Musical HIV

I’ve often been asked, and been unable to answer, how and when the “HIV genome” was deciphered; what “the” genome is, given that we’re told that the pest mutates so rapidly that there are innumerable strains, varieties, and hybrids; what portion of “the genome” is used for measuring viral load. Now, it seems, all those questions can be answered by listening to music whose notes represent the individual nucleotides of “the” complete “HIV” genome as decoded in 2009: What does HIV sound like?
“. . . HIV is an ugly virus in terms of human health. . . . But a new album manages to locate some sonic beauty deep in its genome.  Sounds of HIV (Azica Records) by composer Alexandra Pajak explores the patterns of the virus’s nucleotides as well as the amino acids transcribed by HIV, playing through these biologic signatures in 17 tracks. . . . Pajak took as her basic formula the National Institutes of Health’s record of the retrovirus’ genome and the thousands of coded letters which get transcribed by an enzyme into DNA in a cell once it’s infected. . . . She became curious about the HIV genome, especially when its complete structure was sequenced to single-nucleotide resolution in 2009“.

Intestinal dysbiosis: more and more confirmations

Recently I mentioned a conference presentation from a few months ago that offered support for Tony Lance’s ideas about the role of intestinal dysbiosis in “HIV/AIDS”: probiotic treatment decreased “immune activation” — which is the latest, currently favored mainstream “explanation” for the damage that “HIV” supposedly causes — and increased CD4 counts. Just now I received from Prof. Marco Ruggiero an article that underscores this observation: “Probiotic yogurt consumption is associated with an increase of CD4 count among people living with HIV/AIDS”, by Stephanie L. Irvine, Ruben Hummelen, et al., Journal of Clinical Gastroenterology 44 [2010] e201–e205.

The article is, of course, imbued with mainstream belief, for example “HIV” is blamed for any and every aspect of bad health: “micronutrient deficiencies, diarrhea, and other conditions associated with HIV infection” [my emphasis]. Nevertheless, it cites another 5 articles that report decreased mortality and increased CD4 count merely from increased micronutrient intake especially vitamins B, C, E; and articles associating “HIV” with damage to the gut that is potentially reversible with the aid of probiotics. The latter have also been found to work against the Th1/Th2 imbalance that is one of the characteristics of “HIV/AIDS”. (For a discussion of Th1/Th2 in this context, see Rebecca Culshaw, “Mathematical modeling of AIDS progression:
Limitations, expectations, and future directions”, Journal of American Physicians and Surgeons, 11 [2006] 101-5.)

The fallacy of pre-publication peer review

An alternative title for this piece might be,
“The mainstream conspiracy of peer review”

Somehow it has become the conventional wisdom, within and without the scientific community, that the reliability and quality of science is safeguarded when grants are awarded only after vetting by established experts and research outcomes are published only after approval from established experts.
To the contrary: The important testing of scientific claims occurs only after publication of those claims, whereas pre-publication peer-review serves more effectively to censor truly original advances than to improve the quality of the research literature.
Those points of fact have been known, though, chiefly within history and sociology and philosophy of science and science & technology studies (STS). Few working scientists know anything of those fields, and they labor happily under such illusions as the misguided belief that there’s a universal “scientific method”  that guarantees objectivity and reliability.
The barrier that peer review under mainstream auspices sets against truly innovative work is discovered typically by the individuals who find their ground-breaking advances scorned, censored, rejected, and then rediscovered only after perhaps a very long time, occasionally posthumously. (Stigler’s Law, an illustration of itself,  holds that a discovery is named after the last person to discover it, not the first.) Sociologist Bernard Barber fifty years ago already described the “Resistance by scientists to scientific discovery” (Science, 134 [1961] 596-602). Biologist Gunther Stent four decades ago coined the term “prematurity” to describe scientific breakthroughs that were too far ahead of the mainstream’s conventional views to be accepted (“Prematurity and uniqueness in scientific discovery”, Scientific American, December 1972, 84-93). It took further decades before even the STS communities focused in organized fashion on these insights (Ernest B. Hook (ed)., Prematurity in Scientific Discovery: On Resistance and Neglect, University of California Press, 2002).
Journal editors are in prime position to recognize the wet blanket of banally routine attitudes that peer review throws over original, counter-mainstream claims. Thus Richard Horton, editor of The Lancet, wrote:
“Peer review . . . is simply a way to collect opinions from experts in the field. Peer review tells us about the acceptability, not the credibility, of a new finding” (Health Wars: On the Global Front Lines of Modern Medicine, New York Review Books, 2003: 306).
A full discussion of these matters has been published by Richard Smith, former editor of the British Medical Journal (“Classical peer review: an empty gun”, Breast Cancer Research 2010, 12 [suppl. 4] S13). Smith points out that all the studies of the consequences and effects of peer review as normally practiced have found no evidence for its vaunted benefits:
— “At present, little empirical evidence is available to support the use of editorial peer review as a mechanism to ensure quality of biomedical research”.
— Peer review does not prevent the publication of unimportant banalities that clutter up the literature and lower its quality: “Many studies are never cited once, most disappear within a few years, and very few have real, continuing importance”.
That has long been known, of course, to competent observers in STS, see for example J. R. & S. Cole, Social Stratification in Science , University of Chicago Press, 1973: 228; Henry W. Menard, Science: Growth and Change, Harvard University Press 1971: 99; Derek J. de Solla Price, Little Science, Big Science . . . And Beyond, Columbia University Press 1963/1986, Chapter 2).
It is not surprising, then, that John Ziman estimated that perhaps 90% of research articles in physics journals turn out to be erroneous in some way and thus not worth citing (Reliable Knowledge, Cambridge University Press, 1978, p. 40).
That much of the scientific community as well as science journalists and public pundits about science have remained ignorant of all this is illustrated by the brouhaha of astonishment that came when John Ioannidis showed that much of the medical literature is simply false [“Why most published research findings are false”, PLoS Med, 2005, 2:e124], often because “the standard of statistics in medical journals is very poor” [D. G. Altman, “Poor-quality medical research: what can journals do?” JAMA 287 (2002) 2765-7; “The scandal of poor medical research”, BMJ 308 (1994) 283-4]; so that “less than 1% of the studies in most journals” is “both scientifically sound and important for clinicians” [Haynes, “Where’s the meat in clinical journals?”, ACP Journal Club 119 (1993) A22-3]. Drummond Rennie, an editor of the Journal of the American Medical Association, remarked that “There seems to be no study too fragmented, no hypothesis too trivial, no literature citation too biased or too egotistical, no design too warped, no methodology too bungled, no presentation of results too inaccurate, too obscure, and too contradictory, no analysis too self-serving, no argument too circular, no conclusions too trifling or too unjustified, and no grammar and syntax too offensive for a paper to end up in print”. As I pointed out recently,  the purpose of publishing “research” articles is to pad vitae and lay the ground for getting more grants.
— Pre-publication peer review lacks benefit since it doesn’t ensure quality. It causes damage by censoring important work. Even with journeyman studies that add something potentially useful to the literature, the costs incurred by peer reviewing are not commensurate with any value added by the peer-review process.
— By contrast, peer review does prevent publication of work vindicated later, perhaps much later, as an important advance. Smith fails to cite Barber, however, who may have been the first to offer a host of specific illustrations. Smith does, however, point to the evidence that bias strongly influences reviewers’ opinions, and that abuses occur, not only the willful criticizing of those whose views are not the same as those of the reviewer but even such actual dishonesty as the misappropriation by reviewers of supposedly confidential material.

Smith sums it all up thus: “The problem with filtering before publishing, peer review, is that it is an ineffective, slow, expensive, biased, inefficient, anti-innovatory, and easily abused lottery: the important is just as likely to be filtered out as the unimportant. The sooner we can let the ‘real’ peer review of post-publication peer review get to work the better”.

Richard Smith cites David Horrobin’s critique of peer review, though he fails to mention Horrobin’s founding of Medical Hypotheses, the journal that practiced what Smith and Rennie and Horton preach — until ignorant administrators at Elsevier bowed to pressure from HIV/AIDS vigilantes (€L$€VI€R and the NEW “Medical Hypotheses”).  Smith himself was editor of the short-lived Cases Journal (~2008-2010) whose rationale and practices were similar to those of Medical Hypotheses.

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The degree to which bias, self-interest and vested interests have corrupted science and medicine is illustrated by the fact that editors of leading journals write about the deficiencies of peer review but do not even try to change the system, despite the fact that they are in prime position to do so. Rather they actively collaborate, and entrench the system’s deficiencies: a group of Lancet editors ratified Elsevier’s censorship of Medical Hypotheses, and Horton’s Lancet has itself censored evidence-based critiques of HIV/AIDS theory by Gordon Stewart.
I have myself been editor of a peer-reviewed journal, and I understand the wide latitude that editors have in their choice of reviewers, in holding reviewers to standards of objectivity, and in bringing even counter-mainstream views to wider notice by publishing them together with reviewers’ demurrals. It isn’t necessary for editors of leading journals to just follow the implicit orders of the mainstream’s conventional wisdom; more shame to them for doing so even as they recognize that they shouldn’t. It’s possible to do better. I’ve found, for instance, that the Journal of American Physicians and Surgeons  practices pre-publication peer review in a manner that is useful rather than burdensome: the editor demands that reviewers respond promptly, chooses alternatives when reviewers are tardy or unresponsive, and holds reviewers to evidence-based commentary that helps authors to improve their manuscripts.
However, the almost universal hegemony exerted by current counter-productive practices is illustrated by the fact that Richard Smith’s exposure of the fallacy of pre-publication peer-review was published in Breast Cancer Research rather than where it belongs, in Nature or Science or The Lancet or JAMA or the New England Journal of Medicine, since it is of concern to everyone involved in research and practice in science and medicine.

The hold that current corrupt practices have over academe and medicine and science is further illustrated by the avalanche of books by informed insiders denouncing the corruption — to no visible avail or effect. One is reminded of the continual expressions of horror at the corrupt state of intercollegiate athletics, expressions from the very people whose positions — as university presidents or as members of the Knight Commission  — would seem to make it possible for them to actually do something about it. Instead, the most prominent critical voices are those of university presidents who are safely retired.

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Acknowledgment:
Richard Smith’s article was drawn to my attention by (no relation) Dave Smith, who has himself blogged about the problems with peer review  and the piece by Richard Smith

More professionally published garbage

No sooner had I posted about news not fit to print than TIME Healthland brought the headline,
“Study: Gay Men Are Twice as Likely to Have Cancer”

It took me a little while to find the original source, in part because there are two journals titled “Cancer” and in other part because this ground-breaking announcement had not yet been published and was available only in the “Early View” list on the journal’s website.
The actual report reveals that the headline was utterly misleading: the article concerns relationships between sexual orientation and cancer survivorship, not cancer incidence:
“these data only address self-reported survivorship; therefore, they do not adequately reflect cancer incidence” (Boehmer et al., “Cancer survivorship and sexual orientation”, Cancer DOI: 10.1002/cncr.25950).
Furthermore, the authors themselves list reasons why their “study” should not be taken seriously: it is restricted to a California group and not representative of the groups allegedly being studied, namely, those differing in sexual orientation. The second part of the article’s “Discussion” section explains quite well why the first half, which reports alleged differences by sexual orientation, should be ignored.
But it would not even be necessary to read that far to understand why this was “news” not fit to print. The authors merely searched in data from surveys published in 2001, 2003, and 2005 by the California Health Interview, looking for correlations by sexual orientation. Statistics 101 teaches that if you look for enough correlations you are sure to find some, the actual rate depending upon what criterion you choose as the threshold for “statistical significance”. If the correlations being looked for are inherently plausible, and the typical significance level of p<0.05 is used, perhaps only 1 in 20 “correlations” will be entirely spurious (but at least 1 in 20); if the correlations that seem to pop up are implausible, the rate of false-positive correlations will be considerably higher (see for example R A J Matthews, “Significance levels for the assessment of anomalous phenomena”, Journal of Scientific Exploration 13 #1 [1999] 1-7).
Boehmer et al. “found” a higher incidence of cancer among gay men, albeit not for melanoma, colon cancer, or “multiple cancers”, and a “significantly” lower rate of prostate cancer. How many correlations did they look at for different types of cancer? Perhaps the apparently significant correlations are spurious.
So too with women: “There were no significant differences between lesbians and heterosexual women with respect to their health perception or any of the cancer sites (results not shown). Bisexual women, however, differed significantly from heterosexual women”. How plausible is it that bisexual women but not lesbians differ significantly from heterosexual women in any way at all? I wager that no replication of this “finding” will ever be published. But that does not prevent the authors from claiming that the results identify “bisexual women as a new risk group for cervical cancer”! And they propose that this group be targeted for “screening intervention to reduce the prevalence of cervical cancer in this population”.
For that matter, what conceivable reason is there to look for correlations between sexual orientation and cancer, be it incidence or survivorship? The vaunted (albeit mythical) scientific method begins with a plausible hypothesis of some sort and then seeks to test it against evidence; what was the plausible hypothesis to be tested here?
The authors recommend “interventions that target lesbian and bisexual cancer survivors to improve their health perceptions”. One might wonder why that has any importance at all. Is “health perception” another new medical condition, an illness, to be diagnosed and treated? (Read Selling Sickness by Moynihan & Cassels.),

The Boehmer et al. article illustrates nicely what I had pointed out in the previous post,  that the purpose of publication is to pad vitae and to impress potential research funders; note how the authors emphasize that their findings are novel: “Our novel findings”; “this study’s novelty”; “novel findings”; “new risk group”; and “Future research” will need to identify why health perceptions differ by sexual orientation, calling for more data to be gathered “to identify possible factors, such as discrimination, social support, coping, or the patient-physician relationship”.
Clearly this sets the stage for enough grants to last several working life-times (if one cares to dignify this activity as work). Moreover, future exercises along these lines are guaranteed to bear fruit. After all, it is too superficial to analyze the data only in terms of overall sexual orientation. Obviously the category of gay men ought to be sub-divided into those who always take the passive role, those who always take the active role, and those who switch hit; similarly with lesbians, there needs to be a sub-division into the three analogous groups; and the category of bisexual women, too, should be sub-divided into those who are bisexual lifelong and always, those who begin as heterosexual and later recognize their true inclinations, those who begin and change in the opposite way, and those who make such a change back and forth more than once. In other words, it is easy to identify perhaps as many as a couple of dozen variables worth “studying”; and it can be guaranteed that some startling correlations, really novel “findings”, will emerge if correlations are sought among another dozen or two variables; it’s money in the bank.

The immediate news release about the Boehmer article, published only on-line and awaiting print publication, illustrates the publicity-hunting ethos of contemporary researchers and the determined efforts of the journalists to get there first with everything, thereby flooding the media with untested claims that turn out to be chiefly rubbish, since real science — reliable science — isn’t news.

Policy makers and research funders would do well to ignore authors who praise the novelty of their own findings, especially when those findings are merely the result of indiscriminate data-mining; and they should ban all “statistical” research that relies on frequentist rather than Bayesian approaches, see R A J Matthews, “Facts versus Factions: The use and abuse of subjectivity in scientific research”, in Rethinking Risk and
the Precautionary Principle (Ed: Morris, J.) (Oxford : Butterworth) 247-282 (2000).

“HIV/AIDS” “science” news unfit to print

Scientists understand what the purpose of publishing is: to make a name for oneself, to impress those who dole out research funds, to provide padding for one’s curriculum vitae.
Outsiders don’t always understand this, and journalists are among those outsiders, regrettably. As a result, the media are replete with announcements of scientific breakthroughs that are nothing of the sort. The overall damage may not be obvious, certainly not at once, but it is surely quite high.
For instance, how many women were misled into hope over the announcement, many years ago, that a gene responsible for breast cancer had been found (Elisa Segrave, “Still living in hope”, Sunday Times (UK), 9 July 1995, p. 7-5; review of Kevin Davies & Michael White, Breakthrough: The Quest to Isolate the Gene for Hereditary Breast Cancer, Macmillan)? How many women opted for prophylactic mastectomy because they had that gene?
The truth, of course, was that researchers had found an association, a correlation, between a certain gene mutation and about 5% of cases of breast cancer. Furthermore, by no means everyone with that mutation gets breast cancer. It is still not agreed what the odds are (though of course one can read all sorts of claims about it), and it is still not known  what the undoubtedly several others factors are — even in those women with that particular mutation — that also increase the odds that breast cancer will ensue. Consequently there is no rational way, no objective guidance, for a woman with that gene to estimate the benefit in risk reduction from a mastectomy as against the psychological cost.
The “news” about the discovery of that correlation was not fit to print, as was obvious even at that time since the observation of a mere correlation with a mere 5% of cases should have brought only yawns and an understanding that this sort of thing is suitable for publication in a research journal but not worth mentioning to the wider public. Yet it was ballyhooed all over the media. There are innumerable other such instances. The media, and especially television, need a continual supply of newsworthy material — which doesn’t exist when news is defined as startling as well as new; especially concerning science or medicine, since real science just isn’t news. To the general public “science” means reliable, certain, trustworthy, and nothing can be known to be that if it hasn’t been around long enough to be thoroughly tested under all sorts of conditions and by people with different scientific prejudices and beliefs.
One suspects that journalists are hesitant to apply common sense to matters that seem highly technical. If so, then that would reflect a high degree of ignorance, because the flaws in these “breakthrough” announcements are obvious on quite general grounds and without delving into the technicalities. For one thing, anyone “covering” anything about science or medicine ought to know that a single study, even if published in a peer-reviewed journal, cannot be taken as more than possibly suggestive, even if they have not learned from John Ziman (Reliable Knowledge, Cambridge University Press, 1978, p. 40)that even in physics about 90% of research articles, the “primary” scientific literature, turn out to be wrong in some way.

This general preamble was set off by the press release, picked up by several news media, that a presentation at a forthcoming conference would explain why black men are so much more likely than others to become “HIV-positive”:

“Higher HIV risk in black gay men linked to partner choice, risk perception”
03 May 2011
“[EMPHASES ADDED IN THE FOLLOWING] Young black men who have sex with men (MSM) get infected with HIV nearly five times more often than MSM from other races, even though they don’t have more unprotected sex.
The discrepancy has long mystified public health experts but a new study by investigators at Johns Hopkins and elsewhere now offers a possible explanation for it.
The study found that young black MSM — a group that includes openly gay and bisexual men, as well as those who have sex with men but do not identify themselves as gay or bisexual — select partners and judge these partners’ HIV status in a specific way. These men show a clear preference for masculine men, while also equating masculinity with lower HIV risk. This dynamic, the researchers say, can help explain why young black MSM contract HIV more often than their counterparts from other races.
The results are based on interviews with 35 black men ages 18 to 24 who have sex with men. The most notable findings include an overwhelming preference for masculine partners, accepting masculine partners as dominant in the sex act and leaving to them decisions about condom use, perceiving masculine men as low risk for HIV and feminine men as high risk.
“There may be no difference in HIV prevalence between masculine-looking and feminine-looking men, but because black MSM perceive masculine men as lower risk, their sexual encounters with such men may make HIV infection more likely,” said investigator Jonathan Ellen, M.D., a pediatrician and teen health expert at Johns Hopkins Children’s Center.
In other words, even though young black MSM have unprotected sex just as often as others, they may be having unprotected sex in riskier ways with partners whose HIV status they often miscalculate, the researchers explain.
The findings offer new insight into how black MSM judge risk based on perceptions of masculinity and can help inform public health campaigns to reduce new HIV infections in this disproportionately affected group. The findings, the researchers say, can also guide safe-sex conversations between primary care physicians and patients.
Errol Fields, M.D. Ph.D., currently a resident at Boston Children’s Hospital, was lead author on the research, which he conducted as a graduate student at the Johns Hopkins Bloomberg School of Public Health. Researchers from Children’s Hospital Boston and Emory University also participated in the study.
Source: Johns Hopkins Medicine”

This striving for public attention was a press release from Johns Hopkins, also featured on the Johns Hopkins Children’s Center site, and picked up by EurekaAlert  and ScienceDaily  among many other sites. Yet it’s garbage, and quite obviously so: anyone who disseminates in any media ought to understand the limitations of material collected by interview; and even a moment’s thought will make plain that information from 35 people hardly warrants extrapolation to everyone who is also black, male, gay (or MSM), and aged between 18 and 24.
Possibly a bit more subtle but still hardly recondite is the fact that if you claim to be comparing black men with others, you should actually do so; yet there is no mention of interviews with 18-24-year-olds of other races, to learn whether perhaps they too have the same preferences in sexual partners and (allegedly) mistaken inferences about the risks that those partners might be “HIV-positive”.
That there in fact “may be no difference in HIV prevalence between masculine-looking and feminine-looking men” is hardly a basis for alleging, as the “conclusions” of this “study” do, that there isn’t in fact any difference.
And of course it’s purely speculative that they “may be having unprotected sex in riskier ways with partners whose HIV status they often miscalculate”.
Anyone familiar with the epidemiology of “HIV” would also balk at the claim that black men are “nearly five times” more likely than those of other races to become “HIV-positive”: African-American men are about 7-8 times more likely than white American men, and about 10 times more likely than Asian American men, to be “HIV-positive”. That this “has long mystified public health experts” stems from the mistaken acceptance by those experts of HIV/AIDS theory; others have long offered explanations in terms of race-linked physiology, see several chapters in my book and sources cited there.
That this was work carried out by a graduate student, and that it was featured in a press release from Johns Hopkins, illustrates what I said at the outset about the purpose of “scientific” publication.