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Chocolate is the perfect gift for your molecular biologist mother

 :: Posted by American Biotechnologist on 05-08-2011

Chocolates are probably one of the most common gift ideas on Mother’s Day. While it is great to give a unique gift, one will never go wrong with chocolate.

In addition to its great taste, chocolate has been lauded by the “experts” as having fantastic health benefits.

In honor of Mother’s Day, here’s a great post from The Scientist which I thought would be interesting for all chocolate lovers. Andy McShea is the COO of the Theo Chocolate factory and a former molecular biologist at Harvard University. His research focuses on understanding the characteristics of perfect chocolate at the molecular level and his motto is “better science through chocolate”.

According to The Scientist, McShea had no prior chocolate experience before joining Theo and it was his credentials in assay development that got him the job. I’m a molecular biologist with lots of chocolate (eating) experience….where do I apply?

Check out the Dr. Chocolate for some yummy reading.

Rethinking peer reviewed science

 :: Posted by American Biotechnologist on 04-28-2011

I just read a thought-provoking and controversial article in Nature News by Hidde Ploegh, a professor of biology at the Whitehead Institute of the Massachusetts Institute of Technology in Cambridge.

In “End the wasteful tyranny of reviewer experiments”, Dr. Ploegh argues that the current peer-review process practiced at many high-impact journals is plagued by unnecessary requests for authors to perform wasteful follow up experiments that negilgently delay otherwise justified publication.

Ploegh suggests that reviewer requests are motivated by the attitude that

look, I’ve read it, I can be as critical as the next dude and ask for something that’s not yet in the manuscript

and the feeling that since the reviewers themselves have been subjected to such unreasonable demands, they are simply dishing out their share of ‘what goes around comes around’.

In order to correct this problem, Ploegh suggests that

  1. journals start employing editors who are subject matter experts capable of over-ruling reviewers when necessary
  2. reviewers consider the extra costs that will be incurred by their request for additional experiments
  3. editors decision to go forward with a publication be based on readership demand with reviewer input limited to analyzing the logic or execution of the study

I believe that these suggestions are a welcome breath of fresh air to the young scientific community and will go a long way to speeding up the pace of progress and innovation in academic science.

What are your thoughts?

Making the most of negative results

 :: Posted by American Biotechnologist on 03-02-2011

How often have we lamented that obtaining negative results has stymied productivity and gotten in the way of career progression? After all, no reputable journal will accept negative results, and without publications we may as well throw our science careers out the window.

The problem is that negative results ARE results nonetheless. While they may not be as sexy as positive data, negative data are a consequence of hard work and should be considered just as important as positive data.

One reason for this observed bias can likely be attributed to the early stages of scientific methodology. All scientific experiments start out with background research that leads to a hypothesis. The overwhelming number of scientists hypothesize that treatment A will result in consequence B happening to subject C. Very few scientists will hypothesize that treatment A will not result in any changes to subject C. Who wants to do THAT kind of experiment.

What we often fail to remember is that the hypothesis is really just an educated guess which must honestly be proven to be either correct or incorrect. Unfortunately, only hypotheses that are proven correct end up making it past the cutting room floor of the high-impact journals which is akin to rewarding good guessing over hard work.

In an effort to recognize the important contribution of hard-working scientists who’s experiments have concluded with negative results, an online database called Figshare has been created as a global repository for all the unpublished negative data coming out of hard-working science labs.

The idea is to have scientists publish ALL their negative data in the database. The database is open access and therefore any information stored there can be used freely by other scientists as long as it is properly attributed.

At the very least, such a system helps prevent other scientists from wasting untold amounts of money repeating the same experiment only to eventually come up with similar negative results. Whats-more, should your data eventually be published by another researcher, you will receive a citation and perhaps even an opportunity for collaboration.

As is written on the figshare website:

Unless we as scientists publish all of our data, we will never achieve access to the sum of all scientific knowledge.

Although Figshare cannot replace the thrill of publishing in a top-tiered scientific journal, it should help take away the sting of negative results and lead to an appreciation for all scientific data both positive and negative.

Friendship: It’s all in the genes

 :: Posted by American Biotechnologist on 01-20-2011

NewScientist reported this week on a University of California research study that analyzed the genes of 3,000 pairs of friends looking for genetic differences or similarities that might indicate a genetic predisposition for certain types of friendships.

The study found that close friends share similarities in the DRD2 gene and are less likely to share similarities in the CYP2A6 gene.

Here’s how the story was reported on ABC News:

Journal reference: Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1011687108

Standing Room Only-The Effects of Protein Crowding

 :: Posted by American Biotechnologist on 01-12-2011

One of the biggest challenges for any scientist is to ensure that their experimental model of choice actually mimics natural biological circumstances. While it is one thing to conduct research in a test tube or cell culture dish it is quite another to translate those results into human biology. It is therefore imperative for scientists to choose a research model that most closely resembles its scaled up reality.

Over the past decade, the field of proteomics has experienced exponential growth. With the rise of technologies such as protein crystallography, protein arrays and surface plasmon resonance more information can be gathered on a proteomic-wide scale than ever before. Nonetheless, most proteomic experiments are conducted in-vitro often after protein extraction and clean-up techniques in an environment that is far removed from their cellular milieu. Under such circumstances, one must wonder how biologically relevant results techniques such as protein-protein interaction actually are. In fact, in a recent story published in Chemical and Engineering News (C&EN), staff writer Celia Arnaud describes the often overlooked effect of protein crowding on proteins function and stability.

According to the article, when proteins are packed into a cell (as is often the case under natural biological conditions), excluded-volume effects occur, which means that many things happen simply because molecules occupy space. This circumstance is often compensated on the bench with the addition of chemical agents such as Ficoll, however this is not an ideal way to replicate protein crowding and will not necessarily replicate biochemical conditions found in the cell.

According to Martin Gruebele, a chemist at the University of Illinois, Urbana-Champaign, “Eventually, people will expect that a complete protein data set includes in-cell or crowded studies of various kinds, in addition to the current aqueous buffer data. This is clearly where things will shift in the next five to 10 years.”

For more on the importance of protein crowding see Close Quarters