Genomics

I was digging around for some good examples for a talk I am doing on mutation theory in a few weeks, and came upon this great paper in PNAS – Molecular Origins of Rapid and Continuous Morphological Evolution. Their argument? “tandem repeat expansions and contractions are a major source of phenotypic variation in evolution”. Hmmm…. it almost seems as if these repeats are functioning as parameters to a larger system. That reminds me of something…. Almost like parameterized evolution. The paper has a great image of repeat-based morphological variation, too: . The primary differences in the skulls are nose bends and midface length, which are governed by a repeat sequence in the Runxp-2 gene. By expanding or contracting parts of Read More ›

Big news at Craig Venter’s Synthetic Genomics: Summary: Link 1 Press Release: Link 2 The rhetoric is interesting. What they’ve done is stuck a synthetic genome inside a nonsynthetic cell. Nonetheless, they’ve slipped into talking of a “synthetic bacterial cell.” Indeed, one headline reads “The First Self-Replicating Synthetic Bacterial Cell.” This is hype. If something is going to be called “synthetic,” shouldn’t the whole of it be synthesized and not merely a minuscule portion of it? Also, does such a cell knowably signal design and, if so, why wouldn’t cells untouched by Synthetic Genomics do the same, i.e., implicate design?

Were one to design the encoded DNA “blueprint” of life, would not one incorporate ways to preserve that “blueprint”? The Nobel prize in medicine has just been awarded for discovery of features that look amazingly like design to preserve chromosomes. See:

3 Americans win medicine Nobel for chromosome research

Three U.S. researchers were awarded the 2009 Nobel Prize in Physiology or Medicine for their work on how chromosomes are protected against degradation, the Nobel Foundation reported Monday. Read More ›

Semiotix – Stephen Pain The distinction between “theorising” and “belief” is extremely important because our attitude differs towards them. In a theory the reified concept of the sign does not have an ontological status but an epistemological one. While in belief, the concept has often a clear ontological one. Uexküll believed in his concept of the Bauplan in the same way as Bergson believed in the vital force. The concept of a plan is of course no different from the creationist’s concept of “intelligent design”. Any usage of the Bauplan is further complicated by its ideological usage in The Biological State, Uexküll‘s template for the German State, one that was anti-democratic and in many instances attractive to the Nazi of Read More ›

In informatics metaprogramming is a technique consisting in developing computer programs (sets of instructions) that output other programs. While simple programming means instructions generating data, metaprogramming means instructions generating instructions. In general the prefix “meta” means a thing/cause that stays at a higher semantic/ontological level than another thing/effect (in the case of metaprogramming we have a two-level hierarchy where a parent program creates child programs). For a tutorial introduction to metaprogramming see for example the following Jonathan Bartlett’s brilliant articles:
one, two and three.

DNA contains instructions, biological code for working-out various constructive cellular jobs (making proteins, setting developmental parameters, etc.). Question (inspired by the above ascertainment and readings): does DNA contain also meta-programs beyond simple programs?

Much DNA (outside its coding-for-proteins portions) seems without function (junk-DNA). Is it possible that some junk-DNA is meta-code able to assembly other DNA code? This could be an interesting ID prediction. Many have noted as the information amount contained in the genomes seems really too little to account for the overall complexity of organisms. Metaprogramming would be exactly one of the techniques able to compress the biological information. Read More ›

I’ve heard geneticists say we’re in the middle of a paradigm shift, and that no one really understands what’s going on. I even read an article the other day showing how at least one creature DELETES portions of its own DNA during certain stages of development. Basically, the long-held ideas from even a couple years ago are being modified. Until scientists can look at an arbitrary line of code and say “this does this or that” I would not say any idea is “certain”.

Lamarck’s specific hypothesis had been rejected once Mendel found a mechanism for inheritance. Lamarckism was so obviously wrong. Darwin came up with something that was just the opposite. It was obviously true and easily understandable. It is easy and true within a certain scope, although it’s inadequate to explain certain biological features. Hence the modern synthesis and the current attempt to formulate a new synthesis of ideas, which may or may not succeed. Read More ›