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bob b
April 3rd, 2002, 06:36 PM
For those just dying to see what the cytochrome C discussion is all about I have placed two diagrams on the web displaying the data.

The complete color coded sequences are at:

http://members.aol.com/Bobsbend/cytocc.htm

and a condensed diagram that eliminates all the amino acid positions that are identical among the 22 mammals is at:

http://members.aol.com/Bobsbend/cytoc.htm

Stratnerd
April 3rd, 2002, 06:41 PM
And please refresh us as to your methods of analysis. :up:

Stratnerd
April 3rd, 2002, 08:25 PM
Am I right that your hypothetical common mammal is constructing by, for any particular position, the most frequently occurring amino acid?

Wedge
April 3rd, 2002, 08:53 PM
Originally posted by Stratnerd
Am I right that your hypothetical common mammal is constructing by, for any particular position, the most frequently occurring amino acid?
That's the way I understand bob's analysis. If this is the case then the "common mammal" is simply an "average" of whatever animals make up the "mammal group". A child would be able to see the obvious flaw with this method.

Perhaps bob could answer the following questions about his method of "analysis":

1. On what basis do you select animals for the "mammal group". Is this a priori selection going to bias your results?
2. Why do you do the analysis at the level of "mammal" and not at a higher (e.*., vertebrate) or lower (e.*., primates/rodents/etc.) level?
3. What is your view on the demonstrated fact that the composition of the "common mammal" is heavily influenced by the dominant subgroup of animals? Is this a flaw in the method?
4. Why have you done the analysis this way? What predictions are you testing from evolutionary theory or creationism? How are the predictions tested by the analysis?

Take you time with these bob and feel free to use examples from your data. I won't be back for a few days.

Stratnerd
April 3rd, 2002, 09:02 PM
Wedge et al.,

The problem with using frequency is that it is highly biased towards the most sampled taxa (whatever level you are taking about). In this case it is highly misleading because monotremes, the group accepted (at least by real scientists :p ) as the basal lineage are not even represented.

Even if ALL mammals species were sampled this would greatly bias the sample towards rats(!) since the majority of mammals are such. It would be the same as weighing all mammals and suggesting that this weight was the ancestral mass!

bob b
April 4th, 2002, 02:33 PM
Perhaps bob could answer the following questions about his method of "analysis":

1. On what basis do you select animals for the "mammal group". Is this a priori selection going to bias your results?

It is hard to see how this would bias the results since I have other charts that include all the creatures (fish, reptiles, amphibians, birds, etc) for which cyto c sequences are known and it doesn't seem to affect any conclusions drawn by simply viewing the color coded charts

2. Why do you do the analysis at the level of "mammal" and not at a higher (e.*., vertebrate) or lower (e.*., primates/rodents/etc.) level?

First, there is no "analysis" involved. I present the sequences in their raw form with only the differences highlighted to make it easier to see what is going on between the various organism cyto c. Also as I mentioned above the groups seem to "fall out" naturally so it is logical to view them separately before comparing one group to another.

3. What is your view on the demonstrated fact that the composition of the "common mammal" is heavily influenced by the dominant subgroup of animals? Is this a flaw in the method?

I don't agree that what you have said is true. The reason becomes more obvious when a larger number of animals is viewed in a more comprehensive chart. The orginal chart published by Dobyzansky, et. al. and used in many biology classes even today is similar to what I posted on the Web, but has only 22 creatures on it including representatives from plant, fish, fungi, insect, etc. The common mammal could still be determined from the few mammals on that chart alone and this result stayed essentially the same even when I found and added 11 more mammal sequences to that chart. The only positions in any doubt for mammals are two, 70 and 100. If one looks at other groups of animals those two positions can be resolved because most of the other animals agree with one or the other of the two alternative amino acids. If you like I will change the chart to the alternate amino acid, but this will change none of the conclusions one can make by simply looking at the data. Mice will still be quite distinct from men, more than can be explained by random mutation of the amino acids within the protein.

If you don't believe me look at this chart where I used the alternate amino acid as the "common mammal":

http://members.aol.com/Bobsbend/cytoca.htm

4. Why have you done the analysis this way? What predictions are you testing from evolutionary theory or creationism? How are the predictions tested by the analysis?

I have done no analysis. The data has been left as the raw amino acid sequences of the protein cytochrome c. It has not been altered in any way except that I highlighted those amino acid differences from the most commonly occurring one at each of the various positions.

The evidence speaks for itself in the sense that each person is free to draw whatever conclusions they feel are justified from the data itself. In my own case I find it illogical to believe that all mammals could have been derived from a common ancestor because several of the currently existing forms have sequences that are too close to what that common ancestor would have had to have as a protein sequence. This is despite the fact that all of the creatures would of necessity had the same length of time to diverge by random mutation from that same common ancestor.

What I am saying is that if the cow/pig/sheep sequence was the same as the common ancestor why did mutations not affect their sequence?

Why are the primates so different than other mammals?

Why are mice so different?

Why are whales the same as camels?

juliod
April 4th, 2002, 04:59 PM
I think it is easy to show that all the data is "inevitable". That is, for any set of conserved sequences the same relationships will appear.


What I am saying is that if the cow/pig/sheep sequence was the same as the common ancestor why did mutations not affect their sequence?

You don't have a "common ancestor". You have an "average" sequence. That is, a sequence which is most similar to all of the test sequences. It is inevitable that one or more sequences will be closest to the "average" sequence. This is true even if you use completly random data.


Why are the primates so different than other mammals?

What do you mean by "so" different? This is a highly conserved sequence, and the primates show reasonable divergence. Again, some sample in your group must be the furthest from the "average".


Why are mice so different?

Same answer.


Why are whales the same as camels?

1) They aren't.
2) For a group of sequences of such a highly conserved gene, it is inevitable that some of them should be identical.

Overall score: 2 out of 10.

DanZ

bob b
April 4th, 2002, 05:39 PM
Dan,

>>You don't have a "common ancestor". You have an "average" sequence. That is, a sequence which is most similar to all of the test sequences. It is inevitable that one or more sequences will be closest to the "average" sequence. This is true even if you use completly random data. <<

I think you are in denial.

What would your conclusion be if all lifeform sequences from bacteria to humans had the same amino acid in a particular position except for one particular lifeform? Wouldn't it be logical to assume that the single exception was a random mutation and that the amino acid at that position for all other lifeforms was what the "common" ancestor had in that position?

Note that we can tell if this is the case by looking at a chart that contains all of the known cyto c sequences (which I happen to have in my possession).

The idea that I have looked only at "averages" is not an accurate view of the situation. Almost all of the positions in the chart can be described as the "overwhelming case", not the "average case".

Stratnerd
April 4th, 2002, 06:56 PM
Bob,

>>> described as the "overwhelming case", not the "average case". <<<

The sequence you have constructed is based merely on frequencies, which in this case will be biased towards the organisms sampled AND the naturally occurring diversity of a particular group.

What you have is the most frequently occurring amino acid - that's it! Why do you assume it has anything to do with ancestral-descendent relationships?

Based on almost any cladistic analysis (which uses an outgroup - another missing feature of your chart), monotremes are the hypothethetical ancestral mammal group (also missing from the chart).

If mammals are descended from a lineage with a single species that is still exant and is dominated, species-wise, by another lineage you will never find the hypothetical ancestor and all you will have is the most frequent amino acid for the most diversie lineage.

Stratnerd
April 4th, 2002, 07:19 PM
>>> Why are whales the same as camels?

Based on a phylogenetic analysis, they are actually part of the same lineage and such similarities are expected based on the idea of a shared common ancestor.

juliod
April 4th, 2002, 07:42 PM
Wouldn't it be logical to assume that the single exception was a random mutation and that the amino acid at that position for all other lifeforms was what the "common" ancestor had in that position?

No. That is a common misunderstanding of evolution. All proteins in all organism alive today are "evolved" to exactly the same extent. You can construct a family tree based on relatedness, but you can't draw any conclusions about which amino acids in which positions were "original".

DanZ

bob b
April 4th, 2002, 09:06 PM
Dan,

I think what you just said is totally illogical. What you are saying is that it is possible that every form living today "just happens" to have the same amino acid at a particular position except one, but that this does not say anything about what amino acids were present in that position for any ancestor. If that were the case then how in the world could molecular analysis say anything at all about relationships among ancestors where the DNA/protein sequences are of necessity not known?

If one constructs a "family tree" then this strongly implies ancestral relationships. If this is not so then using the term "family tree" would be a serious misstatement of what the term "family tree" means in the English language.

>>All proteins in all organism alive today are "evolved" to exactly the same extent. <<

This statement is clearly incorrect for the simple reason that mutational theory logically assumes a rate of "evolutionary" change that is dominated by the number of generations (not absolute time) that a particular living form has been evolving.

Thus, living bacterial forms would have been evolving for far many more generations than living primates, even assuming that the primates started evolved from the same original "protocell" that the bacteria did.

juliod
April 5th, 2002, 12:16 PM
If that were the case then how in the world could molecular analysis say anything an all about relationships among ancestors where the DNA/protein sequences are of necessity not known?

You don't talk about relationships between ancestors. You talk about relationships between organisms alive today. This has implications about ancestors.


Thus, living bacterial forms would have been evolving for far many more generations than living primates, even assuming that the primates started evolved from the same original "protocell" that the bacteria did.

Correct, but that's just the reason that you don't want to talk about generations when you mean "time". All organisms have evolved for the same amount of time, but of course very different numbers of generations.

DanZ

bob b
April 5th, 2002, 12:48 PM
Dan,

>>All organisms have evolved for the same amount of time, but of course very different numbers of generations. <<

Since you agree with me that this must be the case if evolution is true, perhaps you would like to revise your earlier statement:

>>All proteins in all organism alive today are "evolved" to exactly the same extent. <<

Looking at the primate and mouse/rat subgroups on the cyto c diagram this is obviously not true.

http://members.aol.com/Bobsbend/cytoca.htm

Here is another diagram which illustrates that an organism that supposedly branched off earlier than the mammal subgroup (a bullfrog) has retained many of the same amino acids that most mammals have, indicating that the mammal "ancestor" undoubtedly also had that same amino acid at that position.

http://members.aol.com/Bobsbend/ctytoca2.htm

juliod
April 5th, 2002, 04:06 PM
I still don't know what you are getting at. Your data all points to evolution, not creation. The data shows descent and relatedness, not individual or group creation.

Evolution reasonably explains all the data, both the similarities and the differences.

Creations fails to explain either the similarities or the differences.

Since Cytochrome C does the same function is every organism that has it, why should there be differences at all if the organisms were all created by a "designer"? On the other hand, if each species was an independant creation, why should groups like primates have similar sequences?

DanZ