Some pics from SciFoo

Finally I downloaded the pics from my camera and posted them to Flickr. Here there are some.

A really funny picture, with a standing Tim O'Reilly at Google and an "Server not found" error on the web browser.

This is the way that a self organized schedule board looks. Personally, I love it, and the overall result was a wild display of creativity. It worked very well, not surprisingly.

Some of the attendants.



People at Google work really hard it seems. Even when you are pissing you can improve your coding! Keep going that way, guys, your work makes our lives easier. And I should learn to use time on that way.

James Randi, our secular saint!

Greg Bear and Kim Stanley Robinson. Soon(?) I will post about their presentations. KSR was already one of my favorite SF writers. Now I like his work even more. I better save my opinion about Bear for later...

The RepRap, the macro almost-self-replicant machine that soon will manufacture its own pieces. A really mind blowing device, even in this early stage of development. If it can deliver its promises it will change a lot of things for a lot of people.

Walking around that wonderful place, I stumbled upon the answer to the Ultimate Question!

A truly Agalmic environment, according to me. Maybe I will write something serious about it when I am done with my thesis. Someday, I guess.

To come: More reviews about SciFoo and some more pics about the Amazing and Depressing things I saw in the US.

Second Day at Scifoo part II

The second session was called “The Future History of Biology” and was by Rob Carlson.
He made a nice comparison between the history of aviation, the history of computing and the future history of Biology. According to Carlson there is a very good parallelism between these technologies. A difficult beginning with a small community of people working in key issues, with impressive achievements by trial and error rather than by any analytical method, (Lillienthal machine, Chanute, Wright bros.), with the achievements separated by years, later a phase where empirical design yields good results, but general rules are still needed (plane design during WWII) and then an age where general principles are at hand and CAD is possible (Boeing). Some people claimed that current aeronautic industry has become stagnated because the expensive that projects are and because there's no market anymore for further developments, compared to the invest they need. I pointed out that biology is not aeronautics. Biology is cheap and self replicant, so in any case if CAD becomes applied to biology the result will be more like current OS development than like designing expensive aircrafts. Some other person said that synthetic biology is impossible to become really successful because modeling the cell is an n-body problem and we lack truly accurate simulations, so, it is not possible to engineer bacteria or other organisms. I said that we do not know the exact solution to Navier-Stokes equations, and that does not prevent us from flying everyday. He called us in a very polite way (again, the eternal politeness of the Americans) ignorants, because only people ignorant of the last 200 years of organic chemistry could be so hopeful about synthetic biology. If we were computers, based in silicon discussing the possibility of this crazy thing called life, I would say he has a point. But we aren't. We are alive, we have ribosomes (something lacked by organic chemists), our bodies do molecules that are extremely complex. He liked to make this phony analogy between systems biology and not being able to travel faster than light and about the possible consequences and about the things we do not see in the universe that we would see if it could be possible to travel faster than light. But, we do see in our body and in our surroundings that in fact it is possible to create complex systems from biological parts. That it might be much more difficult than we think? That we are too happy-go-lucky about the issue? Probably. Maybe it will be tougher than we think and we are a bunch of babblers, but it is not impossible, whether or not n-body problem a cell is not a soup with n pieces of chicken, beef and vegetables. According to that argument electronics is impossible, as we cannot know accurately the position of an electron, and if we cannot know the basics, what hope is there for more advanced applications? That is the reason why we use psionic power for the Internet.
The next session I attended was a presentation by James Randi about several subjects, including homeopathy and psychics. Randi is a terrific speaker and his presentation one of the funniest in Scifoo, like his lucid debunking of homeopathy with the analogy of having to drink 26 swimming pools of water from a homeopathic dilution in order to find a single molecule of claimed active principle in some homeopathic preparations (for others, numbers are even worse!).

After that, I had lunch with Marc Marti Renom, from the Synaptic Leap, to discuss our joint presentation later, then looked for James Randi, for my first session. More about that later.

Some remarks: Yes, the food in Google is as good as the myth says.

Second Day at Scifoo part I

More on Scifoo:

On Saturday I attended to several sessions:

A session on Open Science 2.0, by Bora Zivkovic that was not as productive as I expected. In fact, it gave origin to another session next day, by Alex Palazzo and Andrew Walkingshaw. The session wasn't specially interesting because most of us did not agreed about the direction we should be heading to and about the real effect of blogging, open notebooks and the future of the peer review system. Discussion about tenure was a major issue and showed one of the fundamental disagreements, based on the fact that blogging and keeping an Open Notebook was much easier and risk free when one is a tenured professor rather than a young scientist. I am not worried about the issue and given the fact my thesis advisor is interested in exploring the open side of things, I will probably have an open notebook once I begin my experimental work, if someone is obnoxious enough to not accept me at his lab or at his program because I have blogged or because I have written about strange matter like animal uplifting and economic effects of nanoassamblers, then that person is somebody I do not want to work with. And I am not afraid of not getting grants because of the same reason. Let's put it in another way: I am afraid of that whether open access and open notebooks or without them. Science is a difficult field. But I can understand that people are afraid about blogging and is not as cold blooded about the fact as is my case, after all, I am an undergrad who has almost nothing to lose (and a lot of things to win, I have traveled a lot thanks to my unconventional writing) and a thesis advisor who has proven unconditional approval and almost infinite patience, their situation might be different, being in top universities, extremely competitive places and possibly about to begin their own research, as they are postdocs (And they are so young, man, I am ashamed!). But let me focus on this session, as the facts I have discussed partially belong to the other session on Sunday. In a surprising situation (or perhaps not so surprising), the young scientists told to the old ones to discuss more about the current set of rules about blogging and open access, rather than speculating about the mid term future of publishing, it was nuts. A couple of not-so-young (let's be polite, as Americans are extremely polite) people were besides me talking in whispers and complaining about these kids who dared not to look at the future. Scifoo is a really special conference, it seems. Another traditional complaint that arose was the extreme slowness of the peer-reviewing process in Biology and the subjectiveness of the “impact” or earth-shaking criteria that allow papers being published in certain top-journals.

Among the new things said there were the need about separating the communication of the results from its evaluation (Open Notebooks), suggestions about including criteria for grant selection that encouraged open access. The difference between Open Access and Free Access, this is, freedom to use vs. freedom to read only. The Nature Precedings were not discussed in-depth in this sessions, but I am very happy that people in Nature Publishing Group is going in the right direction. Other interesting ideas were creating a certifying system for scientists, a Science Whuffie (nobody used the term, but I think it's corrrect to call it that way), based not only in publications but in reputation among peers. I think I would do better in that one that in the current system, so I am biased and please do not take my opinion as a neutral one, but I just love that idea.

Bora Zivkovic from the Public Library of Open Science (PLOS) gave some thrilling numbers: So far, in three years, they have published more than 700 papers, 40% of which are rejected for non sound science, as they are open, not uncritical, but earth-shaking-ness is not necessary, they publish now around 30 papers a week. I learned that blogs have been cited in papers and that there are people that say we need alternatives to citation systems, something I had never thought about. Others argued about the current format of papers being doomed in the mid term future, and that the future lies in machine readable formats that we humans learn from without worrying by petty issues, others argued back that papers are now machine-readable, pdf is convertible to text. Wow. Did I say that it was a kind of disappointing session? Yes, it was! A lot of extremely good ideas being overwhelmed by the discussion on more pedestrian issues and extreme disagreement. But I will write more about that later.

Another geek in the con

Finally.
This was the Day 1 of the Scifoo.
I will deliver a presentation about Open Source Biomedical Research and another one about skepticism and rational thinking.
Today's presentation were great, about presenting scientific data in new and innovative ways, the total amount of energy available on Earth, about systems biology and Eau D'E. coli, coli bacteria that smells like banana and about life in space. We had a lot of fun, the Googleplex is amazing and I spotted some big names in science and software development, and in SF too. And in skepticism.

I am barely awake, I will post more tomorrow. But today I met: Kim Stanley Robinson, Greg Bear, James Randi, and a lot of interesting biologists too. And I got a model of a Buckyball!

Preparing my summer trip

Greetings!
This summer I will travel to the US and attend to three conferences: Transvision 2007 in Chicago, the World Future Society annual meeting in Minneapolis and the Science Foo Camp in Mountain View, California. I will speak about OS Biomedical Research in a student meeting associated to TV07, as it seems I am too young and unexperienced to be allowed on the main conference. Anyway, I will try to spread the meme and make more visible the problems that we have here dealing with diseases very well known but that have no cure, because they are not profitable for the industry.

In the WFS meeting I won't deliver any presentation, but I hope to discuss some of my work with the Millennium Project with the MP staff that will be there.

In Mountain View I will be at the famous Googleplex for the Science Foo Camp, new kind of conference, where there is no previous schedule, the contents are determined by the interaction of people. I hope to talk there about my current work at the MP, the importance of future studies, proper science education and skepticism, but also about OS Biomedical Research and the current efforts going in that way like The Synaptic Leap and current research done at my lab, testing the efficiency of already modelled compunds against Chagas' Disease. It would be a lot of fun, and I will try to learn as much as I can.

Here is my abstract on OS Biomedical Research:

Open Source Biomedical Research and Computational Biology can improve drug design and help to fight neglected diseases.

Abstract:

Several hundred millions of people around the world are affected by neglected diseases. One of the challenges they encounter is that the development of treatments for these diseases is not profitable for the private sector, as most of the affected are among the poorest people in the world. These diseases tend to attack people in tropical regions of Africa, Asia and the Americas, often in a chronic way, disabling people for years and causing further poverty and decay, in a downward spiral. Until now, the process of developing new drugs has been cumbersome and expensive, yielding many ineffective or highly toxic products, due to an approach based on random testing of substances.

Now, with new methods in computational chemistry, it is possible to design new drugs in rational way that targets specific parts of a given virus, bacteria or parasite, while it bypasses the equivalent parts in humans. This approach might save a great amount of time and resources previously wasted on useless compounds or on effective compounds against useless targets, which, in turn, could reduce the cost of drug development. However, even with these new tools, most commercial partners are still not interested in developing drugs for poor markets.

A possible solution to this problem is the application of the “Open Source” approach to drug development. The Open Source (OS) approach in software has shown it is possible to create useful, reliable and efficient products through a voluntary, collaborative process. In biology the OS approach could be used for collaborative non-profit research, aiming to avoid the duplication of efforts and the release of patent-free compounds for neglected diseases in a relatively short period of time, thanks to the new computational methods and distributed efforts; moreover, as these methods become increasingly efficient and the available information about pathogens grows (regarding genomes, expression patterns, etc.), a OS collaboration could make the process of drug development even cheaper and more efficient, and even allow for the creation of "backup drugs" to tackle the problem of drug resistance before it appears.

Keywords : Systems Biology, Open Source Biomedical Research, Neglected Diseases.

I am really surprised I got invited to Scifoo, given the extremely high level of the attendees and that I still (yes, shame on me, but I chose to take computational physics too) am an undergrad. But this is a perfect example fof the reasons I created this blog: In this age you don't have to be wealthy or live in the developed world to help to develop new things, to be in contact, to get opportunities like this. Even ten years ago this would have been impossible even in my wildest dreams. This, my readers, is a praise to globalization. I only am sad that many people smart enough to get opportunities like this is lacking a proper education. I dream of the day that is corrected and we, all mankind, can use our brains and hands to solve our current problems.