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Author Topic:   Deep Homology and Front-loading
Genomicus
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(1)
Message 1 of 172 (665909)
06-19-2012 2:46 PM


In a previous thread, I have discussed the concept of front-loaded evolution as a testable teleological hypothesis. This caused a good bit of disagreement, as many of you are quite adamant that FLE doesn’t make any exclusive predictions. Contrary to this, I think FLE does, in fact, make a prediction that the current evolutionary paradigm does not.

Before beginning, let me explain exactly what the front-loading hypothesis is, as some of you have misconceptions about it.


Front-loading is all about designing future states through the present. Here’s how Mike Gene, the guy who first conceived of the idea of front-loading, defines it:

“Front-loading is the investment of a significant amount of information at the initial stage of evolution (the first life forms) whereby this information shapes and constrains subsequent evolution through its dissipation. This is not to say that every aspect of evolution is pre-programmed and determined. It merely means that life was built to evolve with tendencies as a consequence of carefully chosen initial states in combination with the way evolution works.
Front-loading does not allow for a prediction of specific outcomes, at a specific time and place, but does allow that specified outcomes can be made much more likely...”
(The Design Matrix, p. 147).

According to the front-loading hypothesis, one of the objectives of front-loading was the rise of eukaryotes and multicellular life forms. And if multicellular life forms were front-loaded, this can serve as a springboard from which we can make several predictions.

So, how would a designer(s) front-load multicellular life forms through unicellular life forms? You’d simply have to load the first genomes with proteins that would later be utilized by the multicellular life forms. For example, histones seem to be universally required by eukaryotes. Thus, loading the first genomes with histones (or their analogs) would make the appearance of eukaryotes more likely (and front-loading is all about “stacking the deck” in favor of the appearance of multicellular life forms). Without histones in the first genomes, the evolution of eukaryotes is left solely to the blind watchmaker’s tinkering. And without specific information to guide and constrain the path of evolution, such that it is “nudged” in the direction of eukaryotes, there’s no guarantee that histones will evolve. Consequently, the likelihood that eukaryotes would evolve drops considerably. A front-loading designer can make the evolution of eukaryotes much more likely by packing the first genomes with eukaryotic proteins (or their analogs), such that evolution will build around these proteins, eventually producing the objective.

From here we can make a prediction: key eukaryotic proteins will share deep homology with functional but unnecessary prokaryotic proteins.

The homologous protein in prokaryotes will be functional because if the designer loads up the genome with proteins that will only find function millions of years later, these proteins will decay into oblivion, eliminating the whole purpose of front-loading. But if these homologous proteins are unnecessary in that they are not required for the basic prokaryotic cell, then we have a successful prediction of front-loading. Non-teleological evolution does not make this prediction.

This is because, under non-telic evolution, the LUCA’s genome could easily have been a minimal genome that only encodes the proteins absolutely necessary for the existence of a prokaryote cell. Non-teleological evolution does not require this; but nor does it require that the LUCA’s genome encodes more than is necessary. We can summarize this state of affairs thusly: non-teleological evolution makes no predictions regarding the gene/protein content of the LUCA, other than the obvious fact that it would have to encode the proteins necessary for its existence. On the other hand, front-loading specifically predicts that the LUCA will contain more proteins than is necessary for prokaryotic existence. If the front-loader only designed the LUCA such that it encoded the bare minimum required for life (about 250 genes or so), there’s no “stacking of the deck” in favor of the evolution of multicellularity. In short, front-loading, by its very definition, requires the loading of the LUCA’s genome with unnecessary (but functional!) proteins – proteins that are required for the rise of eukaryotes and multicellularity.

I will now briefly address the objections that I’ve come across so far:

1. If evolution can explain something happening, it also predicts that it can happen (source: Dr Adequate). The modern evolutionary theory might be able to explain some biological feature, while an ID hypothesis would predict that biological feature. If the prediction is confirmed, this is evidence for that ID hypothesis, regardless of whether non-telic evolution can explain it or not. Science is built upon a track record of successful predictions, not on whether some alternative model can explain the feature under consideration. Consider the following example. Evolution predicts that if the bacterial flagellum evolved, a number of its components will share similarity with proteins that are more ancient than the bacterial flagellum. Can the hypothesis that the flagellum was engineered explain this? Yes. Engineers very often re-use parts in different systems. But the ID hypothesis does not predict that the flagellar components will share similarity with more ancient proteins. This is because engineers can also design from scratch. So, while ID can explain this, it does not predict it. Which means that, when it comes to similarity, evolution is the superior explanation.

2. Why would the LUCA have a minimal set of genes ? Wouldn't it be expected to have more than the absolute minimum ? Given evolution, rather than design (source: PaulK). In my humble opinion, evolutionary theory – that is, the current biological paradigm – doesn’t make a prediction either way regarding the gene content of the LUCA. Under evolutionary theory, LUCA would not be expected to have more genes than necessary any more than it would be expected to have only the bare minimum. This is because, under non-teleological evolution, the LUCA could have been simply a self-replicating molecule, encoding only a few genes. This population of self-replicating molecules would then diverge, producing different domains of life. But under front-loading, the LUCA would have to have more genes than necessary because there’s no reason to suppose that a minimum gene set could specifically evolve into multicellular life forms, given that there are many directions in which this minimum gene set could evolve. Only a few of the paths consist of multicellular life forms of the type we see today, while the vast majority of possible evolutionary trajectories does not consist of the multicellular life forms we see today. So, to front-load these life forms, you’d need to load the LUCA’s genome with genes that would make the appearance of these life forms more probable.

One more point. I’d like to correct something I stated earlier. Previously, I said something to the effect that these functional but unnecessary proteins in prokaryotes would be so unnecessary that deleting them wouldn’t significantly affect fitness. This is not correct. Deleting them might kill the organism under consideration. Nevertheless, if a given gene is required for one prokaryote, this does not mean that it is required by all prokaryote life forms. So, by “unnecessary but functional” I mean a gene that is not required by the basic prokaryote cell plan but does carry out a functional role in the LUCA.


Replies to this message:
 Message 3 by Dr Adequate, posted 06-19-2012 9:36 PM Genomicus has responded
 Message 7 by PaulK, posted 06-20-2012 12:40 AM Genomicus has responded
 Message 73 by Taq, posted 06-25-2012 12:50 PM Genomicus has responded

  
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Message 2 of 172 (665911)
06-19-2012 3:41 PM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Deep Homology and Front-loading thread in the Proposed New Topics forum.
    
Dr Adequate
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Message 3 of 172 (665929)
06-19-2012 9:36 PM
Reply to: Message 1 by Genomicus
06-19-2012 2:46 PM


Well, try to either have your cake or eat it. If the homologues are sufficiently useful that natural selection would conserve them, then they will in fact be conserved, and their conservation is in fact predicted by the ToE.

Either:

(1) The histone homologues are useless to prokaryotes, in which case FLE does not predict their conservation and can't even explain it either, since no mechanism for conserving them is known (conservative selection being ineffective for this purpose by hypothesis) ...

... or:

(2) The histone homologues are useful to prokaryotes, in which case the ToE predicts their conservation by natural selection.

Edited by Dr Adequate, : No reason given.


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

Replies to this message:
 Message 4 by Genomicus, posted 06-19-2012 9:50 PM Dr Adequate has responded

  
Genomicus
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Joined: 02-15-2012
Member Rating: 4.7


Message 4 of 172 (665930)
06-19-2012 9:50 PM
Reply to: Message 3 by Dr Adequate
06-19-2012 9:36 PM


If the homologues are sufficiently useful that natural selection would conserve them, then they will in fact be conserved, and their conservation is in fact predicted by the ToE.

Yes, but that's not the issue here at all. I said that the FLE would predict that proteins crucial to eukaryotes will share deep homology with proteins in prokaryotes. That's the whole issue here, not whether a protein will be conserved in one lineage or another. In other words, the ToE doesn't predict the existence of histones in prokaryotes; it can explain the existence of histones in prokaryotes, but it doesn't predict it.


This message is a reply to:
 Message 3 by Dr Adequate, posted 06-19-2012 9:36 PM Dr Adequate has responded

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 Message 5 by Dr Adequate, posted 06-19-2012 9:54 PM Genomicus has responded

  
Dr Adequate
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Joined: 07-20-2006
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Message 5 of 172 (665931)
06-19-2012 9:54 PM
Reply to: Message 4 by Genomicus
06-19-2012 9:50 PM


Yes, but that's not the issue here at all. I said that the FLE would predict that proteins crucial to eukaryotes will share deep homology with proteins in prokaryotes.

Well, so does Darwinian evolution. How could they not?

The only way I can think of you could not have such homology is if you had a LUCA front-loaded with two disjoint sets of genes, one for prokaryotes and one for eukaryotes. Which would be a front-loading hypothesis.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 4 by Genomicus, posted 06-19-2012 9:50 PM Genomicus has responded

Replies to this message:
 Message 6 by Genomicus, posted 06-19-2012 10:07 PM Dr Adequate has responded

  
Genomicus
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Member Rating: 4.7


Message 6 of 172 (665932)
06-19-2012 10:07 PM
Reply to: Message 5 by Dr Adequate
06-19-2012 9:54 PM


Well, so does Darwinian evolution. How could they not?

Two points here:

1) Darwinian evolution (that is, the current paradigm) does not predict that crucial proteins in eukaryotes will share deep homology with functional but unnecessary proteins in prokaryotes. By unnecessary I do not mean a protein that offers only little fitness advantage. I simply mean a protein that is not necessary for the basic prokaryotic cell plan. For example, although histones are found in a number of prokaryotes, and are fully functional, they are not required for the existence of prokaryotes. In a world without histones, we'd still have prokaryotes.

2) Unlike front-loading, Darwinian evolution does not necessarily predict that eukaryotic histones will share deep homology with prokaryotic proteins. Why? Proteins not only evolve from coding sequences, but they can also be pieced together from non-coding sequences. A cool example of this is T-urf13, which, IIRC, evolved from rRNA sequences and other non-coding sequences. In short, T-urf13 didn't evolve from any protein-coding gene. It was pieced together from different non-coding sequences. Thus we see that Darwinian evolution could expect that histones (or analogous counterparts) would only be homologous with non-coding regions. In other words, there's no reason, from a Darwinian perspective, why the existence of histones in eukaryotes implies the existence of histones in prokaryotes. Taking this from a Darwinian point of view, the presence of histones in eukaryotes only means that it will be homologous with different chunks of DNA/RNA sequences in prokaryotes - DNA/RNA sequences that are not necessarily functional. This goes against the expectations of front-loading, because you can't really front-load histones by depending on chance to cobble together a histone from "scratch" (i.e., non-coding sequences).

Edited by Genomicus, : No reason given.


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 Message 5 by Dr Adequate, posted 06-19-2012 9:54 PM Dr Adequate has responded

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 Message 8 by Dr Adequate, posted 06-20-2012 5:18 AM Genomicus has responded

  
PaulK
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Message 7 of 172 (665934)
06-20-2012 12:40 AM
Reply to: Message 1 by Genomicus
06-19-2012 2:46 PM


I think that you are using different senses of "predict" here.

We don't know that there isn't a minimal gene set that would enable evolution into something of equivalent complexity to modern animals and plants in the time available. It only seems likely that this is true.

But if we accept that the LUCA is a community of simple organisms sharing genes it is vanishingly unlikely that evolution would only have a minimal gene set to work with.

So, on this basis your "not a prediction" seems to be a stronger statement than your "prediction", which simply can't be the case if you are using a consistent standard.

I would also comment on this:

quote:

This is because, under non-teleological evolution, the LUCA could have been simply a self-replicating molecule, encoding only a few genes.

Even taken as a vague idea, ignoring what we know about the development of early life this seems false. How can a simple self-replicating chemical have genes ?
If we take into account the fact that DNA seems to be a relative latecomer (and ask yourself why we would have evidence pointing to this if life on Earth started with artificial prokaryotes) any LUCA you could find by investigating the homology of genes would necessarily be the product of considerable evolution, with DNA and a gene set already in place - you can't go back to anything earlier.


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

Replies to this message:
 Message 9 by Genomicus, posted 06-20-2012 10:31 AM PaulK has responded

    
Dr Adequate
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Posts: 15927
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Message 8 of 172 (665946)
06-20-2012 5:18 AM
Reply to: Message 6 by Genomicus
06-19-2012 10:07 PM


1) Darwinian evolution (that is, the current paradigm) does not predict that crucial proteins in eukaryotes will share deep homology with functional but unnecessary proteins in prokaryotes.

So the emphasis is on functional but unnecessary?

But then you could say the same of front-loading. What is there in FLE that says that by the modern era, the only homologous proteins won't be those absolutely necessary to both lineages?

2) Unlike front-loading, Darwinian evolution does not necessarily predict that eukaryotic histones will share deep homology with prokaryotic proteins.

How likely, though, is a complete turnover of genes?

A cool example of this is T-urf13, which, IIRC, evolved from rRNA sequences and other non-coding sequences.

Could you clarify --- do you think that this, and things like it, actually happened?

---

You haven't addressed my point about front-loading. What is there in the concept of FLE as such which stops the LUCA from having two non-intersecting sets of genes, one for eukaryotes, one for prokaryotes? Now, I know the evidence is that the LUCA wasn't like that, but if there's nothing to stop a designer from doing something like that, then there's no prediction, is there?

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 6 by Genomicus, posted 06-19-2012 10:07 PM Genomicus has responded

Replies to this message:
 Message 10 by Genomicus, posted 06-20-2012 10:53 AM Dr Adequate has responded

  
Genomicus
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Member Rating: 4.7


Message 9 of 172 (665959)
06-20-2012 10:31 AM
Reply to: Message 7 by PaulK
06-20-2012 12:40 AM


We don't know that there isn't a minimal gene set that would enable evolution into something of equivalent complexity to modern animals and plants in the time available. It only seems likely that this is true.

Would you care to elaborate on this? With a LUCA that has a minimal gene set, there's really no reason to suppose that complex life forms could arise. You'd have to guarantee the rise of mitochondria before you can get complex life forms. And, IMHO, there's no reason to suspect that a minimal gene set consisting of just essential proteins - i.e., DNA replication proteins, ribosomes, key metabolic pathway proteins, and the like - is all that likely to "just happen" to evolve in specific directions that would allow the evolution of mitochondria. In the absence of mitochondria, you won't have complex life forms.

But if we accept that the LUCA is a community of simple organisms sharing genes it is vanishingly unlikely that evolution would only have a minimal gene set to work with.

What does horizontal gene transfer have to do with a minimal gene set? I.e., sure, this LUCA community could be transferring genes, but these genes would be part of the minimal gene set.

Even taken as a vague idea, ignoring what we know about the development of early life this seems false. How can a simple self-replicating chemical have genes ?

A self-replicating RNA molecule could specify a protein sequence.

If we take into account the fact that DNA seems to be a relative latecomer (and ask yourself why we would have evidence pointing to this if life on Earth started with artificial prokaryotes)...

I haven't found any convincing evidence that DNA evolved from RNA. I am aware of a number of papers on the subject, but I'll (hopefully!) discuss this evidence in another thread (so we don't get sidetracked here).

...any LUCA you could find by investigating the homology of genes would necessarily be the product of considerable evolution, with DNA and a gene set already in place...

Yes, but under the FLH, the LUCA isn't the product of considerable evolution. Maybe I'm not getting your point with this statement?


This message is a reply to:
 Message 7 by PaulK, posted 06-20-2012 12:40 AM PaulK has responded

Replies to this message:
 Message 14 by PaulK, posted 06-20-2012 1:18 PM Genomicus has responded

  
Genomicus
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Member Rating: 4.7


Message 10 of 172 (665963)
06-20-2012 10:53 AM
Reply to: Message 8 by Dr Adequate
06-20-2012 5:18 AM


So the emphasis is on functional but unnecessary?

Yes.

But then you could say the same of front-loading. What is there in FLE that says that by the modern era, the only homologous proteins won't be those absolutely necessary to both lineages?

If I understand your question correctly, the answer is: if you loaded the first genomes on earth with proteins "in waiting" that will find their intended function only later, when complex life forms have arisen, then, in the modern era, you can trace this homology back in time. Naturally, these proteins "in waiting" will carry out a function such that it isn't likely that they will be weeded out by natural selection.

How likely, though, is a complete turnover of genes?

Well, it's likely enough to happen.

Could you clarify --- do you think that this, and things like it, actually happened?

Yes. That's what the evidence indicates happened in the case of T-urf13.

You haven't addressed my point about front-loading. What is there in the concept of FLE as such which stops the LUCA from having two non-intersecting sets of genes, one for eukaryotes, one for prokaryotes? Now, I know the evidence is that the LUCA wasn't like that, but if there's nothing to stop a designer from doing something like that, then there's no prediction, is there?

Well, in this case, we'd have an either/or prediction. In other words, FLH predicts either that the LUCA will have functional and unnecessary genes or that the LUCA will have non-intersecting sets of genes.


This message is a reply to:
 Message 8 by Dr Adequate, posted 06-20-2012 5:18 AM Dr Adequate has responded

Replies to this message:
 Message 11 by Dr Adequate, posted 06-20-2012 11:36 AM Genomicus has responded

  
Dr Adequate
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Posts: 15927
Joined: 07-20-2006
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(1)
Message 11 of 172 (665969)
06-20-2012 11:36 AM
Reply to: Message 10 by Genomicus
06-20-2012 10:53 AM


If I understand your question correctly, the answer is: if you loaded the first genomes on earth with proteins "in waiting" that will find their intended function only later, when complex life forms have arisen, then, in the modern era, you can trace this homology back in time. Naturally, these proteins "in waiting" will carry out a function such that it isn't likely that they will be weeded out by natural selection.

But the bit of that that made sense is Darwinian.

Let's try it again.

You make a big deal out of the fact that things that are essential to eukaryotes are merely useful to prokaryotes.

(I must have missed the place where you proved that, but let's take this as true for the sake of argument.)

But where does FLE predict that some things that are essential to eukaryotes are merely useful to prokaryotes? Is not FLE consistent with the idea that everything that is essential to eukaryotes is also essential to prokaryotes?

Well then, if FLE is consistent with that, then it does not predict the opposite of that.

Well, it's likely enough to happen.

But again I have to ask if you believe what you're saying.

If you believe that Darwinian evolution is sufficient to produce a complete turnover of a genome --- then this would be the time for me to point out that you do not deny that Darwinian evolution occurs. You apparently believe in Darwinian evolution plus front-loaded evolution. So if you believe that a complete turnover of the genome is "likely enough to happen" given Darwinian evolution, then you believe that it is "likely enough to happen". In which case, where is your prediction? If you admit that given FLE, it is "likely enough to happen", then FLE has no prediction that it wouldn't happen.

Yes. That's what the evidence indicates happened in the case of T-urf13.

But ...

... you admit that Darwinian evolution did that ...

One of the reasons that it's hard to argue with you is that it's difficult to know what it is that you think. I mean, I know that you're trying to slip ID in there somewhere, but ...

... I'll come back to this point when I know what you wish to say.

Well, in this case, we'd have an either/or prediction. In other words, FLH predicts either that the LUCA will have functional and unnecessary genes or that the LUCA will have non-intersecting sets of genes.

But then you're screwed.

Don't you see?

We can't actually look at LUCA, can we?

We can only look at what's in front of us, the modern genomes of modern organisms.

Now, when you've broadened your hypothesis to saying: "A front-loaded LUCA could be like this, in which case it would explain this; or, alternatively, a front-loaded LUCA could be like that, in which case it would explain that" ... then you've lost the point you were originally meant to be gaining.

We can't look at the genome of LUCA. We can just look at the genomes of the organism that are presently available to us. Now, if all FLE predicts is that we will either see evidence that something is true, or we will see evidence that the opposite is true, then that's not a point in favor of FLE, is it?

You say you have an "either/or prediction". Well, how does that differ from the "either/or prediction" of Darwinism in terms of the phenomena that we can actually observe?

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 10 by Genomicus, posted 06-20-2012 10:53 AM Genomicus has responded

Replies to this message:
 Message 12 by Genomicus, posted 06-20-2012 11:59 AM Dr Adequate has responded

  
Genomicus
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Posts: 815
Joined: 02-15-2012
Member Rating: 4.7


Message 12 of 172 (665971)
06-20-2012 11:59 AM
Reply to: Message 11 by Dr Adequate
06-20-2012 11:36 AM


But where does FLE predict that some things that are essential to eukaryotes are merely useful to prokaryotes? Is not FLE consistent with the idea that everything that is essential to eukaryotes is also essential to prokaryotes?

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.

Now, it appears to me that you're saying "is not FLE consistent with the idea that calmodulin is also essential to prokaryotes?"

The problem is that, simply put, calmodulin is not essential to prokaryotes. The basic prokaryotic cell plan does not require calmodulin. You could design a prokaryotic cell that requires calmodulin, but the basic prokaryotic cell architecture does not require the existence of calmodulin. And this is the key point. This means that saying "is not FLE consistent with the idea that calmodulin is also essential to prokaryotes" doesn't really make sense, because we know that calmodulin isn't essential to prokaryotes.

If you believe that Darwinian evolution is sufficient to produce a complete turnover of a genome...

Well, first of all, you said "turnover of genes;" I didn't think you meant a complete genome. And, come to think of it, the terminology "turnover of genes" is kinda vague in this context. Care to elaborate?

You apparently believe in Darwinian evolution plus front-loaded evolution.

I'm not sure how you're defining Darwinian evolution.

So if you believe that a complete turnover of the genome is "likely enough to happen" given Darwinian evolution, then you believe that it is "likely enough to happen". In which case, where is your prediction? If you admit that given FLE, it is "likely enough to happen", then FLE has no prediction that it wouldn't happen.

No, because FLE has an objective, while non-telic evolution does not. Thus, non-telic evolution could stitch together a protein from non-coding segments of a genome, "just happening" to produce a new protein. In short, if FLE relies on the cobbling together of proteins to reach an objective, it is extremely unlikely that a specific, intended outcome will be produced, given that there are trillions of different possible configurations for pieces of DNA sequences. Non-telic evolution has no goal, so it can cobble stuff together, and stumble on novel functions. Meanwhile, FLE has an objective, and since there are many more possible functions than the FLE objective, it is vanishingly unlikely that the FLE objective will be found. To remedy this, you simply need to load the first cells with proteins that are nearby in sequence space to the objective (or are the objectives themselves).

We can't actually look at LUCA, can we?

Yes, we can. Not directly, of course, but indirectly.

You say you have an "either/or prediction". Well, how does that differ from the "either/or prediction" of Darwinism in terms of the phenomena that we can actually observe?

Well, Darwinian evolution "predicts" that either the LUCA will have a minimal genome, or the LUCA will have more than a minimal genome. Confirmation of any of these "predictions" is compatible with Darwinian evolution. It should be noted that something that predicts every scenario isn't really predicting anything, and this seems to be the case with non-telic evolution when it comes to the gene content of the LUCA. However, FLE is not compatible with the former scenario (that of a minimal genome). Thus, if we find that the LUCA actually did have a minimal genome, FLE will have been falsified. Which means its testable, and that it makes a specific prediction Darwinian evolution does not make.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 11 by Dr Adequate, posted 06-20-2012 11:36 AM Dr Adequate has responded

Replies to this message:
 Message 13 by Dr Adequate, posted 06-20-2012 1:02 PM Genomicus has responded
 Message 72 by Taq, posted 06-25-2012 12:39 PM Genomicus has responded

  
Dr Adequate
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Joined: 07-20-2006
Member Rating: 3.8


Message 13 of 172 (665977)
06-20-2012 1:02 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.

Now, it appears to me that you're saying "is not FLE consistent with the idea that calmodulin is also essential to prokaryotes?"

No, you're missing the point.

You can produce as many cases as you like of things that are essential to eukaryotes and merely useful to prokaryotes. Knock yourself out. It doesn't help

But is there anything in FLE that predicts that such a thing should exist? Would it not be compatible with FLE that everything that's essential to eukaryotes should also be essential to prokaryotes? Where does FLE rule that out?

Well, first of all, you said "turnover of genes;" I didn't think you meant a complete genome. And, come to think of it, the terminology "turnover of genes" is kinda vague in this context. Care to elaborate?

Well, suppose that prokaryotes started off with a certain set of genes, let's call them genes 1 ... 1000. Then gene 1001 arises by the mechanisms you suggest, and substitutes for gene 1 and displaces it, and then gene 1002 arises by the mechanisms you suggest, and substitutes for gene 2 and displaces it ... and so on until every gene in LUCA has been substituted by a gene arising by the mechanisms you postulate.

We can just imagine that happening. But is it likely?

I'm not sure how you're defining Darwinian evolution.

Evolution by known mechanisms: reproduction, mutation, natural selection, lateral gene transfer, recombination ... and so forth.

No, because FLE has an objective, while non-telic evolution does not. Thus, non-telic evolution could stitch together a protein from non-coding segments of a genome, "just happening" to produce a new protein. In short, if FLE relies on the cobbling together of proteins to reach an objective, it is extremely unlikely that a specific, intended outcome will be produced, given that there are trillions of different possible configurations for pieces of DNA sequences. Non-telic evolution has no goal, so it can cobble stuff together, and stumble on novel functions.

* sighs *

But will you make this clear?

You believe, do you not, in random mutation and in natural selection?

Therefore, you believe in "non-telic evolution" don't you?

So don't you believe that "Non-telic evolution [...] can cobble stuff together, and stumble on novel functions"?

To make it clear:

You apparently believe that Darwinian evolution happens. You apparently believe that Darwinian evolution allows for a complete turnover of genes, such that there would be no homology whatsoever between eukaryotes and prokaryotes. Well, in that case your model does not predict that there would be any homology between eukaryotes and prokaryotes, because your model incorporates Darwinian evolution.

You're trying to have your cake and eat it again. If Darwinism allows this sort of thing to happen, then your model also allows this sort of thing to happen, because your model permits Darwinian evolution.

Yes, we can. Not directly, of course, but indirectly.

But as I have pointed out before, our ability to look "indirectly" at LUCA depends crucially on accepting Darwinian evolution. That is the theory which allows us to infer LUCA. If we deny Darwinism, we have no basis on which to say what LUCA looked like.

Well, Darwinian evolution "predicts" that either the LUCA will have a minimal genome, or the LUCA will have more than a minimal genome. Confirmation of any of these "predictions" is compatible with Darwinian evolution. It should be noted that something that predicts every scenario isn't really predicting anything, and this seems to be the case with non-telic evolution when it comes to the gene content of the LUCA. However, FLE is not compatible with the former scenario (that of a minimal genome). Thus, if we find that the LUCA actually did have a minimal genome, FLE will have been falsified. Which means its testable, and that it makes a specific prediction Darwinian evolution does not make.

* sighs *

But again, we don't get to look at LUCA.

Let's look again at the data, according to you.

You claim that:

(1) There are certain proteins that are essential to eukaryotes.

(2) These proteins have homologues in prokaryotes such that prokaryotes would not actually drop dead if deprived of these proteins, but would be significantly disadvantaged if deprived of them.

How does FLE predict this state of affairs? How would I, or you, or anyone, reason from "LUCA was front-loaded" to this conclusion?

Edited by Dr Adequate, : No reason given.

Edited by Dr Adequate, : No reason given.


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

Replies to this message:
 Message 16 by Genomicus, posted 06-20-2012 1:31 PM Dr Adequate has responded

  
PaulK
Member
Posts: 12684
Joined: 01-10-2003
Member Rating: 2.7


(1)
Message 14 of 172 (665978)
06-20-2012 1:18 PM
Reply to: Message 9 by Genomicus
06-20-2012 10:31 AM


quote:

Would you care to elaborate on this? With a LUCA that has a minimal gene set, there's really no reason to suppose that complex life forms could arise.

You're looking at the wrong question. The real question is whether it is possible to engineer a minimal gene set which would encourage the formation of complex life. Given the size of the minimal gene set that you suggest, it seems that that is at least something that could plausibly be true.

quote:

You'd have to guarantee the rise of mitochondria before you can get complex life forms

That would seem pretty difficult to do by front-loading a single organism. Wouldn't it make a lot more sense to engineer eukaryotes with artificial mitochondria - if the engineers chose the symbiotic route at all?

quote:

What does horizontal gene transfer have to do with a minimal gene set? I.e., sure, this LUCA community could be transferring genes, but these genes would be part of the minimal gene set.

If the LUCA is a population of organisms exchanging genes it would be expected to have a greater diversity of genes than if it were a single individual organism. And thus far more likely to have more than a minimal genome (in aggregate).

quote:

A self-replicating RNA molecule could specify a protein sequence.

A notion that only makes sense if we assume a mechanism that can "read" that specification and produce a protein. Which means that we are talking about something more complex than a simple self-replicating molecule

quote:

I haven't found any convincing evidence that DNA evolved from RNA. I am aware of a number of papers on the subject, but I'll (hopefully!) discuss this evidence in another thread (so we don't get sidetracked here).

For the purposes of this discussion it is going to be better if you at least take the leading views of the origin of DNA as possibilities that have to be considered. To the best of my knowledge, the RNA World hypothesis is widely accepted among researchers into the origins of life.

quote:

Yes, but under the FLH, the LUCA isn't the product of considerable evolution. Maybe I'm not getting your point with this statement?

Of course, I was talking about the prevailing evolutionary view. Not that FLH makes any prediction on the matter at all.


This message is a reply to:
 Message 9 by Genomicus, posted 06-20-2012 10:31 AM Genomicus has responded

Replies to this message:
 Message 15 by jar, posted 06-20-2012 1:30 PM PaulK has not yet responded
 Message 19 by Genomicus, posted 06-20-2012 1:44 PM PaulK has responded

    
jar
Member
Posts: 28826
From: Texas!!
Joined: 04-20-2004
Member Rating: 3.1


Message 15 of 172 (665979)
06-20-2012 1:30 PM
Reply to: Message 14 by PaulK
06-20-2012 1:18 PM


Getting rid of bad stuff
Doesn't the prevailing view imply that those things that are seriously damaging to the chance of reproduction will get filtered out?

If so, doesn't the prevailing view imply that random mutations that are NOT seriously damaging to the chance of reproduction get retained?

If that is true, then doesn't the prevailing view predict that random mutations that may be useful in the future but not useful at the moment also do not get filtered out?

In that case, how does the FL model differ? How can you determine is something was intentional or just **** luck?


Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
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Replies to this message:
 Message 17 by Genomicus, posted 06-20-2012 1:35 PM jar has responded

  
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