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Author Topic:   An ID hypothesis: Front-loaded Evolution
Granny Magda
Member (Idle past 154 days)
Posts: 2462
From: UK
Joined: 11-12-2007


Message 46 of 216 (653292)
02-19-2012 6:44 PM
Reply to: Message 45 by bluegenes
02-19-2012 6:12 PM


Re: Miller on Front-Loading
Yes, but the actual results of that would be indistinguishable from a sequence that was simply highly conserved because it was useful. Even where the system served different functions in eukaryotes and prokaryotes, it would still be indistinguishable from conservation with exaptation. We're just left with another situation where the predictions of front-loading are exactly the same as what we would expect from regular evolution.
Mutate and Survive

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Genomicus
Member (Idle past 2057 days)
Posts: 852
Joined: 02-15-2012


Message 47 of 216 (653293)
02-19-2012 6:53 PM
Reply to: Message 37 by Dr Jack
02-19-2012 5:12 PM


quote:
Well, I can flat out tell you the answer to that one: we do. The problem for you is that this isn't, in any way, incompatible with conventional theory. Exaptation is common, and well understood. These genes perform important roles in single celled organisms, and are later exapted to perform different roles in multi-cellular organisms. You need to come up with something that will distinguish your front-loaded genes from simple exaptation.
Further, I'd suggest that your hypothesis should lead to us seeing many, probably most, such multi-cellular genes in prokaryotes - we don't.
I'm not sure if it's just me, but those two paragraphs seem slightly contradictory. On the one hand, you state that "Well, I can flat out tell you the answer to that one: we do [find such homologs in prokaryotes]" and on the other hand you say that "I'd suggest that your hypothesis should lead to us seeing many, probably most, such multi-cellular genes in prokaryotes - we don't." Just saying.
A couple of points to be made here. Morphologically, hearts and brains have no homologous counterparts in unicellular organisms or even some "lower" multicellular organisms. Why then do you think that conventional theory would predict that the genes for the development and function of these organs would have homologs in unicellular organisms?
Secondly, you state that "I'd suggest that your hypothesis should lead to us seeing many, probably most, such multi-cellular genes in prokaryotes - we don't. There are some, yes, but most are not found in bacteria; a few more in Archaea and a decent portion in single-celled Eukarya or in multi-cellular but simply differentiated Eukarya. It seems to me that if front-loading was true we would expect a majority of such genes to be present in all species, would you agree?"
For clarification, I would agree that, under the FLE model, we would expect homologs of these genes in many prokaryote taxa - either in the form of structural or sequence similarity. We have sequenced only a fraction of the biosphere. Thus, this prediction can be potentially confirmed. Based on FLE logic, I predict that we will find many, many prokaryotic homologs of key genes involved in the development and function of metazoa. Does conventional theory predict this? You don't seem to think so.
Consider, for example, Pax-6 and Hoxa-3. Pax-6 plays a key role in the development of the eye, and Hoxa-3 plays a major role in heart development. Based purely on the logic of the conventional theory, would you expect these genes to have homologs in prokaryotes?
Of course it does. Highly conserved proteins have higher sequence identities than average proteins whilst, conversely, proteins not under selective pressure rapidly diverge. Proteins shared between the three domains must be highly conserved and thus will tend to have higher sequence identities.
I don't see how this would be the case. If a protein has homologs in all domains of life, this does not mean that it is necessary for life per se; it means that it is beneficial. And most proteins are, of course, beneficial. This doesn't constrain their sequence identity above average.

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bluegenes
Member (Idle past 2593 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 48 of 216 (653294)
02-19-2012 7:23 PM
Reply to: Message 46 by Granny Magda
02-19-2012 6:44 PM


Re: Miller on Front-Loading
Granny Magda writes:
Yes, but the actual results of that would be indistinguishable from a sequence that was simply highly conserved because it was useful. Even where the system served different functions in eukaryotes and prokaryotes, it would still be indistinguishable from conservation with exaptation. We're just left with another situation where the predictions of front-loading are exactly the same as what we would expect from regular evolution.
Of course. That's why I said on the thread (silly design) where I suggested this one that I'd be interested in seeing predictions that weren't either the same as those of evolutionary theory, or in keeping with it.
Genomicus understands the need for these.

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Blue Jay
Member (Idle past 2814 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 49 of 216 (653303)
02-19-2012 9:30 PM
Reply to: Message 1 by Genomicus
02-19-2012 5:43 AM


Hi, Genomicus.
Welcome to EvC!
It's nice to see an IDist who's taken some time and put some good thought and reasoning into his work.
For my post, I want to focus on this bit:
Genomicus writes:
The front-loading hypothesis proposes that ... [the intentionally seeded] life forms contained the necessary genomic information to shape future evolution, such that the course of evolution was biased in pre-determined trajectories.
Since front-loading predicts biases in the trajectory of evolution, shouldn't we be able to detect these biases by examining patterns in evolutionary trajectories across multiple lineages? For example, if the front-loaders intended to promote the emergence of a certain characteristic, wouldn't we predict that multiple lineages of descendant organisms would evolve that characteristic? Isn't this what "biased evolutionary trajectories" means?
Based on this, wouldn't it be reasonable to argue that characteristics that only emerged once in Earth's evolutionary history probably were not front-loaded into the original propagule? Any technique that biases evolution toward a certain trajectory, yet only results in one out of millions of lineages following that trajectory, was either a very ineffective technique, or an astonishingly complex algorithm that surely even you don't believe was encoded into a single prokaryotic propagule.
Edited by Bluejay, : A redundant redundancy

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
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Jon
Inactive Member


Message 50 of 216 (653307)
02-19-2012 10:04 PM
Reply to: Message 49 by Blue Jay
02-19-2012 9:30 PM


For example, if the front-loaders intended to promote the emergence of a certain characteristic, wouldn't we predict that multiple lineages of descendant organisms would evolve that characteristic? Isn't this what "biased evolutionary trajectories" means?
Legs. Wings. Eyes.

Love your enemies!

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Blue Jay
Member (Idle past 2814 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 51 of 216 (653317)
02-19-2012 11:46 PM
Reply to: Message 50 by Jon
02-19-2012 10:04 PM


Hi, Jon.
Jon writes:
Legs. Wings. Eyes.
So... the first animal was front-loaded?
What about the first prokaryotic progenitor of all life? Why did only one sub-sub-lineage of its descendants manifest these front-loaded characteristics?
Edited by Bluejay, : Rewording

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

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Dr Adequate
Member (Idle past 400 days)
Posts: 16113
Joined: 07-20-2006


Message 52 of 216 (653319)
02-20-2012 12:05 AM
Reply to: Message 1 by Genomicus
02-19-2012 5:43 AM


The front-loading hypothesis proposes that (a) early in earth’s history, the earth (or the solar system) was intentionally seeded with unicellular life forms (i.e., directed panspermia) and (b) these life forms contained the necessary genomic information to shape future evolution, such that the course of evolution was biased in pre-determined trajectories.
"Course" is singular, "trajectories" is plural.
This is not a mere grammatical quibble, I think there's a point that needs addressing here by you or by anyone else with a system of orthogenesis. If the course of evolution is preprogrammed into the first species, then how did its descendants evolve into a lobster and a giraffe? It can be preprogrammed to do one or the other, but how both? How do the same set of genetic instructions tell identical organisms: "Now, you evolve this way but you evolve that way"?
What are your thoughts on this?

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Genomicus
Member (Idle past 2057 days)
Posts: 852
Joined: 02-15-2012


Message 53 of 216 (653320)
02-20-2012 12:08 AM
Reply to: Message 43 by bluegenes
02-19-2012 6:03 PM


Re: The best of error minimizing codes?
I hope you'll agree that I was right to suggest a thread specifically for your front loading hypothesis. You may not like all the reactions, but you're certainly getting some!
Yes, I agree that it was a good idea. I don't mind objective criticism at all, but for the record, for all of you: now that the weekend is over, I won't have that much time to respond to all of you - only one or two responses per day, unless I can muster some more time. This means that I will be only responding to the highest-quality criticisms (e.g., MrJack and bluegenes and bluejay).
That said:
There's an interesting thing about this. While our standard code has certainly undergone selection for error minimization, and seems to be close to its local peak on the fitness landscape, there are plenty of higher fitness peaks elsewhere which nature could have hit if it had happened across a different random code to start with.
Looking at this from the I.D. perspective, it seems like bad news. Our standard code seems a very unlikely choice for your rationally designing frontloaders if they were aiming at error minimization.
Here's a 2007 paper that might interest you.
Paper on the rugged fitness landscape of genetic codes...
I'll take a look at that paper, but there are some things that need emphasizing. That the standard genetic code is not at a global optimum for error minimization really isn't bad news from an ID perspective. This is because there are other functions aside from error minimization that would be optimized, and this is indeed the case in the genetic code, as highlighted by Bollenbach et al., 2007:
As we learn more about the functions of the genetic code, it becomes ever clearer that the degeneracy in the genetic code is not exploited in such a way as to optimize one function, but rather to optimize a combination of several different functions simultaneously. Looking deeper into the structure of the code, we wonder what other remarkable properties it may bear. While our understanding of the genetic code has increased substantially over the last decades, it seems that exciting discoveries are waiting to be made.
Full optimization of one function may significantly reduce the optimization of another. Thus, a balance would have to be made between various functions.
The genetic code is, nevertheless, at a local optimum for error minimization. And the absence of a phylogenetic tree like I describe in my essay, and the fact that this highly optimized genetic code is nearly universal, points to front-loading.
As for your main point about it, I see no reason why any very early more error prone versions should have survived alongside a prokaryote LUCA, and I don't really see the point of your analogy with non-flagellar functional homologies, as these are nothing to do with sub-optimal flagella.
The prokaryote LUCA could easily have had a thoroughly sub-optimal genetic code. This would, in turn, evolve and be fine-tuned, but many detours and by-ways would be explored, with some less optimal genetic codes branching off, producing a phylogenetic tree of genetic codes. There is no reason why this should not have occurred, under the non-telic model.
I'll respond to your other points later.
Edited by Genomicus, : No reason given.

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Blue Jay
Member (Idle past 2814 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 54 of 216 (653324)
02-20-2012 1:04 AM
Reply to: Message 53 by Genomicus
02-20-2012 12:08 AM


Re: The best of error minimizing codes?
Hi, Genomicus.
Genomicus writes:
I don't mind objective criticism at all, but for the record, for all of you: now that the weekend is over, I won't have that much time to respond to all of you - only one or two responses per day, unless I can muster some more time. This means that I will be only responding to the highest-quality criticisms...
No sweat: IDists frequently get swamped here. Nobody will mind if you take a long time to write a high-quality response.
Just so you know, if you start to get too far behind, I intend to yield the floor to others. That will help focus the debate better. And, I consider Mr Jack and Bluegenes superior debaters and superior representatives for the positions I would argue, anyway.
Any threads of discussion you choose not to follow (including mine) can always be revisited some other time.

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

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Genomicus
Member (Idle past 2057 days)
Posts: 852
Joined: 02-15-2012


Message 55 of 216 (653325)
02-20-2012 3:35 AM
Reply to: Message 43 by bluegenes
02-19-2012 6:03 PM


Re: The best of error minimizing codes?
...and I don't really see the point of your analogy with non-flagellar functional homologies, as these are nothing to do with sub-optimal flagella.
The point about the flagellum is that it is predicted by Darwinian evolution that we should find functional pre-cursors, if it did indeed evolve. The same logic holds for the genetic code: we should find sub-optimal pre-cursors. Perhaps a better analogy would be the eye: the human eye is more optimal than, say, the rhinoceros eye, for example. One could build a tree with less optimal eyes in basal lineages, with more optimal eyes in late-branching taxa. That you cannot do the same with the genetic code is interesting, to say the least.
Is the suggestion that the front loaders might be able to predict something like the chance endosymbiotic event that seems to have enabled the evolution of eukaryotes?
Well, for starters, that's assuming that the endosymbiotic event that gave rise to the eukaryotes wasn't planned. The question "how could they front-load that?" is a valid one, but keep in mind that the human race has very little experience in the field of front-loading biological states. I think the answer to this question could be solved if we really thought about it. My personal opinion, of course.
And wouldn't they have to have a very clear idea of the future orbit and physical evolution of the planet itself, not to mention the behaviour of the local star which could radically effect things?
Well, the way I see it is that these front-loaders would have seeded many planets with these life forms. On some planets, these life forms may have gone extinct. Also, convergent evolution at the molecular level seems to indicate that it wouldn't be that terribly difficult to front-load future biological states - the behavior of our local star notwithstanding.

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Genomicus
Member (Idle past 2057 days)
Posts: 852
Joined: 02-15-2012


Message 56 of 216 (653329)
02-20-2012 5:49 AM
Reply to: Message 49 by Blue Jay
02-19-2012 9:30 PM


Hi, Genomicus.
Welcome to EvC!
Thanks!
Since front-loading predicts biases in the trajectory of evolution, shouldn't we be able to detect these biases by examining patterns in evolutionary trajectories across multiple lineages? For example, if the front-loaders intended to promote the emergence of a certain characteristic, wouldn't we predict that multiple lineages of descendant organisms would evolve that characteristic? Isn't this what "biased evolutionary trajectories" means?
In the first place, I'm not envisioning anything like extreme front-loading, where something as specific as the human species is front-loaded. So if I'm understanding you correctly, you're saying that if multicellularity was front-loaded, we should expect multicellular life forms to evolve independently. But this is what is believed to have occurred; that is, that multicellular life forms arose multiple times but many of these lineages went extinct - see here: Puzzling Out The Tree Of Life Of Green Plants.
"Multicellular life was another great idea that almost certainly arose more than once. A one-celled organism has to do everything -- it's a jack of all trades and master of none -- but in a group of cells, individuals can specialize and be very good at one specific thing," Mishler said. "But again, only a very few major lineages made it through to the present, and those all from one basic stock."
And there is good evidence of biased trajectories of important biological features: to name just one example, eyes have evolved independently in different lineages - indicative of a biased trajectory.
Essentially, it would not be reasonable to argue that "characteristics that only emerged once in Earth's evolutionary history probably were not front-loaded into the original," because lineages can be lost through deep time.

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Replies to this message:
 Message 60 by Blue Jay, posted 02-20-2012 3:08 PM Genomicus has replied

  
bluegenes
Member (Idle past 2593 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 57 of 216 (653345)
02-20-2012 9:13 AM
Reply to: Message 53 by Genomicus
02-20-2012 12:08 AM


Re: The best of error minimizing codes?
Genomicus writes:
I'll take a look at that paper, but there are some things that need emphasizing. That the standard genetic code is not at a global optimum for error minimization really isn't bad news from an ID perspective. This is because there are other functions aside from error minimization that would be optimized, and this is indeed the case in the genetic code, as highlighted by Bollenbach et al., 2007:
Yes, that's the answer I was expecting, but it was optimization for error minimization that you mention in the O.P. In fact, the paper suggests that the standard code is frozen some way off even its local fitness peak so far as error correction is concerned. However, the other improved error minimization peaks are so numerous that it would seem unlikely that there aren't those that would achieve better all round balanced function (or more rational design) than the one we've got. The designers had a lot of choice.
Geno writes:
Full optimization of one function may significantly reduce the optimization of another. Thus, a balance would have to be made between various functions.
Correct.
Geno writes:
The genetic code is, nevertheless, at a local optimum for error minimization.
More likely at a local balanced optimum because of the other functions you mentioned, and frozen there (with the few known exceptions) because of the difficulty of traversing valleys to reach other high points (which the front-loaders could have done).
Geno writes:
And the absence of a phylogenetic tree like I describe in my essay, and the fact that this highly optimized genetic code is nearly universal, points to front-loading.
It fits the scenario of an initial random functional code evolving to become optimized, and hitting a local peak on the fitness landscape fairly quickly then getting frozen. The paper suggests that random codes hit their local optimums easily and quickly.
Geno writes:
The prokaryote LUCA could easily have had a thoroughly sub-optimal genetic code. This would, in turn, evolve and be fine-tuned, but many detours and by-ways would be explored, with some less optimal genetic codes branching off, producing a phylogenetic tree of genetic codes. There is no reason why this should not have occurred, under the non-telic model.
The quick and easy arrival at a local balanced optimum would be one very plausible reason, don't you think?
If I'm getting it right, the variations that we do see from the standard code should be rare examples of it traversing slight valleys on the fitness landscape, and hitting other local peaks. They may not be sub-optimal for their circumstances in the balanced sense, even if they are for error correction or other single functions (just like the standard).
Their survival might indicate that a rational seeming option of seeding the planet with organisms containing lots of different codes could have left a number of them with much more radical differences. Different non-local fitness peaks. But we don't see this.
There's one thing that I will say about our standard code. It will be exactly right for doing what it has done on this particular planet regardless of its objective efficiency, and that's a prediction of both a non-telic view of evolution and a pure front-loading telic view. "Side loading" I.D. views do not predict this, and their claim is that what we see happening on the molecular level is inadequate to produce the variety and complexity of life that we see around us, and therefore the constant intervention of intelligent design is required.
There's quite a gulf between your view and that of the side-loaders.

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Jon
Inactive Member


Message 58 of 216 (653352)
02-20-2012 10:14 AM
Reply to: Message 51 by Blue Jay
02-19-2012 11:46 PM


Jon writes:
Legs. Wings. Eyes.
So... the first animal was front-loaded?
What about the first prokaryotic progenitor of all life? Why did only one sub-sub-lineage of its descendants manifest these front-loaded characteristics?
Don't mistake me for someone who thinks front-loading is anything other than stacking stuff unevenly on a trailer. I was just pointing out some characteristics shared across lineages that seem to have a tendency to evolve.
Perhaps they'll become important in the discussion later on. Perhaps not.
Jon

Love your enemies!

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bluegenes
Member (Idle past 2593 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 59 of 216 (653355)
02-20-2012 10:42 AM
Reply to: Message 55 by Genomicus
02-20-2012 3:35 AM


Re: The best of error minimizing codes?
Genomicus writes:
The point about the flagellum is that it is predicted by Darwinian evolution that we should find functional pre-cursors, if it did indeed evolve.
What's predicted is that they should have existed, not that they will necessarily still be around. Like semi-aquatic whale ancestors, for example, or apes with brain sizes half-way between ours and the other extant species, or elephant ancestors with noses three feet long.
Genomicus writes:
The same logic holds for the genetic code: we should find sub-optimal pre-cursors.
Not should, but hypothetically could. But if the pathway to the local fitness peak is easy, and getting off it hard, it seems unlikely.
Genomicus writes:
Well, for starters, that's assuming that the endosymbiotic event that gave rise to the eukaryotes wasn't planned. The question "how could they front-load that?" is a valid one, but keep in mind that the human race has very little experience in the field of front-loading biological states. I think the answer to this question could be solved if we really thought about it. My personal opinion, of course.
I'll try thinking, but it beats me at the moment. It would seem to be part of the general plan, because you described eukaryotes, plants and animals as the objectives. With the plants, there's another such event required as well.
Genomicus writes:
Well, the way I see it is that these front-loaders would have seeded many planets with these life forms. On some planets, these life forms may have gone extinct. Also, convergent evolution at the molecular level seems to indicate that it wouldn't be that terribly difficult to front-load future biological states - the behavior of our local star notwithstanding.
Don't you think that varying the genetic code around lots of different fitness peaks would help in increasing the chances of life taking? Also, if they wanted eukaryotic cells, they could start off with them in the mix, which would seem much more like rational design than relying on an endosymbiotic event.

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Blue Jay
Member (Idle past 2814 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 60 of 216 (653386)
02-20-2012 3:08 PM
Reply to: Message 56 by Genomicus
02-20-2012 5:49 AM


Hi, Genomicus.
Thanks for the reply.
Genomicus writes:
In the first place, I'm not envisioning anything like extreme front-loading, where something as specific as the human species is front-loaded.
Thanks for the clarification: though, I already figured you for someone wouldn't make this argument.
Genomicus writes:
So if I'm understanding you correctly, you're saying that if multicellularity was front-loaded, we should expect multicellular life forms to evolve independently. But this is what is believed to have occurred; that is, that multicellular life forms arose multiple times but many of these lineages went extinct...
Well, I wasn't trying to put forward an example yet: I was trying to establish a conceptual principle whereby we could test the predictions of FLE.
And, yes, there are indeed many lineages of multicellular organisms. As the article you cited mentioned, there are probably at least 5 independent emergences of "true" multicellularity. And, depending on how we define "multicellularity," there are also prokaryotes that can count as multicellular (some cyanobacteria, for instance).
So, based only the single criterion I proposed, I would regard multicellularity as potentially consistent with the front-loaded evolution hypothesis.
Genomicus writes:
And there is good evidence of biased trajectories of important biological features: to name just one example, eyes have evolved independently in different lineages - indicative of a biased trajectory.
My concern with the specific example here (eyes) is that the bias in trajectory only emerges in one "later branch" of the Tree of Life (Metazoa). So, it seems that the capacity to develop eyes isn't rooted at the base of the Tree of Life, but at the base of the animal branch of the Tree of Life.
Unless FLE allows for front-loading within individual branches of the tree, and not exclusively at the base of the tree, I think the proper conclusion is that eyes probably were not front-loaded.
Genomicus writes:
Essentially, it would not be reasonable to argue that "characteristics that only emerged once in Earth's evolutionary history probably were not front-loaded into the original," because lineages can be lost through deep time.
Please observe the parallels between your argument here and a specific statement you made in the OP:
Genomicus writes:
Arguing that the sub-optimal codes once did exist early in life’s history, but vanished once the optimal codes came on the scene (i.e., that they were outcompeted), looks awfully ad hoc.
I will accept your "deep-time" argument if you withdraw your objections to the similar argument in relation to sub-optimal genetic codes.
Edited by Bluejay, : No reason given.
Edited by Bluejay, : No reason given.
Edited by Bluejay, : last time: I swear

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
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