Field of Science

Long time no posting.  Sorry.  I've been working on our new CIHR grant proposal, but for unknown reasons not doing this on the blog.

But I have a point I need to make in the proposal, and to a colleague who's just generously critiqued a draft for us.  I'm having a hard time finding a way to explain what I mean, so, of course, I'll try doing it here.

As you can see from the Specific Aims above, our goal isn't just to investigate the factors affecting transformation, but to incorporate these factors into a predictive model (initially two separate sub-models), and to test this model's predictions against the real transformation seen in a laboratory version of the respiratory tract environment.  Our hope is that this model or its more sophisticated successors can be used to predict clinically important genetic exchange, leading to modifications in drug and vaccine design that minimize the opportunities for specific exchange events.

Proposals typically describe how the results could be used to improve medical treatments, but for basic science this is usually just a 'somebody, someday' hope.  Because the researchers won't themselves be applying their results, there's no incentive to make sure they're in a useable form.  For genetic exchange the outcome has been that, although we have lots of descriptive information about the mechanisms and regulation, and lots of surveys of its significance in natural populations, none of the information can be combined into useful predictions.

We however propose to integrate data collection, prediction development, and prediction testing into one coordinated research program.  This means that the data we generate about uptake and recombination biases has to be in a form that can be incorporated into computer programs that predict uptake and recombination from input genome sequences.  And it means that the predictions of these programs will be tested against reality

Typical journal spam...

Dear Dr. Rosemary,

Greetings from Journal of Fungal Genomics & Biology.

Based on your eminent contribution in the field of fungal genomics and biology, we are glad to invite you to submit Research/Review article for our prestigious Journal, Fungal Genomics & Biology. Your contribution is of great importance for us and it will help our journal to establish its high standards.

You can submit manuscript at
 (OR) by e-mail to

You can submit your valuable articles by mid of September, 2012 so that we can publish in the coming issue (or) as per your interest at your earliest convenience.

Please do not hesitate to contact us for any queries.

Awaiting for your positive response.

With Regards,
XXXXXX (name redacted to protect the guilty)
Editorial office

And no, I've never published ANYTHING on fungal biology.

I tried to get an image of the journal cover, but all the Omics Group page links are broken:

Should women ask for more, or are we punished for being 'greedy'?

A short paper in the Lancet (Bedi et al) compares the sizes of grants awarded to women and to men by the Wellcome Trust, from 2000 to 2008.  Male applicants get, on average, £44,735 more than women.  Women's grants must also be shorter, because the disparity is even more dramatic when funding is calculated per year.

Because women and men have similar success rates for these grants, and the amounts awarded are usually the amounts requested, the authors think the discrepancy is because 'women are systematically less ambitious in the amounts of funding requested in their grant applications.' 

They recommend that mentors 'should ensure that women are as ambitious as men in their outlook, and in their grant proposals'.  But they don't consider the alternative explanation, that women who ask for as much as men do are seen as greedy and undeserving, while women with modest ambitions are rewarded. This might be checked by comparing the the requested amount with the probability of being funded, for men and for women.

Their second recommendation, that 'men should be encouraged to be economical when costing such applications', is of course absurd.

The model that's the goal of our CIHR proposal

In our new CIHR proposal we're going to propose to gather the experimental information needed to make a predictive model of genetic exchange by transformation in the respiratory tract.  I've been trying to lay out the Research Plan by describing the things we want to find out.  But I realized last night that it might be better to start by describing the predictive model we want to generate, and let its requirements determine what we propose to find out.

That was when I also realized that I have no idea what form the model should take!  That is, what would be the input information, and what would be the output.  Let's see if I can do better this morning.

Of course, we don't need to have just one model.  Several different models might be appropriate, to address different questions.  For example, given two H. influenzae genome sequences, what are the relative probabilities of different recombination events?  Of course we couldn't evaluate ALL the possible events, but we could tag the most likely and least likely.  So we'd want to be able to scan the genome sequences of potential donors and flag the segments most likely and least likely to be taken up by competent cells.  And we'd want to scan the genome sequences of potential recipients, flagging the segments most likely and least likely to undergo homologous recombination.

We could do this a different way.  For each potential donor genome, we would evaluate the probability that a given segment would be taken up as a DNA fragment by competent cells.  Then, for the other genome, we'd calculate the probabilities that different parts of this fragment would be recombined into the recipient genome.

Or we could evaluate a pool of DNA sequences with different proportions from different strains or species, again tagging the segments most likely to be taken up, and the effects of changing the proportions from different sources.  And we could consider a population of possible recipients, consisting of strains with different levels of competence and present in different proportions.

OK, I think the post-doc and I are going to spend some time today working on this at the whiteboards in the hall.

A slick puff piece on my research for only £1960!

I just got an email from someone named Simon Jones, offering to publish an article about my research in a publication called International Innovations.  Here's their website.  They appear to be an online publisher of articles about advances in health care research.  Oops, no that was just their health care branch.  They have other branches, for Energy, Environment, Nanomaterials etc.  You can see the whole list here.  They claim to be 'The Leading Global Dissemination Resource'.  (Red text is my highlighting.)

They describe what they publish as 'open access journals', but they're certainly not peer reviewed.  Instead they're collections of puff pieces, intended to make the researcher look good.

The first part of the email was followed by a long collection of lists, of researchers they have written about, topics they've covered, institutions and countries that subscribe, etc.  Far too long to include here.  And after that comes the details:

So the deal is:  For a fee of £1960 (about $3000) they prepare a 3-page glossy article about how great my research is, based on 2-3 hr of input from me.  They apparently do the writing and prepare the figures, and they publish it in their slick online magazine, and perhaps in a glossy paper edition too.  I own the rights, so I can then splash this article around in any way I like - send it to my Dean, post it on my web page, print a glossy brochure to hand out...

Given the copyright promise, it's a bit surprising to see this statement in each issue: 
Copyright reproduction in whole or part by any means without written permission of the publisher is strictly forbidden.  The publisher accepts no responsibility for errors, omissions, or the consequences thereof.  The opinions expressed in International Innovation are those of the individual and not endorsed by Research Media.  Copyright Research Media.
It's also odd that they claim copyright but disclaim any responsibility for the content.

And maybe it's not surprising that the published material nowhere indicates that the researchers being profiled paid for their profiles.

And an application to Cystic Fibrosis Canada

(I wrote this yesterday but forgot to click 'Publish'.)

I've been spending an inordinate amount of time preparing the 'Notification of Intent to Apply for a Discovery Grant' for NSERC, and I submitted that this morning.  I was about to get back to writing the CIHR proposal, but then I remembered that Cystic Fibrosis Canada also makes research grants, and since the CIHR proposal is so strongly focused on respiratory infections I thought I should check these out.

Well, they make about 20 grants per year (about 30% of these are new, success rate for new applications about 25%).  The application deadline is Oct. 3, which is 2 weeks after the CIHR deadline and a month before the NSERC deadline, so that's feasible, especially as what I'd send them would be a modified (reduced?) version of the CIHR proposal.

 They also have an Intent to Apply notification process, and I'd need to email the form tomorrow, August 1.   Our chances probably aren't great, as the proposal isn't close to therapy, but it's worth a try.