Genuine Puzzles In Biology?

So would anyone like to add to the list? What is genuinely puzzling in biology --- what are the questions that need answers and don't yet have them? Whether or not genetic equidistance is the result of epigenetic complexity of organisms or whether it is the result of genetic drift et al. I argue for the former.

"The meaning of this sentence is obscure. However I suspect that if and when you ever elucidate your meaning, this will turn out not to be a genuine puzzle in biology but rather a question to which every biologist knows the answer." The genetic equidistance phenomenon suggests that the number of different residues between two organisms is largely determined by the amount of time since the two species diverged [Margoliash, 1963]. This view not only presupposes that a neutral mutation in a given organism is also neutral in all other organisms, but it also assumes that the epigenetic complexity of an organism does not impose a restraint on the amount of genetic diversity that organism can tolerate. Taft et al. (2007) propose that organismal complexity may be defined as the number and different cell types in that organism, as well as the amount of cellular organization.If the epigenetic complexity of an organism does impose a restraint on the number of mutations that organism can tolerate, then the phenomenon of genetic equidistance would still be manifested, even if all species diverged at the same time. This is because different species can tolerate different levels of mutations, since different organisms have different numbers of cell types.It is difficult to determine whether the phenomenon of genetic equidistance is the result of the amount of time that has passed since two or more species diverged, or whether this phenomenon is the result of the epigenetic complexity of the organisms imposing restraints on the number of mutations tolerated. This is because the number of cell types in organisms has, in general, increased as evolutionary history progressed [Valentine et al., 1994] .I am proposing that this is a genuine problem in biology. I would be more than willing to elaborate on this if I am somehow still being obscure.References:Margoliash E. Primary Structure And Evolution Of Cytochrome C. Proc. Natl. Acad. Sci. U.S.A. 50: 672—9 (1963).Taft, R.J., Pheasant, M. and Mattick, J.S. (2007) The relationship between non-protein-coding DNA and eukarotic complexity. BioEssays 29:288-200.Valentine James W., Collins Allen G., Meyer C. Porter. Morphological Complexity Increase in Metazoans. Paleobiology, 20(1994):2:131-142.

"I'm not a biologist, but it sure seems pretty obvious that it is the result of genetic change, rather than epigenetics. The measurement of genetic distance is done by comparing protein structure of different species, and the protein structure is encoded in the DNA." It's obviously the result of genetic change, but the question is not if it is the result of mere change at the molecular level (since that is very, very obvious). With the observation of the genetic equidistance phenomenon there emerges a paradox: how do we know that this phenomenon is the result of the amount of time that has lapsed since the divergence of two organisms, or whether it is the result of the epigenetic complexity of the organisms imposing a restraint on the number of mutations tolerated in a given protein, since as time progresses, the number of cell types increases. "You didn't actually argue anything. You just asserted." I never suggested, implied, or proposed that I argue for the former in this forum. However, I have argued for the former in other places. Also, you might want to consider not nitpicking on semantic details. Just a thought. "I expect that the biologist members will be be able to refute your argument in pretty short order." You shall see what you shall see.

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Biology rocks!

"You seem to have confused your terms. Epigenetics refers to DNA methylation and histone packaging. Genetic comparisons use the actual DNA sequence, as does genetic drift." I am referring to epigenesis in the context of ontogeny, i.e. in the context of embryological development, where organs arise in a certain order as the result of the interaction of different parts. In short, when I say "epigenetic complexity" I am referring to, firstly, the number of cell types the mature organism has, and secondly the amount of cellular organization and regulation in that organism.
For example, mammals would be more epigenetically complex than yeast. Sea urchins would be considered more epigenetically complex than annelids, despite sharing the same number (approximately) of cell types. This is because the blastomeres of the eggs of annelids lack the regulative properties that are present in sea urchin eggs.

"But what is being suggested here is not that "epigenetic complexity" causes "equidistance" but rather that it limits it. The cause of the (neutral) divergence would still be drift." Genetic drift does cause the phenomenon of genetic equidistance. However, this phenomenon is only manifested when the protein sequence of a less epigentically complex outgroup organism is aligned with the protein sequence of a more complex clade: e.g. the genetic equidistance result is observed if we align a protein sequence of a fish against that of a mammalian organism and reptilian organism.So the question really is not whether genetic equidistance is caused by genetic drift; rather, the question is whether it is the result of the time that has lapsed since divergence or whether it is the result of the epigenetic complexity of organisms. At the fundamental level, it is caused by genetic drift. But note that not all species are equidistant to each other. So, are the patterns of genetic equidistance the result of the time that has lapsed since divergence or is it the result of the epigenetic complexity of organisms. This is the puzzle.
I submit that it is the result of the epigenetic complexity of organisms.Edited by Livingstone Morford, : No reason given.

"Please support this assertion." There are numerous ways to support this assertion. Without getting too detailed, note that flowering plants evolved approximately 125 myr ago, and mammals evolved during the late Triassic period, or about 200 myr ago. Since flowers are less epigenetically complex than mammals, if my assertion is correct, there would be more genetic diversity among flowering plants than among mammals. This is exactly what we observe.Edited by Livingstone Morford, : No reason given.Edited by Livingstone Morford, : No reason given.

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Biology rocks!

"So what we are really looking at is the complexity of the DNA regulatory network." We are also looking at the number of cell types in an organism, and in fact this is the pivotal part of my argument. With regards to genetic drift and genetic equidistance, see my reply to Dr. Adequate.

"Using only conserved proteins with identical function in both species ensures that it's the former and not the latter." The use of conserved proteins (like cytochrome-c) with identical function in both species does not in any way ensure that it is the former. If genetic equidistance is the result of the epigenetic complexity of organisms, we would get the exact same results. I take it that you get the gist of my "argument"? "It's not really a puzzle." Yes it is, because how are we supposed to tell if the genetic equidistance phenomenon is the result of the time lapsed since divergence or if it is the result of the epigenetic complexity of organisms? With respect, you have not specified any method of how we are supposed to do that. "Also, you're frequently using "equidistance" when what you mean is "distance." " I'm glad that there are some people on this forum that pay attention to grammar and meaning of words (I don't mean that sarcastically). However, in this particular case, I think I do mean "equidistance."

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Biology rocks!