Posts Tagged 'science'

New directions and projects

The last year, and the beginning of 2011, has been full of projects, work and other stuff. All this had me away from the blog. As a scientist, sometimes things get really hard to maintain in a specific way. And the blog is the downfall of all the work that I have been doing lately.

Chapter One. Just… Research

For example, here in Chile, the spring (starting in September) becomes THE season of meetings and events. In october, I had the pleasure to participate in the European Wnt Meeting, held on the Karolinska Institutet, Stockholm. Back at home, I had now the opportunity to attend the 5th meeting of the Latin American Society of Developmental Biology (LASDB), featuring important scientists from all the world. It was an incredible experience, to participate in both events. But, as many of you probably know, you come back from these events with your head full of ideas. Translating those into a planned experiment, testing the conditions and getting results can take a lot of time. And I am still in that process.

Chapter Two. About Advocacy

I proposed to an Association of Researchers in Graduate Level” (sort of translation), an idea to promote science in the people, to reach authorities and to promote science in the media, among other things. This campaign has been difficult to develop. The lack of funding, and contacts outside the science world, makes this advocacy campaign an “impossible” plan. I really admire the strength of the “Science is Vital” initiative. But we are far from that success and resources.

Chapter Three. Related Stuff.

I collaborated with some posts on The Node, the more-than-awesome blog and community around the Development journal. I also published some letters in chilean newspapers, about the state of Science in our country. These media included El Mostrador (the first and most important digital newspaper), letters in La Tercera and El Mercurio (the two most prominent printed newspaper), and others.

Conclusions…

It has been interesting. All this work. But I believe that, this year, I will come back to my roots at Astu’s Science Blog. But excluding more discussions regarding Mendeley, Papers and related software. Science life or, more exactly, scientist life, will be my most common topic this year (I hope).

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Swine Flu, Update

First of all, thanks to the team and people of Nature Blogs for accept my blog in their list!

Second… Being a Grad Student, usually I have little time to dedicate to post something really interesting and good-quality content. Today, it’s one of these days (the workbench took all of my day… and now I am getting ready to sleep). But I wanted to recommend these links about the Swine Flu on Nature and Science.

First, an interview from ScienceInsider with Ruben Donis, chief of the molecular virology and vaccines branch at the CDC. I tried to investigate about the genetics of the virus, but it seems that I have to wait to see a paper in a Journal. Anyway, Donis talks in the interview about some interesting features of the virus, and about the history of the Swine Flu. Also check the special from Science here.

Second, the special from Nature is also interesting. By the way… this blogger lives in Chile. Sometimes, here we hear things like “we are so far from everything… we are isolated and safe”. But in the news I watched about the first confirmed case in Peru, next to us. Chile has been very efficient so far in the preparation for the disease and the checking of the tourists and travellers in the International Airport. By now, there are about 42 cases in our country; 16 of them have been ruled out; 26 are being studied, and several of them are people who travelled to Mexico or USA. I guess the meetings and courses around there will suffer by now.

Swine Flu, reloaded

I found some interesting information about the Swine Flu outbreak in Science Insider [1,2]. Two topics are really disturbing: one of them is related with a previous outbreak in 1976. It seems that a swine flu strain swept from a military base in New Jersey, and several soldiers were infected. But only one soldier died. You can read more about this story in [2].
The second topic is very perturbing. The news from ScienceInsider claims that in USA, none of the suspected diseased people have died; all of them had a mild disease. However, in Mexico, 80 deaths are attributed to the virus. One should ask: Why? If these numbers are correct, why in one country, there are no deaths from a virus, but in the next country, there are so many? In this case, one can propose that economical factors are influencing in the outcome of the treatment. But, there is such a difference between USA and Mexico? I could accept a difference maybe between England and Bolivia, for example.
Maybe another explanation can be even more deep. Ona explanation regarding something even more powerful than economics: Single Nucleotide Polymorphisms (SNPs). There is no scientific fact to assume that two populations will have the same genetical background. And, indeed, some mutations are more prevalent in specific genes in specific populations. I have some knowledge about one specific gene: ATP7B. Mutations in this gene is related with the Wilson Disease, and more than 250 mutations have been reported. Strikingly, mutations are “country-specific”. Even between neighbor countries, the differences are surprising. A database with more than 300 mutations has been implemented. And this is only one example.
Being hard with this idea, I can imagine that the influence of genetic variations in the response to pathogens and drugs, for example, will be important when someone is analyzing two populations. And then, we have Genome-Wide association studies: the only available tool that we can use in a quick way to asses two population’s response to an infectious disease, in this case. Are we ready to develop and implement fast and global responses to global threats such as Swine Flu? Of note, a recent news in Science talks about a debate regarding the real value of genome-wide association studies, where some scientists are saying that these studies are not bringing valuable clinical information about diseases, and the trend seems to be the support to full-genome sequencing in patients. That approach could be very useful in the study of diseases such as cancer. But, when we are dealing with global outbreaks, as Swine Flu now, we need to handle all the information available. Including the properties in our genome that can influence the response of a country, or even the entire human kind, to a inminent threat.

References and links:

[1] http://blogs.sciencemag.org/scienceinsider/2009/04/swine-flu-sprea.html
[2] http://blogs.sciencemag.org/scienceinsider/2009/04/retrospective-w.html
[3] Koenig, R. Science, 2009, April 24, Vol. 324, page 448.

The Limits of Automation

“What remain to be determined are the limits of automation” says Ross King and coworkers in a very recent article in Science [1]. The work is interesting: the development of a Robot Scienctist, called “Adam”, which has the ability to generate autonomous functional genomics hypotheses about orphan genes responsible of metabolic reactions. Using the team’s words, the idea is to “originates hypotheses to explain observations, devises experiments to test these hypotheses, physically runs the experiments using a laboratory robot, interprets the results to falsify hypotheses inconsistent with the data, and then repeats the cycle” [2]. Adam is completely independent; only needs the human assistance to restore supplies and to remove waste. Reading the article, it seems that the question is not “are we going to be replaced by robot scientists?”, but “when are we going to be replaced?”

Dr. King and Adam

Dr. King and Adam

I guess that the main bottleneck to that “when” could be the money, specially in our times. In smaller countries, such a robot would be too much expensive. Imagine that in our country (Chile), supplies and reagents are very expensive (sometimes, three or even four times more expensive that the price in USA or Europe). But an additional stone in the road is obvious: at the time, robot scientists could only handle with species such as
Saccharomyces and maybe E. coli. Adam could demonstrate 12 out of 20 hyphotheses generated, and in the case of a specific set of genes, “it sheds light on, and perhaps solves, a 50-year-old puzzle”. Could a Robot Scientist handle with the complexity of species such as frogs, chicks and mice? Even more, when we are discovering that non-coding RNA is extremely important in such organisms [3], we are far from establish a clear and comprehensive picture of the “omics” of Mus musculus and Homo sapiens. Adam work with mutant strains of yeast; how could do the same with humans? It seems that the potential of such devices (as Adam) is restricted, by the meantime, only to “lower” organisms. An additional argument has been proposed [4]. If the advantage of a Robot Scientist is to release human scientists from “wet lab” in order to allow them to work in the interpretation of data, thinking and ultimately writing papers (in summary, high-level creative tasks), are we prepared for such a freedom? Specially when some lab heads still “treat postgrads and postdocs as a cheap source of menial labour, rather than educating them to become tomorrow’s creative research leaders”? [4]. I have to acknowledge the contributions of informatics to our work; nowadays, text and data mining tools are necessary to handle the increasing amount of data, papers and references (literatury now is far from our capabilities; [5]); system biology tools allow us to analyze information and unveil new discoveries and hyphoteses, and even more. However, altough a Robot Scientist could be a valuable tool in our daily work, we have to start thinking and questioning if we are ready for such a change.

References

[1] King et al, Science, Vol 324, 85-89, 2009

[2] King et al, Nature, Vol 427, 247-252, 2004

[3] Amaral et al, Science, Vol 319, 1787-1789, 2008

[4] Nature, Vol 427, 181, 2004.

[5] Waltz and Buchanan. Science, Science, Vol 324, 43-44, 2009

Additional links (with pictures):

[5] http://www.msnbc.msn.com/id/30016175/

[6] http://www.bbsrc.ac.uk/media/releases/2009/090402_robot_scientist.html


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