Archive for February, 2008

Tales from an RNA world: a tempting hypothesis

February 28th, 2008 | Category: Bio

What is the origin of evolution? What ingredients, methods, and environment did life need to emerge as the only known process to generate complex behavior?

For some time now, there has been a minimal hypothesis stating that RNA all by its own could support Darwinian evolution. This notion has been given the name of the “RNA world” conjecture and it is broken down into two notions. The first notion of an RNA world states that an early form of life used RNA as the only genetically encoded component. The second notion goes farther ahead by stating that not only RNA was used as a sole genetically encoded component, but that it was the first one to be used. This means that RNA alone could have spontaneously produced life given certain conditions.

The second notion is of course much less supported than the first one. However, regardless of the notion, when we talk about an RNA world, we explore the concept of life generated by the interactions of RNA with its environment. We give the molecule, with its ribose backbone and its nucleotide language, the center stage in the drama of life.

But how do we prove this? Where to start? One way is to begin inferring how ancient life worked by looking at the present state of it all. In this way, ancient genomes must be inferred and ancient metabolic models deduced from that guess. The problem is that data suggests that the RNA world would have to occur well before the appearance of LUCA (our Last Universal Common Ancestor). However, inferring an RNA only model only by looking at a model of LUCA and the workings modern life is tricky and educated-guess-like at best. Another way to the RNA holy grail is by looking at how was Earth during the early stages of life: its composition, its environment, and its astronomical accidents. An RNA world model that fits Earth’s early state can be theorized and then experimentally proved. This is far more difficult that it sounds because forming a stable strand of RNA spontaneously in an unstable atmosphere and from a restricted set of elements that we think Earth had back then is not easy. There are many complications that rise during the polymerization of ribose in such an environment and many questions of how it can polymerize in the first place.

I certainly believe that there is evidence that points to the way of an RNA world, but there is no model yet of my knowing that can withstand all the critics. One thing that is fascinating about problems like this one, that is, problems that deal with the origin of life, is that, in a sense, we are Universe staring at Universe; a being trying to desperately remember its own moment of Creation. A being trying to remember when it became different to everything else.

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Six out of twelve

February 22nd, 2008 | Category: Uncategorized

Six out of twelve

Have we dwelled in the stars,

In the shining forever

Of a thousand years far.

Taken by time,

Tittered by faith,

We came to our union

In quick  change of fate.

We first came to liking,

In Love’s caverns we danced.

But sooner than later,

Even Love’s grace we surpassed.

We are now truly unknowing

Of which  place we reside.

But it is of no matter,

If I’m by your side.

Six out of twelve

have we channeled ourselves,

And the deeper we delve

In our meaning

In our warmth

The deeper the love, the higher the sadness, the greater the sea.


¡La sesión vive!

February 19th, 2008 | Category: Personal (Espa√Īol)

Desde hace ya m√°s de 10 a√Īos he jugado rol semanalmente. Me han acompa√Īado en mi exploraci√≥n de mundos de fantas√≠a y oscuridad varios compa√Īeros, los cuales tengo la gran fortuna de llamar amigos. Hace poco acab√≥ una saga de historias importante ubicada en “Reinos Olvidados” de D&D 3.5. Durante poco m√°s de cuatro a√Īos cada uno de nosotros cre√≥ m√°s de 4 personajes en promedio, decenas de historias y batallas llenas de epicidad. Cabe resaltar que en una “quest” tuvimos que bajar las nueve capas del infierno, a la Dante, s√≥lo que en vez de Virgilio ten√≠amos a un palad√≠n con Great Smitingx3 (go Valnefein!), en vez de la bella Beatrice ten√≠amos a la hija de un personaje m√≠o (que termin√≥ siendo la reina de la oscuridad…figures) y en vez del cielo ten√≠amos como meta llegar a Faerun. Al acabar tan √©pica saga, un compa√Īero m√≠o mencion√≥ que el trabajo, la escuela, los posgrados, compromisos sociales, etc. iban a espaciar¬† nuestro calendario. En vez de jugar una vez a la semana, jugar√≠amos dos al mes o algo as√≠. Todo mundo, incluy√©ndome, asentimos.

Acto siguiente, yo anuncio que estaré narrando una historia en D&D y por ende quisiera saber cuantos de ellos iban a jugarla de manera constante (una vez a la semana). Sólo uno, el narrador anterior, confirmó su presencia continua. Pasó sólo un día para que recibiera una llamada. El jugador del paladín antes mencionado tenía una idea excelente de un nuevo personaje y confirmó su asistencia a la nueva sesión. Escasos treinta minutos después, recibo un mensaje de otro jugador (el mismo que mencionó los problemas de seguir jugando tan seguido) preguntándome cual sería el nivel del personaje de la nueva sesión. El asunto fue demasiado divertido. Cuando dicen que la sesión está a punto de morir, siempre resulta igual: the session lives to see another saga. =)


Eclipse PermGen Memory Leak

February 15th, 2008 | Category: Computers & 570x0FF

Since updating to eclipse 3.3 in my new Arch linux system I’ve been having trouble with the respected programming IDE. It crashes. Real bad. Frequently. Surfing the web a bit, I have become aware that I am not alone. Many more are reporting the same bug and apparently no one has come with a permanent solution. When eclipse crashes, it writes the following to the .metadata log:

!ENTRY org.eclipse.osgi 4 0 2008-02-15 09:37:14.597
!MESSAGE Shutdown error
java.lang.OutOfMemoryError: PermGen space
!SESSION Fri Feb 15 09:37:15 CST 2008 ------------------------------------------
!ENTRY org.eclipse.equinox.launcher 4 0 2008-02-15 09:37:15.314
!MESSAGE Exception launching the Eclipse Platform:
java.lang.OutOfMemoryError: PermGen space

A memory leak in PermGen space. What’s that? Well, PermGen is short for permanent generation heap space. It is the space where all things that live forever and are not to be garbage-collected reside. These include classes and interned Strings (a better explanation of these entities can be found here). So what’s the deal? Is eclipse loading up to many classes then? Maybe we need more space for our String constants? A temporary solution to these recurrent crashes is to increase our PermGen space (it has 64M size by default) by starting eclipse with the following argument:
-vmargs -Xmx512M -XX:PermSize=64M -XX:MaxPermSize=128M
That gives us 128 megs of Perm space, which ought to ok for almost anything. However, some people are reporting the same error even within a 512M max perm size limit (see the bug report link above). Is this a VM problem? An eclipse problem (which is known for its tendency to hogging memory)? WTF?
I just hope that it is soon fixed and that the temporary solution works (at least temporarily =P).

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