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Author Topic:   Deep Homology and Front-loading
Taq
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Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


Message 133 of 172 (666530)
06-28-2012 11:23 AM
Reply to: Message 128 by Genomicus
06-27-2012 7:46 PM


Re: The Ubiquitin Story
Non-teleological evolution does not predict that ubiquitin will have a prokaryotic homolog because the ubiquitin gene could easily have been pieced together from different pieces of DNA, in much the same way that T-urf13 evolved.

Non-teleological meteorology does not predict that it will rain in Dallas, TX today because it could just as easily not rain today. Therefore, if it rains it is due to rain fairies.

Do you think this is a valid argument? I sure don't. While non-teleological meteorology does not require that specific areas get rain at specific times, it can easily accomodate these observations. In the same way, evolution does not predict that specific proteins will become necessary in future generations. Rather, it accomodates such observations. Ubiquitin fits this model. Non-teleological evolution can easily co-opt a gene in ancestors to fill a necessary role in descendants. That is what it does. You are trying to falsify evolution by pointing to the very observations that it can produce. That makes no sense.

Better yet, please show that it is impossible for non-teleological evolution to create these observations.


This message is a reply to:
 Message 128 by Genomicus, posted 06-27-2012 7:46 PM Genomicus has responded

Replies to this message:
 Message 144 by Genomicus, posted 06-29-2012 1:54 PM Taq has responded

  
Taq
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Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


Message 134 of 172 (666531)
06-28-2012 11:25 AM
Reply to: Message 129 by Genomicus
06-27-2012 8:16 PM


Re: The Ubiquitin Story
More specifically, why the current theory does not predict the presence of ubiquitin homologs in prokaryotes.

It predicts descent with modification, which is exactly what we observe.

Also, in a more a global sense, FLE predicts that key eukaryotic proteins will share deep homology with prokaryotic proteins that are not part of the essential gene set.

This does not differentiate FLE from non-teleological evolution since evolution can produce this same pattern.


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Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


Message 139 of 172 (666559)
06-28-2012 3:03 PM
Reply to: Message 135 by Genomicus
06-28-2012 2:04 PM


Re: The Ubiquitin Story
Okay, here's a simple true/false question: If the Metazoa we see today was the intended outcome of a front-loading scenario, could we make testable predictions from this premise?

In order to be testable predictions they would need to differ from the assumption and differ from known natural mechanisms that you are seeking to replace. So far, you have fulfilled none of these requirements.

No, non-teleological models do not predict that crucial eukaryotic genes will share deep homology with functional but unnecessary (for life) prokaryotic proteins.

Just like non-teleological meteorology does not predict that it has to rain on July 15th, 2016 in Dallas, TX. However, rain that day is consistent with non-teleological meteorology. In the same way, "crucial eukaryotic genes will share deep homology with functional but unnecessary (for life) prokaryotic proteins" is also consistent with non-teleological evolutionary mechanisms.

It is incumbent on you to show that non-teleological mechanisms can not co-opt proteins in subsequent generations.

Read that carefully, then tell me that it's not reasonable, under non-teleological models, for the LUCA to have only a minimal genome and be only a minimal cell.

It's not reasonable under non-teleological models for LUCA to have a minimalist genome. LUCA is a product of many rounds of evolution. LUCA will contain genes that are unnecessary for life by necessary for outcompeting other organisms in a given environment.

What you label unnecessary proteins are beneficial proteins to the organism that carries them. That is why they have been preserved for 3 billion years of evolution. Can non-teleological mechanisms preserve beneficial proteins? Yes. Therefore, it is not a valid testable prediction for FLE.

Can non-teleological mechanisms co-opt beneficial mutations for new purposes through random mutation and natural selection so that they are necessary genes in subsequent generations? Yes, absolutely. This too is not a valid testable prediction for FLE because it does not differentiate FLE from non-teleological processes.

The issue here really isn't whether the non-telic view of life can potentially explain the observation that crucial eukaryotic proteins share deep homology with functional but unnecessary prokaryotic proteins.

Yes, it is. If non-teleological mechanisms can produce the observations then FLE is not supported.


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Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


Message 140 of 172 (666560)
06-28-2012 3:06 PM
Reply to: Message 137 by Genomicus
06-28-2012 2:35 PM


Re: The Ubiquitin Story
1. Non-teleological evolution predicts that key eukaryotic genes will share homology with functional but unnecessary proteins. Essentially then, the non-telic model predicts that the LUCA did not have a minimal genome. Interestingly, however, a number of papers have proposed that the LUCA did, in fact, have only a minimal genome, demonstrating that this is perfectly reasonable under the non-telic model.

A minimal genome for what function? LUCA did not have a single base codon system as the evidence suggests was the case for the first life. Instead, LUCA had a three base codon system, with some 3rd base wobble. Already, LUCA is not a minimalist genome, and we have only looked at the tRNA's.


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 Message 137 by Genomicus, posted 06-28-2012 2:35 PM Genomicus has not yet responded

  
Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


(1)
Message 158 of 172 (667026)
07-02-2012 12:07 PM
Reply to: Message 144 by Genomicus
06-29-2012 1:54 PM


Re: The Ubiquitin Story
That Darwinian evolution can explain an observation does not mean it predicts it.

The stochastic nature of evolution predicts that you will NOT be able to predict a specific outcome millions of years in the future based on a given genome. It is incumbent on you to show that this can be done. You need start with the ancestral sequence for ubiquitin and then show, from first principles, that this sequence is front loaded so that it will become ubiquitous in future generations. You also need to show how other genes will not using those same principles. Until you do so, you are simply painting the bull's eye around the bullet hole.


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Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


(2)
Message 165 of 172 (667176)
07-03-2012 3:55 PM
Reply to: Message 159 by Genomicus
07-03-2012 12:31 PM


Re: The Ubiquitin Story
You have not yet explained why we cannot make testable predictions based on the premise that the Metazoa we see today was the intended outcome of a front-loading scheme.

Your predictions are the same as your assumption. That is the problem. You are assuming that ubiquitin was the goal. You then turn around and claim that it is a prediction.

FLE states that modern genes descended from ancient genes that are unnecessary for life.

So does non-telic evolution.


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 Message 159 by Genomicus, posted 07-03-2012 12:31 PM Genomicus has not yet responded

  
Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


Message 166 of 172 (667178)
07-03-2012 3:59 PM
Reply to: Message 162 by Genomicus
07-03-2012 1:56 PM


Re: I predict "No LUCA"!
Well, we know that endosymbiosis events are not at all implausible occurrences. However, it's not plausible for a specific protein fold to "just happen" to evolve, given that there are many more possible protein folds that could have arisen, many of which would not have contributed to the rise of eukaryotes.

You are assuming that metazoans were the goal. The front loaders may have had different life in mind, but an evolutionary novelty arose that dashed all of their plans. What you keep ignoring is that something other than eukaryotes could have arisen.

If convergent evolution has taught us anything, it is that given specified initial conditions, specific biological objectives can be front-loaded over deep-time.

Actually, it teaches us just the opposite. It teaches us that evolution will find similar solutions from DIFFERENT starting points. That is the opposite of front loading.


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