If working hard is not for you, at least you can look busy...

Via @michaelshermer, I found this series of anti-motivation posters which actually speak the truth very well. Some examples:

Let's blame someone for the scientific illiteracy

I just read the article "Why do people reject science? Here's why ..." by Stephan Lewandowsky, and despite I agree with many of his points, the narrative worries me a little bit. Some comments of mine follow below the quotes:

The historical evidence is overwhelming that some of that opposition has been organised by vested interests, often successfully delaying political and regulatory action that posed a perceived threat to corporate profits. The peer-reviewed literature has clearly identified the subterfuge, distortion and manufacture of doubt with which vested interests delayed the control of tobacco, CFCs and sulphur emissions.

"Vested interests" are not restricted to big corps, they also apply to small corps -- even at the individual level. To fingerpoint at money is not enough (to be fair, the author aknowledges it later), and everybody have expectations of profit, not only "corporations". To have some commercial relation does not transform you in "evil", and to be free from it does not mean you are uninterested. Publicly funded researchers may struggle to keep being publicly funded in similar ways as privately funded ones (Lysenkoism was not a "corporate scam", for instance).

The notion of threat is key to understanding the rejection of evidence; whether it’s by vested interests, by mediocre scientists fearful of becoming outdated, or by the public at large when confronted by inconvenient science. (...) Perhaps most relevant to present public debate are threats to people’s “worldviews” – the very fundamental beliefs people hold about how the world should be organised.

But even outstanding, "altruistic" and handsomely rich sicentists (even as a collective body) can be resistant to evidence and "inconvenient science" -- it is part of the regular, skeptical peer review process. When new science comes up most scientists won't laugh in epiphany, and not because they are particularly evil or stupid. Maybe they need to reproduce the results themselves, or they lack the theoretical background for this specific result (scientist do not have priviledged access to The Truth, they also need to RTFM from time to time), or they genuinely demand that the new research programme must improve over existing methods in explaining all existing evidence. An analogous process of healthy suspicion might take place with the public at large, not because they are averse to progress but because we are averse to risk. Since the public may have simplified/incomplete views of the scientific process the outreach becomes more relevant, and be not only politically agnostic but perceived as so -- if you care to educate the public, that is.

Worldviews come in many shades and forms, but one prominent distinction — popularised by Professor Dan Kahan at Yale University — is between people whose worldview is “hierarchical-individualistic” and those whose worldview is “egalitarian-communitarian”.
Hierarchical-individualistic people (HI from here on) believe rights, duties, goods, and offices should be distributed differentially and on the basis of people’s own decisions without collective interference or assistance. Egalitarian-communitarian (EC) people, by contrast, believe rights and goods should be distributed more equally and society should bear partial responsibility for securing the conditions of individual flourishing.
Like all binary classifications, the distinction between HI and EC worldviews lacks nuance and oversimplifies the complexity of human worldviews.

It simplifies to the point of becoming useless -- it is a straw man version of individualism and a very charitable version of collectivism. Let me guess in what camp the distinguished professor wants to sit in...
This is the problem not only with this analysis, but with several other recent commentaries: if we could classify people between good and bad, it would be very easy to blame bad people for whatever problem we have at hand. First, I don't believe anybody would belong to the HI camp thus described (I don't know prof. Kahan's research so I am based solely on this article's description), since even the usual suspects believe in collective interference, and extreme individualism excludes hierarchy. And by usual suspects I mean those nasty ideological opponents that progressives retort to as "the other".
Second, and more importantly, this fixation in highlighting the differences between "us and them" is for me the definition of evil. Of course, recognizing the differences is natural and desirable (e.g. being capable of telling progressive from conservative ideas). But when this is used in a narrative to blame "them",make "them" responsible for something, or simply believing that detecting "them" is enough to solve the problem, we are paving the way for the destruction of empathy. And as everything else in politics, it usually goes well in the short term, but leads to catastrophic consequences...
We may be binary, but we don't fit into one byte.

In light of these data it’s not surprising there can be yawning gaps between scientific knowledge and public acceptance of that knowledge.

We must remember that the scientific community is also part of the public, and thus ignorant on many subjects. The problem then is when they neglect their own ignorance and treat it as part of their knowledge body. For example the scientist with a pretense of economical knowledge when in fact he is ignorant about it, and propose economically inane solutions as if they were part of the scientific knowledge. That is, they cannot see the distinction between descriptive and normative assertions. (To be clear, they are entitled to join the normative discussion, even as "experts", but not to confuse it with facts).
Scientists are great in determining the boundaries of their ignorance within their fields -- that is, they know quite well what they don't know and what can't be known -- but less so about other fields. The recipe to minimize this is to rely on the respective authorities in the field ("Don't know evolution? Then listen to evolutionary biologists. Not sure about climate change? Then read what experts have been discovering"), but for some reason Economics does not get the same love ("Economists? They are all stoopid"). And it becomes a problem when they step on each other's foot, proudly ignorant and certain of having found the problem on "them".

When you start believing "us and them" helps explaining things...

Conference on Astrobiology at the University of Vigo

Next Wednesday (November 16th) from 10:00 to 13:30 the University of Vigo will host a series of talks and a round table on "Astrobiology: the challenge of searching for life on the Universe today". It will take place at the Auditorium (Salón de actos) of the Experimental Sciences building. Judging by the poster, the talks might be in galician.

PS: I'm not involved in the organization of the event, just spreading the word.

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.

Effects and choices of food

Below there are a few links about recent research on food, as reported by Science Daily. Which means that the reported news are based on press releases -- and as such may be overly optimistic and certainly not the last word on the subject.

"New evidence that caffeine is a healthful antioxidant in coffee":

Scientists are reporting an in-depth analysis of how the caffeine in coffee, tea, and other foods seems to protect against conditions such as Alzheimer's disease and heart disease on the most fundamental levels.

"Coffee reduces breast cancer risk, study suggests":

Recently published research shows that coffee drinkers enjoy not only the taste of their coffee but also a reduced risk of cancer with their cuppa. More detailed research published May 10 in BioMed Central's open access journal Breast Cancer Research shows that drinking coffee specifically reduces the risk of antiestrogen-resistant estrogen-receptor (ER)-negative breast cancer

"Goat milk can be considered as functional food, Spanish researchers find":

Researchers at the University of Granada have found that goat milk has nutritional characteristics beneficial to health. They have determined that goat milk has many nutrients that make it similar to human milk.

"Anticancer effect of mushrooms demonstrated":

City of Hope researchers have investigated compounds in natural foods for their potential anticancer benefits, with a focus on food items that are easily found in grocery stores to ensure greater access and availability. Shiuan Chen, Ph.D., associate chair and professor of City of Hope's Department of Cancer Biology, identified phytochemicals in mushrooms that block the ezyme aromatase from producing estrogen. Controlling aromatase activity can help decrease estrogen levels, which controls and kills hormone-dependent breast cancers. In addition, mushrooms also demonstrate the ability to inhibit cancer call activity and slow tumor growth.

"Resveratrol studies confirms potential health boost":

A University of Florida review of research finds the polyphenol compound known as resveratrol found in red wine, grapes and other fruits may not prevent old age, but it might make it more tolerable. News stories have long touted resveratrol as a cure for various diseases and a preventative against aging.

"Changes in specific dietary factors may have big impact on long-term weight gain":

In a series of three separate studies looking at how changes in multiple dietary and other lifestyle factors relate to long-term weight gain, Harvard School of Public Health (HSPH) researchers found that modest changes in specific foods and beverages, physical activity, TV-watching, and sleep duration were strongly linked with long-term weight gain. Changes in diet, in particular, had the strongest associations with differences in weight gain.

"Are the French becoming bored with wine?":

One of the most familiar aspects of French culture -- its love of wine -- might be lost as successive generations abandon the imaginative representations of wine linked to national identity, according to a study in the International Journal of Entrepreneurship and Small Business. The findings suggest that the transmission of French wine heritage to future generations is in terminal decline.

"It's not an apple a day after all -- it's strawberries: Flavonoids could represent two-fisted assault on diabetes and nervous system disorders":

A recent study from scientists at the Salk Institute for Biological Studies suggests that a strawberry a day (or more accurately, 37 of them) could keep not just one doctor away, but an entire fleet of them, including the neurologist, the endocrinologist, and maybe even the oncologist.

"Red wine: Exercise in a bottle?":

As strange as it sounds, a new research study published in the FASEB Journal, suggests that the "healthy" ingredient in red wine, resveratrol, may prevent the negative effects that spaceflight and sedentary lifestyles have on people. The report describes experiments in rats that simulated the weightlessness of spaceflight, during which the group fed resveratrol did not develop insulin resistance or a loss of bone mineral density, as did those who were not fed resveratrol.

"Research reveals new secret weapon for Tour de France: Beetroot juice":

Winning margins in the Tour de France can be tight -- last year just 39 seconds separated the top two riders after more than 90 hours in the saddle. When every second counts, riders do everything possible to gain a competitive advantage -- from using aerodynamic carbon fibre bikes to the very latest in sports nutrition.

"Molecular gastronomy: Science behind the art of cooking":

Dr Juan Valverde believe that Molecular Gastronomy (a scientific discipline that studies what happens when we cook) has a lot of untapped potential in Ireland.

"Dry onion skin has a use":

More than 500,000 tonnes of onion waste are thrown away in the European Union each year. However, scientists say this could have a use as food ingredients. The brown skin and external layers are rich in fibre and flavonoids, while the discarded bulbs contain sulphurous compounds and fructans. All of these substances are beneficial to health.

"Why diets don't work: Starved brain cells eat themselves, study finds":

A report in the August issue of the Cell Press journal Cell Metabolism might help to explain why it's so frustratingly difficult to stick to a diet. When we don't eat, hunger-inducing neurons in the brain start eating bits of themselves. That act of self-cannibalism turns up a hunger signal to prompt eating.

"Can eggs be a healthy breakfast choice?":

Eggs, one of the most commonly consumed breakfast foods in the United States, have long been a subject of controversy. Are they healthy or are they a high-cholesterol trap? The answer depends on what the hen eats, says a Tel Aviv University researcher.

"Gazpacho ingredients lose vitamin C during preparation":

In summer, more dishes like gazpacho -a cold soup containing raw vegetables, bread, olive oil and vinegar- are consumed. A new study has revealed that ingredients' vitamin C content as well as other organic acids is lower in the resulting mixture, meaning that it should be eaten immediately after preparation.

 "Antioxidant spices, like turmeric and cinnamon, reduce negative effects of high-fat meal":

Eating a diet rich in spices, like turmeric and cinnamon, reduces the body's negative responses to eating high-fat meals, according to Penn State researchers.

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)

Nanatsu no Taizai -- Seven Deadly Sins

For some reason [1] I had this random note with the translations for the seven deadly sins, from the japanese wikipedia. As a reminder that this blog don't need to be so serious, let me share with you this useless piece of information (it also has the spanish and latin terms).

七つの大罪

大罪	たいざい	スペイン語	ラテン語	英語
傲慢	ごうまん	Soberbia	Superbia	Pride
嫉妬	しっと	Envidia	Invidia	Envy
憤怒	ふんぬ	Ira	Ira	Wrath
怠惰	たいだ	Pereza	Acedia	Sloth
強欲	ごうよく	Avaricia	Avaritia	Greed
暴食	ぼうしょく	Gula	Gula	Gluttony
色欲	しきよく	Lujuria	Luxuria	Lust

I forgot to include the romanized reading in the table, they are respectively: gouman, shitto, fun-nu, taida, gouyoku, boushoku, and shikiyoku.


[1] Probably my wife was tired of me asking her the translation of the same term again and again, and suggested me to RTFM.

What I do in my spare time

I create art, and have to explain it a lot:

My work explores the relationship between Bauhausian sensibilities and multimedia experiences. With influences as diverse as Caravaggio and Joni Mitchell, new combinations are synthesised from both explicit and implicit layers.

Ever since I was a teenager I have been fascinated by the ephemeral nature of relationships. What starts out as hope soon becomes manipulated into a manifesto of lust, leaving only a sense of what could have been and the dawn of a new beginning. As wavering replicas become distorted through frantic and repetitive practice, the viewer is left with a new agenda of the corners of our condition.

If you missed the joke, please check the link out. But it still loses for the Post-Modernism Generator, that could replace good part of the Brazilian intellectual elite.

[HT Ed Yong]

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.