Do tell what you mean. Given that Nature has the higher impact factor and, AFAIK, already had it back then, are you insinuating the manuscript was submitted to Nature and rejected?

    remains popular among creationists and those on the lunatic fringe,

    but you repeat yourself,

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  3. 3. Dartian 9:53 am 03/27/2012

    David:
    are you insinuating the manuscript was submitted to Nature and rejected?

    Is it known whether Charig et al. even tried submitting it to Nature in the first place? Or did they reason (in those pre-internet days) that publishing their paper in its American counterpart would be a better tactical move and reach a greater number of people?

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  4. 4. naishd 10:20 am 03/27/2012

    Why Science and not Nature? Charig in particular had a thoroughly ‘British’ approach (though of Jewish-Ukrainian parents), was ex-Cambridge, and it certainly seems to me that submitting to Nature would have been considered the superior option. Then again, Science maybe was considered to have more international appeal, I don’t know.

    Darren

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  5. 5. naishd 10:29 am 03/27/2012

    Text now reads: “The ‘Archaeopteryx is a forgery’ idea remains popular among creationists and others on the lunatic fringe”.

    Darren

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  6. 6. McCarthy_Colin 12:53 pm 03/27/2012

    I went to a talk that Hoyle gave at around that time. An audience member asked him the ‘God’ question and Hoyle replied that he suspected that there had been some form of ‘Cosmic Intelligence’ that had “got itself into trouble” (presumably exploding as another big bang). He implied that process leading to the development of the human brain was a step on the way to the ‘Cosmic Intelligence’ reforming. This statement didn’t do an awful lot for his credibility I’m afraid..

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  7. 7. aaronthemad 3:18 pm 03/27/2012

    I love your posts on fringe theories. Just last week I was showing my wife your 2008 post about ” Aquatic proto-people and the theory
    hypothesis of initial bipedalism”.

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  8. 8. falcon121 5:00 pm 03/27/2012

    That was … hilarious. I have a question though. How far phylogenetically is Compsognathus from Archaeopteryx and the rest of Maniraptora?

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  9. 9. Therizinosaurus 5:09 pm 03/27/2012

    I had always assumed Hoyle et al. were only claiming this for the London and Berlin specimens and weren’t so stupid to think there were no other Mesozoic birds or mammals. Guess even the BANDits need somebody to look down on.

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  10. 10. naishd 5:17 pm 03/27/2012

    Mickey (comment 9): in Archaeopteryx The Primordial Bird: A Case of Fossil Forgery, Hoyle and Wickramasinghe take the time to argue that all known Mesozoic birds other than Archaeopteryx – and, I wish I were joking, but I mean Hesperornis and Ichthyornis – were either just “wading reptile[s]” (p. 33) or perhaps forgeries as well (p. 128).

    falcon121(comment 8): I’ll see if someone provides a useful response before I make time to deal with it.

    Darren

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  11. 11. THoltz 5:30 pm 03/27/2012

    Falcon121: depending on the analysis, Compsognathus might be just outside (((Deinonychosauria + Avialae) + Oviraptorosauria ) + Therizinosauria ); or it could be outside of the above (i.e., Maniraptora) plus Ornithomimosauria; or it can be just outside Tyrannosauroidea plus the above set. So it is pretty far removed phylogenetically (and anatomically) from Archaeopteryx, modern birds, and deinonychosaurs.

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  12. 12. THoltz 5:31 pm 03/27/2012

    That said, back in the 1980s, the anatomy of early members of the various coelurosaurian clades were pretty much not well-known.

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  13. 13. naishd 5:33 pm 03/27/2012

    Yes, thank you, we have >>TOM HOLTZ<< (not exactly a world first, but I'm still allowed to brag).

    Darren

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  14. 14. Heteromeles 5:55 pm 03/27/2012

    I’m still in awe of the idea that viruses can cause scales to spontaneously turn into feathers in a way that’s immediately useful to the organism suffering with the virus.

    I’ve just got to see that happen.

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  15. 15. Halbred 6:27 pm 03/27/2012

    I sense a horrible, direct-to-DVD movie involving crocodiles or, perhaps, _Supergators._

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  16. 16. llewelly 6:39 pm 03/27/2012

    Did Hoyle et al seriously propose the transmorgificaiton event was immediate, rather than taking a longer amount of time that would be difficult to distinguish from immediate in the geological record ?

    (A longer time period wouldn’t save the idea, but it would make it seem less ridiculous.)

    Also, if your cartoon is fair, I’m not seeing why the Paul S. cartoon is unfair.

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  17. 17. naishd 6:41 pm 03/27/2012

    “Also, if your cartoon is fair..”

    Did I say it was? :)

    Darren

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  18. 18. GreatAnarch 7:25 pm 03/27/2012

    A bit bonkers I agree, but it shouldn’t be allowed to overshadow Hoyle’s real reputation. He had the bad luck to come down on the wrong side in some of the major astrophysical controversies of the time. In the one case in which he was inarguably right, the origin of the elements, he was denied a Nobel Prize on a technicality. This seems to have put him at odds with the scientific establishment generally and made him reckless in controversy.
    Panspermia went into eclipse when cosmic rays were discovered (not known in Arrhenius’ time of course). However, since comets can be exchanged between the Oort clouds of stars whenever they make close encounters (close here meaning half a light year), I think it may be too early to write it off completely.

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  19. 19. Heteromeles 8:03 pm 03/27/2012

    I can see the cartoon caption now:

    “Dude, that comet just like totally torqued my scales!”

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  20. 20. Dartian 2:50 am 03/28/2012

    GreatAnarch:
    it shouldn’t be allowed to overshadow Hoyle’s real reputation

    Sorry, but the ‘Hoyle was brilliant in his own field’ excuse doesn’t apply here. Evolutionary biologists aren’t unfairly ridiculing Hoyle (and his henchmen) – Hoyle worked long and hard to earn that ridicule.

    As explained by Darren in the OP, the entire basis of Hoyle’s anti-Archaeopteryx campaign was his belief that these fossils must be forgeries – because Hoyle’s personal pet hypothesis required that. In other words: Hoyle started his ‘research’ with the conclusion, and from that he then proceeded by cherry-picking evidence that – in his opinion – supported his hypothesis while systematically ignoring (and, indeed, refusing to even consider) evidence that did not. To call such behaviour ‘bad science’ would be an understatement. If Hoyle’s reputation has been tarnished as a consequence, it’s his own damn fault!

    he was denied a Nobel Prize on a technicality. This seems to have put him at odds with the scientific establishment generally and made him reckless in controversy.

    The Nobel snub wasn’t what made Hoyle go ‘bonkers’. By all accounts, he had been a pugnacious eccentric (bordering on the unhinged) pretty much throughout his entire career. It seems certain that, by fiercely criticising some of its decisions in public, he had already burned his bridges with the Nobel Committee years before it would perhaps have been his turn to receive the prize (in 1983).

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  21. 21. David Marjanović 9:48 am 03/28/2012

    I had always assumed Hoyle et al. were only claiming this for the London and Berlin specimens and weren’t so stupid to think there were no other Mesozoic birds or mammals.

    So you made an argument from personal incredulity about a gigantic argument from ignorance! :-þ

    Guess even the BANDits need somebody to look down on.

    So true, so true.

    Hesperornis and Ichthyornis – were either just “wading reptile[s]”

    *facecouch*

    That said, back in the 1980s, the anatomy of early members of the various coelurosaurian clades were pretty much not well-known.

    That said, Archaeopteryx has arms as long as its legs. Compsognathus has arms as long as its what, thighs? Almost any idiot can tell the difference between the two at first fucking glance.

    (…making the case of the 6th specimen, which was actually referred to C. at first, even more embarrassing!)

    I’m still in awe of the idea that viruses can cause scales to spontaneously turn into feathers in a way that’s immediately useful to the organism suffering with the virus.

    AFAIK, the idea was that the viruses would generate lots and lots of hopeful monsters, a few of which would turn out to be viable.

    To call such behaviour ‘bad science’ would be an understatement.

    It’s simply not science. Starting from your conclusion is… just… wrong.

    And, well, if he started from his conclusions in his own field, too, he can’t have been brilliant in it. If he didn’t, what made him suddenly go bonkers when he turned his mind to biology?

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  22. 22. GreatAnarch 3:56 pm 03/28/2012

    Does anybody really care if Newton spent much of his life predicting the future from the length of the horns of the Beast of Revelations? It in no way diminishes his work on gravity or mechanics, or casts doubt on the laws of motion. Oliver Lodge attempted to contact the dead: how does harm his scientific reputation, or cast doubt on his work in electricity? Hoyle’s work on nucleosynthesis was fundamental, and would have received a Nobel prize long before 1983 if the 1957 BBFH paper had one fewer author. This forgery allegation is a trivial eccentricity of his later years, best forgotten.

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  23. 23. llewelly 4:43 pm 03/28/2012

    It is essential to remember that even very smart people can develop and advocate wildly incorrect ideas.

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  24. 24. naishd 5:18 pm 03/28/2012

    GreatAnarch (comment 22): I don’t know if you’re responding to my article, or to any of the comments, but I just want to note that my article is about the ‘Archaeopteryx is a forgery’ hypothesis (and the ‘transmogrification by incorporation of alien viruses’ hypothesis) specifically, not about Hoyle’s general legacy or entire body of work.

    Darren

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  25. 25. Heteromeles 5:32 pm 03/28/2012

    Yes, but we shouldn’t revere the silly ideas of smart people, either. Mockery is very egalitarian.

    Besides, I’d rather hammer on Newton for his role as the Warden of the Royal Mint in the “Great Recoinage of 1696. Apparently Newton (along with Locke) were responsible for Britain going on a silver standard for currency. Many people suffered horribly when Britain decided that a silver shilling had a standard value (following Newton’s advice), especially since that face value was lower than its value in silver in the rest of Europe. Eventually Britain went on the gold standard, something that lasted until the end of the Empire (Source: Graeber (2011) Debt, the First 5,000 Years).

    While Newton’s position on coinage may have been related to his religious beliefs, at least his alchemical experimentation didn’t cause hunger and civil unrest.

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  26. 26. llewelly 10:22 pm 03/28/2012

    Argument from authority is a common logical fallacy. And rather than one confined to the ignorant, it turns up again and again in everybody – mostly when we are not even thinking about it.

    So it is important to remind ourselves of the mistakes authorities have made.

    Furthermore – psuedoscientists of all stripes love to find some kooky idea promoted by some scientist of otherwise august reputation, and use them to push their own ideas. Linus Pauling, Kary Mullis, Fritjof Capra, and of course Fred Hoyle, have all been called upon as authorities whose work supposedly supports many a pseudoscientific idea.

    So it’s important to explain how and why their bad ideas are not science.

    And I’m quite disturbed that GreatAnarch seems to be advocating pushing Hoyle’s mistakes under the rug.

    Finally I must admit I’m fascinated by weird ideas.

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  27. 27. Dartian 2:47 am 03/29/2012

    David:
    what made him suddenly go bonkers when he turned his mind to biology?

    Perhaps Hoyle didn’t consider biology a real science, and therefore something so far beneath his contempt that he didn’t even feel the need to apply the Scientific Method to it? I find it hard to think of any other plausible explanation for his behaviour.

    I wonder, by the way, if this whole “Archaeopteryx flap” (as Stephen Jay Gould called it) would ever have taken place if history had played out slightly differently? What if Richard Owen had failed (as he almost did) to procure the first* Archaeopteryx specimen for the British Museum in London, and all the Archaeopteryx fossils had remained in German museums instead? Would Hoyle and Wikramasinghe have taken the trouble to travel to East Berlin (this was during the Cold War, remember) to try and find evidence for their forgery claims? I very much doubt it. It’s much easier (and, at least in this particular case, perhaps also safer) to be a crackpot in your own country.

    * For the purposes of the current discussion, that isolated feather fossil that was earlier discovered at Solnhofen can be ignored.

    GreatAnarch:
    Hoyle’s work on nucleosynthesis was fundamental

    Maybe so, but that’s completely irrelevant in this context. What matters here is Hoyle’s case against the authenticity of the Archaeopteryx fossil(s). Which, as has been pointed out, is severely and thoroughly flawed both regarding its fundamentals as well as its specifics.

    This forgery allegation is a trivial eccentricity of his later years, best forgotten.

    You should tell that to the creationists.

    I also strongly suspect that Hoyle himself would have disagreed with the “trivial” part. All available evidence suggests that Hoyle took this stuff quite seriously indeed. He devoted a huge amount of time, effort, and personal prestige to his anti-Archaeopteryx campaign (which in turn was a part of his wider anti-’evolution by natural selection’ campaign); it was no casual exercise in devil’s advocacy for him.

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  28. 28. Lars Dietz 8:03 am 03/29/2012

    Did Hoyle or his coauthors ever say anything about Archaeopteryx after the rebuttals have been published? In those later Hoyle/Wickramasinghe books that I have seen the topic isn’t mentioned at all.
    By the way, the idea that Archaeopteryx is a fake was already suggested by the anti-Darwinian ornithologist Giebel shortly after the first specimen had been published, but I think he changed his mind after Owen’s monograph came out. The reference is:
    Giebel, C. G. A. 1863 Der lithographirte lithographische Vogelsaurier. Z. ges. Naturw. 21, 526–530 & 22, 338–341

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  29. 29. David Marjanović 8:26 am 03/29/2012

    Newton’s position on coinage may have been related to his religious beliefs

    *facepalm*

    Poisons everything, eh?

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  30. 30. Heteromeles 9:53 am 03/29/2012

    @David: I’m not going to trash Newton’s religious beliefs, considering when he lived and what he knew at the time. After all, he was in the middle of the rise of capitalism, when the old Medieval financial systems were being systematically shredded. I don’t blame him for turning to alchemy (or wherever) for the idea that precious metals were innately precious, and therefore something to give stability. He supported the idea that the stamp on a coin was to guarantee its quality and authenticity (over that of a random lump of alloyed silver), not to use it as a trading marker.

    Let’s also look at the alternative: in 1694, the Bank of England was founded when a group of English and Scottish merchants made a loan of 1.2 million pounds to King William II to finance his war against France. In return, they received the right to become a corporation with a monopoly on issuing banknotes. These banknotes (the first paper money in Europe) were effectively IOUs against the debt that the Crown owed the Bank. In other words, they monetized the debt. This debt has never been repaid, and it can’t be, because if the crown paid off that original debt, Britain’s current monetary system would cease to exist.

    Beginning to see why a silver standard was attractive? Ron Paul’s making a similar argument in US politics today. The problem was that he didn’t back down when it became obvious that his idea only made things worse. That’s where he failed as a scientist, because he didn’t respond to the evidence. Then again, that’s what usually happens in politics.

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  31. 31. Owlmirror 2:46 pm 03/29/2012

    David Attenborough describes the discovery of the first Archaeopteryx (a doctor allowed quarryworkers to pay him in fossils, but the doctor later needed to pay for his daughter’s wedding), including the Hoyle and Wickramasinghe forgery accusation. Attenborough also explained the refutation of the accusation: Since they have the counterpart to the fossil slab, it can easily be seen that the pieces match exactly, with no room for the alleged limestone paste impressed with chicken feathers; and mineral patterns of the stone that contains the feather impressions match exactly on both pieces.

    (How does one cite an audio series?)

    Attenborough, David. 2009. Archaeopteryx. Life Stories S01 E08

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  32. 32. Jerzy New 5:08 pm 03/29/2012

    Not Archeopteryx related: anybody knows the story behind this video?
    http://elcomercio.pe/player/1384898

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  33. 33. naishd 6:16 pm 03/29/2012

    Jerzy: I read that this was a recent event (5th March 2012), happened in Arraial do Cabo, Brazil (not Rio, as some websites say). You’re not supposed to pull dolphins by the tail when rescuing them, but of course the average person doesn’t know this.

    Darren

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  34. 34. GreatAnarch 6:39 pm 03/29/2012

    Darren: No, I was responding to some of the comments rather than the article itself. Hoyle’s real work should not be overshadowed by an aberration.
    I just remembered that I sat next to him once at an astrophysics conference. We had a brief chat between presentations (about my work, not his).

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  35. 35. vdinets 12:33 am 03/30/2012

    Jerzy: looks like they were chasing a school of fish and didn’t give it up in time. Note the boobies in the background.

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  36. 36. naishd 5:54 am 03/30/2012

    The dolphin video is really interesting, since it seems to confirm that cetaceans sometimes get beached when they make dumb mistakes – not necessarily because there was anything wrong with the pod ‘leader’ or because they were under stress or anything like that. They just made a major error of judgement. Perhaps this happens all the time.

    Darren

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  37. 37. David Marjanović 10:42 am 03/30/2012

    That’s where he failed as a scientist, because he didn’t respond to the evidence. Then again, that’s what usually happens in politics.

    Yeah.

    mineral patterns of the stone that contains the feather impressions match exactly on both pieces

    Those patterns are dendrites, branched crystals of rust (red, duh) and managese oxide (black) which are often confused with ferns and other plants by laypeople.

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  38. 38. David Marjanović 10:44 am 03/30/2012

    Off-topic: octopus hunting gulls?

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  39. 39. llewelly 11:59 am 03/30/2012

    David, how do you know that isn’t a poor helpless bird being transformed into an octopod by ALIEN DNA FROM COMETS?

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  40. 40. Heteromeles 12:10 pm 03/30/2012

    @David: why not? There’s something vaguely Lovecraftian about it all, though.

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  41. 41. Jerzy New 7:47 am 03/31/2012

    Re dolphins: I saw no fish, and my interpretation was different. Dolphins were escaping something (possibly other dolphin pod) and switched off their sonar, not to be heard.

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  42. 42. Jerzy New 7:58 am 03/31/2012

    BTW, I often wonder which scientific “truths” of today will be in 50 or 100 years considered outright stupid and lunatics by future scientists? Feel free to suggest some.

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  43. 43. Heteromeles 10:43 am 03/31/2012

    @Jerzy: P-values.

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  44. 44. naishd 12:28 pm 03/31/2012

    Jerzy: the idea that anthropogenic global warming is not happening and that all is ok :)

    Darren

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  45. 45. Heteromeles 12:42 pm 03/31/2012

    @Jerzy: that paying to publish in a subscription-only scientific journal is the only way to secure one’s reputation as a scientist.

    Link to this
  46. 46. llewelly 1:33 pm 03/31/2012

    I think science has had its “Cambrian Explosion”, so to speak, and the primary body plans of science are well-established, and it is not likely that any new ones will arise.

    However, I do think we have some new sources of information opening up, and those will change how we view much of science:

    (a) Global warming will force many species to evolve or die (since human habitats will hinder movement). And evolutionary biologists are already watching this closely. Either way, we will learn a lot about evolution. Sadly it seems likely that for vertebrate biologists this will mostly involve learning a lot about the extinction side of evolution. Nonetheless I expect that within a 100 years or less there will be well documented examples of new vertebrate species evolving while scientists watch.

    (b) Today many phylogenetic studies have one or a handful of individuals standing in for a whole population. However, sequencing costs are falling, so that sample size will expand – probably to a 100 or more in many cases. Expanding sample size from a handful to a hundred can radically change the view of the phenomena. Perhaps we’ll find hybridism has played a much greater role in vertebrate evolution than previously thought. Or perhaps not.

    (c) Information processing techniques, combined with better understanding of the underlying chemistry will enable reconstruction of the highly fragmented DNA samples retrieved from plants and animals dead for 10s of thousands of years. This will enable better calibration of genetic clocks (at least for short time scales), and perhaps a correspondence between how genes have changed over the last few 10s of thousands of years, and how bones (where available) have changed over the last few tens of thousands of years.

    (d) Kepler has discovered a ridiculous number of exoplanets, and its successors will discover more. Expanding our sample size from one to thousands will radically change our view of solar system development.

    (e) Kepler will also change our view of how frequently worlds where life-as-we-know-it is possible.

    (f) However – many of the radical overturnings of scientific ideas happened due to sources of information nobody expected to have – telescopes, measuring the magnetic alignment of crystals in rocks on the Atlantic sea floor, and so on. The really big surprises will come from information sources we don’t actually have today.

    (g) Dark matter is the ether of our time.

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  47. 47. Mike from Ottawa 3:07 pm 03/31/2012

    There are not many opportunities at TetZoo for my kind of pedantry, so I can’t help noting that it’s not “Sir Hoyle”. “Sir Fred Hoyle”, or “Sir Fred” are OK, but one does not refer to a knight by “Sir” followed by their last name. Keep that up and someone will take you for American!

    For those Blackadder fans who may wonder, the “Percy” in “Sir Percy” is obviously the first “Percy” in “Sir Percy Percy”. :-)

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  48. 48. vdinets 3:49 pm 03/31/2012

    41: Small fish would be difficult to see, but you can clearly see boobies attracted to a fish shoal and diving for it.

    42: I can bet my monthly salary that global warming will far exceed all “mainstream” predictions. The same goes for predicted mass extinction rates. I am pretty sure that by the end of the century almost all remaining flora and fauna will survive in small, heavily-managed, zoo-like reserves.

    Another thing I think is safe to predict is that the scientists of today will be despised for clinging to archaic, technically obsolete system of scientific publication. I would expect an emergence of a universal Wiki-like depository, where everyone can publish instantly and have his work reviewed by anyone interested, not just 2 randomly selected reviewers. Mathematicians and physicists already have such a thing, called arXiv.

    And, of course, I expect PSC to be completely dead and forgotten. The cleanup of systematics will take a long time, of course.

    One thing I really would like to know is: will strictly cladistics-based classifications prevail, or will the inconveniences they create force turning back to diagosticability-based systems?

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  49. 49. David Marjanović 11:56 am 04/1/2012

    (e) Kepler will also change our view of how frequently worlds where life-as-we-know-it is possible.

    So far, however, it has found maybe one such planet. Maybe. Yes, “hot Jupiters” are still by far the easiest to discover… but still…

    (g) Dark matter is the ether of our time.

    Why? How else would you explain this and this?

    PSC

    What is that? It seems vaguely familiar, but I can’t remember what it means.

    One thing I really would like to know is: will strictly cladistics-based classifications prevail, or will the inconveniences they create force turning back to diagosticability-based systems?

    This is so confused I don’t even know where to begin.

    I’ll try to begin with the principle. You’re confusing three distinct things: phylogenetics, classification and nomenclature.

    Cladistics is the set of methods used by the science of phylogenetics. This has nothing to do with classification and nomenclature, which are not science but sets of conventions.

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  50. 50. naishd 5:11 pm 04/1/2012

    PSC = Phylogenetic Species Concept.

    Darren

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  51. 51. vdinets 5:31 pm 04/1/2012

    David: let me give you an example. The polar bear is nested within the brown bear; it is more closely related to Queen Charlotte Is population than to all others. The current trend is that all taxonomic units must be monophyletic. So we have to either lump the two species (which makes no sense), or split the brown bear; and since Old World suspecies of the latter are even more divergent that QCI population, we’ll have to split it into lots and lots of spp., some with no or almost no differences in phenotype, and all hybridizing freely and sometimes intergrading into each other. That’s extremely inconvenient. This is not a rare situation: it happens very often on all levels (Cetaceans vs. Even-toed Ungulates, Afrotherians vs. Insectivores, etc., etc.) In fact, any highly modified taxon renders some other taxon paraphyletic. This is going to be a nightmare for everybody in applied biology, teaching etc.

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  52. 52. naishd 5:50 pm 04/1/2012

    Vlad: I’m sure others will produce more authoritative responses, but it just isn’t true that any phylogenetic discovery represents a problem for taxonomy, teaching or communication. Why? Because species are artificial segments of lineages, they are not clades, and they don’t need to be monophyletic. As you know, there isn’t even widespread agreement over what a ‘species’ is (my personal preference is for a ‘diagnostic species concept’ sensu Cracraft).

    This is totally different from the situation with major clades. Yes, artiodactyls are paraphyletic with respect to cetaceans – but why is this a problem? Most people who care now understand that whales are modified relatives of deer and hippos, and those interested in biology are surely interested in teaching this to others.

    Darren

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  53. 53. Heteromeles 7:44 pm 04/1/2012

    Or we can get beyond mammals and get really silly. Let’s take, oh, wheat for an example:

    Bread wheat is an allohexaploid, and contains the following genomes:
    –one from Triticum uratu
    –one from something resembling Aegilops speltoides (possibly Aegilops tauschii, or Aegilops cylindricus. Experts differ).
    –one from Aegilops squarrosa.
    And if you remember your genetics, this becomes allohexaploid because hybrid plants typically undergo meiotic failure as part of becoming a viable organism.

    This used to be taught as wild, diploid einkorn wheat crossed with an Aegilops to produce emmer and durum wheat, which crossed with another Aegilops to produce bread wheat, spelt, etc.

    Most of the ancestors of bread wheat are still extant.

    Note that this situation IS NOT UNUSUAL for the wheat tribe or even grasses in general. It just happens to be better documented in bread wheat, because it’s such an important crop. There are other wild tetraploid Triticums, for example, and spelt is thought to have resulted from at least two independent hybridization events from the parent species. Heck, when I was a TA, we used to collect a naturally occurring intergeneric grass just off campus for use in torturing plant taxonomy students (it was an obvious hybrid).

    The take-away point is that there are more plants than vertebrates out there. There may be even more hybrid plants out there than there are vertebrates. Every time I hear someone blowing the trumpet for phylogenetic species concepts, I ask them to come up with clean approaches to this issue. There isn’t one, but that doesn’t make it irrelevant.

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  54. 54. llewelly 7:47 pm 04/1/2012

    Vlad, I think you have the wrong islands; the QCI are famous for not having any brown bears. It’s a different brown bear population which are closest to polar bears; probably the Alexander Archipelago brown bear population (just to the north of the QCI).

    http://www.polarbearsinternational.org/polar-bears/polar-bear-comprehensive/evolution

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  55. 55. vdinets 9:27 pm 04/1/2012

    llewelly: of course! sorry for the mistake.

    Darren: of course species are clades. They can by polymorphic, they are usually made up of populations, etc. Our own species is made up of dozens of lineages with behaviorally suppressed hybridization, distinct habitat preferences, and facial differences evolved to suppress outbreeding.
    But let’s look at higher levels. Insectivora was a nice, easily defined clade. Now parts of it are in Afrotheria, a clade containing animals with nothing in common from a layman’s point of view.
    Let’s say you are a 3rd grade teacher and I am your pupil. Try explaining to me what an Ungulate is, considering that some of them now have flukes and blowholes :-)

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  56. 56. llewelly 9:36 pm 04/1/2012

    “Dark matter” has exactly one characteristic in common with ordinary matter: it has gravity. In every other respect, it is entirely unlike matter.

    If you bang on a table, you are repelled by the electromagnetic forces between your exterior electrons and the table’s exterior electrons. “Dark matter” has no such interaction; the bullet cluster and its analogues show this quite clearly; they are explainable if and only if “Dark matter” has no electromagnetic properties.

    Now there are neutral particles, neutrinos and neutrons, and so forth, which have mass but no electromagnetic properties. But they do have nuclear properties. Dark matter appears not to; all particle collider searches for “Dark matter” have so far come up empty handed. (But perhaps the LHC will change that.)

    I’ll leave the other properties of matter as an exercise for the reader, but I assure you, “Dark matter” has only one so far detected; gravity. It has nothing else in common with any other sort of matter.

    The scientists who theorized the ether did the best they could to explain the phenomena they had observed, and the scientists who theorized dark matter have done likewise, albeit with far better technology, and better background science.

    But then an unexpected discovery was made; the velocity of light in a vacuum was shown to be constant, irrespective of the velocity of the frame of reference it was measured from. And suddenly a ridiculously stiff medium which suffused everything and impeded nothing no longer made sense.

    That’s how most scientific conclusions get overturned; some new, unexpected observation must occur. Of all the items I listed, all of the others are based on observations scientists have already made; they are interesting changes to watch for, but they aren’t likely to upset scientific conclusions, because they are founded on things scientists have already observed, or they are reaching into areas where scientists really have little more than speculations.

    If there is a new observation which throws dark matter into doubt – that would upset a scientific conclusion. You can’t predict the overturning of a scientific conclusion without making a unlikely statement. Of all my suggestions, my claim that “Dark matter is the ether of our time” is by far the least likely to be shown true. But it is the only one which has any chance at all of overturning scientific “truth”.

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  57. 57. llewelly 9:38 pm 04/1/2012

    Somehow I lost the beginning of my comment, due to the lack of adequate commenting facilities (preview.) Trying again:

    David, ether had exactly one characteristic in common with ordinary matter: it was a wave-conveying medium. In every other respect, ether was entirely unlike matter.

    “Dark matter” has exactly one characteristic in common with ordinary matter: it has gravity. In every other respect, it is entirely unlike matter.

    If you bang on a table, you are repelled by the electromagnetic forces between your exterior electrons and the table’s exterior electrons. “Dark matter” has no such interaction; the bullet cluster and its analogues show this quite clearly; they are explainable if and only if “Dark matter” has no electromagnetic properties.

    Now there are neutral particles, neutrinos and neutrons, and so forth, which have mass but no electromagnetic properties. But they do have nuclear properties. Dark matter appears not to; all particle collider searches for “Dark matter” have so far come up empty handed. (But perhaps the LHC will change that.)

    I’ll leave the other properties of matter as an exercise for the reader, but I assure you, “Dark matter” has only one so far detected; gravity. It has nothing else in common with any other sort of matter.

    The scientists who theorized the ether did the best they could to explain the phenomena they had observed, and the scientists who theorized dark matter have done likewise, albeit with far better technology, and better background science.

    But then an unexpected discovery was made; the velocity of light in a vacuum was shown to be constant, irrespective of the velocity of the frame of reference it was measured from. And suddenly a ridiculously stiff medium which suffused everything and impeded nothing no longer made sense.

    That’s how most scientific conclusions get overturned; some new, unexpected observation must occur. Of all the items I listed, all of the others are based on observations scientists have already made; they are interesting changes to watch for, but they aren’t likely to upset scientific conclusions, because they are founded on things scientists have already observed, or they are reaching into areas where scientists really have little more than speculations.

    If there is a new observation which throws dark matter into doubt – that would upset a scientific conclusion. You can’t predict the overturning of a scientific conclusion without making a unlikely statement. Of all my suggestions, my claim that “Dark matter is the ether of our time” is by far the least likely to be shown true. But it is the only one which has any chance at all of overturning scientific “truth”.

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  58. 58. Heteromeles 11:46 pm 04/1/2012

    Our own species is made up of dozens of lineages with behaviorally suppressed hybridization, distinct habitat preferences, and facial differences evolved to suppress outbreeding..

    Um, I better not show this to my partner, who’s of a very different “lineage” than I am. Of course, I’ve got ancestors from all over Europe and teeth that appear oriental, possibly thanks to Genghis Khan or one of his soldiers, so outbreeding goes back a millennium in my lineage. Probably more.

    Yes, people look different, but there’s as much outbreeding as inbreeding, and habitat preferences are more learned than biological.

    Heck, modern racism didn’t even come about until Christians needed an excuse to enslave Africans. Slavery was illegal in Medieval Europe (due in part to the abuses of the Roman Empire. Note that slavery is not serfdom, although funtionally they’re similar). Slavery became economically desirable for a variety of reasons in the 15th and 16th Centuries, and so people started coming up with theories that others who looked different from “us” (especially those with darker skin) were “inferior,” not quite human, and therefore it was okay to enslave them (see Graeber’s Debt, the first 5000 years for the gory details).

    Given the sorry record of eugenics and scientific racism, I’d say that humans as a species really aren’t a good example of anything other than within-species diversity. The evidence doesn’t go further than that.

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  59. 59. vdinets 11:59 pm 04/1/2012

    Heteromeles: I enjoyed sampling other ethnic groups myself when I wasn’t married, but that’s not the point. In almost every society (and I’m not even sure about “almost”), the percentage of inter-ethnic marriages is lower than expected if mating was completely random. It is not just because every group considers itself the best: there are numerous isolating mechanisms, from simple linguistic differences to cultural taboos. Some groups (including my people, the Ashkenazim) have been so isolated that inbreeding became a serious problem which I am doing my best to alleviate. A century ago one could argue that Jews were on a separate evolutionary trajectory ;-)
    I didn’t get your point about slavery, sorry. What does it have to do with intraspecific systematics?

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  60. 60. Dartian 4:12 am 04/2/2012

    Vladimir:
    Insectivora was a nice, easily defined clade.

    Whoah, you picked one of the worst possible examples to make your point (such as it is).

    There was never any real agreement among zoologists about which taxa did, and which did not, belong to the traditional Insectivora. It was a notorious wastebasket taxon for small, morphologically plesiomorphic mammals that were “not clearly referable to some more distinctive order” (to use G.G. Simpson’s words).

    Now parts of it are in Afrotheria

    It’s worse than that, actually (well, ‘worse’ from your point of view). Most authorities on mammalian taxonomy (e.g., Wilson & Reeder) no longer recognise a taxon called ‘Insectivora’ at all; hedgehogs are in the ‘order’ Erinaceomorpha, whereas shrews, moles, and solenodons are in the ‘order’ Soricomorpha. (And scandentians – which sometimes were and sometimes weren’t considered members of the old ‘Insectivora’ – are neither afrotherians or traditional insectivores, but euarchontoglirans.)

    a layman’s point of view

    And how far do you suggest we should go with this argumentum ad populum? If laypeople think that whales are fish, should zoologists adjust their classification systems to respect those beliefs?

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  61. 61. naishd 5:53 am 04/2/2012

    Vlad: with respect, I don’t think there’s much substance to your main argument – this being that the non-monophyly of many traditional groups presents a problem to communication and teaching. Well, I’ve not only lectured to undergrads at university level, I’ve also taught whole courses on tetrapod diversity, phylogeny and history, and it doesn’t seem to me that people have a problem with any of this stuff so long as it’s explained properly.

    Species: many extant species are clades, since they’re understood to include all descendants of a single ancestor. But, since species evolve from species, species – by definition – cannot be clades across the board: rather, it’s my interpretation that the entities we term ‘species’ are those bunches of closely related lineages that share characters and look alike, yet don’t necessarily include all descendant populations. A ‘species’ is thus a non-monophyletic unit of convenience. As a non-monophyletic unit, it is not a clade.

    Other taxa: people have always appreciated that the membership of taxonomic groups changes over time. I do not under how anyone can have a problem with this – the contents of groups will change continually, for as long as we make discoveries about the world. If we find in future that, say, tarsiers are not close to primates, but are actually afrotherians, I hope you will agree that any taxonomic system should reflect this new position. If you don’t agree, are you really interested in what we’ve learnt about phylogeny? Cetaceans were once excluded from ‘viviparous quadrupeds’, then they were understood to be mammals of some sort, then it was realised that they were somehow close to ‘ungulates’, then it was suggested that they were especially close to artiodactyls, then it was realised that they were deeply nested within Artiodactyla. So, any discussion of what Artiodactyla is must now include the explanation that the group includes not only terrestrial, long-limbed, hoofed taxa, but also a set of highly modified, aquatic forms with flippers, tail flukes and blow-holes. Seriously – what’s the problem here? I’ve never seen anyone have a problem with this. Whales are artiodactyls. Whales are mammals. Tree-based thinking and the idea that clades are nested within others only enhances people’s understanding of evolution and diversity.

    Darren

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  62. 62. David Marjanović 1:16 pm 04/2/2012

    Why? Because species are artificial segments of lineages, they are not clades, and they don’t need to be monophyletic.

    (Depends on the species concept – but, AFAIK, not many people advocate a concept under which species have to be clades. I don’t even know if the PSC is one of those.)

    Darren: of course species are clades.

    “Clade” is a synonym of “monophylum”. It is defined as “an ancestor and all its descendants”.

    Our own species is made up of dozens of lineages with behaviorally suppressed hybridization, distinct habitat preferences, and facial differences evolved to suppress outbreeding.

    …Seriously? Have you got any evidence there isn’t just geographic (and, more recently, cultural) separation at work here?

    But let’s look at higher levels. Insectivora was a nice, easily defined clade.

    LOL. It never was. I once read its diagnosis by G. G. Simpson which included several items like “can be semiaquatic but not too much”…

    Now parts of it are in Afrotheria, a clade containing animals with nothing in common from a layman’s point of view.

    Two options:

    1) Fuck them. Phylogenetics isn’t done for anyone’s convenience, it’s done to understand reality, however messy reality may be.

    2) Educate them. It seems that all afrotherians share extremely delayed tooth replacement, for instance; that’s a character that’s easy to understand for everyone!

    Let’s say you are a 3rd grade teacher and I am your pupil. Try explaining to me what an Ungulate is

    There are no ungulates anymore. Even Artiodactyla and Perissodactyla may not be sister-groups. There’s simply nothing to explain here. :-|

    Now there are neutral particles, neutrinos and neutrons, and so forth, which have mass but no electromagnetic properties. But they do have nuclear properties.

    Well, neutrinos do not react to the strong nuclear force, only to the weak one, which is… weak. And while they have a mass, it’s ridiculously tiny. So I wouldn’t be surprised if the LHC found particles that have a mass but maybe don’t even react to the weak nuclear force.

    Slavery was illegal in Medieval Europe

    Completely untrue – in theory.

    In practice, 1) it was illegal to enslave Christians, and heathens were increasingly hard to come by after 1100 or 1200 or so; 2) slaves were expensive, so pretty much nobody in Europe was able to afford one. There was lots of slave trade through western Europe to the empire(s) of Islam as long as heathens were available.

    Given the sorry record of eugenics and scientific racism, I’d say that humans as a species really aren’t a good example of anything other than within-species diversity. The evidence doesn’t go further than that.

    In particular, all the variation is clinal, and the alleles of different genes have very different geographic distributions.

    Most authorities on mammalian taxonomy (e.g., Wilson & Reeder) no longer recognise a taxon called ‘Insectivora’ at all; hedgehogs are in the ‘order’ Erinaceomorpha, whereas shrews, moles, and solenodons are in the ‘order’ Soricomorpha.

    Why, actually? What’s wrong with Lipotyphla, or Eulipotyphla if you must?

    And isn’t Solenodon the sister-group to the rest of Eulipotyphla, which has in all seriousness been called Eueulipotyphla? In the late 90s, the hedgehogs showed some really crazy long-branch attraction in a few molecular trees, but that’s over, they behave now.

    Other taxa: people have always appreciated that the membership of taxonomic groups changes over time. I do not under how anyone can have a problem with this –

    (Well, creationists do. But that’s really beside the point.)

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  63. 63. vdinets 1:21 pm 04/2/2012

    Darren, I am not suggesting that we establish the preferred taxonomy by conducting a referendum among kindergarten students. But look at the bigger picture. Just a while ago, all living things were divided into clear, intuitively obvious sets. Animals, vertebrates, reptiles, lizards. Now you need a Ph.D to explain to your kid why crocodiles are not related to lizards, why Archea are so different from other germs, and why Flipper is a mutant hippo. I sense an imminent popular revolt here :-)

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  64. 64. vdinets 1:30 pm 04/2/2012

    David: cultural suppression of hybridization is still suppression of hybridization. It can conceivably lead to speciation, and not only in primates (think songbirds).

    And I am pretty sure it’s not all cultural. Most of anatomical differences between ethnic groups are in facial features. It’s the same with almost all other higher primates: look at chimp subspecies, marmozets, guenons, etc., etc. The pattern is too widespread to be without a function.

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  65. 65. John Scanlon FCD 1:55 pm 04/2/2012

    Hoyle did an evening lecture at Sydney Uni while I was an undergrad, mainly on what he regarded as the persuasive evidence for bacteria and viruses existing in space (when introducing viruses to the mix, he remarked ‘May as well be hung for a sheep as a lamb’). It all tied in with his preference for the Steady State over Big Bang; given that the evidence for cosmic expansion was incontrovertible, the assumption that density stayed fairly constant required the creation of additional matter here and there, now and then. This might have been protons and electrons as he’d initially assumed, but he was now strongly attached to the idea that bacteria and viruses were being created ex nihilo throughout spacetime, and make up a large proportion of interstellar dust grains.

    A few years later I picked up a bargain from a remainder pile: ‘Fundamental Studies and the Future of Science’, which is more-or-less the proceedings of a 1982 symposium in Colombo, edited by Chandra Wickramasinghe, and with several contributions by Hoyle including such classics as the interstellar grains paper, the conference epidemic proposed to be caused by a shower of viruses from space (I remembered that making the news earlier, when I mainly knew Hoyle as the author of ‘The Black Cloud’), and a proof (?) that plate tectonics is only possible if the continents float on a layer of gas. There are also papers by Arthur C. Clarke and Fritjof Capra, and many more. Quite entertaining all round – if difficult and obscure in parts – and I think it fairly represents the last decade or so of Sir Fred’s scientific interests and output. No Archaeopteryx, unfortunately.

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  66. 66. llewelly 12:59 am 04/3/2012

    Heteromeles:

    Genes are the elements of selection. If brain power and compute power were free, clades and trees would ideally be constructed for every gene from every organism from which genes could be obtained.

    But that would be a truly ridiculous number of trees – and vast swathes of them would be almost identical, especially when viewed at the granularities most appropriate for studying evolution.

    Mechanisms for grouping similar trees together are absolutely essential.

    Evolutionary cladistics as presently practiced is a bag of statistical tricks for devising trees which are (a) representative of most of the theoretical per-gene trees which are relevant to the populations studied, and (b) show interesting features of evolution.

    In an ideal world, such statistical tricks would be determined based on an in depth understand of the mechanisms of copying, mixing and transferring of genes, particularly at the granularities relevant to the scientific question studied.

    But for historical reasons, the statistical tricks presently in use are subject to anthropocentric bias, and are thus much more appropriate to creatures who copy, mix, and transfer genes more or less the way humans do.

    Plants do not copy, mix, and transfer genes quite the way humans do, so current techniques of evolutionary cladistics work poorly for plants because plants are fucking weird.

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  67. 67. Heteromeles 1:10 am 04/3/2012

    Um, even if we could assign one tree per elemental particle, I don’t think there are enough elemental particles in this universe to calculate gene trees for any major group of organisms. It’s not a matter of free computing, it’s a matter of combinatorial math running into the fundamental limits of the universe. Cladistics will always have to deal with this particular reality, no matter how fast computers get.

    I’d also add that botanists have pioneered some of the tricks used, so the bias exists as much in the researchers as in the techniques. Also, botanists so routinely deal with hybridization that we teach it to undergrads.

    As for weirdness, so far as the world’s concerned, bacteria and viruses are the norm for genomics, fungi and protists are fairly unusual, plants are definitely unusual, and vertebrates are so far on the extreme end of the weirdness spectrum that no technology should be based on them with any expectation of general relevance to the genomes of the rest of the biosphere. Unfortunately, phylogenetics doesn’t reflect this reality.

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  68. 68. Dartian 4:17 am 04/3/2012

    David:
    Why, actually? What’s wrong with Lipotyphla, or Eulipotyphla if you must?

    The most recent update of Wilson & Reeder is from 2005, and at that time, the monophyly of a clade that included hedgehogs, shrews, moles and solenodons was still in doubt. In fact, there’s still no real certainty about (eu)lipotyphlan monophyly today; the solenodons, in particular (as well as the extinct nesophontids), are still difficult to place in the placental tree. By using the respective names Erinaceomorpha and Soricomorpha (both of which were coined by W.K. Gregory in 1910), Wilson & Reeder were probably ‘playing it safe’ – i.e., they named clades with (at the time) relatively undisputed content.

    And isn’t Solenodon the sister-group to the rest of Eulipotyphla

    The most recent results suggest that, yes (bearing in mind, of course, that Solenodon is still a highly under-studied taxon). But, as I said, that wasn’t known in the early oughties.

    has in all seriousness been called Eueulipotyphla

    Yikes, has someone actually used that name in earnest? I thought it was just a tongue-in-cheek suggestion.

    Incidentally, for an insight into the morass that is ‘insectivoran’ nomenclature, systematics and phylogeny, see Symonds (2005). His review is, inevitably, by now slightly outdated, but, among other things, the paper includes the delightfully titled section “Emptying the wastebasket” – which concludes with the slightly defeatist sentence “The wastebasket may have been emptied, but its contents are currently strewn over the floor.” (p. 109).

    Symonds, M.R.E. 2005. Phylogeny and life histories of the ‘Insectivora’: controversies and consequences. Biological Reviews 80, 93-128.

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  69. 69. Christopher Taylor 4:53 am 04/3/2012

    Heteromeles in # 53:

    You’re either confusing species concepts, or confusing the phylogenetic species concept with phylogenetic nomenclature. The phylogenetic species concept, as the term is most often used (the smallest lineage of organisms sharing one or more diagnostic characters), was not so named because it requires species to be monophyletic, but because it was supposed to be the smallest appropriate unit for a phylogenetic analysis (I would have preferred it to have been called something like ‘diagnostic species concept’, but no-one asked me [probably because I would have been less than ten years old at the time]). There have been species concepts proposed that require species monophyly, but they’re not really workable and I don’t think that they’re very popular. In particular, if we do define a ‘species’ as the smallest diagnosable lineage, then referring to a ‘monophyletic species’ is potentially meaningless as, almost by definition, you can’t identify exclusive monophyly at a level below the species.

    If what you’re doing is confusing the phylogenetic species concept with phylogenetic nomenclature, then I agree with you that the situation that you describe is problematic for the latter (and I say that as a supporter of phylogenetic nomenclature). Others disagree with me: it depends on whether you’re willing to accept a classification with overlapping but non-hierarchical taxa (I don’t).

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  70. 70. Dartian 5:28 am 04/3/2012

    Christopher:
    I say that as a supporter of phylogenetic nomenclature

    Weren’t you still on the fence on this issue only a couple of years ago? When did you go over to the Dark Side?

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  71. 71. Heteromeles 6:34 pm 04/3/2012

    About human faces, slavery, and so on. The basic point about slavery is that, 1) as David pointed out, slavery used to be based on religion more than skin color, and 2) racial differences only became important in a context where groups of people had to be classified as inferior because of who they were, not what they believed.

    This is why it’s dangerous to start talking about race as a basis for human cladogenesis. The concept of race as we understand it isn’t that old or objective, and it certainly doesn’t have a lot of biology behind it. For example, “black” contains most human genomic diversity (in phylogenetic terms, we’re all black, because every other race is well-embedded within the African clade. Skin color is irrelevant to blackness in a phylogenetic sense), while “Hispanic” ranges anywhere from people of pure Native American ancestry* to people whose ancestors include Conquistadors, Aztec royalty, and African slaves (in phylogenetic terms, we’re separating out the reticulation events and calling them a separate, incipient clade).

    Both of these terms are considered racial classifications in the US, and are, in fact, used as the basis for medical tests, whether that makes sense or not. I recently got a blood test where the optimal ranges were different depending on whether I was “black” or “non-black,” and I know this testing criterion has been criticized within the medical community for ignoring the genetic diversity of African Americans.

    As I said above, it’s better to regard humans as a complex species, rather than as a group of subspecies.

    *Amusing anecdote about the Chumash tribe of California. A few decades ago, the standard ethnographies said they were all extinct. Then, when the discriminatory laws against Indians were repealed in the 1970s, they suddenly showed up again. Now they have their own reservation and casino. What happened was that they a) realized that being considered Indian was a bad thing around 1900 or before, and b) realized that whites couldn’t tell them apart from Mexicans. Since most of them already had Hispanic surnames (thanks to the Spanish Missions), they simply started calling themselves Mexican-Americans and disappeared into the population. Then, once it was safe to be Indian again, they re-emerged as a tribe. I got to meet a Chumash healer, and her great uncle had been a California state legislator–a “Hispanic” one. That’s race for you.

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  72. 72. Christopher Taylor 6:43 pm 04/3/2012

    Weren’t you still on the fence on this issue only a couple of years ago? When did you go over to the Dark Side?

    I went over to the Dark Side before I had much of an online presence, so you may be misremembering. I have said on more than one occasion that introducing phylogenetic nomenclature is problematic because too many organisms remain poorly known phylogenetically. There are also occasions, such as the aforementioned hybridogenesis events, where I feel that an ‘as phylogenetic as practical’ approach may be preferable to a strictly phylogenetic approach. But these are pragmatic issues rather than theoretical ones.

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  73. 73. vdinets 7:04 pm 04/3/2012

    Heteromeles: Did I even mention race? I think I said “ethnic groups”. There are many more well-defined subspecies (races, or whatever you call them) in H. sapiens than the US classification recognizes. Just in Ethiopia there are at least twenty ethnic groups with distinctive facial features that any Ethiopian can instantly recognize (so they are separate species if you use a diagnosticability-based species concept). And racism is as diverse as races: remember Hutu genocide of Tutsis. When people talk about racism in Russia, they usually mean racism by Slavs towards peoples of the Caucasus, who, ironically, are often called “black” by Russian racists.

    Of course, racial differences have always been important for people. It’s part of our biology to see unfamiliar-looking faces as alien. Even little kids do that. And even in societies where all ethnic groups are equal in terms of status, inter-ethnic marriages are less common than they would be if mating was random. We can, and should, try to overcome those instincts, but it’s unscientific to deny that they exist.

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  74. 74. Dartian 12:33 am 04/4/2012

    Christopher:
    I went over to the Dark Side before I had much of an online presence, so you may be misremembering.

    Well, in 2008, you did write on your blog that “I’m a pretty determined fence-sitter in this case”. (Full article here.)

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  75. 75. Christopher Taylor 2:54 am 04/4/2012

    Excuse me while I sit down with a large plateful of tasty, tasty words.

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  76. 76. David Marjanović 8:06 am 04/4/2012

    Just a while ago, all living things were divided into clear, intuitively obvious sets. Animals, vertebrates, reptiles, lizards.

    There’s very little intuitively obvious about it all. How many people around you, in your family for instance, can reliably distinguish salamanders and lizards? How many even know there is a difference, and neither is a subset of the other?

    Even Linnaeus lumped all salamanders into the species Lacerta salamandra. (Well, till Österdam & Linnaeus described Siren lacertina in 1766 – but that paper makes very clear he was not aware that lizards never have aquatic larvae.)

    And I am pretty sure it’s not all cultural. Most of anatomical differences between ethnic groups are in facial features. It’s the same with almost all other higher primates: look at chimp subspecies, marmozets, guenons, etc., etc. The pattern is too widespread to be without a function.

    Can’t it be neutral?

    Or how about recognition of individuals, which it’s actually used for in social species? That there’s some phylogenetic signal in it is inevitable when facial features are heritable.

    he was now strongly attached to the idea that bacteria and viruses were being created ex nihilo throughout spacetime

    Whoa. That sounds like Randall Munroe setting two kooks loose on each other – except it’s one and the same kook!

    As for weirdness, so far as the world’s concerned, bacteria and viruses are the norm for genomics, fungi and protists are fairly unusual, plants are definitely unusual, and vertebrates are so far on the extreme end of the weirdness spectrum that no technology should be based on them with any expectation of general relevance to the genomes of the rest of the biosphere. Unfortunately, phylogenetics doesn’t reflect this reality.

    How about phylogenetic networks? There are already computer programs for those.

    Yikes, has someone actually used that name in earnest? I thought it was just a tongue-in-cheek suggestion.

    The paper that coins it uses it in earnest. Strangely, it’s not among the 6 Google results. This paper contains the sentence “Eulipotyphla without Solenodon would create the Eueulipotyphla (D. Archibald, pers. comm.)”; that’s it.

    Others disagree with me: it depends on whether you’re willing to accept a classification with overlapping but non-hierarchical taxa (I don’t).

    I’d say that with phylogenetic nomenclature there’s no need for classification. There’s nomenclature (a set of names and their definitions), and there’s its application to a phylogenetic hypothesis; that’s all.

    And even in societies where all ethnic groups are equal in terms of status, inter-ethnic marriages are less common than they would be if mating was random.

    How sure are you that’s not due to language, culture & stuff?

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  77. 77. David Marjanović 8:09 am 04/4/2012

    …Oh. This is the paper that coins Eueulipotyphla, in these two sentences farther down:

    “Should the monophyly of the Eulipotyphla be disrupted, it is almost certainly going to be due to Solenodon lying just outside the remaining Eulipotyphla. In this case, it is suggested that the clade composed of Erinaceidae, Soricidae, and Talpidea be called the Eueulipotyphla (phonetically, the you-you-lipotyphla).”

    So, no, nobody seems to have used it ever since; and Archibald’s original suggestion may have been a joke, though Waddell & Shelley apparently took it seriously for the length of a paper.

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  78. 78. vdinets 9:03 am 04/4/2012

    David: everybody in my family knows the difference between lizards and salamanders! Even my mother has been subjected to high doses of zoology despite her prolonged resistance.
    Back to the subject, of course there were some difficult issues even in the good old days, but you could still describe any large taxon in a line or two of simple English. People here have said that Insectivores were not an obvious grouping, but I remember that the first field guide to mammals I’ve ever read described them as “Small to very small mammals, primarily insectivorous, with short limbs, long pointed snouts, small eyes, and pointed, weakly differentiated teeth.” Sounds simple enough to me. The guide was for Russia, but you only need to add “placental” to make it work worldwide. Now, please try to describe Afrotheria in one sentence :-)

    Note that in some primates (guenons, marmozets) facial features differ strikingly between taxa, but there’s very little variability within each population. It seems likely that they first evolved for hybridization avoidance, and only later were co-opted for individual recognition in apes (not sure if any other primates use them that way). Voice is also used for individual recognition in our species, but does it show any phylogenetic differences? (Actually, I am not sure anyone has checked, but for now it seems like it doesn’t).

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  79. 79. Heteromeles 9:40 am 04/4/2012

    Or compare that with the (current) glomeromycota. When I started my PhD work in the late ’90s, they were an order within Zygomycota. By the time I finished my (ecological) research on them, they were considered their own phylum. This didn’t bother those of us who worked on them, since it was obvious they had little in common with the zygomycetes, aside from appearance. What it showed instead was what happened when researchers started getting a good look at fungal genetics. Glomalean fungi are among the most common fungi on the planet, so it’s roughly equivalent to finding that ants are a separate phylum, and are actually the sister group to vertebrates, despite the fact that they look like insects.

    The problem for mycology is that the morphological appearance of many fungi has nothing to do with what they’re related to. For example, truffles turn out to be a life form, not an evolutionary lineage, and they’ve evolved many, many times independently. Even the glomalean fungi have come up with species that look (and act) like truffles.

    As for bacteria, the point is that they tend to share genes through a variety of mechanisms, and most of our notions of phylogeny assume that this doesn’t happen.

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  80. 80. llewelly 9:59 am 04/4/2012

    “As for bacteria, the point is that they tend to share genes through a variety of mechanisms, and most of our notions of phylogeny assume that this doesn’t happen.”

    This means that for bacteria, organisms are not the proper unit of phylogeny (much as with plants, except bacteria are arguably worse).

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  81. 81. Heteromeles 10:16 am 04/4/2012

    Um, Llewelly, no. If you start getting to the point where “my theory must be right! I know, it applies to genes, not to organisms. Then it all works!” That’s when you’re not doing science any more.

    Theories have to be falsifiable.

    VDInets is doing the same thing by spinning race down to individual small groups, so long as he wins the argument that there’s subspecies within the human species. (example: Rwanda has also been described as “those without shoes killed those who had shoes.” Tutus and Hutsis are different tribes, not different lineages (they intermarried extensively). Genocide refers to death of a people, not a genetic unit. You could theoretically have a genocide of Americans, even though we aren’t a subspecies of humanity).

    Botanists have little trouble talking about species, subspecies, varieties, and hybrids. The problem comes when zoologists come marching in, tell us we’re wrong, there’s a better way to do it based on what they’ve worked out in animals, and try to shoo us out of the way. Then we sit back and watch. Either zoologists’ heads explode, they go back to animals, or they figure out why we’ve been having so much fun, and join us.

    This is pretty similar to what’s going on with dear old Fred Hoyle. Physicists do similar things when they invade biology to prove the innate superiority of physics, and with similar results. It’s all about assumptions based on the academic pecking order colliding with reality.

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  82. 82. vdinets 1:20 pm 04/4/2012

    Heteromeles: if I say “there are subspecies within human species”, it is not a scientific theory and it doesn’t have to be falsifiable. Subspecies is an artificial construct, so it’s a matter of personal taste. What I am saying is that humans qualify for subspecies as well as any mammalian species I can think of.

    As for Rwanda, of course there was some intermarriage. But it was very obviously limited, otherwise there would be no anthropometric differences between the three tribes. As it is, the world’s tallest ethnic group (the Tutsi) shares that tiny country with average-sized Hutu and also with pygmies. How could such a situation be maintained if there was no partial reproductive isolation?

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  83. 83. Jerzy New 5:31 pm 04/4/2012

    A piece to the debate – Anas ducks hybridize often enough to exchange haplotypes, but still not melt into one species.

    http://www.biomedcentral.com/content/pdf/1471-2148-12-45.pdf

    Interesting article, not only undermines the basics of cladistics, but also some species concepts (that common hybridization must lead to meltdown of species barrier).

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  84. 84. Christopher Taylor 5:44 pm 04/4/2012

    Botanists have little trouble talking about species, subspecies, varieties, and hybrids. The problem comes when zoologists come marching in, tell us we’re wrong, there’s a better way to do it based on what they’ve worked out in animals, and try to shoo us out of the way.

    Except that, as has already been pointed out up-thread, many of the original players in the development of phylogenetic nomenclature and species concepts were botanists (e.g. Donoghue, M. J. 1985. A critique of the biological species concept and recommendations for a phylogenetic alternative. Bryologist 88: 172-181, though in this case the ‘phylogenetic species’ is the monophyly-based one I criticised earlier). So characterising this argument as something that zoologists foist onto botanists simply doesn’t reflect reality.

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  85. 85. Heteromeles 12:07 pm 04/5/2012

    It reflects the current reality, not history. I’ll admit that over a decade ago, I had quite a lot of fun messing with some early botanical supporters of the phylocode, in the format of a seminar talk on Triticeae relationships. I learned it as the Triticeae hybridization mandala (which looks a lot like a cobweb), and the phylogenetic tree for this group is an equally tangled mess.

    The point is that the prevalence of hybridization in plants is a buzz saw biologists run into repeatedly, especially when they get consumed by visions of phylogenetic trees, and most especially if they get the idea that animals rule the world and everything else is weird and/or insignificant.

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  86. 86. llewelly 9:23 pm 04/5/2012

    I feel like Heteromeles is arguing that real numbers are bad or psuedoscientific because many physics problems require complex numbers.

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  87. 87. Heteromeles 3:18 pm 04/11/2012

    Not quite. I’m arguing against the notion that real integers are the only numbers worth considering.

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