The $5,000,000 ID Research Challenge

I've been absent for a bit, but now I'm back. I'll post my thoughts here shortly.

And: 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 ProgramI. Front-loaded Evolutiona. 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 Flagelluma. 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?

Double post.Edited by Admin, : Remove content of double post.

Ooops, double post (I keep doing that).

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

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. 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.

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.

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: 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.

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.

And: 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.

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

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

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. 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. God is potential? What does that even mean?

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

Geez, thanks. Now please respond to my points.