27 February 2008

A victim of its own success

The Encyclopedia of Life page, as I expected, was under huge server load yesterday. The webmasters have gone back to its old preview pages rather than its more advanced first release that I posted about yesterday.

Hopefully, it will be back soon so that we can really start to see what the website can do.

26 February 2008

Encyclopedia of Life

The Encyclopedia of Life has finally moved past the preview stage.

It’s been very slow today, the server no doubt reeling under the load of people who have been eagerly awaiting it. But it’s a treat if you can get to it.

This particular database sprang from a TED prize for biologist E.O. Wilson, shown below.

This kind of project has been on the minds of a lot of people for a long time. There are various taxonomic databases out there. The Tree of Life was probably the first major one, and Wikispecies is another. And those projects have been very valuable, but I think it's fair to say they haven't revolutionized the science the way that GenBank did for DNA or that Wikipedia did for general knowledge.

Hopefully, Encyclopedia of Life can be that transformative resource.

No entry for Marmorkrebs – yet! – but there are plenty of crustaceans in the database already. Check out the crayfish page.

25 February 2008

Harvard goes open access

Science magazine is reporting that Harvard University has developed an "Open access" policy.

The resolution authorizes Harvard to place a faculty member's work in a repository that will be available to all at no cost. The researcher would retain the copyright, as in the past, but the university would have a license to release it. Papers would be posted on the Internet upon receipt or following a requested delay. Any author may choose not to participate but would need a waiver from the dean in order to opt out of the system.

I recently wrote about some issues surrounding open access here.

As if to make the point for me, the Science article is locked behind password protection for subscribers.

19 February 2008

Pic of the Moment: 19 February 2008

Marmorkrebs embryo
A Marmorkrebs embryo stained with fluorescent nuclear dye, about half-way through development. From Seitz and colleagues (2005).

12 February 2008

Ideas that spread and research publishing

The rationale for this website was directly inspired by this TED talk by Seth Godin. Early in the talk, Seth presents a simple mantra:

Ideas that spread, win.

I created Marmorkrebs.org to spread an idea: Marmorkrebs are an exciting and fascinating organism for research.

The jury is still out on whether I will win.

But as I've been compiling all the abstracts to research articles, I've noticed that all of them are protected by journal publishers in one way or another. Some are more liberal than others. The Journal of Experimental Biology, for instance, makes everything available to everyone for free after one year.

I support intellectual property rights. For that reason, I only post abstracts of research papers here. I have no intention of archiving research papers that publishers normally protect behind passwords and subscriptions. If those articles are freely and publicly available, that would be another matter; I would archive those. But currently, none are.

It's important to ask what the benefits of limiting information are. For instance, publishing in journals that have a strong reputation can help to establish the credibility of information. Plus, given that many researchers read more abstracts of papers than entire papers, it may not matter if the main text of a research paper is password protected online if the abstract summarizing the most important points can be read freely. There are many books that I know a lot about -- even though I have never read them! -- because I've read so many reviews of them.

It's also encouraging that some journals, which normally protect their research papers and charge fees to get them, are starting to offer authors a choice to allow their papers to be open access. For a fee, naturally.

Issues like this are why you can find a Creative Commons license on this page. I wanted to state specifically that people are free to spread the ideas contained in this blog, provided people follow the scholarly practice of attribution.

These issues of intellectual property are key to scientific communities, particularly young ones like this little Marmorkrebs community. I hope that next time someone has a Marmorkrebs paper to publish, they think about how well they are spreading their ideas.

05 February 2008

Vogt and colleagues, 2008

The Journal of Experimental BiologyVogt G, Huber M, Thiemann M, van den Boogaart G, Schmitz OJ & Schubart CD. 2008. Production of different phenotypes from the same genotype in the same environment by developmental variation. The Journal of Experimental Biology 211(4): 510-523. http://dx.doi.org/10.1242/jeb.008755


The phenotype of an organism is determined by the genes, the environment and stochastic developmental events. Although recognized as a basic biological principle influencing life history, susceptibility to diseases, and probably evolution, developmental variation (DV) has been only poorly investigated due to the lack of a suitable model organism. This obstacle could be overcome by using the recently detected, robust and highly fecund parthenogenetic marbled crayfish as an experimental animal. Batch-mates of this clonal crayfish, which were shown to be isogenic by analysis of nuclear microsatellite loci, exhibited surprisingly broad ranges of variation in coloration, growth, life-span, reproduction, behaviour and number of sense organs, even when reared under identical conditions. Maximal variation was observed for the marmorated coloration, the pattern of which was unique in each of the several hundred individuals examined. Variation among identically raised batch-mates was also found with respect to fluctuating asymmetry, a traditional indicator of the epigenetic part of the phenotype, and global DNA methylation, an overall molecular marker of an animal's epigenetic state. Developmental variation was produced in all life stages, probably by reaction–diffusion-like patterning mechanisms in early development and non-linear, self-reinforcing circuitries involving behaviour and metabolism in later stages. Our data indicate that, despite being raised in the same environment, individual genotypes can map to numerous phenotypes via DV, thus generating variability among clone-mates and individuality in a parthenogenetic species. Our results further show that DV, an apparently ubiquitous phenomenon in animals and plants, can introduce components of randomness into life histories, modifying individual fitness and population dynamics. Possible perspectives of DV for evolutionary biology are discussed.

Keywords: genotype • phenotype • variation • marbled crayfish • development • growth • colour • reproduction • behaviour • sense organs