Of Schemes and Memes Blog

Best of nature.com blogs, SciLogs.com and Scitable: 1 – 7 September

Fighting about ENCODE and junk

A red junk at Tsim Sha Tsui


Brendan Maher reports in the News Blog that  on Wednesday a handful of journals released more than 30 papers describing results from the second phase of ENCODE: a consortium-driven project tasked with building the “ENCyclopedia Of DNA Elements,” a manual of sorts defining and describing all the functional bits of the genome:

Many reactions to the slew of papers, their web and iPad app presentations as well as the news coverage that accompanied the release were favourable. But several critics have challenged some of the most prominently reported claims in the papers, the way their publication was handled and the indelicate use of the word “junk” on some material promoting the research.

First up was a scientific critique that the authors had engaged in hyperbole. In the main ENCODE summary paper, published in this journal, the authors prominently claim that the ENCODE project has thus far assigned “biochemical functions for 80% of the genome.” I had long and thorough discussions with Ewan Birney about this figure and what it actually meant, and it was clear that he was conflicted with reporting it in the paper’s abstract.

Continue to the post to find out more.

Dawn departs Vesta, aims for Ceres


Dawn, NASA’s mission to explore the asteroid belt’s two most massive bodies, has left its first target, Vesta, in a belch of ionized xeno reveals Eric Hand in the News Blog. 

 On 5 September, the probe fired its ion thruster — which creates thrust by using electricity to ionize a store of xenon — and made its way away from the asteroid, ending a campaign to map the asteroid that began in July 2011. Although the science team has had no trouble being seduced by Vesta’s charms — its layered interior points towards a formation process more like a planet’s than a simple asteroid’s — it did have trouble settling on a coordinate system that would pass muster with the International Astronomical Union. Now, Dawn moves towards an appointment in early 2015 with Ceres, the dwarf planet that is thought to harbour substantial amounts of subterranean ice.

Find out more about this mission in Eric’s post. 

Zoologists endorse electronic publication for new species

A new species of Yeti crab (Kiwa puravida) was described online in the journal PLoS-ONE.


Zoologists looking for the ultimate tribute to Stephen ColbertBob Marley and other celebs can now name new species in electronic-only publications, the International Commission on Zoological Nomenclature (ICZN) announced on 4 September, in an editorial in the journal Zootaxa (published in print and online). Ewen Callaway explains more in the News Blog:

Previously, new animal species descriptions were required to be published in print to be considered bona fide.  The decision — by a vote of 23 in favour and 3 against, with one abstention — comes a year after the International Code of Botanical Nomenclature (ICBN) endorsed electronic publication for new kinds of plants (See ‘Botanists shred paperwork in taxonomy reforms‘).

“It’s a relief and a delight that it’s finally fixed,” says Mike Taylor, a vertebrate palaeontologist at the University of Bristol, UK, and a blogger who has long advocated for electronic taxonomy publication. “The very fact that we’re discussing this in 2012 seems sort of silly, when every journal worth mentioning is online and many significant journals are only online.”

Reactions coupled with palladium

This month’s ‘in your element’ article (subscription required) is from Matthew Hartings (or@sciencegeist as he is known on Twitter) who proposes the bold idea that, rather than carbon, it is palladium that has assumed the role of most important element in many a famous organic reaction.

Another interesting aspect in the history of palladium is that its incredibly practical role initially stemmed from curiosity. Francis Phillips, Professor at Western University (which now goes by the name of theUniversity of Pittsburgh), came across an example of palladium’s catalytic activity as early as 1894, while studying gases in Pennsylvania. Of course, he didn’t exactly start using palladium to couple all sorts of organic molecules through carbon–carbon bonds, and others must be credited for their role in understanding and developing this reactivity — read the article to find out the roles in particular of Smidt and Heck. But still, in 1894 Phillips had described the reaction of olefins over palladium and noted that no CO2 was formed. The rest, as they say, is palladium-catalyzed chemistry.

More details can be found in the Sceptical Chymist Blog.

Benjamin Franklin

Lightning Rod Atop a Statue

SciLogs blogger, Paige Brown, reflects on the life of scientist and journalist Benjamin Franklin in her latest post.

Benjamin Franklin, as he described himself in his autobiography, impressed me with his apt for reading and writing and his overall scientific curiosity. Not to mention his intellectually satirical way of writing that had me smiling as I read his recollections of his youth. With only a modest formal education, Franklin was famous and even revered in his own day for his accomplishments as a printer, author, politician, inventor, scientist, civic activist and diplomat, among the many other roles he fulfilled during his life.

Socially Assistive Robots that Care

The latest Soapbox Science post is by Maja Mataric´, a professor of Computer Science, she talks about socially assistive robots that care:

Robotics research is increasingly turning to the challenges of HRI inherent in the myriad of robotics applications that are coming in the next few decades.  These include robotics technologies for caregiving of end-user populations which include the elderly aging-in-place (i.e., living in their homes as long as possible), those ageing in institutions, as well as stroke patients, children with autism, and other social and developmental disorders, and many others.


Learn more about socially assistive robots and how they may impact the future in Maja’s post. 

Surviving the PhD write up

SciLogs blogger, Pete Etchells, offers some top tips for surviving your PhD in his latest blog post:

1. Look after yourself. It’s an obvious one, but also one that’s really easy to neglect. Now, more than ever, you’ll need a clear and focused mind to gather your thoughts and ideas into a coherent written entity. That’s not going to happen if you hole yourself up in a darkened room, living off beans on toast and noodles. Eat healthily, take time to exercise (or at least get out of the house/office), don’t cope by drinking, and leave off the cigarettes.

Feel free to share your own tips in his comment thread.  

Digital Data Storage in DNA

Over at Scitable,Eric Sawyer‘s latest post looks at a recent paper exploring the possibility of using synthetic DNA to store digital information of human design:

We have a data problem. The future of science seems to be big data, and that’s challenging and expensive to store. The CMS experiment at the Large Hadron Collider alone generates 1 terabyte of data every second and, more poetically, in its projected lifetime the LHC will give us a dataset comparable in size to a library containing every single word spoken by every human who has ever lived2. Big science aside, the internet and social media generate large quantities of digital information.

In their paper, George Church and colleagues combine recent advances in DNA synthesis and sequencing to create a data storage chip made of DNA. In the DNA chip they stored a HTML file of a synthetic biology book, containing 53,426 words of text, 11 black and white JPEG images, and a computer program written in Java. Since DNA contains four bases, two computer bits can be encoded per DNA base: e.g., A = 00, C = 01, G = 10, T = 11. The authors of this paper however decided to use a one base per bit code, A = 0, C = 0, G = 1, T = 1, which allows for many synonymous encodings to avoid sequences that are difficult to sequence such as long repeats.

Google Doodle

Mohammed Yahia reports in the House of Wisdom blog, this week Google featured a new doodle, celebrating the anniversary of Abu Raihan Al-Biruni, a Muslim scholar often regarded as one of the greatest scientists of the medieval Islamic period:

Al-Biruni, a Persian scientist who spent the first part of his life in modern-day Afghanistan, is credited with bringing Indian science to the Islamic world – often given the title of “founder of Indology”. Little is known of his early life. He even claims he never knew his father nor his family origins. He was engaged in science at an early age, publishing his first book on cartography when he was 22 years old. Like most scientists of the era, he was a polymath, excelling and writing about various topics from astrology and mathematics to geology and anthropology.

Learn more about Al-Biruni in Mohammed’s post. 


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