Linux dominates in supercomputing

Nothing new under the Sun, but the very interesting presentation makes it very cool to see. I just got to this article at BBC about the Top500 supercomputer list, where a very nice Treemap graph presents supercomputers according to their computational power. By selecting the Operating System, the dominance of Linux is staggering, confirming its status of de-facto standard for high-performance computing. Again, nothing new under the Sun, but it is interesting to see it in such strong visual representation.

Craig Venter programs a bacterium from scratch

As you probably heard in the news, Craig Venter, the American biologist best known for starting up Celera Genomics and sequencing the human genome, achieved another big success. He created a fully working new bacterium, programming its DNA from scratch.

Like a computer having hardware and software, a bacterium has a set of components that execute the software written in the DNA to create proteins. For quite some time, the strategy was to put small pieces of new DNA into full genomes, so to add a new piece of genetic code to synthesize a new protein, typically a pharmaceutical drug. For example, people with diabetes must periodically use insulin, a small protein which is normally produced by a fully functional pancreas. If the pancreas does not produce insulin, then diabetes arises. A solution is to inject insulin from outside, but this small protein must be produced somehow. The technique used to produce it is the Recombinant DNA: A small piece of DNA specifying the code to produce insulin was inserted into a normal bacterium (Escherichia coli, the same that lives in your gut). The altered bacterium duplicates, and millions and millions of daughter cells now produce the proteins their genetic code specifies for, like they were small chemical laboratories. Since specification for insulin has been introduced in their DNA, these millions cells also produce the precious insulin, which is then extracted, purified and sold for diabetes treatment.

At the Craig Venter Institute, they went further. They didn’t add something new to a bacterium. They took all the DNA contained in one, throw it in the dumpster, put another DNA completely designed on a computer, and let it go. This has been done some time ago, but this artificial bacterium was not able to reproduce, until some time ago. Yesterday the paper has been finally published on Science: “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome“, marking the fact that the hardware (the mechanism that synthesize proteins) can be programmed at will by totally replacing the software (the DNA). In the most superior example of computer programming skills, the JCVI now controls a chemical computer. Venter walks the path of Wohler, once again demonstrating that life has nothing magic, but it is just a chemical system, obeying the rules of chemistry in a fascinating self-sustaining, self-replicating system made of order and chaos.

What are the consequences of this achievement? What can we do with a totally programmable, reproductive chemical laboratory ? Well, it’s not that easy. Actually this achievement is great, a milestone that will probably earn Craig Venter the Nobel Prize very soon, but to go from this achievement to practical uses for humankind we are a bit far, although not that much far. Having such control will allow so endless possibilities that are almost difficult to imagine right now in their completeness, but we can start from:

  1. production of now expensive proteins to cure diseases, similar to the insulin case, reducing the cost and increasing the effectiveness of therapies.
  2. production of bacterial species able to consume and transform substances that are toxic for us
  3. bacterial species able to deliver a pharmacological payload near the source of the disease. Today we inject stuff in our body, for example to kill cancer, but we poison every single cell, even the good ones. What if a bacterial species is able to detect and attach to a tumor, and then start producing an anticancer drug right there ?
  4. production of electricity from biological sources. Take wood or sugar, let bacteria digest it and promote electricity creation (a so-called microbial fuel cell). It’s clean, renewable and easy to control. We already do something similar with Biosensors to evaluate the amount of glucose in blood.
  5. production of biofuels from garbage or pollutant, like used plastic.
  6. understand how a simple system like a bacterium works will give us the chance to understand more complex systems

Yes, some will probably be scared at the idea of such inane level of control: biological weapons, superbugs… danger! danger!… but if you really stop for a moment, check some history, and think deep, you realize that biological warfare is nothing new: people in the middle ages threw corpses hit by plague beyond castle walls to kill the opponents via biological warfare; humanity does not need to create a powerful bacterium as a weapon: a large amount of them are already available in nature, ready to be harvested, and they could go straight on the tip of some rocket ! Being scared that this new technology could be used by mad, aggressive people as a weapon is not an issue. Again: the biological weapon is already out there, since the very beginning. This is the reason why biological weapon stockpiling and production has been banned since 1972 (Biological Weapon Convention) and only defensive research is allowed and pursued.

In fact, if you think about it, understanding how bacteria work is actually the only way to find effective protection, and not only from human madness…There is a bigger menace out there to be worried about: the pure, crystalline natural cruelty, wiping thousands and thousands of species out with not a blink of compassion since 4 billions years. In 1918, the so called spanish flu wiped out 6% of the world population of that time. Six percent. We humans do not accept this harsh treatment from cruel nature, and we found a way to understand its mechanisms and use them at our own advantage. Our life today is twice as long and many times safer than the life of our ancestors, just 100 years ago: think about living in a world with no anesthesia, no penicillin, no anticancer drugs, no social security or medical assistance, with sounding remedies like skull trepanning, bloodletting, or Hirudotherapy.

Are you really scared of the 21th century ? I’m not.

Eight molecules that changed the rules of the game: Benzene

Rule changed: stimulated research to explain electronic resonance.

Benzene

Benzene

Except for its nice regular hexagonal shape, benzene is not a nice compound. It is toxic, carcinogen, highly flammable, burns with a very dirty and smoky flame, and if it is not enough, it made chemists go crazy for one hundred years. The latter point is interesting for our discussion. Why, you may ask ? It has to do with its structure and a bunch of data that didn’t add up for quite a long time, starting from its discovery, in 1825. It took more than one hundred years to finally understand what was going on, and it required the development of a whole new scientific discipline: quantum chemistry.

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About class attributes, semantics and microformats

I just got to this post by Richard le Guen via the referrals to my blog, and I feel it’s important to clarify my point.

So, let’s describe the problem. In HTML, you describe the layout of your information. How the information will look like is “presentation” and is managed via a so called Cascading Style Sheet, or CSS. Change the CSS, the visual aspect changes.

To bind the entities you describe in HTML with how they will appear, you use a standardized attribute, the class. An example is:

<div class="info">This is a message</div>

In this example, the info label is the class assigned to the content of the <div> HTML tag. Now you can change its appearance with a CSS directive like

.info {
   color: blue;
   font-size: 13px;
}

if you want the text to appear blue and of a given size. So far so good.

One of the problems in todays’ web is to give semantic meaning to things, so that a computer can extract the information and do smart things with it. Unfortunately there’s no clear way to perform this (well, there is, but we would get into an argument too complex to be described here).

Enter microformats: the point of microformats is to grant semantics through ad-hoc class names that are not only used as a representational reference into the css, but also are assigned to a well-defined meaning. Example:

 <div>
   <div>Joe Doe</div>
   <div>The Example Company</div>
   <div>604-555-1234</div>
   <a href="http://example.com/">http://example.com/</a>
 </div>

can be endowed with semantic meaning if you use the hCard microformat

 <div class="vcard">
   <div class="fn">Joe Doe</div>
   <div class="org">The Example Company</div>
   <div class="tel">604-555-1234</div>
   <a class="url" href="http://example.com/">http://example.com/</a>
 </div>

With this solution, a computer can now understand meaning out of the class attribute, and do smart things like aggregating data, and allow searching on it.

Some time ago, on Jeff Atwood blog, coding horror, a point was made about microformats and their problems. In particular to the fact that (citing Jeff) “the crux of microformats is overloading CSS classes“, and I tended to agree, considering technically wrong to overload CSS classes with meaning. Richard objected that the very definition at the W3 consortium about class attributes is also “For general purpose processing by user agents”, which convincingly includes hCard scrapping tools.

On this, Richard is right, and I’m torn on my previous stance. The point is that the class attribute is indeed specified as a general purpose tool, which specifically and most frequently is used for stylization purposes. Microformats are, from the formal point of view, a totally legitimate use of the class attribute. Nevertheless, when you overload classes with meaning you can incur in all the problems Jeff Atwood points out, and you should be very, very careful, or chaos will ensue. Formal approval for a usage is not always indicative of a safe practice, but in this case the problem arises from the fact that we tend to think at class names as something that has a meaning only within our web application. With microformats, this meaning extends outside the boundaries of our self-contained world, and this conflictual view can produce problems.

Edit : Another issue worth reporting is namespacing. The fact that you grant semantic meaning to a given class attribute means that a given string, say “vcard” conveys a specific meaning which is unique. If you take every possible available string in the world, they belong to a unique, flat namespace. Now, RDF-based semantics approach uses namespacing to distinguish different meanings granted to the same string by using, instead of a trivial string, a URI. In microformats, and in the approach used by microformats, you don’t have namespacing, but you have containment. For example, the class “tel” in the vcard microformat can be distinguished by another “tel” (for example, indicating a table cell on the same webpage) by the fact that the one in the microformat matches the selector “.vcard .tel”. It’s sort of namespacing, although with a different mechanism, and it’s done and built through the containment relationships among HTML elements.

It’s mind bending if you think about it, but once you see how it works, it’s kind of smart. It’s not as complex and demanding as RDF, not as powerful as OWL-based ontology description, but it can work for simple to medium complexity semantic data.

Translations!

I decided to add a rather demanding additional requirement to my blogging activities: I added multiple language support. From now on, posts will also be available in Italian, by selecting the proper option on the top-right corner of the page.

I will not post only when both translations are available. Instead, I will continue blogging in English and progressively translate bottom-up the English posts, until I catch my current flow. Under no circumstances I will delay a post in order to get it in both languages. It would become too demanding. I will keep translating efforts for low inspiration times. This post, however, represents an exception. It is in both languages from the start.

One hundred posts!

Dear all,

in August 2007 I started this blog with the classic Hello World post. Today, in April 2010, what started as a simple just-for-fun experiment has become an active part of my life and curriculum. This post marks my 100th post, with an average of slightly more than 3 posts per month.

During this time, the blog went from no readers and hits to almost 7000 visits per month, and the trend is growing

ForTheScience visits/month trend

Similar case with the feeds: there are 23 RSS readers connected to the updates. These are small, big numbers: the critical fact is that I am doing something that people use and enjoy.

I want to thank every person interested in what I write. I’m not a professional writer, nor I wanted to create a blog to act as a journalist, and this stance will stay. I just wanted, and want for the future, to keep my mind open, read things, poke others with some interesting scientific facts and findings, provide scientific programming hints for issues I discover and solve. When this happens, I will post it here.

What is coming up now at this important milestone can be summarized with the following points:

  1. I will try hard, harder, and even more harder to get a ticket to The Amazing Meeting 2010 in London, and provide full coverage of the events as I did last year. The people I met at TAMLondon 2009 were incredible and enjoyable. The show was exhilarating and witty. I will get on board again this year if I win the hunt for tickets.
  2. I will complete the series of the “eight molecules”: after Ether, Penicillin, Cisplatin and Urea, we are halfway through. More interesting molecules are coming, stay tuned.
  3. I will keep a random post frequency, although I will try to normalize at around a post every 15 days.
  4. Expect more videos and pics. I officially started walking around with my camera all the time.

Again, thank you all for reading.

Eight molecules that changed the rules of the game: Urea

Rule changed: demonstrated that organic compounds had no mysterious “vital energy”

Urea

Urea

The synthesis of urea is a fascinating and critical event. It sent a shocking quake through many open questions in chemistry, and answered them with a cold hard fact with no chance of misunderstanding. It slain one theory, vitalism, and was in front line to promote the discipline of “organic chemistry”, the chemistry of carbon compounds.

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The Meissner-Ochsenfeld effect: levitating magnets

Recently, I had the chance to see a presentation of cool scientific magic: the Meissner-Ochsenfeld effect.

What you can see here is a magnet (the yellow-red cylinder) levitating above a small dish of superconductive material, and consequently free to spin in mid-air. The superconductor must be kept at liquid nitrogen temperature (-196 degrees C) to provide this effect, a limitation that is slowly being removed by research on high-temperature superconductivity. Due to its complete diamagnetism, the superconductor completely expels the magnetic field, and pins the magnetic flux lines around it. I’m not familiar at all with the physics involved in this phenomenon, but I believe it has one of the strongest “Oooh” factors ever in terms of popular scientific dissemination. For this reason, I chose this to be my first YouTube video.

Eight molecules that changed the rules of the game: Cisplatin

Rule changed: revolutionized the treatment of cancer

Cisplatin

Cisplatin, formula [PtCl2(NH3)2] is a very simple compound of the precious metal platinum. It revolutionized the treatment of some types of cancer, in some cases with almost total chance of success, and it can be considered to full extent the “penicillin for (some, unfortunately) cancer treatment”. Read More »

Unscientist awards, a prize for unscientific spokespeople

This is something interesting. What about a prize for unscientific claims: “the Unscientist award”? At the moment, only Patrick Lockerby (the author of the  post linked above) proposes such prize according to the following rules: the potential candidate must either make use of an already debunked argument, a logical fallacy, or (verbatim) “self-aggrandising puerile prosey posturing”, to reach and strongly support an unscientific conclusion going against scientific evidence.

It can be safely assumed that hordes of candidates are available out there.

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