|
Register | Sign In |
|
QuickSearch
EvC Forum active members: 64 (9163 total) |
| |
ChatGPT | |
Total: 916,419 Year: 3,676/9,624 Month: 547/974 Week: 160/276 Day: 34/23 Hour: 1/3 |
Thread ▼ Details |
Junior Member (Idle past 4795 days) Posts: 28 From: New Mexico Joined: |
|
Thread Info
|
|
|
Author | Topic: Genetic Equidistance: A Puzzle in Biology? | |||||||||||||||||||||||||||||||||||||||
crashfrog Member (Idle past 1488 days) Posts: 19762 From: Silver Spring, MD Joined:
|
The predominant force of genetic change is genetic drift; however, the question is what causes the phenomenon of genetic equidistance. Genetic distance is measured primarily on non-coding regions to minimize the effect of selection, so, by definition, your model of equidistance being the result of increased selection against mutations in more complex organisms is false.
|
|||||||||||||||||||||||||||||||||||||||
Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4
|
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). How then do you explain the fact that the yeastchaonoflagellate distance is equal to the yeast<->human distance? The simple fact is that the genetic distance do not follow simple complexity connection lines.
|
|||||||||||||||||||||||||||||||||||||||
Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
Genetic distance is measured primarily on non-coding regions to minimize the effect of selection, so, by definition, your model of equidistance being the result of increased selection against mutations in more complex organisms is false. Actually, this isn't correct. Non-coding regions of DNA evolve much too rapidly to provide useful information across large evolution distances. You'd use non-coding regions to compare human populations, for example, but they're useless for comparing humans and yeast.
|
|||||||||||||||||||||||||||||||||||||||
PaulK Member Posts: 17825 Joined: Member Rating: 2.2 |
quote: Your calculation is obviously incorrect. It assumes that the locations of the changed residues are statistically independent, which is false. For instance any residue which changed in the human lineage since the most recent common ancestor but remained the same in both of the others would be a shared difference, Assuming (as you do) that all residues are equally likely to change (IMHO probably incorrectly), and trusting your numbers we can estimate the number of residues that fall into this category. Since roughly half the difference should appear in each lineage, the number of residues that have actually changed since the common ancestor will be about half the genetic distance, thus I shall estimate this number of changes as 7. So we have 7/105 changed in the human lineage and 98/105 unchanged in each of the others. My estimate is therefore 7/105 * 98/105 * 98/105 * 105 ~= 6 While this would be a very rough estimate of the number of residues that are different from the human in both the frog and the alligator, it is still better than yours - and far closer to the value you report.
|
|||||||||||||||||||||||||||||||||||||||
Theodoric Member Posts: 9142 From: Northwest, WI, USA Joined: Member Rating: 3.3 |
I am afraid discussion with Livingstone will be like arguing with a brick wall.
He seems to have already made up his mind on a lot of things and discussion may be futile. I think it is important that those that are debating with him understand where he is coming from. These snippets I have found on the web give a good idea of how his arguments here tie into his overall beliefs.
quote:No webpage found at provided URL: Source quote:No webpage found at provided URL: Source quote:No webpage found at provided URL: Source And that evidence? quote:No webpage found at provided URL: Source Damn, that might make a great thread. I might have to start a topic on the bible and colours. Edited by Theodoric, : Fix links Facts don't lie or have an agenda. Facts are just facts
|
|||||||||||||||||||||||||||||||||||||||
molbiogirl Member (Idle past 2663 days) Posts: 1909 From: MO Joined: |
I'm not sure you know any biochemistry. Crash, he claims to be a biochemist.
LM writes: Being the author of two technical papers in biochemistry (manuscript under review), I can understand most technical terminology The Golden Gnomon Huang-jin Shi-zi: Some paper concludes that complex organism has more functional bases
|
|||||||||||||||||||||||||||||||||||||||
crashfrog Member (Idle past 1488 days) Posts: 19762 From: Silver Spring, MD Joined: |
You're right, of course. My bad.
|
|||||||||||||||||||||||||||||||||||||||
molbiogirl Member (Idle past 2663 days) Posts: 1909 From: MO Joined: |
If complexity has some relationship to diversity, then how do you explain the significant differences within taxa?
For example:
... among fish, marine species showed a significantly higher heterozygosity than the geographically restricted freshwater species ... And:
... among mollusks, the terrestrial pulmonates were substantially less polymorphic than marine bivalves or gastropods ... Just a moment... And how would you explain these findings?
Genetic diversity is largely higher (i) in species living in broader environmental spectra, (ii) in large species with patchy population structure and limited migration, as well as in solitary or social species, and (iii) species with small body size, annuals or long-lived perennials that are older in time with diploid chromosome numbers, primarily out-crossed, and plant species reproducing sexually and pollinated by wind. Species with the above characteristics harbor, generally, more genetic diversity than their opposite counterparts. Genetic diversity is correlated and predictable by 3-4 variable combinations of ecological, demographic, and life-history variables, largely in this order.
Nevo E. (2001). Evolution of genome-phenome diversity under environmental stress. Proc. Natl. Acad. Sci. USA 98:6233-6240. Nevo E, Beiles A, and Ben-Shlomo R. (1984a). The evolutionary significance of genetic diversity: Ecological demographic and life history correlates. Lect Notes Biomath 53, 13-213. ABE: Another question. Can you explain this quote from Shi?
However, for macroevolution of distinct species of different biological complexity such as yeast versus drosophila or orangutan versus human... The Golden Gnomon Huang-jin Shi-zi: Some paper concludes that complex organism has more functional bases That is, why are humans and orangs "of different biological complexity"? Edited by molbiogirl, : No reason given.
|
|||||||||||||||||||||||||||||||||||||||
molbiogirl Member (Idle past 2663 days) Posts: 1909 From: MO Joined: |
No, it's not. If Shi Huang says this, Shi is wrong. Really wrong, Crash.
Shi writes: Dr. Shi Huang has now come up with a more complete theory unifying epigenetics and genetics. His new theory, the maximum genetic diversity hypothesis ... explains more facts than Darwinism and has yet to meet a single exception within its domain of application. From a book review he posted on Amazon. Gotta love the third person.Amazon.com And:
Shi writes: Thus, macroevolution is the opposite of microevolution. While randomness is good and a source of innovation/variation for microevolution, it is mostly harmful for macroevolution of greater complexity and must be suppressed. Shi writes: Most of today's species are terminally highly derived or differentiated. So, macroevolution would be extremely rare in today's Earth. Shi writes: Chimpanzee is closer to orangutan or gorilla than human is in DNA. The Golden Gnomon Huang-jin Shi-zi: Some paper concludes that complex organism has more functional bases Edited by molbiogirl, : No reason given.
|
|||||||||||||||||||||||||||||||||||||||
molbiogirl Member (Idle past 2663 days) Posts: 1909 From: MO Joined: |
LM. Can you explain this to me?
Shi writes: The genetic non-equidistance to a more complex outgroup despite equidistance in time or genealogy, as described here, shows that higher sequence similarity to a complex outgroup cannot be used to infer closer genealogical relationships. Nature Precedings Why can't sequence similarity be used to infer closer genealogical relationships?
|
|||||||||||||||||||||||||||||||||||||||
Livingstone Morford Junior Member (Idle past 4795 days) Posts: 28 From: New Mexico Joined: |
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 noun Edited 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. Biology rocks!
|
|||||||||||||||||||||||||||||||||||||||
Percy Member Posts: 22480 From: New Hampshire Joined: Member Rating: 4.8 |
Livingstone Morford writes: I used to be a young-earth creationist, but that changed when I did a thorough examination of the evidence against young-earth creationism...I am eighteen years old Could I suggest to you (and to everyone else) that your views are probably still in a state of rapid flux?
I wish to emphasize that it is a far cry from authoring papers on biochemistry than actually being a biochemist. Uh, okay. Here's what you originally said:
Being the author of two technical papers in biochemistry (manuscript under review)... If by this you mean you have had one paper published and one under review at legitimate biochemistry journals that seek to publish original contributions, then could I further suggest to you that making original contributions in the field of biochemistry is probably the best definition of a biochemist one could have. --Percy Edited by Percy, : Grammar.
|
|||||||||||||||||||||||||||||||||||||||
Dr Adequate Member (Idle past 305 days) Posts: 16113 Joined: |
This makes no sense. Every single amino acid can be found in every single human cell, so there's no such thing as a substitution that would be "incompatible" with the cell. He jus means a deleterious point mutation.
No, this makes no sense. Protein A may not be expressed in X, Y, or Z, or it may be subject to alternate splicing such that the mutation in the gene for A is in a region that is not expressed in one of those cells. And really, there's no such thing as "cell type", there's just different patterns of gene expression and regulation in different cells. The fact that two different cells may have different patterns of gene expression really doesn't say anything at all about which mutations will prove fatal in which cells. But it is a priori less likely that a mutated protein will be neutral with respect to its function in the brain and the liver and the pancreas and the bone marrow and ... so on ... then with respect to its function in a single cellular environment. This still leaves certain questions: (1) What is the magnitude of this effect?(2) What is the magnitude of this effect in the proteins used in molecular phylogeny? (3) What in the world can this have to do with IDiocy?
|
|||||||||||||||||||||||||||||||||||||||
crashfrog Member (Idle past 1488 days) Posts: 19762 From: Silver Spring, MD Joined: |
I promise not to hold it against you that you are young, or early in your academic career. I am not particularly further along myself. And I would never hold it against someone for being open and honest about how their views have changed, since mine change all the time.
The only thing I will try to pin you on is where you make authoritative claims of fact that are wrong. I hope you (and others, like Taz) will do the same to me when I do it. Thanks for sharing. Now I'll share - 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. Most deleterious mutations are deleterious because the structural change to the protein eliminates its function, and that function is crucial to the life of the cell. 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." There's just nothing in biochemistry that would allow you to confidently make the prediction you're making, to wit: that an increase in cell diversity in a given species is going to result in more mutations being deleterious instead of neutral. The vast majority of proteins in a cell have the same function regardless of what kind of cell they're in.
|
|||||||||||||||||||||||||||||||||||||||
crashfrog Member (Idle past 1488 days) Posts: 19762 From: Silver Spring, MD Joined: |
But it is a priori less likely that a mutated protein will be neutral with respect to its function in the brain and the liver and the pancreas and the bone marrow and ... so on ... then with respect to its function in a single cellular environment. I don't think a priori you can make such a statement, since there's too many confounding factors. Most proteins in the cell have no idea whether they're in a liver cell, or a brain cell, or a pancreatic cell. Obviously cell environment has an effect on which mutations prove to be deleterious, because some of that effect is the result of changes in a protein's interactions with other components of the cell environment. But to predict the effect of diversity of cell environment on a mutated protein (and vice-versa) you need a finer-grained study than "liver cell; muscle cell."
What is the magnitude of this effect in the proteins used in molecular phylogeny? Well, it's a standard practice in constructing phylogenies to use proteins with identical function across the compared clades. That would seem to rule out any effect of diversity of cell environment. Cytochrome c is going to be highly conserved regardless of what kind of cell we're talking about.
|
|
|
Do Nothing Button
Copyright 2001-2023 by EvC Forum, All Rights Reserved
Version 4.2
Innovative software from Qwixotic © 2024