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Author Topic:   Deep Homology and Front-loading
Genomicus
Member (Idle past 256 days)
Posts: 852
Joined: 02-15-2012


Message 31 of 172 (666036)
06-21-2012 10:48 AM
Reply to: Message 29 by PaulK
06-20-2012 4:39 PM


So long as it encourages the development of complex life forms, it doesn't matter what the genes code for. They need not be analogs of proteins used by known life.

True, but proteins that encourage the development of multicellularity and Metazoa etc. aren't likely to be found in a minimal gene set, because such genes only encode the bare necessity, which means there'd be no "front-loading." There's a difference between simply designing the first life forms and specifically engineering it such that it front-loads the appearance of complex life forms.

That is the very assertion that I am disagreeing with. Given 250 distinct proteins it is simply not clear that they would be insufficient for front loading, given the modest goals assumed.

Yes, but you're forgetting that these 250 distinct genes would also have to be part of a minimal gene set. So, you'd need to get one of the genes necessary say, for the Krebs cycle, and engineer it such that it actually does nudge evolution in the direction of complex life forms. Or you could take SecY, which AFAIK is a necessary protein for life, and engineer it so that it biases evolution in favor of multicellular life. But then, once you do that, there's no reason to suspect that we'd have something that looks like SecY anymore. And, unless you have evidence suggesting otherwise, there's nothing inherent in SecY that would bias evolution towards the development of complex life forms, is there?


This message is a reply to:
 Message 29 by PaulK, posted 06-20-2012 4:39 PM PaulK has responded

Replies to this message:
 Message 36 by PaulK, posted 06-21-2012 1:16 PM Genomicus has responded

  
Genomicus
Member (Idle past 256 days)
Posts: 852
Joined: 02-15-2012


Message 32 of 172 (666038)
06-21-2012 10:59 AM
Reply to: Message 30 by Dr Adequate
06-20-2012 9:44 PM


No, that's where you ducked my point.

Elaborate, if you please.

For example, what's to stop LUCA from having two parallel sets of genes, one for prokaryotes and one for eukaryotes?

I already explained this: we have an either/or prediction in this case. Under front-loading, either the LUCA has more than a minimal genome, or LUCA has two parallel gene sets.

Darwinian evolutionary models also generate either/or predictions. For example, the specific evolutionary hypothesis that the bacterial flagellar system arose from the type III secretory system predicts that either the type III secretory system is a pre-cursor to the flagellum and thus pre-dates the origin of the flagellum, or both systems share a common ancestral system that is essentially a type III secretory system.

Okay, I think I understand what you mean with this one. All FLE predictions (that I am aware of) include things that are possible under "Darwinism." However, there are some possible scenarios in Darwinian evolution that isn't allowed by FLE.

Which? Mutation still happens, doesn't it? And natural selection? And lateral gene transfer? And recombination?

Anything that can happen under Darwinian mechanisms can happen under the FLE hypothesis, since it does not deny the existence of those mechanisms.

You will note that I said "there are some possible scenarios in Darwinian evolution that isn't allowed by FLE." At this point, I wasn't talking about mechanisms. I was talking about scenarios. And one scenario that is perfectly acceptable under Darwinian evolution is that the LUCA had only a minimal genome. Such a scenario is not, however, compatible with FLE.

False.

Really? Why?

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 30 by Dr Adequate, posted 06-20-2012 9:44 PM Dr Adequate has responded

Replies to this message:
 Message 33 by Dr Adequate, posted 06-21-2012 11:14 AM Genomicus has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


(1)
Message 33 of 172 (666039)
06-21-2012 11:14 AM
Reply to: Message 32 by Genomicus
06-21-2012 10:59 AM


Elaborate, if you please.

Well, in that you didn't actually answer it.

I already explained this: we have an either/or prediction in this case. Under front-loading, either the LUCA has more than a minimal genome, or LUCA has two parallel gene sets.

Darwinian evolutionary models also generate either/or predictions.

True. But your claim was that (in this respect) FLE had greater specificity than Darwinism. If you now admit that FLE could have been done so that there'd be no homology at all between eukaryote and prokaryote proteins, then your point has vanished. We might see homology, we might see none. Or we could see any degree of homology, depending on how much overlap there was between the two gene sets. Also, the overlap could have only included absolutely essential proteins. Your "either/or prediction" is that in the case of any given protein, either we'll see homology between eukaryotes and prokaryotes or we won't. That seems to cover everything. Adieu predictive specificity.

You will note that I said "there are some possible scenarios in Darwinian evolution that isn't allowed by FLE." At this point, I wasn't talking about mechanisms.

Ultimately, this seems to be a distinction without a difference. Darwinian evolution allows every scenario that is allowed by the mechanisms. If you admit the mechanisms, you admit the possibility of every such scenario.

Really? Why?

Well, we can't see LUCA. You have no reason to suppose that, just because the histone genes are not absolutely essential to modern prokaryotes, they were not absolutely essential to LUCA. Maybe in this respect it was more like a eukaryote.

(BTW, I have no idea where you're getting the information about these proteins. Presumably this came up on another thread. Could I have a reference please? Thank you.)

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 32 by Genomicus, posted 06-21-2012 10:59 AM Genomicus has responded

Replies to this message:
 Message 34 by Genomicus, posted 06-21-2012 11:54 AM Dr Adequate has responded

  
Genomicus
Member (Idle past 256 days)
Posts: 852
Joined: 02-15-2012


Message 34 of 172 (666042)
06-21-2012 11:54 AM
Reply to: Message 33 by Dr Adequate
06-21-2012 11:14 AM


Well, in that you didn't actually answer it.

Is this your question?

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?

If so, then you might want to elaborate. Because reading it from here, it looks like you're basically saying "is there anything in common descent that predicts ERVs should exist? Would it not be compatible with common descent that ERVs do not exist? Where does common descent rule that out?" Ignoring, of course, the simple observation that ERVs do in fact exist, and from this observation we can generate a prediction.

True. But your claim was that (in this respect) FLE had greater specificity than Darwinism. If you now admit that FLE could have been done so that there'd be no homology at all between eukaryote and prokaryote proteins, then your point has vanished. We might see homology, we might see none. Or we could see any degree of homology, depending on how much overlap there would be between the two gene sets. Also, the overlap could have only included absolutely essential proteins. Your "either/or prediction" is that in the case of any given protein, either we'll see homology between eukaryotes and prokaryotes or we won't. That seems to cover everything. Adieu predictive specificity.

A couple of points:

1. The same thing could be said for Darwinian evolution. There's nothing in Darwinian evolution preventing the LUCA from having parallel gene sets, is there?

2. More importantly (I suppose a case could be made that it's unlikely from a Darwinian standpoint to have parallel gene sets in LUCA), the predictive value of the FLE does not lie only in the homology aspect, but in the fact that this homology is shared with prokaryotic proteins that are unnecessary for life.

So, we could summarize the FLE predictions in this manner:

a. Either crucial proteins in eukaryotes will share deep homology with prokaryotic proteins that are functional but unnecessary, and phylogenies will show that prokaryotes and eukaryotes are related,

b. Or phylogenies will indicate that eukaryotes and prokaryotes arose independently.

Simply put, FLE predicts that either (a) eukaryotes and prokaryotes are evolutionarily related - in which case, the prediction that key eukaryotic proteins will share deep homology with prokaryotic proteins naturally follows, or (b) eukaryotes emerged independently from prokaryotes.

Confirmation of either of these two general predictions wouldn't boost the case for front-loading because non-teleological evolution also makes those predictions. However, from these predictions we can glean other predictions, predictions that are made exclusively by the front-loading hypothesis, and thus confirmation of these predictions is what we're looking for.

If you admit the mechanisms, you admit the possibility of every such scenario.

All the Darwinian scenarios are possible, but that doesn't mean they actually happened in the past. And FLE requires that the possibility of the LUCA having only a minimal genome is not actually what happened.

Well, we can't see LUCA. You have no reason to suppose that, just because the histone genes are not absolutely essential to modern prokaryotes, they were not absolutely essential to LUCA. Maybe in this respect it was more like a eukaryote.

Do you agree that the basic prokaryotic cell plan does not require all the proteins necessary for the eukaryote and multicellular life? If so, then you must admit that it is possible that the LUCA did not require eukaryotic proteins. That this possibility was not manifested, however, is what front-loading argues. In other words, under non-teleological evolution, it is possible for the LUCA to have been structured such that it did not require key eukaryotic proteins. But if this is found to be the case, and moreover it is discovered that the LUCA did not in fact have key eukaryotic proteins, FLE is effectively falsified? Make sense?

BTW, I have no idea where you're getting the information about these proteins.

I'm not quite sure what information you're referring to.

For the record: after plowing through some literature, I discovered that histones actually aren't universally required by eukaryotes, being absent in a number of fungi (the paper I read was from 1971 though, so things very possibly have changed since then).


This message is a reply to:
 Message 33 by Dr Adequate, posted 06-21-2012 11:14 AM Dr Adequate has responded

Replies to this message:
 Message 35 by Dr Adequate, posted 06-21-2012 12:50 PM Genomicus has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 35 of 172 (666047)
06-21-2012 12:50 PM
Reply to: Message 34 by Genomicus
06-21-2012 11:54 AM


If so, then you might want to elaborate. Because reading it from here, it looks like you're basically saying "is there anything in common descent that predicts ERVs should exist? Would it not be compatible with common descent that ERVs do not exist? Where does common descent rule that out?" Ignoring, of course, the simple observation that ERVs do in fact exist, and from this observation we can generate a prediction.

Given that ERVs exist, we can predict something else, namely the pattern of their distribution. But what you're doing is given that histone homologues exist in prokaryotes, you're predicting the existence of histone homologues in prokaryotes.

It's just the same as the giraffophile designer I was talking about on the other thread. Given the hypothesis of a designer, we can't predict giraffes. So you throw in the premise that the designer wanted to make giraffes. Hurrah, now we can predict giraffes! Such specificity the hypothesis has! Yay!

In the same way, the designer might have made all sorts of decisions about what LUCA should be like. You need to add onto the FLE hypothesis the additional ad hoc supposition that the front-loading was done so as to produce the outcome we see. And then, lo and behold, your hypothesis predicts the outcome we see.

I could do the same with Darwinism. Let's add to the known mechanisms of Darwinism the hypothesis that the sequence of mutations and the selective pressures were just such as to produce the observed outcome. Whoopidie-do-dah, now I have just as much predictive specificity as you do. But I've done it the same way --- by adding in, ad hoc, extra hypotheses that fit my theory to the facts but do not follow from my theory.

Is this your question?

The question was: "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?"

Now, your solution seems to be to add in, ad hoc, the hypothesis that the designer didn't design things that way. Also apparently he likes giraffes but not unicorns.

1. The same thing could be said for Darwinian evolution. There's nothing in Darwinian evolution preventing the LUCA from having parallel gene sets, is there?

2. More importantly (I suppose a case could be made that it's unlikely from a Darwinian standpoint to have parallel gene sets in LUCA), the predictive value of the FLE does not lie only in the homology aspect, but in the fact that this homology is shared with prokaryotic proteins that are unnecessary for life.

Except that it doesn't predict that, does it?

To see that this is so, consider the case in which the homologous proteins were in fact all essential. Would that be cause for us to say: "Front loading definitely didn't occur, then. If there was a designer, there would definitely be inessential proteins in prokaryotes homologous to essential proteins in eukaryotes. We now know for certain that life had no designer and that LUCA was in no way a product of intelligence"?

No, of course not. It would give us no warrant to say that whatsoever. In which case it is not a prediction of FLE or of any other form of ID that such a homology should exist. If seeing ~X does not falsify theory T, then theory T does not predict X.

Do you agree that the basic prokaryotic cell plan does not require all the proteins necessary for the eukaryote and multicellular life? If so, then you must admit that it is possible that the LUCA did not require eukaryotic proteins. That this possibility was not manifested, however, is what front-loading argues. In other words, under non-teleological evolution, it is possible for the LUCA to have been structured such that it did not require key eukaryotic proteins. But if this is found to be the case, and moreover it is discovered that the LUCA did not in fact have key eukaryotic proteins, FLE is effectively falsified? Make sense?

I can't make sense of this as an answer to what I wrote.

My point was this. You suppose that LUCA had inessential proteins. You point to histones as an example of this. That LUCA had histone-like proteins you (rightly) deduce from the fact that they (or their homologues) are present in both prokaryotes and eukaryotes. But you also seem to be claiming that we know they were inessential to LUCA because we know that they are inessential to modern prokaryotes. But that is not a legitimate deduction. In this respect, LUCA might have had more resemblance to a modern eukaryote than to a modern prokaryote. Or not, of course. Who can say?

I'm not quite sure what information you're referring to.

About the role played by histone homologues in modern prokaryotes.


This message is a reply to:
 Message 34 by Genomicus, posted 06-21-2012 11:54 AM Genomicus has responded

Replies to this message:
 Message 38 by Genomicus, posted 06-21-2012 4:05 PM Dr Adequate has responded

  
PaulK
Member
Posts: 15554
Joined: 01-10-2003
Member Rating: 3.1


Message 36 of 172 (666048)
06-21-2012 1:16 PM
Reply to: Message 31 by Genomicus
06-21-2012 10:48 AM


quote:

True, but proteins that encourage the development of multicellularity and Metazoa etc. aren't likely to be found in a minimal gene set, because such genes only encode the bare necessity, which means there'd be no "front-loading." There's a difference between simply designing the first life forms and specifically engineering it such that it front-loads the appearance of complex life forms.

That's the assumption that I am challenging. Given that we know that proteins may have multiple uses, plus the possibility of near variants having still more uses 250 different proteins should give you quite a range of options to encourage the development of complex life.

quote:

Yes, but you're forgetting that these 250 distinct genes would also have to be part of a minimal gene set.

No, I'm not.

quote:

So, you'd need to get one of the genes necessary say, for the Krebs cycle, and engineer it such that it actually does nudge evolution in the direction of complex life forms. Or you could take SecY, which AFAIK is a necessary protein for life, and engineer it so that it biases evolution in favor of multicellular life. But then, once you do that, there's no reason to suspect that we'd have something that looks like SecY anymore. And, unless you have evidence suggesting otherwise, there's nothing inherent in SecY that would bias evolution towards the development of complex life forms, is there?

I'm not sure that I understand your argument here. Obviously we can't require that the front-loaded gene set would necessarily do things the way earthly life does them - that would be begging the question. So obviously we don't have to have something looking like SecY nor do we have to have the precursors to the Krebs cycle. All we need is a set of proteins that will work as a minimal life form while strongly encouraging the development of more complex life forms. You say that it can't be done, not even by your hypothetical designers, with their unknown capabilities. BUt I'm still waiting to see a real reason.


This message is a reply to:
 Message 31 by Genomicus, posted 06-21-2012 10:48 AM Genomicus has responded

Replies to this message:
 Message 39 by Genomicus, posted 06-21-2012 4:18 PM PaulK has responded

  
bluegenes
Member (Idle past 792 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 37 of 172 (666053)
06-21-2012 2:15 PM
Reply to: Message 26 by Genomicus
06-20-2012 3:24 PM


I predict "No LUCA"!
Genomicus writes:

There are many problems and challenges facing the FL hypothesis. It's a shaky hypothesis at the moment.

Yes. For one thing, Genomicus, I don't think your predictions make sense on more than one level. Surely the best way to front load a planet "stacking the deck" in favour of multicellular life would be to include eukaryotes along with prokaryotes, and to have as many of each as possible. Also, if there were forms of multicellular life that could be engineered to live and photosynthesise in the early seas, then those would be included. So, a reasonable prediction might seem to be "no LUCA" on such a planet. But there are problems with that also, because we know nothing of the designers, the processes they used, and their technical capabilities.

I think what you're doing with your predictions is a bit like one of our "sideloading" I.D. types suggesting a hypothesis to explain turtles after having observed their existence. "The designer wanted and created turtles" requires and predicts turtles, whereas for evolutionary theory they are compatible, but not a prediction. You can surely see what's wrong with this. A general sideloading hypothesis doesn't actually predict turtles at all. Indeed, I'm not aware of anything specific that the general sideloading idea predicts.

Can the general idea of front loading make any specific predictions when we know nothing about actual process and nothing about the level of technical knowledge the designers had?


This message is a reply to:
 Message 26 by Genomicus, posted 06-20-2012 3:24 PM Genomicus has responded

Replies to this message:
 Message 41 by Genomicus, posted 06-21-2012 4:38 PM bluegenes has responded

  
Genomicus
Member (Idle past 256 days)
Posts: 852
Joined: 02-15-2012


Message 38 of 172 (666055)
06-21-2012 4:05 PM
Reply to: Message 35 by Dr Adequate
06-21-2012 12:50 PM


Given that ERVs exist, we can predict something else, namely the pattern of their distribution. But what you're doing is given that histone homologues exist in prokaryotes, you're predicting the existence of histone homologues in prokaryotes.

No, I'm not. It goes like this: given that protein X is required for eukaryotic existence, I predict that protein X likewise exists in prokaryotes, which is expected from front-loading. So, no, it's not a giraffophile designer. I'm using histone as an example because we know it's present in both eukaryotes and prokaryotes. But there are a number of important eukaryotic proteins that we only find in eukaryotes (e.g., Pax-6), but - given front-loading - I expect we'll eventually find functional homologs in prokaryotes.

Now, how does the non-teleological model explain the origin of Pax-6? The same way it explains the origin of nylonase or T-urf13, and the like. Or maybe small blocks of functional protein modules were randomly mixed and matched, "just happening" to result in Pax-6. So we really wouldn't predict deep homology (i.e., statistically significant similarity) of Pax-6 with prokaryotic proteins under the non-teleological model.

The question was: "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?"

Now, your solution seems to be to add in, ad hoc, the hypothesis that the designer didn't design things that way. Also apparently he likes giraffes but not unicorns.

Sigh. I keep answering this question. Is it true or is it false that proteins required by eukaryotes are not required for the existence of carbon-based life (more specifically, DNA-based life)? If that is true, then we have our FLE prediction: proteins universally required by eukaryotes will share deep homology with proteins in prokaryotes that are not required for the existence of life.

To see that this is so, consider the case in which the homologous proteins were in fact all essential. Would that be cause for us to say: "Front loading definitely didn't occur, then. If there was a designer, there would definitely be inessential proteins in prokaryotes homologous to essential proteins in eukaryotes. We now know for certain that life had no designer and that LUCA was in no way a product of intelligence"?

I think you're missing a crucial point. You say "consider the case in which the homologous proteins were in fact all essential." I assume by that you mean that these proteins are essential to both eukaryotes and prokaryotes. But it is an objective fact that eukaryotes require proteins that are not required by all types of prokaryotic life forms. And from here is where we get our prediction.

My point was this. You suppose that LUCA had inessential proteins. You point to histones as an example of this. That LUCA had histone-like proteins you (rightly) deduce from the fact that they (or their homologues) are present in both prokaryotes and eukaryotes. But you also seem to be claiming that we know they were inessential to LUCA...

No, that's not the point. Whether they are inessential to LUCA specifically is not relevant. What's relevant is whether these proteins are essential to all prokaryotic life forms.

Again, I'll condense the prediction down to this:

1. FLE involves loading the first genomes with proteins that will later be used by eukaryotes - proteins that are required for the rise of eukaryotes (e.g., calmodulin), but are not required for the existence of prokaryotes.

2. FLE therefore predicts that eukaryotic proteins will share deep homology with proteins in prokaryotes that are functional but unnecessary for the existence of prokaryotic life forms as a whole, regardless of whether for some reason or another LUCA required these proteins.


This message is a reply to:
 Message 35 by Dr Adequate, posted 06-21-2012 12:50 PM Dr Adequate has responded

Replies to this message:
 Message 40 by Dr Adequate, posted 06-21-2012 4:37 PM Genomicus has responded

  
Genomicus
Member (Idle past 256 days)
Posts: 852
Joined: 02-15-2012


Message 39 of 172 (666056)
06-21-2012 4:18 PM
Reply to: Message 36 by PaulK
06-21-2012 1:16 PM


That's the assumption that I am challenging. Given that we know that proteins may have multiple uses, plus the possibility of near variants having still more uses 250 different proteins should give you quite a range of options to encourage the development of complex life.

And:

All we need is a set of proteins that will work as a minimal life form while strongly encouraging the development of more complex life forms. You say that it can't be done, not even by your hypothetical designers, with their unknown capabilities. But I'm still waiting to see a real reason.

Actually, PaulK, the burden of proof is on you to provide evidence for the assertion that one can design a gene set that both functions as part of the minimum genome and also encourages the development of Metazoa etc. (incidentally, such a strategy for front-loading would be a pretty clumsy design since with only 250 genes you'd have to front-load the appearance of a whole bunch of proteins necessary for the rise of eukaryotes and Metazoa).

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 36 by PaulK, posted 06-21-2012 1:16 PM PaulK has responded

Replies to this message:
 Message 42 by PaulK, posted 06-21-2012 5:05 PM Genomicus has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 40 of 172 (666057)
06-21-2012 4:37 PM
Reply to: Message 38 by Genomicus
06-21-2012 4:05 PM


No, I'm not. It goes like this: given that protein X is required for eukaryotic existence, I predict that protein X likewise exists in prokaryotes, which is expected from front-loading.

But that isn't a prediction of FLE as such, is it? If prokaryotes lacked histone homologues, you'd just shrug and say that they dropped out of the prokaryote lineage just as (I presume you would have to say) the ability to synthesize peptidoglycan dropped out of the eukaryote lineage.

If it wouldn't damage FLE if they weren't there, then FLE doesn't predict that they'll be there.

Sigh. I keep answering this question.

That's as may be; but you keep getting the answer wrong.

Is it true or is it false that proteins required by eukaryotes are not required for the existence of carbon-based life (more specifically, DNA-based life)? If that is true, then we have our FLE prediction: proteins universally required by eukaryotes will share deep homology with proteins in prokaryotes that are not required for the existence of life.

Well, no. You've already admitted that FLE is consistent with having two completely separate suites of genes, one for eukaryotes, one for prokaryotes. In which case, FLE does not predict any homology.

I think you're missing a crucial point. You say "consider the case in which the homologous proteins were in fact all essential." I assume by that you mean that these proteins are essential to both eukaryotes and prokaryotes. But it is an objective fact that eukaryotes require proteins that are not required by all types of prokaryotic life forms. And from here is where we get our prediction.

Or: "I think you're missing a crucial point. You say "consider the case in which giraffes did not exist." But it is an objective fact that giraffes exist. And from here is where we get our prediction." Quite so. You got your "prediction" from seeing what was true and then retconning your hypothesis.

Look, it's very simple. It would be consistent with front-loading that all the homologous proteins were essential to both eukaryotes and prokaryotes. The world isn't like that, but there would be nothing about FLE as such that would prevent the world from being like that. In which case FLE does not predict that the world is not like that.

You keep stumbling on this point. Obviously if you constrain your hypothesis with reference to what you know post hoc to be true, then you can get it to predict true things. But it goes round in a circle. "FLE could have produced that. But we don't observe that. Therefore, FLE didn't produce that. Therefore the front-loading was done in such a way as not to produce that. Therefore FLE predicts that we won't see that."

As I've pointed out, I could do exactly the same thing. "Darwinism could have produced unicorns. But there are no unicorns. Therefore the mutation and selection events were such as to produce no unicorns. Therefore, Darwinism predicts an absence of unicorns". But Darwinism as such predicts no such thing. I had to throw in some extra hypotheses which were tailor-made to account for the absence of unicorns --- an ad hoc hypothesis to explain a post hoc observation.


This message is a reply to:
 Message 38 by Genomicus, posted 06-21-2012 4:05 PM Genomicus has responded

Replies to this message:
 Message 44 by Genomicus, posted 06-21-2012 6:31 PM Dr Adequate has responded

  
Genomicus
Member (Idle past 256 days)
Posts: 852
Joined: 02-15-2012


Message 41 of 172 (666058)
06-21-2012 4:38 PM
Reply to: Message 37 by bluegenes
06-21-2012 2:15 PM


Re: I predict "No LUCA"!
For one thing, Genomicus, I don't think your predictions make sense on more than one level. Surely the best way to front load a planet "stacking the deck" in favour of multicellular life would be to include eukaryotes along with prokaryotes, and to have as many of each as possible. Also, if there were forms of multicellular life that could be engineered to live and photosynthesise in the early seas, then those would be included. So, a reasonable prediction might seem to be "no LUCA" on such a planet.

What do you mean by "no LUCA"? Do you mean that modern life would have evolved from a pool of different species? I have no problem with that, and I don't think the scientific evidence does either.

Bacteria are by far the best terra-formers, so there's a good reason why they'd be in the original pool. Simple eukaryotes (i.e., "eukaryotes" that had not yet undergone the endosymbiosis event) may have been present as well.

I think what you're doing with your predictions is a bit like one of our "sideloading" I.D. types suggesting a hypothesis to explain turtles after having observed their existence.

Well, we've got a lot of key proteins in eukaryotes that are not found in prokaryotes. So we can actually make a prediction from FLE that isn't ad hoc, namely that we'll find homologs of these proteins in prokaryotes. Note that Darwinian evolution doesn't really predict this (I explain the rationale for this statement in my latest reply to Dr Adequate).

Can the general idea of front loading make any specific predictions when we know nothing about actual process and nothing about the level of technical knowledge the designers had?

Well, in the first place I'm taking supernatural, omnipotent designers off the table.


This message is a reply to:
 Message 37 by bluegenes, posted 06-21-2012 2:15 PM bluegenes has responded

Replies to this message:
 Message 43 by Dr Adequate, posted 06-21-2012 5:25 PM Genomicus has responded
 Message 45 by bluegenes, posted 06-21-2012 7:28 PM Genomicus has responded
 Message 47 by Dr Adequate, posted 06-21-2012 8:51 PM Genomicus has not yet responded

  
PaulK
Member
Posts: 15554
Joined: 01-10-2003
Member Rating: 3.1


Message 42 of 172 (666061)
06-21-2012 5:05 PM
Reply to: Message 39 by Genomicus
06-21-2012 4:18 PM


quote:

Actually, PaulK, the burden of proof is on you to provide evidence for the assertion that one can design a gene set that both functions as part of the minimum genome and also encourages the development of Metazoa etc. (incidentally, such a strategy for front-loading would be a pretty clumsy design since with only 250 genes you'd have to front-load the appearance of a whole bunch of proteins necessary for the rise of eukaryotes and Metazoa).

No, I don't have to support assertions that I haven't actually made.

But to support the point I DID make:

The hypothetical designers would be free to choose any set of proteins that would work. They would, for instance be completely free to choose completely unrelated proteins. They would NOT be limited to using the proteins used by Earthly life.

Proteins are versatile and can be and are co-opted for different uses.

Mutation may enable other functions in proteins.

250 proteins is quite a large number.

Taking these considerations into account it seems to me that the hypothetical designers could do a far better job of enabling the development of complex organisms using a simple 250 gene single-celled organism than evolution could.
(Which does raise the question of how you could consider the evolution of modern life plausible at all - according to you it would have to start with something greatly inferior to something you consider inadequate).

But let us get to the real point. f

For your argument to be truthful you need a consistent standard for "prediction".

That is you need a satisfactory standard that YOUR views satisfy, while the arguments from the evolutionary side do not.

That is rather difficult when your view is just an assumption that seems intuitive.

So, do you have a stronger argument that actually deals with the issues, or are you just going to evade the problem ?


This message is a reply to:
 Message 39 by Genomicus, posted 06-21-2012 4:18 PM Genomicus has responded

Replies to this message:
 Message 51 by Genomicus, posted 06-21-2012 10:17 PM PaulK has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 43 of 172 (666064)
06-21-2012 5:25 PM
Reply to: Message 41 by Genomicus
06-21-2012 4:38 PM


Ubiquitin
Well, we've got a lot of key proteins in eukaryotes that are not found in prokaryotes. So we can actually make a prediction from FLE that isn't ad hoc, namely that we'll find homologs of these proteins in prokaryotes.

Very well.

Consider ubiquitin, a highly conserved protein found in all eukaryotes, which marks down proteins for proteasomal degradation. This article lists it among the proteins unique to eukaryotes. (Later on, we might look at some of the others.)

Now, according to WP: "The proteasomal degradation pathway is essential for many cellular processes, including the cell cycle, the regulation of gene expression, and responses to oxidative stress." It seems, then, that ubiquitin is indispensable to eukaryotes.

And yet according to this article: "No ubiquitin homolog has been found in prokaryotic genomes sequenced thus far".

Prokaryotes instead use a protein known as prokaryotic ubiquitin-like protein, which is functionally analogous but non-homologous.

So, if you're right about what FLE predicts, then goodnight FLE. But wait! I can just hear you now. "It is a matter of objective fact that ubiquitin has no prokaryotic homologue. Therefore, FLE doesn't predict that there should be one ..."


This message is a reply to:
 Message 41 by Genomicus, posted 06-21-2012 4:38 PM Genomicus has responded

Replies to this message:
 Message 52 by Genomicus, posted 06-21-2012 10:26 PM Dr Adequate has responded

  
Genomicus
Member (Idle past 256 days)
Posts: 852
Joined: 02-15-2012


Message 44 of 172 (666072)
06-21-2012 6:31 PM
Reply to: Message 40 by Dr Adequate
06-21-2012 4:37 PM


But that isn't a prediction of FLE as such, is it? If prokaryotes lacked histone homologues, you'd just shrug and say that they dropped out of the prokaryote lineage just as (I presume you would have to say) the ability to synthesize peptidoglycan dropped out of the eukaryote lineage.

I find it suspicious that when I said "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" you made no issue of it. Yet, now that we are discussing FLE you're bringing up the possibility of homologs being lost in various lineages.

In other words, if you want to bring up that aspect of all of this, then you've got to admit that Darwinian evolution actually doesn't predict that the bacterial flagellar components will share homology with more ancient systems. Kewl.

Why would you have to admit this? Precisely because these homologous counterparts could have been loss over deep time, erasing any evidence of pre-cursor homologs to the bacterial flagellum system. You sure you want to go down that path, Dr Adequate?

Let me put it another way. Go ahead and argue that since proteins can be lost over deep time, FLE actually doesn't predict that key eukaryotic proteins will share homology with prokaryotic proteins. But, at the same time, you have to be consistent and admit therefore that any homology the flagellar system shares with more ancient systems isn't evidence for the evolution of the flagellum, precisely because, by your argument, evolution does not predict this homology.

I'll respond to your other points later.


This message is a reply to:
 Message 40 by Dr Adequate, posted 06-21-2012 4:37 PM Dr Adequate has responded

Replies to this message:
 Message 46 by Dr Adequate, posted 06-21-2012 8:49 PM Genomicus has responded

  
bluegenes
Member (Idle past 792 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 45 of 172 (666075)
06-21-2012 7:28 PM
Reply to: Message 41 by Genomicus
06-21-2012 4:38 PM


Re: I predict "No LUCA"!
Genomicus writes:

What do you mean by "no LUCA"? Do you mean that modern life would have evolved from a pool of different species? I have no problem with that, and I don't think the scientific evidence does either.

I'm suggesting that, on any hypothetical planet that was front loaded with the deck stacked in favour of multicellular life, the equivalent of eukaryotes and whatever simple multicellular organisms that could survive should be there.

Geno writes:

Bacteria are by far the best terra-formers, so there's a good reason why they'd be in the original pool. Simple eukaryotes (i.e., "eukaryotes" that had not yet undergone the endosymbiosis event) may have been present as well.

Why take the chance of key endosymbiotic events taking place? Intelligent deck-stacking doesn't need to. If you want such things to arrive, make them. I'm suggesting that, on my hypothetical planet, the array of life that might have existed here one to two billion years ago would have appeared immediately as the first life on that planet (tailored to its circumstances, of course).

Genomicus writes:

Well, we've got a lot of key proteins in eukaryotes that are not found in prokaryotes. So we can actually make a prediction from FLE that isn't ad hoc, namely that we'll find homologs of these proteins in prokaryotes. Note that Darwinian evolution doesn't really predict this (I explain the rationale for this statement in my latest reply to Dr Adequate).

But why does FLE predict this? As we've agreed, the frontloaders could've made their own eukaryotes. Also, as Darwinian processes take place after the frontloading, then why should we expect all important proteins in modern eukaryotes to have homologues in modern prokaryotes even if the FrontLoaders didn't think of making their own eukaryotes?

Genomicus writes:

Well, in the first place I'm taking supernatural, omnipotent designers off the table.

Me too. For an evidence based case, it's best to assume biological aliens. However, as I suggested, this still makes it hard to make predictions when we know nothing of their technical ability and the processes used. Intuitively, it does at least give us a reason why, being multicellular life forms themselves, they might be interested in the kind of project you're suggesting!

Of course, critics of your hypothesis might wonder, if it took 4,000,000,000 yrs for intelligent biologists to emerge from this "stacked-deck" biosphere, how long it took for them to emerge on their "unstacked-deck" planet.

Maybe we can at least get a Sci-fi novel out of this, if nothing else.

Edited by bluegenes, : missing word


This message is a reply to:
 Message 41 by Genomicus, posted 06-21-2012 4:38 PM Genomicus has responded

Replies to this message:
 Message 66 by Genomicus, posted 06-22-2012 10:16 PM bluegenes has responded

  
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