ADVANCES IN ECOLOGICAL SPECIATION (AES) Conference, Portugal, 29-30 April 2013

I just received the following info about the AES Conference:

ADVANCES IN ECOLOGICAL SPECIATION (AES) Conference, CIBIO/UP, Portugal, 29-30 April 2013

LIVE BROADCAST of the AES Conference!

We are happy to announce that the AES Conference can be followed Live on streaming from http://tv.campusdomar.es/directo.html

If you want to join us please check out the program of the AES Conference from our website (http://www.aes-cibio.org/). The Live broadcast will be on Portugal local time (UTC/GMT+1hour).

Invited Speakers:

Dolph Schluter (Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, Canada)
Felicity Jones (Friedich Miescher Laboratory of the Max Planck Society, Tubingen, Germany)
Walter Salzburger (Zoological Institute, University of Basel, Switzerland)
Sebastien Renaut (Botany Department, University of British Columbia, Vancouver, Canada)
Roger Butlin (Department of Animal and Plant Sciences, University of Sheffield, UK)

You can also follow the AES Conference on:

https://www.facebook.com/AdvancesInEcologicalSpeciation

https://twitter.com/aes_cibio

The conference videos will be available afterwards at the Campus do Mar website, and you can dowload the book of abstracts right now.

eLife pursuing the niche of exclusiveness

Which I don't blame them really, they are better positioned than others to explore the limelight publications. I just read this FAQ about it:

Helping your findings achieve maximum reach and impact – Your article will be selected by notable life science colleagues from around the world and published alongside work that is judged to be amongst the most outstanding in its field. Impact statements from editors, along with plain language summaries and commentary from thought leaders will help to explain the significance of the work.  And, your article will be immediately and freely available to the world.

It's also mentioned the confidentiality of the editorial process, remuneration of academic editors, and it's emphasized their distinction from megajournals (PLoS ONE?), in that they are really into potential impact. My comments on twitter:

mixed feelings about @eLife_sciences. Looks perfect, except for emphasis on impact (glamour?) ow.ly/b0j2G
— Leonardo Martins (@leomrtns) May 18, 2012

some fields/subfields are just not attractive. And we are seeing a raise of poor works w/ high impact. good impact measures take time (1)
— Leonardo Martins (@leomrtns) May 18, 2012

and peer reviewers are not that good at evaluating impact and technical soundness at once. Editors might be better at evaluating impact (2)
— Leonardo Martins (@leomrtns) May 18, 2012

but still, real impact is a posteriori, At first we can mostly say if it sells -- and TV is here to show us how it ends. (3)
— Leonardo Martins (@leomrtns) May 18, 2012

OTOH I understand there is a niche to be filled by "next gen" publications, of more "exclusive" research (4)
— Leonardo Martins (@leomrtns) May 18, 2012

The level field of potentially significance is uneven, including its overlap with novel research -- a novel method might not be as fancy as an old method on a novel data set, or an old data set on a novel computing facility. Furthermore there is the problem of field glamour: an editor pressed to chose between two equivalent papers from fields A and B may consistently attribute more impact to field B. And we have been seeing that controversial research sells, non-replicable research sells, big names with loose oversight sells, and publication bias is a problem with devastating consequences for science. And corrections to flawed research do not sell, small niche development do not sell.
What I wanted to stress out but I was reaching my twitter-fu limits is that it's on "impact/significance" that reviewers can weight in with all weird subjectivities. So to help solving the increasing complains about peer review, publications should really reduce or eliminate reviewers' right to clairvoyance. In many cases reviewers can really spot a game-changing manuscript or detect a dull result. But in many other cases they will even unconsciously see more platitudes than there actually are, or praise a work because of its implications neglecting its truthfulness, or even mistake a poor phrasing for an uninteresting paper. And the secrecy of the review process encourages such behavior. I'm not saying to get rid of impact projections, but please don't leave it to reviewers -- the fact that academic editors are being paid can be a good justification for them assuming this responsability (maybe this is their plan anyway.)
There's much more to be said, lins to be linked, but my coffee break is over -- and I might be missing relevant information about it. In the end I really like the idea of eLife, although it seems to be taking a very conservative approach -- perfectly understandable given the risk aversion of stablished brands, but a shame to see one of the best recent opportunities lost (e.g. to offer post-publication impact evaluation,  to accredit peer reviewers by publishing their reviews, allow updates on article, and so many other ideas that in my naiveté I thought scientists might be willing to explore.)

Workshops in August: Bayesian phylogenetics on UC Berkeley and Statistical Genetics course in Barcelona

From Evoldir (check the links for more info):

Eighth annual Statistical Genetics Short Course

• When: Monday, 22 August - Friday, 26 August
• Where: Barcelona, Spain. Hosted by Centre Nacional d'Analisi Genomica (CNAG)
• more information here

Each day will include hands-on computer exercises using statistical genetics computer programs, especially the Mendel software package, with its new graphical front-end.

We will cover the general theory behind the methods as well as emphasize the practical aspects needed to give the best chances of success. The Course is designed to assist people who will be performing statistical analyses to discover the genetic basis of complex traits. The methods covered are appropriate to both human and non-human populations.

Mini-symposium on Bayesian inference of phylogeny

• When: August 15 - 16 (talks), August 17 - 19 (workshop on RevBayes for interested developers)
• Where: UC Berkeley campus

There will be a mini-symposium on Bayesian inference of phylogeny to be held on the UC Berkeley campus from August 15th to 19th. There will be two days of talks (August 15th and 16th) on various aspects of Bayesian inference as it applies to the phylogeny problem. The following three days will be a workshop for people interested in developing for the RevBayes program. RevBayes implements an R-like language for specifying complex evolutionary models and (attempts) to perform solid statistical estimation of a model's parameters.

Confirmed speakers include: Michael Jordan (UC Berkeley), Ian Holmes (UC Berkeley), Jeff Thorne (NCSU), Fredrik Ronquist (Swedish Natural History Museum), Jeet Sukumaran (KU), Sebastian Hoehna (Stockholm University), Tracy Heath (UC Berkeley), and John Huelsenbeck (UC Berkeley)

Newly lauched Open Access journals of interest

Almost two years ago I compiled a list of new "Open Access" publications, many of which turned out not to be Open Access at all. Here is a list of other Open Access (to the best of my knowledge) journals released since then. I tried to make sure that these journals are indeed Open Access (as opposed to "free to read" but still prohibiting other uses), but please feel free to correct me in any case.

• mBio

As ASM's first broad-scope, online-only, open-access journal, mBio offers rapid review and publication of the best research in microbiology and allied fields. The new journal continues ASM's nonprofit publishing mission and is edited by scientists involved in active research.

• SAGE Open

SAGE Open is a new open access publication from SAGE. It publishes peer-reviewed, original research and review articles in an interactive, open access format. Articles may span the full spectrum of the social and behavioral sciences and the humanities.

• BMJ Open
  

BMJ Open is an online-only, open access general medical journal, dedicated to publishing medical research from all disciplines and therapeutic areas. The journal publishes all research study types, from study protocols to phase I trials to meta-analyses, including small or potentially low-impact studies.

• G3: Genes, Genomes, Genetics

G3: Genes, Genomes, Genetics meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of Genetics, with an emphasis on research issuing from the emerging style of genetics research, with its increasing reliance on genome sequence information. G3 publishes: 1) Research of interest to a wide range of biological disciplines, including microbiology, mycology, zoology, botany, and agriculture; 2) Research in established and emerging model organisms; 3) Research in human and medical genetics;

• Scientific Reports

Online and open access, Scientific Reports is a primary research publication from the publishers of Nature, covering all areas of the natural sciences. Hosted on nature.com -- the home of over 80 journals published by Nature Publishing Group and the destination for millions of scientists globally every month -- Scientific Reports is open to all, publishing technically sound, original research papers of interest to specialists within their field, without barriers to access.

• Open Research Computation

Open Research Computation publishes peer reviewed articles that describe the development, capacities, and uses of software designed for use by researchers. Submissions relating to software for use in any area of research are welcome as are articles dealing with algorithms, useful code snippets, as well as large applications or web services, and libraries. Open Research Computation differs from other journals with a software focus in its requirement for the software source code to be made available under an Open Source Initiative compliant license, and in its assessment of the quality of documentation and testing of the software.

• Open Biology  [update: added on 2011.08.10]

"The Open Biology Editors and Editorial Board are practising scientists who will actively engage in the review of submitted papers. Our intention is to publish research of the highest quality and to ensure a fair and speedy review process. I hope that by streamlining the review system and putting  everything into the hands of active scientists, that we can do something valuable for our respective communities. Above all, I want Open Biology to be a high profile journal run by biologists for biologists; where acceptance of a paper is based on quality and merit rather than the headline."

Professor David Glover, Editor-in-Chief

And the announcement of three big research organizations planning to launch an Open Access journal for Biomedical and Life Sciences":

The Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust announced today that they are to support a new, top-tier, open access journal for biomedical and life sciences research. The three organizations aim to establish a new journal that will attract and define the very best research publications from across these fields. All research published in the journal will make highly significant contributions that will extend the boundaries of scientific knowledge.

Talk at UVigo: Fine-grain parallelism of MrBayes on multi- and many-core architectures, by Frederico Pratas

Announcement I received about an invited talk at my building, since my group is part of the Galician Network of High Performance Computing (R-GHPC2). I guess the talk will be given in english -- at our meetings we usually find a common ground between english, spanish, galician and portuguese.

Thursday, June 30th of 2011, 12:00 PM
Room 3, Wing B, ground floor of the Experimental Sciences building, University of Vigo

Fine-grain parallelism of MrBayes on multi- and many-core architectures
Frederico Pratas, from the Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento (INESC-ID), Lisboa, Portugal

Currently, we are facing a situation where applications exhibit increasing computational demands. In particular, we observe a considerable increase of complexity in algorithms due to both the increasing amounts of data available for analysis (e.g., genomic databases) and the need for more accurate and precise results (e.g., more complex particle interaction models). In this talk we address how MrBayes, a bioinformatics application that performs Bayesian inference of phylogenetic trees, can benefit from modern multi- and many-core computing architectures. We focus on exploiting fine-grain parallelism by distributing the evaluation of the conditional likelihoods (cl). Namely, we use different types of architectures: General-purpose Processors, Graphics Processing Units (GPU) and Cell Broadband Engine (Cell/BE). Besides, reconfigurable hardware can also be used as a very efficient co-processing solution to accelerate this type of applications. Therefore, we also consider the design steps and implementation of MrBayes on Field Programable Gate Arrays (FPGAs). Overall the results show that, although we can efficiently accelerate the computation of cl on GPUs and FPGAs due to their characteristics, there are still important constraints related with the access to the data in the main memory, which incurs in huge overheads. The general-purpose processors show the best results in terms of speedup.

This talk is supported by the Galician Network of high Performance Computing.
PS: In a previous communication, the address was "Room S4, Wing C, 2º floor" but there should be no problem since they are very near.

This week's readings

Lift the veil of secrecy over peer review - New Scientist:

But the authors of the protest letter suggest a compromise, which should make abuses easier to spot while preserving the main strength of peer review: keep anonymity, so scientists aren't discouraged from being critical, but publish the reviews and editorial correspondence. Indeed, The EMBO Journal already does this.

For justice to be seen to be done more widely, other journals should follow this lead. Like democracy, peer review may be flawed but it's the least-worst system we've got. It should be nurtured, through exposure to a little more sunlight.

To be a science ignoramus is simply not on - Times Online:

To ordinary people our top universities often seem somewhat elite and mysterious where arcane subjects are explored. Universities should foster a culture of open access and strengthen educational activities in the community and in schools.

In the past, the mark of a civilised person was an appreciation of Shakespeare, Thucydides, Rembrandt and Beethoven. Today the pursuit of science is so demanding that scientists are more likely to neglect their cultural inheritance. Perhaps, by broadening our own interests, we scientists may also help non-scientists see science more as part of our culture.

Are We Training Too Many Scientists? - The Scientist:

Career disappointment for postdocs is not just about finding a job, it's finding a job that is rewarding: one that pays reasonably well and offers a career path. The recent prospects for PhDs - rising numbers of postdocs, few tenure track positions, and poor funding - do not live up to that expectation. (...) The unintended consequence of the shortage of faculty positions was longer postdoctoral fellowships as young scientists received low wages, endured little job security or respect, and delayed starting families while waiting for a job.

Shrinking budgets + skyrocketing subscription fees = UC boycott of NPG  - Adventures in Ethics and Science:

Scientific publication, after all, isn't just about keeping score. It's also about communicating findings, ideas, techniques, and conclusions. And NPG surely has no monopoly on the technologies by which that communication can -- and will -- take place.

I also made a comment on the NatureNews report about the last Brazilian scientific meeting - which had very nice talks as well (link in pt_BR).

PS: HT to @BioMedCentral for some of the links.

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.

Anything goes on the internet

The "Special report: Living in denial" issue of the New Scientist (12 May 2010) has some interesting articles. Two excerpts below.

When a sceptic isn't a sceptic (by Michael Shermer):

A climate sceptic, for example, examines specific claims one by one, carefully considers the evidence for each, and is willing to follow the facts wherever they lead. A climate denier has a position staked out in advance, and sorts through the data employing "confirmation bias" - the tendency to look for and find confirmatory evidence for pre-existing beliefs and ignore or dismiss the rest.
(...)
It has, for example, become fashionable in some circles for anyone who dares to challenge the climate science "consensus" to be tarred as a denier and heaved into a vat of feathers. Do you believe in global warming? Answer with anything but an unequivocal yes and you risk being written off as a climate denier, in the same bag as Holocaust and evolution naysayers. (...) When I say "I believe in evolution" or "I believe in the big bang", this is something different from when I say, "I believe in a flat tax" or "I believe in liberal democracy".
(...)
What sometimes happens is that people confuse these two types of questions - scientific and ideological. Sometimes the confusion is deliberate. Denial is one outcome. Thus, one practical way to distinguish between a sceptic and a denier is the extent to which they are willing to update their positions in response to new information.

Questioning science isn't blasphemy (Michael Fitzpatrick):

As philosopher Edward Skidelsky of the University of Exeter, UK, has argued, crying denialism is a form of ad hominem argument: "the aim is not so much to refute your opponent as to discredit his motives". The expanding deployment of the concept, he argues, threatens to reverse one of the great achievements of the Enlightenment - "the liberation of historical and scientific inquiry from dogma". Don't get me wrong: the popular appeal of pseudoscience is undoubtedly a problem. But name-calling is neither a legitimate nor an effective response.
(...)
Such attempts to combat pseudoscience by branding it a secular form of blasphemy are illiberal and intolerant. They are also ineffective, tending not only to reinforce cynicism about science but also to promote a distrust for scientific and medical authority that provides a rallying point for pseudoscience.

I also liked Jim Giles's article about how easy it is to spread a lie, and how hard to fix it nowadays.

High Performance Computing conferences in Galicia - May 2010

Next week there will be two meetings here in Galicia on HPC (that I am aware of, at least). The first is Tuesday, on Santiago the Compostela:

Título: Open Cirrus Cloud Computing Testbed
Ponente: Dejan Miljicic, Senior Researcher at HP and Managing Director OPEN CIRRUS
Data: 18 de Maio do 2010
Hora: 11:30h.
Lugar: Sala de Presentaciones do CESGA (Avda. de Vigo s/n)

ABSTRACT:
There are a number of important and useful testbeds, such as PlanetLab, EmuLab, IBM/Google cluster, and Amazon EC2/S3, that enable researchers to study different aspects of distributed computing. However, no single testbed supports research spanning systems, applications, services, open-source development, and datacenters. Towards this end, we have developed Open Cirrus, a cloud computing testbed for the research community that federates heterogeneous distributed data centers. Open Cirrus offers a cloud stack consisting of physical and virtual machines, and global services, such as sign-on, monitoring, storage, and job submission. By developing the testbed and making it available to the research community, we hope to help spur innovation in cloud computing and catalyze the  development of an open source stack for the cloud. In addition to presenting Open Cirrus, this talk will also include a number of important research effort currently undergoing in Open Cirrus, such as Cloud Sustainability Dashboard, OpenNet, ExaScale Data Center, Mercado (Cloud Services market Places), Federation of Open Cirrus and Planet Lab/GENI, etc.

And the second is the Workshop of the Galician Network of HPC, here in Vigo, on Friday:

Aplicaciones de la Supercomputación

Programa

Fecha: 21 de Mayo de 2010
Lugar: Salón de Actos del Edificio de Ciencias Experimentales, Campus Universitario, Universidad de Vigo, Vigo

Horarios

09:50 Apertura y presentación del WorkShop e invitados

10:00 Iain S. Duff - STFC Rutherford Appleton Laboratory, Oxfordshire, UK and CERFACS, Toulouse, France
Título: The solution of really large linear systems arising from discretizations of three-dimensional problems

10:45 Alexandros Stamatakis - Technische Universität München, Germany
Título: Orchestrating Phylogenetic Likelihood Computations on Parallel Architectures

11:30 Coffee Break

12:00 Andrew Gettelman - National Center for Atmospheric Research, Boulder, CO, USA
Título: Simulating Earth's Climate and Chemistry with the Earth's Biggest Computers

12:45 Clausura del WorkShop

Soon it will take a Ph.D. to rap

Here is the latest addition to the list of academic contributions to rap. In a sense.

A few other ones after the break:

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"...

When Science meets politics and likes it - update on Climategate

This week's round-up of interesting commentaries:

• Professor Judith Curry's lucid commentaries on the dotearth and ClimateAudit blogs
• Janet D. Stemwedel nails down the relevant ethical implications of the case - she elegantly avoids politically contentious issues
  
• The Curmudgeon is not happy about the vindication of the creationists (great read)
• Phil at Andrew Gelman's blog is surprised at how scientists buy the skeptic arguments (his analogy was not appropriate, but this was fixed in the comments)
  
• Daniel Henninger talks about the danger of allowing for a postmodernist politicization of Science
• Andrew Revkin shows that the "contrarians-deniers-skeptics" are not alone in having too many strings attached (here, here, and here you can see examples supporting this view)
• Chris Mooney and Matthew C. Nisbet seem to be outraged that the "contrarians-deniers-skeptics" dared to frame Climategate. And they thought that they had a monopoly on this rhetoric trick... to make things worse, they try to fix it by reframing it as a dispute between left and right wings. This name-calling always work against reason (in this case, science).
• Gavin Baker points that the solution to many of these issues relies on Open Access.

update 2009.12.14: I just realized that Andrew Gelman is not the only one to write on his blog, some posts are written by a mysterious "Phil". I corrected the entry.