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Author Topic:   The $5,000,000 ID Research Challenge
Taq
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Posts: 7971
Joined: 03-06-2009
Member Rating: 4.5


Message 16 of 285 (671924)
08-31-2012 12:46 PM
Reply to: Message 14 by ringo
08-31-2012 12:16 PM


Re: Create life
That sounds like more of a historical question than a scientific one. "Could it happen?" is easier to detemine in the lab than "Did it happen?"

It is a scientific question, and one that the theory of evolution is able to answer. We can observe evolution in the lab, so we know that it can happen. We can then ask if it did happen in the past, and we can run experiments to see if it did. We can do this by looking for transitional fossils or by comparing genomes. It is a scientifically testable proposition.

I am asking for ID creationists to come up with the same testable hypotheses, and then describe the equipment that they will need to test it.


This message is a reply to:
 Message 14 by ringo, posted 08-31-2012 12:16 PM ringo has responded

Replies to this message:
 Message 17 by ringo, posted 08-31-2012 12:58 PM Taq has responded

  
ringo
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From: frozen wasteland
Joined: 03-23-2005
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Message 17 of 285 (671926)
08-31-2012 12:58 PM
Reply to: Message 16 by Taq
08-31-2012 12:46 PM


Re: Create life
Taq writes:

We can observe evolution in the lab, so we know that it can happen. We can then ask if it did happen in the past, and we can run experiments to see if it did.


Suppose we create life in the lab using our intelligence. Knowing that it "could" happen either by intelligence or by evolution, how would you tell which way it "did" happen?
This message is a reply to:
 Message 16 by Taq, posted 08-31-2012 12:46 PM Taq has responded

Replies to this message:
 Message 18 by Taq, posted 08-31-2012 1:07 PM ringo has acknowledged this reply

  
Taq
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Posts: 7971
Joined: 03-06-2009
Member Rating: 4.5


Message 18 of 285 (671928)
08-31-2012 1:07 PM
Reply to: Message 17 by ringo
08-31-2012 12:58 PM


Re: Create life
Suppose we create life in the lab using our intelligence. Knowing that it "could" happen either by intelligence or by evolution, how would you tell which way it "did" happen?

That is the $5,000,000 question, isn't it.

I would love to see an ID supporter try and answer that question.


This message is a reply to:
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Replies to this message:
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Tanypteryx
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Posts: 2250
From: Oregon, USA
Joined: 08-27-2006
Member Rating: 5.3


Message 19 of 285 (671929)
08-31-2012 1:46 PM
Reply to: Message 18 by Taq
08-31-2012 1:07 PM


Re: Create life
I predict that you will not get a credible answer from any of the ID proponents on the board.

$5,000,000 will buy a lot of lawyers and so far the ID proponents in the U.S. have spent all their time and money on finding gullible state legislators and school board members to demand equal time for ID in the science classes.

Research is a concept and a word that their brains seem unable to process.


What if Eleanor Roosevelt had wings? -- Monty Python

One important characteristic of a theory is that is has survived repeated attempts to falsify it. Contrary to your understanding, all available evidence confirms it. --Subbie

If evolution is shown to be false, it will be at the hands of things that are true, not made up. --percy


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Genomicus
Member (Idle past 136 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 20 of 285 (671931)
08-31-2012 2:23 PM


I've been absent for a bit, but now I'm back. I'll post my thoughts here shortly.
  
Genomicus
Member (Idle past 136 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 21 of 285 (672060)
09-02-2012 8:11 PM
Reply to: Message 1 by Taq
08-30-2012 12:39 PM


Some people claim that ID researchers are ignored and persecuted, the result of which is that ID researchers can not get research money to study ID.

So what if they did get $5,000,000 to spend on a new research facility? What would they spend it on? That is the challenge for this thread. Show us what the ID research program would actually need to do, what equipment would be needed to do this research, and how you would prioritize the money in this laboratory. Show us what a real ID research program would look like.

And:

I am asking for ID creationists to come up with the same testable hypotheses, and then describe the equipment that they will need to test it.

For the moment, I'll ignore your use of the phrase "ID creationists."

I think the best angle of research ID proponents could do would be to go out and test specific ID hypotheses. Thus, I envision a sort of "Biological Intelligent Design Research Program," which would consist of outlining ID hypotheses, methods for testing them, and finally actually testing these hypotheses.

What follows is a rough sketch of what my ID research program would look like.

Outline of an ID Research Program

I. Front-loaded Evolution

a. Gene content of the LUCA
1. Prediction: Given front-loaded evolution, the gene content of the LUCA should exceed that of the minimum number of genes required for life. In short, the LUCA should possess information that is unnecessary to life but is required for the rise of the complex life forms we see today.
2. Method: A variety of bioinformatic techniques can be used to test this prediction of front-loaded evolution (e.g., phylogenomic approaches).

b. The role of cytosine deamination in the origin of key Metazoan genes
1. Prediction: It should be noted that the below discussion is not a necessary prediction of front-loading. However, the “Increasing Hydrophobicity Effect” (IHE) hypothesis is a teleological hypothesis that ties in with front-loading, and it can be tested. What is the IHE hypothesis? Mike Gene proposed the IHE hypothesis back in 2007 in his book The Design Matrix. See here for more details. To quote Mike Gene: “…a set of originally designed proteins may have been designed such that they could exploit the effects of C-T transitions, in essence channeling original designs in a direction to increase the chances that a buried, secondary design is extracted. And such events may have been tied to front-loading. (Figure 7) For example, proteins that played essential roles in the evolution of multicelluarity may have been spawned from the IHE. This scenario portrays at least some evolutionary events as an interaction between four dynamics: random mutation, mutation rigged by natural law, intelligent design, and natural selection. This hypothesis also makes a prediction that can be tested. For example, if the multicellular state was front-loaded with life’s design, we would expect to find conserved, multicellular-specific proteins have crucial FLIYWVMCS residues that can be explained by C-T transitions relative to their ancestral state.”
2. Method: Ancestral sequence reconstruction, and identification of functionally important residues in multicellular-specific proteins are useful tools for testing this prediction of the IHE hypothesis.

II. Engineering and Molecular Machines: The Bacterial Flagellum

a. Engineering of the flagellum
1. Prediction: If the components of the bacterial flagellum were directly engineered, we expect that molecular clocks will place their divergence times in the pattern predicted by the design hypothesis (see here).
2. Method: Standard molecular evolution techniques apply here to determine the molecular clock divergence times of flagellar components and their non-flagellar counterparts.

b. The functional optimality of the ur-flagellum
1. Prediction: If rational engineers designed the original bacterial flagellum, we could reasonably predict that this ancestral flagellum (the ur-flagellum) was at least as functionally optimal as the modern variants. Evolutionary theory, on the other hand, makes no such prediction, because under the evolutionary model the flagellum was cobbled together from proteins that at first fitted with each other only loosely, producing function but not at an optimal level. Further fine-tuning over time gradually converted this original flagellum into the efficient ones we see in nature today. However, from a design perspective, the originally (designed) flagellum was fully functional and optimal at the start.
2. Method: Reconstructing the ancestral sequences of the flagellar components allows us to build a probable ancestral ur-flagellum in the cell. The usual biochemical methods can then be used to assess its functional optimality.

This is only a brief outline. I have other ideas, but it would take a bit of time to go through all of them so I've provided only a few.

Thoughts?


This message is a reply to:
 Message 1 by Taq, posted 08-30-2012 12:39 PM Taq has responded

Replies to this message:
 Message 24 by PaulK, posted 09-03-2012 1:46 AM Genomicus has responded
 Message 25 by Taq, posted 09-04-2012 1:24 PM Genomicus has responded

  
Genomicus
Member (Idle past 136 days)
Posts: 852
Joined: 02-15-2012


Message 22 of 285 (672061)
09-02-2012 8:13 PM
Reply to: Message 1 by Taq
08-30-2012 12:39 PM


Double post.

Edited by Admin, : Remove content of double post.


This message is a reply to:
 Message 1 by Taq, posted 08-30-2012 12:39 PM Taq has not yet responded

  
Genomicus
Member (Idle past 136 days)
Posts: 852
Joined: 02-15-2012


Message 23 of 285 (672062)
09-02-2012 8:14 PM


Ooops, double post (I keep doing that).
  
PaulK
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Posts: 15204
Joined: 01-10-2003
Member Rating: 3.4


Message 24 of 285 (672084)
09-03-2012 1:46 AM
Reply to: Message 21 by Genomicus
09-02-2012 8:11 PM


Predictions should really be in terms of what we expect the experiments/investigations to find, and I think you need more detail there.

On the specific examples:

Ia) Unguided evolution doesn't predict a minimal LUCA, so quantification is required for this prediction to be any use at all.
(Added: And what of the possibility that there was no single LUCA, rather a population exchanging genes. Would this be taken as falsifying FLE ? If not, how would you take it into account ?)

Ib) Equally we should expect some examples of this given unguided evolution. Quantification is required before this is any use at all.

IIa) I think that the prediction should be clarified. I believe that the point is that there are "ID" changes required to build a flagellum (which occurred in so short a time as to be negligible) plus later drift which occurred at the measured rate. Since the argument requires some quantification of the changes required these values should also be used to estimate the expected divergence times.

IIb) I assume you mean a simulation rather than actual experiment ? As usual the prediction would require far more quantification, not least a measure of optimality.

Edited by PaulK, : No reason given.

Edited by PaulK, : No reason given.


This message is a reply to:
 Message 21 by Genomicus, posted 09-02-2012 8:11 PM Genomicus has responded

Replies to this message:
 Message 26 by Genomicus, posted 09-04-2012 6:31 PM PaulK has responded

    
Taq
Member
Posts: 7971
Joined: 03-06-2009
Member Rating: 4.5


(1)
Message 25 of 285 (672175)
09-04-2012 1:24 PM
Reply to: Message 21 by Genomicus
09-02-2012 8:11 PM


a. Gene content of the LUCA
1. Prediction: Given front-loaded evolution, the gene content of the LUCA should exceed that of the minimum number of genes required for life. In short, the LUCA should possess information that is unnecessary to life but is required for the rise of the complex life forms we see today.

This really doesn't separate ID from other existing, unguided mechanisms for the production of LUCA. However, you could convince me otherwise.

What experiments would you run to show that these unnecessary parts were the product of design and not unguided contingent processes that came before LUCA?

1. Prediction: It should be noted that the below discussion is not a necessary prediction of front-loading. However, the “Increasing Hydrophobicity Effect” (IHE) hypothesis is a teleological hypothesis that ties in with front-loading, and it can be tested. What is the IHE hypothesis? Mike Gene proposed the IHE hypothesis back in 2007 in his book The Design Matrix. See here for more details. To quote Mike Gene: “…a set of originally designed proteins may have been designed such that they could exploit the effects of C-T transitions, in essence channeling original designs in a direction to increase the chances that a buried, secondary design is extracted. And such events may have been tied to front-loading. (Figure 7) For example, proteins that played essential roles in the evolution of multicelluarity may have been spawned from the IHE. This scenario portrays at least some evolutionary events as an interaction between four dynamics: random mutation, mutation rigged by natural law, intelligent design, and natural selection. This hypothesis also makes a prediction that can be tested. For example, if the multicellular state was front-loaded with life’s design, we would expect to find conserved, multicellular-specific proteins have crucial FLIYWVMCS residues that can be explained by C-T transitions relative to their ancestral state.”

Sharpshooter fallacy. If evolution took a different turn and favored A-T transitions instead you would be talking about how proteins that evolved though A-T transitions were front loaded. You are simply taking the result and painting a bull's eye around it. This is a major problem for all of your approaches.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 21 by Genomicus, posted 09-02-2012 8:11 PM Genomicus has responded

Replies to this message:
 Message 32 by Genomicus, posted 09-05-2012 7:01 PM Taq has responded

  
Genomicus
Member (Idle past 136 days)
Posts: 852
Joined: 02-15-2012


Message 26 of 285 (672216)
09-04-2012 6:31 PM
Reply to: Message 24 by PaulK
09-03-2012 1:46 AM


Predictions should really be in terms of what we expect the experiments/investigations to find, and I think you need more detail there.

I'm pretty sure I said what we'd expect to find from an ID perspective.

Ia) Unguided evolution doesn't predict a minimal LUCA, so quantification is required for this prediction to be any use at all.
(Added: And what of the possibility that there was no single LUCA, rather a population exchanging genes. Would this be taken as falsifying FLE ? If not, how would you take it into account ?)

At the same time, unguided evolution does not predict a non-minimal LUCA. It makes no prediction at all regarding the gene content of the LUCA. I'm not quite sure what you mean by "quantification" in this context.

Regarding the possibility that there was no single LUCA, but instead a population exchanging genes: from a front-loading viewpoint I'd still expect that these organisms will have unnecessary (but functional) genes. That is, if we track back in time to the population from which the current domains diverged, this population will contain a bunch of unnecessary genomic information.

Ib) Equally we should expect some examples of this given unguided evolution. Quantification is required before this is any use at all.

As stated above, I'm not sure what exactly you mean by "quantification." Also, IMHO the argument that "equally we should expect some examples of this given unguided evolution" is of dubious merit. From a non-teleological perspective, cytosine "just happened" to be part of the genetic code. Thus, there's no reason why protein sequences containing cytosine-encoded amino acid residues should be poised to evolve into different proteins with different functions. If we found examples of multicellular-specific proteins that evolved through massive cytosine deamination events in a precursor gene this would only make sense from a teleological perspective because such proteins could only feasibly evolve from a protein with a specified initial condition. In other words, given a random protein sequence, there's no reason at all why cytosine deamination events should turn it into a protein with another function. But from an ID point of view, the initial protein sequence is designed such that it is specifically constructed to utilize cytosine deamination to evolve into a novel protein. Although this is slightly off-topic, there is another issue at play here as well. The non-telic position must explain why it is that the genetic code is arranged such that cytosine deamination almost always results in increased hydrophobicity. This makes sense if a designer wanted to front-load novel protein folds, but it doesn't make much sense from a non-telic point of view. More on this later.

IIa) I think that the prediction should be clarified. I believe that the point is that there are "ID" changes required to build a flagellum (which occurred in so short a time as to be negligible) plus later drift which occurred at the measured rate. Since the argument requires some quantification of the changes required these values should also be used to estimate the expected divergence times.

Okay. Am I correct in saying that your issue here is that I haven't provided the predicted divergence times for the flagellar proteins and their non-flagellar counterparts?

IIb) I assume you mean a simulation rather than actual experiment ? As usual the prediction would require far more quantification, not least a measure of optimality.

I mean an actual experiment. The ancestral flagellar sequences would be reconstructed and then actually translated in the cell such that we have a pretty good idea of what the ur-flagellum looked like and how it functioned.

With regards to optimality: this can be estimated from an engineering context. For example, the flagellar motor is pretty efficient in its energy conversion. I'd predict that the motor of the ur-flagellum was just as efficient, while a Darwinian perspective doesn't make this prediction.

I'm still a bit puzzled by what you mean by "quantification." Where is the quantification, for example, in the prediction of common descent that we will see a pattern of geographic distribution of life forms (as described by Darwin in his Origin of Species)?

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 24 by PaulK, posted 09-03-2012 1:46 AM PaulK has responded

Replies to this message:
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Taq
Member
Posts: 7971
Joined: 03-06-2009
Member Rating: 4.5


Message 27 of 285 (672222)
09-04-2012 7:43 PM
Reply to: Message 26 by Genomicus
09-04-2012 6:31 PM


At the same time, unguided evolution does not predict a non-minimal LUCA. It makes no prediction at all regarding the gene content of the LUCA. I'm not quite sure what you mean by "quantification" in this context.

Then you seem to agree that your scheme does not differentiate itself from other unguided processes since it is explicable in either model.

If we found examples of multicellular-specific proteins that evolved through massive cytosine deamination events in a precursor gene this would only make sense from a teleological perspective because such proteins could only feasibly evolve from a protein with a specified initial condition. In other words, given a random protein sequence, there's no reason at all why cytosine deamination events should turn it into a protein with another function.

Where did you show this?

The non-telic position must explain why it is that the genetic code is arranged such that cytosine deamination almost always results in increased hydrophobicity.

More to the point, why would a telic position predict this? Why not a decrease in hydrophobicity to encourage interaction with polar molecules?

I mean an actual experiment. The ancestral flagellar sequences would be reconstructed and then actually translated in the cell such that we have a pretty good idea of what the ur-flagellum looked like and how it functioned.

I really, really doubt that this can be done, but that certainly would be an interesting experiment. If anything, this comes closest to meeting the challenge.


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PaulK
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Posts: 15204
Joined: 01-10-2003
Member Rating: 3.4


Message 28 of 285 (672243)
09-05-2012 2:00 AM
Reply to: Message 26 by Genomicus
09-04-2012 6:31 PM


quote:

I'm pretty sure I said what we'd expect to find from an ID perspective.

But NOT in terms of what the actual experiments or investigations would find. You only talked about the findings we would infer from that.

quote:

At the same time, unguided evolution does not predict a non-minimal LUCA. It makes no prediction at all regarding the gene content of the LUCA. I'm not quite sure what you mean by "quantification" in this context.

I'd say that unguided evolution more strongly predicts a non-minimal genome than FLE, for reasons I've already given - and that you haven't been able to refute. Further, the hypothesis that the LUCA was not a single organism but a population of organisms, exchanging genes through lateral transfer is the only hypothesis to predict a non-minimal genome with absolute certainty

Quantification, of course, would start with the idea of "how far from minimal" - how many extra genes. At least if you assume that the LUCA is a single organism you could come up with a genome far enough from minimal that it is more plausibly due to FLE than unguided evolution.

quote:

Regarding the possibility that there was no single LUCA, but instead a population exchanging genes: from a front-loading viewpoint I'd still expect that these organisms will have unnecessary (but functional) genes. That is, if we track back in time to the population from which the current domains diverged, this population will contain a bunch of unnecessary genomic information.

As an aggregate the population MUST contain genes which are unnecessary to a single organism. Each member of the population is a functioning organism without the differing genes found in other members. That the aggregate would be a non-minimal genome is a certainty. If you're arguing that individual organisms would be non-minimal the question is how you could tell. Reassembling individual organisms within the population would be far more difficult than producing a genome for a single LUCA (itself hugely difficult).

quote:

As stated above, I'm not sure what exactly you mean by "quantification."

Then you've really no business writing these proposals. If something is expected to happen MORE OFTEN given FLE than it is given unguided evolution then you need to work out how often it is expected to happen for each, in advance of the investigation which will try to work out how often it happened.

quote:

Also, IMHO the argument that "equally we should expect some examples of this given unguided evolution" is of dubious merit. From a non-teleological perspective, cytosine "just happened" to be part of the genetic code. Thus, there's no reason why protein sequences containing cytosine-encoded amino acid residues should be poised to evolve into different proteins with different functions. If we found examples of multicellular-specific proteins that evolved through massive cytosine deamination events in a precursor gene this would only make sense from a teleological perspective because such proteins could only feasibly evolve from a protein with a specified initial condition. In other words, given a random protein sequence, there's no reason at all why cytosine deamination events should turn it into a protein with another function. But from an ID point of view, the initial protein sequence is designed such that it is specifically constructed to utilize cytosine deamination to evolve into a novel protein.

Of course you miss the point, Given that these mutations occur naturally and without guidance, SOME of them will have given rise to useful new functions by pure chance.

quote:

Although this is slightly off-topic, there is another issue at play here as well. The non-telic position must explain why it is that the genetic code is arranged such that cytosine deamination almost always results in increased hydrophobicity. This makes sense if a designer wanted to front-load novel protein folds, but it doesn't make much sense from a non-telic point of view. More on this later.

You're going to have to give a reason why this is a problem before i accept it.

However there IS another point. This is exactly the sort of trick that would allow an FLE engineer to reduce the number of genes that were required in the initial life form. When arguing for a non-minimal genome you were clearly arguing that they would not use these tricks. Obviously there is a tension between the two arguments...

quote:

Okay. Am I correct in saying that your issue here is that I haven't provided the predicted divergence times for the flagellar proteins and their non-flagellar counterparts?

No, the point is that you have not sufficiently detailed the model that predicts these divergence times. (Actually you haven't explained why there would be any homologues at all given that your hypothesis would tend to lead to the expectation that they would not exist).

quote:

I mean an actual experiment. The ancestral flagellar sequences would be reconstructed and then actually translated in the cell such that we have a pretty good idea of what the ur-flagellum looked like and how it functioned.


I think you will find that such work is more often done by simulation.

quote:

With regards to optimality: this can be estimated from an engineering context. For example, the flagellar motor is pretty efficient in its energy conversion. I'd predict that the motor of the ur-flagellum was just as efficient, while a Darwinian perspective doesn't make this prediction.

That really depends on the evolutionary path, though...

quote:

I'm still a bit puzzled by what you mean by "quantification." Where is the quantification, for example, in the prediction of common descent that we will see a pattern of geographic distribution of life forms (as described by Darwin in his Origin of Species)?

Of course Darwin was not performing an experiment (the data was in and needed to be explained) and the signal was very strong (meaning that quantification was largely moot). But you are proposing experiments and we don't know how strong the signal will be. So we want to work out how strong a signal we should expect given your hypothesis versus how strong a signal we should expect given unguided evolution. As your experiments are written it is quite possible that the result would actually support unguided evolution - and you would be touting it as evidence for ID.

And THAT is why you need quantification.


This message is a reply to:
 Message 26 by Genomicus, posted 09-04-2012 6:31 PM Genomicus has not yet responded

Replies to this message:
 Message 29 by Percy, posted 09-05-2012 8:30 AM PaulK has responded

    
Percy
Member
Posts: 18591
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.0


(4)
Message 29 of 285 (672252)
09-05-2012 8:30 AM
Reply to: Message 28 by PaulK
09-05-2012 2:00 AM


My Take
I don't understand the nitpicking about Genomicus's research proposals. If the ID crowd were actually engaged in any of the investigations he proposes I, for one, would be applauding. I'd still think the research was unfounded upon any real world observations, but at least it would be actual research on ID. It would be a welcome break from all the dishonest portrayals of evolution they usually engage in.

--Percy


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 Message 28 by PaulK, posted 09-05-2012 2:00 AM PaulK has responded

Replies to this message:
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PaulK
Member
Posts: 15204
Joined: 01-10-2003
Member Rating: 3.4


Message 30 of 285 (672256)
09-05-2012 8:55 AM
Reply to: Message 29 by Percy
09-05-2012 8:30 AM


Re: My Take
I wouldn't cheer. The investigations as proposed are very susceptible to false positives, to the point that it appears that a "positive" result is almost inevitable, no matter what the truth is - which makes them scientifically useless. Pointing that put goes beyond nit-picking.
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