Friday, July 31, 2015

The onion test or the protozoa test?

Regarding the onion test, I would like to say it is asking the wrong question. One should be asking is: why the simple organism protozoa kind has a genome size variation range from the small to large of ~20000 fold, or why flowering plants ~2000 fold, whereas mammals only less than 10 fold? Don't even try to invoke time of evolution as the reason as mammals and flowering plants appeared about the same time. The actual numbers cited here came directly from the a paper by the author who invented the onion test (see Figure 1 in the paper). 

From the onion test author: “the onion test simply asks: if most eukaryotic DNA is functional at the organism level, be it for gene regulation, protection against mutations, maintenance of chromosome structure, or any other such role, then why does an onion require five times more of it than a human?”

Answer: 99.9% of human genome is functional for internal construction purposes while 0.1% is for normal variations among humans and for adaptation to environments. HIV is 20% vs 80%. Onions have a large fraction of their genomes for adaptive purposes, which can be freely changed without much effect on its internal integrity (in this sense, junks). So, to say most human DNA is functional for its construction does not necessarily precludes one from saying that most onion DNA is not or most HIV DNA is not for construction. So the question why does an onion require more (functional genomes in terms of construction purpose) is not a valid question. No one is saying so and it does not. No one, at least I am not, is saying that every species has the same proportion of functional genomes (in terms of internal construction not much related to adaptation). So, the onion test has a straw man premise. What onion does have more than human does, or an HIV virus does more than human does, is that it has more fraction of its genome as the so called junks (that in fact play adaptive roles in response to environments). Once you accept as you did that some species can tolerate more junks, the size of the junks, whether 1x or 5x of human genome size, is irrelevant.

So, why portozoa have the largest variation in genome size? Protozoa are all unicellular, which is the key. They are hence all simple relative to multicellular organisms. Simple systems can tolerate more random error type of variations in their building parts, including the dimensions or amounts, which just means a large stdev from the ideal form. So, if a part for a toy car is specified to have a length of 10000 +/- 9999, then both 19999 or 1 will be allowed random errors. 

All researchers in the field base their papers on the infinite sites model, which says there are infinite number of neutral or junk sites for any genome regardless whether it is human or onion. They do not acknowledge that different species tolerate different amounts of junks. They don't think that monkey or mouse or onion can tolerate more junks than humans do. or maybe they do in their heart but at least they disregard that in their work.I think they are going to have a hard time answering my protozoa test.

Palazzo AF, Gregory TR (2014) The Case for Junk DNA. PLoS Genet 10(5): e1004351. doi:10.1371/

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