Saturday, October 17, 2009

The Onion Test -- Answered

In his blog, biologist T. Ryan Gregory coined the phrase “Onion Test”. The blog entry starts like this:

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

Why would anyone one think that there is a universal function for “junk” DNA? Doesn’t it make more sense that there are a multitude of functions performed by “junk” DNA and that it may take hundreds of years of tedious research to figure out what it all does? It’s a hubris assumption for a scientist to think that the vast majority of DNA is junk just because he doesn’t know what it does. Frankly, I haven’t yet seen a good reason to call any of it junk based upon what it looks like. Do I think there is some junk? Sure -- that would be an expected result of entropy. However, I would be way more inclined to believe 5% was truely junk rather than 97%.

Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?

What could some onion “junk” DNA be used for? Well, unlike humans, onions can't control their environment or move away from it. Onions have no choice but to adapt. It could be that onions were designed with a lot of adaptive capacitance allowing its descendents to change into different kinds of onions that could thrive in many different environments. Deletion of DNA used for adaptive capacitance could then still easily result in a viable onion. It would be an onion with less adaptive capacitance than the original but still able to produce offspring that could thrive in the current environment. Multiple lines of deletion of DNA used for adaptive capacitance could also result in speciation and account for the various DNA sizes for different species of onion.

The idea of adaptive capacitance is hardly far-fetched. We already know that stem cells change into other types of cells even though most of the cell types that derive from stem cells have the same DNA coding. In fact, this hypothesis that some non-coding DNA may serve as adaptive capacitance has already been unwittingly tested at least once. PZ Myers describes the experiment in his blog here. To summarize, the experiment involved moving 10 lizards out of their environment to the tiny island of Pod Mrcaru. After only 36 years these lizards changed into a different kind of lizard. There were changes to their skulls, limbs and even personality. Even more remarkable is the fact that their digestive system “evolved” cecal valves allowing them to digest a broader range of plant material. It’s just plain silly to think that this could be the result random mutation and natural selection over the course of just 36 years (could someone please do the math). This could only happen if previously existing information in the collective genomes of these lizards was selected in response to the environment.


At 8:18 PM, March 10, 2010, Anonymous Anonymous said...

2 points:
1. While you refer to Gregory's Onion Test, you do not address the question it raises which is: Why is there such a discrepancy between gene/DNA size/content and species -- if one supposes a "design", shouldn't there be consistency? You argue rhetoric and innuendo(Well, unlike humans, onions can't control their environment or move away from it. Onions have no choice but to adapt), but not science. Writing code is not the imprimatur for scientific approach.
2. The example of the evolution (or "evolution" as you term it) of the lizard you use to demonstrate that "junk DNA" was put there to allow for alterations of the organism to adapt to its environment: In other words, like the OAK tree inherent in the acorn, life (other than human life) has all this extra machinery to allow invocation of alternate physiologies when required -- sort of like Batman's utility belt.
1. It is not clear, nor is it evident, that this species of lizard DOES have this "junk DNA".
2.To assume that the capacity for adaptation is "adaptive capacitance" due to "junkDNA" is post hoc ergo propter hoc fallacy, and NOT science.
3. Is there a point to "allowing" pre-defined adaptation to new environments, other than providing a "curiosity game" for humans disguised as scientists?
3. The use of "well junk DNA really isn't junk because it is now proven that organisms need it" is NOT proof that "there see: the Biologists got that wrong, so they are wrong about evolution also" [Richard Deem]. That is not science, either.


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