Do I even have to mention this week’s top story in science? Nah.
“I’m more and more inclined to think that we can actually penetrate at least some of the steps by which nature invented the code.” — Charles Carter
The genetic code is one of biology’s few universals*, but rather than being the result of some deep underlying logic, it’s often said to be a “frozen accident” — the outcome of evolutionary chance, something that easily could have turned out another way. This idea, though it’s often repeated, has been challenged for decades. The accumulated evidence shows that the genetic code isn’t as arbitrary as we might naively think. And more importantly, this evidence also offers some tantalizing clues to how the genetic code came to be.
This origins of the genetic code has long been a research focus of University of North Carolina biophysicist Charles Carter, and his UNC enzymologist colleague Richard Wolfenden. They authored a pair of recent papers that suggest behind the genetic code are actually two codes, reflecting key steps in its evolution. Dr. Carter kindly agreed to answer some questions about the papers, which present some interesting results that add to the growing pile of evidence that the genetic code is much less accidental that it may seem.
These papers deal with the machinery that implements the genetic code. Conceptually the code is simple: it is a set of dictionary entries or key-value pairs mapping codons to amino acids. But to make this mapping happen physically, you need, as Francis Crick correctly hypothesized back in 1958, an adapter. That adapter, as most of our readers know, is tRNA, a nucleic acid molecule that is “charged” with an amino acid.
But the existence of tRNAs creates another coding problem: how does the right tRNA get paired with the correct amino acid? The answer to this question is at the heart of the origin of the genetic code, and it’s the subject of these two recent papers. More about this story, as well as the first part of my interview with Dr. Carter, is below the fold. Continue reading “Where Does the Genetic Code Come From? An Interview with Dr. Charles Carter, Part I.”
Science is increasingly focusing on whole environments – ranging from our guts to the ocean – exploring how all the parts of a system work together to function in a healthy way. Lucie Libotte’s 2014 work, Dust Matters, now on exhibit at the Science Gallery in Dublin, creates art from one of the inescapable elements of our domestic environment – dust.
In a kind of “citizen sciart” project, Libotte had a group of friends in various areas of the UK collect dust from their homes. She then fired the dust as a coating on ceramic vessels, which look strikingly varied. Says the artist, “Dust Matters’ aim is to re-evaluate this ‘dirt’, and convey the value of dust as an indicator of our environment, showing how it reflects our daily life and traces our journey through the world.”
Libotte’s work is part of an exhibition at the Science Gallery called HOME\SICK: POST-DOMESTIC BLISS, which “looks at the meanings of home, from rubbish to robots and microbes to micro-dwellings, asking whether the changing nature of home is for better or worse.”
HOME\SICK, which runs through July 17, features the work of many other artists, scientists and designers, including the microbial bellybutton stylings of Finch & Pea friends Rob Dunn and Holly Menninger of North Carolina State University.
You can get lots more information about the show at the Science Gallery website.
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.
Researchers have discovered seven new species of miniature frog – all from the genus Brachycephalus – living in the Atlantic Rainforest of Brazil. In a fascinating case of geography influencing evolution, each species lives on a separate mountaintop and has evolved a different skin color and texture. Rachel Feltman’s article in The Washington Post has much more detail about the tiny (less than 1 cm long!) frogs and the paper that introduced them to the world.
The frogs are not, of course, actually new. I’m sure they’ve been living peacefully on their mountaintops, minding their own business, for many years until a bunch of scientists came along to discover them. Sorry, little guys. If the tourists start bothering you, band together and use your toxins.
The Finch and Pea 