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Author Topic:   Genetic Equidistance: A Puzzle in Biology?
crashfrog
Inactive Member


(1)
Message 16 of 89 (596908)
12-17-2010 7:53 PM
Reply to: Message 12 by Livingstone Morford
12-17-2010 6:25 PM


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.


This message is a reply to:
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Dr Jack
Member (Idle past 440 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


(1)
Message 17 of 89 (596920)
12-18-2010 5:00 AM
Reply to: Message 9 by Livingstone Morford
12-17-2010 6:22 PM


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 yeast<->chaonoflagellate distance is equal to the yeast<->human distance?

The simple fact is that the genetic distance do not follow simple complexity connection lines.


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Dr Jack
Member (Idle past 440 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 18 of 89 (596921)
12-18-2010 5:02 AM
Reply to: Message 16 by crashfrog
12-17-2010 7:53 PM


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.


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PaulK
Member
Posts: 15617
Joined: 01-10-2003
Member Rating: 2.9


Message 19 of 89 (596926)
12-18-2010 7:08 AM
Reply to: Message 11 by Livingstone Morford
12-17-2010 6:24 PM


quote:

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


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.


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Theodoric
Member
Posts: 6878
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 3.3


Message 20 of 89 (596935)
12-18-2010 9:47 AM
Reply to: Message 8 by molbiogirl
12-17-2010 2:03 PM


Re: Just FYI for everyone
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:
Hello, my name is Livingstone Morford (Morford being an alias and a variation of my real name, for anonymity).

I am a staunch Intelligent Design proponent, and an avid opponent of Darwinian evolution.



Source

quote:
(1) I hold that evolution can occur to an extent. There are some things that the mindless processes of evolution can achieve, but there are some things that are beyond the edge of evolution (Behe 2007). This edge is defined by limited evolutionary potential (Pitman 2004). This limited evolutionary potential is limited due to biochemical and molecular constraints. In short, there is a gap that separate between protein-based structures. This gap can be defined as such: a gap of neutral stretches of amino acids (neutral in that they do not confer any advantage), so that natural selection cannot select for these sequences. This means that evolution must evolve very specified structures solely through random mutation, which is blind. This gap that separates protein based systems from each other, if on the order of 100 amino acids, means that the odds of that protein evolving is 20^100, a massive number. This is the limits to evolution.

Suppose for example, that amphibians had protein Y, and reptiles had protein X, which amphibians did not have. Further suppose that protein X demands over 100 specifically arranged amino acid residues in order to function. This would mean that amphibians could not evolve into reptiles since evolution could not produce that protein. This is how there are limits to evolution.

(2) How was life designed on earth? I advance a model where the intelligent designer designed life through a mechanism, namely through the recombining of DNA sequences of different organisms to engineer other organisms (recombinant DNA). There are many more details to this of course, such as directed mutagenesis, etc., but I only covered the main mechanism. Directed enzyme mutagenesis can easily account for the design of protein structures.

(3) I accept the creationist views that view intelligent design as a science, but I oppose those views that hold that intelligent design is not a science, or that it is a work of Satan, or anything like that. In short: I can be a creationist's best ally when debating a staunch evolutionist who opposes both creationism and intelligent design, but I will also defend intelligent design theory from those creationists who hold that it is not science, etc.

In Christ,
Livingstone Morford



Source

quote:
I have used this argument for the Bible's divine origin against atheists so many times, and it's always a little bit funny when they get stumped:
http://www.idscience.org/.../an-amazing-new-biblical-finding

Source
And that evidence?

quote:
The Bible mentions five colors in Hebrew: red (adom), Yellow (tzahov), green (yerakon), blue (tchelet) and magenta (argaman). One curious observation is immediately apparent, in that this list not only includes the primary colors - red, yellow and blue but it also includes the only two other colors green and magenta that are necessary to produce the complete color palate for four color printing. As interesting as this observation is it pales in comparison to a discovery made by Haim Shore a professor of Statistics and Engineering at Ben-Gurion University. What Professor Shore discovered is that the numerical values of the Hebrew words for these colors is correlated with the spectral wave frequency for these colors.

Hebrew is an alpha numeric language - in that every letter is also equal to a number. So if you add the values of each letter you get a number for the total value of the word. This is commonly used in “gematria”, the Rabbinic Cabalistic system of Biblical interpretation and prophesy, but what Shore did is not gematria. After calculating a total value for each word, he then plotted them on a graph. He plotted the numerical value of each word on the horizontal graph and the color’s wave frequency on the vertical axis . To Shore’s amazement he discovered that the graph yielded a straight line.

“It’s a universal principle of engineering that if you have two sets of data, you put them in ascending order, plot one set on the horizontal axis and the other on a vertical axis and if they fall on a straight line, that means that both data sets are measuring the same thing, only on a different scale. “I was astonished. The five points on the graph formed a straight line, which means that the names of the colors related directly to their wave frequencies.” It was purely a statistical analysis Shore said,”I didn’t manipulate a single number in doing the analysis.” “When I saw this result I was stunned.” “I was completely astonished. Then I went on to other words in the Hebrew Bible, plotting the value of the letters against known scientific data. The whole thing blew me away.” Shore went on to investigate similar cases in the Bible and so far has preformed over 20 different analyses with statistically verifiable findings, for example he has found a similar correlation between numerical word value a planetary diameters.

Shore began as a Bible skeptic and did not expect to make any of these findings. He says that he does not want to tell anyone what his findings mean but their theological implications are unavoidable.



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

This message is a reply to:
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molbiogirl
Member (Idle past 977 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 21 of 89 (596944)
12-18-2010 11:40 AM
Reply to: Message 14 by crashfrog
12-17-2010 7:10 PM


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

http://thegoldengnomon.blogspot.com/...r-first-axiom-of.html


This message is a reply to:
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crashfrog
Inactive Member


Message 22 of 89 (596945)
12-18-2010 11:58 AM
Reply to: Message 18 by Dr Jack
12-18-2010 5:02 AM


You're right, of course. My bad.

This message is a reply to:
 Message 18 by Dr Jack, posted 12-18-2010 5:02 AM Dr Jack has acknowledged this reply

  
molbiogirl
Member (Idle past 977 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 23 of 89 (596950)
12-18-2010 12:47 PM
Reply to: Message 12 by Livingstone Morford
12-17-2010 6:25 PM


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 ...

http://www.sciencemag.org/content/312/5773/570.full

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...

http://thegoldengnomon.blogspot.com/...r-first-axiom-of.html

That is, why are humans and orangs "of different biological complexity"?

Edited by molbiogirl, : No reason given.


This message is a reply to:
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molbiogirl
Member (Idle past 977 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 24 of 89 (596956)
12-18-2010 2:57 PM
Reply to: Message 15 by crashfrog
12-17-2010 7:43 PM


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.
http://www.amazon.com/review/R160K7033BB22Y

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.

http://thegoldengnomon.blogspot.com/...r-first-axiom-of.html

Edited by molbiogirl, : No reason given.


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molbiogirl
Member (Idle past 977 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 25 of 89 (596962)
12-18-2010 3:54 PM


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.

http://precedings.nature.com/documents/3794/version/1

Why can't sequence similarity be used to infer closer genealogical relationships?


  
Livingstone Morford
Junior Member (Idle past 3109 days)
Posts: 28
From: New Mexico
Joined: 12-13-2010


Message 26 of 89 (597028)
12-19-2010 12:44 AM


A General Response To Comments Regarding My Character
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!

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Percy
Member
Posts: 19046
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.4


Message 27 of 89 (597041)
12-19-2010 7:36 AM
Reply to: Message 26 by Livingstone Morford
12-19-2010 12:44 AM


Re: A General Response To Comments Regarding My Character
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.


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Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 8.3


Message 28 of 89 (597062)
12-19-2010 10:35 AM
Reply to: Message 14 by crashfrog
12-17-2010 7:10 PM


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?


This message is a reply to:
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crashfrog
Inactive Member


Message 29 of 89 (597070)
12-19-2010 12:28 PM
Reply to: Message 26 by Livingstone Morford
12-19-2010 12:44 AM


The Crash Promise
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.


This message is a reply to:
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crashfrog
Inactive Member


Message 30 of 89 (597072)
12-19-2010 12:32 PM
Reply to: Message 28 by Dr Adequate
12-19-2010 10:35 AM


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.


This message is a reply to:
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