Archives de avril 2008

Gene therapy success ‘reverses’ blindness


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Evolution happens, just like shit


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ScienceDaily Picks

Hypnosis: The Key To Unlocking The Delusional Mind?: (Apr. 29, 2008 ) — Researchers at Macquarie University have developed an original new approach to the study of delusions, using hypnosis to temporarily create typical delusional beliefs in otherwise non-delusional people.

This study has laid the groundwork for future experiments which will examine the features and parameters of hypnotic delusions, the impact of challenging the delusions, and whether role-playing participants display the same behaviour as genuinely hypnotised participants, » they explain. « Using hypnosis we expect to get a real sense of how to investigate, understand and confront delusional beliefs in a more effective way.

Well, well, well, maybe that means the future of religions is badly shaped 🙂

Watering Tomato Plants With Diluted Seawater Boosts Levels Of Antioxidants: (Apr. 29, 2008 ) — Watering tomatoes with diluted seawater can boost their content of disease-fighting antioxidants and may lead to healthier salads, appetizers, and other tomato-based foods, scientists in Italy report. »

And you don’t need to use salt for the salad?

Are Nanobots On Their Way?: (Apr. 29, 2008 ) — The first real steps towards building a microscopic device that can construct nano machines have been taken by US researchers. Writing in the International Journal of Nanomanufacturing, researchers describe an early prototype for a nanoassembler. »

Asimov died too early

Evolutionary Intricacies Of Rickettsia Pathogens Revealed: (Apr. 29, 2008 ) — Scientists from the Virginia Bioinformatics Institute (VBI) at Virginia Tech and the University of Maryland School of Medicine have unveiled some of the evolutionary intricacies of rickettsial pathogens by analyzing over a decade’s worth of genomic data. Some species of Rickettsia are known to cause harmful diseases in humans, such as epidemic typhus (R. prowazekii) and Rocky Mountain spotted fever (R. rickettsii), while others have been identified as emerging pathogens and organisms that might possibly be used for the development of biological weapons. »

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détente dominicale

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PLoS ONE Picks

Kerkhoven RM, Sie D, Nieuwland M, Heimerikx M, De Ronde J, et al. (2008 ) The T7-Primer Is a Source of Experimental Bias and Introduces Variability between Microarray Platforms. PLoS ONE 3(4): e1980. doi:10.1371/journal.pone.0001980 🙂

Guyader S, Burch CL (2008 ) Optimal Foraging Predicts the Ecology but Not the Evolution of Host Specialization in Bacteriophages. PLoS ONE 3(4): e1946. doi:10.1371/journal.pone.0001946

Rempel H, Calosing C, Sun B, Pulliam L (2008 ) Sialoadhesin Expressed on IFN-Induced Monocytes Binds HIV-1 and Enhances Infectivity. PLoS ONE 3(4): e1967. doi:10.1371/journal.pone.0001967

Lissek S, Peters S, Fuchs N, Witthaus H, Nicolas V, et al. (2008 ) Cooperation and Deception Recruit Different Subsets of the Theory-of-Mind Network. PLoS ONE 3(4): e2023. doi:10.1371/journal.pone.0002023

Bryan MJ, Burroughs NJ, Spence EM, Clokie MRJ, Mann NH, et al. (2008 ) Evidence for the Intense Exchange of MazG in Marine Cyanophages by Horizontal Gene Transfer. PLoS ONE 3(4): e2048. doi:10.1371/journal.pone.0002048

Rands SA, Whitney HM (2008 ) Floral Temperature and Optimal Foraging: Is Heat a Feasible Floral Reward for Pollinators? PLoS ONE 3(4): e2007. doi:10.1371/journal.pone.0002007

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Spot The Fake Smile

This experiment is designed to test whether you can spot the difference between a fake smile and a real one

It has 20 questions and should take you 10 minutes

It is based on research by Professor Paul Ekman, a psychologist at the University of California

Each video clip will take approximately 15 seconds to load on a 56k modem and you can only play each smile once

Just got 14 out of 20 correct 😦

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John Templeton Foundation – censorship – backstage

My e-mail message concerning the censored comment I left at the Templeton Conversation « Belief » page, received a prompt response, thanks to Charles Harper I suppose. Previous experience showed that other people wasn’t quite responsive.

Gary R, Chief External Affairs Officer of JTF was the main contact. He granted permission to display his messages, so below the fold you will find the whole thing, to be able to make a personal judgement of the behavior of JTF and of how I see it.

One of the sentences of the original commentary seem to be the most problematic.

JTF’s activity seems to fit the definition of scienligion, a softer than the ID creationism, denying the characterization of creationism, say as Miller, a roman catholic christian, who’s credo is a God creator of the universe

Gary R qualifies it as erroneous information about the JTF, without pointing to it specifically in his first message, but we came to it relatively quickly.

It’s a fact that JTF worked against Creation Science and Intelligent Design creationism, the first one being completely ridiculous, the second one using an approach too political for theJTF‘s standards [#] and not good science. That doesn’t mean that JTF don’t promote creationism. Science isn’t the main aim of JTF, Science and Religion is.
One can call them theistic evolutionists, evolutionary creationist, soft creationists, crypto-creationist or whatever other term he likes to differentiate them in the continuum of creationist approaches, the fact that they promote religions asserting the existence of a creator god remains constant and it will not change any soon. The visible part of the iceberg being the efforts to prove, or at least avoid the lost of the last traces of credibility of the idea, that the universe have a sense, a teleological (philosophical, religious) position, implying a beginning and purpose to reach an aim, purpose of a deity creator of the universe. This is the typical monotheistic religions message, say christians, who’s credo clearly states this belief at the very first sentence: « We believe in one God, the Father, the Almighty, maker of heaven and earth, and of all that is, seen and unseen… « 

The way JTF is perceived seems to be more important for Garry R then its real nature. His main concern is how people will perceive the foundation if they understand that they promote creationism. The concern is visible by the way the motto of the foundation changed recently, going from « Science and Religion » to « Big Questions ».
One would expect from such a powerful organization an educational effort to explain people the distinction between the different forms of creationism, to differentiate their way to consider the creation of the universe.
Instead, as this episode showcase, they try to avoid by any means the characterization as creationists, even in a sentence differentiating them from their last-in-date colleague, the ID movement.

The way Gary R dealt with my comment is quit immoral (by atheist’s standards at least, lying for Jesus may be considered moral for some people). As I understand the word « conversation » it’s all about bringing different versions together. JTF‘s a posteriori presented editorial standards exclude the expression of opposite opinions.
Somehow Gary R seems to be able to cut the majority of my message as moderator, but he, or some other of the JTF‘s people, is unable to reply to it, discuss it, converse. Maybe after all their open-mindness have nothing to do with open-minds, but just with the closed-mindness characterizing usual proselytes.
Censorship to avoid the expression of undesirable opinions is a common trait of propagandists/communicators with a narrow ideological field, lacking arguments to support their position if scrutiny concerns not only the front of the decorum but also what lies behind. Now, after this episode my feeling that JTF is of that kind of propagandists is quite stronger.

Crude censorship would be to just no accept the comment. That’s what I expected.
Gary R made it worse by editing it. Without warning that he did so, neither in the comment, or to me. He just arranged the decorum as he likes it.
Expecting what? That I wouldn’t see he done so? That I would accept his manipulation and leave the truncated and meaningful comment under my name? That I would accept the worse of censorships, the display of accommodated opinions?

When one become aware that such censorship is practiced in a conversation page, the assertion of Gary R « we are happy to represent all points of view in this discussion » (emphasis mine) seems ridiculous; how many comments aren’t displayed and how many are truncated, arranged by Gary R?

The second message from Gary R made me laugh.

You must know that the terms « creationist » and « creationism » have very distinctive meanings in the US. They describe an anti-science movement that denies evolutionary theory and challenges the well-established findings of evolutionary biology. JTF works very hard to counter the influence of this movement, and I can’t allow a posting on our website to say that we are « creationists.

At least he makes it clear that « creationism » is what bother him.

But that wasn’t the funny part. Let me explain: My first contact with JTF, was through a french non for profit association, the Université Interdisciplinaire de Paris (Interdisciplinary University of Paris, nothing to do with academia anyway) and in particular Jean Staune, it’s perpetual General Secretary, whom Charles Harper consider to be a fascinating and deep person of principle and vision.
Things become funny when one knows the ideological anti-darwinism of Staune, who calls himself super-evolusionnist adhering even to neo-lamarckism (denier of evolutionary theory), the way he purposefully ignores any part of the scientific literature opposing his views (anti-science) and critic of darwinians views imputable to fanatism and ideology for him, including (?) the one of Ken Miller.
JTF seems to be UIP’s principal founding agency actually. If JTF works hard to counter this kind of movements in the USA, they seem to be quite helpful and willing to expand them in France/Europe.
Now, that’s funny, isn’t it?

Maybe Gary R ignores that kind of activities of the JTF. I don’t. Maybe he don’t see clearly that the foundation finance (relatively heavily) such denials of evolutionary theory and well-established findings of evolutionary biology and he truly thinks that this is not so. I don’t.

Maybe he should be kept more informed about how the foundation’s money is used, quite useful in his position as Chief External Affairs Officer. Maybe he would then be able to understand that I didn’t mischaracterized JTF, even by his standards.

At his third message, Gary R introduce « editorial standards » that weren’t displayed on the conversation page. He misrepresents the fact that editorial standards may include censorship as a technique to avoid controversial opinions to be expressed. « Censured », « censorship », the words are used between quotes, probably to avoid to be in full contact with them, as « creationism ». Well, he is not convincing. Hypocrisy.
The truth is mostly that (emphasis mine):

JTF works very hard to counter the influence of this movement, and I can’t allow a posting on our website to say that we are « creationists. »

I intentionally left the « we are ‘creationists' » part, as it may be replaced by whatever statement that don’t fit the decorum the JTF display.
Dear Gary R, please accept as a small souvenir of this brief contact the following definition:

censorship |ˈsensərˌ sh ip|
the practice of officially examining books, movies, etc., and suppressing unacceptable parts : details of the visit were subject to military censorship.

from the New Oxford American Dictionary.
You may want to reconsider the title of your position as Chief External Affairs Officer and Website Censor, for better visibility.

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Mechanism Of Epigenetic Inheritance Clarified

Mechanism Of Epigenetic Inheritance Clarified: (Apr. 24, 2008) — Although letters representing the three billion pairs of molecules that form the ‘rungs’ of the helical DNA ‘ladder’ are routinely called the human ‘genetic code,’ the DNA they comprise transmits traits across generations in a variety of ways, not all of which depend on the sequence of letters in the code.

Papier fort intéressant que celui de Anna Kloc, Mikel Zaratiegui, Elphege Nora and Rob Martienssen. “RNA Interference Guides Histone Modification during the S Phase of Chromosomal Replication”, présenté par ScienceDaily, montrant que l’héritabilité épigénétique est basée sur les séquences géniques après tout, conditionnée par les conditions environnementales. (si, si, il y a des personnes qui en doutent 😉 )

D’habitude, je donne les liens vers les rapports de ScienceDaily sans plus, mais ici je m’arrête excédé, encore une fois, mais celle-ci au dessus du seuil de tolérance, par le propos du présentateur. Lisez moi ça :

Long DNA molecules almost miraculously cram into cell nuclei that are almost a million times smaller than they are.

Merde alors, s’il y a un miracle c’est surtout que la personne qui a écrit cette phrase travaille encore dans un service de nouvelles scientifiques !

Bien sûr les noyaux ne sont pas un million de fois plus petits que les molécules d’ADN qu’ils contiennent, ADN qui occupe une fraction minoritaire du volume du noyau. L’explication de la condensation autour des histone suit dans le même paragraphe.
Ainsi, ce n’est pas l’ignorance qui est à l’origine de cette absurdité et j’ai du mal à comprendre à qui est adressé le côté sensationnel de la phrase; certainement pas aux biologistes intéressés par l’épigénétique.

Il y a des petites choses comme ça qui m’agacent dès le premier café de la journée…


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Gene regulatory networks and embryonic specification

Leroy Hood a le beau rôle du défenseur de la biologie des systèmes qui présente un bijou du domaine, le travail de Oliveri, Tu et Davidson, publié dans le même numéro des PNAS (Global regulatory logic for specification of an embryonic cell lineage)

C’est Timothée qui a attiré mon attention sur les deux papiers, et je ne pensais pas vraiment les regarder de près avant quelques jours, une autre projet de blogging étant en cours et accaparant mes périodes caféinées. Mais au moment de fermer le pdf du papier de Hood mon oeil est tombé sur ce paragraphe :

In this issue of PNAS, the article by Oliveri, Tu, and Davidson (5) is the most powerful demonstration to date of how a dynamically changing, complete GRN can explain virtually every aspect of skeletal-cell development in the sea urchin larva over its first 48 h. The authors focus on specification of the skeletogenic micromeres that ultimately differentiate into skelet al cells exhibiting mineralization. The idea is to determine …

Un GRN complet ? Avec son comportement dynamique ? Qui explique le développement des cellules squelettiques ? Soient-elles de l’oursin, ça sonne intéressant au moléculariste qui s’est vaguement intéressé au développement, au moins pour trois raisons :

  1. la méthode utilisée pour bâtir le GRN,
  2. le potentielle de ces approches qui peuvent se passer de données génétiques massives pour aborder certains sujets,
  3. un time will tell qui est en suspens quelque part dans mes blogs.

Davidson peut agacer certains, il a réalisé néanmoins un tour de force qui est en passe de marquer la biologie de façon profonde. Il justifie clairement la biologie des systèmes qui n’a pas eu un accueil chaleureux de la part de toutes les personnes qui s’occupent de biologie et je fais essentiellement allusion ici aux biologistes classiques. La notion de système n’est pas très proche du raisonnement basé sur l’organisme, l’espèce… On commence à la toucher en parlant d’écosystème, et les évolutionnistes et écologistes étaient rapides à chopper l’idée, on l’évoque clairement pour les biologistes moléculaires qui se sont un peu éloignés de la démarche de la génétique, non pas parce qu’il n’aiment pas mais parce qu’ils disposent d’outils qui permettent de voir plus rapidement et plus.

Quand on a vécu le passage du Northern Blot au micro-array et à la WMISH on comprend facilement ce dont je parle.

Nous sommes en train de changer d’ere. Le Modeste Biologiste que je suis commence à pouvoir envisager de se servir du 454 pour passer en deux semaines de boulot ce qui prenait 7-8 mois, avec l’espoir d’avoir un vision plus claire du problème qui le préoccupe.
Et cette façon d’envisager les chose en grand, pour disposer de données suffisantes pour aborder nos problèmes, change non pas seulement notre façon de travailler à la paillasse, mais aussi, et surtout, notre façon de poser les problèmes.

Le travail de Davidson et al. servira de plate-forme pour le développement d’autres projets du même genre, dont il suggère la faisabilité, longuement mise en doute par les experts décideurs. Je jubile personnellement, ayant vu le plus gros projet que j’ai mis en place être balayé simplement, parce que le rapporteur « ne voyait pas l’intérêt que présentait l’étude de l’expression génique sur plusieurs types cellulaires à la fois » !

Il y a une autre conséquence qui n’est pas directement visible, mais qui est d’aussi grand intérêt que la compréhension détaillée du développement avec l’espoir que l’on puisse y baser des approches thérapeutiques pour corriger certains défauts; la partie luxe.
La biologie synthétique bénéficiera de ce genre d’approches, pour disposer de blocks géniques spécialisés à une tache particulière, qui pourraient être utilisés tels quels pour le transfert de compétences, définis par la constitution d’un réseau GRN plutôt qu’à leur participation à un ensemble métabolique (par exemple).

La phrase que l’éditeur (ou Hood lui-même ?) a fait ressortir « Sophisticated computational studies must be driven by good bilogy » est amusante. Pas en soi, mais à cause des réactions qu’elle a suscité autour de moi, et je suppose un peu partout où des bioinformaticiens ou des modernisateurs du vivant traînent. 7/9 des personnes que je connais et qui se sont prononcées à son sujet se sont montrées agacées. Excellent !

J’apprécie une bonne branlette intellectuelle, que ce soit de la science-fiction, des casse-têtes ou des mots-croisés pour se dégourdir l’esprit. Et j’apprécie également le côté ludique du travail scientifique. Mais ladite branlette intellectuel ne trouve pas sa place dans le travail scientifique, ce que plusieurs personnes semblent ne pas concevoir.

Entre l’observation, les données, et les modélisations (sophisticated computational studies), il est nécessaire de placer une compréhension profonde du sujet abordé (good biology). Sinon on s’en remet à la chance pour produire quelque chose qui correspondrait à a réalité; et plus un système est complexe, plus cette chance est plutôt faible. Ou pire, on part d’une idée préconçue et on essaie de faire coller les données à ses croyances (pas nécessairement religieuses). Les résultats sont plutôt catastrophiques.

L’approche de Davidson est en ceci exemplaire : les résultats théoriques obtenus par les modélisation sont testés in vivo, pièce par pièce, avant que les modèles validés ne soient proposés à a communauté scientifique. Il y a peut-être de la place pour une amélioration, qui pourrait venir dès lors que des méthodes plus sensibles seront disponibles, pour ajouter des éléments aux GRN, des éléments qui échapperaient aux techniques disponibles actuellement. Mais déjà, ce qui est disponible est du solide.

Dans la présentation de la méthode, que ce soit par Davidson lui-même ou par Hood, on trouve exprimées les précautions d’usage (soulignées par moi):

The general approach was as follows:
(i) a list of all identified DNA-binding domains (proteins) was determined from the complete genome sequence (it is believed that this list is relatively complete);
(ii) dynamic quantitative PCR (QPCR) was used to ascertain which of these regulatory genes were present during embryogenesis;
(iii) the spatial localization of these regulatory genes was determined by whole-mount in situ hybridization for up to 48 h (and was believed to be sufficiently sensitive to observe low-abundance transcription factors);
(iv) all of the micromere-expressed transcription factors were suppressed individually by morpholinos, and the resulting perturbations (network linkages) in gene expression were recorded dynamically across the 48-h time period by QPCR; and
(v) a delineation of the cis-regulatory structures for several genes in the network was used to check the architecture of the GRN.

Mais il n’y a pas que l’expression des précautions qui est exemplaire. Il y a aussi la démarche de vérification expérimentale qui devrait inspirer ceux qui ont des approches brouillonnes qui aboutissent à des conclusions aberrantes (suivez mon regard virtuel qui lorgne du côté de Cairn, Fleury, McFadden, Ogryzko and Cie).

Vous savez quoi ? C’est vraiment de la bonne (science)! Que vous soyez intéressé par le développement de l’oursin ou non, lisez les deux papiers. Ils méritent d’être utilisés pour l’enseignement de la biologie dans la section « exemple à suivre ».

Pour répondre à une question qui m’a été posée en direct et qui risque d’arriver dans les commentaires : non, je ne compatis pas avec ceux qui pourraient voir leur rêves de détermination non génétique du développement égratignés par ce genre de résultats.

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John Templeton Foundation censorship

update added at the end of this post


  1. Honorable people doesn’t practice censorship and/or heavily truncate comments left on their website.
  2. John Templeton Foundation’s people practice censorship and/or text truncation
  3. John Templeton Foundation’s people aren’t honorable

A couple of days ago I posted a commentary to JTF’s website, at the « Does science make belief in God obsolete? » page. The commentaries are moderated before publishing and mine was published almost 24 h later. It was slightly modified, the title (which I hadn’t provided) being added: RE: Kenneth Miller. OK, I had Ken Miller’s answer in mind, but I gave my comment a more general take.

That isn’t a problem. But latter, they edited my text, taking out what they didn’t like, leaving a reconstructed paragraph that I never wrote!

Quite the same kind of censorship one could expect from DaveScot at Uncommon Descent. Now, on your screens from John Templeton Foundation people. Enjoy.

Out of context! Truncated to their convenience. Not even the warning one could expect from an editor when editing is necessary, and they do have my e-mail address, you know, just the usual « required field ».

Can one trust that kind of people? I think not.

I was wondering, how comes the JTF is supporting local (French) neo-creationists censoring negative comments. Now I know, same kind of people.

Do I need to say that I’m pissed-off?

For before/after screen captures go here

Just sent this mail :

To: Webmaster

Cc : Pamela P. Thompson (as Vice President for Communications), Clio A. Mallin (as Communications Coordinator), Charles Harper (hoping that this will not be considered as a minor mistake) and Kenneth Miller (my comment being labeled by JTFs staff as RE: Kenneth Miller)


A recently posted comment at the « » page of JTF’s website, a « Templeton Conversation » about « Does science make belief in God obsolete? » was heavily edited.
I didn’t received any notification about the changes of the content of my message (and yes, I did checked the spam folder of my e-mailer, just in case).
The result is quite afar from my argument. You can check Before/After screen capture at

The behavior is unacceptable. A conversation isn’t possible if you reserve the right to edit comments as you like to make them soft and hide critics. The name of such behavior is censorship. Worse than censorship. It would be just censorship if you just had deleted the comment. There is also manipulation of my phrases out of context.

There are two alternatives:
1 – You restore my comment at it’s initial content, and in this case there is a possible conversation.
2 – You delete the reconstructed comment as it does not correspond to my opinion. ASAP.

Whatever your decision, the case was posted at the Web already, and I’ll take care to publicize the way the JTF conceives the term « Conversation ». []

Please, keep me informed,

Antoine Vekris

PS copy will be included at

Update 23 april 2008, 20:00 CEST

Charles Harper replied to my message and he forwarded it to the competent persons. Thank you Dr Harper.
Gary, from the JTF, contacted be to explain the situation he created by editing my comment. He is the one guilty and he apologies for. He deleted the comment (option 2). I would like to thank him publicly for doing so. Below the fold my reply to his message. Lire la suite »

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