Deep Homology and Front-loading

Message 3 of 172 (665929) 06-19-2012 9:36 PM

Reply to: Message 1 by Genomicus 06-19-2012 2:46 PM

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.

Message 5 of 172 (665931) 06-19-2012 9:54 PM

Reply to: Message 4 by Genomicus 06-19-2012 9:50 PM

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.

Message 8 of 172 (665946) 06-20-2012 5:18 AM

Reply to: Message 6 by Genomicus 06-19-2012 10:07 PM

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?

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

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.

Message 11 of 172 (665969) 06-20-2012 11:36 AM

Reply to: Message 10 by Genomicus 06-20-2012 10:53 AM

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.

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.

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.

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.

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

Reply to: Message 12 by Genomicus 06-20-2012 11:59 AM

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, 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?

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

* 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.

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.

* 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.

Message 23 of 172 (665987) 06-20-2012 2:05 PM

Reply to: Message 16 by Genomicus 06-20-2012 1:31 PM

* sighs, bangs head against desk *

You don't seem to have got the hang of this whole prediction thing.

Look, suppose you said that giraffes confirm FLE because FLE predicts giraffes.

And then I come back saying: "But is there anything in FLE that predicts that giraffes should exist? Would it not be compatible with FLE that there should be no giraffes? Where does FLE rule that out?"

And then you riposte with: "Huh? It's not FLE that rules that out, it's basic observations that rule it out."

These "basic observations", of course, being that we can see giraffes.

Don't you see that in order for a theory to predict X, it has to rule out not-X? You can't say: "My theory predicts X ... OK, I grant you it doesn't rule out not-X ... but we can see that X". Well in that case your theory hasn't made a prediction. We've just seen X.

But unless you claim that it is a prediction of Darwinism that there should most likely have been a complete genomic turnover, then you must acknowledge that it is a prediction of Darwinism that there should be homologies.

But if you admit that Darwinian evolution can and does take place, then none of your predictions can be based on the premise that it can't and it didn't.

Therefore, you must admit that FLE permits anything that ToE permits. In which case FLE can never be more specific in its predictions than ToE.

Yeah, all known mechanisms, plus common descent.

I would be the first to admit that "Darwinism" is not the best word for that, but for want of a better, I'll go with that.

No. That is not the definition of front-loading.

If you were clear enough, then I think that you yourself would reject your own ideas.

Edited by Dr Adequate, : No reason given.

Message 24 of 172 (665990) 06-20-2012 2:37 PM

Reply to: Message 23 by Dr Adequate 06-20-2012 2:05 PM

You are the counsel for the prosecution.

You: If John stole the money, then the money would be missing. The money is missing. Therefore John stole the money.

Me: But that doesn't show that Tom or Dick or Harry didn't steal the money. To pin the crime definitively on John, you'd have to show that if John didn't steal the money, then the money would still be in the till.

You: But it is a matter of basic observation that the money is not in the till!

That doesn't get us anywhere. It is common ground that someone stole the money, and that it is therefore missing. But in order to pin the crime on John you have to prove that if it wasn't for John the money wouldn't be missing. Otherwise the fact that the money is missing isn't evidence against John.

Message 27 of 172 (665999) 06-20-2012 4:01 PM

Reply to: Message 25 by Genomicus 06-20-2012 3:16 PM

And I should like you to answer that point rather than another one.

Where does it do that?

But so far as I can see, you believe in both.

In which case your range of predictions includes anything that Darwinism says is possible, and so cannot have greater specificity than Darwinism.

But, one more time ...

WE CAN'T SEE LUCA.

Any predictions have to be about what we can see in the present. If you admit Darwinian mechanisms, then anything that Darwinian mechanisms allow us to see in the present is allowed by your hypothesis. Which therefore cannot be more specific in its predictions than Darwinism.

No. That is not part of the definition of front-loaded evolution.

Edited by Dr Adequate, : No reason given.

Message 30 of 172 (666018) 06-20-2012 9:44 PM

Reply to: Message 28 by Genomicus 06-20-2012 4:33 PM

No, that's where you ducked my point.

But that is still not an answer to my question.

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

Now, please note once more that it is not to the point to observe that this the evidence we have now shows that this didn't happen --- in order for there to be a prediction, you need to show that the very concept of FLE precludes doing it that way.

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.

False.

Message 33 of 172 (666039) 06-21-2012 11:14 AM

Reply to: Message 32 by Genomicus 06-21-2012 10:59 AM

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

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.

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.

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.

Message 35 of 172 (666047) 06-21-2012 12:50 PM

Reply to: Message 34 by Genomicus 06-21-2012 11:54 AM

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.

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.

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.

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?

About the role played by histone homologues in modern prokaryotes.

Message 40 of 172 (666057) 06-21-2012 4:37 PM

Reply to: Message 38 by Genomicus 06-21-2012 4:05 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.

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

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

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.

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.

Message 43 of 172 (666064) 06-21-2012 5:25 PM

Reply to: Message 41 by Genomicus 06-21-2012 4:38 PM

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 ..."

Message 46 of 172 (666081) 06-21-2012 8:49 PM

Reply to: Message 44 by Genomicus 06-21-2012 6:31 PM

I never said it did. You did. There is in fact no a priori reason why they should still be hanging around. They might well have been lost instead. There's nothing in Darwinism per se that says this shouldn't have happened. If you want to admit that you were wrong about this too, go right ahead.

Edited by Dr Adequate, : No reason given.

Message 47 of 172 (666082) 06-21-2012 8:51 PM

Reply to: Message 41 by Genomicus 06-21-2012 4:38 PM

In which case, once again, FLE does not predict any deep homologies at all.