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.
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.
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.
quote: 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.
So far as I can tell this "distinction" relies on a double standard. Under both hypotheses we expect extra genes in the LUCA. In the case of non-telic evolution the fact that we can't guarantee it is used to disqualify it as a prediction, in the case of FLE this criterion is ignored. Without a real distinction there's no case here.
quote: 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."
There still doesn't seem to be much of a case here. Or even an attempt to provide an analysis. There is a pretty limited selection of bases that are likely to be available, so analysing the alternatives would seem to be the next step but I don't see any sign of that having even been tried.
The other point is that if this can happen, then it is likely that it has happened at some point in evolutionary history. The only interesting claim is that a "hidden" structure was designed in, but we can't determine that just by finding a case where C->T transitions have produced useful genes.