Why blogging is good (also for your thesis)

Sometimes I wonder if my blogging activity is harmful for the progress of my thesis. But, if we take into account that the topics I blog about are the same that are covered in my thesis, I think that not only it doesn't harm but it's actually doing me good:

      1. I get to read a lot of articles, not only about my research topic but also many others conceptually related to the whole area. This helps to acquire a broad perspective of where my project fits and helps developing an integrative frame of mind.

      2. I write reviews of recent articles as well as original essays. Doing so, my scientific writing skills improve, especially exercising scientific texts reading comprehension, ability to synthesize the main ideas (mine or from other people's papers) and the actual writing skills (scientific redaction, english grammar).

      3. Since the blog is information-rich, web searching tools (Google, for example) will bring people interested in what I write about, therefore I will gain a lot of feedback, both from specialists --who will correct me, if I'm wrong; giving me publicity among fellows of the field, and, in the end, increasing my contacts network-- as well as from aficionados of all levels --who will serve me to test my divulgative speech.

Allow me to spare a bit of modesty here: even my bosses agree that my writing skills are good and keep improving, which will become handy for articles and future project submissions.

However, it seems that I'm the only enthusiastic evo-blogger in my institute (Evo-bloggers in het IBL). And that's in spite of having our own blog server!

To be honest, I didn't know we did have one until I received a mail about the weblog of the 'Instituutsraad', and I guess that I'm not the only one. In fact, I still don't know how do they work (who can post and/or comment and how to) but I think it is definitely a good move for the Institute (only if all the sections would get to use them, and for more than a simple on-line blackboard).

And not only the departments as such, but the individuals themselves, should start using the new technologies. Not only is good for yourself (as I wrote above), but also for the whole community: you are helping to enrich the web with information, helping with the difussion of knowledge.

Quoting Rino Zandee, from the Theoretical Biology Section (and showing less and less modesty):

Er zouden meer AIO' s [en stafleden] het goede voorbeeld van Max moeten volgen.

A thorny parallelism

Featuring: the 'Three-spine' stickleback, Gasterosteus aculeatus

This small fish (barely a few inches long) lives in marine or fresh-water environments. They happen to be very common and, as it seems, easy to maintain in the lab (like most of the fish smaller than 10 cm). And there a number of research groups "lobbying" for stablishing it as a model system, especially for evo-devo studies.

What makes it be so especial? Something really curious: sea populations, like the japanese (JAMA) in the figure, have an "armour" in the posterior part of the body but fresh-water populations, like the Paxton Lake (PAXB) in the figure, don't.

(Alizarin-red tinction, staining bone elements; bar length is 1 cm, fish in real size.)

Don't you find something strange here? Fresh-water populations are isolated from each other, so, how is it possible that all of them have the same phenotype? Two explanations can be proposed: either the difference is due to an environmental cue in the development (what would make the delights of eco-devo'ers) or that there has been massive parallel evolution.

We know that the reason is the latter because the phenotype is inherited even if there is a change in the environment, but now we also know which gene is responsible for the parallelism. Pamela Colosimo and coworkers describe in a Science article the identification of the allele that causes the phenotypic differences. Yes, that's right, all (but one) the fresh-water populations with 'low' morph share the same allelic variant of the gene Ectodysplasin (eda) whereas sea-water populations present the normal variant (Eda). And in the article they not only describe the identification of the gene, no. They also make functional studies that effectively prove that the gene found is necessary and sufficient for triggering the phenotypic change.

This figure is particularly revealing. In the northern hemisphere map you can find the locations of the samples used for the phylogenetic analysis. Blue for 'low' morphs, red for 'complete' morphs. The tree in C is obtained using 193 SNP's (single nucleotide polymorphisms) found in 25 different loci randomly chosen; it should reveal the actual phylogenetic tree of the fish populations. The tree in B is obtained using the respective sequences for the Eda locus. The correlation between morph and allele is almost 100%, only one japanese population (NAKA) has the normal allele, showing an example of convergent evolution, rather than parallel.

What can we deduce from all this? First, that the eda allele has to be present in a very small frequency in the sea-water populations because all fresh-water populations have the same allele; such a high sequence identity is impossible to explain by independent mutations. That, and that 'something' in common must be in all fresh-water environments, not an epigenetic cue but a selective pressure that promotes the fixation of the low morph allele (otherwise, the fixation by genetic drift in all those populations would mean that the frequency of the allele in sea-water populations had to be huge, which is not the case; this is even more evident since there is at least a case of the same phenotype occuring via a different mutant genotype).

What do you think? Population genetics and developmental genetics, all together thanks to genomics. It seems true that this fish has everything!

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1. P. F. Colosimo et al. (2005), Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles Science 307:1928-1933
2. G. Gibson (2005), The Synthesis and Evolution of a Supermodel Science 307:1890-1891

From DNA to Diversity, 2nd edition

From DNA to Diversity
Molecular Genetics and the Evolution of Animal Design
Second Edition
By: Sean Carroll, Jennifer Grenier, and Scott Weatherbee



In this landmark work, the author team led by Dr. Sean Carroll presents the general principles of the genetic basis of morphological change through a synthesis of evolutionary biology with genetics and embryology. In this extensively revised second edition, the authors delve into the latest discoveries, incorporating new coverage of comparative genomics, molecular evolution of regulatory proteins and elements, and microevolution of animal development.

Free donations or in request of evaluation are accepted. ;-)

And I have barely finished reading the first ed (2001) that I bought last year. If I had known.... Do you think I will be able to give it back? I still have the ticket... XD

The tough life of a professor

If for some (most) of the Ph.D students their thesis are like carrying the Ring to Mordor, they can find some support knowing that professors are as stressed as we are.

OK, right you are; they earn as much as 4 times more salary. And they have permanent possitions. Yes, true, they seldom appear in the lab and even so they are authors in every paper.

Now I come to think about it, there's no support for us there. Suffering seems only starting with the thesis and the only comfort for bearing the load is that bosses are also f**k'd up. Bad of many, consolation of... students.

From the article in Mare I link above, I wish to comment the poll made among the professors of my university. It reflects that they devote only a 6% of their time to their Ph.D. students. Ahem. How many students has the average professor here? Let's say from 4 to 6. That would mean from 1 to 1.5% of their time per student. According to the official working schedule (38 hours per week), that is 1 and a half to 2 hours. According to the alleged real working schedule (60 h.p.w.), it would be in between 2 and a half and 3 hours. It seems a lot to me ;-)

By the way, if you get to the bottom of the article, it's worth reading Renata Fontana's opinion about life in Leiden and the Netherlands in general. XD