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Author Topic:   Deep Homology and Front-loading
Taq
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Message 72 of 172 (666274)
06-25-2012 12:39 PM
Reply to: Message 12 by Genomicus
06-20-2012 11:59 AM


Let's take a look at calmodulin (CaM) as an example. Calmodulin binds to calcium and is found universally among eukaryotes. This fact, coupled to the observation that its sequence identity is exceptionally conserved across taxa, suggests that eukaryotes require calmodulin for their existence. In a world without calmodulin (or a functional analog), would eukaryotes exist? Probably not.
This quote exemplifies the problems with FLE. It is Texas Sharpshooting, plain and simple. The Texas Sharpshooter falacy is where a sharpshooter makes the claim that he can hit a target the size of a quarter from 1,000 yards away on the first try. The sharpshooter fires his shot into a crowded suburb, finds the bullet hole (presumably in the side of a house), and draws a quarter sized bull's eye around the bullet hole. Voila, amazing sharpshooting exhibition, right?
This is exactly what FLE is. It assumes that the biodiversity we see today is the biodiversity that was intended. Genomicus is drawing the bull's eye around the bullet hole. What Genomicus just can't understand is that eukaryotes DID NOT NEED TO EVOLVE. There is nothing in the history of life that requires the existence of eukaryotes, much less eukaryotes with calmodulin. NOTHING. It is a happenstance of occurences that resulted in eukaryotes evolving. If we went back in time before eukaryotes emerged could we use FLE to predict that eukaryotes would emerge, and that they would all require calmodulin? No. Genomicus has not put forward one methodology within FLE for predicting which proteins will become important in future lineages. None. All FLE does is look at what did evolve and then claim that this was the target. This is Texas Sharpshooting.
Even worse, the predictions of FLE are exactly what we would predict from the non-teleological process of evolution. Evolution is descent with modification. What is the prediction of FLE? Descent with modification. FLE can not, and does not, differentiate itself from observed non-teleological processes. FLE is sliced neatly away by Occam's Razor.

This message is a reply to:
 Message 12 by Genomicus, posted 06-20-2012 11:59 AM Genomicus has replied

Replies to this message:
 Message 74 by New Cat's Eye, posted 06-25-2012 2:35 PM Taq has replied
 Message 96 by Genomicus, posted 06-26-2012 2:00 PM Taq has replied

  
Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


(2)
Message 73 of 172 (666276)
06-25-2012 12:50 PM
Reply to: Message 1 by Genomicus
06-19-2012 2:46 PM


From here we can make a prediction: key eukaryotic proteins will share deep homology with functional but unnecessary prokaryotic proteins.
This is also what we would expect from non-teleological processes like evolution. In fact, Hermann Muller predicted that evolution would produce these relationships clear back in 1918:
quote:
Most present day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect which it produced upon the "reaction system" that had been brought into being by the many previously formed factors in cooperation; thus a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous elementary parts or factors, and many of the characters are factors which, when new, where originally merely an asset finally become necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former. It must result, in consequence, that a dropping out of, or even a slight change in any one of these parts is very likely to disturb fatally the whole machinery . . . [emphasis mine]
"Genetic Variablity, Twin Hybrids and Constant Hybrids, in a Case of Balanced Lethal Factors", by Hermann J Muller, in Genetics, Vol 3, No 5, Sept 1918, pp 422-499.
You also make the mistake of equating unnecessary with useless. You leave competition out of the equation. Let's use cars as an analogy. We could design a car with a bare minimum of parts. This car would be functional, but it would be slow, wouldn't corner well, and would be very unsafe. However, it would fulfill its role as a mode of transportation. As we all know, life is about competition. What traits are passed on is the result of competition for limited resources. To model this situation, let's have the cars race each other. How well would this minimalistic car do? Not well at all. It would lose rather horribly.
One of the MAJOR problems with your model is assuming that a minimalistic genome comprised of only "necessary" proteins would be viable. It wouldn't.

This message is a reply to:
 Message 1 by Genomicus, posted 06-19-2012 2:46 PM Genomicus has replied

Replies to this message:
 Message 103 by Genomicus, posted 06-26-2012 3:53 PM Taq has replied

  
Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


(2)
Message 75 of 172 (666297)
06-25-2012 3:55 PM
Reply to: Message 74 by New Cat's Eye
06-25-2012 2:35 PM


I was going to mention to Geno that it looked like he already liked FLE, and then went looking for evidence that can be shoehorned into it, rather than coming to a conclusion of FLE from the evidence that he had found.
Quite right. A more scientific approach would be to derive the ancestral genome and then demonstrate from first principles which genes were front loaded without pointing to modern genomes. Geno doesn't do this. At best, he claims that unnecessary genes will be passed on to subsequent generations where they would either be selected against if they became completely useless, or selected for if they evolved a more important role. This is evolution, no front loading needed.
Geno might as well predict that of the millions of lottery tickets, one of them will be a winner. In fact, the lottery is front loaded so that a specific ticket will win. Which ticket is the lottery front loaded for? Well, you have to wait for the drawing to figure that out. IOW, FLE is nothing more than the hope of some supernatural guidance in a nominally non-teleologic process.

This message is a reply to:
 Message 74 by New Cat's Eye, posted 06-25-2012 2:35 PM New Cat's Eye has replied

Replies to this message:
 Message 76 by New Cat's Eye, posted 06-25-2012 4:57 PM Taq has replied
 Message 78 by bluegenes, posted 06-25-2012 6:16 PM Taq has replied
 Message 105 by Genomicus, posted 06-26-2012 4:24 PM Taq has replied

  
Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


(1)
Message 77 of 172 (666307)
06-25-2012 5:48 PM
Reply to: Message 76 by New Cat's Eye
06-25-2012 4:57 PM


I don't know enough about genetics, how would you derive the ancestral genome?
Through a consensus sequence. Let's say that you had the following three sequences:
seq 1: ATAA
seq 2: AATA
seq 3: AAAC
-------------------
con : AAAA
The consensus sequence would be AAAA since the majority of the three sequences have an A at each position. The methodology is based on the rules of parsimony where it is assumed that common sequence is ancestral instead of the same independent mutation in several lineages. You can also incorporate the phylogeny into the reconstruction. Of course, the more ancient the sequence the more phylogeny and sequence data you will need and the less confidence you will have in the sequence. However, it would seem to be the most obvious starting place for the FLE hypothesis, but it would appear that Geno is starting clear at the other end.
How would you go about showing that some of the stuff we find in the earliest forms of life contain evidence of incorporating intelligently desinged genomic sequences and/or proteins?
The first thing I would look for is sequences that are designed solely for the benefit of the designer, such as those found in lifeforms that we design (e.g. GM foods).
If I was front loading a genome then I would want to make sure it does the job I want it to do when it gets to that point. That would mean having some sort of mutation protection for that sequence.

This message is a reply to:
 Message 76 by New Cat's Eye, posted 06-25-2012 4:57 PM New Cat's Eye has replied

Replies to this message:
 Message 79 by New Cat's Eye, posted 06-25-2012 8:27 PM Taq has replied

  
Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 88 of 172 (666349)
06-26-2012 11:11 AM
Reply to: Message 79 by New Cat's Eye
06-25-2012 8:27 PM


With your meaningfully helpful example, that assumption seems shaky at first. But I guess that depends on the size of the sequence. What sizes are we talkin'?
What are the chances that the same mutation will occur at the same base in 5 different species? Quite slim. It is possible, but improbable.
As to size . . . as large as possible. If you are trying to reconstruct the entire ancestral genome then you will try to find ALL of the shared DNA you can. You need to keep in mind that DNA will be lost in different lineages, so phylogenetic information is also important to determine when that deletion occurred.

This message is a reply to:
 Message 79 by New Cat's Eye, posted 06-25-2012 8:27 PM New Cat's Eye has replied

Replies to this message:
 Message 92 by New Cat's Eye, posted 06-26-2012 12:58 PM Taq has replied

  
Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 89 of 172 (666351)
06-26-2012 11:32 AM
Reply to: Message 78 by bluegenes
06-25-2012 6:16 PM


To say fair, Genomicus seems to deliberately steer clear of implying the supernatural.
Fair enough. However, we can't have an infinite regress of natural designers. There had to be a first set of natural designers at some point in our Universe's history. Therefore, we already know that non-teleologic natural mechanisms are capable of producing intelligent designers like us. There is every reason to believe that we are those First Designers, the first in a chain of intelligent design.
Perhaps I have jumped the gun in accusing Genomicus of proposing a supernatural teleological force . . . time will tell.
If the hypothesis is that this planet was seeded with the intent of producing metazoa, then I'd suggest that we should see instant biodiversity and no LUCA, because that would be the best way for the designers to minimize risk of complete extinction. More importantly, we should see the maximum possible engineering of shortcuts towards the production of complex metazoa, given the circumstances of the early planet.
Quite right. If the intent was for metazoans to arise in the future, why not make them straight away? We can deduce from our own technological evolution that it would only take a few decades between designing our first prokaryote and our first eukaryote. Even more, we could easily tweek simple metazoans from our own ecosystem to fit the environs of a distant planet. Do you want oxygen in the atmosphere? Dump some genetically modified algae into the planet's oceans.

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Replies to this message:
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Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 90 of 172 (666352)
06-26-2012 11:38 AM
Reply to: Message 83 by Genomicus
06-25-2012 10:19 PM


Re: The Ubiquitin Story
So, from a front-loading perspective, the designers would load up the first genomes with the basic ubiquitin structure, such that it could be easily co-opted into a role that is necessary for the rise of eukaryotes.
How did you determine that ubiquitin structure was intended for use in metazoans? How did you rule out the possibility that other proteins were destined for this role, but evolution caused ubiquitin to fill this role instead.
But if you don't put the basic ubiquitin structure in the first genomes, you'd have to depend on Darwinian mechanisms to come up with that structure, prior to the origin of eukaryotes.
This would only be true if the evolution of complex life required the existence of the ubiquitin fold. You haven't shown that anywhere. You are acting as if the biodiversity we see today is the only way it could have been. I see no reason why this is true. If ubiquitin did not evolve and life took a different route towards complex multicellular life then you (or possibly and intelligent being like you) would be talking about how this other protein was front loaded. You are painting the bull's eye around the bullet hole.
Given that there are many possible protein folds that have not been "found" by evolution in the history of life on earth, ubiquitin could have been one of those structures that never arose - in which case, eukaryotes might very possibly not have arisen.
But something else would have.

This message is a reply to:
 Message 83 by Genomicus, posted 06-25-2012 10:19 PM Genomicus has replied

Replies to this message:
 Message 116 by Genomicus, posted 06-27-2012 1:48 PM Taq has replied

  
Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 91 of 172 (666353)
06-26-2012 11:43 AM
Reply to: Message 82 by Genomicus
06-25-2012 9:48 PM


It's an argument based on what we know about biology: life requires a fairly specific core set of genes . . .
Actually, we don't even know if life requires DNA, much less a certain set of genes. Again, you are painting the bull's eye around the bullet hole. You are taking one result out of possibly billions and claiming that this is the only way of doing it. You are assuming that eukaryotes and metazoans were the goal instead of demonstrating that they are the goal.

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 101 of 172 (666388)
06-26-2012 2:45 PM
Reply to: Message 92 by New Cat's Eye
06-26-2012 12:58 PM


Doesn't that depend on the length of the sequence?
It depends on the mutation rate and the size of the genome. For most metazoans, the chances of the same mutation moving to fixation in two separate populations is low enough that it can be ignored for most purposes, but it should always be lurking in the background.
Seems to me that the phylogeny speeks better, I don't see how you could come to much of a conclusion from the sequences.
You might be interested in this article:
quote:
Heidmann and his colleagues set out to re-activate one family of HERVs, called the HERV-K(HML2) family, an evolutionarily young family of retroviral elements. They aligned HERV-K(HML2) elements, determined their consensus sequence, and then constructed a retrovirusPhoenixfrom the consensus sequence by mutating existing HERV-K(HML2) copies.
In addition, the researchers showed that Phoenix could form particles capable of infecting mammalian cells in culture. Infectivity was very low, presumably because host cells have evolved mechanisms to resist uncontrolled virus propagation, as has been repeatedly observed for retroviruses from experimental animals.
Phoenix Rising - Heidmann, Pierron, Dewannieux
I'm not liking Geno's approach... but don't get me wrong folks, I'd love to see some good evidence showing some planning involved in the evolution of life on Earth.
I do appreciate Geno bringing a breath of fresh air into these discussions. At least he has an informed opinion even if it turns out to be wrong.

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 102 of 172 (666392)
06-26-2012 3:24 PM
Reply to: Message 96 by Genomicus
06-26-2012 2:00 PM


Now that we've defined our terms, I ask the following question: in what way do I have "a large amount of data at their disposal, but only focuses on a small subset of that data. Random chance may give all the elements in that subset some kind of common property"?
That would be easy. You are focusing on what evolution did instead of what could have evolved. You claim that ubiquitin was front loaded while ignoring all of the other proteins that did not become functionally important in the metazoan lineage. You are looking for a bullet hole, and then painting a bull's eye around it.
One of the premises of Darwinian theory is that all species are related by common ancestry.
No it isn't. It is one of the CONCLUSIONS. It is what the evidence demonstrates. We don't need to assume common ancestry. We can demonstrate it. I am asking you to do the same for FLE.
Meanwhile, the premise of the front-loading hypothesis is that the Metazoa etc. that we see today was the result of intent.
Then I challenge that premise. Demonstrate that metazoans are the result of intent. Demonstrate that ubiquitin was intended to become functionally necessary in eukaryotes and how you are able to determine which proteins will become necessary in future generations.
Suppose, for example, that we received a radio signal from space that consisted of a long string of prime numbers. From here, it would be perfectly reasonable to hypothesize that the sequence of the radio signal was the intended outcome by some alien intelligence.
This is a poor analogy for a process that occurs through non-intelligent process (i.e. biological reproduction) right in front of our eyes.
Please read the OP and respond to the specific points I make there, where I argue that there is a prediction of the FLE that we would not make from the non-teleological model.
There is really only one point worth replying to which is the main point:
"From here we can make a prediction: key eukaryotic proteins will share deep homology with functional but unnecessary prokaryotic proteins. "
This is consistent with non-teleological evolution as well. You have not distinguished FLE from evolution in a testable manner. Since we can observe evolution in action, but lack any observation of your supposed designers, then it makes us wonder why evolution is not a satisfactory answer for the data in hand.
Edited by Taq, : No reason given.

This message is a reply to:
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Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 104 of 172 (666396)
06-26-2012 4:06 PM
Reply to: Message 103 by Genomicus
06-26-2012 3:53 PM


No, Hermann Muller predicted that traits that are at first merely beneficial can become necessary. He did not predict anything at all along the lines that crucial eukaryotic proteins will share deep homology with functional but unnecessary (for life) prokaryotic proteins.
"Functional but unnecessary" is the same as beneficial. They are one in the same. If these proteins did not produce beneficial function in prokaryotes then they would not be around 3 billion years later. They would have long since accumulated knockout mutations and gone the way of the dodo. In order for a protein to stick around in lineages it needs to be preserved by positive selection.
At one point, under the non-teleological model, life consisted of only a few genes. In arguing against the possibility that the LUCA could have, under the non-telic model, consisted of only a minimal genome, you are going against what a number of scientific papers have proposed or implied.
An organism with a minimal set of genes necessary for reproduction will go extinct as it is outcompeted by organisms that have functional but unnecessary genes that allow it to gain access to more resources. Any organism resembling LUCA would have those types of genes as LUCA is already well along a path of evolution. LUCA is not the first life. It is the last common ancestor of all extant life. Universally shared genes makes up the minimum genome for LUCA, not the entire thing.
You still have not demonstrated that the life we see today was even intended, much less intended by your proposed designers. You need to show us the bull's eye without a bullet hole in it, and then show us the bull's eye with the bullet hole in it. Do you understand what I am saying?

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Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 106 of 172 (666401)
06-26-2012 4:49 PM
Reply to: Message 105 by Genomicus
06-26-2012 4:24 PM


Since when did the supernatural, gods, deities, etc., enter this discussion?
When purpose is assigned to natural processes. That is usually where such discussions lead. Perhaps I have jumped the gun on this one . . . time will tell.

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 108 of 172 (666436)
06-27-2012 10:54 AM
Reply to: Message 107 by Genomicus
06-26-2012 6:07 PM


Re: The Ubiquitin Story
My point is that loading the first genomes with an ubiquitin-related fold allows it to be easily co-opted into the role used by eukaryotes.
This is true no matter what the origin of ubiquitin is, and is easily accomplished by non-teleological processes.

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 124 of 172 (666466)
06-27-2012 2:42 PM
Reply to: Message 116 by Genomicus
06-27-2012 1:48 PM


Re: The Ubiquitin Story
If we assume, for sake of argument, that the Metazoa we see today was the intended outcome of a front-loading scheme, we can make testable predictions regarding biotic reality.
If you assume your conclusion then you can not make testable predictions. That's the problem.
However, if we follow the line of thought that Metazoa were, in fact, the intended outcome of front-loading, from here we can make real predictions that are not made by the non-teleological model.
Those predictions exactly mirror non-teleological models. FLE states that modern genes descended from ancient genes. Non-teleological models make the SAME PREDICTION.
The non-telic view of life does not require that prokaryotes have ubiquitin homologs.
The non-telic view of weather does not require that it rain in Dallas, TX today. However, it is certainly a possibility for non-telic meteorology, is it not? The same for ubiquitin homologs. Non-telic mechanisms are clearly capable of co-opting ancestral genes for roles in subsequent generations.

This message is a reply to:
 Message 116 by Genomicus, posted 06-27-2012 1:48 PM Genomicus has replied

Replies to this message:
 Message 135 by Genomicus, posted 06-28-2012 2:04 PM Taq has replied
 Message 159 by Genomicus, posted 07-03-2012 12:31 PM Taq has replied

  
Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 125 of 172 (666467)
06-27-2012 2:43 PM
Reply to: Message 120 by Genomicus
06-27-2012 2:04 PM


Re: The Ubiquitin Story
No, because rain is predicted from plain ole' meteorology.
Shared genes between eukaryotes and prokaryotes are predicted from plain ole' evolution.
Edited by Taq, : No reason given.

This message is a reply to:
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