Panmere

From Science Daily:

Researchers at Texas A&M University’s Artie McFerrin Department of Chemical Engineering have discovered how certain types of bacteria integrate the DNA that they have captured from invading enemies into their own genetic makeup to increase their chances of survival.

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Examining E. coli bacteria, Wood found that the bacteria developed a means of not allowing the phage to replicate and leave the cell of its own volition. Once the phage was effectively “captured,” the bacteria incorporated the phage’s DNA material into its own chromosomes. This new diverse blend of genetic material, Wood says, has helped the bacteria not only overcome the phage but also flourish at a greater rate than similar bacteria that have not incorporated the phage DNA.

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This distinct advantage is helping scientists understand why bacteria carry about 10-20 percent of genes that aren’t their own. Simply put, carrying the virus DNA allows bacteria to increase their chances of survival by producing diverse progeny – something Wood says is extremely important when the bacteria choose to move to a new environment through a process known as dispersal.

Dispersal occurs, Woods says, when the bacterium can no longer glean the nutrients it needs from its surroundings or when other environmental conditions, such as temperature, have become unfavorable. Wood found that through an elaborate regulation method, the bacteria are able to retain the virus DNA or expel it. It’s an interesting trade off, as retaining the virus DNA helps the bacteria grow faster but reduces its motility, which is needed when seeking out new environments, Wood explains.

Remarkable. These bacteria are GMOs (genetically modified organisms); more specifically, they are transgenic organisms. However, they have achieved these modifications using endogenous (internally-supplied) DNA modification processes, rather than through the exogenous means of tedious laboratory manipulation.

Question: Are endogenously produced transgenic organisms inherently any more or less dangerous than exogenously produced transgenic organisms?

From Nature Editor’s Summary:

The origin of life on Earth required — at some point — the synthesis of a genetic polymer from simple chemicals. The leading candidate for this role is RNA, but although ‘activated’ ribonucleotide molecules (the building blocks of RNA) can polymerize without enzymes, no plausible route had been found by which the ribonucleotides could have formed. Now a team from the University of Manchester has found such a route. They also show that a widely held assumption about ribonucleotide synthesis — that the molecules formed from pre-existing sugar molecules and RNA bases — isn’t necessary for RNA to have formed on prebiotic Earth.

The relevant articles are linked on the Editor’s Summary page.

Yet another article on how artificial life is just around the corner. This one is from New Scientist: “Second Genesis: Making New Life“.

In the May-June 2009 issue of American Scientist, is a featured article entitled “Origin of Life“  [1]. In summary:

The authors investigate the metabolic evidence, reaction thermodynamics and chemical logic of the primordial autocatalytic cycle and conclude not only that it can explain the origin of life, but also that the appearance of life was very likely an inevitable side effect of the laws of thermodynamics.

The authors offer the following analogy of their proposal [bold added]:

Consider the requirements of the U.S. Interstate highway system. The system includes an enormously complex network of roads; major infrastructure devoted to extracting oil from the Earth, refining oil into gasoline and distributing gasoline along the highways, a major industry devoted to producing automobiles; and so on. If we wanted to explain this system in all of its complexity, we would not ask whether cars led to roads or roads led to cars, nor would we suspect that the entire system had been created from scratch as a giant public works project. It would be more productive to consider the state of transport in preindustrial America and ask how the primitive foot trails that must certainly have existed had developed into wagon roads, then paved roads and so on. By following this evolutionary line of argument, we would eventually account for the present system in all its complexity without needing recourse to highly improbable chance events.

In the same way, we argue, the current complexity of life should be understood as the result of a multistep process, beginning with the catalytic chemistry of small molecules acting in simple networks—networks still preserved in the depths of metabolism—elaborating these reaction sequences through processes of simple chemical selection, and only later taking on the aspects of cellularization and organismal individuality that make possible the Darwinian selection that biologists see today. Our task as origin-of-life researchers is to look at the modern highways and see what they reveal about the original foot trails.

The theme here is that the relevant pre-life chemistry necessary for creating life (”the foot trails”) was, comparatively speaking, quite simple. The authors then go on to argue that the origin-of-life process was further facilitated by the necessities of thermodynamics, which favored the formation of particular chemical cycles:

[W]e consider a primordial reductive citric acid cycle the most likely route from geochemistry to life—the rivulet that formed at the top of the energy hill, through which the pond of energy began its thermodynamic escape. We then ask how, from this simple beginning, could the complexity we see in the modern cell arise.

Given that their discussion is of pre-cellular chemistry, so that the discussion centers on subsets of chemical flows freely embedded in some larger context of sinks and sources, it seems somewhat problematic to invoke thermodynamics for these inherently open subsystems; however, set that aside. What seems more interesting to me is that if all the origin-of-life problem required was some comparatively simple chemistry, and a thermodynamically favorable environment, then….why have we not yet created life in the lab? Certainly, we ought to be able to construct the appropriate vessels, “soups”, and thermodynamic conditions to facilitate the formation of life; indeed, as the authors state, life should be “inevitable”.

One could perhaps appeal to some statistical argument about the frequency of such creation, or to some pesky technical issue, as to why this has not yet been done. However, this strikes me as somewhat weak; it would seem reasonable to expect that there could be produced at least a compelling proto-life example, based on these premises. But where is it?

Another possibility is that the authors’ premises are wrong to begin with, and that the origin-of-life process did not go from simple chemistry to complex to cellularization. Indeed, there is no a priori reason to expect that the origin-of-life problem is solvable specifically by reductionist means. As such, life could indeed still be “inevitable” — it may simply be that the conditions for its arising required a much more complex set of chemical conditions and environmental forcings than typically envisaged. This would not mean that the origin-of-life problem is inscrutable or unsolvable, far from it; however,  it would mean that the problem is perhaps much more tightly coupled to the organizational complexes of pre-biotic chemistry and conditions than to the particular chemical cycles which became codified in the organisms themselves. By this account, the details of the codified chemical cycles are best thought of as residue; it is the organization of the system which is key.

In terms of the author’s analogy of highways and foot trails: the task would not be to look at the modern highways and see what they reveal about the original foot trails, but instead to look at the modern highways and see what they reveal about the nexus of conditions that caused the particular organization of roadways which resulted.

References

[1] Trefil, J., Morowitz, H., Smith, E. “Origin of Life“. American Scientist. 97(3):206. DOI:10.1511/2009.78.206.

Aloisius Louie’s new book, More Than Life Itself: A Synthetic Continuation in Relational Biology [1], is now listed on Amazon.com. The book is not yet available, but the listing states the publication date as May 31, 2009. On the product page, you can sign up to be notified by email when the book becomes available.

[1] Louie, Aloisius H. 2009. More Than Life Itself: A Synthetic Continuation in Relational Biology. Ontos-Verlag, Frankfurt. 388 pp.

     ISBN-13: 978-3-86838-044-6. ISBN-10: 3868380442.

Excerpted from The Wall Street Journal:

In Massachusetts, a young woman makes genetically modified E. coli in a closet she converted into a home lab. A part-time DJ in Berkeley, Calif., works in his attic to cultivate viruses extracted from sewage. In Seattle, a grad-school dropout wants to breed algae in a personal biology lab.

These hobbyists represent a growing strain of geekdom known as biohacking, in which do-it-yourselfers tinker with the building blocks of life in the comfort of their own homes. Some of them buy DNA online, then fiddle with it in hopes of curing diseases or finding new biofuels.

But are biohackers a threat to national security?

The full article notes that one defense of such biohackers is “that Mother Nature is more likely than any home hobbyist to create dangerous new pathogens. They cite the current A/H1N1 “swine flu” virus, which is a made-in-the-wild brew of human, bird and pig influenzas.” This defense, however, is weak on two points: 1) the possibility of naturally occurring pathogens does not mitigate the danger of man-made pathogens, and 2) the frequency of such naturally occurring pathogens is chance-based, whereas the intentional actions of malicious biohackers could greatly increase the frequency of man-made pathogens.

Ultimately, though, people cannot be isolated from microorganisms. Unlike, say, isolating fissionable nuclear materials from most people, microorganisms are essential for our survival and permeate our existence. Also, the empirical evidence is that the vast plethora of intentionally genetically modified organisms to date have not been a scourge or a plague. On the other hand, there is no a priori definable line between “safe” and “unsafe” biohacking, given that each genetic modification ventures into new territory for which we have either no models, or very simplistic ones, as to the effects of such modified organisms on local and global ecosystems.

It would seem that biohacking will only increase over time, as our understanding of genetic manipulation increases, and the tools and additional raw materials become more sophisticated and more readily available. For good or ill, for good or ill.

Edit:

Also see: Schmidt, M. “Diffusion of synthetic biology: a challenge to biosafety“. Systems and Synthetic Biology 2(1):1-6. DOI:10.1007/s11693-008-9018-z