When intellectual dishonesty becomes a crime: Nature and its cynical promotion of bad science.

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Early in October 2008 an article proposing a new, earlier year of origin for HIV-1, the pandemic AIDS virus, was published in Nature. For several reasons I, and scientists whom I know, considered this article a travesty, and one that spoke volumes about the conduct of Science in the 21st Century.

The principal author of the article, "Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960", was Michael Worobey, an ambitious young Canadian scientist who had recently been appointed - while still in his early thirties - to head the laboratory of Ecology and Evolutionary Biology at the University of Arizona, in Tucson.

Worobey's article dealt with huge mathematical calculations done on "super-computers". In reality, however, it was a mish-mash of arguments about the likely date of the beginnings of the AIDS pandemic, which concluded that the first example of HIV-1 must have existed in humans in or around 1908. Unfortunately, Worobey's calculations were based on a scientific model (the "phylogenetic clock", or "molecular clock") that is entirely bogus when applied to a lentiretrovirus such as HIV-1. The results he came up with are therefore equally spurious.

Within days of the article's publication, I posted a detailed riposte to his work on this web-site. Entitled "HIV-1 in 1908? Another sad comedy of errors from Michael Worobey ", this essay cited scientific and historical evidence that demonstrated that several of Worobey's assertions and assumptions were incorrect. It also demonstrated that he has played a dubious and covert role in this controversy for at least the last seven years.

Shortly after this, I was approached by an eminent molecular biologist who suggested that we submit a letter of response to Nature. (Most scientists who oppose the bushmeat theory of origin are forthright in private, but afraid to put their heads above the parapet publicly, lest they suddenly lose their funding. This man was an exception.) We immediately agreed to collaborate. The letter we wrote was just 400 words long, and I think constituted a pithy and apposite response to Worobey's piece, but within days it had been rejected. However, the editor concerned did suggest that we could perhaps instead submit another form of response to Nature, called a "Brief Communication Arising", which we duly proceeded to do. Nature's rules for such submissions require that a copy be sent to the author of the initial article, and we therefore e-mailed a copy of our new 650-word submission to Worobey, inviting his comments. Nature allows 2 weeks for authors to respond to such approaches, but Michael Worobey did not send any form of reply. A further 10 days elapsed before Ursula Weiss, one of the senior editors at Nature, sent a brief e-mail to state that our submission had been rejected. The reasons she gave were as follows: "This section of Nature is extremely oversubscribed, so we can consider only a very few of the critical comments we receive. We mainly consider those contributions that challenge key conclusions of the published paper in question. In the present case, while we appreciate the interest of your comments, we do feel that this is the case, and therefore cannot offer to consider your paper for publication in our Brief Communications Arising section." This is basically a pro forma response with (I suspect) a little bit added on. I found it an unconvincing and inadequate explanation (even allowing for the fact that she appears to have omitted the word "not" from "we do feel that this is the case"), but since it was sent from a web address that did not accept incoming mail, it did not allow opportunity for either reply or comment.

We then sent a slightly adapted version of our submission first to The Lancet, and then to the British Medical Journal (which had published not only Koprowski's original "preliminary report" of his African vaccination trials in July 1958, but also a series of letters and articles expressing frank criticism of several aspects of his polio vaccine research). Both journals replied courteously, but later declined to publish on the basis that the most relevant journal to publish our submission would clearly be Nature. This may have been correct, but it was also Catch-22, in that it is now clear that Nature has little if any intention of publishing anything that ran counter to the scientifically flawed, but politically sustainable, bushmeat theory advocated by Worobey and his allies.

I have no problems with The Lancet or the British Medical Journal, with whose views on this I feel some sympathy, even if it would have been refreshing had one of them shown the courage to publish and be damned on such a key topic.

I do, however, have a considerable beef with Nature, to which journal I have, down the years, submitted at least four carefully-worded letters of response on the subject of AIDS origins, all of which have been rejected.

I think it is now high time for me to make a frank public statement about Nature and its nefarious role in this debate. The fact that Nature regularly publishes alleged "refutations" of the OPV theory and that it does so to enormous fanfare, the fact that it has competed vigorously with its rival Science in order to publish such "refutations", and the fact that it has never published an exposition of the OPV theory, or allowed a single paragraph of space to any proponent of the OPV theory, reveal that the rejection slips from Nature have nothing whatsoever to do with the volume of correspondence that that journal receives. Instead, they are reflections ofNature's determination to promote an explanation for how AIDS began that is supported only by certain powerful governments, and by a perversion of sound scientific method.

To those with some experience of molecular biology, the limitations and flaws in the work of Michael Worobey and his fellow-bushmeat proponents, such as Beatrice Hahn, Paul Sharp and Bette Korber, are readily evident. Many scientists with whom I speak on this topic respond with rueful laughs. Some of them, the more forthright, go on to define the work of the aforementioned scientists on this topic as occupying a range falling between "bullshit" and "complete bullshit".

The version of events that Nature promotes as "truth" is that the AIDS pandemic began when a hunter was accidentally exposed to the ancestral virus when he was capturing or butchering a chimpanzee; that this happened in or or near south-eastern Cameroon, and that it happened in or around 1908. There is powerful scientific and historical evidence to counter every one of these assertions, and yet Nature has negated good scientific practice by promoting this deeply flawed version of events whilst continually ignoring and suppressing alternative views. The major alternative hypothesis of origin of AIDS is the oral polio vaccine (OPV) theory which (as I can prove by historical documents and eye-witness testomonies) is considerably more plausible than the bushmeat theory. Yet it provides a version of events that might well cause political embarrassment (and even class action law suits) in certain countries, notably in the USA and to Belgium, the former colonial master of the Democratic Republic of Congo, Rwanda and Burundi, where these trials were staged. Nature has published one deeply biased book review about "The River", but otherwise has never published a single paragraph attempting to explain the arguments and evidence supporting the OPV hypothesis of origin.

In short, on this particular topic, Nature has abandoned the most basic principles of scientific enquiry. Instead the journal has consistently acted as if it is a stooge of certain powerful governments and interst groups.

It is clear that some, if not all, of Nature's editors are bright enough to realise that they are promoting poor (or perhaps I should write "controversial") science as if it were proven fact. That they continue to actively promote such flawed arguments demonstrates that on this topic at least, Nature has betrayed its own declared principles as an organ that seeks to promote scientific knowledge and impartiality.

In making this accusation, I would especially single out three individuals: the editor-in-chief of Nature, Philip Campbell, who bears overall responsibility for the publication; one of the senior editors, Ursula Weiss, who seems to preside over the journal's virology coverage; and the retrovirologist who (according to an ex-employee of Nature) exerts an inordinate degree of control over HIV/AIDS coverage in the journal, Robin Weiss.

After the publication of "The River" and the subsequent death of Bill Hamilton, Professor Weiss (one of the surviving co-organisers of the Royal Society meeting) encouraged me to submit my hypothesis to the cold harsh glare of Science, so that honest and impartial scientists could determine whether or not it had merit. A few months later I visited him in London; he confirmed my invitation to speak at the Royal Society meeting, but then warned me that I had "better behave myself". As it turned out, I behaved pretty well, whereas he behaved like a scoundrel, inviting an altered and clearly one-sided set of speakers and then giving a hopelessly biased closing speech. One year later, he gave another grossly partisan closing speech at the Accademia Nazionale dei Linceiin Rome, the other venerable institution which, at the prompting of Bill Hamilton, had decided to stage a conference about the origins of HIV and AIDS>. This time I was so disgusted that I got up and walked out, shouting that Weiss's speech was "a disgrace". I know that Weiss is also a powerful influence on the AIDS coverage in Nature's main rival, Science (even if Science is actually more of a sister publication than a rival).

[I have never been able to find out whether Ursula Weiss and Robin Weiss are in any way related, and would welcome any input from readers on this point. I suspect that they are not, and that they merely speak with a common voice on this topic.]

Here let me add a word of perspective. In 2000, just after the publication of the paperback version of The River, I was invited to speak at Hay-on -Wye, and also invited to dinner by the family that organises the Festival. There I met the (I believe) recently-retired editor-in-chief of Nature, John Maddox. I asked him if he'd read the book, and he said that he had. What did he think?, I asked. "You've proposed a plausible hypothesis, and it would cost 300 million to put it to the test", he answered. If he meant pounds, or even dollars, then I think his estimates were about a thousand times too high. But the point is that when it's not a public performance, some people atNature sing a very different song.

My gut feeling about the current situation is that intelligent people like these do not make mistakes of this type by accident. They do so because they decide that it would be in their material or political interests to do so. I hereby accuse the three individuals mentioned above of betraying the very principles of science by publishing and promoting shoddy and misleading closed-shop articles about the origins of AIDS. I challenge them to allow me similar space in their journal to publish an alternative view, a view which I believe would be more scientifically sustainable. If they fail to allow me this, then I will have no alternative but to conclude that by their consistent ignoring of the evidence on such a crucially important subject, and by their consistently counter-intuitive promotion of anti-science, they are guilty not just of opportunism and a lack of integrity, but also of a moral and intellectual crime that is equivalent to the most serious of legal crimes. And I shall continue to accuse them accordingly.

If they fail to meet my challenge, then I will have no alternative but to conclude that the roles that they have played in this debate are every bit as reprehensible and odious as the roles played by those who are getting huge grant funding in order to create the flawed (but politically expedient) origins-of-AIDS science that Naturepublishes, and also by those who developed and administered that experimental polio vaccine in Africa 50 years ago, individuals who since that time have consistently lied about what they actually did out there. Over the years I have gradually collected the evidence that proves the claim made at the end of that last sentence, and I have put copies of that evidence in several places.

I should perhaps add that I am writing all this in the full knowledge of the laws of libel. If the aforesaid individuals don't like my claims, then they can take me up on my challenge and invite me to write an article for publication inNature....or if they prefer they can take me to court, and we can argue our respective positions there, under the watchful eye of the public.

I copy below the text of the response of the "Brief Communication Arising" that my co-author and I submitted toNature, so that those who visit this site can make up their own minds about the pros and cons. (I have, however, omitted the name of my co-author, who agrees with me that there is little to be gained by publicly revealing his identity at this particular moment, now that our letter has been rejected.)

Ed Hooper, December 1st, 2008.

(This posting is made on World AIDS Day 2008, more than 50 years after the first arrival of HIV-1 in humans, and more than 27 years after the first official recognition of AIDS as a new disease entity. It is written in respectful memory of all those who have suffered through the emergence of this dreadful condition.)


How AIDS began: an alternative explanation.

Michael Worobey's finding of new fragments of HIV-1 originating from Leopoldville/Kinshasa in 1960[1] is important, especially when the two previous earliest samples, globally, of pandemic HIV-1 Group M (dating from 1959 and 1976) came from inhabitants of the same Congolese city. It is therefore regrettable that the analysis, both in Worobey's letter and in the commentary by his supporters and fellow "bushmeat origin" proponents, Sharp and Hahn[2], ignores the synchronicity of time and place of these earliest HIV-1(M) viruses, and instead focuses on the entirely theoretical estimate of 1908 for the first HIV-1(M) infection in a human.

This hypothetical start-date depends on three assumptions: (a) that the mutation of HIV-1 occurs at a constant rate, which can be measured by a "relaxed molecular clock"; (b) that any recombinant viruses can be identified and excluded from the HIV-1 dataset studied; and (c) that all the HIV-1(M) viruses seen today result from one original transfer of the M group's ancestral virus, SIVcpz, from common chimpanzee to human. However, all three assumptions are controversial. Phylogenetic dating is valid for organisms that evolve through mutation, like DNA-based viruses, but HIV-1 is the most recombinogenic virus known and some 90% of its evolution occurs through recombination.[3] Worobey addresses this briefly, stating "Despite initial indications that recombination might seriously confound phylogenetic dating estimates, subsequent work has suggested that recombination is not likely to systematically bias HIV-1 dates in one direction or the other". His supporting reference, however, is far more cautious, and assumes that most recombination will occur among the "terminal branches", the most recent HIV-1 sequences in the dataset.[4]

He ignores the alternative scenario, the oral polio vaccine (OPV) theory of origin, which proposes that different strains of chimpanzee SIV that had recombined in culture were transferred to man via an experimental OPV made locally in Africa, and administered to almost 1,000,000 vaccinees of all ages in the Belgian territories of Africa (including Leopoldville) in 1957-60[5]. Such recombined SIVs would feature at the very heart of the phylogenetic tree, not on the terminal branches; furthermore, not being recognisable as recombinants, they could not be excluded from the geneticists' datasets. Under such circumstances, as Schierup has observed, "it is not valid to use a phylogenetic method to obtain the time estimate."[6]

And even if HIV-1 phylogenetic dating were legitimate, how could geneticists distinguish a single introduction in 1908 of the progenitor of HIV-1 Group M from, say, 8 - 12 introductions in the late 1950s of various SIVcpz recombinant strains that fall at the basal node of each known subtype of HIV-1(M)?

Worobey has previously declared the OPV theory of AIDS origin "refuted". He claimed that the chimpanzees involved in the 1950s OPV experiments in the Belgian Congo were Pan troglodytes schweinfurthii from "the vicinity of Stanleyville" [now Kisangani], where, he asserted, a form of SIVcpz genetically more distant from HIV-1(M) than the SIVcpz from Pan troglodytes troglodytes (Ptt) chimps from Congo Brazzaville and Cameroon was found.[7] But he is incorrect. More than 400 common chimpanzees (Pan troglodytes) of largely unrecorded subspecies and over 80 pygmy chimpanzees (Pan paniscus) were co-caged and group-caged at Lindi Camp, just outside Stanleyville. They were captured from 200,000 square miles of rain forest, extending as far west as Coquilhatville (now Mbandaka)[8], then a major chimpanzee collecting centre. Indeed, in 1955 two Ptt apes were purchased here by the same team that later supplied Lindi Camp.[9] Chimps from Coquilhatville/Mbandaka have routinely been brought to Stanleyville/Kisangani on the Congo ferries and sold[10] - and the presence of at least one Ptt among Stanleyville's chimpanzee experimentees is confirmed.[11] Only 60 of these 500-odd chimpanzees survived the 1956-60 experiments.[12] Congolese and Belgian technicians confirm that in the Laboratoire Médical de Stanleyville tissue cultures were being made from chimpanzee cells, and OPV batches were being prepared.[13] We contend that the bushmeat theory is not the only, or indeed the strongest, explanation for how AIDS began.

[650 words]

References:

1] M. Worobey et al., "Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960". Nature; 2008; 455; 661-664.

2] P. Sharp and B. Hahn, "Prehistory of HIV-1" [News and Views]. Nature; 2008; 455; 605-6.

3] S. Wain-Hobson, A. Meyerhans et al., "Network analysis of human and simian immunodeficiency virus sequence sets reveals massive recombination resulting in shorter pathways"; J. Gen Virol.; 2003; 84; 885-895. A. Jung, S. Wain-Hobson et al., "Multiply infected spleen cells in HIV patients", Nature; 2002; 418; 144.

4] P. Lemey, O.G. Pybus, M. Worobey et al., "The molecular population genetics of HIV-1 Group O";Genetics; 2004; 167; 1059-1068.

5] O. Bagasra, "HIV and Molecular Immunity: Prospects for the AIDS Vaccine", [Natic, MA: Eaton, 1999]. E. Hooper, "The River: A Journey to the Source of HIV and AIDS" [Boston: Little Brown; London: Allen Lane/Penguin, 1999].

6] M.H. Schierup and R. Forsberg, "Recombination and phylogenetic analysis of HIV-1", Atti dei Convegni Lincei; 2003; 187; 231-245. [Available from the www.aidsorigins.com web-site.]

7] M. Worobey, P.M. Sharp, B.H. Hahn et al., "Origin of AIDS: contaminated polio vaccine theory refuted". Nature. 2004; 428(6985); 820.

8] F. Deinhardt, Lindi databook (covering 53 of the Lindi chimps); 1959.

9] Databook of chimpanzee materials stored at Musée Royal de l'Afrique Centrale, Tervuren, Belgium, 1998 edition.

10] Personal communications, 2004 and 2005, from G. Hensenne (regarding the 1950s) and K. Ammann (regarding the 1980s).

11] M.M. Vastesaeger, R. Delcourt, "L'atherosclerose experimentale du chimpanzé. Recherches preliminaires." Acta Cardiol. 1965, 20 (Suppl 11), 283-297.

12] E. Hooper, "Dephlogistication. New developments in the origins of AIDS controversy"; Atti dei Convegni Lincei; 2003; 187; 27-230. E. Hooper, "The
latest scientific evidence strongly supports the OPV theory", 2005. [Both these papers, and others, are available from www.aidsorigins.com

13] "The Origins of AIDS", Galafilm/MFP television documentary (91 minute version), 2003.

Authors:

Edward Hooper and one other, whose name is here omitted.