Author: Mike White

Genomes, Books, and Science Fiction

Great Experiments in Science Publishing

It’s a great time to follow scientific publishing: right now there are some innovative and even radical experiments happening. Open access has, of course, been the biggest (and most successful) experiment. But figuring out how to run a good journal without a paywall is more of an economic innovation, rather than an innovation in how we communicate science. There are other fascinating experiments underway that go beyond open access.

PLOS One goes all-in on post-publication peer review, publishing papers after a review for methodological soundness, and letting the community decide whether the work is significant. eLife tries to make the traditional publishing approach less wasteful by forcing editors and reviewers to talk to each other to produce a consensus review. Faculty of 1000, PeerJ, and The Winnower are trying various more radical experiments in peer review. And Academia.edu and ResearchGate are both trying to harness the power of social media to help researchers communicate their work with each other.

These are fascinating experiments, but do they work? It’s a hard question to answer, but in my latest Pacific Standard column, I take a look at a recent study by Academia.edu, which found that papers posted to their site had a citation advantage — on average, 83 percent more five years after publication. The study is not published in a peer-reviewed journal (for now), but it’s out there for the community to review: the authors have released all their code and data alongside the report.

The question of whether there is a citation advantage for certain types of publications (e.g., open access journals) has been controversial and hard to resolve. There are clearly many potentially confounding variables that have to be controlled for if you want to make a convincing case. The Academia.edu study takes a stab at this, and it is a provocative attempt to get the scientific publishing community to focus not just on the question of open access in general, but specifically on how it’s implemented:

Beyond Academia.edu, our work raises questions about how characteristics of venues matter for open access citations. To our knowledge there has been no research on what features of open access repositories or databases make articles easier to discover, and to what extent that leads to increased citations.

As Academia.edu’s founder, Richard Price told me, we need to explore whether savvier use of social media tools will make for a better publishing system, one that helps people find work that otherwise would have gone unnoticed:

Certain open access platforms are push networks: articles are pushed out to followers on upload, and sometimes there are viral properties where followers can re-share the article with their followers. A tentative conclusion is that push networks with viral properties generate more exposure for papers, and this exposure leads to citations.

Standing Up For Basic Research

I don’t like getting drawn into partisan fights when it comes to science, because federally funded research has generally had broad bipartisan support in Congress for more than a half-century. But there is no point in denying that the funding bill that just passed the House is a blatantly partisan effort by GOP leaders to impose their political ideologies — which include climate change skepticism — on our research agenda.

As I discuss in my recent Pacific Standard column, curiosity, and not partisanship should drive our scientific agenda when it comes to basic research. That’s generally been the rule at our basic science agencies, and the current leadership of the House of Representatives doesn’t like it.

This week, the House passed a highly partisan funding bill that would dramatically and disastrously reshape our science agencies along the lines of GOP preferences. Among the mischief attempted by these lawmakers is an push to slash funding for earth sciences at NASA and the NSF, in a poorly disguised effort to dial back climate change research. Representative Bill Foster (D-IL), a physicist, put it best: this bill reflects “the majority’s efforts to impose their own personal beliefs and ideologies on the process of scientific discovery.”

Fortunately, the White House has issued a veto threat. And its Office of Science and Technology Policy is pushing back against the GOP leadership’s misleading claims that they’re just trying to get the NSF and NASA to focus on “core science” or research that’s “in the national interest.” The OSTP has started a Twitter campaign under the hashtag #BasicResearch: Continue reading “Standing Up For Basic Research”

You can’t do transformative science without wasting money

This is a great statement by Eric Lander from an interview he gave to James Fallows at The Atlantic last year:

“When will genomics cure cancer?”

Young scientists who need to look at 100,000 cancer samples, or do functional tests inhibiting all the genes in the genome, or explore the use of chemicals in ways they never could before—they need an NIH [National Institutes of Health] that is able to place bets. With sequestration, and the NIH budget falling by about 25 percent in real terms over the past decade, the people reviewing grants naturally become more conservative. When there’s less money, reviewers don’t want to run the risk of wasting money on something that doesn’t work.

I’ve got to tell you, if you aren’t prepared to waste money on things that might not work, you can’t possibly do things that are transformative. Because for every successful transformative idea, there’s five times as many nonsuccessful transformative ideas. Nobody knows how to figure out in advance which ones they’re going to be.

I don’t agree with everything Lander says in the interview – specifically, the statement that we’ll have a “complete catalogue” of disease genes in another five or six years has no basis in reality. But overall, he makes some great points about the transformative potential of genomics.

My picks for weird post-apocalyptic SF

BlueprintsPKmech.inddThis week I’ve contributed to SF Signal’s Mind Meld. The question is essentially what science fiction you’d bring to a wedding:

Something old, something new, something borrowed. . .

Recommend three books to our readers out of your list of favorites: An older title, a newer title, and title you discovered because you borrowed it from a friend or a library.

Go check out all of the great responses. My answer focuses on, as you may have guessed, post-apocalyptic SF. The best SF book I ever borrowed from a friend was Dhalgren, a marvelous and very weird New Wave beast that takes place in a fictional ruined city. To go with Dhalgren, I picked two other outstanding weird post-apocalyptic classics, something old (The Night Land of 1912), and a strange new book that more people should read (the 2012 Blueprints of the AfterLife). Head on over and whet your appetite for some very weird post-apocalyptic SF.

Mark Ptashne on the “incoherent and counterfactual world” of epigenetics

Ptashne again cuts through epic epigenetic confusion of transcription factors versus histone marks, cause versus effect.

“The Chemistry of Regulation of Genes and Other Things”:

As I have described, where the activated gene encodes the activator itself, we have memory: a self-perpetuating state of gene expression transmitted by regulatory proteins distributed to daughter cells as cells divide.

These now obvious ideas seem to be hard to accept for some. Ignoring the specificity problem and in the search for some alternative solution to the memory problem, they have created an incoherent and counterfactual world, one in which chromatin structure determines the activity of transcription factors (recruiters) rather than the other way around. Chromatin structure is usually meant to imply histone modifications, which somehow have acquired the name epigenetic modifications. The literature is replete with studies of histone modifications presented as studies of “epigenetics,”… Continue reading “Mark Ptashne on the “incoherent and counterfactual world” of epigenetics”