[Coral-List] Re: Coral model for functional genomics

Robert W. Buddemeier buddrw at kgs.ku.edu
Fri Jan 6 17:40:32 EST 2006


 From waaaaay outside the genetics/genomics communities, it sounds to me 
like a key question might be whether the ideal candidate would be a 
versatile, stress-tolerant and well/broadly adapted species, or one that 
would hit the panic button, try hard, and die quickly whenever something 
went wrong.  I could envision arguments either way -- if the former, 
then P. lobata would be hard to beat, but if the latter, maybe not.

On other counts, a couple of sociopolitical observations.
First, there is (in my opinion) never any such thing as consensus in the 
coral reef community.  Especially in a forum of the self-selected, those 
with strong but unsupported opinions will back off in the face of good 
arguments (but not change their minds), and/or really knowledgable 
people will not 'waste their time' contesting the loud and persistent.  
Either way you wind up with an apparent agreement by default, with some 
irritated people on the other side primed to slap back when they get a 

Second, what to do about it (assuming that you are on the side of the 
angels)?  If the negative reviewers seem to be be people trying to 
feather their own nests by advancing their pets over all comers, it 
should be possible to make some well-educated guesses about who they are 
and list them in the "possible reviewers to be excluded" section.  This 
is legitimate, but should not be undertaken thoughtlessly.  First, I 
would suggest a heart-to-heart talk with the program officer.  Would a 
replay go back before the same panel?  Would he/she necessarily re-use 
some of the same reviewers for a resubmission?  It might be that if you 
lay out what you see as the issues clearly and objectively, he/she would 
fold that into the next review selection process, or make some 
observations that would help you deal with the issues in your rewrite.  
And, if you have a program officer who knowingly sends your proposal to 
hostile (as opposed to rigorous) reviewers, it's a signal to stop 
wasting your time there. If you do go back in to the same program, it's 
important to document responses to the previous reviews; 
"clarifications" are preferable, but it sounds like you might have to do 
some flat-out rebuttal -- if so, be polite but very very clear.

Personally, I still like P. lobata -- but the identity thing might be an 
issue -- I think it grades imperceptibly into P. lutea over their mutual 
ranges, and I don't know if anyone has attacked the question of 1 vs 2 
spp and how to tell (in addition to not being a genomist I'm also not a 
taxonomist -- easier to have opinions that way).

Good luck.  It sounds interesting and important enough to persist in 
trying to do something, even if that takes compromising or fighting.

Bob Buddemeier

Mikhail Matz wrote:

> The major argument against Porites that still remains is the notable 
> absense of any genomic resourses for this coral, whereas there are 
> already some ESTs for others  - Acropora palmata (4017), Montastraea 
> faveolata (2156) and Acropora millepora (promised to be made available 
> soon  from David Miller's lab). Also, there are already some 
> microarrays developed for A. millepora.  Those corals have a 
> head-start and seem to be favorites, so why betting on a dark horse?..
> The arguments in favor of Porites which I recall from the previous 
> discussion are:
> 1. Porites as a genus is an important reef builder both in Caribbean 
> and Indo-Pacific
> 2. It is not considered particularly endangered anywhere, so there is 
> minimal concern about field sampling (quite unlike A. palmata, for 
> example)
> 3. grows rapidly
> 4. easy to handle and keep in the lab
> 5. transmits its symbionts vertically, so there must be minimal 
> genetic and gene expression variation due to zooxanthellae (I think 
> this one is really important for genomics)
> 6. is easier for biochemistry and molecular work that Acropora and 
> Monstastrea (according to Craig Downs).
> Another concern that I received is that since Porites lobata is not a 
> branching type it will be difficult to separate pieces (nubbins) for 
> experiments; but here I was simply unfortunate to encounter a reviewer 
> who did not try it with Porites and does not know how easy it is to 
> saw its soft skeleton into neat chunks of any size required (as well 
> as to saw off a larger piece in the field, for that matter). Let's 
> disregard this one.
> Misha
> Michel Pichon wrote:
>> Misha,
>>  Before one can go any further, if would be useful  (indeed 
>> necessary)  to know on what grounds/ Porites lobata/ is deemed 
>> unsuitable for coral genomics. Have you got such a piece of 
>> information  ?
>>  Cheers,
>>  Michel
>> -- 
>>         Professor Michel PICHON, Directeur d'Etudes
>>      Laboratoire des Ecosystemes aquatiques tropicaux & mediterraneens
>>        Ecole Pratique des Hautes Etudes
>>         Universite de Perpignan
>> 66860 PERPIGNAN Cedex
>>    Ph: 33 (0)4 68 66 21 94  Fax  : 33 (0)4 68 50 36 86
>>      email : pichon at univ-perp.fr   
>> -- 
>> Ce message a été vérifié par *MailScanner* 
>> <http://www.mailscanner.info/>
>> pour des virus ou des polluriels et rien de
>> suspect n'a été trouvé.
>> CRI Université de Perpignan 

Dr. Robert W. Buddemeier
Kansas Geological Survey
University of Kansas
1930 Constant Avenue
Lawrence, KS 66047 USA
e-mail: buddrw at ku.edu
ph (1) (785) 864-2112
fax (1) (785) 864-5317 

More information about the Coral-List mailing list