Tag Archives: v-src

To Resign over an Editorial Decision You Disagree With

What would you do if you were serving on the editorial board of a scientific journal which had just published a manuscript that you knew was seriously flawed. Moreover, you knew that publication of the manuscript might seriously undermine global public health? That was the circumstance of cell biologist Klaudia Brix, Professor of Cell Biology, Jacobs University Bremen, Germany, when, in 2011, the Italian Journal of Anatomy and Embryology (IJAE)—the official publication of the Italian Society of Anatomy and Histology—published a paper by infamous AIDS denialist, Peter Duesberg, which reiterated his already discredited argument that HIV (the human immunodeficiency virus) does not cause AIDS (1). Brix resigned in protest from the IJAE editorial board. But why is that noteworthy? Remarkably, she was, for a time, the only member of the journal’s 13-person editorial board to do so, despite other members having similar misgivings over the decision to publish the paper. Afterwards, Heather Young, an anatomy and neuroscience researcher at the University of Melbourne, likewise resigned from the IJAE editorial board. Here is the background to this state of affairs.

Peter Duesberg is not the only AIDS denialist. However, he has been the most infamous of the AIDS denialists. HIV is a retrovirus, and Duesberg is the only AIDS denialist who also happens to be an expert retrovirologist. In fact, Duesburg was at one time a highly esteemed retrovirologist. In 1985 he was elected to the U.S. National Academy of Sciences; mainly for his 1970 discovery, with Peter Vogt, of the first known retroviral oncogene—the Rous sarcoma virus v-src.

AIDS denialist, Peter Duesberg
AIDS denialist, Peter Duesberg

Duesberg first put forward his denialist view in a 1987 paper in Cancer Research (2), which asserted that AIDS results from drug abuse, parasitic infections, malnutrition, and antiretroviral drugs. In Duesberg’s assessment, HIV is just another opportunistic infection. He has maintained that view since then, despite overwhelming evidence to the contrary. Consequently, he is looked upon as a pariah by the scientific community.

Even though Duesberg’s denialist views have been rejected by AIDS experts, Duesberg’s standing as a retrovirologist enabled him to yet influence some public health officials. In 2000, Duesberg was serving on a panel advising Thabo Mbeki (President of South Africa after Nelson Mandela) on how to manage the South African AIDS outbreak. Although Mbeki was an able and intelligent leader, he accepted Duesberg’s denialist view that HIV was not the cause of the South African AIDS epidemic. Thus, Mbeki allowed the South African outbreak to get completely out of control (3). Two independent studies later concluded that over 300,000 South African AIDS deaths would not have occurred if the Mbeki government’s public health policy had not followed the denialist view. Many thousands of South African AIDS victims, including infants, would have been spared infection if the government had publicized that AIDS is an infectious disease, and if it had made antiretroviral drugs available, particularly to pregnant women (1).  See Asides 1 and 2.

[Aside 1: The reasons why Mbeki assented to Duesberg’s denialist view are not clear. One possibility is that Mbeki held strong anti-colonialist and anti-West sentiments—born of having come of age during South Africa’s apartheid era—which led him to see his country’s AIDS crisis as a means by which the West sought to exploit his nation. To that point, he may have doubted the efficacy of expensive antiretroviral drugs, which were available only from large Western pharmaceutical companies. Moreover, the cost of treating the 5 million or more HIV-infected South Africans with those drugs would have exceeded the annual health department budget of his poverty-stricken nation by a factor of ten. Mbeki did accept that AIDS is the consequence of a breakdown of the immune system. But he was inclined to believe (or at least claimed) that poverty, bad nourishment, and ill health, rather than a virus, led that breakdown; a stance that enabled him to justify treating poverty in general, rather than AIDS in particular. Duesberg defended Mbeki in his publications, denying that hundreds of thousands of lives were lost in South Africa because of the unavailability of anti-retroviral drugs. But in 2002, after Mbeki suffered political fallout from the consequences of having acceded to Duesberg’s views, he tried to distance himself from the AIDS denialists, and asked that they stop associating his name with theirs.]

[Aside 2: The 2000 International AIDS Conference was taking place in Durban (a city in the South African province of KwaZulu-Natal) at the same time that Mbeki’s AIDS panel was convening in Johannesburg. Consequently, the denialist views expressed by Mbeki’s panel were also being heard in Durban. This prompted the so-called “Durban Declaration,” signed by over 5,000 scientists and physicians, and published in Nature, which proclaimed that the evidence that HIV causes AIDS is “clear-cut, exhaustive and unambiguous”.]

Well before Duesberg submitted his paper to IJAE, the arguments put forward in the paper had already been appraised and rebuffed by the scientific community. Indeed, the paper had previously been rejected by several other journals. The first submission was to the Journal of Acquired Immune Deficiency Syndromes (JAIDS), a peer-reviewed medical journal covering all aspects of HIV/AIDS. The JAIDS editors found that Duesberg’s contentions in the paper were based on a selective reading of the scientific literature, in which he dismissed all the vast evidence that HIV is the etiologic agent of AIDS. Not surprisingly, JAIDS rejected the paper, with one peer reviewer even warning that Duesberg and co-authors could face criminal charges if the paper were published.

After JAIDS rejected the paper, Duesberg  submitted a revised version to Medical Hypotheses (4). Like the original paper sent to JAIDS (as well as the version accepted by IJAE), the paper submitted to Medical Hypotheses contained data cherry-picked to cast doubt on HIV as the cause of AIDS. Nonetheless, Medical Hypotheses accepted the paper. However, the paper never went to press. But first, what was the explanation for the seemingly bizarre decision to accept the paper?

The answer laid in the fact that Medical Hypotheses was the only journal of its parent publisher, Elsevier, that did not use peer review; instead relying on its editorial board to select papers for publication. In any case, before the accepted paper went to press, prominent AIDS researchers, including Nobel laureate Francoise Barre-Sinoussi (co-discoverer that HIV is the cause of AIDS, 5), complained to Elsevier that the paper would have a negative impact on global healthcare, and requested that the paper be withdrawn.

Elsevier responded to these protests by asking the editors of another of its journals, The Lancet, to oversee a peer review of the paper. The Lancet editor sent the paper to five external reviewers, each of whom found that it contained numerous errors and misinterpretations, and that it could threaten global public health if it were published. Elsevier then permanently withdrew the paper.  Elsevier also instituted a peer-review policy at Medical Hypotheses (and fired the journal’s editor, who resisted the change).

The Medical Hypotheses incident resulted in more notoriety for Duesberg when the University of California, Berkley, where Duesberg is still a professor of molecular and cell biology, bought charges of misconduct against him for making false scientific claims in the paper, and for a conflict-of-interest issue. Apropos the latter, Duesberg did not reveal that co-author David Rasnick had earlier worked for Matthias Rath, a German doctor and vitamin entrepreneur, who sold vitamin pills as a therapy for AIDS. Duesberg was later cleared of both charges. But the next iteration of paper, to IJAE, did not respond to these allegations.

Duesberg regarded Elsevier’s actions as another example of “censorship” imposed by the “AIDS establishment.” Undeterred however, he submitted a revision of the paper to IJAE, which that journal then accepted, prompting Klaudia Brix and Heather Young to resign from that journal’s editorial board. The IJAE paper contained the same cherry-picked data and discredited assertions that were rejected earlier by JAIDS and Elsevier.  Moreover, publication of the paper still posed a threat to global public health. What then was behind the IJAE decision to publish?

Here is what happened. The paper was “peer-reviewed” by IJAE, but by only two reviewers; one of whom was Paolo Romagnoli, the IAJE editor-in-chief, who is neither a virologist or an epidemiologist but, instead, a cell anatomist. Consequently, the paper underwent only one external review, and there is no information regarding whether the lone external reviewer was an AIDS expert. One board member (who did not resign) later commented: “Only one [external] reviewer in my mind is not enough for manuscripts of a sensitive nature… (6)” [But this comment too is a bit troubling. Bearing in mind that the paper contained numerous errors and misinterpretations, would those have been okay if the paper were not of a “sensitive nature”?]

One also might ask why a journal that specialized in anatomy and embryology would consider a paper about the cause of AIDS. To that point; Klaudia Beix gave, as a reason for her resignation from the IJAE board, her belief that a journal should function within its scientific “scope” (6). So how did Romagnoli, the IJAE editor-in-chief, justify his decision to consider the paper?  He did so by asserting that it dealt with “issues related to the biology of pregnancy and prenatal development and with the tissues of the immune system (6).” But despite Romagnoli’s contention, the only mention of embryology in the paper was a short comment in the abstract: “We like to draw the attention of scientists, who work in basic and clinical medical fields, including embryologists, to the need of rethinking the risk-and-benefit balance of antiretroviral drugs for pregnant women, and newborn babies (1).”

As for Romagnoli’s reliance on only two reviewers, he justified that stance on the fact that the reviewers had concurring opinions. Moreover, he claimed that his criteria for selecting reviewers—apparently irrespective of their expertise—was to choose individuals (himself included) who he believed would not reject a paper merely because it challenged prevailing opinion.

But is there any possibility that Duesberg might be right? The answer is virtually none whatsoever. An earlier post noted: “…the evidence that HIV causes AIDS is, without exaggeration, overwhelming. Consider just the following. Data from matched groups of homosexual men and hemophiliacs show that only those who are infected with HIV ever develop AIDS. Moreover, in every known instance where an AIDS patient was examined for HIV infection, there was evidence for the presence of the virus. These data have been available for years, and Duesberg should have been aware of them. What is more, there has been the enormous success of antiretroviral therapy in changing AIDS from a nearly invariably fatal disease, into a manageable one, for many HIV-infected individuals (3).”

Even so, Duesberg is not regarded as a pariah by AIDS experts merely because his views concerning the connection between HIV and AIDS challenge accepted wisdom.  Instead, as asserted by Harvard University AIDS epidemiologist, Max Essex, Duesberg has sustained a “dangerous track of distraction that has persuaded some people to avoid treatment or prevention of HIV infection (6)”.

A scientist mounting a long-time challenge to the “establishment,” and being ridiculed for his views, before eventually being vindicated, makes for a very good story. However, such instances are very rare. Exceptions include Howard Temin (7) who hypothesized reverse transcription, and Stanley Pruisner (8) who hypothesized prions—infectious agents that contain no nucleic acid genome. Both researchers had to endure widespread ridicule for several years. But, and importantly, irrefutable evidence eventually accumulated to support their hypotheses. And, finally, both were awarded Nobel Prizes. But Duesberg has not been vindicated and, almost certainly, he  never will be.

References:

1. Duesberg PH, et al., 2011. AIDS since 1984: no evidence for a new, viral epidemic – not even in Africa. Italian Journal of Anatatomy and Embryololgy 116:73–92. http://fupress.net/index.php/ijae/article/view/10336/9525

2. Duesberg P, 1987. Retroviruses as carcinogens and pathogens: expectations and reality. Cancer Res. 47:1199–220. PMID3028606.

3. Thabo Mbeki and the South African AIDS Epidemic, Posted on the blog July 3, 2014.

4. Duesberg PH, et al., 2009. WITHDRAWN: HIV-AIDS hypothesis out of touch with South African AIDS – A new perspective. Medical Hypotheses. doi:10.1016/j.mehy.2009.06.024. PMID19619953.

5. Who Discovered HIV, Posted on the blog, January 24, 2014.

6.  Corbyn Z. 2012. Paper denying HIV–AIDS link sparks resignation: Member of editorial board quits as editor defends publication. Nature doi:10.1038/nature.2012.9926.

7. Howard Temin: “In from the Cold, Posted on the blog December 14, 2013.

8. Stanley Pruisner and the Discovery of Prions: Infectious Agents Comprised Entirely of Protein, Posted on the blog December 15, 2016.

 

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Tony Hunter and the Serendipitous Discovery of the First Known Tyrosine Kinase: the Rous Sarcoma Virus Src Protein

In 1911 Peyton Rous, at the Rockefeller Institute, discovered the Rous sarcoma virus; the first virus known to cause solid tumors (1). Although Rous’ eponymous virus also would be known as the prototype retrovirus, his discovery generated only scant interest at the time, and would not be recognized by the Nobel Committed until 65 years later! [Nobel prizes are not awarded posthumously. Fortunately, Rous had longevity on his side. He died 4 years after receiving the prize, at age 87.]

In 1976 Harold Varmus and J. Michael Bishop, then at the University of California San Francisco, discovered that the Rous sarcoma virus oncogene, v-src, as well as the oncogenes of several other tumorgenic retroviruses, actually were derived from cellular genes that normally play an important role in controlling cell division and differentiation (2). Moreover, Varmus and Bishop showed that these cellular “proto-oncogenes” can be altered by mutation, to become “oncogenes” that contribute to cancer. [Varmus and Bishop received the 1989 Nobel Prize in Physiology or Medicine for their discovery of proto-oncogenes.]

But what is the actual activity of the protein coded for by the normal cellular c-src, and by v-src as well? The story of that discovery is rather delightful and begins as follows.

In 1978, Raymond Erikson and coworker Marc Collette, then at the University of Colorado Medical Center, were the first researchers to isolate the Src protein. They accomplished this by first preparing lysates from avian and mammalian cells, which had been transformed in culture into tumor cells by Rous sarcoma virus. Next, they precipitated those lysates with antisera from rabbits that bore Rous sarcoma virus-induced tumors. The premise of their strategy was that antibodies from the tumor-bearing rabbits would recognize and precipitate proteins that were specific to cells transformed by the virus .

With the Src protein now in hand, Ericson and Collette next sought its function. They initially asked whether Src might have protein kinase activity (i.e., an activity that adds a phosphate group to a protein.). This was a reasonable possibility because protein phosphorylation was already known to play a role in regulating various cellular processes, including cell growth and differentiation.

Ericson and Collette tested their premise by incubating their Src immunoprecipitates with [γ-32P] ATP (i.e. 32P-labelled adenosine triphosphate). In agreement with their proposal, they found that the antibody molecules in the Src immunoprecipitates had been phosphorylated. [Note that Src’s protein kinase activity was simultaneously and independently discovered by Varmus and Bishop.]

Ericson and Collette also carried out control experiments that were particularly revealing. When the same rabbit antisera was used to immunoprecipitate extracts from normal cells, or extracts from cells infected with a transformation-defective mutant of Rous sarcoma virus, no signs of protein kinase activity were seen in those immunoprecipitates. What’s more, the protein kinase activity was found to be temperature sensitive in immunoprecipitates from cells infected with a mutant Rous sarcoma virus that was temperature-sensitive for transformation.

These control experiments confirmed that the protein kinase activity in the immunoprecipitates was coded for by the virus. What’s more, they confirmed that the kinase activity of the retroviral Src protein plays an essential role in transformation. Furthermore, when taken with the earlier findings of Varmus and Bishop, they implied that the kinase activity of the cellular Src protein plays a key role in the control of normal cell proliferation.

While Erickson and coworkers were carrying out the above experiments in Denver, Walter Eckhart and Tony Hunter, at the Salk Institute, were looking into the basis for the transforming activity of the mouse polyomavirus middle T (MT) protein. [Unlike Rous sarcoma virus, which is a retrovirus, the mouse polyomavirus is a member of the Polyomavirus family of small DNA tumor viruses. SV40 is the prototype Polyomavirus.]

Tony Hunter
Tony Hunter

Since Erickson’s group was finding that Src expresses protein kinase activity, Eckhart and Hunter asked whether the polyomavirus MT protein might likewise be a protein kinase. Thus, as Erickson and Collette had done in the case of Src, Eckhart and Hunter examined immunoprecipitates of MT to see if they too might express a protein kinase activity, and found that indeed they did.

Interestingly, it was not known at the time of these experiments that MT actually does not express any intrinsic enzymatic activity of its own. Instead, MT interacts with the cellular Src protein to activate its protein kinase activity. See Aside 1.

[Aside 1: For aficionados, MT is a membrane-associated protein that interacts with several cellular proteins. Importantly, the phosphorylation events carried out by MT-activated Src cause a variety of signal adaptor molecules [e.g., Shc, Grb2, and Sos] and other signal mediators [e.g., PI3K and PLCγ] to bind to the complex, thereby triggering a variety of mitogenic signaling pathways. These facts were not yet known when Eckhart and Hunter were doing their experiments.]

At the time of these experiments, serine and threonine were the only amino acids known to be phosphorylated by protein kinases. In fact, Erikson and Collette, as well as Varmus and Bishop, believed that threonine was the amino acid phosphorylated by the Src kinase (see below). Consequently, Hunter asked whether the polyomavirus MT protein likewise would phosphorylate threonine. [Recall that MT actually does not express any intrinsic enzymatic activity of its own.]

Hunter’s experimental procedure was relatively straightforward and reminiscent of Erikson’s and Collette’s. It involved incubating immunoprecipitates of MT with [γ-32P]ATP, hydrolyzing the immunoglobulin, and then separating the amino acids in the hydrolysate by electrophoresis. But, to Hunter’s surprise, the position of the labeled amino acid in his electropherogram did not correspond to that of either threonine or serine.

Hunter was well aware that tyrosine is the only other amino acid with a free hydroxyl group that might be a target for the MT kinase activity. And, while there was no precedent for a tyrosine-specific protein kinase, Hunter proceeded to ask whether the polyomavirus MT protein indeed might phosphorylate tyrosine.

Hunter began by synthesizing a phosphotyrosine molecule that could be used as a standard marker against which to compare the labeled amino acid in a repeat of his earlier experiment. And, to his pleasure, Hunter found that the amino acid that was phosphorylated by the MT kinase activity ran precisely with the phosphotyrosine standard marker in his new electropherograms.

But why had other researchers not detected tyrosine phosphorylation earlier? It was partly because phosphotyrosine accounts for only about 0.03% of phosphorylated amino acids in normal cells. The remaining 99.97% are phosphoserine and phosphothreonine. But, again, that is not the entire explanation. The rest is truly precious.

In Hunter’s own words, he was “too lazy to make up fresh buffer” before doing his experiments. Had the buffer been fresh, its pH would have been the usual 1.9; a pH that, unbeknownst to all at the time, does not separate phosphotyrosine from phosphothreonine during the electrophoresis procedure. The pH of the old buffer that Hunter used in his experiment had inadvertently dropped to 1.7; a pH at which phosphotyrosine is resolved from phosphothreonine. That fact enabled Hunter to discriminate phosphotyrosine from phosphothreonine for the first time. Thus, Hunter attributes his hugely important discovery to his laziness.

The finding that tyrosine is the amino acid phosophorylated  by the polyomavirus MT protein kinase activity led Hunter and his Salk Institute-colleague Bart Sefton to ask whether Src too might phosphorylate tyrosine, rather than serine or threonine (4). Indeed, they found that the retroviral Src protein, as well the normal cellular Src protein, function as tyrosine-specific protein kinases. [Recall that it became clear only later that MT actually has no intrinsic enzyme activity of its own and that it acts through Src.] Moreover, the levels of phosphotyrosine were 10-fold higher in cells infected with wild-type Rous sarcoma virus than in control cells, consistent with the premise that Src’s protein tyrosine kinase activity accounts for the altered growth potential of those cells.

Subsequently, Stanley Cohen, at Vanderbilt University, discovered that the epidermal growth factor (EGF) receptor contains an intrinsic protein-tyrosine kinase activity, further underscoring the importance of protein-tyrosine kinases in the normal control of cell proliferation. [Cohen shared the 1986 Nobel Prize in Physiology or Medicine with Rita Levi-Montalcini for their discoveries of growth factors, including EGF.] Subsequent studies identified additional receptor protein-tyrosine kinases, such as the fetal growth factor (FGF) receptor, and non-receptor protein-tyrosine kinases, such as Abl, each of which activates a mitogenic intracellular signaling pathway.

Tony Hunter and coworkers went on to demonstrate that protein-tyrosine kinases play key roles in additional crucial cellular processes, including cellular adhesion, vesicle trafficking, cell communication, the control of gene expression, protein degradation, and immune responses. Moreover, discoveries regarding the role of protein-tyrosine kinases in cell transformation and cancer gave rise to a promising new rational approach to cancer therapy; i.e., the targeting of protein-tyrosine kinases. For example, the drug Gleevec, which inhibits activation of the Abl and platelet-derived growth factor (PDGF) tyrosine kinases, was approved by the U.S. Food and Drug Administration for the treatment of chronic myelogenous leukemia and several types of gastrointestinal tumors.

References:

  1. Howard Temin: “In from the Cold,” Posted on the blog December 14, 2013.
  2. Harold Varmus: From English Literature Major to Nobel Prize-Winning Cancer Researcher, Posted on the blog January 5, 2016.
  3. Collett, M. S. and R. L. Erikson, 1978. Protein kinase activity associated with the avian sarcoma virus src gene product. Proc. Natl. Acad. Sci. USA 75: 2021-2024.
  4. Hunter, T., and B. M. Sefton. 1980. Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc. Natl. Acad. Sci. USA 77:1311–1315.

Harold Varmus: From English Literature Major to Nobel Prize-Winning Cancer Researcher

Harold Varmus and J. Michael Bishop changed cancer research in a fundamental way in the 1970s, when they discovered proto-oncogenes at the University of California at San Francisco (UCSF). Proto-oncogenes are cellular genes that normally play an important role in controlling cell division and differentiation. However, Varmus and Bishop found that proto-oncogenes can be altered by mutation, to become oncogenes that contribute to cancer. When Varmus and Bishop first began their collaboration in 1970, cancer research was, for the most part, focused on epidemiology (e.g., studies linking smoking to lung cancer) and empirical approaches to therapy (e.g., radiation and chemotherapy).

Harold Varmus, Cancer Researcher, Nobel Laureate, Director of the NIH
Harold Varmus, Cancer Researcher, Nobel Laureate, Director of the NIH

The discovery of proto-oncogenes is a pertinent topic for our Virology blog because it depended crucially on Varmus and Bishop’s earlier finding that retroviral oncogenes are mutated versions of cellular genes that retroviruses “captured” from their host cells. Varmus and Bishop hypothesized and then demonstrated that since retroviral oncogenes are versions of genes that actually are part of a normal cell’s genetic makeup, mutations in those genes, or their inappropriate expression, can lead to cancer. The v-src gene of Rous sarcoma virus was the first retroviral oncogene that Varmus and Bishop showed is derived from a cellular genome (1).

Varmus and Bishop continued searching for proto-oncogenes in the 1980s. Varmus also began investigating HIV (also a retrovirus and the cause of AIDS). In 1989 Varmus and Bishop were awarded the Nobel Prize in Physiology or Medicine for their discovery of proto-oncogenes.

In the early 1990s Varmus stepped out from his role as a research scientist to take up the cause of public funding for biomedical research. In 1993 President Bill Clinton acknowledged Varmus’ efforts in that regard, as well as his stature as a scientist, by appointing him to serve as Director of the National Institutes of Health (NIH). Thus, Varmus became the first Nobel laureate to head the NIH.

In 2000 Varmus left the NIH to accept the presidency of the Memorial Sloan-Kettering Cancer Center in New York. In 2010 Varmus returned to the NIH, this time appointed by President Barak Obama to serve as director of the National Cancer Institute (NCI). In 2015 Varmus was back again in New York where he is the Lewis Thomas University Professor of Medicine at Weill-Cornell Medical College.

Varmus was featured in two earlier blog postings. The first of these described how he mediated the dispute between Robert Gallo and Luc Montagnier over the right to name the AIDS virus (2). The second posting covered some of the political and social dilemmas Varmus faced during his days leading the NIH (3).

Here, we relate first how Varmus opted for a career in biomedical science and, second, how his collaboration with Bishop came about. This is an interesting tale because Varmus’ remarkable career as a science researcher, administrator, and spokesperson happened despite his initial intention to become a teacher of English literature. Indeed, his career in science did not begin until after he earned an M.A. degree in English from Harvard University, and then spent four years in medical school preparing for a career in clinical medicine.

We begin our story in 1950 as Varmus recounts how, as a ten-year-old, he witnessed his physician father receive a call that conveyed shocking news: “one of my mother’s favorite cousins, a robust man in the middle of his life, had just been diagnosed with leukemia. Of course, I did not know very much about leukemia, but I did know immediately from my parents’ expressions–and within a few weeks, from our cousin’s death—that his disease was a veritable tidal wave.” [All quotations are from Varmus’ book The Art and Politics of Science (4), in which he reflects back on his entire career.]

His cousin’s leukemia actually resulted from a mutation in one of the genes that Varmus would discover more than two decades later. And Varmus notes just how far the science in general had progressed during that 25-year interim: “…when my father heard about our cousin’s leukemia, biologists were not even sure that genes were made of DNA, had no idea how genetic information could be encoded in genes, and, of course, had no way of knowing that cancers are driven by mutations.”

Varmus was urged by his father to prepare for a career in medicine. Nonetheless, when Varmus enrolled as a freshman at Amherst College he strongly favored studying the humanities. Thus, he “toyed with the idea of majoring in philosophy (ultimately too abstract), physics (ultimately too hard), and English literature (ultimately selected).”

Throughout his undergraduate days, Varmus envisioned preparing for an academic career teaching literature. Still, he dutifully fulfilled premed requirements to keep open the possibility of obliging his father’s wishes that he become a medical doctor. Yet he never considered majoring in biology. “I couldn’t understand how some of my close friends (among them, some now distinguished scientists) could spend long afternoons and evenings incarcerated in a laboratory, when they could be reading books in a soft library chair or reciting poetry on Amherst’s green hills.”

Varmus began having doubts about his career choice when his Amherst College classmate Art Landy (later a well-known molecular biologist at Brown University) won an Amherst biology prize that allowed him to attend a 1961 international biochemistry meeting in Moscow. Importantly, Landy invited Varmus to accompany him to the Moscow meeting, where Varmus learned that Marshal Nirenberg had deciphered the genetic code. “Even though I did not understand its meaning or its importance at the time, I was not oblivious to the excitement around me…Scientists seemed likely to discover new, deep, and useful things about the world, and other scientists would be excited by these discoveries and eager to build on them. Would this be true of literary critics and teachers?”

Notwithstanding these misgivings, Varmus continued on his path to a career in English literature after graduating from Amherst College in 1961, earning an M.A. in English from Harvard in 1962 (his focus was on Anglo-Saxon poetry). But his uncertainties about his future only grew stronger. “Despite outward signs that I had chosen a life of studying and teaching literature, soon after starting my graduate work at Harvard I began to suffer some further internal doubts about abandoning medicine. The graduate curriculum in English literature was not especially onerous, but it felt like a prolongation of college. Most of my courses were heavily populated with Harvard and Radcliff undergraduates.” Varmus leaves the impression that he looked upon much of his course work at Harvard as a tiresome chore.

Varmus was also aware of the enthusiasm of former Amherst College classmates who were then studying at Harvard Medical School. “Occasionally, on Saturday mornings, I traveled across the Charles River to join some Amherst classmates at Harvard Medical School, while they sat in the Ether Dome at Massachusetts General Hospital, entranced by diagnostic dilemmas discussed at the weekly pathology conference. These stories struck me as far more interesting than those I was reading, and my medical school friends expressed general excitement about their work. They also seemed to have formed a community of scholars, with shared interests in the human body and its diseases and common expectations that they would soon be able to do something about those diseases…These Saturday excursions probably account for an influential dream I had one night about my continuing indecision. In that dream, my future literature students were relieved when I didn’t turn up to teach a class, but my future patients were disappointed when I didn’t appear. It seemed I wanted to be wanted.”

So, Varmus finally came to grips with his qualms about a career teaching English literature, hastily preparing an application to Harvard Medical School and biking across the frozen Charles River to deliver it just in time to meet the deadline. But it was to no avail, since the dean of admissions thought Varmus was “too inconstant and immature” for medical school.

Varmus next sent off an application to Columbia University’s College of Physicians and Surgeons (P&S). His interviewer at Columbia was an esteemed physician named David Seegal, who also happened to be rather literate. Seegal asked Varmus if he might translate the Anglo Saxon phrase Ich ne wat. “This was easy; it simply means ‘I don’t know.’” Seegal used his question as a lead-in to discuss why a physician might admit fallibility to a patient. In any case: “By the fall of 1962, I was happily enrolled at P&S, helped for the first, but not the last, time by someone’s exaggerated appreciation of my competence in two cultures.”

Now ensconced at P&S, Varmus thought he might become a psychiatrist; an ambition stoked by an interest in Freud and by his winning of an essay prize at P&S in psychiatry. But, he found his “first hour alone in a room with a psychotic patient to be more difficult and less interesting than an hour reading Freud.” So, Varmus’ interests in medical school turned from the “elusive mind” to the physical brain and then, more generally, to diseases that might be explained by known physiology and biochemistry.

When graduation from medical school was impending, Varmus had to consider his career options more deliberately than he had in the past. A key factor was the Vietnam War, which was in progress, and which he and many others of that era vehemently opposed. “I was determined not to serve in it. Medical graduates were subject to the draft; however, we did have the more palatable option of two years training at one of the agencies of the Public Health Service. For most of my classmates with academic ambitions similar to my own, the NIH was the favored choice. As the largest biomedical research campus in the world, it offered unequaled opportunities to learn virtually any form of biomedical research…”

Varmus confesses that he had a “woeful lack of laboratory credentials.” Nonetheless, he entered the competition for one of the coveted research slots at the NIH. But, because of his lack of research experience, he was not encouraged by most of the NIH laboratory chiefs who interviewed him. However, one of them, endocrinologist Jack Robbins, suggested to Varmus that he speak to Ira Pastan; a young endocrinologist who, at that time, was interested in the production of thyroid hormones.

As Varmus relates, “The recommendation proved to be wise and fateful. My schooling in literature turned out to be more important than my interest in endocrinology, Ira’s field, because Ira’s wife Linda, a poet, had often complained that Ira’s colleagues seldom talked about books…When matches were announced I was told I would become Ira’s first clinical associate, having been passed over by the more senior investigators. This outcome could not have been more fortunate.”

But, before Varmus could take up his position at the NIH, he received a “shocking phone call” from Pastan, to the effect that he (Pastan) was giving up his work on thyroid hormones because he and colleague Bob Perlman “had made a shocking discovery about gene regulation in bacteria.” Pastan and Perlman found that cyclic AMP is a major regulator of bacterial gene activity, and that it plays a similar role in animal cells—findings which led Pastan to pioneer the field of receptor biology in animal cells.

The discovery by Pastan and Perlman had important consequences for Varmus. First, it immediately forced him to give up his plan to train in endocrinology. Instead, Pastan assigned Varmus to find out whether cyclic AMP augments bacterial gene expression by increasing transcription of mRNA. Second, as explained below, Pastan’s new research direction led to Varmus’ introduction to and fascination with virology.

So, Varmus was now a budding molecular biologist. But, since he had no prior research experience, his first days in the Pastan lab were a near disaster, leading Pastan to half jokingly ask, “Now remind me why I took you into the lab.”

In any case, Varmus worked closely with Pastan to develop a molecular hybridization assay to measure transcription of E. coli lac mRNA. [Their specific the goal was determine whether the mechanism by which cyclic AMP reverses catabolite repression of the E. coli lac operon is by enhancing transcription of lac mRNA.] And, they used an E. coli phage, which had incorporated the lac operon into its genome, as their source of isolated lac operon DNA. Thus, Varmus was introduced to virology. [Aficionados, note, “These experiments with the lac operon proved to be analogous in several ways to experiments that revealed the first proto-oncogene a few years later.”]

The satisfaction that Varmus derived from his research in Pastan’s lab caused him to reconsider his aspirations for a career in clinical medicine, and instead to think about a future in biomedical research. He thought he might next try his hand at cancer research, motivated in part, by his mother’s breast cancer, first diagnosed in 1968, to which she succumbed two years later. But there were other factors at work as well. In particular, Varmus’ use of the E. coli phage in Pastan’s lab led to his fascination with virology. And his interest in virology was relevant to his new plans because the DNA and RNA tumor viruses held immense potential for cancer research. 1970s technology could not identify which one of the tens of thousands of cellular genes might have mutated to result in a cancer. However, that technology was potentially able to identify which of the handful of a tumor virus’ genes might underlie its ability to transform a normal cell into a tumor cell.

That line of thought led Varmus to apply for a research position in Renato Dulbecco’s lab at the Salk Institute. [Dulbecco would win a share of the 1975 Nobel Prize in Physiology or Medicine for his pioneering studies of the DNA tumor viruses (5).] However, reminiscent of Varmus’ unsuccessful application to Harvard Medical School, he was “rebuffed by not one but two letters from his (Dulbecco’s) secretary.”

While the rejection from Dulbecco was a disappointment, it would be another of the seemingly providential happenings in Varmus’ career. In the summer of 1969 he chanced to visit Harry Rubin, an eminent Rous sarcoma virus researcher at U Cal Berkeley. Rubin, who had earlier introduced Howard Temin to virology (another auspicious happening; see reference 6), told Varmus about a new group at UCSF that had begun to study retroviruses. Importantly, the goal of the UCSF group was to discover cancer-causing genes. Thus, Varmus stopped over at UCSF, where he met members of the group, including a smart young virologist named Mike Bishop. Varmus reports, “we recognized from the first moments that we were destined to work together.”

Varmus came to Bishop’s lab in 1970 as a postdoctoral fellow. However, their relationship quickly evolved to one of equals, and they made all of their major discoveries in the 1970s and 1980s as a team, and they rose together through the UCSF academic ranks. Bishop relates that their bond formed not just by a shared fascination with cancer viruses but “by our mutual love of words and language.” Varmus, for his part, notes that “after many years of ambivalence and indecision…I appeared to be headed in a clear direction, even if not towards medicine or literature.”

References:

1. Stehelin D, Varmus HE, Bishop JM, Vogt PK., 1976. DNA related to the transforming gene(s) of avian sarcoma viruses is present in normal avian DNA. Nature 260:170-173.

2. How the Human Immunodeficiency Deficiency Virus (HIV) Got Its Name, posted on the blog February 4, 2014.

3. The Politics of Science: Vignettes Featuring Nobel Laureate Harold Varmus during his Tenure as Director of the NIH, posted on the blog June 2, 2014.

4. Varmus, H. 2009. The Art and Politics of Science, (W. W. Norton & Company).

5. Renato Dulbecco and the Beginnings of Quantitative Animal Virology, posted on the blog December 3, 2013.

6. Howard Temin: “In from the Cold”, posted on the blog December 14, 2013.

The Politics of Science: Vignettes Featuring Nobel Laureate Harold Varmus during his Tenure as Director of the NIH

During his extraordinary career, Nobel laureate Harold Varmus practiced science and served science with distinction. The vignettes that follow are, for the most part, about Varmus’ service to science during his tenure (1993-1999) as director of the U.S. National Institutes of Health. But first, we begin with a brief account of Varmus’ most significant scientific accomplishment.

In 1976, Varmus and collaborator Michael Bishop reported that retrovirus oncogenes (cancer-causing genes) are versions of genes that actually are present in the genomes of normal cells (1). Indeed, retroviruses acquired their oncogenes by “capturing” them from the genomes of their host cells. Perhaps the most singularly important conclusion to be drawn from Varmus’ and Bishop’s finding is that since retroviral oncogenes are versions of genes that are actually part of a normal cell’s genetic makeup, mutations in those particular cellular genes, or the inappropriate expression of those genes, might lead to cancer.

Varmus’ and Bishop’s findings led to a mushrooming of discoveries in cell signaling, cell growth, and cell differentiation (see Aside 1). Moreover, their discoveries are increasingly relevant clinically, as recounted below in the main text.

[Aside 1: The v-src gene of Rous sarcoma virus was the first retroviral oncogene that Varmus and Bishop showed is a version of a cellular gene. Next, in 1978, Raymond Erikson and coworkers isolated the Src protein. Then, Erikson’s research group and that of Bishop and Varmus independently discovered that Src has protein kinase activity. Protein kinases add phosphate groups to a specific target protein, generally triggering its activity. (Actually, Src phosphorylates itself, thus regulating its own activity.)

At the time that Erikson isolated Src, all protein kinases were believed to add phosphate to serine and threonine residues on their target proteins. Then, in 1980, Tony Hunter and Bart Sefton discovered that Src adds phosphotes to tyrosine residues. Thus, Src was the first known protein tyrosine kinase.

Stanley Cohen then discovered that the epidermal growth factor (EGF) receptor too is a protein tyrosine kinase, underscoring the role of tyrosine kinases in the control of normal cell proliferation, while also affirming the notion that inappropriate phosphorylation of a cellular protein can lead to cancer.

These discoveries led to a burst of research activity in cell signaling, and to the discovery of additional tyrosine and serine/threonine protein kinases, many of which act in mitogenic signaling pathways. What’ more many of the cellular genes encoding these proteins were initially discovered as retroviral oncogenes. For details on these points, see Virology: Molecular Biology and Pathogenesis.]

[Aside 2: An earlier posting on the blog, Renato Dulbecco and the Beginnings of Quantitative Animal Virology, noted that Renato Dulbecco shared the 1975 Nobel Prize for Physiology or Medicine, in recognition of his opening up the study of transformation by the DNA tumor viruses (i.e., the polyomaviruses, papillomaviruses, and adenoviruses). How then did analysis of transformation by the oncogenic retroviruses (i.e., the RNA tumor viruses) complement analysis of the DNA tumor viruses?

As suggested above; studies of the oncogenic retroviruses led to the identification of cellular signaling pathways that positively govern cell replication (i.e., that trigger cell growth). In contrast, studies of the DNA tumor viruses led to insights into cellular processes that negatively regulate cellular replication; in particular, processes affected by the key cellular tumor suppressor protein, p53, which activates apoptosis in cells that attempt to divide without having appropriately passed cell cycle checkpoints. The DNA tumor viruses affect transformation by inactivating tumor suppressor proteins. See Virology: Molecular Biology and Pathogenesis for details.]

[Aside 3: Varmus tells us that early in his career, in the late 1960s, he looked for places and people that might offer research training in the tumor viruses. “However, when I wrote to the already famous virologist Renato Dulbecco, at the Salk Institute in La Jolla, just North of San Diego, for a postdoctoral position, I was rebuffed by not one but two letters from his secretary (2).” See Aside 2.]

In the days before Varmus and Bishop published their findings, many cancer researchers actually were reluctant to believe that cancer has an underlying genetic basis. This was partly because it was not yet possible to clone and sequence genes, and there were no other apparent methods by which to identify putative cancer-related genes. [The means by which Varmus and Bishop made their breakthrough discovery are recounted in the Appendix, below.] In recognition of their discovery, Varmus and Bishop were awarded the 1989 Nobel Prize for Physiology or Medicine.

Varmus looked back on all aspects of his career in his 2009 autobiography, The Art and Politics of Science (2). [Unless otherwise noted, all of the quotations that follow are from Varmus’ 2009 memoir.] Here, are his remarks on the clinical significance of his and Bishop’s Nobel Prize-winning findings:

“In recent years, after our prize was awarded, mutant proto-oncogenes and the proteins they encode have become critical tools for the classification of cancers and promising targets for drugs and antibodies—treatments that have, in some cases, proven to be effective for a significant and growing number of cancers, including leukemias and lymphomas, lung, gastrointestinal, and kidney cancers: and cancers of the breast.”

In 1993, Varmus was named by President Bill Clinton to serve as Director of the U.S. National Institutes of Health; a position he held through 1999. As such, he was the only Nobel laureate to ever serve as the NIH director and he was also the first NIH director to also run an active laboratory. What’s more, during his tenure as director, he managed to nearly double the NIH’s research budget.

nih clinical center NIH Clinical Center

One of Varmus’ major responsibilities as the NIH director, and also one of his most contentious ones, was to apportion research dollars among the individual NIH institutes and programs. Why was there contention? As might be expected, the directors of the individual institutes actively advocate for their shares of the NIH budget. But, a further source of contention was Congress, in which the most ardent NIH supporters were generally motivated by their interest in a particular disease or program. What’s more, public advocacy groups likewise championed their own favored disease. Consequently, as Varmus explains:

“Apart from the difficulties of predicting where and how discoveries will arise, the priority-setting process can be ugly—for instance, when advocates refuse to recognize, or to care, that funds for their disease must come from funds being spent elsewhere, including funds used for a disease important to another group of advocates.”

Here is one such instance that Varmus notes:

“One of my first exposures to this problem occurred soon after I arrived at the NIH, when I received a call from my own former congresswoman, Nancy Pelosi, asking me to add $50 million to the budget for AIDS research. As the representative from one of the districts most heavily affected by the epidemic, her wishes were understandable. Since she was a member of the House Appropriations Committee for the NIH, she was in a position to try to increase funds for AIDS research when the subcommittee was debating the size of the NIH budget, without taking the money from some other research program. But, in the period of spending caps, she had presumably been unsuccessful in negotiations with her fellow committee members and was now trying to fulfill a promise to her constituents by asking me to shift funds from some other budget categories into the OAR (Office of AIDS Research) account. I declined as politely as I could.”

Varmus notes that it can difficult to refuse such requests (demands?) when they come from powerful people; especially so when the come from the President. For instance, President Bill Clinton “requested” that $10 million more be spent on spinal cord research; this coming after he spent an afternoon with recently paralyzed actor, Christopher Reeve.

“But the President’s wishes are always obeyed. When the next accounting was made of disease-specific spending at the neurology institute (formerly known as the National Institute of Neurological Diseases and Stroke, or NINDS), the funds for spinal cord research were accordingly higher, and funds for other purposes were lower.”

Here is an additional example, this time involving the vice-president:

“But Vice-President Al Gore posed a potentially serious dilemma for the NIH late in 1997 when he proposed that the National Cancer Institute (NCI) should receive a much larger share than the other institutes in the record-breaking $1 billion budget increase that the president was going to request for the NIH for fiscal year 1999. Possibly as a result of promises made to cancer research advocates, possibly because of personal concerns about cancer (his sister died of lung cancer at an early age), possibly because cancer research was popular politically, Gore asked that the cancer institute’s budget grow at twice the rate accorded the others.”

Varmus continues:

“I was very unhappy about this. The differential rates of growth were not in accord with clearly defined medical needs or with carefully considered scientific opportunities. No major changes in disease rates or outcomes and no sudden developments in cancer research made the needs for the NCI any greater than those for brain disorders, metabolic diseases, or infections. By any measure, the NCI was already the largest institute by a considerable margin, and Gore’s plan would further accentuate the differences. And, of course, there would be strong negative reaction from the supporters of the other institutes when the plan was announced. But, he was the vice-president, and conceivably the next president, so the idea of arguing with him on this issue was not appealing.”

However, Varmus had an ally in Donna Shalala, the Secretary of Health and Human Services (HHS), who supported his position. And, with her help, Varmus was able to take the issue directly to Gore:

“… we were able to reach a rapprochement when I pointed out that many institutes did cancer research, not simply the NCI, and he was very pleased to learn this. That gave us an opening for a compromise: we would ensure a relatively large increase for cancer research, but it would be spread among all the institutes that could be said to do cancer research.”

[Aside 4: Varmus was featured in an earlier posting on the blog that recounted how, in 1986; he resolved the dispute between Luc Montagnier and Robert Gallo over the right to name the AIDS virus (3). It’s been said that Varmus developed diplomatic skills while resolving the naming dispute that served him well as Director of the NIH. The following comment from Varmus shows his subtle diplomacy when interacting with the directors of other government agencies that he competed against:

“Often the best way to support the NIH and science in general was to make a magnanimous gesture toward the other agencies, emphasizing their importance in an increasingly interdisciplinary world of science and hoping the gesture would be reciprocated. This strategy was appreciated by my colleagues in other disciplines, helped to dispel jealousies about our fiscal success, and is remembered as a hallmark of my time at the NIH.”]

Irrespective of any political considerations, the setting of research priorities is an inherently difficult process. The following quotation points up the often conflicting scientific and public health considerations that Varmus took under consideration when determining research priorities. And, bearing in mind his recounting of Nancy Pelosi’s request for additional funding for AIDS, these remarks also demonstrate that he was hardly insensitive to the AIDS issue:

“For much of my time at the NIH, I was castigated by advocates for research on heart disease because the NIH was spending about as much on AIDS research as on studies of heart disease, even though there were about twenty times more deaths from heart disease than from AIDS in the United States each year. The arguments tended to ignore other important facts: that AIDS was a new and expanding disease, that it is infectious, that it is devastating large parts of the world, or that age-adjusted death rates from heart disease have fallen by two-thirds in the past 50 years.”

Elsewhere Varmus notes: “Of course, very different impressions can be produced by the use of different criteria—the number of people living with a condition, the number who die from it each year, the age adjusted death rate, the number of healthy individuals at risk, the number diagnosed each year, the annual medical expenditures, the annual cost to society, or the degree of pain and suffering. These are legitimate aspects of the nation’s burden of disease, but they are crude tools for deciding how to spend research dollars appropriately.”

Another difficulty that Varmus had to contend with was that laypeople, both in Congress and in public advocacy groups, often did not appreciate that science usually works best when scientists are free to investigate the particular issues that most intrigue them. And, when biomedical scientists follow their own inclinations, they often focus on basic or fundamental questions that may seem to have no apparent clinical relevance. Yet, and importantly, the knowledge gained from untargeted basic research may have a more positive affect on the understanding and treatment of a particular disease than all of the clinical research specifically targeted at that disease. [Indeed, the Nobel Prize-winning research of Varmus and Bishop is a good example of that very point.]

Speaking to that notion, Varmus said the following in a June 2009 interview with Catherine Clabby in American Scientist:

“Look at what pride people take now in advances made in diabetes and cancer research and infectious disease research. Almost all of it is based on recombinant DNA technology, genomics and protein chemistry. These are methods that grew out of basic science that was funded for years and years in a non-categorical way.”

Still and all, while basic research often may lead to significant clinical advances, Varmus acknowledges that the NIH still must have programs that are targeted at public health concerns:

“One of the potential strengths of the NIH is its ability to encourage scientists throughout the country to pay greater attention to underserved and deserving problems, even when the opportunities may not be obvious. Simply by encouraging attention to such problems—autism, rare neurological diseases, imaging methods, emerging infections, or bioengineering, to mention a few areas promoted during my tenure—new ideas may emerge to create those opportunities.”

But, Varmus adds:

“In this regard, the NIH must walk a narrow line: to respond responsibly to public health needs and yet to provide the freedom for investigators to exercise their imaginations as freely as possible.”

[Aside 5: An earlier posting on the blog, Jonas Salk and Albert Sabin: One of the Great Rivalries of Medical Science, described how the National Foundation for Infantile Paralysis financed the crusade against polio in the pre-NIH days of the 1950s. But, the Foundation’s efforts went beyond merely raising money for research. It also attempted to provide direction to the research, which often placed it at odds with its grantees. That was so because the principal goal of Harry Weaver, the Foundation’s director of research, was to bring a vaccine to the public. In contrast, most of the Foundation’s grantees were more interested in investigating basic virological issues, such as poliovirus transmission, replication, and dissemination.]

Research involving human embryonic stem cells was a particularly contentious issue that Varmus dealt with as NIH director. Stem cell research “attracted controversy mainly because the cells are obtained from human embryos, linking stem cell research to historical battles over abortion and over the legal and moral status of the human embryo and fetus.”

Yet Varmus took up the cause for stem cell research because “embryonic stem cells were likely to have the potential to develop into many specific tissue types…if so they could be used to repair damaged tissues or to treat chronic degenerative diseases of the brain or spinal cord, endocrine organs (such as pancreatic islets), muscles, joints, or other tissues.”

In 1993 Varmus assembled the Human Embryo Research Panel, tasked to advise him on what types of stem cell research might be suitable for federal funding. Not surprisingly, an immediate hullabaloo followed the panel’s recommendation that in vitro fertilization might be used to create embryos, from which stem cells could then be derived. Varmus remarked on the reaction to the panel’s recommendation as follows:

“Although well received by scientists who were watching its work, the panel’s report ignited a storm of government opposition; even within the liberal Clinton administration…the White House was in shock from the Democratic Party’s loss of control of both congressional chambers in the midterm elections held a month earlier. Democrats across the nation, especially those at the highest ranks of the Clinton administration, were concerned about a shift in the electorate toward the conservative policies of Newt Gingrich and his Republican revolutionaries, and already anxious about the presidential election of 1996…I remember getting a call from Leon Panetta, then the White House chief of staff, telling me that I was supposed to repudiate some of the panel’s recommendations, in particular any that might permit the use of federal funds to create embryos for research purposes. I refused to reject the recommendations of my panel summarily. I was not fired, as the tone of Panetta’s call had threatened.”

Although Varmus wasn’t fired for his independence, the Clinton White House quickly issued an executive order forbidding the use of federal funds to create human embryos for research. Varmus attributed the political pushback to the undue influence (“on the conduct of science in a diverse society”) of a few conservative religious groups. Varmus went on to say:

“Few arguments can seem as insulting to medical scientists as the claim that we are ethically irresponsible when we toil to extract stem cells from donated early human embryos, which would otherwise be destroyed, and use them for beneficial, potentially lifesaving purposes.”

Varmus lamented the fact that President George W. Bush limited federal funding for stem cell research during his administration. Nevertheless, stem cell research was being done even during the Bush presidency, although it was supported by the private sector and by several states (California, New York, Massachusetts, Wisconsin and others). Yet because potential stem cell investigators would need to obtain funding from less well-endowed non-federal sources to do this research, it is likely that many were discouraged from entering the field.

Varmus also fought a difficult and frustrating battle to secure federal funding for needle-exchange programs. By way of background, intravenous drug abusers were accounting for one-quarter of all new HIV infections in the United States. And, while other industrialized nations had needle-exchange programs that were successful at reducing the number of new HIV infections, many powerful individuals in the United States, including General Barry McCaffrey, head of the Clinton White House Office on Drug Control, regarded efforts to make drug use safer to be the equivalent of condoning drug use.

In 1998, HHS Secretary Donna Shalala, using evidence compiled by Varmus, advised President Bill Clinton that needle exchange programs were proven to be effective at preventing HIV transmission and, moreover, they did not increase drug use. Nevertheless, the President did not lift the ban on federal support for needle exchange programs.

By coincidence, the day that Clinton announced his decision not to lift the ban, Varmus and his wife were having dinner with Rahm Emanuel, who, at that time, was a domestic policy advisor in the Clinton White House. Interestingly, the liberal Emanuel was not sympathetic to lifting the ban. Instead, he believed that doing so would open the Democratic Party to charges that it was soft on drugs. At any rate, not lifting the ban did not enable the Democrats to regain either house of Congress. Varmus adds:

“The only satisfaction we received was the later admission by Bill Clinton, speaking at an international AIDS conference in Spain, less than two years after he left the White House, that his failure to lift the ban on funding needle exchange was wrong and one of the worst decisions he made during his presidency.”

Another of the good fights that Varmus fought on behalf of science was to establish new approaches to publishing scientific papers. His purpose was to enhance access to the scientific literature by taking advantage of new opportunities being offered by the internet and by new computational tools. His efforts resulted in two important new ways in which scientific research is published, stored, and retrieved; specifically, public digital libraries and “open access” publishing.

Varmus credits Stanford biologist Pat Brown with pushing him, in 1998, to think about improving access to the scientific literature by making the most of the internet. Brown had earlier worked with Varmus and Bishop on retroviral integration in the 1980s.

Varmus was still the NIH director when he helped to launch PubMed Central; the NIH’s full-text public digital library for the biomedical sciences, and the first of its kind. [In contrast to PubMed Central, PubMed is the NIH’s on-line archive of titles, authors, and abstracts. Access to full text articles was possible via PubMed, but only if one had a personal subscription to the particular journal, or had access via their institution.] But, many scientists and journal publishers were initially opposed to PubMed Central. Consequently, in 2000, after Varmus had left the NIH, he and Brown, together with Mike Eisen, a computational biologist at Berkeley (who had worked as a post-doc with Brown), took more vigorous steps to promote it:

“Pat, Mike, and I wrote a short declaration of purpose—we called it a pledge, publishers called it a boycott—in which we said that one year hence, the signatories would no longer submit articles, provide reviewing or editing services, or purchase individual subscriptions to journals that had not agreed to deposit their articles with PubMed Central.”

Thirty thousand scientists worldwide signed the pledge, but most didn’t. One reason for the lack of wider support was that leading scientists typically strove to have their papers published in the most prestigious journals, and most of those journals had not bought in to the open access idea. Journal publishers were opposed because their revenues from subscriptions would be undermined by the open access model.

Since most journal publishers were not willing to participate in PubMed Central, Varmus, Brown, and Eisen decided to found open access journals themselves. They began by creating two outstanding journals, PLoS (for Public Library of Science) Biology and PLoS Medicine. Their business model was to use author’s fees to cover publication costs, usually paid from research grants. [Incidentally, no favorably reviewed paper would be turned away for inability to pay the fee. All of the PLoS journals can be seen by anyone, anytime, at http://www.plos.org.]

The public access situation began to change dramatically in 2007 when a coalition of leading scientists, open access publishers (including PLoS), and concerned members of Congress advocated for a policy that would require all scientific papers reporting NIH-funded research to be deposited in PubMed Central. This cause came to fruition when President George W. Bush signed the 2008 appropriations bill, which included a clause making the NIH public access policy the law of the land.

So, wrapping things up, considering that the NIH director’s job can grind one down with its “incessant and inevitable conflicts,” why did Varmus put up with it? His answer is he enjoyed it:

“Above all, there was the pride, excitement, and (at times) historical significance of being the leader of the largest funding agency for medical research in the world. The position represents medical science and the good things it does for the country, if not the world. I felt this when working within the administration, when speaking to members of Congress, when talking to reporters, and when addressing the public at commencement exercises, and elsewhere.”

Varmus left the NIH to become President of the Memorial Sloan-Kettering Cancer Center in New York City; a position he held from 2000 until 2010. He then returned to the NIH, where he serves as director of the National Cancer Institute.

In the Epilogue to his memoir (2), Varmus refers to the work of scientists, and its potential benefit to society, as follows:

“Scientists may work and compete as individuals, but the competitive efforts are ultimately directed to the construction of a common edifice, knowledge of the natural world. There are few other fields in which such fierce independence serves the public good in such a transparently shared fashion”

But he adds: “…our knowledge does not improve the societies in which we live unless other kinds of actions, both political and pragmatic, are taken.”

References:

1. Stehelin D, Varmus HE, Bishop JM, Vogt PK., 1976. DNA related to the transforming gene(s) of avian sarcoma viruses is present in normal avian DNA. Nature 260:170-173.

2. Varmus, H. 2009. The Art and Politics of Science, (W. W. Norton & Company)

3. How the Human Immunodeficiency Deficiency Virus (HIV) Got Its Name, on the blog

Appendix:

Varmus and Bishop turned to nucleic acid hybridization to test their hypothesis that v-src might be a version of a cellular gene. They could not use the complete Rous sarcoma virus genome as a probe for the putative cellular src gene, because the complete virus genome might have detected endogenous retrovirus sequences within the cellular genome, rather than a cellular src gene per se. So, they needed to generate a more specific probe.

In the days before recombinant DNA procedures, Varmus and Bishop cleverly generated their specific src probe by making use of a transformation-defective mutant of Rous sarcoma virus, isolated earlier by Peter Vogt. The important feature of this mutant virus was that its src gene was deleted.

Varmus and Bishop generated their src-specific probe by first using reverse transcriptase to make a radioactively labeled, single-stranded DNA copy of the entire standard Rous sarcoma virus genome, which contains the src gene. This cDNA was then fragmented and annealed to an excess of RNA genomes of the src deletion mutant. The only DNA fragments that did not anneal were those containing only src sequences. These single-stranded DNA fragments could be separated from the annealed product and used as the src nucleic acid hybridization probe.

Using their cDNA probe, Varmus and Bishop were able to demonstrate the presence of src not only in the genomes of normal chicken cells, but also in the genomes of many other vertebrates as well, including humans (reference 1). These experimental findings led to the remarkable conclusions that the cellular src gene was present early in vertebrate evolution and that it has remained conserved to this day.

More experiments of this kind demonstrated that other highly oncogenic retroviruses contain other oncogenes of their own, which likewise have their counterparts in normal cell genomes. Indeed, each of the known retroviral oncogenes corresponds to a gene present in a normal cellular genome, and each of these retroviral oncogenes appears to be derived from a cellular genome.

But, why did Varmus and Bishop suspect that v-src might have originated as a cellular gene? In part it was because Steve Martin had earlier isolated a mutant of Rous sarcoma virus that was temperature-sensitive for transformation, but not for replication. Why would a virus carry a gene that it did need for it to replicate?