Tuesday, October 30, 2007

XO Laptops for Uruguay: The wheels are spinning!

Finally the OLPC foundation makes a solid deal with a country. Uruguay just bought 100,000 machines and is expected to buy 300,000 more in the next two year. Eventually every kid from Uruguay will have his or her laptop. I hope this is only the first purchase of XO laptops, since it was taking too long for the orders to begin. I hope that also the price keeps falling and eventually will be affordable for poorer countries. However, what I am expecting eagerly is to see the effect exerted on the children and teenagers who have massive access to XO laptops and can get connected and network between themselves and with the world. In my education video games played a very important role, even the silly video games we had in my days, I learned English because I wanted to solve puzzles and play RPGs, these games made me think hard and be the builder and main character in a story rather than looking passively at it.
Computers came much later and gave me tools that have been invaluable later, even if I cannot code in the way I wish, and now with e-books, if a child likes to read he won't have to re read several times the same books, as I had to, since there will be a huge variety of books, much more that s/he could ever read.

I am so damn happy today for the clusters of new possibilities open now for these children, and I think that thanks to effort like this one the Internet will be a much more fascinating and complex place in ten years.

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Saturday, October 27, 2007

Arthur Kornberg, RIP

A great loss for Biology:


It would be a great time to re read his wonderful book. For the love of enzymes.

May his legacy be honored by us.

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Monday, October 22, 2007

Grow muscles as a Marvel character or The Real Mighty Mouse

MIT Technology review has a very interesting piece about a new kind of drugs that could help with muscle degenerating conditions and also could trigger the growth of additional muscle mass in normal individuals. The drugs act upon certain proteins that regulate the growth of muscle mass, concretely myostatin that blocks such growth and follistatin, which enhances it, both of them belong to the Transforming Growth Factor beta superfamily of proteins.

Knocking out myostatin and overexpressing follistatin causes mice to grow muscles four times bigger than wild type mice. It was known that myostatin played a significant role in the growth of muscular tissue, and that mutations of it have arisen naturally in several breeds of animals such as cows, sheep and dogs. Mimicking the myostatin receptor and thus preventing the binding of myostatin to its real target in mice causes an increase of 60% in muscle mas in a month. Trials are expected to begin in early 2008.

Here is a picture that compares a wild type mice and a myostatin lacking, follistatin overexpressing mouse:

The possibilities open by this are incredible, not only for the sick people, but also for the astronauts, in order to avoid loss of muscle due to microgravity and for people who just want to increase their muscles without years of effort. Since it seems that the muscular increase due to this drugs is likely to have much less secondary effects than steroids, I do not see any reason to not to allow these drugs in athletic competitions, given the fact that these competitions are separated from traditional ones, where non-enhanced athletes must remain and where all enhancing shall be severely punished, but, for the Enhanced Leagues, everything that is not health threatening must be allowed. It is time for those who are not blessed for the genetic lottery to use the technology to become competition athletes if they wish so. I do not know why somebody who achieves a record thanks to a striking mutation that his/her opponents lack, and lots of effort is morally superior to somebody who "cheats" and use pharmacological help and lots of effort to to achieve exactly the same effect in performance given by this hypothetical mutation.

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Tuesday, October 16, 2007

Lava lamps and DNA or Thermal Cyclers for everybody

A new breakthrough in technology will allow cheap and ubiquitous PCR diagnosis:

A pocket-sized device that runs on two AA batteries and copies DNA as accurately as expensive lab equipment has been developed by researchers in the US.

The device has no moving parts and costs just $10 to make. It runs polymerase chain reactions (PCRs), to generate billions of identical copies of a DNA strand, in as little as 20 minutes. This is much faster than the machines currently in use, which take several hours.

To cycle through these temperatures, a conventional PCR machine heats and cools a large metal block holding multiple tubes containing samples of DNA and the material needed to make copies.

In the new device, created by graduate student Nitin Agrawal, a centimetre-wide loop of tubing wraps in a vertical ring around a set of three metal rods. The rods, together the size of an AA battery, are kept at three different temperatures. With this set-up, the parts of the tube closest to each block are heated differently.

This keeps the liquid flowing through the millimetre-wide tube, and so the DNA and building blocks cycle automatically through the three temperatures needed for PCR. "It's similar to how a lava lamp works," says Ugaz.

As the fluid is heated, it becomes less dense and more buoyant, so it flows upward. When the fluid cools in another part of the loop, it becomes denser and moves down. And because the device only heats the three small blocks of metal, it also runs off just two AA batteries.

This brings new and incredible perspectives, from setting finally a Global Epidemiology Network, scanning in real time samples from thousands of places in situ and at a much lower cost to the creation of new markets for DNA testing for inherited conditions and infectious diseases in poor countries. Low profit, billions of potential clients. I am sure that it is bound to happen in a short period of time. And a lot of collateral business opportunities will bloom, once the devices are working.

A picture of this gadget:

I feel very optimistic about this, this is only one of the many "leapfrogging" devices that will make the development of willing poor countries easier and swifter. India sure will take advantage of this. Venezuela, in the other hand, isn't, we are too busy buying AK 47s.

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Saturday, October 13, 2007

Vatican: Keep the good work, guys!

It is a fact that the catholic hierarchy is rotten almost completely, from head to toe. So, it is not surprising to see while the Archbishop of Mozambique, Francisco Chimoio is still on his post, despite his filthy lies about AIDS tainted condom and retroviral drugs, an unnamed high rank priest has been suspended after the Vatican found he was gay. Yet a lot of priests were simply moved after they found they were raping young boys and girls.

This might not be surprising, but it is shocking, nauseating and disgusting. To see that the ones who claim to have the moral authority of the world, the ones who claim to be the voice of the creator of the Universe in Earth, are far more concerned for consensual sex between two adult males than for vile slander aimed at killing as many people as possible, because what Chimoio said wasn't only about condoms, but also about retroviral drugs. It is very difficult for me to imagine what kind of thoughts are in Chimoio's mined, but maybe Roderigo Borgia would be able to understand the sickness, perversion and deceit inside this poisoner's mind.

But for those of us who think that the Vatican is a negative force in society this is great. There is no better way of exposing them than letting them be themselves, showing their true disregard for human life, their false piety and their hypocrisy. Catholic believers are mostly sincere, but their leaders are not, as this sad case shows us. They are more interested in condemning those who deviate from the official doctrine than in punishing those who do harm to spread that doctrine. Nothing has changed since the last 1000 years, it seems.

But, fortunately, despite Chimoio and his followers and predecessors (Once I read a letter of a priest to a newspaper claiming similar things about the condoms), medicine and technology are creating new opportunities for people who would otherwise have a death sentence. And activism is making these marvels available to more and more people each year. Here is the endearing and brave story of a man who is healthy, happy and well thanks to this combination of ingenuity and altruism. Charles story brings tears to my eyes, both of cheer because of him, and of sorrow by all those millions who are not as lucky as him, but in any case, this is an ode to life and happiness, the complete negation of the love of this Archbishop for death and misery that keeps people in the necessary fear for not questioning their beliefs. Some day we will have a cure and a vaccine and that day despite you, Archbishop, and despite all the fear mongers, life will prevail.

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Friday, October 12, 2007

Transhumanism 101

From my friend George Dvorky's blog, Sentient Developments:

Some basic info about H+ delivered by some of the most known faces in H+: Nick Bostrom, Anders Sandberg and Aubrey de Grey.

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Monday, October 8, 2007

I'd kill for initial conditions

Long frustrating weekend, trying to run the model of Guerra. I did exactly what the thesis said, the kinetic equations are right, the differential equations are right too, the names of each constant and variable are right, hell, I even corrected mistakes in nomenclature. And still the model does not run according to his results. I guess the initial conditions are not the correct ones, since I find singularities or imaginary solutions when I run the model (after hours of running the NDSolve command, btw). The initial conditions are not explicitly stated on the thesis, neither there is an appendix with the code of the model. Neither I can find an online model (As I can find Bakker's model of Trypanosoma brucei glycolysis) in Mathematica. I guess I'll have to learn XML and Cellml. JITT for me, it seems, although I am getting tired of not making any process despite all I am learning.

I will try more things before giving up, besides I still have to run the model in Fortran.

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Ten Commandments of Systems Biology

From Computational Biology news, a superb blog by Animesh Sharma:

Commandments in Systems Biology:

Joseph X. Zhou notes Prof. Denis Nobel's on systems-biology in the blog.
Commandment 1 (C1): Gene itself has no functions.
C2: Transmission of information is NOT one-way
C3: DNA is not sole transmitter of inheritance
C4: Theory of biology Relativity
C5: Gen ontology will fail without high-level insight
C6: There is not “genetic program”
C7: There is no program at any other level
C8: No program from any level, including brain
C9: Life is the self integrated process, not an object or substance.
C10: There are many more to be discovered, the theories of biology do NOT yet exist. Seeking theory/ies is real challenge in system biology.
I do not like C10. What about evolution? If we are talking only about Systems Biology it might be true, but if we are talking of all Biology, then C10 is plainly wrong. And C1, well, what is any
part of a biological system without the other parts, C9 states it clearly?
It could be rewritten to be more accurate, I think.

Despite my objections these seem to be some interesting principles worthy of more discussion.

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Help Interpol to trap this bastard

This _____ depicted here (Sorry, my English is not good enough to express with words what I think about crap like this) thought that cheap photoshopping was going to save him from being recognized. He abused 12 young boys in Asian countries in front of a camera.

If you have seen him report to the police and help to save children from this monster.

I am happy that the Internet is also helping to get pedophiles instead of just getting them in touch and helping them to lure children:

LONDON (Reuters) - Interpol said on Monday it was hopeful of identifying a serial pedophile after posting his picture on the Internet in an unprecedented public appeal that drew hundreds of responses from around the world.

"We have already ... hundreds of responses from the public globally as to who this person could be," Kristin Kvigne, assistant director of Interpol's Trafficking in Human Beings Unit, told BBC World television.

We can change things if we help. We just must not be indifferent.

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Friday, October 5, 2007

Why Chagas' Disease matters

Chagas’ Disease, or American Trypanosomiasis, is one of the world’s most extended lethal parasitic infections. It is also the main cause of heart failure in Latin America. Around twenty million people are already infected, and each year this figure increases by fifty thousand. The population living in areas of infectious risk is around one hundred and twenty million people, roughly a quarter of Latin America’s population.

Despite all these facts this disease remains unattended because its insidious nature, although its mortality rate is high, it kills years, and even decades after the infection, frequently from heart failure, which figures in registrations as the official cause of death, eclipsing the role of the disease and diminishing its importance in the official registers. Often the person remains impaired during the last years of his life, unable to do any physical labour. In an urban environment this would not be a problem, but most of the affected live in rural areas, dependant of farming, inflicted with poverty, far away from the managers, a calamity that goes unnoticed by city-dwellers. All these facts combine to make Chagas’ Disease a silent tragedy that not only sever lives but distort them, making them unproductive and vulnerable long time before the death occurs.

Currently there are no effective treatments against Chagas’ Disease. The compounds already used, Nifurtimox and Benznidazole have plenty of side effects, besides they are only effective at the early stages of the infection, which are often unnoticed, in later stages, they are totally ineffective. Hopefully, new therapeutic alternatives are being designed, tailor made to attack the parasite without interfering with the host metabolism. Among the new approaches to deal with Trypanosoma cruzi are targeting the systems that allow the parasite’s consumption of glucose, its sole source of energy in the bloodstream and its systems for sterol synthesis, both necessary for the survival of the parasite. Several compounds that target the enzymes responsible for these systems have been successfully assayed, showing in vitro and in vivo activity against the parasite, besides having low or no detectable toxicity in cultured macaque cells and mice.

However, drug development is still a expensive endeavor and we might have to wait for long time before a cure is achieved.

More info about Chagas' Disease:

Doctors without borders

And a rough translation of a fragment of "Chagas, a silent tragedy", by Eduardo Galeano:

It doesn't explode like bombs, it doesn't sound like shots. Like hunger, kills silencing. Like hunger, kills the silent ones: to the ones who live condemned to the silence and die condemned to oblivion. Tragedy that doesn't sound, sick people that do not pay, a disease that doesn't make any sell. Chagas' disease is no business that attracts pharmaceutic industry nor subject interesting to politicians or journalists.

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Wednesday, October 3, 2007

Top Ten most interesting extra solar planets


Great list of extrasolar planets. The youngest, the oldest, the smallest, the biggest, the closest, the farthest. All of them are there. If you are an astronomy geek, you should not miss it. If you aren't you neither should miss it.

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Tuesday, October 2, 2007

About my thesis. Soon, first results

I have decided to make public the preliminary models and kinetic results from my thesis. I will post some code here, but most likely I will upload the files (Fortran files and Mathematica notebooks, unfortunately I am not going to be able to do it 100% on FLOSS) somewhere. The title of the thesis is: "Control y regulación de la Glicólisis en Trypanosoma cruzi: Un enfoque teórico-práctico", which translated would be something like "Control and regulation of Trypanosoma cruzi's Glycolysis: A theoretical-practical approach". I will make a model of T. cruzi's Glycolisis based on Ordinary Differential Equations and an Metabolic Control Analysis of the model, trying to find which enzymes and/or transporters comprise the majority of the control of the glycolytic flux of the pathway. According to Solomon Nwaka and Alan Hudson, in their paper Innovative lead discovery strategies for tropical diseases, published in Nature RFeviews, Drug Discovery, November 2006 finding proper targets is important because:

Many compounds active in protein-based assays are inactive in whole cells.
This can be due to failure to enter intact cells but can
also occur because the chosen molecular targets are not
in fact essential to the microbes. The latter issue sug-
gests that more work on target validation is needed to
increase confidence levels in the selection of protein
candidates for Hight-Throughput Screening campaigns. The initial challenge of
identifying molecular targets that are crucial to parasite
survival, coupled with the identification of whole-cell
active compounds, is formidable (...)
My favorite analogy to explain to my family what the hell I am doing is to ask them if they have a gun, few bullets and a car is coming to them at 100 kph, will they aim to the rear-view mirrors? I tell them I try to find the vital parts of the parasite that can be targeted in a safe way, without risk to us in order to not waste bullets against non relevant targets, since resources for research are scarce here. We have chosen to model T. cruzi's glycolysis because this pathway is very particular in trypanosomatids, it is physically located inside an special organelle called the glycosome. the enzymes are regulated in a non traditional
fashion, do not share a lot of similarity with mammalian enzymes and glycolysis is essential for the survival of the parasite. Besides this, there is a whole research line on these kind of models for other trypanosomatids, but not in T. cruzi. I have spotted some mistakes on the kinetic equations of some of the models I am basing my work on and therefore, improved models of other kinetoplastids could be developed too, if there is enough time. And I think that besides replicating the work for T. cruzi, it is also possible to develop some original research concerning these models. Stay in touch.

PS: Around the weekend I should post/upload a corrected version (minor details of transcription and nomenclature) of Daniel Guerra's model of Trypanosoma brucei's glycolysis in his doctoral thesis from 2005, Glucose Metabolism of Trypanosoma brucei and Leishmania mexicana.

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