Tabitha M. Powledge

It’s not just that Jesse’s treatment was bungled, although it apparently was. There’s been lots of bungling in other trials as well, and other ambiguous deaths. It also turns out that researchers have routinely flouted the government’s rules governing gene therapy — especially the requirement to report all “adverse events” following the experiments. “Adverse events” means any serious reaction or side effect. Researchers have failed to disclose a stunning number of adverse events in gene therapy trials: more than 700. And counting.

Adverse-events reporting was not invented just to drive scientists bananas and give bureaucrats paper to shuffle. Accurate reporting is crucial to the future of gene therapy — in fact, to clinical research in general. All scientists working on a new treatment need to know when something bad happens in experiments on people, because it gives them clues about what to do, and what not to do, and where to go from here.

“Reporting of adverse events is a joke; it hasn’t worked for years,” declares Penn’s Center for Bioethics director Arthur Caplan, who contends that this sort of misbehavior infects all experiments on people. “Gene therapy is getting close scrutiny at the moment, but human-subjects research has had serious problems of noncompliance for ages.”

Granted, Caplan doesn’t qualify as a wholly disinterested observer. Caplan, whose center is associated with the now-vilified Institute for Gene Therapy, was consulted about the conduct of its gene therapy studies, including Jesse’s. But he has also been a professional research-watcher for decades, and his observation that gene therapy is not a special case is correct. The failures of oversight, the absence of monitoring, the plain old sloppiness that pervaded clinical gene therapy research at Penn (and, we now know, many other clinical gene therapy studies) infiltrates all kinds of human-subjects research.

Human research has come a long way since the so-called Tuskegee experiment. From the 1930s through the early 1970s, the government studied the natural history and course of untreated syphilis in a large group of black men with the disease. The men were not told they were infected. Not only was treatment withheld, the Public Health Service actively intervened to keep the men from being treated by other agencies, such as the U.S. Army. In the uproar that ensued when the syphilis study came to light, Congress legislated safeguards to protect human subjects, and these measures have been tinkered with and added to over the years. Hence the requirement to report “adverse events.” But the practice of using human volunteers to test new treatment still is far from the humane, honest, careful way of making progress against disease that it should be.

Prompted in part by the flap over gene therapy, and timing it brilliantly to coincide with the Penn report, Donna Shalala’s Department of Health and Human Services has just presented Congress with draft legislation setting up more regulations. One of its ideas is financial penalties — up to $250,000 per researcher and $1 million for the offending institution.

Imposing fines seems a bit bizarre for research infractions, but it does give the government some middle-of-the-road punishment options. Currently the choices are total annihilation — that is, shutting a research program down — or a slap on the wrist. The latter consists of sending the errant researcher a letter saying he has been naughty and he must promise not to do it again.

Caplan suggests a useful approach would be unannounced inspections and audits. But NIH’s Office of Protection from Research Risks has tried that. In the past couple of years, OPRR has shut down hundreds of human research programs (not involving gene therapy) at seven major U.S. institutions. Our government’s response? It’s moving OPRR out of National Institutes of Health and into Shalala’s office and changing its name to Office of Human Research Protections. This is supposedly a promotion, but some think the move will only serve to undermine its power. Shalala’s office has also declined to consider the OPRR director behind the surprise raids — a spunky candidate for herohood named Gary Ellis — to head the new office. (Translation: They fired him.)

Which suggests that the U.S. government is not hugely serious about beefing up protections for human research subjects. And that this is not the last time you will hear sad stories like Jesse Gelsinger’s.

Which is a shame for everyone — not just the victims of scientific bungling. The dazzling idea behind gene therapy is that you can treat a disease, perhaps even cure it, by transferring new genes into a patient’s cells. The notion has captured the imaginations of ambitious and competitive scientists all over the world. The possibilities are indeed amazing. Gene therapy might mean cures not just for the odd exceedingly rare genetic disease like Jesse’s, but also exceedingly common disorders like cancer and heart disease.

But after more than a decade of frantic work — 300-plus clinical trials on 6,000-plus patients — gene therapists have not much to show for their exertions. At the end of April, French researchers announced an apparent cure in two children with “Bubble Boy” disease, which is caused by a single faulty gene. The kids’ immune systems now function well, a year after scientists transferred working copies of the gene into their bone marrow. The researchers warned everybody not to get too excited about short-term results, however. They won’t be sure they have really cured the disease for many years. So the score stands at one probable success, a couple of ambiguous possible maybe successes, and that’s about it.

Still, the news from France — the first nice thing to happen in the field since Jesse’s death — had gene therapists dancing in the streets. Penn’s is just one of several investigations launched in the wake of Jesse’s death, and their findings have been grim. Gene therapy is in a heap of trouble. The trouble is not just technical, it is also political. And much of it is self-inflicted.

“In my medical school I was taught that gastric ulcer is due to hurry, worry and curry,” says Nikhil Dhurandhar, Ph.D., who was educated in Bombay and is now an assistant professor at Wayne State University in Detroit. He is talking about the disease that is everybody’s favorite example of biomedicine’s new infectious paradigm. For decades the medical party line was that ulcers were stress-induced and incurable, the archetypal ailment of the Age of Anxiety — except that almost all ulcers are caused by a bacterium, Helicobacter pylori, and can be easily, permanently and inexpensively cured in less than a month with antibiotics. Researchers first described the relation between H. pylori infection and ulcers in 1983, but their findings were scoffed at for years and incorporated into the medical canon only recently.

Dhurandhar is on a similar mission, but meeting less resistance. Backed by a powerful mentor, obesity researcher Richard Atkinson of the University of Wisconsin, Dhurandhar is slowly amassing evidence that some proportion of obesity — at this point his work suggests, scarily, that it may be a very large proportion — is the consequence of infection by a virus.

Most of this research has been done in animals, but some small human studies, so far mostly unpublished, back it up. The latest published contribution appeared last month in the International Journal of Obesity and Related Metabolic Disorders. The paper reported on experiments in which Dhurandhar and his colleagues inoculated chickens and mice with a human virus they suspect of promoting fat gain. It did: The infected animals gained two-thirds more fat than uninfected control animals.

The virus, designated Ad-36, is one of 50 adenoviruses known to infect people. In an electron microscope, adenoviruses look a bit like the World War II mines used to block shipping channels — spherical and studded with spikes that help them attach to host cells. Despite that ominous configuration, most appear to be benign. A few cause respiratory infections, pinkeye and diarrhea.

As for Ad-36, it doesn’t seem to give diarrhea or colds to Dhurandhar’s birds and rodents, at least. “They are quiet for a day or so, and then they bounce back,” he says.

A handful of viruses are known to make animals fat, which is how Dhurandhar — who operated obesity treatment centers in India before he came to the U.S. nearly a decade ago — got interested in them. An unexpected characteristic of these infections is that when the animals get fat the levels of cholesterol and triglycerides in their blood plummet. Increased body fat is generally accompanied by increased cholesterol and triglycerides, which ferry fats around in the blood.

In a study published in 1997, Dhurandhar examined blood from patients in Bombay looking for antibodies against an adenovirus that was epidemic among Indian chickens — and which killed them after making them fat. He found viral antibodies in 10 of his 52 human patients, evidence that they had been exposed to the virus at some time in their lives. The 10 tended to be fatter than the other patients, and also tended to have lower cholesterol and triglycerides.

Dhurandhar says he has strengthened the case in a U.S. study. In findings presented at conferences and in a paper Dhurandhar says has been submitted for publication, Ad-36 antibodies turned up in 100 of 313 obese subjects, but in just four of 92 lean controls. In short, nearly one in three fat Americans in Dhurandhar’s study showed evidence of prior infection with the virus, compared with only one in 20 slim ones. Moreover, the infected subjects also had lower-than-usual cholesterol levels.

Dhurandhar’s provocative results, especially the human studies, must, of course, be replicated before they can be fully accepted. But the reactions of other obesity researchers, at first skeptical, have become cautiously friendly, at least in public. One measure of Dhurandhar’s increasing credibility is that top obesity researchers have joined the advisory board of the Rochester Center for Obesity Research, the nonprofit center he has set up to do human studies in collaboration with the weight management center at Crittenton Hospital in Rochester, Mich. These scientists include Atkinson, who is president of the American Obesity Association, and John P. Foreyt, a professor at the Baylor College of Medicine in Houston. The National Institutes of Health has given Dhurandhar money to screen other human adenoviruses for fat-promoting effects.

But as Dhurandhar points out, even if the results of his studies hold up, many questions remain. “We don’t know what role the virus plays. Is it that you need a viral infection and a high-fat diet? If you have just the infection but not a high-fat diet, maybe you won’t gain weight. Or is it some other factor that has to go together with viral infection for obesity to be expressed? We don’t know.”

To add, um, weight to his thesis, Dhurandhar and his colleagues have also studied twins, a traditional means for ferreting out genetic and environmental causes of disease. They screened a group of 90 pairs of identical twins for Ad-36 antibodies, throwing out the pairs in which both twins tested the same — positive or negative — for the virus. In the remaining 26 twin pairs, where one twin possessed the antibodies and the other did not, the positive subjects had significantly higher body weight and body fat than the antibody-negative twins, says Dhurandhar, who is seeking funding to expand the twin study. “I believe that’s the closest one can come to showing the role of this virus in humans,” he says.

This sort of indirect evidence of a relation between viral infection and obesity in humans is probably the best we can expect. One of the Australian researchers who finally established that ulcers are caused by a bacterial infection got so fed up with being hooted at by his colleagues that he put his mouth where his convictions were. He swallowed some H. pylori — and promptly got ulcers. But he also had faith that his stomach pain could quickly be vanquished with antibiotics. There is no such magic bullet for infectious adiposity, if it exists. And even if regulatory agencies would permit direct human tests, it’s hard to imagine thin people volunteering to swallow Ad-36 and then sit around — perhaps for years — waiting to get fat.

“In humans we say we have a strong association, not a causation,” says Dhurandhar. “So we have to collect circumstantial evidence, something like smoking and cancer.” The circumstantial evidence includes continuing searches for viral antibodies and traces of the virus itself. The virus has been detected in infected animals but, so far, not in people.

Dhurandhar is also doing laboratory investigations of how a virus might make people fat. In these studies, Ad-36 seems to speed up the conversion of a kind of pre-fat cell into full-fledged fat cells, known as adipocytes. His hypothesis is that the virus is doing what viruses do, commandeering human DNA and getting it to make viral proteins, in the process ratcheting up the adipocyte production rate.

Dhurandhar has been inundated with beseeching e-mails from hundreds of distended and desperate people. Sadly, he has nothing to offer them — for now, at least — except the conventional, notoriously unsuccessful advice: diet and exercise.

But some day, if the infection theory of fatness holds, Dhurandhar thinks it would not be too difficult to develop an Ad-36 vaccine that could be administered to everybody early in life, like polio vaccine. “But right now we are far from that,” he cautions.

Another possibility is antiviral drugs. But before developing a pill, scientists would want to know how long the virus remains in the bodies of the fat. “Does this virus just turn genes on or off, and go away, but the body goes on to become obese? That’s one scenario,” says Dhurandhar. “The other is that the virus stays in your body and continues to make you fat. In that case one could add an antiviral to other therapies.”

If researchers continue to fail to find traces of the virus itself in the antibody-positive obese, that could mean that the infection itself is long gone, rendering antiviral drugs useless. On the bright side, it could also mean that virally induced obesity isn’t contagious.

“At this point we don’t know whether it’s an acute or a chronic infection,” Dhurandhar says. “It may be that a virus makes a person fat, but once they’re obese, then what they’ve got to do is eat less and exercise more.”

In a slightly cheering bit of news, he says, a small pilot study of people undergoing drug treatment for obesity has shown that those with the Ad-36 antibodies lost weight faster than those who were antibody-free. Dhurandhar thinks that might mean that someone who gets fat as a result of a viral infection may not be predisposed to gain weight — unlike those of us who chose our ancestors unwisely and are therefore genetically more resistant to weight loss.

Which might mean that fat germs are less fateful than fat genes.

“Maybe,” says Dhurandhar, “but we don’t know right now.”

“It’s the first to show that a particular part of the brain involved in learning is active after you learn,” says Sean P.A. Drummond, a psychiatry professor at the University of California at San Diego, who has used brain imaging to study how sleep deprivation impairs people’s ability to learn.

Using the brain imaging method called positron emission tomography, or PET scanning, scientists observed the brains of study subjects as they slept after learning what neuropsychologists call a “reaction task.” (They pressed buttons in response to symbols flashed at them.) There are several studies showing that both lab animals and people get better at this kind of thing after a night’s sleep. These subjects did too.

But the PET scans went on to show, for the first time, that their brain activity patterns during sleep were quite similar to the patterns generated when they were awake and learning the button-pressing routine. The scientists concluded that the sleeping brain was probably stabilizing and strengthening memories of the task via something like a series of instant replays. In a word, it was practicing.

These brain patterns manifested themselves only during that stage of sleep known as REM (for rapid eye movement, because your eyes dart madly around beneath your lids at this sleep stage). REM sleep happens four or five times a night, and folklore has it that dream time is REM time. The truth is that dreaming goes on all night, at every sleep stage. But REM sleep dreams do tend to be our most vivid and memorable, and are probably more frequent than other dreams.

“We can see exactly where this extra activity is, and it happens only during REM sleep,” says one of the study’s authors, Carlyle Smith, a psychology professor at Trent University in Peterborough, Ontario. “These people show great improvement when you test them the next day. What else could that extra neuronal activity during REM sleep be about? It’s only in the group that learns, exactly what you’d predict you would see.”

Late in his career Freud himself seemed to lean this way. He was constantly revising “Dreams,” and in a 1925 update he veered away from emphasizing dream content to declare: “At bottom, dreams are nothing other than a particular form of thinking, made possible by the conditions of the state of sleep.” That is not so different from what many sleep researchers say now. They tend not to speak of dreams; the term they often use is “mentation.”

Although neuroscientists have long sneered at Freud’s notions, they do not agree among themselves what dreams and REM sleep are for. The idea that they are related to learning and memory is just one of several theories. (Let us eschew discussion of dreams as portents, despite divination’s 4,000-plus years of history and the steady stream of dream books that continue to advise on existential crises and selection of lottery numbers.)

Another hypothesis presents REM sleep as a way to process negative emotions. A Finnish researcher proposes that dreams are a protective mechanism that arose long ago in evolution as a way to simulate threatening events and rehearse possible responses. A group of Harvard researchers has long argued that dreams are meaningless; they are simply our desperate attempt to make sense out of random discharges from the most primitive parts of the brain, to weave them into something like a coherent story line.

Gina Poe, who studies learning and sleep in rats and directs the undergraduate neuroscience program at Washington State University, signs on to the memory consolidation idea, but suspects that memories are also deleted during REM sleep; we may be getting rid of an unnecessary duplicate copy of some memory we have shipped off to our permanent archives.

It is entirely possible that each of these (except divination) is at least partly right. “This study does provide evidence for the memory-consolidation hypothesis specific to REM sleep, but that is not mutually exclusive with any of the other theories,” says Drummond. “However, teasing apart and getting to the relative contribution each may make to the truth is going to be very difficult — if it is possible at all.”

The reaction-time test the researchers employed is primarily a test of motor skills — muscle memory. It’s a task not unlike learning to touch-type. At first you have to think about what you’re doing, but with a little practice, your movements quite soon bypass consciousness and become automatic.

Would the results be similar if researchers could figure out a way to watch REM sleep after the sleepers were exposed to higher-level learning, especially verbal learning such as lists of words or a new language? Both Drummond and Poe suspect that the answer is yes, but it needs to be nailed down. “This is a very nice first step,” Drummond says. “To really link memory consolidation to REM sleep though, we need to replicate this with higher, more complex, language-based learning.” Confirming that point will not be easy technically. But it is a pretty important question in our famously information-driven society.

There are satisfying hints in the research literature that confirmation is likely to be forthcoming eventually. Joseph De Koninck, a psychology professor at the University of Ottawa, has studied students in intensive total-immersion language courses. De Koninck’s subjects quickly increased the amount of REM sleep they got, and the students who were doing the best increased their REM sleep the most. People learning a new language commonly dream they are speaking the language, and, most intriguing, the good students in this study began to have those dreams sooner than their less able classmates. De Koninck believes that dream content is not itself involved in learning, but rather mirrors the degree of competence the dreamer has achieved.

The next step, Poe suggests, would be to pair a PET learning study with studies of REM sleep deprivation — and enhancement. Yes, it is possible to enhance REM sleep. Increase the surrounding temperature, and/or deliver certain auditory tones that have been shown to lengthen and intensify REM sleep. (Musicians take note; there’s an unoccupied niche here.)

Could we boost learning by increasing REM sleep? It’s possible, Poe says cautiously. However, heed her warning: “There might be a threshold above which you’ve spent too much time in REM sleep. You may be erasing too many things.”

What to do until the scientists sort all this out? Don’t pull all-nighters. Don’t bother cramming just before a test. Study hard, but stay warm and get a good night’s sleep. In short, listen to your mom.

It won’t. The heads of the projects themselves mention that often. The public project’s leader, Francis Collins of the National Human Genome Research Institute, cautions, “There is much left to be done.” The private project’s leader, Craig Venter of Celera Genomics Corp., said that Monday was “not a very important moment except that it’s the beginning of what we can do with it.”

Why all this modesty from the masters of an accomplishment that President Bill Clinton likens to Galileo’s and Lewis and Clark’s, that Tony Blair hails as “the first great technological triumph of the 21st century?” Because Collins and Venter know some things that CNN and its ilk aren’t telling you.

For starters, nearly 66 percent of the data in the publicly funded project is in “draft” state, an acknowledgement that the DNA sequences are larded with mistakes. Collins likes to call the human genome sequence “our own instruction book.” Well, your new instruction book is full of errors: factual errors and typographical errors. The original plan was to fact-check, spell check and proofread each of the millions of DNA sequences at least 10 or a dozen times to purge the goofs in analysis — an inevitable consequence when the project comprises more than 3.1 billion pieces of information. But in the indecorous and very public race between the taxpayer-funded and the commercial HGPs, prudence was shed along with good manners. HGP officials, public and private, have settled, albeit temporarily, for half the amount of proofreading they know must eventually be done.

Your instruction book is also missing 15 percent of its pages. In addition to the errors, there are tens of thousands of gaps where the DNA has not been sequenced at all. Public and private scientists alike have waved away the gaps as inconsequential, but that’s not entirely true. “It’s impossible to answer whether the gaps are important,” says Samuel Aparicio, a genome scientist at Cambridge University. “There will be genes that weren’t known that will turn up in the gaps, and the gaps have to be closed. But the significance of having 90 percent of the sequence online is to help to show them.”

And here’s a human genome factlet that hardly anybody ever mentions. The projects have completely excluded a kind of highly condensed DNA called heterochromatin from sequencing. That’s about 7 percent of the human genome, and there are probably some genes in it. Not many, but some.

The unfinished state of gene knowledge is such that a few weeks ago genome scientists began to make bets on the number of human genes. Nobody knows how many there are. So far the wagers by the people who are likely to know range wildly from 27,000 all the way to 200,000. The wagering will remain open until 2003 because one thing genome scientists do know is that the human DNA sequence isn’t anywhere near finished yet. Even when it is, picking out genes from the mass of other DNA will be very tough. (Genes are estimated to occupy only 3 percent of the human genome.)

On the other hand, the exact number may not matter much. This we have now learned from investigating the genes of other creatures. The mapping and sequencing of the DNA in a couple of organisms has been completed in the last year or two. The simple nematode Caenorhabditis elegans — that’s a tiny soil worm to you — turns out to have more than 18,000 genes although it possesses a paltry 959 cells. But the fruit fly — which, although also tiny, is much more complex and human-like than C. elegans — has some 5,000 fewer genes than the worm (about 13,600). Gerald Rubin, who headed the fruit-fly genome project at Berkeley, points out, “Complexity is not in any simple way related to gene number.”

This was a real shocker for the researchers, who are just as anthropocentric as the rest of us. For years they had casually estimated the human gene number at about 100,000. Most of them have now reduced their estimates drastically. At this writing, genome scientists have placed 228 bets on the human number. Half of them have wagered that there are fewer than 54,000 human genes. Two just-published estimates from highly respected genome scientists are in the 30,000s. Collins himself has joined the accelerating trend to lowball guesses; his wager is 48,011. Nobel laureate David Baltimore, perhaps taking his cue from the project leader, told the readers of Sunday’s New York Times that 50,000 seemed about right to him.

In short, a great many genome scientists now believe we possess only two or maybe three times as many genes as a worm the size of a pinhead that resides in the dirt beneath our feet. And yet the planet continues to turn.

That lowered estimate has also been a shocker for capitalists who fund the research because they hope to exploit it. Uber-genomicist Venter has reported an encounter — culture clash is more like it — with the late Wallace Steinberg, an entrepreneur who backed early stages of Venter’s work on the human genome. When Venter speculated in print that there might be only 60,000 or 70,000 human genes, he got a furious call from Steinberg. “What the hell do you think you’re doing, saying there are only 60,000 genes?” Steinberg reportedly shouted. “I just sold 100,000 genes to SmithKline Beecham!” (The giant drug company had agreed to a big deal giving it access to Venter’s database, which is Celera’s product.) To Steinberg, individual genes were a commodity. More was better.

If not gene number, then what makes us so much cooler than worms? Part of the answer may be proteins. Proteins carry out the activities of cells, and making proteins is what genes mostly do. But a gene can be involved in construction of a number of different proteins, each of which can perform a different job. Another part of the answer may lie in regulation of a gene’s behavior; controlling what cells it’s active in; and when and how much or little protein it churns out.

What this means is that the really interesting part of the Human Genome Project has hardly begun. Most of it still lies, iceberg-fashion, in databases and gene chips and the brains of scientists — and scientists unborn — all over the world. Only 7,000 or so human genes out of the hypothetical 48,011 have even been named, and genome researchers know something about the function of only a fraction of those.

The intriguing part, the hard part, the useful part — figuring out what each gene is up to, and how each gene conducts itself with all the others — all lies in the future. At the announcement on Monday, Venter predicted that the analysis will take most of this century. Lots more information about what specific genes do must be acquired before the HGP starts paying off in the widespread medical wonders you have been promised. That’s the real human genome project. And it won’t be complete in your lifetime.