viernes, septiembre 07, 2007

A system, not a replicator. Autopoiesis vs Natural Selection at the origin and definition of life

The topic of the origin of life and the possibility of artificial synthesis of life in the lab shows SOME signs of catching up with conceptual advances defended in the 70's by Maturana and Varela.As reported by science journalist Carl Zimmer, Carol Cleland, a philosopher, is working at NASA on this topic.

"When people try to define life, they choose a few of the features of living things and make them the very essence of life. And that, Cleland and Chyba argue, is a mistake. "We don't want to know what the word life means to us. We want to know what life is," says Cleland"

This is the same way Maturana and Varela introduced the problem 34 years ago. They rejected definitions of life that were merely empirical-descriptive lists such as homeostasis, reproduction, and DNA. They emphasized that the search must be to identify the process itself from which these properties emerge; More than a description, a "theory of life" is needed. Cleland provides a good example to illustrate this point:

"In this sense, scientists who try to define life today make the same mistake that alchemists did in the Middle Ages. Alchemists tried to define substances by their properties, without any understanding of the underlying chemistry. Water, for example, was defined according to its ability to dissolve different solids. This definition led alchemists into confusion. Since ice couldn't dissolve anything, it couldn't be water. Alchemists gave the name "water" to things that we know now are nothing of the sort. They called nitric acid aqua fortis, or strong water, because it could dissolve most metals. Aqua regia, or noble water, was actually a mixture of hydrochloric acid and nitric acid that was powerful enough to dissolve even gold and platinum, the so-called noble metals. Searching for a better definition of water would have not gotten alchemists out of this mire. A solution only came in the 18th century, as scientists formulated a theory of chemistry. The behavior of water and other substances suddenly makes a lot of sense when you realize that they are all composed of atoms, which are in turn composed of smaller particles. Chemists can now say water is H2O. However, "'Water is H2O' isn't a definition," says Cleland. "It's a discovery."

However, Cleland then takes a wrong turn; she proposes that a defintion of life is impossible. I agree that in absence of a theory of life, defining life is nothing but a "barbaric" description. But once we DO have a theory of life, definitions should not only become possible, but they may allow an "acid test" for the clarity of the theory. Cleland's posture seems a bit mysterianist to me, as if no true theory of life will ever be possible. For instance, without a theory of life, how can we know if "having DNA" is or not directly related to life? Cleland certainly does not think that genes are crucial:

"Cleland, for example, doubts that Darwinian evolution, the core of the NASA definition of life, is essential. "I think those arguments are weak," she says. She envisions alien microbes filled with enzymes but lacking genes. The enzymes build more enzymes and the microbes split in two. They couldn't evolve through Darwinian evolution, because they wouldn't have genes. But they might still change, as their environment changed. Cleland doesn't claim any evidence that such things exist, but she argues that scientists can't rule them out"

Cleland's problem is that she does not have any truly sound THEORETICAL response if she were required to explain why she thinks DNA is unnecessary. We know already that many scientists would refuse to acknowledge such extraterrestrial things as truly alive; we cannot naïvely hope that the discovery of such extraterrestrial life would provide an empirical shortcut to "eliminating DNA" on what is truly a conceptual, and not an empirical, problem. After all, they can reply right back to Cleland that she cannot rule out the future discovery in other planets of autocatalytic self-replicating molecular "genes". Would she say those cannot be life? Why, exactly?

Because Maturana and Varela's autopoiesis is a systemic theory of life, it has no requirement for the presence of any particular type of molecule such as DNA; therefore, this theory explains why having DNA is not a requisite. According to Maturana and Varela's theory of organisms as "Autopoietic machines":

"An autopoietic machine is a machine organized (defined as a unity) as a system of processes of production (transformation and destruction) of components networked in a way such that: (i) through their continuous interactions and transformations they generate the processes (relations) that produced them; and (ii) constitute the machine as a concrete unit in physical space"

They emphasize that the production of components and the borders of this well-defined topological unit help produce each other: a distributed network. It is a little system; not a "selfish" self-replicator. Importantly, reproduction is not a requisite of the definition (yes, you can be a mule and still be autopoietic). Reproduction can occur as a RESULT of the growth and fracture of a previously existing autopoietic system; Maturana and Varela point out that many things can reproduce that are not autopoietic systems nor universally acknowledged as living (for instance, crystals, viruses, and prions).
The exclusion of reproduction from the core of the theroy of life is a pretty conspicuous difference from the "darwinian" perspective on the origin of life; according to those theories, the first life forms were self-replicating, reproducing molecules (RNA is a clear favorite), "genes" in themselves. This would put in motion a darwinian process of natural selection of favorable mutations, that therefater would have added DNA, membrane, proteins, etc. To ensure better self-replication, of course.
Now, as final words, allow me to indulge in some biochemical speculation (despite this not being my area). I dare say that it is becoming increasingly clear that no molecule of RNA complex enough to self-replicate can be produced without some vesicle or "border" separating it from the outer environment; nowadays most researchers seem to be trying to fit one biochemical cocktail or another into some kind of membrane or miscela of some kind. It seems probable to me that the new more impressive claims of "synthetic life" in the future will involve such little systems. Probably nothing too impresive will be coming from any isolated self-replicators....

-A. Vargas

Maturana, Humberto & Varela, Francisco ([1st edition 1973] 1980). Autopoiesis and Cognition: the Realization of the Living. Robert S. Cohen and Marx W. Wartofsky (Eds.), Boston Studies in the Philosophy of Science 42. Dordecht: D. Reidel Publishing Co.

jueves, septiembre 06, 2007

Origen de una adaptacion

Quería compartir con ustedes esto que aparece en el último Nature: Se trata del funcionamiento de las mandíbulas accesorias en la morena, una anguila muy parecida a la que veíamos en plena acción terrestre en un post anterior. Observarán que, recordando una de las más entrañables criaturas de la ciencia ficción, la morena posee DOS pares de mandíbulas; hay un segundo par interior que puede proyectarse hacia afuera y que la anguila usa para tragar objetos grandes que sujeta con las mandíbulas más anteriores, como se aprecia en éste video
Se los quería comentar porque me parece una vez más que estamos ante un excelente ejemplo de un monstruo esperanzado; es más, me parece un caso patente de la transformaciñon homeótica del segundo arco branquial, que desarrolla la identidad mandibular del primero. Sabemos experimentalmente que pueden obtenerse transformaciones homeóticas alterando el entorno embrionario en el que se desarrolla un elemento esquelético; experimentos que van desde los transplantes, la mera aplicación de ácido retinoico, hasta la más moderna técnica de cambiar la expresión genética en los tejidos circundantes, especialmente genes Hox en el caso de los arcos branquiales. A ver si observamos esta expresión en la morena y sacamos un nature...jaja

Obviamente, un cambio repentino como una transformación homeótica no puede decirse producto de una acumulación producida por un proceso de selección direccional. Tiene más que ver con una lógica mucho más estructuralista, con las posibilidades de desarollo (campo epigenético?) que ofrecía el ancestro de la uso para tragar, es una de tantas felices coincidencias que sabemos que continuamenete se producen en esta DERIVA natural...

Mehta RS, Wainwright PC (2007) Raptorial jaws in the throat help moray eels swallow large prey. Nature 449:79-82.

miércoles, septiembre 05, 2007

One classic “tradeoffs” of sexual reproduction is the risk of acquiring sexual transmitted diseases. But if we now consider that many microbial and viruses associations survive or have been integrated inside the eukaryotic organism (ie “mutualistic”), this allow us to consider sexual contact as a chance to acquire symbiotic associates. In aphids symbiotic bacteria are inherited maternally, this has been demonstrated to be very conservative in parthenogenetic populations. One way to acquire the symbiont is by ingesting it in diets or by microinjections. Alternatively during sexual reproduction, male-borne symbionts can be acquired by females and subsequently transferred to sexually or parthenogenetic generated offspring. This transference is stable trough generations and can establish inheritable acquired characters such as defense towards natural enemies or resistance to heat.

This is the case of the worldwide distributed pea aphid Acyrthosiphon pisum (Hemiptera: Aphididae). In this insect, besides the main Buchnera aphidicola simbiont (that is required for “normal” development and reproduction), other three bacterial symbionts may be present: Candidatus “Hamiltonella defense”, Candidatus “Serratia symbiotica”, and Candidatus “Regiella insecticola” (all members of Enterobacteriaceae). Different aphid population can present from zero to all of those bacterias. Aphids (in their native habitats) usually have all female parthenogenetic reproduction from spring to autumn, then a single generation of sexually reproducing offprings is born (this is related with the shortening of the photoperiod), as a result of copulation these females will lay overwintering eggs and restart the cycle of parthenogenetic reproduction (Fig.1).

Figure 1: Schema of aphid life cycle using A. pisum as example

During copulation, male insects transfer sperm as well as other substances produced from accessory glands. In this, sexually transmitted viruses and bacteria can be transferred to the female. In the case of the pea aphids symbionts present in the male aphid gonads (Fig. 2) R. insecticola can be transferred to the female by the seminal fluid. This has been tested simulating the sexual reproduction season in laboratory strains with and without the different bacterial symbionts and it was demonstrated that copulation between a male carrier with a non infected female can result in a venereal horizontal transmission of the bacterial symbionts! (Moran & Dunbar, 2006).Thus the female and the following parthenogenetic strain generated acquire the symbiotic association.

Interestingly, the acquired association between the aphid and the different Enterobacteriaceae could generate changes in the organism relation with the environment such as the acquired ability to survive parasitoid wasp infections, fungal pathogens, and expansions in the insect niche thanks to acquired ability to use other host plant or to become resistant to a broader range of temperature.
This show again the relevance of understands the organism as a creative onto-phylogenetic dynamic process of development. Better than to focus only on the phenotypic filter as a motor of evolutionary processes.

Figure 2: Localization of the symbionts within the male reproductive system (from Moran & Dunbar, 2006) by using FISH probe matching the 16S rRNA sequence of R. insecticola (green and bright yellow) and with propidium iodide DNA counterstain (red), (Scale bars, 0.1 mm.).



Moran NA & Dunbar HE (2006) Sexual acquisition of beneficial symbionts in aphids. PNAS, vol. 103, 34, 12803–12806.