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.


Friday, June 01, 2012

PLoS Biology highlights article on Data Management Literacy

Dealing with Data: A Case Study on Information and Data Management Literacy, an article in the Community section of the PLoS Biology website, discusses the changes in data management compelled by the deluge of data, and the recognition that it was not being managed rationally or well.
In an era of Linked Open Data and the Semantic Web [10], research today comprises information in many forms: blogs, tweets, database entries, and grant reports that could be made available as Linked Data. The launch of new initiatives to accelerate publication and use of new and emerging technologies to enable improved data presentation [11] has spurred further conversations about enabling data-driven “publications” whereby the data itself is cited [12]. Further, it has been suggested that publications should be evaluated based on whether they have enriched content to provide interactivity, available datasets, and machine-readable metadata [13].
...Scientists today need to rely on data management not just at the end of a project, but during its whole life cycle. Thus, it's imperative that we develop the tools to handle data effectively and efficiently as we continue to consume and generate it. As a step towards facilitating quality data management practices, NIH has recently announced support for informationists to work on currently funded research grants [16].
... Libraries are an under-recognized resource in the field of data and information literacy. Librarians have increasingly become experts in data management because of their combined knowledge of new data sharing standards, information science, and the Semantic Web [24]. For instance, the eagle-i curation team consists of Semantic Web experts, ontologists, librarians, and domain curators. Information literacy has always been a topic of interest to research librarians, and it is natural that their role is expanding to include topics surrounding data curation and access.

Tuesday, May 29, 2012

Nat'l Academies Pre-print Report on Discipline-Based Education Research

This 270 page "synthesis study" collects the literature and assesses research on approaches to undergraduate science education.  I haven't read the report, just skimmed the 19-page Executive Summary. 

Most reports by the National Academies can be read online for free, including this one.  From the Exec. Summ.:
DBER scholars have devoted considerable attention to effective instructional strategies and to students’ conceptual understanding, problem solving, and use of representations. Key findings from DBER are consistent with cognitive science research and studies in K-12 education.

To gain expertise in science and engineering, students must learn the knowledge, techniques, and standards of each field. However, across the disciplines, the committee found that students have incorrect understandings about fundamental concepts, particularly those that involve very large or very small temporal and spatial scales. Moreover, as novices in a domain, students are challenged by important aspects of the domain that can seem easy or obvious to experts, such as problem solving and understanding domain-specific representations like graphs,
models, and simulations. These challenges pose serious impediments to learning.

DBER clearly shows that research-based instructional strategies are more effective than traditional lecture in improving conceptual knowledge and attitudes about learning. Effective instruction involves a range of approaches, including making lectures more interactive, having students work in groups, and incorporating authentic problems and activities.

To enhance DBER’s contributions to the understanding of undergraduate science and engineering education, the committee recommended:
  • Research that explores similarities and differences among different student
  • Longitudinal studies—including studies of the K-12/undergraduate transition— to better understand the acquisition of important concepts and factors influencing retention.
  • More studies that measure outcomes other than test scores and course performance, and better instruments to measure these outcomes.
  •  Interdisciplinary studies of cross-cutting concepts and cognitive processes.

Tuesday, May 01, 2012

Inexpensive ethylene sensor reported

Megan Scudellari reported in The Scientist on April 30 in "Sensor Measures Produce Ripeness," on a 25 cent ethylene sensor developed by chemists at MIT that could help grocers and shippers gauge the ripeness of fruits and vegetables.
The sensor, described April 19 in the journal Angewandte Chemie [International Edition], is made of an array of tens of thousands of carbon nanotubes modified with copper atoms, which bind ethylene and allow scientists to measure the amount of gas present. The researchers successfully tested their sensors on bananas, avocados, apples, pears, and oranges, accurately determining their ripeness.
The inexpensive devices could someday be attached to cardboard boxes of produce and scanned with a handheld device to reveal the contents’ ripeness, said [MIT's Timothy] Swager. Then, grocers would know when to put items on sale before they get too ripe.
If you are a member of the University of Massachusetts Amherst community, you can read the Angewandte Chemie article using the library's subscription.
  • On campus, use this link.  
  • Off campus, use this link - you will need to authenticate yourself using an OIT username and password, and navigate to the full text of the article.

As a past student of post-harvest physiology, I suspect this device could be a real boon to the industry and the consumer, and result in much less wasted produce.

Friday, April 06, 2012

...and, NPR story on Bears in Northampton, MA

Local story goes national.

Apparently, some people in Northampton don't realize that feeding wild bears is a bad idea.
Wildlife officials are pushing for a city law to make feeding bears illegal, so they'd have little reason to leave their natural habitat. The problem is, mother bears have already taught their cubs that chomping on discarded pizza crusts is a lot easier than picking berries in the woods. For the next generation of bears, this may actually be their natural habitat.
Another angle from, with a link to the abc40 news segment.

Two UMA Science stories (Center for CASA and Geckskin) on WFCR

This morning, on the local public radio station, WFCR, in their Morning Edition Extra segment, the first two stories spotlighted useful scientific research at UMass Amherst.

The first was a piece on the work at a new Engineering Research Center, CASA, or, Center for Collaborative Adaptive Sensing of the Atmosphere. David McLaughlin, associate dean of the School of Engineering, described the next generation of weather doppler to help speed up severe weather warnings. Currently, there is an average of 12 minutes between warning being issued and tornado striking, and 80% are false alarms. Solution is to use a higher number of lower and smaller radar installations, networked, like cell phone networks. Finer resolution should result.

This segment was followed by another on a UMass Amherst interdisciplinary team working on developing dry adhesives. As discussed in an interview with biologist Duncan Irschick and polymer scientist Al Crosby, they have looked to the gecko for inspiration.  Their work has produced an adhesive which will allow heavy loads to hang from smooth walls, and removing the load from the wall easily and quietly.  Geckskin's commercial applications could be myriad; military uses are also likely.  More info here.

Tuesday, February 07, 2012

Petition to boycott Elsevier journals up to [nearly] 4500 signatures

Elsevier, a scientific publisher, has recently raised the ire of scientists and mathematicians (and librarians) concerned about the rise in journal prices, business practices, and lobbying stances taken by academic publishers.

Well-known mathematician, Tim Gowers, in a piece on his Gowers’s Weblog, was the proximate cause of the latest campaign in reaction to these issues.  He took a stand on Elsevier's practices and positions, namely, the high cost of their journals, the bundling many journals in packages for academic libraries, their 'ruthless' reactions when libraries object to this practice, and their support for the Research Works Act (which would discourage the open access publishing movement) and SOPA and PIPA.  That a prominent mathematician would publicly proclaim his refusal to publish in, or engage in reviewing or editing Elsevier journals caught the attention of the scientific community. It inspired Tyler Neylon to put up an online petition, The Cost of Knowledge, where scientists could register their commitment to boycott Elsevier in those specific ways.

In the time it has taken me to write these words, the number of signatories went from 4479 to 4492.  I will check one more time before I finish this post.

Elsevier, naturally, doesn't  agree with Mr. Gower.  A piece in The Scientist outlines their position - it didn't make a lot of sense to me, so I will leave it to my readers to judge for themselves.  I hasten to add that Elsevier is merely one of the scholarly publishers with these issues, albeit one with the highest priced journals.  It's a complex market/situation/issue.  I wouldn't recommend the Wikipedia article on this topic (Serials Crisis) as it currently stands. If you would like to know more about it, please contact me.

Librarians have been shouting about these issues for a long time - we are on the front line in the struggle to provide access to the academic literature. One could say that we have done such a good job that the problem was obscured to most people - they could get the stuff they needed, so why would they complain? One of the points that Elsevier does not address in The Scientist piece is that the rate of inflation for academic journals  overall has been about 8% per year - much higher than nearly everything else in the economy, including the rise in tuition and fees to students, or academic salaries.  (I've been looking for reasonable sources for this contention but I can't lay my hands on it right now - will provide later.) It has occurred to me that  perhaps commercial publishers are milking the situation as hard as they can now because they see the writing on the wall, so to speak - their cash cow is nearly spent.

Tim Gowers's blog is thoughtful - he had no intention of starting a movement, and he is moving on to looking for alternatives to Elsvier.  I particularly liked reading his post "What's wrong with electronic journals."

The petition just went over 4500.
Note: 9 Feb they are approaching 5000 signers.
6 April, approaching 9000

Tuesday, January 03, 2012

Reinventing the Research Library: The MIT Libraries in the 21st Century

I was looking at the videos MIT Libraries have posted, and this one caught my eye. It's on the long side (8+ min) but nicely done.  Of particular note to me, starting at about 5:46, they discuss MIT's commitment to open access - as far as is possible, all articles published by MIT faculty are also housed in their archives, and available to anyone with internet access. The Institute Archive is part of the Libraries.

Video: Reinventing the Research Library