Archive for June, 2011

A Tree of Eukaryotes v1.3a

June 30, 2011 Leave a comment

On Skeptic Wonder, a science blog focussing on protist and evolution, whereas the actual scientist himself works on Arabidopsis.

In his latest post, he makes another attempt of making a tree of eukaryotic life (thus excluding bacteria and archea).

Categories: Interesting link

One Math Museum, Many Variables

June 30, 2011 Leave a comment

For everyone who finds mathematics incomprehensible, boring, pointless, or all of the above, Glen Whitney wants to prove you wrong.

He believes that tens of thousands of visitors will flock to his Museum of Mathematics, to open in Manhattan next year, and leave invigorated about geometry, numbers and many more mathematical notions.

“We want to expose the breadth and the beauty of mathematics,” said Mr. Whitney, a former math professor who parlayed his quantitative skills into a job at a Long Island hedge fund. He quit in late 2008 with connections to deep pockets and a quest to make math fun and cool.

Link to NY Times article.

Categories: Interesting link

Will The iPad Replace Paper Lab Notebooks? 7 Issues That Need to be Overcome

June 30, 2011 Leave a comment

Re-post of a recent blog-post on Bitesize Bio by Rory Mcneil.


In April 2010, just after the release of the iPAD, Jode Plank wrote an article for Bitesize Bio asking whether the iPAD will replace lab notebooks.  Fast forward a year and a bit, and I’d like to put my head above the parapet and answer the question:  Yes!  With the iPAD now a roaring success, Android tablets beginning to make a mark, and a Windows tablet in the offing, the clamour is growing among scientists to use the iPAD in the lab. IMHO, it’s only a matter of time before tablets, led by the iPAD, are playing a central role in the lab and, ultimately, replace paper lab notebooks.

But what will it take to make this happen?  Here are seven issues that need to be overcome:

1.  Price

Tablets are not cheap.  Who is going to pay for them?  The lab?  The institution?  Individuals in the lab?  Will tablets will come to be seen as an essential piece of personal lab equipment, i.e. like a computer, or a personal accessory, like a cell phone?  I would argue that, like a laptop or a netbook, they will be in an in between category: something that belongs to the individual, but is sometimes used in the lab.    Early adopters are already buying tablets (mostly iPADs) themselves and exploring how they can be used now and might be used in future with additional functionality, and in some cases PIs are finding funding to purchase tablets for all lab members.  But as tablets come to be seen as more and more essential, more labs and institutions will buy them for or supply them to scientists.  So a mixed funding model is likely to emerge, at least in the interim.

2.  ‘Spillage’

Comments like the following made in a comment to Jode’s article are often put forth as a reason that tablets are inappropriate in the lab environment and will never replace the trusty paper notebook:  “Acid burns, spills, burns and too many falls.  I doubt the iPAD would resist a normal lab use.”  What’s my view on that?  This is a transitional issue that will be overcome as usage grows.  If the demand is there, usable protective covers will be produced.  And let’s not forget that plenty of other portable electronic devices are already common in the lab; think barcode scanners, for example.

3.  Accessibility

One of the main reasons that people are reluctant to abandon paper notebooks for electronic lab notebooks is the convenience and utility of pen and paper — you don’t have to boot up a paper notebook, it’s always at hand.  The new generation of tablets, however, are always on and don’t need to be rebooted.  So that objection is quickly becoming historical.

4.  Writing

Another advantage of pen and paper is that you can jot down notes and make sketches. Tablets, however, now support direct input with a stylus.  So the inability to write on a screen is also quickly becoming historical.

5.  Acceptance

What if your PI is attached to paper lab notebooks and doesn’t like the idea of ‘going electronic’?  In the short term, that clearly is a major barrier to uptake of tablets in the lab.  But a growing number of PIs are not just accepting tablets in the lab, they are pushing their uptake.  As is the case with all new product categories, the curve of adoption needs to start with early adopters before it spills out into the mainstream.  But that is not a long term barrier, just a matter of time.

6.  Familiarity

An issue you don’t see that much discussion about is to me crucial.  This is that paper lab notebooks are so familiar, like a trusted friend and companion where your life, or your research life at least, is recorded.  The working equivalent of a personal diary or journal.  How could you possibly give that up?  Most scientists have opted not to do so when the alternative is using a software program that runs on a computer.  Yes there are some enthusiasts, many of them mac users, who have always viewed their laptops with the same devotion that scientists have for their paper notebooks.  But they are the exception, not the rule.  The iPAD has changed the game.  People have the same personal relationship with the iPAD they have with their cell phone.  They love it!  And I’m betting that that will be a key factor in enabling the iPAD to do what electronic lab notebooks have failed to do:  get scientists to transition away from paper lab notebooks.

7.  Notetaking and Sharing

So that’s it then, the pieces are in place for the transition to gather pace?  Not quite.  There is still one crucial missing piece in the puzzle.  That’s because when people look at transitioning from paper to electronic they actually want to do more than they could in a paper notebook.  They expect to be able to take full advantage of the power of the web in organizing, sharing and archiving their data.  That’s true of individuals, and it’s even more true of labs looking at electronic solutions.

So the missing piece in the puzzle is software that allows easy entry and manipulation of experimental and sample data, and controlled sharing of that data, in a way that fits snugly into existing workflows and post-research writing up and publication of results.  I’m predicting that the advent of software with these characteristics on tablets will be the trigger that pushes tablets into mainstream lab use.

What do you think?

Link to original post with some interesting comments at the bottom.

Categories: Interesting link

Panda’s are more diverse then Caucasian humans

June 30, 2011 1 comment

The survival of species is often linked to both population size and genetic diversity. With the latter we mean, that the more variation is present in a population, the more cards that species can bring to the table for selection. The graph above is taken from the recent publication of the Tasmanian devil‘s (Sarcophilus harrisii) genome in PNAS. As the name suggests, the Tasmanian devil can only be found on the island discovered by Abel Tasman. In the last several years, the number of Tasmanian devils has been in sharp decline, due to the a transmittable virus that causes facial cancer and ultimately death. In an attempt to divert the Tasmanian devil from it’s cousin’s faith, the extinction of the Tasmanian tiger, the genetic diversity of various Tasmanian devils was assessed. Rather then just relying on a rather expensive nuclear genome sequencing approach, the researchers decided to look at mitochondrial DNA. And that is what the figure above shows, the average number of mitochondrial SNPs between individuals of the same species. The bar colors also add information, namely, red = endangered species, blue = just fine (for now), and black = extinct. As for the mammoth and Tasmanian tiger mitochondia, they used museum samples. A similar approach was used for the Tasmanian devil’s mitochondria. When we compare the European human to the critically endangered panda bear, it appears that the vegetarian bear has a more genetically diverse mitochondrial genome then your average corporate businessman/CEO.

Link to the original paper.


Categories: Interesting link

Post(-PhD | -doc)

June 29, 2011 Leave a comment

Some of you are almost done with their PhD and have started to look for a life after your PhD. Many many options await you and the most obvious one is of course a postdoc. But how do you find a good postdoc position and do you even want to do a postdoc to begin with. Below are the first few paragraphs of a great piece from the Science Careers website (part of Science magazine).


Whether you’ve just started graduate school, are halfway through, or are finishing your Ph.D., it’s never too soon to start thinking about the next step. For many Ph.D. scientists, the “next step” is a postdoc.

A postdoc is nearly always required for tenure-track faculty positions, especially for positions in research. But here’s a shocker for those of you who haven’t peered out of the windows of the ivory tower. Only a small minority of science Ph.D.s ever achieve a tenure-track position. A recent Federation of American Societies for Experimental Biology study showed that in 2001 only 14.1% of biomedical scientists surveyed 5 to 6 years post-Ph.D. had tenure-track faculty positions. That’s down from 34% 20 years earlier. Although the statistics don’t address this, it’s safe to say that a relatively small fraction of the remaining 85.9% will ever get a tenure-track position. Sure, the percentages vary from field to field but not by much. Tenure-track professorships are rare no matter what kind of science you do. So if it’s time to start looking for a postdoc, it’s also time to take a good, hard look at your prospects and your long-term plans.

What are the options? They are too numerous to mention. That’s the problem with so-called alternative careers: More people with Ph.D.s work in these careers than in traditional careers, but they’re so diverse that they’re difficult to categorize. Some Ph.D. (and M.D.) scientists go on to work in regulatory affairs. Some choose science policy. Others become editors. Still others become outstanding schoolteachers. Others choose industrial research–for which a postdoc is not a bad idea but may not be essential. (Of three recent hires into drug-development staff positions at one “big pharma,” two were hired straight from their organic chemistry Ph.D.s; only one had any postdoc experience.)

Scientists with advanced degrees do all sorts of work. They typically find the transitions into their new careers easy. And they almost always find the new work very rewarding. Yes, folks, there is intelligent life outside the academy, not to mention more family-friendly policies and better working conditions. So if you have doubts about your evolving bench career, now is a very good time for some serious introspection. Pay a visit to your institution’s career office. And check out Next Wave’s Index of Monthly Feature Indexes. With hundreds of essays about and by scientists in dozens of careers, this is undeniably the best resource available for scientists considering their away-from-the-bench options.

Still with us? Still want to know how to go about finding a postdoc? Then let’s get started.

Click here to read the complete article.

Categories: Uncategorized

UC Entrepreneurship Academy, September 12-16

June 29, 2011 Leave a comment

A message from the Designated Emphasis in Biotechnology (DEB):

We’d love to have you participate in the upcoming UC Entrepreneurship Academy, September 12-16, 2011. This is a unique opportunity (we are one of the few universities to offer this program) for science and engineering researchers to spend a week learning business development and how to evaluate their ideas and research for potential market and business opportunities.

Apply online by August 22 but the earlier you apply, the earlier we can accept you!

Apply online >>

Hosted by the Center for Entrepreneurship, the one-week intensive will provide you with:

  • a five day intensive on exploring the market opportunities surrounding your ideas and your research
  • daily seminars and interactive sessions taught by leading venture capitalists, angel investors, and entrepreneurs
  • the tools to communicate the broader potential of your research
  • a networking dinner with industry sponsors, entrepreneurs, venture capitalists and angel investors,
  • evening mentoring sessions with industry executives and investors

“I am where I am today because of the amazing, life-changing experience as a Business Development Fellow.”
Riccardo LoCascio, DEB Alum, Kauffman Postdoctoral Fellow, Business Development Fellow 2006

Nicole Starsinic
Associate Director
UC Davis Center for Entrepreneurship

Categories: Recent News

Fwd: It’s impact time

June 29, 2011 Leave a comment

Re-post from report from Nature NewsBlog, writen by Richard van Noorden.

Once a year, information company Thomson Reuters publishes updates to a measure of popularity that every science journal displays in lights: its ‘impact factor’. This event, which happened again yesterday, always produces a slightly embarrassed buzz among science journal editors. They appreciate the absurdity that a journal’s impact (a fuzzy, multi-dimensional concept) should be reported publicly by a single number; and the bias that some journals must score more highly because the communities they serve tend to cite each other more often (citations being the key measure on which the impact factor is based). And you won’t find any thinking person who doesn’t condemn how the impact factor has been abused for wider evils – such as judging the quality of scientists or research articles by the impact factor of the journals where they are published. (This, as one bibliometrician put it in a Nature special issue on metrics, is a ‘mortal sin’).

In fact, abuses of the impact factor have been roundly criticized by all. For criticisms from Nature, see ‘Not-so-deep impact’, a still-relevant 2005 editorial that explains how research assessment “rests too heavily on the inflated status of the impact factor”. Or, for an up-to-the-minute reflection after yesterday’s updated figures, this blog from Nature Materials editor Joerg Heber. Thomson-Reuters also explain how the impact factor should be used. Many researchers are now looking at other ways to judge scientists and research papers.

But the impact factor abides, and journal editors across the world have been checking to see how they have moved in the impact rankings, or where new journals are placed. (You can follow their buzz on twitter, and for one newbie’s take, Nature Chemistry have blogged at The Sceptical Chymist about the details of their first impact factor). To that end, here’s a ladder of this year’s top 20 and their movements from last year. Reviews journals (which don’t publish original research) are left un-named; the CA-A Cancer Journal for Clinicians is off the top of the charts at 87.9. Data from Thomson Reuters Journal Citation Reports.

Link to original article.

Categories: Interesting link