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Schierup and Forsberg's paper: recombination as a problem in phylogenetic dating

A recent revert took out a paper listed in Google Scholar as MH Schierup, R Forsberg - Recombination and Phylogenetic Analysis of HIV-1. ATTI DEI CONVEGNI LINCEI-ACCADEMIA NAZIONALE DEI LINCEI, 2003 - Accademia Nazionale dei Lincei; 1998, which questions the validity of the phylogenetic dating of HIV. The scanned paper has page numbers (231-245) and was most likely published as a chapter on the conference noted here: Origin of HIV and Emerging Persistent Viruses, Rome, 28-29 September 2001 Published as Atti dei Convegni Lincei, 2003, Vol. 187, ISBN 88-218-0885-8.

The authors are well-accredited biomedical researchers; the lead author, Schierup, has a paper Consequences of Recombination on Traditional Phylogenetic Analysis (free access) which GScholar says has been cited 179 times. Most of these citations appear to be from prestigious biology journals such as Genetics, PNAS, Annual Reviews in Genetics, ect. So there's a pretty good argument for including the paper: it has been published, and even it hadn't, the lead author is indisputably an expert in recombination and phylogenetic analysis. Even if we don't want to use this paper, the authors cite two previous papers from 2000, one in Genetics, the other in Molecular Biology and Evolution. The Consequences article noted above is the Genetics article, and here (free access) is the other one. In the latter article, they do reference HIV as suffering from the recombination problem. (It is a "letter to the editor", but so is the 2008 Nature article referenced here.) A 2006 article referencing the Consequences article has describes a test for recombination [1].

By the way, it doesn't really look like the authors are using the problems in phylogenetic dating to support the OPV AIDS hypothesis. They don't even mention the hypothesis. They're just saying that phylogenetic dating relies on an assumption of a lack of recombination, and thus could be (and likely are) confounded and "invalid". It would be nice to find a recent review of the AIDs origin which discussed this problem. Recent reviews of the AIDS origin seem scarce, but there's PMID 16092503 (I don't have access), PMID 15966105 (no access), PMID 15682876 (no access either). I have access to PMID 16873637, but it doesn't mention this issue, focusing largely on nonhuman primates and their tolerance of SIVs. II | (t - c) 00:22, 12 January 2009 (UTC)

Certainly a solid review of HIV molecular dating would be a better source than a news article for a date as specific as the "1908" currently given in the OPV section; this entire article could stand a thorough combing-through to correct some apparent contradictions. However, I don't think the solution to these minor problems includes claiming (particularly when sourced to a website making inflammatory comments about individual scientists) that molecular dating is impossible: that's not remotely in line with consensus, and many dating efforts have examined where and when recombination may have occurred. Sharp PM et al. note that recombination can happen when one individual is infected with diverse strains from different sources. In the case of one recombinant these authors discuss, the recombination took place before the species jump. Researchers don't just ignore the possibility of recombination, and the possibility of recombination does not invalidate dating approaches unless clear proof is present.
Incidentally, and neither here nor there, the article or conference report in question is often cited by defenders of the OPV hypothesis, including Hooper in a 2005 letter to American Scientist. Keepcalmandcarryon (talk) 22:44, 12 January 2009 (UTC)
I didn't say it was impossible, and neither did Schierup. But it presents a problem which seems to be taken seriously, given the number of citations to Schierup's Genetics article. In science, a possible confounder does not make the conclusion conclusive -- rather, it implies that the conclusion should be interpreted cautiously and stated with a qualifier. Lemey et al.'s paper Tracing the origin and history of the HIV-2 epidemic use somewhat cautious language, citing Schierup. II | (t - c) 02:27, 16 January 2009 (UTC)
What changes do you propose? Keepcalmandcarryon (talk) 23:16, 16 January 2009 (UTC)
I think this is settled. I apologize for coming off a bit snappish with my earlier reply. II | (t - c) 20:55, 22 January 2009 (UTC)
Describing one's own journey of intellectual discovery in the article text, especially in the absence of references, is unlikely to settle anything. Keepcalmandcarryon (talk) 17:33, 27 January 2009 (UTC)
Do you have access to Nature? The text I added is taken as closely as possible without copyrighting from Worobey's Nature article. Wearing your POV so blatantly on your sleeve, assuming bad-faith, and deleting without reading references isn't very productive behavior for article-building. II | (t - c) 18:34, 27 January 2009 (UTC)

Article title

There was a proposal a couple of years ago (see higher up on this page) to change the title of this article to "Origin of AIDS". It didn't get any opposition but wasn't followed up. I would propose making this change now because this is simply more fluent English. Any objections? Phil Bridger (talk) 21:42, 24 January 2009 (UTC)

Genetic studies section

I have removed the "Genetic studies" section as repetitive. The Africa-Haiti-US spread hypothesis was covered previously, using the same study, making the first paragraph superfluous. The phylogenetic paper dating the jump to human population in Africa had also been presented previously. The additional, recently introduced text in the second paragraph, while a fine description of editor II's discoveries of how recombination does or does not affect dating, was not particularly encyclopaedic or well-sourced. The third paragraph seemed somewhat peacockish for a paper that basically says lentiviruses have been around for a long time. I see it as irrelevant (or relevant only in an obscure, non-encyclopaedic and tangential way) to an article on AIDS origin. Keepcalmandcarryon (talk) 17:40, 27 January 2009 (UTC)

"The additional, recently introduced text in the second paragraph, while a fine description of editor II's discoveries of how recombination does or does not affect dating, was not particularly encyclopaedic or well-sourced". What does this sentence mean? It was sourced to Worobey's paper. Genetic studies are a rich area for studying the origin of AIDs and certainly deserves its own section. I'm restoring the text. Improve, don't delete. II | (t - c) 18:14, 27 January 2009 (UTC)
Follow-up note: deleting the scholarly references on phylogenetic dating and integrating it into "cases" timeline doesn't make much sense. Yes, the 2007 study is noted in the cases timeline, referenced to a pop. press article. Deleting the section wouldn't be doing any favors for the interested reader, who most likely wants a slightly in-depth discussion of how these numbers are found. Most likely we will see further articles on the subject directed at the genetic avenue as well. II | (t - c) 18:43, 27 January 2009 (UTC)
The conclusions of Worobey's paper and other "genetic studies" have already been presented in this article. The section is redundant and thus non-encylopaedic. What is not redundant in the section is original research and synthesis. You seem to have concluded previously that recombination makes dating the HIV jump difficult or impossible, based upon your own research, including reading a fringe website. You then correctly came to the conclusion that phylogenetic research does not support this conclusion. While I congratulate you for taking the time to research and learn this, your thought process history does not really have a place in the article on AIDS origin.
You wrote, "Genetic recombination had earlier been thought to seriously confound such analysis". Earlier? By whom? ...and continued "but later work suggested that recombination is unlikely to systematically bias results, although it is expected increase variance." What do you mean by "unlikely" or "systematically bias"? You also write, "The results of the study supported this view and unambiguously indicated that HIV evolves reliably." Evolves reliably? Unambiguously?
Redundant and problematic sections, riddled with original research and confusing weasel words, are best deleted.
As for the references, this article could certainly use better references and rely more on peer-reviewed sources and less on popular press. I wrongly assumed that the reference had been given previously in the article; in any case, the bot rescued it. Keepcalmandcarryon (talk) 18:52, 27 January 2009 (UTC)
Did you notice that when I added those sentences [2], I said I was fleshing out the paper? I'll just quote from Worobey's 2008 article in Nature:

Despite initial indications that recombination might seriously confound phylogenetic dating estimates6, subsequent work has suggested that recombination is not likely to systematically bias HIV-1 dates in one direction or the other, although it is expected to increase variance7.

If you want to read the full article and get those references, email me. Scientists are expected to cite research which does not necessarily support their points of view. We should try to do the same on Wikipedia. II | (t - c) 19:03, 27 January 2009 (UTC)

I see: you cherry-picked a sentence that agreed with your own experience from a primary source and plagiarised it, giving your source, of course, but not indicating you had quoted it. I trust this is not representative of your writing habits.

In any case, the issue here is not "points of view" but whether a) points described in detail earlier in the article should be repeated in a separate section; and b) minor points from the primary literature (such as the technical issue of what influence recombination has on phylogenetic dating or whether the discovery of a retrovirus in Madagascar has implications for antiretroviral design) merit inclusion in an encyclopaedia. Keepcalmandcarryon (talk) 19:13, 27 January 2009 (UTC)

If we were to put quotes around every single complicated, technical statement in these types of article -- which have to be cited very closely to the source -- these articles would be nothing but a mess of quoted sentences. I'll admit that one is questionable especially since I forgot to put the cite after the sentence, but it's no more questionable than your bad faith insistence that I've committed original research without even reading the source. Your opinion is that recombination is a minor technical issue. As I showed above, Schierup, who is not a fringe figure, doens't think that it is a minor technical issue. Neither, obviously, does Worobey. Anyway. I think you need to understand that your opinion of what merits inclusion is probably not the same as many other people, and we have a bias towards including highly reliable sources. I don't think I've encountered many people as quick to hit the delete trigger on reliable sources. Feel free to improve by moving around, rewording, and perhaps condensing, but I don't think any of the information in the "Genetic studies" section should go. II | (t - c) 19:21, 27 January 2009 (UTC)
I apologise for not recalling this particular sentence from my earlier reading of the paper. As for plagiarism, your "questionable" sentence would have consequences if I caught it in my classroom. I appreciate that it can take time and effort to rephrase a sentence, but the result of such effort is preferable to stealing another's work and attempting to conceal one's behaviour by changing a word or two. Keepcalmandcarryon (talk) 19:35, 27 January 2009 (UTC)
Technically, if one switches the phrasing and uses the same words, it's still called "plagiarism". Yet this is Wikipedia. When we cite technical work, we need to use the authors' words. Yet a page made up entirely of quoted words would be ugly. Sometimes I forget to put quotes around those words or forget to change the wording substantially. Also, a good author will typically steal the most obvious and efficient phrasing of a sentence. I'm not trying to "steal" credit for their work -- if you think about it, that's really a pretty absurd accusation. Also, just because Worobey doesn't spend a lot of time on the subject doesn't mean it is not important. The idea something which could "seriously confound" results is a minor technical issue is absurd from a scientific perspective. II | (t - c) 19:42, 27 January 2009 (UTC)
Agreed on the last point. But this is not a scientific paper, and we should take care to remember the audience and the subject of the article. In a scientific paper, it's certainly appropriate (and necessary) to address the various confounders of a study on HIV dating. In addition to recombination, a few that come to mind are: tissue storage methods and how they influence RNA or DNA integrity; the use of RNA versus DNA sequences; PCR artifacts; perhaps most importantly, the strengths and drawbacks of the mathematical models one uses. In my opinion, these factors are too technical to include in a general article on AIDS origins....unless they are introduced and explained clearly.
Why, then, is recombination included but no other potential confounders?
Perhaps I am being overly critical of one section when the entire article is in fairly poor shape, but I'm still not understanding the repetition and selectivity. Keepcalmandcarryon (talk) 20:39, 27 January 2009 (UTC)
I haven't noticed any of these things in the papers I've glanced at. They don't seem to be mentioned by Worobey or other HIV phylogenetic dating papers. However, every molecular phylogenetics paper I've glanced at mentions recombination as a possible confounder. The more recent (2007-2008) say it's not going to systematically bias the results but will increase variance. Recombination generated a lot of publications and scientific interest in the early studies (pre-2006), and is still mentioned. Leading edge research considers it to be less of a problem. This is what our article says, and what it should say. But if you can find other confounders mentioned as significant, I do think they should be included in appropriate areas. If they're mentioned in Worobey's paper, then here. However, if they're general problems with the dating models, connecting them to Worobey's paper or HIV phylogenetics introduces a bit of original research, and they probably belong in the molecular phylogenetics article. II | (t - c) 21:07, 27 January 2009 (UTC)

The following sentence "In addition, the time frame falls into place (...) lemurs later developed immunity to the virus strain and survived an era when the lentivirus was widespread among other mammalia." sounds to me as suggesting that the Middle Miocene disruption may have been in part due to SAIDS. This would be a bold theory indeed! Is there any evidence for it? Otherwise the sentence should be modified so as not to suggest this. 20:00, 1 October 2010 (UTC) —Preceding unsigned comment added by MCSmarties (talk • contribs)

Re: Origins

With respect to the changes made to the HIV Origins entry, there are a few problems here:

1) The goal of Wikipedia is to provide objective information, not to disseminate popular opinion.
2) Although none were conclusively verified, many of Edward Hooper's claims are in fact plausible and compelling.
3) The most logical thing to do then is to either provide a full discussion of both sides, *or* simply supply a brief, non-accusative summary of the theory, allowing people to do further research of the theory, if they so wish (as I have done).

I think you're Sebastian Garth. I believe that you are incorrect about several things regarding Wikipedia articles:
  1. Actually, the goal of Wikipedia is to be WP:NPOV (neutral), and not to give WP:WEIGHT (undue weight) to fringe ideas. I'm not an expert around here, but I know enough about AIDS and HIV to say that the edits you propose are fairly fringe.
  2. In fact, the literature quote completely rejected Hooper's claims. To state that they are plausible and compelling is what they call around here WP:NOR (original research).
  3. Lastly, Wikipedia articles don't have to discuss both sides, especially if one side is not supported by citations and sources, or if it's fringe.
I would suggest you gain some sort of support here before making large changes. SciMedKnowledge (talk) 19:34, 10 April 2009 (UTC)



1.a) The tone of the section was unequivocally *not* neutral.
1.b) I, too, feel that it is important not to give weight to *unsubtantiated* claims. I took this into account when I made the edit.
1.c) Unfortunately, intelligent conclusions are not always popular. This does not make them 'fringe', just unpopular.
2) Yes, and in a similar manner, established institutions have rejected scientific thoeries that later proved to be correct. In the interest of being objective and neutral, we should consider the validity of all claims.
3) Fair enough, but until then, the section should be reworded for neutrality.
4) The changes I made would not have been so 'major' had the section not been so biased. You should be less concerned with how much support I may or may not have and more for your responsibility toward others to represent objective information.

[[User:Sebastiangarth|Sebastian Garth]http://en.wikipedia.org/w/index.php?title=Talk:Origin_of_AIDS&action=edit&section=37] (talk) 20:45, 10 April 2009 (UTC)


Discussion: Wording of OPV theory

The prior wording for this article does not meet NPOV standards. This is clearly a sensitive topic. In order to be both nonprovocative and neutral, I chose a simple "passing" reference to the theory, and then the note that the generally accepted view was that it was incorrect. This is my wording:

The hypothesis that HIV/AIDS originated from polio vaccine research in Africa was advanced by the journalist Edward Hooper in his book "The River".[18][19] This hypothesis has been largely discredited by the scientific community.[20][21]

I feel it is a fair and balanced treatment of the topic without lending any undue credance to the theory. What are the arguments against this wording? Better yet, can the two versions be merged in such a way that everyonce is satisfied? Sebastian Garth (talk) 00:22, 12 April 2009 (UTC)

Your edits introduce weasel words. Note "largely discredited" & "aspects of" instead of "rejected" & "basic claims". It may have been your intent to summarize portions of the article, but you did so at the expense of scientific documents pointing to the contrary position. Your analysis should be backed up by a preponderance of evidence, not in spite of it.ˉˉanetode╦╩ 02:33, 12 April 2009 (UTC)
I disagree with the characterization of "largely discredited" as weasel words. They merely indicate a general form of consensus, unlike phrases such as "widely discredited", "completely discredited", and similar exaggerated phraseology. Short of saying something like "discredited by some in the scientific community", I'm not sure how to put that in less "weaslish" terms. Incidentally, "popularized", "rejected by the scientific community", "Subsequent research has falsified", and "suggests" *are definitely* weasel phrases, and yet they somehow fell beneath your radar. Furthermore, simply reverting my changes without making any concessions whatsoever is really undiplomatic and totally unconstructive. It would benefit everyone here if we could find a middle ground. If we can commit to that then we will make some real progress in resolving this disagreement. Sebastian Garth (talk) 03:48, 12 April 2009 (UTC)
The problem is that exaggeration runs perpendicular to neutrality, especially in medical articles. Your phrasing, or rather your opinions, were substituted in place of cited, verifiable facts. Subsequent research did reject the OPV hypothesis, you can't largely discredit something. Research does indeed suggest, as in the meta-analysis of studies can be used to falsify otherwise perceived trends. Formal and informal academic reviews, such as the cited text from Nature, serve to elucidate the conclusions reached by the academic community at large. I suggest you brush up on the scientific method and basic terminology before you attempt to wield words like "undiplomatic" or [sic]"unconstructive" in an irrelevant context. ˉˉanetode╦╩ 04:24, 12 April 2009 (UTC)
First of all, I didn't insert a single opinion into the article, so there is nothing to verify. The relevant citations that were originally there were left intact. My contention from the very beginning has been the biased and single-sided nature of the section. I am certain that my concerns are not unfounded, and I am urging you to give the matter the proper consideration that it deserves. So please, rather than resort to using insults or acting disrespectfully, let's concentrate on finding a middle ground so that everyone can move on. Sebastian Garth (talk) 05:29, 12 April 2009 (UTC)
What you are saying basically contradicts what you are doing. If you aim to avoid disrespect, then please avoid any demands of "concession". Wikipedia isn't a democracy, any appearance of consensus on medical research described in articles must strive to accurately reflect reality. Your attempts to implement vague and relative tone where none is needed can only be seen as attempts to obfuscate scientific findings. Your concerns are rather obvious and I do understand them, but I am not obliged to be sympathetic or easily swayed by diplomacy when dealing with editorial issues. Content comes first. In this case, we are dealing with a pathology that has been thoroughly investigated by the medical establishment and dismissed. ˉˉanetode╦╩ 06:13, 12 April 2009 (UTC) Further, I'd like to point out that so far no less than three editors have rejected your proposed changes. ˉˉanetode╦╩ 06:21, 12 April 2009 (UTC)
Sebastian is correct, consider me one more editor in support of his proposed changes. Anetode is another editor who wears his POV on his sleeve.173.53.175.220 (talk) 18:44, 17 June 2009 (UTC)
The OPV hypothesis has been roundly rejected by the scientific community. Unless and until someone resuscitates this dead theory, it has been "rejected". Keepcalmandcarryon (talk) 16:24, 18 June 2009 (UTC)

British printer case

I suggest we remove the British printer AIDS case from this article - the section heading states "History of known cases and spread", and the British printer case was unequivocally not AIDS (there is universal agreement on this). Any objections? —Preceding unsigned comment added by 71.198.251.93 (talk) 04:23, 23 May 2009 (UTC)

Relevance of phylogenetic dating to OPV

From http://www.aidsorigins.com/content/view/214/2/: "Using their molecular clock, Worobey's team use the 1959 and 1960 HIV-1 samples ... in order to predict that HIV-1 has been in existence since 1908. If they were not so wedded to these two faulty principles [single point of origin and the molecular clock], they might examine a much simpler and more logical explanation. This is that the emergence of the two earliest examples of HIV-1 from the same city (Leopoldville/Kinshasa) and within a year of each other suggests that there might have been a causative event in that city in the years immediately preceding 1959 and 1960.

Was there such a candidate event? There was indeed [the vaccinations]"

In order words, the relationship of the phylogenetic dating to OPV is a deeply ambiguous one. At the moment, our article clearly implies that the phylogenetic dating disproves OPV. But this is itself original research. The phylogenetic dating study, in itself, says nothing at all about OPV. Indeed, the argument above is that OPV is strengthened, not weakened, by the discovery of the 1960 sample. I suggest we either keep my original edit or remove the sentence on phylogenetic dating from the OPV section: it is presently being used to argue against OPV, and this is not defensible. User20090521 (talk) 05:33, 23 May 2009 (UTC)

The author of that "source" of yours is Edward Hooper, a famed AIDS denialist whose theories have been discredited by science. I thing your constant addition of these unsupported claims could be considered problematic. SciMedKnowledge (talk) 22:38, 24 May 2009 (UTC)
I agree that this is problematic. This a topic that has been widely subjected to scientific study, so we should base it on peer-reviewed scientific sources, not a conspiracy-theory website self-published by someone with no qualifications in this field. Phil Bridger (talk) 23:06, 24 May 2009 (UTC)

WP:MEDRS: "The fact that a statement is published in a refereed journal does not make it true."

Let's look at the research cited in note 14 that has "shown the basic tenets of the OPV theory to be false".

1) Rambaut et al, arguing (not proving) the structure of HIV-1 phylogenies in the DRC to be counter-indicative of multiple cross-species transmissions. This is a theory, and a theory can't falsify another theory. To argue that it does is WP:NOR.

2) Poinar et al, showing that batches of the vaccine prepared outside Africa don't contain chimp DNA. The OPV theory is that the vaccine was amplified in chimp tissue in Africa; senior lab attendants confirm this. The results are exactly what the OPV theory would predict.

3) Worobey et al, showing that SIV in the DRC is only 70% similar to HIV-1. But a) the closest SIV ever found is only 80% similar; b) the chimps in the camp where the vaccine was prepared came from all over Africa; and c) recombination of SIVs amongst chimps in the camp would result in any individual strain of SIV diverging substantially from HIV-1. The results are entirely consistent with what the OPV theory would predict.

4) Blancou et al, showing that batches of the vaccine prepared outside Africa don't contain chimp DNA. The OPV theory is that the vaccine was amplified in chimp tissue in Africa. The results are exactly what the OPV theory would predict.

5) Berry et al, showing that batches of the vaccine prepared outside Africa don't contain chimp DNA. The OPV theory is that the vaccine was amplified in chimp tissue in Africa. The results are exactly what the OPV theory would predict.

The refutations are astonishingly weak.

If the above points are now accused of sourcing to Edward Hooper, please remember that Hooper is the author of several papers with W D Hamilton, the most respected evolutionary biologist of the 20th century, including one paper that appeared in The Lancet. W D Hamilton stated that he was 95% certain of the truth of the OPV theory, described Hooper as the most knowledgable person regarding the origin of AIDS in the world, and wrote the forward to The River. The River has the explicit and unconditional backing, as a reliable source, of one of the most respected scientists that has ever lived. If The River is not a reliable source, W D Hamilton is not a reliable source when he explicitly states that it is. If W D Hamilton is not a reliable source, vast swatches of accepted evolutionary theory on Wikipedia will have to go too.

Wikipedia is an objective source, not a mouthpiece for the scientific community. This is a crucial point in assessing how Wikipedia should report issues affecting the reputation and interests of the scientific community as a whole. I further draw attention to WP:MEDRS: "Make readers aware of any uncertainty or controversy." The article presently doesn't do this. We need to state the prevailing scientific consensus along with the fact that the scientific community's position is not de facto an objective one. Any editor taking this to mediation with the above points would have a very strong case. BBrihem (talk) 05:53, 3 July 2009 (UTC)

I'm afraid you may be misunderstanding how Wikipedia approaches scientific topics. Wikipedia's "point of view", if you will, is by default that of the scientific community, i.e. the established experts. There is no concern about what is ultimately "true" or "false", only what is verifiably reported by independent sources with a reputation for fact-checking. At the moment, Hooper's theory has been reported in the popular press (i.e., in outlets with little or no relevance to WP:MEDRS) and has been universally rejected by the experts (i.e. independent scientists who publish in peer-reviewed scientific journals, the highest-quality reliable sources). Perhaps W.D. Hamilton does indeed support Hooper, but your opinion (or mine) of an individual scientist is of little import to a Wikipedia article.
Should the scientific community one day come around to your position, namely, that Hooper was right, this article should and will be altered to reflect the changing expert consensus. Until that day, it's pointless to add caveat after caveat about how it's only the "scientific community" that rejects Hooper's hypothesis. After all, the scientific community is the authority of central importance to Wikipedia on such matters. Keepcalmandcarryon (talk) 15:19, 3 July 2009 (UTC)
I would also point out that W. D. Hamilton died before most of the research into this subject took place, so he can't be cited in support of any position based on the results of that research. Phil Bridger (talk) 15:48, 3 July 2009 (UTC)
BBrihem writes, "please remember that Hooper is the author of several papers with W D Hamilton, the most respected evolutionary biologist of the 20th century, including one paper that appeared in The Lancet". GoogleScholar and NCBI searches return only one paper written by Hooper and Hamilton, a "viewpoint" article in The Lancet. This article summarises interviews conducted by Hooper and unless I'm mistaken does not appear to include any biological research. Keepcalmandcarryon (talk) 14:22, 6 July 2009 (UTC)
Also, and of importance to this debate, this sole article by Hooper and Hamilton is not about the OPV hypothesis. Keepcalmandcarryon (talk) 14:24, 6 July 2009 (UTC)

Remove OPV hypothesis from artice?

The OPV hypothesis should be excised entirely per WP:MEDRS. This hypothesis has never been widely accepted and is not supported by reliable sources. It is already covered in AIDS origins opposed to scientific consensus, where it belongs. Keepcalmandcarryon (talk) 16:00, 3 July 2009 (UTC)

I agree. The hypothesis should be covered as a historical and cultural phenomenon, which is a separate topic from the actual origin of AIDS, and is covered by AIDS origins opposed to scientific consensus. There is a see-also link in this article to help anyone looking for such information. Phil Bridger (talk) 17:18, 3 July 2009 (UTC)

A theory on the origins of AIDS that the most respected evolutionary biologist of the 20th century stated he was 95% certain of the truth of, and which the most respected scientific institution in the world organized a conference specifically to discuss, clearly needs to be present in an encyclopedia article on the origins of AIDS, along with the fact that the scientific community now states the theory has been disproven. It would be hard to find another encyclopaedia article on the origins of AIDS that doesn't even mention the OPV theory.

I understand from Phil Bridger's first comment above that Hamilton -can- be cited in support of any position based on the result of research prior to his death, and that is what my changes do: they reference no work other than The River, which Hamilton, a reliable source, explicitly and unconditionally stated was a reliable source. (The source for Hamilton's being 95% certain of the truth of the OPV theory is his own wife.)

I am a little concerned about Keepcalmandcarryon's assertion that on Wikipedia "There is no concern about what is ultimately "true" or "false". I think this is belied in WP:MEDRS: "The fact that a statement is published in a refereed journal does not make it true." This passage in WP:MEDRS a) shows a clear concern for what is ultimately true or false, and b) makes it clear that we cannot automatically repeat the assertions of the scientific community as fact.

(I'd appreciate it if Keepcalmandcarryon retracts the allegation that my position is that Hooper is right: nothing in what I have written explicitly or implicitly states this. Nobody knows if the OPV theory is true.)

Regarding the removal of the whole section, I believe the conclusion a reasonable person would draw on reading this discussion page is that it is possible the two of you are deliberately shifting the goalposts of the dispute prior to mediation: attempting to make the dispute about whether the section should be retained or not, rather than about whether the changes should be accepted. You have both been heavily involved in editing this page: why have the two of you not removed this section before?

WP:MEDRS:

"Neutrality and no original research policies demand that we present the prevailing medical or scientific consensus ... Although significant-minority views are welcome in Wikipedia, such views must be presented in the context of their acceptance by experts in the field."

W D Hamilton's work is a) that of an expert, and b) that of a significant minority. Keepcalmandcarryon is clearly incorrect in stating that the theory "has been universally rejected by the experts". The question is how much weight Hamilton's views should be given in the article. It could well be argued that even the changes I have made are not adequate in giving an objective picture of this. What do other editors think? This is a very highly-charged issue, and people who feel strongly about this (on either side of the debate) probably need to make themselves known. BBrihem (talk) 23:48, 3 July 2009 (UTC)

The OPV hypothesis is not accepted by a significant minority of scientists. W.D. Hamilton is deceased. The OPV hypothesis is little more than a conspiracy theory that has been conclusively rejected by the consensus of the scientific community, among other reasons due to phylogenetic studies. That's not my opinion, it's what's reported by the reliable sources. As such, this hypothesis has no place in an article on the origin of AIDS. Keepcalmandcarryon (talk) 17:11, 4 July 2009 (UTC)
Perhaps a look at autism would help BBrihem understand what a legitimate medical controversy is and is not. In the scientific community, there is considerable debate about which genetic linkages are responsible for autism, in which combinations, as well as controversy about if and how environmental factors can contribute. There is also a major pseudoscientific movement placing childhood vaccinations at fault for autism. "Major" meaning played out in the pages of major newspapers and magazines, written up in countless books, embraced by celebrities and even finding some voice in medical journals. Yet this hypothesis remains unproven pseudoscience and is not granted its own section in the Wikipedia article, per WP:MEDRS. In comparison, the OPV hypothesis of HIV/AIDS is extremely obscure. In my opinion, it should not even receive mention here; if it does, then in a brief sentence lumping it together with other conspiracy theories such as AIDS denialism and government weapons development. Keepcalmandcarryon (talk) 17:24, 4 July 2009 (UTC)
The point about Hamilton's views is that they were formed before the research was undertaken that refuted the OPV hypothesis, so they can't be said to be any part of any current consensus. I have little doubt that if he had lived to see the results of this research he would have accepted that the hypothesis had been refuted, as all other scientists in this field have done. This is the way science works. People come up with hypotheses, which may be accepted as plausible, as Hamilton appears to have done in this case, but once experiments have refuted a hypothesis, as in this case was done after Hamilton's death, science moves on. Phil Bridger (talk) 17:37, 4 July 2009 (UTC)
Some further thoughts. Firstly I don't think it's helpful to say that "the two of" us are moving the goalposts - I have had no discussion outside of this page with Keepcalmandcarryon about this or (as far as I can recall) any other issue, so we are not acting in concert. The only reason that I didn't remove the section earlier was simply that I didn't think of doing so, but when Keepcalmandcarryon did it I saw that it was the right thing to do. Also nobody is trying to remove coverage of this topic from Wikipedia. Although this hypothesis has been rejected by the scientific community it is still an important part of the history of science and of popular culture, and is rightly covered in depth in its own article, in AIDS origins opposed to scientific consensus (linked from this article, and a rather ugly title but that's a separate discussion) and in Edward Hooper. I can see that you won't be convinced just by Keepcalmandcarryon and me, so I would welcome it if you would start a wider discussion. I'm not too sure myself about which of the arcane Wikipedia processes would be best for this (I'm aware of mediation and requests for comment but have never been involved in either, and given the nature of Wikipedia I'm sure there are other possible avenues), but I will be happy to cooperate in any such process that you wish to invoke. Phil Bridger (talk) 18:19, 4 July 2009 (UTC)
I, too, would welcome the involvement of additional editors. However, WP:MEDRS is clear on the point in question: the OPV hypothesis does not have the calibre of sources we need for a medicine-related article such as Origin of AIDS. The apparent support for this theory from W.D. Hamilton is noteworthy and should be mentioned in his biography and on the appropriate page for pseudoscientific AIDS origin theories, particularly since he died while trying to confirm the OPV hypothesis, but his support does not constitute a significant minority opinion in the scientific community any more than the support of Peter Duesberg, once a highly-respected scientist and leader in his field, renders AIDS denialism a valid scientific opinion for the purposes of Wikipedia. Keepcalmandcarryon (talk) 13:47, 6 July 2009 (UTC)

OPV theory

I've spent some time with the autism issue Keepcalm mentions and I agree with everything he/she says about it. Closer to home, the response to AIDS denialism is a perfect example of the scientific community calmly and competently doing what it's there for.

But the pseudoscience surrounding autism (say) wasn't a theory one of the world's most famous authorities on the subject declared himself 95% convinced of. Given Hamilton's support, you cannot reasonably lump the OPV theory alongside the genuinely wacky stuff. It is qualitatively different; and unless you want a new section called "Origin of AIDS theories the Royal Society devoted a conference to", I don't see how it can possibly disappear from the main page.

Some other points: I wouldn't dream of directly accusing either of you of deliberately moving the goalposts of the dispute. I do think that someone studying this discussion page might wonder, however, as I suspect it's a common tactic prior to mediation. I'd also appreciate it if Keepcalm retracts his allegation that my position is that Hooper is right: it really isn't. More seriously, I think that to delete the entire section without suggesting this first on the discussion page is not mature editing, as this is a huge issue, and edits as controversial as this should always be flagged in advance.

Let's get some other editors' thoughts. For anyone new to this:-

- the wife of the eminent scientist referenced below (Bill Hamilton, now deceased) had this to say: http://uow.edu.au/arts/sts/bmartin/dissent/documents/AIDS/Bozzi03.pdf.

- A news story on one of the scientific community's stated refutations of the theory is here: http://news.bbc.co.uk/2/hi/health/3645323.stm.

- A response to this refutation by the author Bill Hamilton explicitly stated was a reliable source: http://www.aidsorigins.com/content/view/190/2/.

Phil/Keepcalm/anyone else: please do add to this section if you think it is unfairly slanted. BBrihem (talk) 11:34, 5 July 2009 (UTC)

When a section of a medicine-related article doesn't conform to Wikipedia standards for such articles, it should be deleted or moved to another, more appropriate article. AIDS origins opposed to scientific consensus is the appropriate article. The OPV hypothesis is not accepted by the scientific community, and it is not accepted even by a significant minority of scientists. Whatever W.D. Hamilton, a single individual who died ten years ago, may have thought of the hypothesis is interesting but of little relevance, since the OPV hypothesis has never garnered significant support in the pages of sources conforming to WP:MEDRS. In fact, even the pseudoscientific theories of AIDS denialism have occupied more pages in peer-reviewed journals. Keepcalmandcarryon (talk) 13:55, 6 July 2009 (UTC)

RfC: how should Wikipedia report a controversial theory on the origin of AIDS?

A theory that AIDS accidentally emerged through polio vaccinations in the 1950s found extremely strong support from at least one eminent scientist, W D Hamilton, but subsequently the scientific community (in Nature and elsewhere) states the theory has been disproven. An author W D Hamilton explicitly stated was a reliable source says the refutations of the theory are nonsense, and may be due to the scientific community and corporate worlds having a vested interest in convincing the general public the theory is false. I suggest that the section on the theory in the origin of AIDS article is headed "Rejected by the scientific community", and says "The scientific community states that the theory has been shown to be false." Others prefer the section is headed "Refuted", and states "The theory has been shown to be false." BBrihem (talk) 11:44, 5 July 2009 (UTC)

Support from one prominent scientist does not make a significant minority opinion that should be covered as part of the current state of scientific knowledge. Many individual respected scientists have embraced all manner of bizarre hypotheses, many of them more outlandish than the OPV hypothesis. This doesn't mean that these ideas should be considered relevant to medicine-related articles. Incidentally, W.D. Hamilton died in 2000; since then, a large number of reports published, unlike the OPV hypothesis, in peer-reviewed journals, confirm phylogenetic estimates of HIV origins long before the polio vaccine was introduced. There's simply no support for having a section on this rejected hypothesis in a medical article; a sentence acknowledging the existence of this and other pseudoscientific theories would suffice. Keepcalmandcarryon (talk) 14:01, 6 July 2009 (UTC)
What large number of papers are you talking about? The "conclusive" little letter by Worobey et al. in Science came out in 2008. Brian Martin (professor]|Brian Martin]], who has followed this whole thing closely, has said that he's talked to several scientists who think the hypothesis is reasonable but just aren't up for stirring the pot anymore. Deleting any mention of the OPV AIDS hypothesis is premature. II | (t - c) 16:30, 6 July 2009 (UTC)
I have not, and no one else has, suggested deleting all mention of the hypothesis. However, per WP:WEIGHT and WP:MEDRS this fringe hypothesis should not have its own section in a medicine-related article. Wikipedia articles derive from reliable sources, and science/medicine articles have strict standards; what this or that professor heard other scientists say is hardly a strong source. And by the way, to my knowledge, W.D. Hamilton was not a Nobel laureate. Keepcalmandcarryon (talk) 16:37, 6 July 2009 (UTC)
Hmm, you're right about Hamilton. My bad. One good source which isn't used currently is American Scientist's 2004 article on the issue, The Puzzling Origins of AIDS. The author, Jim Moore, has a PhD in biological anthropology from Harvard [3]. When you say a large number of papers have "disproved" the hypothesis, you're probably referring largely to Worobey's papers. Moore directly criticizes the unscientific way that the evidence has been exaggerated:

Contamination of OPV is the only one of the four current theories that is readily falsifiable: Finding the HIV-1 group M virus in a tissue sample that predated the suspect vaccine would eliminate this possibility'. So far that has not happened. Still, many investigators give the theory little weight for other reasons, which has led to the widespread belief that the theory has been definitively disproved. In 2001, for example, Science magazine published a piece titled "Disputed AIDS Theory Dies its Final Death," and Nature ran one under the heading "Polio Vaccines Exonerated." Earlier this year Nature also published "Origin of AIDS: Contaminated Polio Vaccine Theory Refuted", a surprising title given that this theory ostensibly died three years ago.

As of now, I don't think the HIV-1 group M virus has been found in such a tissue sample, but if it has, please show me a source. On the other hand, Moore does say that the evidence is against the OPV hypothesis, and he discusses the phylogenetic analysis. If you don't have access to the paper send me an email. I'm no expert on phylogenetic analysis, but if you mix up the viruses together for a while, I imagine it might be confounded more than these phylogenetic estimates expect. Phylogenetic analysis cannot definitely disprove the hypothesis. II | (t - c) 16:56, 6 July 2009 (UTC)
II, the American Scientist article would be a fine source for the AIDS origins opposed to scientific consensus article, which is where OPV, AIDS denialism and the various weapons lab/genocide theories find their proper home. This is a medicine-related article, with different sourcing requirements. As for your opinions on phylogenetics, your points are well taken, but we must defer to phylogeneticists for the final word. And phylogeneticists, as published in the peer-reviewed literature per WP:MEDRS, seem to think that genetic analyses have conclusively disproven the OPV hypothesis. The rest of the scientific community seems to agree. Keepcalmandcarryon (talk) 17:12, 6 July 2009 (UTC)
This theory is too significant to go without mentioning in this article. Also, it is clear that carryon's opinion is in the minority here. Please stop reverting.98.115.14.193 (talk) 21:36, 6 July 2009 (UTC)
Again, the OPV hypothesis has even less support in the scientific literature than AIDS denialism, which itself is a pseudoscientific set of hypotheses. AIDS denialism doesn't belong in a medicine-related article, and neither does the OPV hypothesis. This isn't my opinion; it's derived from a Wikipedia guideline called WP:MEDRS. Any number of edit-warring sockpuppets and new users will not change this. Keepcalmandcarryon (talk) 21:41, 6 July 2009 (UTC)

Thanks to all for the responses. By the way: you literally can't use the phylogenetic dating to disprove the OPV theory. The two earliest samples of HIV-1 are from a vaccination town. They differ genetically by 12%. So Worobey says "Okay, let's assume these samples are from a single point of origin, and then backdate to that point" and traces their divergence back to 1908. But if the samples -weren't- from a single point of origin, a genetic difference of 12% is exactly what you'd expect if you inoculate 1 million different people with vaccine prepared from hundreds of different chimps from all over the Congo.

But nobody with a phD in virology or a related discipline ever makes this obvious point - only Hooper. And Hooper isn't a member of the scientific community. So when Worobey states this argument constitutes a refutation, and because nobody in the scientific community ever states otherwise, it's reported in the media as -objectively- being a refutation. Should Wikipedia do the same? BBrihem (talk) 22:12, 6 July 2009 (UTC)

I think you make the point very well against including this information in the article. Why, when nobody with a PhD in virology or a related discipline ever makes this point, should we treat it as anything like obvious? The experts say that this is a refutation. A pop-culture journalist with no qualifications in the subject and a book to sell says that it isn't. Isn't it obvious how any encyclopedia with any claim to be serious should treat this? And are we really supposed to believe that all of the researchers and peer-reviewers and journal editors who have studied this subject are involved in a massive cover-up operation, which is the only way that this hypothesis could possibly have any credence? If that's the way we are to build this encyclopedia then let's have a section in Apollo 11 saying that the moon landing might have been faked. Phil Bridger (talk) 22:38, 6 July 2009 (UTC)
There's not a conspiracy, but there is the fact that Worobey and many of the other scientists are personal friends of the scientists who are accused of the creating AIDs (unintentionally). Further, these scientists sometimes argue that the OPV AIDs hypothesis leads to vaccine paranoia. Both of these make it unsurprising that scientists aren't really being honest about the theory's plausibility. If the kidney cells were used to grow the polio viruses and contained SIV, then certainly it could have caused HIV to appear. There's no dispute about that. The dispute comes because the chimps nearby Koprowski didn't carry the right SIV (P. t. schweinfurthii rather than P. t. troglodytes). Could you comment on the American Scientist article (linked above), which is written by a PhD in biological anthropology? Email me if you don't have access. He's a neutral third-party, not a proponent of the OPV hypothesis, but honestly describes it. The theory has not been definitely "disproven". On the other hand, the "hunter hypothesis" is not a super-compelling alternative considering that Africans lived nearby the chimps for such a long time, but HIV appeared only a couple years after OPV was used in the area. II | (t - c) 00:53, 7 July 2009 (UTC)
Rankiri's point is excellent. For science- and medicine-related articles, we must focus on reliable sources and the current state of scientific knowledge. Including an entire section on one selected, rejected fringe theory is unacceptable, especially when this theory has its own article and is also covered in the alternative hypotheses article. I've added a brief concluding section on the pseudoscientific theories, linking to their articles.
II, I would remind you that the talk page is not meant for discussion of the merits of the OPV hypothesis. Our role is to present the current state of scientific knowledge from reliable sources. What this anthropologist or that sociologist has written about the relative strengths of various hypotheses, and what we think about their arguments, is a matter for discussion in another forum. Keepcalmandcarryon (talk) 15:45, 7 July 2009 (UTC)
An encyclopedia article called 'Origin of AIDS' that does not mention a hypothesis the most influential evolutionary biologist of the late 20th century was 95% convinced of is failing its readers.
WP:MEDRS states "Make readers aware of any uncertainty or controversy." The sensible reading of this is to briefly reference Hamilton, and then state that the scientific community has now rejected the theory. BBrihem (talk) 18:32, 7 July 2009 (UTC)
Again, I fear you're misunderstanding WP:MEDRS. This "uncertainty or controversy" is uncertainty or controversy within the scientific community, published in reliable sources. There is no significant controversy within the medical community on this point. A single evolutionary theorist who died ten years ago is not a significant minority within the scientific community, even if your high opinion of him is justified. In any case, Hamilton never published any works on this hypothesis in peer-reviewed journals, so his opinion, while quite interesting and certainly admissible in other Wikipedia articles if properly sourced, is of no relevance to this particular article.
I agree that the hypothesis should be mentioned. It is mentioned, and links to the main articles are given. I would suggest that unless OPV hypothesis proponents can provide OPV hypothesis-supporting sources satisfying WP:MEDRS, they focus their attention on the more appropriate articles, such as AIDS origins opposed to scientific consensus and OPV AIDS hypothesis. Keepcalmandcarryon (talk) 19:19, 7 July 2009 (UTC)
As with your unretracted comment that my position is that Hooper was right, you assign to me a subjective stance on Hamilton that I don't possess. I'm simply repeating what was said by a Royal Society member at his memorial, and Richard Dawkins has said similar. BBrihem (talk) 19:52, 7 July 2009 (UTC)
It really doesn't matter whether it's your position or that of Richard Dawkins, or whether you truly support the OPV hypothesis or are merely promoting it on Wikipedia; Hamilton never published a defense of the OPV hypothesis in the peer-reviewed literature, so his opinions do not have the type of sources needed for inclusion in this article. Keepcalmandcarryon (talk) 20:07, 7 July 2009 (UTC)
Claiming sock-puppetry is not a valid excuse for acting against consensus. It is you who is misunderstanding WP:MEDRS, Keep.98.115.14.193 (talk) 18:44, 25 July 2009 (UTC)
  • Outside comment I think that the OPV hypothesis is both disproven and unimportant. Mentioning it here is unnecessary. Mentioning it before AIDS denialism is very strange. I think that the best alternative is to lump it together in the sentence about bioweapons, e.g., Some conspiracy theories allege that HIV was created in a medical or bioweapons laboratory, perhaps as an agent of genocide, or as an accident.
    Additionally, the OPV summary here is misleading, because the most (then-)popular variant of the OPV idea was entirely about HIV's spread through Africa, not about HIV's actual origin. It should be obvious that, for HIV to be spread through an HIV-contaminated vaccine, the virus must have existed prior to contaminating the batch of vaccines. (Spontaneous generation was rejected a very long time ago, and non-existent viruses cannot contaminate anything.) WhatamIdoing (talk) 17:10, 28 July 2009 (UTC)
Agreed. I've removed it. Keepcalmandcarryon (talk) 20:39, 29 July 2009 (UTC)

Sock puppets

Looking through the article history, I've noticed that a large number of one-time and/or single-purpose IPs, along with several single-purpose accounts, have made most of the OPV hypothesis-promoting changes to this article. Based upon their language and editing patterns, I suspect they may be the same person or co-ordinating as meat puppets. I have begun an investigation at WP:SPI, where I encourage any of the accused to give their side of matters. I've alerted BBrihem, but there are simply too many (and mostly dormant) IPs and accounts to alert each separately. Keepcalmandcarryon (talk) 22:59, 6 July 2009 (UTC)

Yes, I don't agree with 98.115.14.193 that Keepcalm is necessarily in the minority here, because of the potential for this. I've just posted the following:-

"I am User20090521: I didn't make a note of my password when I returned to Wikipedia to look at this page a month later. I don't think this could possibly be said to be "Using an alternate account to mislead others" (SPI guidance page), and I'd appreciate it if an enquiry states as much. I am none of the other usernames/IP addresses listed, and I have no meatpuppets."

I hope Keepcalm agrees with the above, and I'd still appreciate it if he/she retracts the allegation that my position is that Hooper is right. It isn't: we just don't know the truth of this. I wish I did. My concern is with the gap between the scientfic community's statements and the cause of objectivity, and how Wikipedia best addresses this. I'm inclined to agree with him/her that some of the above might be the same user(s), and I hope they tell us this if so, but I also suspect that a) there are genuinely many users who would agree with my suggested changes, and b) a majority vote would be for the section on the OPV theory to be retained.

Please could the others named in the sockpuppet enquiry help with the enquiry, as this affects the standing of all of those concerned about this issue, and this is far too serious a topic to be diverted by this kind of thing. BBrihem (talk) 00:25, 7 July 2009 (UTC)

From the enquiry:

"Clerk, patrolling admin and checkuser comments: Sebastiangarth and BBrihem are technically unrelated to each other and to the IPs (hundreds of kilometers apart). -- Luk talk 13:09, 8 July 2009 (UTC)

Per CheckUser evidence above, I am will be taking no action. Tiptoety talk 02:25, 9 July 2009 (UTC)" BBrihem (talk) 02:37, 9 July 2009 (UTC)

Alternative hypotheses

User:ImperfectlyInformed has added material to "Alternative Hypotheses== that is decidedly mainstream and, in fact, repeats material already included in the article. For example, the idea that bushmeat practices, colonial disruption, and unsterile injections (including vaccination needle reuse) could have synergized to allow rapid SIV-HIV evolution. The Chitnis, Rawls and Moore source is already cited in this regard. As I stated in a previous edit summary, II is more than welcome to supplement with additional reliable sources in the appropriate section. To place these "mainstream" ideas in the same category with AIDS denialism and bioweapons charges is, however, questionable and I would maintain misleading.

In addition, the "Katrack" source (Katrak, possibly?) is not PubMed listed and is probably not an ideal source to use here. Keepcalmandcarryon (talk) 14:54, 23 July 2009 (UTC)

Hmm. Have you read the abstract of Preston Marx's paper? It says this:

The genetic distance from SIV to HIV and the mutational activity needed to achieve this degree of adaptation to human hosts is placed within a mathematical model to estimate the probabilities of SIV completing this transition within a single SIV-infected human host. We found that the emergence of even one epidemic HIV strain, following a single human exposure to SIV, was very unlikely. And the probability of four or more such transitions (i.e. HIV-1 groups M, O and HIV-2 subtypes A and B) occurring in a brief period is vanishingly small. We conclude that SIV cannot become a zoonosis, but requires adaptive mutations to become HIV. Some modern event must have aided in the transition of SIV to HIV.

It is not exactly the same as the "cut hunter" theory. Similarly, in his American Scientist article Moore distinguishes between the cut hunter theory and the "colonialism" theory. So does Katrak. Multiple sources distinguishing between theories, with no sources considering them essentially the same, suggests that we should follow the sources. While Katrak's article isn't PubMed-indexed, it's of decent quality and freely-available -- certainly higher quality than news articles from NPR, USAToday, and the BBC. On the other hand, these probably do fit better in the "Method of spread" section, since they do assume that the SIV originally came from a cut hunter, so I put them there. II | (t - c) 19:21, 23 July 2009 (UTC)
Regarding this revert: if your only complaint is that I noted that the coauthors were Moore's graduate students, we can talk about it and remove it if necessary, although it is something Moore himself stated in his 2004 American Scientist article. Certainly none of the introduced sources are as unreliable as Breitbart, NPR, BBC which previously supported that section. II | (t - c) 21:12, 23 July 2009 (UTC)
Names aren't needed, and my impression of reliable sources is that a reputable news organisation, summarising the conclusions of science for a general audience, is probably a better source for this sort of an article than a non-listed journal piece by an author with no obvious publication record in this area. Keepcalmandcarryon (talk) 14:52, 24 July 2009 (UTC)
Both the Preston Marx and Chitnis article are primary sources. Katrak is a secondary source; a medical professional who can comment on their articles, and does so decently. Incidentally, the only inaccuracy you removed in your edit was the one sourced to NPR in the preexisting "consensus" version, presumably "summarizing science". There is no vaccine for African trypanosomiasis. II | (t - c) 18:22, 24 July 2009 (UTC)
Potential inaccuracies I removed included the declaration that humans and SIV have coexisted for thousands of years, the implication that a (single?) modern event precipitated the spread of HIV and that HIV first appeared in the 1930s. Keepcalmandcarryon (talk) 20:45, 24 July 2009 (UTC)
You're correct about trypanosomiasis. The previous language was "Vaccination campaigns against illnesses such as sleeping sickness", which was inaccurate. Today, there are experimental vaccines, but these weren't around during the time in question. A more accurate statement would have been "vaccination campaigns against smallpox and treatment of illnesses such as sleeping sickness". Keepcalmandcarryon (talk) 21:00, 24 July 2009 (UTC)
The statement that humans and SIV have coexisted for thousands of years comes from Preston Marx et al.'s abstract. Is it controversial? Do you have any papers which disagree? All papers I've seen on the topic speak similarly. The HIV appearing in the 1930s was confusingly worded, but both Preston Marx et al. and Chitnis et al. argue that HIV probably appeared sometime around that time (earlier than the first recorded HIV/AIDS case in the 1950s). II | (t - c) 21:26, 24 July 2009 (UTC)
Yes, it is controversial and is contradicted by recent phylogenetic work. I don't have the references on the computer I'm using at the moment, but I'll attempt to add them in the near future. Keepcalmandcarryon (talk) 00:40, 27 July 2009 (UTC)
I'd still like to see those references. II | (t - c) 19:59, 6 August 2009 (UTC)
I'm sorry I haven't had the time to look up these references again, but I'm pleased to refer you to an excellent information resource where you could perhaps have a look. Keepcalmandcarryon (talk) 20:29, 7 August 2009 (UTC)
What an unsurprisingly snarky remark. I quickly came up with another Marx et al article from 2004 (PMID 15525322) which says "Human exposure to SIV is thousands of years old, but AIDS emerged only in the 20th century". Heeney et al 2006 (PMID 16873637) don't mention this new research. I'll give you a couple months, and maybe I'll try to do some digging myself. However, we have a 2001 research article (PMID 11405938) which says "all of the primates that carry these SIVs have been in close contact with humans for thousands of years without the emergence of epidemic HIV", and the 2004 article saying the same thing. On the other hand we have you saying Marx et al's statement is outdated. The onus is on you to bring references. My experience is that you're not nearly as good at reading and researching science as you think you are, so I'm definitely not going to take your word for it. I think it's a bit sad (though unsurprising) that you can't remember where you saw this. II | (t - c) 00:16, 8 August 2009 (UTC)
I'm pleased that my snarkiness entertains you. May it sustain you through the sadness my unsurprisingly poor, nay abysmal, scholarship has so regrettably caused you. In my shame and self-disgust, I assure you that your firm but thoughtful words have motivated me to redouble my efforts to find the references you seek. Keepcalmandcarryon (talk) 22:10, 10 August 2009 (UTC)
Props for handling snideness gracefully, although I never said that your comments entertain me. Since my frank words are motivating for you, I'll admit that I think rude behavior is trite on Wikipedia (and I'll admit that I'm as bad as anyone). Assuming you are sincere, good luck finding those references. II | (t - c) 18:17, 11 August 2009 (UTC)

(Out) Since I don't consider myself any more of an expert than ImperfectlyInformed on the details of relaxed molecular clocks, etc., it would be both silly and, possibly, a violation of the Talk Page guidelines to turn this discussion into yet another fruitless debate. So I'll try to keep this short. The idea, which II imputes to Marx, that humans have been in contact with potentially transmissible SIV for thousands of years without transmission, does not appear to be the current scientific consensus. In fact, I'm not sure there is a solid scientific consensus on this issue. Consensus is that HIV-1 was transmitted about 100 years ago, HIV-2 somewhat more recently and that multiple transmission events occurred, resulting in various clades or groups of viruses in the human population. My impression is that there's little consensus for the hypothesis that specific SIVs go all the way back to speciation. But I don't think there's enough known to say for sure that human-transmissible SIVs are 100s vs. 1000s of years old.

The relevant question is: How long have humans been in contact with SIVs that could be transmitted to them? Not: how long have humans been in contact with SIV? or how long have humans been in contact with other primates? Humans have been in contact with other primates as far back as one draws the species line. Since SIV, unlike FIV, S/HTLV-I, is not generally thought to go back to speciation, humans have therefore probably been in contact with SIV for as long as SIV has existed. So how long have humans been in contact with the particular strains of SIV that are thought to have been transmitted to them in the last century or so? This question is addressed in a recent publication by Wertheim and Worobey (PLoS Comput Biol. 2009 May;5(5):e1000377) entitled "Dating the age of the SIV lineages that gave rise to HIV-1 and HIV-2." The authors conclude that, unless all HIV and SIV dating estimates are "seriously compromised", SIV appears to be very young, with their results placing the "most recent common ancestor for SIV in sooty mangabeys and chimpanzees at 1809 (1729–1875) and 1492 (1266–1685), respectively". When did the first primate-to-human transmission take hold? The authors estimate that "HIV-1 group M and the SIVcpz sequence that lies immediately basal to it shared an MRCA in 1853 (1799–1904), and HIV-1 group N and its sister SIVcpz shared a MRCA in 1921 (1885–1955)"...so sometime after those dates.

In light of these results, obtained using the latest molecular clock models and drawing on many samples to train the clocks, a review written today could not well state that humans definitely have been in contact with transmissible SIV for thousands of years without transmission. And, in fact, this isn't the first evidence against "thousands of years"; in at least one review, even Marx acknowledges the possibility of hundreds of years. One of the other sources I mentioned (this will take you back!) is Querat G et al, "Nucleotide sequence analysis of SA-OMVV, a visna-related OvLV: phylogenetic history of lentiviruses" in Virology 1990. These authors suggest that the last common ancestor of sheep/goat and primate lentiviruses could have been found as recent as 430 years ago, implying an even more recent radiation than that suggested by Wertheim's evidence. Keepcalmandcarryon (talk) 22:54, 12 August 2009 (UTC)

Thanks a lot for explaining this. I agree that there's certainly no consensus. Some discussion of this is probably worth adding to the article. Marx doesn't really seem to cite much for his statements that SIVs are way old (his statements which were nevertheless published in the two abstracts). II | (t - c) 00:24, 14 August 2009 (UTC)
Glad to do what little I can, and I agree that more of this should be added to the article. Let's work on it. Keepcalmandcarryon (talk) 15:13, 14 August 2009 (UTC)
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