Manuscript accepted for publication!

Genomic annotation and transcriptome analysis of the Danio rerio hox complex with description of a novel member, hoxb13a

My first article as first author has been accepted (at last). The honoured journal will be Evolution and Development. I would have preferred Developmental Biology or Genomics (if preferences really matter, I would have preferred Nature best; in due time ;-) but one of my bosses thought (with a lot of reason) that it would be of a lot of interest for evo-devo people and therefore it should be easyly accepted there.

Quite the opposite.

The content doesn't almost overlap with the journal editorial line (which is a bit old-fashioned, to be honest). However the editors received it quite enthusiastly but they have had many problems finding referees. The big-bosses must be terribly bussy refereing for Nature or such, and the rest of the contacts of the editorial board seemed overwhelmed.

Finally, two months and a week after submitting the manuscript, we have the favorable comments back and the green light for publication from the editors. Now we have just to send the final version and pay the editorial ;-)

Does anybody want a piece of cake?

Mosasaurus in the Netherlands

During the Easter holidays I went to Maastricht and Aachen. Here you have a couple of pictures I shot when we passed by the Natuurhistorisch Museum Maastricht to visit an old pal of mine (the pictures aren't that good and I wasn't in my best times, either) :

Laura, much more affectionate than me, as usual, tried to kiss him ;-p

Our bony friend is a Mosasaurus hoffmani, a marine reptile of the Cretaceous (no, it's not a dinosaur). The generic name, Mosasaurus, means 'reptile of the Meuse', river called Maas in Dutch. The first fossil of this kind of animals was found as long ago as 1780 in a quarry by Maastricht area. In the wikipedia we can find more stuff about the discovery. Doctor Hoffman was a fossil hunter and through his epistolar contacts made public the discovery. When the French revolutionaries occupied the Netherlands, they took the fossil to París, so Cuvier himself was able to study it. The father of Paleontology made the first scientific description of the animal and give it its name, almost 50 years after it was found.

It's a pity that the picture I took of the fossil as it was found wasn't good. By the way, another museum for the 'to see' list: the Teylers Museum of Natural History, in Haarlem; the oldest public museum of the Netherlands. In its funds we can find an specimen of Archaeopteryx and, odd enough, they have found recently that they also had a mosasaur recovered before Hoffman's, but also from the Maastricht limestones. Interesting, huh?

Stirring up the primordial soup

I've discussed in the past about the primordial soup. Some scientists believe that this soup was a 'letters soup' indeed. They call it the RNA world, where RNA was both a genetic repository and a catalytically active molecule. In modern day 'soups' (our cells), the RNA is an intermediary between DNA (genetic info store) and proteins, but there are some species of RNA that have a catalytic activity -- the ribosomic RNA is the responsible of forming the peptide bond.

How could both functions of RNA coexist and allow a sort of molecular evolution to take place (and eventually lead to the first living cell)? It's supossed that a particular kind of RNA existed in those times, a ribo-RNA-polymerase. Taking a RNA molecule as template, it should be able to catalyse the synthesis of an exact copy (with a small margin of error, without mutation there can't be evolution). Most mechanisms proposed so far involve the formation of an intermediary double stranded RNA: the polymerase should create first a complementary copy of the target molecule and then another complementary copy of this one (therefore with the same sequence as the original template) should be synthesised.

This poses a problem: the formation of double stranded RNA will act as a sink of active RNA molecules, because it's more stable but catalytically inactive. William Taylor has thought about this issue and came up with a possible solution ¹: RNA polymerases add nucleotides to the growing strand by the 3' end. Why not the 5'? If a polymerase followed a template reading the sequence from 3' to 5' and adding new nucleotides also from 3' to 5' (instead of from 5' to 3'), then the two strands would have complementary sequence but would not be able to hybridise. And this mechanism will leave the new molecule available (even before it has been completed) for another polymerase to start synthesising the complementary copy of it, thus achieving the replication of the original without a dsRNA intermediate.

However, I think that if today's RNA polymerases do synthesise with that particular polarity, thus creating perfectly complementary strands, it would be for a very good reason. Maybe the Watson-Crick pairs can't form if the two strands are not anti-parallel (this will make the proposed mechanism not suitable because no sequence complementarity could be achieved). Maybe the energy needed to catalyse a 5' extension is much higher. I don't know about these issues, but more in depth thermodynamic studies should be done before giving more relevance to Taylor's proposed mechanism. But still is a jolly good idea.

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1. William R. Taylor Stirring the primordial soup Nature 434, 705 (07 April 2005)

The Pope and the Scientists

I know that the death of the Pope is not news any more, but there is something I would like to comment:
Pope praised for partial conciliation of science and religion [Nature 434, 684 (07 April 2005)]

Catholic researchers and bioethicists have responded to the death of Pope John Paul II with tributes to his efforts to achieve reconciliation between faith and science. And some are optimistic that his successor will keep on the same path.

Maybe the catholic ones are happy about that, but others aren't that happy, including me and those who defend the use of embryonic stem cells in scientific research:

The Polish Pope had a strong personal interest in science and worked to reduce hostility between the scientific community and the Roman Catholic Church. Nonetheless, his strict rejection of abortion, embryonic stem-cell research and contraception, including the distribution of condoms to help contain AIDS, drew him into conflict with some scientists.

Others have told much and in length about the absurdity of his position concerning AIDS and contraception, but I have the feeling that in this issue they will, in the future, recognise that they were wrong. Of course it will be when it won't matter any more and will not help fighting AIDS now. If it took more than 400 years to acknowledge their wrong doing with Galileo's affaire...

In 1980 at Cologne Cathedral, Germany, John Paul declared that there was "no contradiction" between faith and science. He said on several occasions that the concepts of the Big Bang and darwinian evolution were more than mere hypotheses. In 1992, he officially rehabilitated Galileo Galilei, conceding that the Church was wrong to arrest him.

I would like to call your attention to the sentences in bold letters. There might not be a contradiction, but the use of 'mere' referring to two scientific hypothesis sounds pretty despective to me. Maybe they don't know that scientific hypothesis are something very different from 'mere' hypothesis, as for example, any god's existence.

Of course faith and science are compatible. As far as faith doesn't oppose scientifically well stablished facts... Not doing so, that what creationists do, is mere stupidity.

Blogalia is having a massage

blogalia

blogalia is having a massage.

blogalia is getting a massage and will return soon.