Thursday, May 15, 2014

Life's New Language

Artistic DNA molecule. Flicker/Keith Ramsey
For one who follows the world of biological news, one but can't help but have seen the news flash of "alien DNA" being incorporated into bacteria. It seems that many are praising the scientists as if it were some great and humanitarian leap for our progeny. However, is the hype accurate?

Yes, it is quite interesting that a group of scientists, Floyd Romesberg and team from Scripps Research Institute, were able to manufacture chemicals that were quite different from DNA's four bases: adenine, thymine, cytosine and guanine (A, T, C and G respectively). To be frank it think the research is quite interesting. 
The bases engineered by Romesberg’s team are more alien, bearing little chemical resemblance to the four natural ones (1).
These new alien DNA bases, d5SICS and dNaM, were integrated into the microbes genome - this is the core of all the hubbub. Enzyme machines that help copy and translate the genetic code were able to interact with these novel bases.

Some are saying that we may be able to manufacture new drugs and unprecedented cures come from this research. In other words, with new letters one will be able to make new genetic words, which will expand the potential protein results.

My Perspective

However, I do have ten observations concerning this study, some on the skeptical side:
  1. Great, they accomplished adding new, man-made bases to a bacteria's DNA. But at this time the cell has no way of making more, if the microbe's human farmers discontinue supplying the cells with these bases, these bases will no longer be coded within the cell. Traditional bases will replace these artificial bases places.
  2. These bases are said to add information potential of the genome. This may be good, however, even with our computer systems, with only two "alphabets" (0 and 1), we are able to make images, videos, text, music, manufacture complex 3D objects and you name it. DNA already has twice as many "alphabets" as our technology, four bases (not counting the 64 codon combinations and used to put together 20 amino acids).
  3. OK, we have two new bases, so what about the RNA and all the protein complexes that help make protein? Yes, we can copy the text, but what about protein manufacturing? It is one think to copy text, but it is another to use text to build an aircraft. There is a whole level of magnitude above this accomplishment needed to even think about making protein.
  4. Proteins are made up of amino acids. The are attached to something called tRNA and are used to help build protein. So one is going to have to build "machines" help specify new amino acids to the correct new bases that make up the tRNA. Where will these machines come from? How will they be coded? What molecular machines will be automated to make them? There is a vicious loop going on here.
  5. To make protein, we need amino acids. Even if we get amino acids to "stick" to the novel tRNA and rRNA, we have to get the amino acids to form protein.
  6. We finely make a new protein. But form equals function. In other words, a protein needs to be folded just right for very specific jobs. Little machines, called chaperons, help fold proteins in the correct and usable shapes. Where are these new chaperons coming from for the new proteins with new types of amino acids? In other words, new code and new machines will have to be designed to fold the new proteins into correct orientations to even be potentially usable.
  7. They credit the origins of our current nucleotide bases to evolution through deep time. No intelligent source is invoked. However, it took a group of intellectual researchers over fifteen years to just get these microbes to uptake and replicate these artificial letters. This does not count the many other researchers, since the 1960's, who also have been attempting to work toward this goal. It took intelligence to get as far as they did, how could a blind, undirected process come up with four bases? It is even worse than that, think about it, as of now, the microbes can't even uses these bases for anything. They just sit there and get replicated. This hole system is irreducible complex, unless all the parts were in place in the first cells, the original bases would not have functioned.
  8. Along with this, we only know of information arising through intelligent minds. It is the inferences to the best explanation and the law of uniformity. Pure naturalism is not enough. As said on the point above, this study demonstrates this argument lucidly.
  9. Lead researcher Romesberg said the following within a piece in Nature: "If you read a book that was written with four letters, you’re not going to be able to tell many interesting stories" that is why these new bases are important, they will extend the informational content (1). Again, sounds good except for when one looks at even a simple cell, one is totally amazed by the stunning design and complexity. It makes our greatest accomplishments seem like foolish children's play. The biological story is one of the most interesting "stories" that can be told!
  10. Lastly, a quote from Romesberg states the following: "This shows that other solutions to storing information are possible and, of course, takes us closer to an expanded-DNA biology that will have many exciting applications—from new medicines to new kinds of nanotechnology" (2). Why does it seem as if all cutting edge (maybe on the offbeat side) "research" is argued  to help with health, medicine or improve technology? It seems to me that they trying to validate their research by saying "hey, this sounds a little silly, but it really does have importance." OK, maybe I am cynical, but that's what it sounds like!

(1) Callaway, Ewen. "First life with 'alien' DNA"
(2) Scripps Research Institute Scientists Create First Living Organism that Transmits Added Letters in DNA 'Alphabet'.

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