Science aficionados should have appreciated yesterday’s Science Times in The New York Times. The section always does a good job with special issues focusing on single subjects, which have, in the past, included evolution, space exploration, and healthcare.

Yesterday’s package, about genomics, was no exception. As we reported here last May, while the field of epigenetics has been gaining ever more attention since the human genome was decoded nearly ten years ago, it’s still an intensely mysterious field. Traditionally, scientists believed that heritable genes, or short pieces of DNA, governed our individual physical and psychological characteristics. It has become evident, however, that a number of external molecular factors affect those genes in poorly understood ways. When we published our column in May, the news was mostly about “gene expression,” and the idea that certain genes could be turned “on and off.” The Science Times ratcheted up this genomic rethinking even further with a handful of articles that report how scientists are fundamentally rethinking the definition of a gene:

In this jungle of invading viruses, undead pseudogenes, shuffled exons and epigenetic marks, can the classical concept of the gene survive? … These new concepts are moving the gene away from a physical snippet of DNA and back to a more abstract definition.

In the same piece, a scientist tells the Times’s Carl Zimmer that “I think it’s a paradigm shift in how we think the genome is organized.” Other articles discuss the nitty-gritty of RNA and a novel theory of the genome’s relationship to mental disorders. There are also excellent graphics and an glossary of genetics terms, which seems particularly appropriate given that evolving definitions seem to be the point of the section (Knight Science Journalism Tracker has a full round-up here). At any rate, the Science Times’s work is a great example of journalism staying current with science and finding a way to a tell story with no obvious news peg (save for the fact that it’s been almost 100 years since Danish geneticist Wilhelm Johanssen coined the term “gene,” which, thankfully, is not overemphasized).

The genomic package was so good, in fact, that it may have caused some readers to overlook the other notable science article in yesterday’s paper, which appeared on the cover of another (Thanksgiving-inspired) special section called Giving. It’s an unexpected place for science, perhaps, but it provides a hook to another seemingly pegless but imminently important story. This one is about the private medical research foundations, each geared toward curing a specific disease, that are bridging the gap between government-funded basic research and applied therapies.

The Times’s account, by business writer Joe Nocera, focuses on the eponymous foundation created by actor Michael J. Fox, who has Parkinson’s disease. In its attempts to find the cause of and cure for that neurological disorder, Nocera writes, the Fox Foundation, “has joined a small but growing group of what might be called activist disease foundations — foundations that operate with speed and urgency and a business model completely unlike the traditional foundation model, or the National Institutes of Health, for that matter.”

Essentially, what sets the Fox Foundation apart is its business-oriented, rather than philanthropy-oriented, approach. Instead of growing its grant-making endowment, Fox is concerned with getting money to researchers that need it, and actively monitoring the return on that investment. The kind of return the organization expects, however, is also different.

There are generally two paths that biomedical research can follow: basic (which is usually publically funded) and applied (which is usually privately funded). The problem is that discoveries produced by the former can take an astoundingly long time to evolved into the medicines and therapies produced by the latter. The Fox Foundation wants to improve upon that system by focusing on “translational” research—“meaning the applied biology research it paid for was intended to eventually translate into a treatment or a drug.”

That’s no easy task. As Nocera notes up high in his piece, “Collectively, [such foundations] spend hundreds of millions of dollars each year. And yet — and here is the rub — the diseases they are trying to cure remain stubbornly uncured.” That frustrating reality comes through just as forcefully in an article by Sharon Begley in the current issue of Newsweek, headlined “Where Are the Cures?” Her piece mentions Fox, as well as number of other foundations, but focuses on the systemic problems that inhibit research:

The nation’s biomedical funding and training system are set up to do one thing, and they do it superlatively: make discoveries. That is what scientists dream of, that is what gets them published in leading journals (the coin of the realm in academia) and that is what gets them grants from the National Institutes of Health. Here’s what doesn’t get them any of those: the grunt work that [Hans] Keirstead did to turn his spinal-cord breakthrough [injecting stem cells into rats with severed spines in order to cure paralysis] into something that can be tried in patients.

These barriers to “translational” research (studies that move basic discoveries from bench to bedside) have become so daunting that scientists have a phrase for the chasm between a basic scientific discovery and a new treatment. “It’s called the valley of death,” says Greg Simon, president of FasterCures, a center set up by the (Michael) Milken Institute in 2003 to achieve what its name says. The valley of death is why many promising discoveries—genes linked to cancer and Parkinson’s disease; biochemical pathways that ravage neurons in Lou Gehrig’s disease—never move forward.

Begley’s piece then takes a political twist (the only apparent peg for the story, though it appears down low) with the mention that “The next administration and Congress have a chance to change that, radically revamping the nation’s biomedical research system by creating what proponents … call a ‘center for cures’ at NIH. The center would house multidisciplinary teams of biologists, chemists, technicians and others who would take a discovery such as Keirstead’s and nurture it along to the point where a company is willing to put up the hundreds of millions of dollars to test it in patients.”

Whether or not that idea will come to fruition remains to be seen. According to the Democrat and Chronicle in New York, however, the University of Rochester is building a $76.4 million Clinical and Translational Science Institute that will be the “first building of its kind in the nation.”

At any rate, both the Times and Newsweek deserve credit for drawing attention to these rather profound changes in the fields of genomics and biomedical research. Without immediate and obvious news pegs, these wide-angle, forward-looking stories are not easy to tell in the modern media climate, yet the emerging trends expressed therein are likely to one day have significant impacts on human health.

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Curtis Brainard is the editor of The Observatory, CJR's online critique of science and environment reporting. Follow him on Twitter @cbrainard.