Genetic Equidistance: A Puzzle in Biology?

Here I wish to discuss my thesis that the phenomenon of genetic equidistance presents a problem in biology: how do we know if this phenomenon is the result of the amount of time that has lapsed since any two or more organisms have diverged, or is it largely the result of the epigenetic complexity of organisms imposing restraints on the amount of mutations those organisms tolerate? Indeed, if the epigenetic complexity of an organism does impose a such restraint, then the genetic equidistance result would still be observed, regardless of the time that has lapsed since divergence.On a slight tangent, if this was the case, then functionally redundant protein sequences cannot always give us accurate conclusions with regards to phylogenetic relationships. Edited by Adminnemooseus, : Add a blank line - Because I had nothing easy better to do.

Google "genetic equidistance" and you'll get the necessary information.To quote Wikipedia,
"The genetic equidistance phenomenon was first noted in 1963 by E. Margoliash, who wrote: "It appears that the number of residue differences between cytochrome C of any two species is mostly conditioned by the time elapsed since the lines of evolution leading to these two species originally diverged. If this is correct, the cytochrome c of all mammals should be equally different from the cytochrome c of all birds. Since fish diverges from the main stem of vertebrate evolution earlier than either birds or mammals, the cytochrome c of both mammals and birds should be equally different from the cytochrome c of fish. Similarly, all vertebrate cytochrome c should be equally different from the yeast protein." For example, the difference between the cytochrome C of a carp and a frog, turtle, chicken, rabbit, and horse is a very constant 13% to 14%. Similarly, the difference between the cytochrome C of a bacterium and yeast, wheat, moth, tuna, pigeon, and horse ranges from 64% to 69%. Together with the work of Emile Zuckerkandl and Linus Pauling, the genetic equidistance result directly led to the formal postulation of the molecular clock hypothesis in the early 1960s. Genetic equidistance has often been used to infer equal time of separation of different sister species from an outgroup."Edited by Adminnemooseus, : Add the quote box for the quoted material, etc.

Well, no, we're not. The function of proteins like cytochrome c or ribosomal subunit 16S aren't related to cell type, because the function is so basic every kind of cell in every kind of organism needs to perform it. All of your cells, regardless of type, are engaging in protein synthesis and electron transport activity, or else they're dead. I’m not sure you get the gist of my argument. For example, an ontogenic amino acid substitution in a human protein must be compatible with every one of the different cell types found in the human organism (every cell, that is, that contains the protein), while an amino acid substitution in say, a yeast protein must be compatible with only one cell type.
An analogy may (in a theoretical sense) be useful here. Say you have protein A. And you have cell type X, Y, and Z. Any substitution mutation in protein A must be compatible with all three cell types. Meanwhile, if you only have cell type X, then protein A needs only to compatible with X (analogy a la Dr. Shi Huang).
In light of this elaboration, I don’t think your above argument is pertinent. Cell type and cell diversity is going to have no effect whatsoever on these highly conserved proteins, and that's how we know that accumulated differences between homologous genes in different organisms really do reflect evolutionary time. If the number of cell types in an organism does not impose a restraint on how many mutations are tolerated, then what is your explanation for the observation that conserved sequences in simple organisms are always conserved in complex organisms, but the reverse is not necessarily true? Also, why is it that simple organisms that have been diverging for the same amount of time as complex organisms generally display more genetic diversity?
The proposition that the number of tissues in an organism does not impose a restraint on the amount of mutations tolerated is in conflict with Xun and Zhixi (2007), where we see:
To maintain normal physiological functions, different tissues may have different developmental constraints on expressed genes. Consequently, the evolutionary tolerance for genomic evolution varies among tissues.And,
We conclude that tissue factors should be considered as an important component in shaping the pattern of genomic evolution and correlations. Well, but it's not. We know it's not because, again, genetic distance is being measured only on genes that have nothing to do with cell type, cell diversity, or epigenetic complexity. See my elaboration above. Also note that the genetic equidistance phenomenon is manifested in many proteins, not just proteins which have high levels of functional complexity. I’m starting to get the idea that you really don’t quite understand my assertion — and that’s probably my fault for not being clear enough.
Regardless of how complex an organism you are, your mitochondria engage in electron transport and your cells express proteins. True, but you are not attacking my argument. The more complex an organism is, then the less substitutions the cytochrome-c of that organism can tolerate, since any given substitution must be compatible with all the different tissues. By only measuring the genetic distance on proteins that have identical function between the compared species regardless of complexity, like cytochrome c and ribosomal subunit 16S. See my elaboration.References:Xun Gu, Zhixi Su. Tissue-driven hypothesis of genomic evolution and sequence-expression correlations. PNAS, 104 (8): 2779-2784 (2007).

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Biology rocks!

the quick answer is that we know that genetic distance is the result of time and not a pattern of increasing constraint on organisms, because we measure genetic distance based on genes that are subject to far greater restriction as a result of function than they could possibly be subject to as a result of increasing complexity - cytochrome c, ribosomal subunit 16S, and so on.Firstly, as I pointed out earlier, the genetic equidistance phenomenon is manifested in many proteins, and not only proteins that have high levels of functional complexity. Secondly, with regards to your statement that genetic distance is measured in genes that are subject to far greater restriction as a result of function than they could possibly be subject to as a result of increasing complexity, let us realize that neutral amino acid substitutions are allowed in cytochrome-c. However, what I am arguing is that a neutral amino acid subsitution in yeast cytochrome-c is not necessarily neutral in a considerably more complex organism because that substitution must be compatible with all the different tissue types found in that organism. Under your model, humans would exhibit less genetic distance from yeasts than trout do, but what we observe is that both humans and trout exhibit equidistance from yeasts Genetic distance between a complex clade and a simpler outgroup is equivalent to the genetic diversity of the simpler outgroup. Therefore, the distance between trout and yeast and between humans and yeast is determined by the genetic diversity of yeast and not that of the trout or human (a la Dr. Shi Huang). For more background information, you might want to read Dr. Huang’s paper on the maximum genetic diversity hypothesis.

and the fact that this pattern is observed in highly conserved genes supports the concept of molecular clocks Your position cannot be reconciled with particular observations from protein sequences, particularly one observation. A ClustalW alignment of the cytochrome-c sequences of homo sapiens, the alligator, and the frog, reveal that the frog and the alligator are equidistant to humans by 13 residues each. Of these 13 different residues, 7 of them are located in the same position in the alligator and the frog.
To calculate how many of these positions should be shared, based on chance and probability, the following may be done:The chance for a position to be different between human and frog is 13/105.
The chance for a position to be different between human and alligator is 13/105.
The number of positions that would overlap based on chance: 13/105 x 13/105 x 105 = 1.6
In a word, the molecular clock would predict that only 1.6 differing positions (differing from the human cytochrome-c) would be shared by the alligator and the frog. However, this is not the case, as 7 differing positions are shared by the alligator and the frog. This is explained by the thesis I am arguing for, but how does the molecular clock explain this?For a more detailed summary of this feature, see Huang, Shi. The Overlap Feature of the Genetic Equidistance ResultA Fundamental Biological Phenomenon Overlooked for Nearly Half of a Century. MIT Press Journals — Biological Theory, 5(1): 40 — 52 (2010).

Can I assume that by "genetic diversity" you are referring to the coding regions of DNA? Yes. If so, then you run into the problem that Taq raised in the last thread. Respectfully, the problem that Taq raised is irrelevant. The predominant force of genetic change is genetic drift; however, the question is what causes the phenomenon of genetic equidistance. At the fundamental level, it is the result of genetic drift. But is the assumption that genetic distance is determined by the time lapsed since divergence correct? I think not.On a slight tangent, I did a PubMed search of genetic equidistance in pseudogenes and found no results. Does anyone know if the phenomenon of genetic equidistance is prevalent in pseudogenes?

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Biology rocks!

I was trying to think of a way to test your ideas. They’re not mine. I was thinking of comparing sponges, mammals, and fungi to see if they were genetically equidistant. Let me understand this. You’re going to be aligning the protein sequences of what clade to what simpler outgroup? Of these three taxonomic groups you suggest, fungi would be the simplest. Hence, the more complex clade consisting of mammals and sponges would be aligned against the simpler outgroup. Sponges and mammals will be equidistant to fungi.

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Biology rocks!

Before I reply to the actual arguments advanced by my opponents, I wish to respond to various comments made about myself as a person.
Firstly, I assure you that I am not as much of a brick wall as Theodoric makes me out to be. I used to be a young-earth creationist, but that changed when I did a thorough examination of the evidence against young-earth creationism. Moreover, my posts which you refer to are nearly half a year old, and since then my position on biological origins has changed to a degree. In short, if I find evidence that goes against my beliefs, I do not stubbornly cling to those beliefs.Regarding molbiogirl's statement that I have claimed to be a biochemist, I wish to emphasize that it is a far cry from authoring papers on biochemistry than actually being a biochemist. I am not a biochemist, and have never claimed to be. I am eighteen years old (I fully respect those of you who have obviously had more experience in this than I have), and in my first year of majoring in biochemistry. To suggest that I ever claimed to be a biochemist would be quite a leap in reality. Any objections?
I think this should clear the record of where I am coming from, and having responded to that, I will now respond to a most voluminous amount of text.P.S. Sigh, this will take a while. And I didn't get much sleep last night either. So don't expect me to reply to all of you on this one night. Edited by Livingstone Morford, : apostrophe s for possessive proper nounEdited by Livingstone Morford, : No reason given.Edited by Livingstone Morford, : No reason given.Edited by Livingstone Morford, : No reason given.Edited by Livingstone Morford, : No reason given.

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Biology rocks!

Due to the large volume of responses to my posts, I will respond to those posts which I think are the most pertinent and most important to this topic. If someone feels like their post deserves a response, please inform me.That said,

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Cytochrome c isn't in the environment of the cell, it's buried deep in the intermembranous space of the mitochondria, and from that perspective all cells are basically the same.

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Although the cytochrome-c is located in the mitochondria, this does not imply that it does not have an affect on biological activity outside the mitochondria.

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I think the most fruitful line of attack is the way in which you characterize a deleterious substitution mutation as an "incompatibility with cell type." I think this is a unclarifying way to look at mutations. A deleterious amino acid substitution in cytochrome c, for instance, is going to be lethal to the cell regardless of cell type because electron chain activity is critical for meeting the cell's energy budget Some number of mutations are going to be deleterious because they change the way the protein interacts with other components of the cell, or they may introduce a new interaction with the cell, but actual cell type isn't going to have much to do with that. Interaction-based deleteriousness happens at a finer grain of cellular environment than "this is a liver cell; this is a muscle cell."

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You suggest that there is no such thing as a substitution that would be incompatible with the cell type. Or more precisely, that the harmful affects of a substitution (or other type of mutation, so long as it is not synonymous) are not exclusive to only certain tissues. However, observations from biology tell a different story. Can your position be reconciled with say, the observation that brain specific genes evolve slower than immune specific genes, or that members of the nAChR family are more constrained when they are in the central nerve system than those in the peripheral nerve system? With respect, I beg to differ on the grounds that your position will have difficulty in explaining away the data presented by Miyata et al. (1994), where we see that:
A molecular phylogenetic analysis of tissue specific isoforms that are identical to one another in function but differ only in tissue distribution revealed frequent gene duplications and rapid accumulations of amino acid substitutions during the early evolution of chordates where rapid evolution at the tissue or organ levels is thought to have occurred. And,
Members that are virtually identical to each other in function, but differ only in tissue distribution often form a single cluster (subgroup) on the phylogenetic tree.
And,
As we showed above, molecules are constrained more or less from tissues or organs (i.e., global constraint) and liberation of functional constraints at the tissue level result in the rapid accumulation of genetic variations as demonstrated by the blind mole rat crysallin [Hendrik et al., 1987]. Thus the relaxed constraint at the phenotypic level in the early evolution of chordates may permit many isoform duplications as well as rapid accumulation of amino acid substitutions. Also, you might want to explain away the observations made by Zhang and Li (2004),
Do housekeeping genes, which are turned on most of the time in almost every tissue, evolve more slowly than genes that are turned on only at specific developmental times or tissues? Recent large-scale gene expression studies enable us to have a better definition of housekeeping genes and to address the above question in detail. In this study, we examined 1,581 human-mouse orthologous gene pairs for their patterns of sequence evolution, contrasting housekeeping genes with tissue-specific genes. Our results show that, in comparison to tissue-specific genes, housekeeping genes on average evolve more slowly and are under stronger selective constraints as reflected by significantly smaller values of Ka/Ks. According to Kuma et al., 1995:
we compared evolutionary rates of kinase domains between members of the Ig family and showed evolutionary properties characteristic of family members: a wide difference of evolutionary rates among members, a correlation of evolutionary rates between different domains in a molecule, and the tissue dependence of evolutionary rate. These evolutionary properties could not be understood by local constraint along, but rathery they suggest the presence of a global constraint derived from higher levels like tissues or organs, because the structure and function of the kinase domain and those of the Ig domain are similar between different members. Thus the evolutionary rates are expected to be similar between members, if the global constraint is less important. Also,
"Evidence suggests the presence of an alternative constraint derived from higher levels: cells and tissues consist of many molecules, interacting directly or indirectly with each other. Functional alternations of molecular would influence more or less the functions of higher levels like cells or tissues where the molecules are involvedWe report here evidence suggesting that the global constraint derived from higher levels like tissues or organs actually exist and that the evolutionary rates of family members are strongly influenced by tissues where they are expressed specifically. And,
To maintain normal physiological functions, different tissues may have different developmental constraints on expressed genes. Consequently, the evolutionary tolerance for genomic evolution varies among tissues. Here, we formulate this argument as a "tissue-driven hypothesis" based on the stabilizing selection model. Moreover, several predicted genomic correlations are tested by the human-mouse microarray datafor genes with the same expression broadness, we found that genes expressed in more stringent tissues (e.g., neurorelated) generally tend to evolve more slowly than those in more relaxed tissues (e.g., hormone-related). We conclude that tissue factors should be considered as an important component in shaping the pattern of genomic evolution and correlations. (Gu and Su, 2007)Until these observations can be explained away, I believe that I am compelled to hold to the position that a neutral substitution in a simple organism is not necessarily neutral when that protein is present in more cell types.In passing, I might add that Newgard et al. (1986) report that mammalian genes present in muscle tissue have a higher G+C content than those genes expressed in the liver.References:Miyata T, Kuma K, Iwabe N, Nikoh N. A possible link between molecular evolution and tissue evolution demonstrated by tissue specific genes. Jpn J Genet., 69(5):473-80 (1994).Hendriks W., et al. The lens protein alpha A-crystallin of the blind mole rat, Spalax ehrenbergi: evolutionary change and functional constraints. PNAS, 84(15): 5320—5324 (1987).Zhang Liqing, Wen-Hsiung Li. Mammalian Housekeeping Genes Evolve More Slowly than Tissue-Specific Genes. Molecular Biology and Evolution, 21(2): 236-239 (2004).Kuma K, Iwabe N, Miyata T. Functional constraints against variations on molecules from the tissue level: slowly evolving brain-specific genes demonstrated by protein kinase and immunoglobulin supergene families. Mol Biol Evol., 12(1):123-30 (1995).Gu X, Su Z. Tissue-driven hypothesis of genomic evolution and sequence-expression correlations. PNAS, 104(8):2779-84 (2007).Newgard C.B., et al. Sequence Analysis of the cDNA encoding human liver glycogen phosphorylase reveals tissue-specific codon usage. PNAS, 83(8): 8132 — 8136 (1986). Edited by Livingstone Morford, : No reason given.Edited by Livingstone Morford, : No reason given.

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What direct effect does cytochrome c have on biological activity outside the mitochondria?

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At the fundamental level, everything in the cell is connected. That does not mean that there is a direct effect on biological activity outside the mitochondria.

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No, I don't suggest that. I suggested the exact opposite - that there were many mutations whose degree of deleteriousness depends entirely on the interactions of the protein with other cellular components.

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So do you, or do you not, agree that a substitution in a protein in one cell type can have a different effect if that same substitution occurred in the same protein but in a different cell type?

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In many cases, the cell can only function because things are not connected.

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And..? There are still many biological networks involved in the cell.

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Well, ok, but a minute ago you seemed to be reasoning from the assumption that there was.

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There is a difference between a direct effect and a mere effect, however discernible.

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This is certainly something that happens. There's not any reason to think that it happens in enough cases to substantially throw off our confidence in molecular phylogenies.

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Okay, so finally we agree on one thing: and that is that a neutral substitution in a protein in one cell type is not necessarily neutral in another. It happens enough to be detected in phylogenetic analysis [e.g., Miyata et al., 1994]. I cited six papers to the effect that tissues do constrain the substitutions in proteins — in some cases tissues constrain a protein one hundred times more than other tissues [Kuma et al., 1995].References:Miyata T, Kuma K, Iwabe N, Nikoh N. A possible link between molecular evolution and tissue evolution demonstrated by tissue specific genes. Jpn J Genet., 69(5):473-80 (1994).Kuma K, Iwabe N, Miyata T. Functional constraints against variations on molecules from the tissue level: slowly evolving brain-specific genes demonstrated by protein kinase and immunoglobulin supergene families. Mol Biol Evol., 12(1):123-30 (1995).

I still don't see what this has to do with cdesign proponentism. So I guess because I happen to disagree with the orthodox view that the phenomenon of genetic equidistance is best explained by the time lapsed since divergence, and since I am proposing another model, that all of a sudden means that I am using this as evidence for intelligent design? Am I missing something? Yes.

No I have not suddenly vanished and decided to never return. Rather, the last few days have been quite busy for me, and now have the time to devote my energies on responding to my opponents. However, given the large amount of posts I need to respond to, this will take a while.
Just saying...

There certainly does seem to be a lot of attempts to refute the model I am advocating. So all of you can imagine just how much time is required to respond to all of your posts. Regardless,

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Yes, there are. The cell is such a complex place that you really can't say, except in the specific, whether or not mutations are related to cell type diversity.

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I take it that the specific is a reference to the examples I cited above (see the citations I provided)? While we cannot boldly assert as fact whether or not mutations are related to tissue diversity, we can make this assertion with a fair degree of confidence, given the evidence for it.Since it seems like you are building a case around cytochrome-c, and since I believe you are suggesting that some proteins are under tissue constraints while others, such as cytochrome-c, are not, then I would be interested to hear what your thoughts are on the evidence that cytochrome-c is also under tissue constraints. Before I begin, it is suggested that one reads up on the overlap feature of the genetic equidistance result, or else the remainder of this post may appear to be gibberish.
Namely, the overlap feature of the genetic equidistance result [see, for example: Huang, 2010] (note: the paper I am citing is in fact peer-reviewed).
To name an example of this feature (and I might advise that anyone with a rudimentary knowledge of protein alignments can confirm what I am saying here): human cytochrome-c differs from the fruit fly cytochrome-c in 22 positions; and human cytochrome-c differs from the yeast cytochrome-c in 36 positions. Of the 22 variant residues between humans and fruit flies, 17 of these residues are also different between human and yeast cytochrome-c.
How many overlapping residues is predicted in your model?
Huang (2010) states that,
The chance for a position to be different between human and yeast is 36/102; the chance for a position to be different between human and drosophila is 22/102; the number of overlap positions should be: 36/102 x 22/102 x 102 = 7.76— based on probability. However, the actual number of overlapping residues is 17. This observation is completely consistent with the model I am advncing, but it is not at all compatible with the model you are advocating. Note that the overlap feature is observed in not just cytochrome-c, but in many proteins. Thus, the overlap feature indicates that cytochrome-c is under tissue constraints, as are all proteins.
Any attempt to refute this feature must take into account the following:
1) The number of overlap positions follows probability when organisms of similar complexity are compared, such as different yeast strains. However, when organisms of different complexity are compared, the number of overlap positions violate probability theory.
2) Remarkably, in tissue-specific proteins that are not subject to as stringent constraints as other proteins, the overlap feature follows probability. An example may be cited here. When the alpha-crystallin of the chicken and the elephant is compared against the alpha-crystallin of humans, we find the elephant alpha-crystallin differs from human alpha-crystallin by 8 residues; of these 8 variant positions, 6 (out of 29) of them are also variant in the chicken alpha-crystallin: i.e. there are 6 overlap positions. A cursory alignment among seven different organisms will reveal that approximately 50 residues are conserved and therefore not subject to as many mutations. So, even though the alpha-crystallin protein is 173 aa in length (in humans), we substract 50 residues. Thus, the most realistic calculation of how many overlap positions we would expect in your model is as follows:
The chance for a position to be different between human and chicken is 29/123; the chance for a position to be different between human and elephant is 8/123; the number of overlap positions should be: 29/123 x 8/123 x 123 = 1.89, falling short of the 6 actual overlap positions.
Now, if we align the alpha-crystallin of the chicken and the blind mole rat against the human alpha-crystallin, we end up with different results.
The chicken alpha-crystallin differs from the human protein by 29 residues; the blind mole rat protein differs from the human protein by 17 residues. Of these 17 variant residues, 5 are overlapping positions. Now it’s time to plug in our calculations. The chance for a position to be different between human and chicken is 29/123; the chance for a position to be different between human and the blind mole rat is 17/123; the number of overlap positions should be: 29/123 x 17/123 x 123 = 4.0, a number very close to the actual number of overlap positions. These results are very remarkable because the alpha-crystallin of the blind mole rat are not under tissue constraints (the tissue where alpha-crystallin is located is nonfunctional in the blind mole rat, hence the lack of tissue constraints).
So we see that for proteins that are not under tissue constraints, the number of overlap positions follows what we would expect based on probability. It is because of this that I must conclude that cytochrome-c is under tissue constraints. I certainly am willing to be corrected as to why my assertion is not valid, but the above evidence will have to be refuted first.I realize that PaulK has attempted to refute the overlap feature, but his refutation has failed to take into account the above two points I delineated above, and I hope to demonstrate the other errors in Paul's rebuttal (emphasis on the word "hope").P.S. Having done this, I will labor on more replies to my other opponents. Stay tuned. Edited by Livingstone Morford, : No reason given.

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Biology rocks!

While I am attempting to gather the time to muster a more adequate response to all of you (patience is a virtue, so I've heard), I will make a quick note to molbiogirl's post:
You will please note that I was not referring to Dr. Huang's MGD paper, but rather his paper on the overlap feature of the genetic equidistance result -- and that paper was peer-reviewed and is published in the MIT Press Journal of Biological Theory. Does that satisfy you?

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Biology rocks!