Saturday, July 29, 2017

How many manuscripts to review?

Question from a colleague about how many manuscripts to review:

I saw your note about being awash with review requests on Twitter. 

I'm just curious what your opinion is on the number of papers we should agree to review per month; i.e. What is professionally responsible?

I still learning the rules here on when is OK to say no to things.

My fairly off-the-cuff response (although it is something I've thought about over the years): 

Well, I don’t think there is any rule at all against saying ’no’; especially to review a paper. 
Before agreeing to review, I must:

1. Be very interested to read the manuscript
2. Confident I am qualified to critique at least 1 major aspect of the paper
3. Not be reviewing more than 2 other manuscripts already at the time (unless REALLY interested in it)
4. Feel I have a reasonable chance to be able to complete it in the timeframe they request (ie not too swamped with other stuff at the time). 

I suppose my rule of thumb-calculus is that every paper requires 2-3 reviewers (although more if submitted more than once), so to break even, we’d need to review 2-3 manuscripts for every publication — but don’t forget to divide by the number of co-authors of all your publications. So, for me, my papers have at least 2-3 co-authors almost always. Therefore, reviewing 1 paper for every publication feels fair to me. I’ve never discussed this with anyone before, so there could be some flaws in my logic.

But honestly, I don’t think about the quota, I think about #1-4. I get enough requests that agreeing to the interesting ones leads to enough (based on my rule-of-thumb calculus; which others may disagree with, of course).

If declining, I try to do so quickly, and recommend someone else.  

Also, I sometimes ask grad students to review papers that I”m asked to do. If they are new at it, I read their review, and let the editor know about that. It is good training for them, and can save a little time for me doing the full review. A few journals now have a formal process for that, I think it might be common in molecular biology.

Tuesday, February 14, 2017

Exaptation vs Neo-functionalization vs Co-option

I just reviewed a paper that equated Neo-functionaliztion, exaptation, and co-option - using the terms interchangeably. My first instinct was that this was a problem, but it took me a while to work through my thoughts on it; including influential twitter discussion with Vincent Lynch. I thought I would put my thoughts here, in case they are useful or objectionable to anyone.

In my understanding of the terms, “Neo-functionalization” implies that a *duplicated* structure (usually a gene, but not always) gains a new function. As Vinny puts it:

"b/c neofunc is a process in which a homologous character maintains ancestral function"

Exaptation” implies no such duplication. A classic example is feathers - their original function was probably insulation, and their exapted function is flight. Here, there is no substantive change in the exapted structure (or at least that is not the point) - instead, exaptation is a change in function at one level of biological organization.  The point is that selection can fix a structure with one function that is later exapted for another function.

Co-option is a bit similar to both neo-functionalization and exaptation; but I think there are subtle differences. Co-option has become a dominant term in gene expression, and I think even in other contexts (unlike co-option and neo-functionalization) usually examines two levels of structural organization at once. For example, co-option of a gene is inferred when we discover expression in a new place (or perhaps time). Co-option is a copying of expression, but not a duplication of the gene’s structure. Expression is an element of function, but not really the same as the organismal functions usually in play in exaptation. I think people use co-option similarly in morphology where a structure is moved to a new place to become part of another structure that was already there.

Unfortunately, co-option is a very vague and diffuse term in general, and I think is used in ways more extensively than I suggested in the previous paragraph.

For one thing, co-option is sometimes used to describe a duplicated element (see Ganfornina et al 1999 for some examples). For another thing, co-option refers to both pattern and process (mentioned in Oakley, 2007). It is used both to describe a pattern where a gene seems to be expressed in unrelated places, and to describe the mechanism that causes such gene expression. It's like the early days of "species", where species meant both the elements and the process.

Ganfornina M.D., S├ínchez D. 1999. Generation of evolutionary novelty by functional shift. Bioessays. 21:432–439.

Oakley T.H. 2007. A review of Gene Sharing and Evolution: The Diversity of Protein Functions, by Joram Piatigorsky. Evol. Dev. 9:514–516.