Wednesday, October 09, 2013

Science magazine section - "Scientific Communication" - October 4, 2013

Just in time for Open Access Week later this month (October 21-25), Science has published a section on scientific publishing, a topic regarding which they surely are not unbiased. 

I love the infographic,  The Rise of Open Access, by Randall Monroe of xkcd fame which claims that new scientific papers are published at an accelerating rate, currently about one every 20 seconds, and that since 2011, half of new papers are open access. That part of the article comes from an article by Jocelyn Kaiser in another issue of Science (DOI: 10.1126/science.341.6148.830).

There are other worthy pieces in this section, but the one that got my goat was a piece by John Bohannon, "Who's Afraid of Peer Review", an account of his sting operation, sending a scam article to a large number of open access journals to see which of them would catch its problems in their peer review systems. He made some valid points, but overall, I think the project was flawed by not including non-open access journals. The inferences drawn by him and others (see/hear the report on NPR) make it seem like the problems arise from open access rather than from poor peer review. Other bloggers  have written more articulate posts about the shortcomings (see Peter Suber's or Michael Eisen's). 

Science is hosting a live chat session on this issue with the article's author and several others including Eisen, on Thursday, Oct 10, 2013 at 3pm EDT.

Friday, May 03, 2013

A camera that sees like an insect

Here's in interesting use for low-res optics designed to imitate compound eyes.  Biomimetics in action!

Insect-Eye Digital Camera Sees What You Just Did

from National Geographic Magazine - Phenomena

Friday, November 09, 2012

From In the Loop: "Climate modeler identifies trigger for Earth’s last big freeze"

Alan Condron, a Research Assistant Professor in Geosciences at UMass Amherst, and his collaborator, Peter Winsor from University of Alaska Fairbanks, have published an article in the current issue of Proceedings of the National Academy of Sciences. Using a new model, they propose a theory about how the meltwaters from the Laurentide Ice sheet, 12,000 years ago, are likely to have triggered the Younger Dryas, an abrupt cooling of the northern hemisphere, which interrupted a warming trend, coming out of a period of glaciation.
“This episode was the last time the Earth underwent a major cooling, so understanding exactly what caused it is very important for understanding how our modern-day climate might change in the future,” says Condron of the Climate System Research Center.
... “Our results are particularly relevant for how we model the melting of the Greenland and Antarctic Ice sheets now and in the future. “It is apparent from our results that climate scientists are artificially introducing fresh water into their models over large parts of the ocean that freshwater would never have reached. In addition, our work points to the Arctic as a primary trigger for climate change. This is especially relevant considering the rapid changes that have been occurring in this region in the last 10 years.”
 See more details on this story in the campus In the Loop , Tuesday, November 6.

The full text of the original research article, "Meltwater routing and the Younger Dryas" doi:10.1073/pnas.1207381109  is available to the UMass Amherst community through the DOI link.

Thursday, November 08, 2012

Prenatal learning in wrens - mind-boggling!

The title of this news article in Nature, 8 November, "Wrens teach their eggs to sing" is a little misleading - Superb Fairywren (Malurus cyaneus) mothers are teaching their offspring to make a specific begging call that allows them to distinguish between their chicks and cuckoo hatchlings.  They start calling to the eggs about 10 days before they hatch, and the hatchlings must make this call in order to be fed.  Apparently, cuckoo eggs hatch earlier than those of the wrens, but they aren't capable of learning the call in time.  The cuckoo nestling will push unhatched wren eggs out of the nest. This 'secret password' mechanism allows the parents to waste less time feeding a chick that isn't their own; they will abandon the lone cuckoo chick to start on another brood.

Superb Fairywren photo from Wikimedia Commons by JJ Harrison
Superb Fairywren (Malurus cyaneus) photo by JJ Harrison
The finding was discovered by accident by researchers at Flinders University in Adelaide by Sonia Kleindorfer's team.
They were recording inside the birds' domed nests in search of anti-predator calls when they noticed that female fairy-wrens were singing to their unhatched eggs.  When Kleindorfer and her team analysed recordings made over the full nesting cycle, they found that the wren nestlings in a given nest all had the same begging call, which was unique to their nest. [My emphasis] That call contained a signature element present in the call the mothers had made while incubating the eggs, and in the call she used to solicit food from the father. When the researchers broadcast a foreign nestling call at the nests, both the female and male adult birds refused to feed the chicks.
Cross-fostering the wren eggs, i.e.,  switching the eggs in the nest with the eggs of another wren pair before the parents started making the calls, showed that the specific call was learned, not genetic. The system isn't perfect, though. One cuckoo species,  is always identified by the wrens, but another succeeds in finding the right password call some of the time. "Kleindorfer says there is evidence that, in the latter species, the cuckoo nestlings attempt to guess the password by trying out different calls."

I have always found it amazing that parents of parasitized species don't recognize the cuckoo chicks as intruders without a mechanism like this.  Other species, such as cowbirds have the habit of parasitizing other species's nests.

The original research was published as a report in Current Biology, [in press, corrected proof, at this time] "Embryonic Learning of Vocal Passwords in Superb Fairy-Wrens Reveals Intruder Cuckoo Nestlings"

Friday, October 26, 2012

"Lamarck and the Missing Lnc" - from The Scientist

Nice overview by Kevin B. Morris in the cover story of The Scientist, Lamarck and the Missing Lnc, of the work in epigenetics which is challenging the basic tenet of evolution that random mutation is the only source of change in genetics.

As I understand it, serious challenges to an individual's survival may cause heritable changes in the ability of the DNA to express particular regions of the genetic code.  "Long noncoding RNAs (lncRNAs) are transcripts generally expressed from regions of 'junk' DNA that are not thought to code for proteins" but now it seems they may be controlling the expression of the genes, controlling when and how much of a particular protein is produced by the cell.  Suppression of the expression caused by an environmental challenge may be heritable.
(See images 1: The Epigenetic LNC, 2: A Mechanism for a Targeted Change, and 3: Directing Evolution)

Back in the dawn of genetics, Jean-Baptiste Pierre Antoine de Monet, Chevalier de la Marck, often known simply as Lamarck, theorized that traits formed in an individual's life would then be passed on to it's offspring; for example, a giraffe could develop a long neck because it stretched it reaching for forage up high, and their offspring would inherit longer necks as a result. Lamarck's theory has been a prime example of a thoroughly de-bunked scientific theory for decades.

These developments don't exactly support Lamarck's theory, but there is more than a whiff of Lamarckism about them.  And, there do seem to be holes in the strict Darwinism now.  Exciting times!

Monday, August 13, 2012

"Whither Science Publishing?" in The Scientist

The Scientist has an issue focusing on science publishing, it's problems, strengths, and future.  This includes discussion of open access publishing, peer review, funder mandates, etc., and it polls a wide range of opinion.