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Author Topic:   Genuine Puzzles In Biology?
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 136 of 153 (596604)
12-15-2010 7:47 PM
Reply to: Message 133 by Livingstone Morford
12-15-2010 7:20 PM


A touch of context
I'm a biochemistry major with a focus in genetics and even I had to look up "genetic equidistance":
quote:
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."[2] 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.[3] Genetic equidistance has often been used to infer equal time of separation of different sister species from an outgroup.[4][5]
Molecular clock - Wikipedia

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Livingstone Morford
Junior Member (Idle past 4773 days)
Posts: 28
From: New Mexico
Joined: 12-13-2010


Message 137 of 153 (596605)
12-15-2010 7:47 PM
Reply to: Message 129 by nwr
12-15-2010 8:53 AM


"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.

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molbiogirl
Member (Idle past 2641 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 138 of 153 (596609)
12-15-2010 8:42 PM
Reply to: Message 133 by Livingstone Morford
12-15-2010 7:20 PM


This is because different species can tolerate different levels of mutations, since different organisms have different numbers of cell types.
Please support this assertion.
It seems to be the heart of your argument.

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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 139 of 153 (596617)
12-15-2010 10:13 PM
Reply to: Message 134 by Livingstone Morford
12-15-2010 7:30 PM


Livingstone Morford writes:
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.
It is my impression that genetic distance is usually measured on proteins that are particularly unlikely to be affected by the kind of influences that you suggest.

Jesus was a liberal hippie

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 140 of 153 (596624)
12-15-2010 10:48 PM
Reply to: Message 137 by Livingstone Morford
12-15-2010 7:47 PM


To summarize: the greater the number of cell types in an organism, the less likely it is that a given mutation to protein-coding DNA will be neutral, since it would have to be neutral with respect to all the disparate cellular environments in which the protein is active. Hence, other things being equal, we should expect a lower rate of neutral mutations in the coding DNA of more complex organisms.
That has a certain innate plausibility.
It would not really be a problem for the application of genetic clocks, since these are already known to tick at different rates in different groups of organisms. No-one is currently assuming a uniform rate across all organisms.
Your question doesn't really fit the remit of this thread, since the question is whether this effect exists to any significant degree. This thread is about things that are known to be true and which make you ask why is that true and how did it come about.
What you have is not a puzzle in that sense, merely an open question.

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Dr Jack
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Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 141 of 153 (596642)
12-16-2010 5:19 AM
Reply to: Message 133 by Livingstone Morford
12-15-2010 7:20 PM


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.
If this were the case, shouldn't we expect to see, for example, shorter distances between all mammals and yeast than choanoflagellates and yeasts, whereas - in fact - the distances are very similar.

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 142 of 153 (596678)
12-16-2010 1:28 PM
Reply to: Message 137 by Livingstone Morford
12-15-2010 7:47 PM


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.
So what we are really looking at is the complexity of the DNA regulatory network.
If we are going to relate this to DNA sequence divergence then we need a good idea of how many bases are involved in this network and the specific bases in those DNA sequences that are under selection. There could also be spacing issues between regulatory sequences and the genes they are regulating, so indels have to be considered as well.
I think even the most modest estimates would find that the majority of bases are selectively neutral, so genetic drift would still be the cause of the majority of differences.

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 143 of 153 (596680)
12-16-2010 1:31 PM
Reply to: Message 140 by Dr Adequate
12-15-2010 10:48 PM


To summarize: the greater the number of cell types in an organism, the less likely it is that a given mutation to protein-coding DNA will be neutral, since it would have to be neutral with respect to all the disparate cellular environments in which the protein is active. Hence, other things being equal, we should expect a lower rate of neutral mutations in the coding DNA of more complex organisms.
That has a certain innate plausibility.
However, coding DNA makes up a tiny portion of the whole genome, somewhere around 3%. In this model, the other 97% of the genome is diverging through drift so the predominant force of genetic change is still drift.

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 144 of 153 (596682)
12-16-2010 1:38 PM
Reply to: Message 139 by nwr
12-15-2010 10:13 PM


It is my impression that genetic distance is usually measured on proteins that are particularly unlikely to be affected by the kind of influences that you suggest.
Selection is hard to put into the calculations so population geneticists try to use selectively neutral DNA seqeunces that can be readily identified (especially for genomic position to rule out duplication events). One good source for these sequences is pseudogenes, which is exactly what this group used:
A molecular approach to estimating the human deleterious mutation rate - PubMed

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Tupinambis
Junior Member (Idle past 4655 days)
Posts: 18
Joined: 12-12-2010


Message 145 of 153 (596687)
12-16-2010 1:56 PM
Reply to: Message 132 by Taz
12-15-2010 3:44 PM


Re: fear of snakes
I have not actually studied this subject matter but everything I'm saying is based on personal observations. I don't necessarily believe that humans really have an ingrained fear of anything that is strange to us, increasing fear with increasing strangeness. I think the ordinary person would have a much stronger reaction to a rat in their house than a slug or an earthworm.
I still believe that it has more to do with certain features of certain animals that we fear than the animals themselves. I think baby snakes are cute. If it starts to puff up and hiss at me though I'd probably be nervous around it. I'm not afraid of the Tegu which is my avatar even when he grows into an adult because of his calm demeanor. If, as an adult though, he starts hissing and whipping at me, I'd probably be afraid to be near him.
A better example is probably in order here. If I see a red fox running accross the street I would probably be more enraptured by it than anything else. If it starts to approach me though, I'm heading back inside and locking the door.
As per arthropods, I still don't know. Crabs look a lot more like spiders than centipedes do, but people are more afraid of centipedes and spiders than they are of crabs. If someone encountered a spider the size of a "blue land crab" they'd probably soil themselves. I should probably take into account the fact that terrestrial crabs evolved relatively recently (I think....). The thing about crabs though is that they're relatively intelligent and will run away from you if you approach them. Spiders and centipedes aren't. Our fear of them may be related to how they display little to no fear of us, and they're not pointlessly slow like a slug.
As for most animals, if its not afraid of you and its not an oblivious prey item, there's probably a reason for its apparent confidence.
Edited by Tupinambis, : No reason given.

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Livingstone Morford
Junior Member (Idle past 4773 days)
Posts: 28
From: New Mexico
Joined: 12-13-2010


Message 146 of 153 (596762)
12-16-2010 7:40 PM
Reply to: Message 135 by Dr Adequate
12-15-2010 7:34 PM


"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.

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 147 of 153 (596763)
12-16-2010 7:45 PM
Reply to: Message 146 by Livingstone Morford
12-16-2010 7:40 PM


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
Using only conserved proteins with identical function in both species ensures that it's the former and not the latter. That's why protein phylogenies are usually performed on genes for proteins like cytochrome c, or the 16S ribosomal subunit.
This is the puzzle.
It's not really a puzzle.
Also, you're frequently using "equidistance" when what you mean is "distance."

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Replies to this message:
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Livingstone Morford
Junior Member (Idle past 4773 days)
Posts: 28
From: New Mexico
Joined: 12-13-2010


Message 148 of 153 (596784)
12-16-2010 9:25 PM
Reply to: Message 138 by molbiogirl
12-15-2010 8:42 PM


"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.

Biology rocks!

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Livingstone Morford
Junior Member (Idle past 4773 days)
Posts: 28
From: New Mexico
Joined: 12-13-2010


Message 149 of 153 (596785)
12-16-2010 9:28 PM
Reply to: Message 142 by Taq
12-16-2010 1:28 PM


"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.

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Livingstone Morford
Junior Member (Idle past 4773 days)
Posts: 28
From: New Mexico
Joined: 12-13-2010


Message 150 of 153 (596792)
12-16-2010 10:33 PM
Reply to: Message 147 by crashfrog
12-16-2010 7:45 PM


"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."

Biology rocks!

This message is a reply to:
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