Sao Paulo Advanced School of Astrobiology - SPASA 2011

I received this announcement from an alumnus friend, who is one of the organizers.

Sao Paulo Advanced School of Astrobiology -SPASA 2011 -- Making Connections

The applications are open for the "Sao Paulo Advanced School of Astrobiology – Making Connections (SPASA 2011)", promoted by the Department of Astronomy of the Universidade de Sao Paulo and by the Sao Paulo Research Foundation (Fapesp), Brazil.

Location: University of São Paulo, São Paulo, Brazil
Date: December 11 -- 20, 2011
Home Page: www.astro.iag.usp.br/~spasa2011
Target audience: Undergraduate, graduate students and early career post-docs in biology, physics, astronomy, chemistry, earth sciences and related areas.
Application Deadline: September 20, 2011, through the event website.
Language: English

Objective: Astrobiology is a multidisciplinary field that aims to study origin, evolution, distribution and future of life on the Universe, with a broad and multidisciplinary scope, requiring a constant dialogue between different areas. This is a new and very promising scientific research field, with the ambitious goal of seeking for answers to some of the most complex scientific questions. The SPASA aims to bring together renowned experts from different countries with students of different fields in a multidisciplinary event that will address some of the general themes of research in astrobiology, as well as more specific topics in the frontier of science that are being developed worldwide. Stimulating the connection between topics and the exchange of knowledge among the participants is the main goal of the event.

Selected participants from all countries will have travel and accommodation expenses covered by the Sao Paulo Research Foundation.

some more links from iEvoBio

Continuing with my twitter voyeurism of iEvoBio, here are some web pages (softwares and servers) mentioned today at the meeting:

• http://geophylo.appspot.com/
• http://datadryad.org/
• http://www.treebase.org/treebase-web/home.html
• http://ispecies.org/
• http://iphylo.org/linkout/Main_Page
• http://code.google.com/p/biodiverse/
• http://www.cs.auckland.ac.nz/~remco/DensiTree/DensiTree.html
• http://packages.python.org/DendroPy/
• http://code.google.com/p/beagle-lib/
• http://phylo.bio.ku.edu/software/sate/sate.html
• http://code.google.com/p/dadi/
• http://bioinfo-srv1.awh.unomaha.edu/phylomarker/
• http://www.iplantcollaborative.org/grand-challenges/about-grand-challenges/current-challenges/iptol/tree-visualization
• http://cortana.biochem.dal.ca/software/
• http://www.tolkin.org/
• http://gramene.org/
• http://www.pypop.org/
• http://www.stat.wisc.edu/~ane/bucky/index.html
• http://picante.r-forge.r-project.org/
• http://mol.colorado.edu/
• http://code.google.com/p/gensent/
• http://code.google.com/p/treezip/

There is also a Nature Preceedings collection  about the event that is certainly worthwhile to take a look.

(I might update this entry later if other links appear. Stay tuned!)

some links from iEvoBio - the poor guy's bookmarking

OK, let me just note down these interesting links discussed at iEvoBio - I'm not there but the tubes are - while I prepare for SMBE next week.

• http://leptree.net/
• http://www.evoio.org/
• http://www.nexml.org/
• https://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS
• http://www.evolutionaryontology.org/
• http://www.eol.org/
• http://lifewatch.eu/
• http://www.cate-project.org/
• http://scratchpads.eu/
• http://kiwi.cs.dal.ca/GenGIS/Main_Page
• http://prefuse.org/doc/api/prefuse/data/Tree.html
• http://www.cs.nmsu.edu/~cdaostore/
• http://markov.uoregon.edu/software/phyesta/
• http://gmod.org/wiki/Main_Page
• http://www.obofoundry.org/cgi-bin/detail.cgi
• http://www.ibarcode.org/nextgen
• http://www.dnabank-network.org/
• http://www.dataconservancy.org/
• http://phylotouch.jsphylosvg.com/
• http://code.google.com/p/phylobox/ and http://phylobox.appspot.com/
• http://exon.niaid.nih.gov/nexplorer/
• http://synthesis.eol.org/news/eol-treemap-viewer and http://kurie.github.com/EOL-tree-viewer/#COL
• https://www.phenoscape.org/wiki/Phenex
  

via @rdmpage and @phylogenomics (this blogpost will be updated a few times...)

Geno-luddites on the rise

There is a very nice, though short discussion on the cut-and-paste of a bacterial genome onto its cousin at Edge's Reality Club. This comment by Nassim N. Taleb called my attention:

If I understand this well, to the creationists, this should be an insult to God; but, further, to the evolutionist, this is certainly an insult to evolution. And to the risk manager/probabilist, like myself & my peers, this is an insult to human Prudence, the beginning of the mother-of-all exposure to Black Swans.

And if I understood correctly his position, we shouldn't do anything that exposes us so much to Black Swans. I agree that some aspects of this research (and all the news coverage that followed)  downplays the role of evolution. But as reminded by PZ Myers in the same discussion, there is a much larger number and variety of naturally-occurring threats to us. (HT @aerocleber).

PS: The title comes from this post, brought to my attention by @phylogenomics.

God and Darwin in the Land of the Sun

For 59% of the Brazilians, humans are the result of millions of years of evolution, but guided by a supreme being, according to a Datafolha survey. On the other hand, 25% of the participants believe that the human being was created by god less than 10 thousand years ago and another 8% think that evolution takes place without god's intervention. The proportion of creationists was higher among lower income and less educated people. The dataset was composed of 4158 people older than 16 years old. I cannot provide more details now since 1) the full newspaper article is behind a paywall and 2) these surveys tend to be poorly designed, with ambiguous terms (e.g. in the free version of the article they mention the terms "Darwinists" and "creationists" along with the descriptions...) so that I should look at the details before commenting.

My impression is that this theistic evolution view of Brazilians reflects the catholicism to which many people loosely identify with - those self-proclaimed "non-practicing" catholics. The creationists are more frequent among the protestant churches, like the conservationist Marina Silva who is now a candidate for presidency. She has strong ties with religious movements and when questioned about her defense of the teaching of creationism backpedalled using the "let the children decide" argument.

Paraphrasing the great journalist Josias de Souza, Brazilians believe more in president Lula (76%) than in the evolution of the species.

PS: The post title is a reference to the cult Brazilian movie Black God, White Devil.
PPS: most links are in portuguese...

How many microbes live on Earth?

Jonathan Eisen posted on his twitter an  interesting news on BBC about his most recent publication on Nature ("A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea", Nature 462:1056-1060). First of all, congratulations for the nice work! Since the original BBC article is in Spanish, I have tried to translate it here. You will soon realize that neither English nor Spanish are my first languages; I'll fix the mistakes as they are spotted by someone, and I assume responsibility for the remaining errors.

Scientists from US and Germany presented the first issue of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) that collects all living microorganisms on Earth.

It is expected that the publication - whose details appear on Nature Magazine - help researchers to better understand the several roles played by the microorganisms on this planet. It is estimated that the Earth harbors around one nonillion (1 followed by 30 zeros) microbes and despite around 2000 microorganisms already have their genomes deciphered, a large number remains unexplored. The Encyclopedia is being compiled by the Joint Genome Institute under the US Department of Energy, and the German Collection of Microorganisms and Cell Cultures.

Only single-celled ones

"This is a rich sample of the diversity of microbe genomes" says professor Jonathan Eisen, main author of the investigation. "To rely on a better sampling of the whole tree of life give us a better reference point to predict gene functions" he adds. The encyclopedia includes all prokaryotic organisms of the planet, which means the unicellular organisms. Unlike eukaryote organisms like us, yeast and the fungi, the prokaryotic cells don't have a membrane covering their DNA. This organisms are divided in two large groups: the Bacteria, which include the small minority of pathogens that makes us sick, and the Archaea, which are organisms that can survive in extreme environments like thermal waters. Up until now there have been sequenced around one thousand prokaryotic genomes. Almost all of them are pathogenic organisms.
According to professor Eisen "it has been like tracing a world map and including only three cities". Now the new encyclopedia analyzes the main representatives of the big branches of the prokaryotic family tree and the present study shows 56 genomes of this group. As explained by the scientists, even though it is known that microbes can exchange genes with other species (a process called lateral transfer) their position in the family tree, called phylogeny, is more important when we want to pinpoint where new genes appear and how they spread.

The beginning

"Microbes are mediators in almost all known biological processes of the planet" says professor Eddy Rubin, project leader. "And the sequencing of their genomes have revolutionized our understanding of the diverse roles they play". The information obtained with this first group of 56 organisms, adds the scientist, may help researchers in improving processes like biofuel production, bioremediation (to "clean" contaminated surroundings), and the way by which carbon is sequestered in the environment. According to the investigators, this is just the beginning of the project and they expect to be able to sequence all the diversity of microorganisms on Earth, including the hundreds or maybe thousands of microbe genomes currently unknown.  "The known phylogenetic diversity of Bacteria and Archaea is huge, with hundreds of big lineages and probably millions or hundreds of millions of species" says professor Eisen. "This encyclopedical project is starting from the top - with the big phylogenetic groups - with 100 genomes from all tree. "But we are just scratching the surface in the characterization of Earth's diversity" adds the researcher.

My only dispute in this article is that they lead to the impression that all single-celled organisms are prokaryotes. Yes, they fix that in the next sentence when they mention yeasts - which are (mostly?) unicellular - as eukaryotes, but then (unless my semantic interpretation is wrong) they introduce another misunderstanding since yeasts are fungi. But now I understand how hard it must be to convey concepts like phylogeny or Archaea to a broad audience. And I am not sure if "leader" is the best translation for "director"...

Misconceptions about evolutionary terms

I recently saw an article in Evolution:Education and Outreach (doi:10.1007/s12052-009-0187-3) where the authors utilized the word "evolutionism" in the abstract. "Evolutionism", as well as "Darwinism", are not words I usually encounter on scientific publications, given their ideological/rhetoric connotation. But it happens that the authors are Brazilian (like myself), and I must admit that the usage of terms is more loose in terra Brasilis. Nonetheless I still wish we become more careful about the usage of words...

Yes, I know the definition from the dictionary, and that "evolutionism" was popularized by Herbert Spencer to promote social Darwinism (whose only connection to Darwin's work was a misappropriation of what he interpreted as "survival of the fittest"), and that the term "Darwinism" was coined by A.R. Wallace to refer to the principle of natural selection in Darwin's work. But continuing on my newest tradition of aggregating other material from the net, here are some links to comments about these loaded words.

Evolutionism @ http://en.academic.ru:

Creationists tend to use the term evolutionism in order to suggest that evolution and creationism are equal in a philosophical debate. (...) Most scientists object to the terms "evolutionism" and "evolutionist" because the -ism and -ist suffixes accentuate belief rather than scientific study. Conversely, creationists use those same two terms partly because the terms accentuate belief, and partly perhaps because they provide a way to package their opposition into one group, seemingly atheist and materialist, designations which are considered to be irrelevant to natural science.

Wikipedia entry for Evolutionism:

In the modern scientific community the term is an anachronism and is considered redundant as the overwhelming majority of scientists accept evolution, and so it is not used. To say someone is a scientist implies evolutionary views. In the creation-evolution controversy, creationists often call those who accept the validity of the modern evolutionary synthesis "evolutionists" and the theory itself as "evolutionism." Some creationists and creationist organizations, such as the Institute of Creation Research, use these terms in an effort to make it appear that evolutionary biology is a form of secular religion.

The Evolution-Creation Struggle @ Living the Scientific Life [February 20, 2006]:

Let me make this clear: evolutionism is not evolutionary science and evolutionary biologists are not necessarily evolutionists. Evolutionary biology comprises a set of interrelated facts that support a testable theory describing the mechanisms that result in evolutionary change in living organisms throughout time. (...) By contrast, evolutionism provides spiritual and ideological philosophies built on or around a scientific narrative (namely, evolution) and proposes a progressive worldview based on directed mechanisms of organic change.

"Dogmatic Darwinists" - An Instance of the Misleading Rhetoric of the Anti-Evolutionists @ The Panda's Thumb [March 31, 2004]:

Calling evolutionary scientists "Darwinists" is simply a way of marginalizing mainstream science and scientists. The same could be said about the term "evolutionists," as it carries the connotation of someone fighting for belief in evolution (religious-style) instead of scientists working on evolution, whether it be biologists, geologists, paleontologists, biochemists, etc.

Let’s Get Rid of Darwinism @ Opinionator Blog - NYTimes.com [July 15, 2008]:

Then there are the words: Darwinism (sometimes used with the prefix “neo”), Darwinist (ditto), Darwinian. Why is this a problem? Because it’s all grossly misleading. It suggests that Darwin was the beginning and the end, the alpha and omega, of evolutionary biology, and that the subject hasn’t changed much in the 149 years since the publication of the “Origin.”

Good riddance, Darwinism @ Laelaps [July 16, 2008]:

I've
never liked the term "Darwinism." To me it has always been more of a watchword that might indicate that I was talking to a creationist, a term I generally do not encounter unless I'm  reading or hearing an argument against a straw-man version of evolution. (I'm not a big fan of "evolutionist," either.) It may have been useful in the past, when evolution by natural  selection (as popularized by Darwin) was competing with other systems like Neo-Lamarckism and orthogenesis, but today it doesn't have any relevance.

Darwinism @ The Frontal Cortex [July 16, 2008]:

If "Darwinism" should be a synonym for anything it should be the ideology of unrepentant materialism (theory of everything that didn't depend on any unknowable and intangible   forces), which is the underlying philosophy of modern science.

Down with Darwinism! @ Gene Expression [July 17, 2008]:

Do we talk about Newtonism? Einsteinism? We do talk about Epicureanism, Platonism, Neo-Platonism, Aristotelianism, etc. I think that says it all....

I Don't Like the Word Darwinism Either @ Mike the Mad Biologist [July 17, 2008]:

Of course, creationists will always call evolutionary biology Darwinism. One reason is that they don't know what they're talking about, and so, party like it's 1859. The other reason is that they can't afford to acknowledge that evolutionary biology is a dynamic growing field that successfully and continuously meets the challenge of new data.

Darwinism is Dead @ evolgen [July 17, 2008]:

Anyone who talks about "Darwinism" or "evolutionists" gets my attention. That's not to say that any use of those terms is incorrect. But they are often used as framing devices by creationists, and those frames get carried over into the lay discussion of biology.

Darwinism now affects intelligent design film! @ Evolving Thoughts (comment by Bob O'Hara) [April 13, 2008]:

Darwinism has never been about science, it's been about politics and being generally unpleasant to anyone who's inferior to us.

The Supposed Dichotomy between Creationism and Evolution @ National Center for Science Education [Spring, 1983]:

Among scientists the term [evolutionism] is an anachronism. There are no more "evolutionists" among biologists than there are "round-earthers" or "heliocentrists" among    astronomers, "Einsteinians" among physicists, or "antiphlogistonists" among chemists. We may say of a person that he or she is right-handed because there are many who are  left-handed, but we would never say of someone that he or she is "one-headed" simply because to say he or she is a person implies as much. So too, to say a person is a scientist encompasses the fact that he or she is an evolutionist. In scientific circles the term is redundant and is, therefore, never used.

Darwin as a False Idol @ evolgen [November 1, 2006]:

'Darwinism' is a meaningless term in biology. Yes, Darwinian selection has meaning (as a synonym for positive selection), but what the hell is Darwinism? Aside from a term creationists  use instead of saying 'evolution', Darwinism is as vacuous a word as creationism is a science. Stop referring to evolution as Darwinism if you respect science.

On the incoherence of "Darwinism" @ Evolving Thoughts [April 15, 2007]:

For a long time now, I have had troubles with the use of the word "Darwinism". Not just by creationists and antiscience advocates like IDevotees, but by scientists themselves. (...) Basically, when a term has no definition, or has too many definitions, it cannot be a term capable of being defined. But there is another way the term might have some reference - as a name. That is, as the name of a historical sequence of events. (...) So given these caveats, "Darwinian" can only mean "natural selection", which is historically problematic because Darwin's real originality lay not in that notion, but in the recognition that life diversified in a historical tree, which we call Common Descent" or "Phylogeny".

Ummm...what? @ From the Quantum to the Cosmic [March 26, 2008]:

During the Q&A session one young man stood up and asked Dawkins why he used the term Darwinism when referring to the theory of evolution. While noting that it is still common to do so in England, most American scientists eschew the term because of the manner in which it plays into the hands of creationists. We don't speak of Newtonism or Einsteinism, the young man pointed out, and referring to the theory of evolution as "Darwinism" might give some the mistaken view that evolution is nothing more than a religion or cult of personality.

Now here's the really amazing thing: despite being about 30 years the young man's senior, Dawkins thoughtfully assented. He agreed that the young questioner had a point, one which he hadn't fully considered before. Perhaps "Darwinian" has it's place, but maybe "Darwinism" should be retired as too likely to be misconstrued. We in the audience saw a respected writer and science advocate who was willing to reevaluate himself and his choice of expression, and we all loudly applauded Dawkins' open-mindedness and willingness to change. It was a great moment.