An ID hypothesis: Front-loaded Evolution

Hi Genomicus and welcome to EvC Forum!

So, I have a couple of questions;

How does this front-loading work? What is the mechanism?

Can you show me an example of front-loading in a genome?

Are there front-loaded genes that exist now? How would we tell?

How would we differentiate between an organism whose gene had been front-loaded and one that had merely evolved?

Mutate and Survive

For example, if we wanted to front-load molecular machine X, we could design molecular machine Y into the first genomes.

Merely using the phrase "molecular machine" does nothing to establish a mechanism. It is clearly a place-holder term that is standing in for an actual specific mechanism.

Am I to assume that you are doing this because you cannot name a specific mechanism?

Subsequent deletion of several components in molecular machine Y would unveil molecular machine X.

How exactly is that supposed to be achieved? How does the genome "know" which elements are to be deleted and which are to be retained?

Possibly, we might have a real example of this in the biological world. Within the bacterial flagellum, an export system seems to be embedded. Deletion of the cap and hook proteins, and the motor proteins, would result in a protein export system that could mediate interactions between prokaryotes and eukaryotes.

The problem with this is that it sounds very much like an evolutionary origin for the flagellum. It sounds like it would be equally compatible with the regular Theory of evolution.

Another way to front-load a biological system would be simply to make the appearance of that biological system much more probable. Suppose we wanted to front-load blood. In this case, we would endow the first life forms with homologs of hemoglobin, which would carry out an important function so that they don't decay over time as a result of natural selection and genetic drift. So, if the first life forms had homologs of hemoglobin, the blind watchmaker wouldn't have to tinker around, eventually happening to "land" on hemoglobin. The homologs of hemoglobin would already be in place.

So to follow on from that, can you show me that any such example has indeed occurred? Can you show me a front-loaded gene that has been taken up? And can explain how you differentiate it form one that merely evolved?

By this do you mean an example of a genome that was front-loaded?

No, I mean a gene that has been front-loaded but has not yet been, shall we say, "activated"? In other words, can you show me any allele that has been front-loaded but is not yet actively expressed in any extant organism?

According to the front-loading hypothesis, genes that are important to multicellular life were front-loaded. Thus, Pax-6 genes, which are important in developmental pathways, would have been front-loaded from homologs in bacteria.

Why choose multi-cellular life? It seems a bit random, was it picked out of a hat? Why not hypothesise that life was front-loaded to produce Archaea? Or bacteria?

Of course, I might hazard a guess. It's because the organisms that ID lobbyists really want to think have been front-loaded are humans. Because we're special. After all, Jesus does love us...

How can we tell? In the first place, deep homology of these genes with prokaryotic genes would be indicative that they were front-loaded;

Once again, this is indistinguishable from the consensus ToE, where the common ancestry of leads to homologous genes. In fact, a shared evolutionary heritage is pretty much part of the definition of a homologous gene. This seems to be another instance of this idea being unfalsifiable.
Are you saying that it is impossible for a non-front-loaded sequence to be highly conserved? I don't think it is.

So given that independently evolved sequences can be just as highly conserved, I fail to see how this can differentiate evolved systems form front-loaded ones.

You'd have to look at the broad biological context of the gene; determine its prokaryotic homolog and check their level of sequence conservation.

But again, that tells us nothing. It only tells us that the sequence is highly conserved. It does not tell us whether the conservation is due to front-loading or whether it is due to it simply being a useful and thus evolutionarily successful sequence.

It sounds to me like your hypothesis is lacking an actual mechanism, is based upon circular logic and assuming the consequent. It also smells, more than a little, of a convoluted Christian apologetic, wherein humans are the result of front-loading by the Christian god.

Mutate and Survive

Edited by Granny Magda, : No reason given.

I'd prefer to spend my time (and I haven't got too much of it) discussing biological origins with the likes of MrJack or DWIII, and not with those of you who seem to be fond of making snide remarks (e.g., "It also smells, more than a little, of a convoluted Christian apologetic, wherein humans are the result of front-loading by the Christian god").

It's not my intent to be snide, only to be truthful. I apologise if I have offended you, but I hope you can appreciate that I must call it as I see it. I don't want to soft-soap you, I think that would be patronising and would ultimately do you a disservice.

ID, as a movement, is a form of Christian apologetic. All of its leading lights are Christians, most of its supporters are Christians, the rest Muslims and other theists. There are only one or two non-theistic supporters. We know for a fact that there is a continuity between "creation science" and ID; we have the documents to prove it. So calling this hypothesis an apologetic is simply the truth as far as I am concerned.

Or are you going to tell me that you are not a Christian?

Meanwhile I would appreciate any response to the rest of my post.

Mutate and Survive

Hi Mr J,

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.

I found an interesting comment from Ken Miller on this. He suggests that if front-loading were real, we would see the exact opposite of what Genomicus suggests; we would see enormous mutation rates on any front-loading sequences. They would be inactive and thus unchecked by natural selection. Those portion of the genome would be subject to runaway mutation.

quote:

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This means that billions of years ago a humble prokaryote was packed with genes that would be turned off for hundreds of millions of years before they produced the eukaryotic cilium, and genes for blood clotting proteins that would pass more than a billion inactive years in genetic "cold storage." And what happens during those billions of years? As any student of genetics will tell you, because those genes are not expressed, natural selection cannot weed out genetic mistakes. This means that mutations will accumulate in these genes at breathtaking rates, rendering then hopelessly changed and inoperative hundreds of millions of years before Behe says that they will be needed.

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I have to agree with that. If any gene were front-loaded it would have to have yet further (as yet conveniently undetected) mechanism to guard against this.

Mutate and Survive

Ooh! Genomicus has a blog! He proposes this answer to the above problem;

quote:

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How can this problem be overcome? There’s a pretty simple solution, actually. If proteins A1, B1, and C1 are given functions such that their sequence identity is well conserved, and thus their 3D shapes, this problem is overcome.

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Is it just me or does that sound exactly like exaptation?

That's just exaptation, or at least it's indistinguishable from exaptation. So again, the best evidence for front-loading is exactly the same as what we'd see if consensus model evolution were true.

Mutate and Survive

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

Hi Chuck,

Can anyone someone lay his position out for me in laymans terms? Is he arguing that evolution was front loaded by a creator/deity? Or is he arguing for the IDist POV along with the likes of Behe and Meyer?

Well if I remember correctly, Behe goes as far as to say that he suspects the designer to be the Christian god. Certainly Genomicus doesn't go that far. If you take a look at his blog, particularly this post, he expresses his frustration at many within ID over their insistence on dragging theism into the mix. He sees this - quite correctly - as being counter to good science. Here's a quote;

quote:

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When I look at the posts over at UncommonDescent, it is obvious to me that a change needs to occur within the mainstream ID team. At least 50% of the posts at UncommonDescent, aren’t even remotely relevant to ID and biological origins (well, I suppose by some stretch of the imagination they could be just a tiny, tiny bit relevant). Consider the title of one of the posts at UncommonDescent: “Survey results: Only 5.3% of general philosophers of science accept or lean towards theism.” Now what on earth does theism have to do with biological intelligent design? I really don’t know. Does theism have anything to do with the theory of gravity? Not really, and if the mainstream proponents of ID are genuinely interested in developing a rigorous hypothesis of biological origins, then the theistic language will have to be dropped (or at least minimized). I mean, c’mon, UncommonDescent spends a whole bunch of time devoted to attacking atheism, promoting theism, etc. But what does this have to do with the origin of the bacterial flagellum, for example? If you’re truly interested in biological origins, then we don’t need to be sidetracked by the theism/atheism debate, which is a whole other topic.

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Now I come close to agreeing with him here. ID is indeed far too steeped in religion. Where I differ from Genomicus' position is in his view that "theistic language" is what needs to minimised in ID. I think that's wrong. I think that the real problem is not merely theistic language, but the whole focus of ID. The problem is not that the posters at Uncommon Descent have misunderstood the point of ID, it's that Genomicus has misunderstood the point. That point is that ID exists solely for the purpose of Christian apologetics, specifically, getting those apologetics into schools. It's not just the language, it's the whole ideology.

For ID to produce the kind of good science that Genomicus seems to honestly desire, it would have to abandon it's dishonest approach to the subject. It would have to become something totally different to what it is today. It would have to drop it's political and religious aims and concentrate solely on the data. But then of course, it would no longer be ID science, it would just be science.

This is another topic I admit, but it might make an interesting thread when we've finished with this one.

If you want more on the science side of things, check out Genomicus' blog. It's quite good as these things go and it has a lot of material on this subject. I still don't think he's right, but it should be of interest to you.

Mutate and Survive

Well, under the FLE hypothesis, the origin of eukaryotes and Metazoa and plants and animals was not a matter of mere chance, but a matter of chance and direction. In other words, the first genomes anticipated the rise of these taxa and this increased the likelihood of their origin.

Hold on, aren't you jumping the gun here?

Why should we assume that eukaryotes were the intended result?

You've shown homologies between modern prokaryotes and modern eukaryotes, but why should it then follow that the eukaryotes are the ones that the front-loader is interested in? Why can't it be the other way around and the modern prokaryotes are the intended outcome?

You appear to be kind of assuming your conclusion here.

Of course, I could hazard an educated guess at why ID/front-loading enthusiasts prefer to think that metazoans are the intended outcome, but you won't like it...

Mutate and Survive

In my first essay, I stated that a premise of the FLE hypothesis is that eukaryotes and Metazoa were front-loaded. This is the premise of front-loading, and the one from which we can draw testable predictions.

But you're just asserting that. There is no reason to assume it. That completely undermines any arguments based upon the assumption.

And no, I don't think I'd particularly care for your guess about why the FLE posits this as an initial premise, precisely because you'd guess that it's because of theology. That's simply not true

It may not be true for you personally, but the fact remains that the purpose of the ID movement is not the way you seem to want to paint it. I fear that you have been had. If you are truly interested in unbiased scholarship, then the ID lobby are not your fellow travellers.

It's based on the notion that if humans were to seed a planet and front-load, we would almost certainly choose to front-load Metazoa and try to front-load intelligent life forms, would we not?

But that's not any kind of valid reasoning, that's just bias. You are assuming that the front-loader would make something that resembles us just because that what you or I would make. You are founding your whole argument upon an unsupported assumption based upon anthropomorphic bias.

Ummm, because prokaryotes were around for about a billion years before eukaryotes came on the scene.

But that doesn't mean a thing. Maybe the front-loader aimed for bacteria, got what he wanted and life has progressed on its own terms since that time, no front-loading required.

Besides, modern prokaryotes haven't been around for billions of years. One could easily argue that some recently evolved eukaryote was the intended outcome. Perhaps the recently evolved nylon-eating bacteria were the intended outcome.

Come to that, we could decide that blue-footed boobies were the intended outcome. Or absolutely any organism you care to name. This lack of specificity strikes me as a pretty major flaw.

Mutate and Survive

It's the premise of the FLE. We can draw testable predictions from it; if confirmed, it would no longer be an assumption.

But there's absolutely no reason to prefer it over any other hypothesis, right?

I am perfectly aware that the ID movement has a religious agenda. Did I say the ID lobby were my fellow travelers? The problem, though, is that the FLE hypothesis was not proposed by the ID movement

So whose idea was it exactly? Where does it originate?

The ID movement guys would far rather prefer intelligent intervention over front-loading, IMHO.

The latter is merely a less direct version of the former.

Anyways, I'm not a part of the ID movement, I don't share their obvious (and awfully unscientific) religious agenda, so the point is...?

It just seems odd that you would be so interested in this idea. It does seem to be popular within the ID community and it doesn't seem to have any traction elsewhere.

Yes, maybe it did. What predictions would you propose for this idea?

Exactly the same as you cite for eukaryote front-loading; conserved sequences and such. The real problem is that the evidence that one would expect for prokaryote front-loading would not differ one iota from what you predict for eukaryote front-loading. nor would either differ in the least from what we would expect for normal evolution.

why didn't the front-loader put modern prokaryotes on earth from the start?

Is that question only just occurring to you? Genomicus, we might as well ask why the "front-loader" didn't just go straight for the blue-footed boobies, day one. Why bother with any of this?

As far as I can tell, the only reason to assume that metazoans were the intended outcome is pro-metazoan bias and anthropomorphism.

Mutate and Survive

That depends on the amount of evidence the other hypotheses have.

Given that your primary competition is the Theory of Evolution, probably the best evidenced theory in all science, that would seem to leave you high and dry.

Mike Gene formulated the front-loading hypothesis.

So your primary source for this is a single pseudonymous blogger? One who admits that he is not a biologist? That's even more perplexing. Also, given the fact that Gene is a major contributor to Telic Thoughts - a blog that is lousy with theism - this does little to counter the charges of stealth theism. This absolutely is an ID hypothesis, whether its originator has differences with the mainstream ID movement or not.

Actually, the predictions would differ. If modern prokaryotes were front-loaded from previous prokaryotes, and eukaryotes were not front-loaded, we would not predict that prokaryotic homologs of protein components of the eukaryotic flagellum would be more highly conserved in sequence identity than the average prokaryotic protein, for example.

I think you're wrong about that. In fact that would be a necessity of your argument.

For starters, we would expect the eukaryote line to be more conserved, because prokaryotes generally mutate faster than prokaryotes, engage in LGT, etc.

If the genes in prokaryotes that you describe as homologous to eukaryote genes are functional, then it is perfectly possible that they have achieved the aim of the front-loader with that function. The continuing presence of the same gene sequences in eukaryotes is simply a result of the front-loading and its conservation mechanism (whatever that might be). You can't assume that the flagellum is the function that was front-loaded; it might just as easily be the homologous function in the prokaryote.

If the proteins in prokaryotes have been preserved by some sequence preservation mechanism, then that mechanism would have to be present in the eukaryote as well, given their common heritage. Either that or you have a situation where the preservation mechanism gets switched off in later lineages and that seems like a huge stretch of the imagination.

I've already responded to this claim, but here it is again:

In other words, homologs of the core, necessary IFT proteins would be designed into the first genomes. They�d be given a function, such that their basic 3D shape is conserved over deep-time. If they were given a function where their 3D shape would be substantially changed over deep-time, then the front-loading designer couldn�t possibly hope that when these proteins associated, their shapes would complement each other correctly such that a cilium could arise.

But if they are performing a vital function in prokaryotes, then the ToE does indeed predict that they would be highly conserved. They have a function after all.

From here, we can develop our FLE prediction. The non-telic hypothesis for the origin of the cilium does not require or predict that the prokaryotic homologs of IFT proteins be well-conserved in sequence identity. In fact, it�s certainly possible that the non-telic hypothesis predicts that most of the prokaryotic homologs of the core IFT proteins will be loosely conserved in sequence identity: a protein that is not under stringent functional constraints will be more likely to be co-opted into a novel role by chance without being deleterious.

But they are performing a function, that was a requirement of the kind of proteins we're talking about.

In your model, these sequences are conserved because they are front-loaded with a function.

In the standard model they are highly conserved simply because they have evolved a function.

You can't point to proteins that you yourself claim to be functional and then say "Look! They're highly conserved! That's not what we would expect under the ToE if they had no function". They have a function. That's enough to explain why they are conserved. We're talking about some of the most ancient adaptations for multicellularity after all. What's more, defective IFT proteins specifically are associated with a raft of hideous maladies, so that would seem to provide ample reason that they should be conserved in either model.

Thus, under the front-loading hypothesis, we would predict that important proteins in eukaryotes, animals, and plants will share deep homology with unnecessary but functional proteins in prokaryotes.

I don't see anything that prevents that from being equally true the other way around.

I don't see what's to prevent such an astonishingly proficient entity from creating a whole ecosystem; clearly they are superlative gene-engineers, why impose arbitrary limits upon them?

The suggestion made by Bluegenes would also make sense. Why not start with a simple eukaryote? That would be pretty robust and it would avoid the need for chancy freak events like the origins of mitochondria or chloroplasts.

Or alternatively, just being patient would seem to be a better bet. The front-loader could have waited for an ecosystem to develop and then inserted his target organism.

but IMHO my argument does not answer my question to you of why the FL designers wouldn't seed the earth with modern prokaryotes in the first place - according to this alternative FL hypothesis you're "advocating."

Well I did mention nylon-eating bacteria. For a bacterium to eat nylon, some kindly metazoan must first come along create nylon. Many modern prokaryotes are every bit as environment-dependent as eukaryotes. If the target organism were nylon-eating bacteria or the latest strain of swine flu, it too would flounder on the early Earth.

This line of reasoning strikes me as all being a bit post hoc to be honest.

Mutate and Survive

Edited by Granny Magda, : No reason given.