Trouble at CIHR continues

Looks like CIHR continues to have trouble with the Project Scheme Live Pilot. Applicants are waiting for results of the competition to release today, and by the sound of it there was an unintended early release for some applicants that included the names of their reviewers. The message from CIHR is below (emailed to applicants today):

ResearchNet funding decision release incident

This is to advise that at 21:30 on July 14, 2016, a system breakdown caused by a local power failure resulted in ResearchNet releasing funding decisions for the Project Competition prematurely. In addition reviewer names were accessible for a maximum of 49 applicants for 17 minutes. Corrective actions were immediately undertaken and the system was restored to normal operating status. Reviewer names can no longer be accessed. CIHR is in the process of advising each of the reviewers whose name could have been accessed.

At this time, competition results are being released as scheduled. CIHR sincerely regrets this situation and recognizes its significance given the importance of confidentiality in the peer review process. CIHR is currently assessing the technical cause of this incident with ResearchNet in order to ensure that it is not repeated. 

Canadian Institutes of Health Research

This is clearly a big issue for the integrity of the review process. Its good to hear it was caught early, but this is not an encouraging development for an already controversial process. The most recent developments have been covered by CBC and Science magazine.

NSERC-funded research open access policy

It looks like the earlier draft policy on open access for federal Tri-council funding in Canada has been made official. NSERC grants starting after May 1, 2015 will have to comply with the new policy. This seems similar to many other agencies, such as the NIH, which require access within 12 months of publication.

The “deposit elsewhere after publishing” model is usually referred to as “green” open access, and many journals now support this model after funding agencies have begun requiring it. This is usually a zero-cost option for the authors (which is a good thing.) “Gold” open access (where the authors pay a fee at the time of publication to allow immediate OA) costs grant money, and is not always an option when budgets are tight.

ACS journals allow users to deposit their work after 12 months in a repository, such as PubMedCentral, for NIH funded work. Presumably a similar policy will be developed for NSERC. RSC journals also allow OA archiving, as does Nature Publishing Group, Wiley, Elsevier, and others. Some of these (like Elsevier) are journal-specific, and may be worth reviewing before submitting a paper for review.

Open access repositories that NSERC funded chemists are likely to use include PubMedCentral, PubMedCentral Canada, and Institutional Repositories.

 

Posttranslational modifications – What are these things stuck to my protein?

If you took introductory biochemistry, you are probably familiar with the most common biopolymers: nucleic acids (DNA & RNA), proteins, and carbohydrates. The roles of the first two polymers are probably best encapsulated in what is known as the central dogma of molecular biology (coined by Prof. Crick).

Essentially, DNA stores the sequential coding information, it is transcribed into RNA which delivers specific fragments (as mRNA) which become translated into protein sequences. The proteins tend to be the functional molecules in the cell which catalyze chemical change or form essential structures in the cell (and generate the phenotype of the cell/organism). So what happens after translation (posttranslation, and the namesake of this blog)?

Posttranslational modifications (PTM) are chemical changes that happen to proteins after the coding sequence has been converted into a protein. By defenition, these changes are not encoded directly by genetic information. There are many examples, with glycosylation (attachment of a carbohydrate) and phosphorylation (attachment of a phosphate) being some of the more prevalent examples (here is an excellent review on the subject).

So, what do these modifications do? (The real answer is a long one – so I’ll just include some highlights.) A lot of these modifications change the function of the protein. As an example, some sulfotransferase enzymes are inactive as their primary sequence, but when the active site residues are modified (by an enzyme known as FGE) the enzyme becomes active. Some modifications actually control which proteins interact with each other, a mechanism that is essential in immune cell response (among many others.) PTM can also change the stability, shape, or flexibility of proteins.

One of the problems in this field is that PTM, since they aren’t directly encoded, aren’t easy to predict (i.e. things get messy). Think of it this way: if the genetic information stored in DNA is the blueprint of a house, PTM end up being the tweaks and changes that our builder might include that we didn’t specifically ask for (but might even be needed to make things work). This one feature, which leads to complexity and variability, is a large part of why we know a lot less about PTM than we do about, say, DNA. As a result, to study these modifications we have to go in and specifically see what modifications took place in a given cell or condition.

Open access publishing in Bio/Chemistry – Whatever happened to PLoS Chemistry?

I’ve been a fan of the open access (OA) movement for a while. However, I can’t say that I’ve voted with my feet: I typically publish in society/specialty journals that are not open access. Of course, some of these publishers now give you the option of paying them to make your paper OA, so they can argue that one can still publish in those venues and just pay to allow access to your work.

I’m not a fan of this model – having an essentially random sampling of papers does not make for a good presentation to the reader, nor does it address the idea that an open archive of research data and conclusions is a benefit to the community. I would argue that opting to pay OA charges at these closed journals is basically supplementing the journal’s advertising budget with your research grant. At the end of the day, if readers want full access they must get their libraries to pay for the rapidly growing cost of closed journal subscriptions.

Which brings me to the subject of this post: What are the best OA venues for chemists to publish their work right now? I’m specifically interested in “gold road” journals, those that make their content freely available immediately upon publication. Here’s the list I put together in an hour or two of searches, I was targeting Organic Chemistry, Chemical Biology, Biochemistry, and related fields. I doubt this is exhaustive, and I’d appreciate any suggestions from others. (Journals listed with current publication charge, and number of articles published in 2013):

Clearly PLoS One is the largest venue, Scientific reports seems to be growing (about a 3X increase from 2012-2013). I hadn’t realized until now that Molecules, Arkivoc, and the Bielstein journals were OA. Some of the ones low in the list may need some incubation time to reach critical mass. I ruled out some smaller journals if they were not indexed on Web of Science, PubMed, or SCOPUS. Any others that I’m missing?

There was once some talk of a PLoS Chemistry, but I can’t seem to find any indications that its happening. I don’t see many of these venues competing with premier society level journals without buy-in from leaders in the field. My impression is that this has allowed the PLoS brand to take off, with a few of those journals having become top-tier venues.

Its worth noting that archive servers are a mechanism for OA publishing. This is dominant in some field (but sadly lacking in Chemistry/Bio):

bioRxiv.org is the new kid on the block here, and it remains to be seen how readily preprint servers are become adopted in biomedical research.

On the scientific endeavor

I’ve been making an effort to include writings from prominent chemists to my personal reading list. My favourite source is the Profiles, Pathways, and Dreams series put out by the ACS (but now out of print.) These are autobiographical accounts of careers in chemistry, and often feature great snippets of stories about other famous chemists or bits of philosophy.

Here is a quote from the late Prof. R. Lemieux which is worth a read [for context, this quote follows a story about Johnson adding Lemieux to a publication after discovering that the two were investigating the same problem through discussion at a meeting]:

“This statement about Bill Johnson is not characteristic of many scientists, even perhaps of the majority. Especially since Sputnik, many job seekers have rendered the practice of science more of a trade than a profession. Unfortunately, many opportunists have risen above their level of competence and used every known “business” trick to stay involved. The most common ploy is a form of plagiarism based on misconstruing the contributions of others by making a vague reference to their work in a first paper, which thereafter is the only one quoted. It is remarkable that the need to survive can so condition the mentality of some scientists that they refuse to acknowledge that results presented at scientific conferences and in person or in private communication are, in fact, published (made public) results. A more serious threat to the orderly development of science is the evolution, through inbreeding, of editorial boards of prestigious journals, who do not realize that they are about the only ones who hold their publications in such high esteem. I mention these matters because I consider it best that young people contemplating a scientific career realize from the start that science is very much part of the real world and has in its ranks a full quota of stuffed shirts, flim-flam artists, opportunists, exploiters, and even full-fledged buccaneers. At the same time, young would-be scientists must realize that, to participate fully in this noble profession, they should feel free at all times to talk openly about their work. To my mind, the best part of a scientific career is to talk about what you have discovered when it is “hot,” which normally means prior to formal publication. I consider this a most precious freedom that must be defended at all times and with great vehemence if necessary.”

From – “Explorations with Sugars,” by R. U. Lemieux in Profiles, Pathways, and Dreams: Autobiographies of Eminent Chemists, American Chemical Society, Washington, DC, 1990, pg 41.

Although this series is out of print, many copies are floating around in used book shops. I use ABEbooks to dig these up, sometimes at pretty reasonable prices.