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Author Topic:   The $5,000,000 ID Research Challenge
Genomicus
Member (Idle past 734 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 734 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 734 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 734 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).

  
Genomicus
Member (Idle past 734 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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Genomicus
Member (Idle past 734 days)
Posts: 852
Joined: 02-15-2012


Message 32 of 285 (672277)
09-05-2012 7:01 PM
Reply to: Message 25 by Taq
09-04-2012 1:24 PM


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

Yes, but a fundamental distinction needs to be made. In one instance (the non-telic model), we are simply able to explain the potential observation that the LUCA had unnecessary genomic information. On the other hand, the front-loading hypothesis predicts that the LUCA had unnecessary information. Confirmation of predictions is a very crucial part of science, and a track-record of successfully confirmed predictions is what catalyzes the elevation of a scientific hypothesis to the level of theory.

It would be relatively simple to falsify front-loading. If it was found that the LUCA possessed only those genes necessary for life, the front-loading hypothesis would have been effectively falsified. Thus, it is possible to test the hypothesis, and it is the testing of ID hypotheses that would make up an ID research program. This is what this challenge is all about, after all, if I am not mistaken.

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.

Two points:

1. When it comes to cytosine deamination specifically, there is nothing in evolution that would have caused A-T transversions (sorry Taq, but the phrase "A-T transitions" is technically incorrect) to be favored precisely because it is chemistry that causes cytosine deamination. In short, we are met with the following objective fact: cytosine is part of DNA, and cytosine is prone to deamination. If DNA was engineered, then we need to account for why cytosine was chosen instead of a base that was not so prone to deamination (indeed, it has been argued that no engineer would use cytosine as a base in DNA because of this). Curiously, if we look to the genetic code, we see an interesting pattern: the vast majority of non-synonymous mutations that result from C --> T transitions increase hydrophobicity. We therefore have the first basic step in the scientific method: make an observation. Next, we can ask questions, such as "why has this pattern been chosen for the genetic code?" Then you form a hypothesis: from an ID perspective, a plausible explanation for this pattern is that it can be exploited for front-loading, such that an initially designed protein fold can turn into a completely novel fold quite quickly through multiple cytosine deamination events. It would be an effective mechanism for producing key multi-cellular specific proteins, particularly for molecular machines that have system-dependent parts. Next, we'd go out and experimentally test this hypothesis. Then the results would be analyzed and we'd determine if the hypothesis has been falsified or strengthened. I fail to see how following the scientific method ends up as the "Sharpshooter fallacy."

2. You've brought up the Sharpshooter fallacy before, and it's a quick way to dismiss the various hypotheses I have discussed before (e.g., the design hypothesis proposed in the "Nature's Engines and Engineering" thread, and front-loading). However, IMHO you've never really succinctly defined how I'm using the Sharpshooter fallacy. The whole ID position is that some of the actually existing features of life were designed. So if one were to argue that the flagellum was designed based on its discontinuity from the rest of the biological universe, you could easily say "Sharpshooter fallacy." But there really wouldn't be any rational basis for that. A much better approach would be to examine if the flagellum actually does have discontinuity from the rest of the biological world.

So how precisely am I using the Sharpshooter fallacy, and what exact definition of the Sharpshooter fallacy are you using?

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 25 by Taq, posted 09-04-2012 1:24 PM Taq has responded

Replies to this message:
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Genomicus
Member (Idle past 734 days)
Posts: 852
Joined: 02-15-2012


Message 100 of 285 (683128)
12-07-2012 6:16 PM
Reply to: Message 95 by Taq
12-05-2012 3:43 PM


Re: spend it on space exploration/ Brain research.
Douglas Axe is doing work in a laboratory, but it turns out to be lame attempts to disprove evolution and not anything that is directly testing ID.

What he tried to do is take two enzymes that are proposed to have developed from a common ancestral sequence, and then show that you can not get one from the other through a series of mutations. What he did was commit the Crocoduck fallacy. He tried to show that one modern enzyme could not evolve into another modern enzyme. Of course, we know that this is not how evolution works.

I respectfully disagree with your interpretation of Doug Axe's work ("The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway"). The point of the study, as I understand it, was not to demonstrate that since the two enzymes could not plausibly evolve into another, they did not evolve. Rather, the point was that it is not very plausible for one enzyme to evolve into another one with a different function. I do have issues with Doug Axe's argument and study, which I will not outline here at the moment.


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Genomicus
Member (Idle past 734 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 101 of 285 (683131)
12-07-2012 6:26 PM
Reply to: Message 98 by Taq
12-07-2012 11:11 AM


On Testing Intelligent Design
I am looking for something much more concrete. I am looking for experiments that actually put ID at risk just like every other hypothesis in science.

At best, I think we can both agree that ID is not in the position to construct scientific hypotheses. If this is the case, then the challenge will have to be revisited.

The problem is that the ID movement, as characterized by the Discovery Institute, is quite obsessed with disproving Darwinian evolution, instead of constructing a positive hypothesis of intelligent design. Some of the leading proponents of ID admit as much; for example, Paul Nelson has said that:

Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as ‘irreducible complexity’ and ‘specified complexity’-but, as yet, no general theory of biological design.

Nevertheless, there has been precious little effort within the ID movement to propose a testable design hypothesis. If the ID movement is to make any significant progress in academia, it will have to divorce itself from any religious underpinnings and formulate a hypothesis of biological design. Unfortunately, a lot of ID proponents are content with merely finding flaws in the current theory of biological origins. This has got to change within the ID community, or else we'll see a continual decay in the movement.


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Genomicus
Member (Idle past 734 days)
Posts: 852
Joined: 02-15-2012


Message 153 of 285 (687608)
01-14-2013 12:24 PM
Reply to: Message 149 by tesla
01-13-2013 5:01 PM


Re: Sigh.
Tesla,

I don't think you're at all providing a testable ID hypothesis. If you want an idea of what kind of testable hypotheses we're asking you to provide, see my message 21. To be sure, my proposals have had a fair share of criticism. But they might give you a rough idea of what we're looking for.


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 Message 149 by tesla, posted 01-13-2013 5:01 PM tesla has acknowledged this reply

  
Genomicus
Member (Idle past 734 days)
Posts: 852
Joined: 02-15-2012


Message 174 of 285 (687747)
01-16-2013 9:55 AM
Reply to: Message 168 by Phat
01-15-2013 2:14 PM


Re: Hypotheticals
But I think IDists are far from conceding that it could happen. Their desired outcome is that intelligence is necessary but our intelligence is insufficient. Any research they did would be shooting themselves in the foot.

And:

And I would agree that our intelligence is insufficient...at least as far as creating anything much bigger than the Panama Canal or a super collidor.

Of course, we are rapidly approaching the day where human intelligence will be able to create synthetic life. See, e.g., Rasmussen et al., 2003.
This is not a problem for ID (unless one has a religious agenda). If anything, it adds support to the plausibility of the notion that an intelligent civilization somewhere in the universe could have designed biological life. Naturally, the origin of life is a historical question, and not merely a question about plausibility. So we must not only establish the plausibility of the intelligent design of life, but also provide evidence for that view. But, hey, a whole bunch of the evidence that supports the RNA world hypothesis merely supports its plausibility. For example, observations which demonstrate that RNA can catalyze its own replication say nothing about whether self-replicating RNA was indeed the precursor to modern cellular life.

Reference
Steen Rasmussen, Liaohai Chen, Martin Nilsson, Shigeaki Abe, 2003. Bridging Nonliving and Living Matter. Artificial Life, 9(3): 269-316.

Edited by Genomicus, : No reason given.


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Genomicus
Member (Idle past 734 days)
Posts: 852
Joined: 02-15-2012


Message 179 of 285 (688517)
01-23-2013 9:53 AM
Reply to: Message 177 by tesla
01-23-2013 9:47 AM


Re: Chicken or the Egg?
What I'm saying is there is no magical science of I.D.

I.D. is the chapter of science that includes the acceptance of the potential of God, and wishes to seek God through legitimate science.

No, ID is the proposal that life on earth was designed by some intelligence or intelligences. It has nothing to do with gods.


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Genomicus
Member (Idle past 734 days)
Posts: 852
Joined: 02-15-2012


Message 185 of 285 (688554)
01-23-2013 2:05 PM
Reply to: Message 181 by tesla
01-23-2013 1:10 PM


Re: Chicken or the Egg?
God defined: " higher being/intelligence/consciousness/ (other definitions?)

That's not the standard definition of God, though, is it? By that definition, an alien race with just a little more intelligence than us would be deities. Let's stick to established definitions instead of making up our own


This message is a reply to:
 Message 181 by tesla, posted 01-23-2013 1:10 PM tesla has responded

Replies to this message:
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Genomicus
Member (Idle past 734 days)
Posts: 852
Joined: 02-15-2012


Message 186 of 285 (688558)
01-23-2013 2:30 PM
Reply to: Message 182 by tesla
01-23-2013 1:22 PM


Re: Chicken or the Egg?
A technologically advanced life form that split DNA between their species and a species of earth to create 'man' would be 'God' in the eyes of some. I.D. states intelligently designed, by some designer.

Really? Such advanced life forms would only be "God" in the eyes of someone who has little mastery over the English language. ID states intelligently designed by some designers, but there's no need to bring deities into the discussion.

God is defined in many different ways, but every definition I know includes superior knowledge and/or consciousness.

It includes superior knowledge but that's not the only characteristic attributed to deity. Again, let's not start making up our own definitions. If you want a definition of God, you may examine the contemporary philosophical literature on the subject.

So all I'm getting from you is ignoring all that data I have just stated in a simple post, that God is potential, and it's time we explore those potentials with legitimate science, and reach out to the religious who already seek God with all their minds and hearts (and money) to give those of us who desire to know, a path to begin seriously looking.

God is potential? What does that even mean?


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Genomicus
Member (Idle past 734 days)
Posts: 852
Joined: 02-15-2012


Message 193 of 285 (688589)
01-23-2013 6:42 PM
Reply to: Message 189 by tesla
01-23-2013 5:30 PM


Re: Chicken or the Egg?
You are not very educated are you?

That may be true. My education, or lack thereof, however, is irrelevant to this discussion.

How about an etymology of the word God since you’re so convinced I'm using it wrong. Shall we?

Yes, we could go down that route. Or you could see how the contemporary philosophy literature defines "God." This is not to say that there is any fixed definition of "God." But of all the definitions philosophers will offer up, none of them amount to merely a being that possesses higher intelligence than humanity.

God is potential? What does that even mean?

It means you do not have any understanding of the English language.

Mmk.


This message is a reply to:
 Message 189 by tesla, posted 01-23-2013 5:30 PM tesla has responded

Replies to this message:
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Genomicus
Member (Idle past 734 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 197 of 285 (688598)
01-23-2013 7:28 PM
Reply to: Message 196 by tesla
01-23-2013 7:18 PM


Re: Chicken or the Egg?
I had thought you were educated and giving me a hard time.

Geez, thanks. Now please respond to my points.


This message is a reply to:
 Message 196 by tesla, posted 01-23-2013 7:18 PM tesla has responded

Replies to this message:
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