Mass-Media Star

Does anybody know why this picture of Gould has the symbol of Antena3 (an Spanish TV broadcasting channel) if I took it from the Stephen Jay Gould Archive?

More on Meyer's creationist paper

As you may remember, not so long ago I comented on the fact that S.C. Meyer, a well-known defender of the intelligent design theory (basically, the modern version of the Natural Theology of Paley), has managed to put forward a review in a peer-reviewed journal. You can find it at Evolucionarios (telling the truth, you can also find it in the original source at the Discovery Institute, but I don't want to put a link to that).

The issue has atracted a lot of atention, as expected. A search in Google with the full title of the article gives 13.500 hits. And all that in less than two months, only one since it's available on-line. At the National Center for Science Education site (an organisation devoted to defend the teaching of the evolutionary theory) you can find a follow up of the story, as you can also do at The Panda's Thumb "The "Meyer 2004" Medley".

Soon after its publication, several members of the Biological Society of Washington (the one that publishes the journal in which the article came; it only has 250 members) declared their repulse for the publication. In fact, the BSW has issued an statement repudiating the article, recognizing that it "represents a significant departure from the nearly purely taxonomic content for which this journal has been known throughout its 124-year history", and that the BSW endorses the declaration of the American Association for the Advancement of Science on the ID theory.

But creationists don't mind this, especially the ID ones. They are quite happy withe media coverage achieved, mainly because now they will be able to manipulate the situation even more. All the criticism is inquisition-like, they say. I can already imagine how future meetings of academic comitees will be when creationism defenders use the article as "evidence" of the lack of support of the evolutionary theory and that the ID theory is at least equally respectable and that then ID theory should be taught in schools.

All this noise even though, as I already said, a thorough analysis has been performed at The Panda's Thumb. Let me quote their conclusion:

"There is nothing wrong with challenging conventional wisdom — continuing challenge is a core feature of science. But challengers should at least be aware of, read, cite, and specifically rebut the actual data that supports conventional wisdom, not merely construct a rhetorical edifice out of omission of relevant facts, selective quoting, bad analogies, knocking down strawmen, and tendentious interpretations. Unless and until the “intelligent design” movement does this, they are not seriously in the game. They’re not even playing the same sport."

How came, then? If the BSW is ashamed of what happened, how is it possible that they published the article in the first place? Saying it hurts, but this is a case of editorial corruption. The former editor-in-chief, Richard von Sternberg, is a well-known advocate of the ID and, although he denies it, he is a creationist by heart*. He claims that the reviewing process was as usual, but the current editor says that the article should have been rejected because the topic doesn't match the line of the journal, even without regarding the actual content. He also says that Sternberg didn't follow the usual procedure because instead of passing the article to an associate (quite logical, sure there wasn't any appropiate because the journal doesn't publish articles of that sort) he took it for himself. Sternberg afirms that he received favourable reports from three independent prestigious referees, although he doesn't tell who they were nor in which fields of expertise they are so prestigious (in fact, he only gave information about their academic possitions; doesn't it look like an authority criterium?).

In conclusion, it's shameful. A corrupt editor (and, if we take into account that his task is to judge the quality of a paper before publishing it, we can also "sue" him for prevarication), fellow (friend?) of the author, manages to divert the journal he works for from the topic it covers to achieve what it wasn't possible before: that an article that lies and hides the truth on purpose appears in the scientific bibliographical corpus. From right now I predict which paper is going to be the most cited in the creationist world and I foresee that others will follow if the precedent of this infamous couple spreads.

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* Sternberg contacted The Scientist because he was concerned that some in the science community have labeled him and Meyer as creationists. "It's fascinating how the 'creationist' label is falsely applied to anyone who raises any questions about neo-Darwinian evolutionary theory," he said. "The reaction to the paper by some [anti-creationist] extremists suggests that the thought police are alive and well in the scientific community."
However, the Baraminology Study Group views biological creation as happening instantly, rather than through evolutionary descent. Meyer's Discovery Institute is an open pro-ID center, and the Palm Beach Atlantic University of which he is an associate fellow states in its guiding principles that "To assure the perpetuation of these basic concepts of its founders, it is resolved that all those who become associated with Palm Beach Atlantic (...) must believe in the divine inspiration of the Bible (...); that man was directly created by God; (...)"
Are they creationists, the two of them, or not ?

Microarray Analysis of Hox Genes in Zebrafish

Here I am again. I've been off for a while, so let me talk about my talk of last Thursday. I wanted to make a post before, right after my talk, but when I finally managed to escape from the symposium (sadly, I missed the drinks :-( I wrote something that in the end was lost in the cyberspace :'-(

The talk was quite OK, taking into account the circumstances. I finished it the night before the presentation, but it didn't make any difference. The issue here is that I didn't want to give the talk, I was appointed to do so without asking, and whereas the rest of the people were at least finishing Ph.D. students, hence with a lot of results to show, I had to present the results of 4 months in the lab -- that fit into 3 slides. The rest of the presentation was about the whole project and mainly future plans. Unsurprisingly I only got a question, and it was from a guy from my lab (I guess he did ask so I had at least a question).

Alas, it's now done and over. I will present something properly in due time and that will be the important one. By the way, for those of you interested in what I am doing, here goes the abstract:

Microarray analysis of hox genes in the zebrafish
Maximiliano Corredor
Institute of Biology, Leiden University, The Netherlands.

Hox genes are a family of transcription factors of high relevance in development. These genes are clustered in genomic complexes and the arrangement of individual genes within these clusters correlates with their spatio-temporal pattern of expression. We have analysed the genomic organization of the hox genes in the zebrafish, comparing previous knowledge with the recently available genomic sequence in order to have the more complete picture of their organization possible. By doing so we have found a gene previously undescribed, hoxb13a. Some preliminary data of its expression patterns will be shown.
Using the information obtained, we will develop a microarray to characterise their pattern of expression in key developmental and physiological processes, mainly fin development and regeneration. This will lead us to a better knowledge of the regulation of the hox genes in these processes, their downstream targets and particularly analyse the importance of changes in temporal patterns of gene expression.


That was all, folks!

The Selective Brake

The critics of the Darwinian theory of evolution often comment on the “negative” effect of Natural Selection. How can a destructive force (elimination of the less-fit) generate anything?

This argument can come in two flavours. The obvious one stresses the apparent paradox. Selection destroys, limits variation, so how can it generate anything that wasn’t already there? This always reminds me of Michelangelo’s famous saying about his sculptures: they are already there; I only remove the unnecessary bits. Has anyone any doubt about the creativity of Michelangelo?

The more subtle argument relays on the “braking effect” of selection on the speed of evolution. This comes from a true fact. Since not all the mutations are beneficial for the survival, then not all of them are preserved; in fact a tiny fraction of all possible or actual mutations is selected favourably, the vast majority is selected against. It has been mathematically proved that the maximum speed of evolution (that is, the rate of fixation in a population of the new mutations) is equal to the mutation rate. Then selection is actually braking the speed of evolution, isn’t it?

Well, yes. But you may also want to consider what happens to individual mutations. If selection didn’t play any role, mutations of any sign will become fixed at constant rate. It’s even possible that a beneficial mutation may be lost due to genetic drift. However, if selection is taking place, any advantageous mutation will spread in the population faster than what it would have by chance alone. Positive selection speeds up evolution for every individual advantageous mutation.

If by evolution we mean change, selection is indeed a brake. But it is a biased brake since it only stops the fixation of deleterious mutations. For the other kind, the “good ones”, selection accelerates their fixation.

But we may think of evolution as a succession of improvements (as indeed it is: every population is better fit for its environment) and then if it weren’t for selection, the rate of evolution would be much slower.

Look out! I'm giving a talk

Next Thursday, September the 23, 2004, I give my first "big" talk. The "event" is part of a symposium about "Signals in Biology" organized by the Institute of Biology, Leiden.

I'm not saying it here neither for vanity (I don't even want to give it!), nor for inviting you to come (who would be so insane to come to the Netherlands just for my 15 minutes of glory? OK, I concede it, there are many other people talking about interesting things too).

I'm saying it because that means I shall (should) be busy the coming week preparing it (true, I wait for the very last moment to prepare it, but what can I do if the experiments don't work as they should the first time?) so I don't think I'll be able to post anything these days.

Cheers,
Max

Peer-reviewed paper defends theory of intelligent design

Intelligent Design creationists have managed to put their first paper in a peer-reviewed journal, although of a low impact factor: the Proceedings of the Biological Society of Washington (S. C. Meyer, Proc. Biol. Soc. Wash. 117, 213–239; 2004), according to Jim Giles (Nature 431, 114, 09 September 2004).

How came? I'll try to give a couple of hints:
1. The author, Stephen Meyer, belongs to the Discovery Institute, Seattle, Washington. Where did you say that this bilogical society was? Washington too.
2. The editor who supervised the review process and finally accepted the article is Richard Sternberg, who also happens to be in the editorial board of "Baraminology Study Group", a publication about "scientific investigation on creation biology".

Intelligent design creationists are taking advantage of the academic positions they hold to introduce favourable references into the scientific literature. This establishes a serious precedent, since until now they only counted with non-reviewed literature and their manipulation of other people's work (to great concern of the authors).

By the way, the article has already been contested in The Panda's Thumb.
Link to the discussion in Evolucionarios (in Spanish).

Lynn Margulis: Symbiogenesis and the origin of the nucleus and undulipodia

At Leiden University, in the Institute I work at, there are several research groups devoted to symbiotic or parasitic relationships. On September the 6 a symposium was held: "Acquired Genomes: Evolutionary consequences of endosymbionts", taking advantage of the presence of Lynn Margulis in the city as a guest speaker for the Faculty of Science official opening of the academic year. The talks of that meeting were mainly about Wolbachia. Although the topic is most interesting, today I would like to focus on the talk given by the main speaker:

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Evolutionary Consequences of Endosymbiosis: Origin of the nucleus
Lynn Margulis
University of Massachusetts/Amherst, USA

No substitute exists for direct study of microbes in nature. Some serve as modern analogues of the origins of cells as integrated communities of bacteria and protoctists in anoxic environments. We base our model of the origin of the nucleus on current observations of relevant live organisms. We arrange our observations into a plausible evolutionary sequence that led from prokaryotes to the origin of the first nucleated cell. The nucleus is postulated to evolve after the archaebacterium and eubacterium merged to form the symbiotic ancestor of amitochondriates (archaeprotists) protists. Descendants of these swimming archaeprotists today thrive in organic-rich anoxic habitats where they are amenable to study. Eukaryosis, the origin of nucleated cells, occurred by the middle Proterozoic Eon prior to the deposition in sediments of certain well-preserved microfossils i.e., Vandalsphaeridium (Vidal, 1998) and spiny spheres in the Doushantou cherts of China (Knoll, 2003).

Our evolutionary scenario for nucleus origin in archaeprotist ancestors is based on observations by L.R. Cleveland (1892-1971) and Harold Kirby, Jr. (1900-1952). Intrinsic to our model is Cleveland's detailed work on cell motility, i.e., movements of undulipodia, the mitotic spindle and‚ “attraction spheres” (centriole-like organelles) in mitosis as well as on Kirby's concept of "mastigont multiplicity" (Kirby, 1994). Prokaryotic symbionts (Thermoplasm-like archaebacteria + motile eubacteria) began as components of the karyomastigont from which the nucleus was released. We posit that the acquisition and genomic integration of microbial symbionts extends far beyond the origin of the nucleus. Indeed it seems to be the major mode of evolutionary innovations and speciation in eukaryotes. Accumulation of random mutations plays a modulating rather than creative role in the origins of species. Two short videos illustrating these points will be shown.

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To tell the truth, the talk was quite amusing, especially the videos shown about "dancing" spirochetes. However, few news were presented to those who were already familiar with her work, in particular her last book "Acquiring Genomes". Among the new things, I must mention that she openly admits that there is no evidence of nucleic acids associated with centrioles or any other MTOC (microtubule organizing centre). Alas, this doesn't stop her insisting on her idea about a spirochete-archaean symbiosis as the source of the very first proto-eukaryotic cell.

Why does she push still this idea forward, then? Besides her well-known stubbornness, because an electron-micrograph of a spirochete (she didn't mention which species, as far as I remember) shows a quite clear resemblance with an undulipodium (eukaryotic cilia and flagella) since two pairs of "microtubules" could be observed (I shan't call them microtubules until I see the anti-tubulin staining); let's remember that undulipodia (almost) always have a 9+2 symmetry formula (nine pairs surrounding a central pair).

Another reason favouring the endosymbiotic scenario for the origin of the motile elements is of biochemical character. The metabolism of the archaea supported by Margulis as closest relative to the one that gave rise to eukaryotic cytoplasm, Thermoplasma, is sulphur-reducing: it can convert the sulphur abundant in its habitat into sulphide. Spirochetes can in turn oxidise the sulphide into sulphur again. This is a good reason to establish a symbiotic relationship (a similar hypothesis has been proposed for explaining the symbiotic origin of mitochondria; it's called the hydrogen theory), and more importantly, it appears that there is evidence for a sulphur metabolic cycle. Unfortunately, Margulis didn't give any reference for that besides a personal communication of someone (I don't remember the name) that has developed a "sulphurometer" in order to measure sulphur metabolites inside erythrocytes, having found proof of such a "futile" metabolic cycle.

Personally, I wouldn't mind recognizing an endosymbiotic origin for undulipodia. It's a reasonably well-argued hypothesis and some circumstantial evidences are on its side. Since all eukaryotes have microtubule cytoskeleton – what allows them to have an enormous versatility of form and movement – it is one of the most crucial acquisitions of protoeukaryotic history. The problem is that Margulis is convinced that this supposed symbiosis came prior to the mitochondrial one, and that as a result the most distinctive eukaryotic feature evolved. She is not the only one arguing that the nucleus is a secondary result of the first eukaryotic symbiogenesis. The authors behind the hydrogen theory also speculate about this in their model.

In a meeting held in France ("The Origin of the Nucleus", Les Treilles, 7-13 July 2004; editorial comment in Science) several models were debated, but the one that convinces me most is the syntrophic model: metabolic symbiosisàsymbiogenesisànucleated protoeukaryote. This scenario stands both for the hydrogen theory (mitochondria first) and Margulis' theory (spirochete-undulipodia first).

What arose first (assuming that the spirochete story is true), the flagellum or the mitochondrion? That's a good question. All eukaryotes have microtubule cytoskeleton, but not all eukaryotes have mitochondria. Eureka! Lynn would say. But not. Because the fact is that the absence of mitochondria is a derived character, no matter how much she resists to it – she continues to say that the most primitive extant eukaryotes are mitochondria-less anaerobic protist. If there was once an amitochondriate protoeukaryote, it has not left amitochondriate descendants. Facts rule, so for the time being, I support mitochondrion as first endosymbiont and nucleus origin as a result of that symbiogenesis. If the hypothesis of the undulipodia is ever proved, I'll begin to ask myself about what happened first.

I've used several times the word 'symbiogenesis'. In her book "Acquiring Genomes", Lynn and her son Dorion Sagan, basically propose that symbiogenesis – evolutionary consequence of symbiosis – is the main cause for the origin of new species, insisting on the old argument about "simple accumulation of random mutations can't generate new species". Furthermore, it is proposed a new definition of 'species' that takes that into account: different species have different genome compositions. Unfortunately, they easily fall into circular argumentation because as soon as they postulate their new definition, they use it to demonstrate that new species can only originate by genome-wide changes, being the fusion of two (or more) genomes the main mechanism for new species origin.

It's a pity that her extremely relevant discoveries on early eukaryotic evolution be tarnished for her confusion over "orthodox science". During the talk she mentioned several times that her financial support had been removed because of her search of heterodox ideas, blaming the "neodarwinist establishment" for that. After her talk I had the opportunity to ask her how does symbiogenesis exactly take place. To me it was obvious that the answer is by Natural Selection, but she answered in a most Lamarckian way: the initial symbiosis is a behavioural one, it is then strengthened by metabolic bonds, then a physical permanent interaction takes place and finally the genetic materials are fused. No matter how hard I tried, I couldn't make her to acknowledge that the only way that sequence can evolve is by the accumulation of selected random mutations.

In any case, she is a lovely person and she had the friendly detail of kindly dedicate me her book (another more for my collection! :-)

A webpage about Margulis' theory for the origin of undulipodia (in Spanish).
Discussion about the issue at Evolucionarios (also in Spanish).

Article about hydrogen hypothesis for the origin of mitochondria: W. Martin and M. Müller, Nature 392, 37 - 41 (05 March 1998);
editorial comment in Nature: W. Ford Doolittle, Nature 392, 15 - 16 (05 March 1998);
editorial comment in Science: G. Vogel, Science, 279, 1633-1634 (13 March 1998).

Article about another syntrophic hypothesis: D. Moreira and P. López-García, J Mol Evol 47, 517-530 (November 1998).

I hope to have time to look for more references on eukaryotic nucleus origin.

Está bien lo que bien acaba...

... pero nadie se atreve a juzgar por según cómo empiezan las cosas...

Después de una serie de problemillas técnicos afortunadamente resueltos (ejem, ejem. ¡Uy, qué tos más tonta...! ;-) , ya hay una versión visible y utilizable de Evolucionarios en Blogalia. Cierto, aún faltan unos cuantos retoques, pero es totalmente operativa la bitácora, así que ha llegado el momento de tomar una decisión.

Bueno, en realidad ya la he tomado, que si no no escribiría esto.

Creo que lo mejor es mantener los dos sitios como "imágenes". Pero no un espejo cualquiera, no, sino un espejo mágico que transforma lo que refleja.... vamos, que voy a mantener un sitio por idioma. A partir de ahora, aquí sólo publicaré en inglés (y en castellano en caso de que alguien comente en español, que nunca se sabe a dónde le llevan a uno los enlaces). El otro sitio queda reservado para los mensajes en madrileño (y en algún otro idioma si se diese el caso de que algún perdido apareciese por ahí).

Esto quiere decir que desde ya me fijo la tarea de enviar simultáneamente los mensajes (o posts, irsus acostumbrando) en ambos idiomas, uno a cada sitio. Por supuesto, los comentarios son tema aparte, y cada sitio tendrá los suyos. Ya me encargaré de enlazar convenientemente si en algún momento algo dicho en un sitio es relevante en el otro. Supongo que esto le vendrá bien a mi inglés escrito...

A los que no controlen inglés, que vayan modificando sus vínculos en el menú de favoritos.
A los bilingües, espero que no se me líen con tanto jaleo de sitios... ;-)
A todos, nos vemos aquí, allí, o donde siempre.

¿Mudanza a Blogalia?

Este fin de semana he estado cruzando unos emilios con PaleoFreak en los que me sugería mudarme a Blogalia, el 'host' de su blog. Como quiera que su blog es la pauta a seguir que me he fijado, igual la mudanza viene bien, sobre todo porque parece que allí dejan estructurar el sitio un poco más. O igual aquí también se puede y soy yo el que no sabe cómo.
Con lo que me conteste el administrador de Blogalia veré cómo va eso de mudar el sitio. O igual saco un clon. Ja veurem.

The Panda's Thumb

Cuando se menciona 'el pulgar del panda' es habitual que el aficionado a la biología evolutiva piense en un magnífico ensayo de S.J. Gould, aquél que comenta cómo el "pulgar" de este animal no es un auténtico dígito, sino un hueso de la muñeca. Maravilloso ejemplo de constricción filogenética (los antepasados de todos los carnivora perdieron el pulgar) y a la vez del poder de la selección natural para diseñar adaptaciones a partir de lo disponible.
Pero este 'post' se titula así porque, quizá inspirados por el trabajo de Gould como defensor de la evolución y crítico del creacionismo, gente de la Universidad de Ediacara (Australia) ha creado un 'blog' dedicado a eso, a defender la evolución de los ataques creacionistas.
Me he enterado de su existencia por el artículo que ayer comentaba de Nature, ese sobre el primer 'paper' de un creata. Jim Giles, el autor de dicho editorial, lo cita como fuente de la refutación de los argumentos creacionistas de S. Meyer, así que o bien es un sitio de bastante importancia, o bien Jim está implicado en su desarrollo ;-)
En cualquier caso, es algo a tener en cuenta, sobre todo por aquellos que gustan de lidiar con el toro creacionista.

El PaleoFreak

La idea de iniciar un blog se la debo a El PaleoFreak, uno de los participantes habituales de Evolucionarios. Gracias a su excelente sitio en Blogalia he descubierto que existe este mundo. Nunca fui mucho de escribir un diario (hasta que empecé en el laboratorio, y mis sudores me sigue costando) pero me he acostumbrado a "forear" así que necesito un lugar donde exponer mis ideas.
El que visite su blog descubrirá lo que es tener pasión por algo: los pterosaurios en especial, dinosaurios sensu lato en general y mucha afición a la iconografía alrededor de estos "bichos".
Espero que este sitio llegue a ser la décima parte de bueno que el suyo.
Lo dicho, gracias Paleo.
Otro buen propósito: logar que las entradas sean lo más escuetas posible. Aunque por otro lado, si este sitio es mio, y yo soy así de charlatán, ¿por qué tengo que comedirme? Recordadme que decida qué es lo que quiero, desahogarme escribiendo o que otros lleguen a leerme ;-)

Evolucionarios

Y para estrenar el blog, nada mejor que un poco de propaganda

El 8 de Agosto de 2001, presionado por la falta de libertad que imperaba en los foros de Terra.es, creé la comunidad virtual (ahora grupo, a secas) de Evolucionarios en MSN.com. Desde entonces hemos llegado a ser la comunidad más activa en la categoría de biología (español) y he de reconocer con orgullo que la calidad es muy buena.
Como herederos de un foro de debate, la vida comunitaria gira alrededor de los Foros. En principio se crearon varios paneles de mensajes con la intención de tener organizados temáticamente los debates. La práctica nos ha enseñado que esta clasificación no debe interpretarse en modo absoluto, sino como una ayuda al recién llegado para encontrar algo relacionado con un tema en concreto.
Aparte de los Foros, también hay otros paneles de mensajes: tenemos un tablón donde se anuncian convocatorias o se pide información práctica (se de alguien que encontró su tema de doctorado en un anuncio, así que no dejeis de mirar si buscais promoción!); también contamos con una Revista de Prensa donde se cuelga una selección de las más recientes evo-noticias aparecidas en los medios de comunicación y las revistas científicas. Supongo que no costará mucho hacer algo parecido aquí.
Un proyecto en crecimiento es la Biblioteca, donde contamos con un catálogo de libros interesantes para el aficionado a la Evolución, así como paneles de mensajes para sugerencias y críticas.
Además de lo ya mencionado, la comunidad cuenta con un salón de charla y un amplio archivo de Documentos, Fotos y Citas célebres.
Para participar en los debates y usar algunos de los recursos es necesario ser miembro; la admisión es totalmente libre, no hace falta superar ningún baremo de conocimientos ni por supuesto el pago de ninguna cuota. Somos ya 500 pero aún nos parece pequeña, así que únete!

Como os podeis imaginar, administrar todo eso no es tarea fácil, pero cuento con la inestimable ayuda de Xac Mazo, co-fundador y sobre todo amigo desde los viejos tiempos de los foros terráqueos, así como la de otras personas que comparten con nosotros esta manía de divulgar y debatir la ciencia evolutiva. Lamentablemente, el cargo conlleva cierta responsabilidad y llevo cierto tiempo preocupado con la posibilidad de que se identifique mi posición como administrador principal con una autoridad en materia de debate que no tengo ni quiero tener (aunque mi manera de argumentar parezca todo lo contrario), así que creo que será buena idea iniciar este blog como una especie de diario (comentado) con mis pensamientos y opiniones. A ver en qué termina la cosa.

It's Evolution, Baby!

Nothing in Biology Makes Sense Except in the Light of Evolution

Hace ya unos cuantos años me dió por participar en unos foros de debate sobre evolución. Con el correr del tiempo los que allí participábamos decidimos montar una comunidad virtual (http://groups.msn.com/Evolucionarios). Ahora la moda son los blogs, así que aquí me teneis.

La verdad es que ser el administrador de una comunidad llega a pesar sobre tu libertad de expresión, de modo que el propósito de este sitio es simplemente poder exponer mis puntos de vista sobre la evolución (y ya puestos, sobre cualquier otra cosa :-)

A ver qué tal sale el experimento. Saludos cordiales,
BioMax