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Protein Sequence Homology


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#1 roohif

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Posted 05 June 2011 - 06:01 AM

I've been studying protein sequence homology for a little while now, and in my mind it is the strongest line of evidence to support common descent (in the same vein as DNA sequence, ERV and pseudogene homology).

Just to be clear, the argument being made is that independent protein sequence trees converge not just on each other, but also on a consensus tree that is constructed using morphological data (that is, the fossil record and extant organisms). I understand that with a stochastic process like mutation there are bound to be discrepancies in the trees when compared to a consensus tree, but these discrepancies should fall within reasonable statistical boundaries.

I was wondering what creationists think the flaws are in protein sequence homology? Why is it that proteins that have no apparent correlation to phenotype/morphology converge on a consensus if it is not due to common descent?

Does anyone have any SPECIFIC examples of protein sequence trees that they feel do not give a reasonable approximation of the consensus tree?

Thanks.

#2 ikester7579

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Posted 05 June 2011 - 08:46 AM

I've been studying protein sequence homology for a little while now, and in my mind it is the strongest line of evidence to support common descent (in the same vein as DNA sequence, ERV and pseudogene homology).

Just to be clear, the argument being made is that independent protein sequence trees converge not just on each other, but also on a consensus tree that is constructed using morphological data (that is, the fossil record and extant organisms). I understand that with a stochastic process like mutation there are bound to be discrepancies in the trees when compared to a consensus tree, but these discrepancies should fall within reasonable statistical boundaries.

I was wondering what creationists think the flaws are in protein sequence homology? Why is it that proteins that have no apparent correlation to phenotype/morphology converge on a consensus if it is not due to common descent?

Does anyone have any SPECIFIC examples of protein sequence trees that they feel do not give a reasonable approximation of the consensus tree?

Thanks.

View Post


I don't much of anything about what you are talking about because I have not get that far yet in my research. But, since you bring up the fossil record I can input this:

"Living fossils" disprove the fossil record as actually being a record for evolution. The fossil record did not record that they survived until present time. if it did, the fossils of the living fossil would have been found in the layers above the original showing that it survived, and did not change. But "every" living fossil has this problem concerning the supposed fossil record. So why does "every" living fossil have this problem?

So for common descent and the consensus tree to be supported by the fossil record (which you included in this thread), the record has to be more accurate. Living fossils prove that it is not.

Example of the flaws living fossils expose concerning the supposed fossil record:
The coelacanth fish is found about 8 layers down and alive today. Why is it not found in any layer in between showing it survived and did not change? The sea pen is found in the lowest layer and alive today. Same problem of not being found in any layer in between showing it survived.

Exposing these flaws shows that the fossil "record" is not an accurate record. Or maybe you have an explanation for such gaps

And here's the kicker. Being that the Bible says that the flood started by the breaking up of the fountains of the deep. means that the burying, and layering process, started in the water. Which also mean that the lowest layers will only consist of ocean living creatures. Which is what we find. And because the burying process was so fast all the sediments coming up with the water would bury each sea creature according to where it lived in the water. Bottom dwellers first, mid water dwellers second, and top dwellers last. And that is exactly how we find them.

And then you might say: where's all the water for the flood?

Suddenly, there was somewhere to put water deep inside the mantle. “You can have oceans and oceans of water stored in the transition zone,” says Jay Bass of the University of Illinois in Urbana-Champaign. “It’s sopping wet stuff.” Researchers think wadsleyite can hold as much as 3·3 per cent water by weight. It may not sound like much, but there could be an awful lot of wadsleyite.

    According to Smyth, models of the mantle’s composition suggest that at the depths where wadsleyite is stable, between half and three-quarters of the material is the right stuff for making this mineral. “If the region between 400 and 525 kilometers were, say, 60 per cent wadsleyite, and that phase was saturated at 3·3 weight per cent, that’s ten oceans of water,” says Smyth. But Dan Frost, an experimental petrologist at the Carnegie Institution of Washington’s Geophysical Laboratory in Washington DC, thinks the mantle could contain even more water.

    Frost says that solidified lava that has erupted at mid-ocean ridges contains glass that can be analyzed for water content. His research team has calculated how much water the lava’s parent material in the mantle must have contained. “It ends up being between 100 and 500 parts per million,” he says. And if the whole mantle contained 500 parts per million of water, Frost calculates that would be the equivalent of 30 oceans of water.

http://www.ldolphin....deepwaters.html


Scientists scanning the deep interior of Earth have found evidence of a vast water reservoir beneath eastern Asia that is at least the volume of the Arctic Ocean.
The discovery marks the first time such a large body of water has found in the planet’s deep mantle.

http://www.livescien...ered-earth.html


A seismologist at Washington University in St. Louis has made the first 3-D model of seismic wave damping — diminishing — deep in the Earth’s mantle and has revealed the existence of an underground water reservoir at least the volume of the Arctic Ocean. It is the first evidence for water existing in the Earth’s deep mantle.

http://www.physorg.c...ws90171847.html


A seismologist has made the first 3-D model of seismic wave damping, or diminishing, deep in the Earth’s mantle and has revealed the existence of an underground water reservoir at least the volume of the Arctic Ocean.

http://news.wustl.ed...Pages/8749.aspx


For the fossil record to support evolution and be accurate, it would also have to support simple life forms in the lowest layer. The flood on the other hand would not. if complex life existed as a bottom dweller, it would be buried in that layer just because of that. The trilobite has complex systems and fully formed organs. There is no tree to it, or coming from it. So the fossil record more supports the flood then evolution.

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#3 jason777

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Posted 05 June 2011 - 10:44 AM

I've been studying protein sequence homology for a little while now, and in my mind it is the strongest line of evidence to support common descent (in the same vein as DNA sequence, ERV and pseudogene homology).

Just to be clear, the argument being made is that independent protein sequence trees converge not just on each other, but also on a consensus tree that is constructed using morphological data (that is, the fossil record and extant organisms). I understand that with a stochastic process like mutation there are bound to be discrepancies in the trees when compared to a consensus tree, but these discrepancies should fall within reasonable statistical boundaries.

I was wondering what creationists think the flaws are in protein sequence homology? Why is it that proteins that have no apparent correlation to phenotype/morphology converge on a consensus if it is not due to common descent?

Does anyone have any SPECIFIC examples of protein sequence trees that they feel do not give a reasonable approximation of the consensus tree?

Thanks.

View Post



It would depend on how you define homology. Some people assume homology with anything in common (i.e. the protein in the flagellum only shares 20% homology with ATPase).

Posted Image


Could we honestly claim homology with only 20%? Evolutionists certainly do.


L-KFN7JH0Ic?version=3


Creation predicts created kinds, so how would you reconcile the differences between an elephant and a jellyfish or a blade of grass with a humming bird? If you can't correlate all of the biological kingdoms (only closely related species), then how could you reach an assumption of common descent?






Enjoy.

#4 roohif

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Posted 05 June 2011 - 10:50 PM

I don't much of anything about what you are talking about because I have not get that far yet in my research. But, since you bring up the fossil record I can input this

View Post


The argument I'm making doesn't actually depend on the accuracy or validity of the tree derived from the fossil record, merely that such a tree has been constructed.

The trees constructed by protein/DNA sequences attempt to group individual point mutations and/or the subsequent amino acid changes in the sequence that would give a logical path of descent. [[ It might be a good idea to read the pinned Cytochrome C topic to get a better idea of what I'm talking about. ]]

The punchline is that these trees consistently overlay each other, but they use independent data to get there. For example, the tree constructed using Cytochrome C data can be overlaid on the tree constructed using morphological data, even though there is no known reason why these two sets of data should be correlated - except if they shared a common ancestor.

The same works for every protein that I have tested; and that is the basis for the original questions - are there examples that clearly don't fit within the framework; and what is the creationist explanation for these trees?

#5 roohif

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Posted 05 June 2011 - 11:05 PM

Creation predicts created kinds, so how would you reconcile the differences between an elephant and a jellyfish or a blade of grass with a humming bird? If you can't correlate all of the biological kingdoms (only closely related species), then how could you reach an assumption of common descent?

View Post


Good point, and it is true that the deeper you delve into the tree, the less statistical certainty there is behind those branches. To be honest, it is enough for me to conclusively demonstrate that humans descended from apes - the rest is gravy.

I guess in return, I would ask if you thought that whales and hippos are the same "kind"? What about dogs and seals? Horses and rhinos? These relationships are consistently borne out by multiple sets of independent data, and common descent is the only explanation that makes sense of it.

Before anyone asks me to present some evidence, can someone tell me how to post an image??? ;)

#6 jason777

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Posted 06 June 2011 - 05:02 AM

Good point, and it is true that the deeper you delve into the tree, the less statistical certainty there is behind those branches.


So, your convinced by cherry picking closely related groups? I believe in creation because all of the evidence fits its predictions - not just pieces of it.

To be honest, it is enough for me to conclusively demonstrate that humans descended from apes - the rest is gravy.


Are you sure about that?

"In spite of recent findings, the time and pace of origin of order Primates remains shrouded in mystery."
(Elwyn L. Simons (Dpt of Geology and Geophysics, Yale University, USA and Co-Editor of Nuclear Physics), 'The origin and radiation of the primates'. Annals New York Academy of Sciences,vol. 167, 1969, p. 319)

"There are no fossils available as plausible ancestors of the primates, leaving the primate tree without a trunk."
(Martin, R. D., 1993. Primate Origins: plugging the gaps 363:223-233)

"Modern apes, for instance, seem to have sprung out of nowhere. They have no yesterday, no fossil record. And the true origin of modern humans--of upright, naked, toolmaking, big-brained beings--is, if we are to be honest with ourselves, an equally mysterious matter."
(Lyall Watson (anthropologist), 'The Water People,' Science Digest, Vol 90, May 1982, pg. 44)

From a large-scale perspective, the human and chimp Y chromosomes were constructed entirely differently. On the human Y chromosome, there were found four major categories of DNA sequence that occupy specific regions. One can think of this in terms of geography. Just as a continent like Europe is divided into countries because of different people groups, so are chromosomes with different categories of DNA sequence.

Not only were the locations of DNA categories completely different between human and chimp, but so were their proportions. One sequence class, or category containing DNA with a characteristic sequence, within the chimpanzee Y chromosome had less than 10 percent similarity with the same class in the human Y chromosome, and vice versa. Another large class shared only half the similarities of the other species, and vice versa. One differed by as much as 3.3-fold (330 percent), and a class specific to human "has no counterpart in the chimpanzee MSY [male-specific Y chromosome]."

As far as looking at specific genes, the chimp and human Y chromosomes had a dramatic difference in gene content of 53 percent. In other words, the chimp was lacking approximately half of the genes found on a human Y chromosome. Because genes occur in families or similarity categories, the researchers also sought to determine if there was any difference in actual gene categories. They found a shocking 33 percent difference. The human Y chromosome contains a third more gene categories--entirely different classes of genes--compared to chimps.


New Chromosome Research Undermines Human-Chimp Similarity Claims

I guess in return, I would ask if you thought that whales and hippos are the same "kind"? What about dogs and seals? Horses and rhinos? These relationships are consistently borne out by multiple sets of independent data, and common descent is the only explanation that makes sense of it.


No. There isn't any evidence that they are the same kind and there is no evidence from the fossil record that any of these closely related groups share a common ancestor. There is only dogs,seals,hippos, etc. in the fossil record.

There are no ancestors of dinosaurs or evidence of evolution within the dinosaur families.

Posted Image

Trilobites just appear out of no where and there are no transitions between the different orders. With 20,000 species, we should see thousands of transitions.

Posted Image

Cambrian jellyfish

Posted Image

Before anyone asks me to present some evidence, can someone tell me how to post an image???


Create a photobucket account and post images from it.

#7 roohif

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Posted 06 June 2011 - 06:14 AM

So, your convinced by cherry picking closely related groups? I believe in creation because all of the evidence fits its predictions - not just pieces of it.


No. Read what I wrote again, carefully. The deeper trees can still be significant at a 1% or 5% confidence interval, but why not just cut to the chase when you can demonstrate - to an obscenely high degree of accuracy - one controversial relationship?

No. There isn't any evidence that they are the same kind and there is no evidence from the fossil record that any of these closely related groups share a common ancestor. There is only dogs,seals,hippos, etc. in the fossil record.


I'm not interested in the fossil record. This thread is about protein sequence homologies - please try to stay on topic. If it helps, I'm quite happy to go back and remove the reference from the original post, and build a tree based only on the morphology of extant species only.

The DNA and protein sequence trees consistently place those pairs as close relatives, based on their patterns of shared mutations. Now either those mutations are tailored for the individual organisms, or they got there by common descent. You need to demonstrate the former, or construct a tree that violates the consensus.

Create a photobucket account and post images from it.

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Thanks.

#8 MarkForbes

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Posted 06 June 2011 - 06:49 AM

...I was wondering what creationists think the flaws are in protein sequence homology? Why is it that proteins that have no apparent correlation to phenotype/morphology converge on a consensus if it is not due to common descent?
...

View Post

On a general note. The flaw with homology is that it simply assumes "common descent" for animals, not consider any other reasons for commonalities. How about common creator as a reason for commonalities - especially, if it's not corelating to phenotype or morphology. Concerning pseudogenes /junk DNA (which in many cases have been proven to be useful and functional after all), they wouldn't be selected for in the evolutionary model. Their presence all over the animal kingdom won't be prove for evolution, but to the contrary a problem for evolution as they are in totally different animals without having changed over millions of years of evolutionary genealogies.

#9 jason777

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Posted 06 June 2011 - 02:56 PM

Hi roohif,

No. Read what I wrote again, carefully. The deeper trees can still be significant at a 1% or 5% confidence interval, but why not just cut to the chase when you can demonstrate - to an obscenely high degree of accuracy - one controversial relationship?


Alright, so your saying common descent can't be correlated in all the biological kingdoms, but circular reasoning in closely related groups is significant? In my mind, common descent means that all life shares a common ancestor not just humans and apes.

The DNA and protein sequence trees consistently place those pairs as close relatives, based on their patterns of shared mutations. Now either those mutations are tailored for the individual organisms, or they got there by common descent. You need to demonstrate the former, or construct a tree that violates the consensus.


Could you give us some specific proteins and tell us why you believe it proves common descent. I'm sure that the DNA comparison in Y chromosome violates the consensus view since it puts chimps and humans at ~70% similarity instead of the old 98% claim.



Enjoy.

#10 Bruce V.

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Posted 06 June 2011 - 11:21 PM

I've been studying protein sequence homology for a little while now, and in my mind it is the strongest line of evidence to support common descent (in the same vein as DNA sequence, ERV and pseudogene homology).

Just to be clear, the argument being made is that independent protein sequence trees converge not just on each other, but also on a consensus tree that is constructed using morphological data (that is, the fossil record and extant organisms). I understand that with a stochastic process like mutation there are bound to be discrepancies in the trees when compared to a consensus tree, but these discrepancies should fall within reasonable statistical boundaries.

I was wondering what creationists think the flaws are in protein sequence homology? Why is it that proteins that have no apparent correlation to phenotype/morphology converge on a consensus if it is not due to common descent?

Does anyone have any SPECIFIC examples of protein sequence trees that they feel do not give a reasonable approximation of the consensus tree?

Thanks.

View Post


Do you have a link where I could obtain more information on your post please?

It is my understanding that molecular sequencing has really unraveled the TOL (homology) especially at the lower levels.

You are right that evolutions strongest points have to do with common decent. For example, we see junk DNA of a higher organisms that matches that of a lower organisms. That could be proof, but we are finding that so called junk-DNA has purpose. If that is so, than we Creationist can rightly state that our creator used common design. Why reinvent the wheel?

Common decent also does not describe "how" something evolved. Evolution needs viable mechanism that describes how real morphological differences occur. How does something that appears to be designed occur by strictly naturalist means? Random mutation and natural selection have demonstrated little. Same goes with gene duplication followed my random mutation. Without a viable morphological mechanism evolution, by strictly naturalist means, is dead.

#11 Bruce V.

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Posted 06 June 2011 - 11:33 PM

Hi roohif,
Alright, so your saying common descent can't be correlated in all the biological kingdoms, but circular reasoning in closely related groups is significant? In my mind, common descent means that all life shares a common ancestor not just humans and apes.
Could you give us some specific proteins and tell us why you believe it proves common descent. I'm sure that the DNA comparison in Y chromosome violates the consensus view since it puts chimps and humans at ~70% similarity instead of the old 98% claim.
Enjoy.

View Post


I just leaned this. Is this the article you are referring to?

Interesting quote from the article.

To understand why regions in the human genome can differ in their evolutionary history, it needs to be acknowledged that genetic lineages represented by DNA sequences in the extant species trace back to allelic variants in the shared ancestral species. In here, these variants persist until they join in their most recent common ancestor (MRCA). Some genetic lineages, however, do not coalesce in the progenitor exclusively shared by humans and chimpanzees. They enter, together with the lineage descending from the gorilla, the ancestral population of all 3 species, where any 2 of the 3 lineages can merge first. Thus, in two-thirds of the cases, a genealogy results in which humans and chimpanzees are not each other's closest genetic relatives. The corresponding genealogies are incongruent with the species tree. In concordance with the experimental evidences, this implies that there is no such thing as a unique evolutionary history of the human genome. Rather, it resembles a patchwork of individual regions following their own genealogy.


So now, when a gene points in the wrong evolutionary direction, evolutionists just assume that the allele in question didn't become fixed into the population of our ancestors at the same time as most of the rest of the genome. Yet it also used to explain away why a whopping "23% of our genome" does not place humans as most closely related to chimpanzees, contradicting the standard evolutionary tree.

Is the statement that "The human genome is a mosaic with respect to its evolutionary history" just a sanitized way of saying that vast portions of our genome tell contradictory stories about our alleged ancestry with apes'?

#12 ikester7579

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Posted 07 June 2011 - 09:54 AM

The argument I'm making doesn't actually depend on the accuracy or validity of the tree derived from the fossil record, merely that such a tree has been constructed.

The trees constructed by protein/DNA sequences attempt to group individual point mutations and/or the subsequent amino acid changes in the sequence that would give a logical path of descent. [[ It might be a good idea to read the pinned Cytochrome C topic to get a better idea of what I'm talking about. ]]

The punchline is that these trees consistently overlay each other, but they use independent data to get there. For example, the tree constructed using Cytochrome C data can be overlaid on the tree constructed using morphological data, even though there is no known reason why these two sets of data should be correlated - except if they shared a common ancestor.

The same works for every protein that I have tested; and that is the basis for the original questions - are there examples that clearly don't fit within the framework; and what is the creationist explanation for these trees?

View Post


Or a Creator using the Common Template for all life.

So that I better understand what you are trying to do here, how about explaining, in detail, why a Creator should not use a Common Template (RNA DNA) for all life.

Questions:
Does not the common ancestor thing supposedly work because of the "common template" (RNA DNA) that all life share? And if we remove the common template, does not the common ancestor idea break down?

You can make any evidence "conform" to evolution as long as you "leave out" the parts that put that evidence into question. Like the supposed fossil record and living fossils problem. Ignore the problem as you do, does not make it go away. Not addressing the issue to one subject you brought up, only show me that you know how damaging this is but would prefer to ignore it. Conformism is not science. It's a self made truth and self made reality for a "wanted" truth. It is also the reason that 99.9% of all claimed evolution processes have to be animated. Evolution is only provable in a virtual world where any reality can be sold to the masses as long as a good animator is doing the animation. If you don't believe this, I will start another thread and you can show all of the "actual" observed processes of evolution. How big of a thread do you think that will be for a supposed true proven fact with mountains of empirical evidence?

Side note: You want a really good example of information being left out to make it "conform" to evolution? In the claim where we are about 2% different from chimps, do you know the actual numbers that 2% came from? In other words, what number does that 2% represent? The 2% thing is what supports the common ancestor claim, right? So it also supports the subject you bring up.

Also, why are the actual numbers the 2% came from not printed in any school text books? Are you guys claiming that school children cannot do simple math, or maybe they can, and that's what scares you? For I see no other reason to leave out this information unless the truth about evolution cannot be told?

#13 ikester7579

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Posted 07 June 2011 - 09:57 AM

I just leaned this.  Is this the article you are referring to?

Interesting quote from the article.
So now, when a gene points in the wrong evolutionary direction, evolutionists just assume that the allele in question didn't become fixed into the population of our ancestors at the same time as most of the rest of the genome. Yet it also used to explain away why a whopping "23% of our genome" does not place humans as most closely related to chimpanzees, contradicting the standard evolutionary tree.

Is the statement that "The human genome is a mosaic with respect to its evolutionary history" just a sanitized way of saying that vast portions of our genome tell contradictory stories about our alleged ancestry with apes'?

View Post


It's basically "whatever" makes evolution work had to happen (conformism). Even our genes have to conform.

#14 Fred Williams

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Posted 07 June 2011 - 04:26 PM

Just to be clear, the argument being made is that independent protein sequence trees converge not just on each other, but also on a consensus tree that is constructed using morphological data (that is, the fossil record and extant organisms)...
I was wondering what creationists think the flaws are in protein sequence homology? Why is it that proteins that have no apparent correlation to phenotype/morphology converge on a consensus if it is not due to common descent?

Does anyone have any SPECIFIC examples of protein sequence trees that they feel do not give a reasonable approximation of the consensus tree?

View Post


Sure, Cytochrome C! Obviously you didn’t read the pinned Cytochrome C thread very carefully. I provided the sequence without the animals, and an evolutionist took the bait and failed miserably. Why? Because he didn’t have the animals matched to the data ahead of time to influence his interpretation of the data. Here were the results:

29% of his analysis fit the current evolutionary dogma, however 80% of these also fit creationist baramin relationships.
47% neither confirmed or denied current evolutionary dogma or creation baramin relationships
24% contradicted the current evolutionary dogma

You mentioned COX1, and said it was a better choice since it’s less conserved. Are you willing to share with the audience what determination (aka “assumption”) was used to label it “less conserved”? This should be fun!

[somewhere in Australia someone is squirming in their chair right now, because if they answer honestly it totally exposes the illusion of their argument]

Fred
PS. To post an image, it needs to reside on a webpage somewhere, then you point to it using the IMG tag (it is a box above the box when you are editing your message).

#15 roohif

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Posted 07 June 2011 - 07:06 PM

On a general note. The flaw with homology is that it simply assumes "common descent" for animals, not consider any other reasons for commonalities. How about common creator as a reason for commonalities - especially, if it's not corelating to phenotype or morphology.

View Post


Why is a common creator a bad explanation? Pretty simple, once you understand how the trees are constructed. A reminder that this tree construction has nothing to do with evolution (yet), the data can be meaningless and arbitrary.

Posted Image

The image above is something I whipped up that shows you how you would go about building a tree using only the four strings at the bottom: OCAOO, OOAOD, ODOBO and OOOBE. The first string is most similar to the second string, and the third string is most similar to the fourth string. You could draw out the common characters in the first and second strings, and make a guess that the node that joins the two looks something like O?AO?, where the second character could be C or O, and the fifth character could be O or D.

For the third and fourth strings, the parent string would be O?OB?; the second character could be O or D, and the fifth character could be O or E. Using both nodes, we can see that the O gets the most "votes" for both the second and fifth characters. We can use this information to fill out the intermediate strings: OOAOO and OOOBO.

Using the same logic we can deduce that the string at the root of the tree is either OOOOO or OOABO, but we'll choose OOOOO for the sake of simplicity. Remember again that this method has nothing to do with evolution, we're just trying to group these strings into a tree-like structure so that the distance between branches correlates to the difference in the strings. If I were to ask you to place the string OCAOE in the tree, hopefully most of you will place it under the first branch rather than the fourth, even though it shares the E in the fifth character. The algorithm takes into account the patterns of similarites and differences to construct the tree.

The point of this thread though is to demonstrate that when you use protein sequence data to construct a tree like the one above, it gives a very good match to trees built from independent data (such as morphology, physiology, pseudogenes, ERVs, other proteins, etc.) and that requires an explanation.

The creationist explanation is of course that similarities are due to a common designer. So let's use Cytochrome C as the example. If this protein was the result of a common creator, then the obvious explanations would be:

a) The creator chose a single identical protein sequence and placed it in each "kind" of animal, and the sequences you see today are different simply because of random mutations over the last few thousand years, or

b) The creator tailored each sequence to be specific to each "kind" of animal - based on it's morphology, phsyiology, or some other characteristic.

The problem with the first explanation is that the odds of pairs of animals such as the whale and hippo, dog and seal, human and chimpanzee having the same mutations from the original sequence are astronomical.

For the second explanation to be valid, you would need to tell me the specific characteristic of the animal in question, and then explain the correlation. This is a tough ask for our example protein - Cytochrome C - firstly because its function is quite well understood, and secondly, it's been demonstrated pretty conclusively (through transgenic studies) that there isn't a correlation.

Concerning pseudogenes /junk DNA (which in many cases have been proven to be useful and functional after all), they wouldn't be selected for in the evolutionary model. Their presence all over the animal kingdom won't be prove for evolution, but to the contrary a problem for evolution as they are in totally different animals without having changed over millions of years of evolutionary genealogies.


Can you give me an example of a pseudogene that is in "totally different animals" that you think breaks the idea of common descent?

Of course pseudogenes have little to no selective value - I don't think you will get any arguments from evolutionists on that. Surely the Vitamin C pseudogene ("GULO") has been discussed on this forum before? Will have to dig it up at some point.

#16 roohif

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Posted 07 June 2011 - 07:29 PM

Alright, so your saying common descent can't be correlated in all the biological kingdoms, but circular reasoning in closely related groups is significant? In my mind, common descent means that all life shares a common ancestor not just humans and apes.

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Please read the Wikipedia articles on statistical significance and confidence intervals. In laymans terms (which are technically different to the actual definition), if something is significant at a 1% confidence interval, it means you can be 99% sure that your results didn't come about by accident. So, yes, they can be correlated in all the kingdoms, but you can only be 95% or 99% sure, depending on how far you go back.

Could you give us some specific proteins and tell us why you believe it proves common descent.


I think you might be missing the point of the thread - that being all the proteins (and their resulting trees) I've looked at overlap pretty nicely with each other, and that requires an explanation. I'm happy to provide trees for individual proteins on request, and I'll add them to my photobucket album.

In the absence of any reasons that point to these protein being individually designed, we have to go with the explanation that we DO KNOW would give us these results: mutation and heredity, otherwise known as common descent.

I'm sure that the DNA comparison in Y chromosome violates the consensus view since it puts chimps and humans at ~70% similarity instead of the old 98% claim.


(For the purposes of this thread, I don't particularly care what the percentage similarity is between chimps and humans; my argument stands by itself. I'm sure there is a different thread discussing that particular issue.)

#17 roohif

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Posted 07 June 2011 - 08:01 PM

Do you have a link where I could obtain more information on your post please?

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On which part in particular? I've just posted a comment below which explain some of the ideas. Send me a private message if it doesn't explain what you were asking about.

It is my understanding that molecular sequencing has really unraveled the TOL (homology) especially at the lower levels.


Well I guess that's the purpose of the thread - to see if any of the counter-claims hold any weight. Can you list some specific molecular sequences (be they proteins, DNA, ERVs, etc) that throw the Tree of Life into doubt?

You are right that evolutions strongest points have to do with common decent. For example, we see junk DNA of a higher organisms that matches that of a lower organisms. That could be proof, but we are finding that so called junk-DNA has purpose. If that is so, than we Creationist can rightly state that our creator used common design. Why reinvent the wheel?


By junk DNA, do you mean pseudogenes? Or just the bits and pieces of DNA scattered around the genome? The Vitamin C pseudogene in primates is pretty clearly a "broken" version of the gene found in the other mammals, and that would seem like a very odd thing for a creator to do. Again, the pattern of similarities and differences suggests common descent. If the Vitamin C pseudogene had a purpose, I think it would probably be incidental to its intended purpose of creating Vitamin C (not really knowledgeable about junk DNA, happy for people to send me links via private message).

Common decent also does not describe "how" something evolved. Evolution needs viable mechanism that describes how real morphological differences occur. How does something that appears to be designed occur by strictly naturalist means? Random mutation and natural selection have demonstrated little. Same goes with gene duplication followed my random mutation. Without a viable morphological mechanism evolution, by strictly naturalist means, is dead.


I think declaring the theory "dead" just because you can't think how something complex might have evolved, is a little premature. Some things are lost to the past, and we may never know how they came about. We've only been able to study genetics for about 50 years now, and the two experiments that come to mind are the nylonase enzymes, and the Lenski E. coli experiment; both of which demonstrated - at a DNA level - how new functionality came to be.

#18 roohif

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Posted 07 June 2011 - 08:15 PM

I just leaned this. Is this the article you are referring to?

http://mbe.oxfordjou...0/2266.full.pdf

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Pretty interesting article at first glance, and appears to be suggesting that humans were part of a ring species with chimps and gorillas. Will take me a few days to read and understand it properly, and then see what the implications are for common descent.

#19 roohif

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Posted 07 June 2011 - 08:41 PM

So that I better understand what you are trying to do here, how about explaining, in detail, why a Creator should not use a Common Template (RNA DNA) for all life.

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I agree. Using DNA and RNA does not exclude a creator from any explanation. In fact, for the purposes of this thread, I'm quite happy to accept for the sake of argument that the creator made the first living cell, fully functional, with all those pesky abiogenesis problems taken care of.

Questions: Does not the common ancestor thing supposedly work because of the "common template" (RNA DNA) that all life share? And if we remove the common template, does not the common ancestor idea break down?


As above, I don't think it points either way. If though, there were two methods of storing this sort of information (that is, DNA/RNA and something else) then I think that would point away from a creator, and towards a second genesis. In other words, if we couldn't compare DNA and RNA sequences then the "Common Designer" argument goes out the window.

You can make any evidence "conform" to evolution as long as you "leave out" the parts that put that evidence into question. Like the supposed fossil record and living fossils problem. Ignore the problem as you do, does not make it go away.


I'm not ignoring it, I just don't see it as relevant to this thread. I'm doing my best to keep it on topic, and I'm not about to go dig up the deep oceans looking for coelacanth fossils to prove you wrong. Surely there is another thread where living fossils are discussed?

Side note: You want a really good example of information being left out to make it "conform" to evolution?


Can you draw a phylogenetic tree from the information? If you can, then I'd love to see it. If not, then it doesn't belong in this thread. And no, the "2% thing" is not what I use to support common ancestor claims. My claim is that trees constructed using sequence data overlap each other, which can't be an accident. If that explanation is not common descent, then what is it?

#20 roohif

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Posted 07 June 2011 - 09:36 PM

Sure, Cytochrome C! Obviously you didn’t read the pinned Cytochrome C thread very carefully. I provided the sequence without the animals, and an evolutionist took the bait and failed miserably.

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Of course I read it carefully. The user numbers gave some rough calculations by plugging the number of differences into a spreadsheet. Then the user shpongle came along and built a proper phylogenetic tree using specialised software. They were both launching a space probe: numbers used Newton's laws of motion, shpongle used the Theory of Relativity.

DNAunion, PhilC and then myself point out that the challenge has been met, and we have all asked for an explanation. You thought that a family tree couldn't be constructed, yet shpongle created one. Can you explain (preferably in the pinned thread) why his tree is not a good match for the evolutionary tree of life?

You mentioned COX1, and said it was a better choice since it’s less conserved. Are you willing to share with the audience what determination (aka “assumption”) was used to label it “less conserved”? This should be fun!


By "less conserved" I mean that it appears that a bigger proportion of the sequence is open to mutation. This is a simple observation of the data, not an assumption. I could tally up the actual numbers if you like?

If there are more characters in the sequence open to mutation, then the software has a better chance of tracing the patterns of similarities and differences. Cytochrome C, on the other hand, has quite a few positions that are invariant, and many more that seem to only accept one of a handful of amino acids. There have been studies on this. Some amino acid substitutions cause the protein to mis-fold, while others have no effect.




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