Eric Holloway: Honest Questions on Information Theory

@EricMH you seem to be making an honest effort to bridge the gap of understanding between us. I’ve been engaging with you for a while now. I’m going to be thinking carefully about how to most efficiently and clearly make the point to you, given how you specifically are thinking about this.

I’m not sure when I’ll get time and inspiration. I don’t want you to think I’m blowing you off either. I think its possible we could turn the corner together on this.

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3 posts were split to a new topic: The Great Computational Biologists Are All ID?

Great. I’ll continue working on the experiments you suggested. But, I think the main takeaway from this exchange is there is empirical work that can be done on this question, which is the minimal ID position. At the very least, ID can be empirically shown to be wrong and falsified, which would be great. And that makes ID a scientific hypothesis, though a potentially wrong headed hypothesis.

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The only way I can agree with this is if we are clear that ID, in this case, cannot refer to divine intelligence. With that restriction, it is a valid and worthwhile effort. Modifying it thusly, I could also agree:

At the very least, ID can be empirically shown to be wrong and falsified, which would be great. And that makes ID (of divine intelligence) a non-scientific but important hypothesis, though a potentially wrong headed hypothesis.

Detecting divine-design I think is a valid effort that could be valid, evidential, and science-engaged. I’d encourage such an effort, but only think it could work with sustained and explicit engagement with theologians and philosophers. They have to be part of the conversation too.

A simple proof would be the difference between the probability distribution generated by the system dynamics and a significant enough observed divergence from this distribution. Essentially the same thing as CSI.

Why is this restriction necessary to make it science? If halting oracles are necessary to explain what we see, and physical processes cannot be halting oracles, then the necessary explanation for our world is a divine intelligence. That is just deductive logic.

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You don’t have to agree. I holds this view of theological, philosophical, and scientific reasons. I’m just telling you what I can agree with, and I already have explained why on the forums several times.

Yeah, I know. Except we’ve shown that it is, in practice, not possible to compute this probability distribution (Predictability Problems in Physics). Admittedly this is for physics rather than biology, but biology is more complex. Eventually, I’ll get around to showing you what ASC is actually telling us, and how we are applying things like it to understand biology. When I have the time, it will clarify how it doing something very different than “design detection”.

Moreover, even when you are computing FI, you are not computing it correctly (Swamidass: Computing the Functional Information in Cancer). This thread on cancer was just for you @EricMH. I make immediate sense to the physicists, and they can follow my math. It also clarifies the error being made in Durston’s work, and the rest of the ID literature with an example. I hope you can look at that closely and understand it.

It is deductive logic with flawed premises.

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I have a question for you @EricMH. I’ve been really impressed by your sustained engagement here. I haven’t seen a hint of unkindness from you. Frustration at times, but very rarely. You seem to be genuinely engaging with what I am saying, and with others. You also seem to be acknowledging limitations in ID as you come to see them. I have a lot of respect for that.

You also worked closely with Robert Marks and Bill Dembski and the rest of the ID informatics crew. I imagine you are friends with all of them too.

Tell me what it was like working with them? Are they equally engaged with thoughtful critique as you? Would they also admit if they made a mistake, even if it was small? Are they contemplative about these things in the same way you seem to be?

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More or less. As with your side, there is a sort of polemic going on that makes either side unwilling to admit something is a mistake or unknown, unless it becomes really clear. Doesn’t impress me for both of you. At least it is understandable, though not excusable, with the ID crowd, since there is real persecution going on there.

However, my subjective opinion is the ID side is better at being honest about their shortcomings, and being conservative in their pronouncements. Especially Dembski, Marks, Ewert and Montanez. Marks and Ewert especially have shot down a whole lot of my ideas, because they thought the ideas didn’t hold water. I’ve also seen you change your mind a bit in our discussions, and that “builds trust” as you put it.

The worst at admitting their shortcomings, are at places like The Skeptical Zone, or people like Shallit and Tom English. Tom English especially, because he actually seems to know what ID is saying, and agrees with it (or at least cannot disprove it), but would rather insult and harass people like Ewert.

And it is this last group that has been some of the most influential in convincing me to be interested in ID. Why must they spend so much time insulting and harassing ID people, and disproving a lot of strawman arguments instead of disproving ID itself, if there is nothing to it?

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Very good question. It seems very insecure, doesn’t it?

I agree about @Winston_Ewert, as I’ve seen this firsthand. I like him.

Can you point me to any place where Dembski or Marks has been “being honest about their shortcomings”, or retracted an error, or identified fallacious ID arguments that have been put in public?

For example, take a look at this:

Did Dembski ever explain why this paper is not valid, and explain how they went wrong? Why is it still on the DI publication list?

Don’t know anything about this. But, a cursory glance at the abstract makes it seem legit. I’d be curious what rebuttals there are.

I know Dembski has refined his explanatory filter to CSI. Don’t know of anything wrong he has said that requires retraction.

I have seen a lot of, what seems to me, false hysteria regarding his claims in general. It is understandable why he wouldn’t want to cater to that crowd.

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@evograd take the honors on this one?

I remember coming across a comment in some blog by Dembski stating that he abandoned the Explanatory Filter (which he initially put forward in his 90s book The Design Inference) in favor of CSI.

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From my blog post:

2. Vladimir I. shCherbak and Maxim A. Makukov, “The ‘Wow! Signal’ of the terrestrial genetic code,” Icarus, Vol. 224 (1): 228-242 (May, 2013).

This one is interesting. It purports to show a “wow signal” in the standard genetic code – the code that determines which codons are translated into which amino acid. The authors claim that they have detected a signal (mathematical pattern) in the genetic code that can’t be explained naturally, and therefore points to the genetic code being intelligently designed by ET. There are a myriad of problems with this, the key one being that the analysis boils down to numerology. PZ Myers wrote a blog post on this paper shortly after it was published, which I would recommend everyone read. I’ll be paraphrasing him and some other commentators. Numerology is the practice of juggling arbitrary numbers around in an arbitrary fashion in order to find some of kind interesting patterns, which are then proclaimed to be somehow meaningful.

The paper chooses to assign a “nucleon sum” to amino acids, which are equal to the sum of protons and neutrons in a given amino acid. This sum can be calculated for the R group and for what the authors call the “B group” – the “backbone” of the amino acid that is common to all amino acids. They chose the sum of protons and neutrons (the atomic mass) in the amino acid instead of the atomic number, the number of electrons, the number of quarks, the number of bonds, any sum of any subset of these, or any kind of numerical value of the molecular shape of each amino acid without justification. They chose to add the numbers rather than any other mathematical function without justification. They smoothed over any inconvenient quirks in the data – for example proline has a B group with a nucleon number of 73 while all the others have 74, so the authors casually move a hydrogen atom from proline’s R group to the B group without justification. 74 is important because it’s 2*37, and 37 is a special prime number to the authors because if you sum all the digits of 111, 222, 333 etc to equal 3, 6, 9 etc, and then divide the 3-digit number by it’s sum (111/3, 222/6, 333/9 etc) the answer is 37! Why is this interesting mathematical phenomenon relevant to the genetic code? The authors give no justification.

Based on this mountain of arbitrariness the authors report some interesting patterns in the genetic code. For example when they create 2 columns of codons, where each row consists of a codon and it’s mirror image (e.g. ATC CTA, which could just as easily be arranged in the columns as CTA ATC), then it’s possible to arrange the codons in such a way that the sum of the R group nucleon numbers in each column both equal the same value: 703. How is this number special? No particular reason. They report several of these kinds of patterns, all based on the same kind of arbitrary rules, and conclude that since these patterns can’t be explained in functional terms (there’s no reason for the genetic code to show such “special patterns”), they indicate a “wow” signal matching SETI’s criteria. This is messy because mixed in with all the numerology there are real functional relationships between codons at some levels which could serve to slightly increase the chances of finding some patterns when you go looking for them.

We don’t yet fully grasp how the standard genetic code evolved, but there are plenty of studies that offer very plausible hypotheses along the way. This is briefly discussed in PZ’s blog post so check that out. shCherbak and Makukov’s paper doesn’t provide convincing evidence that the genetic code was designed with a special “wow” signal at all.

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Dembski’s 2005 paper conflates probability and expected value, and he has an example where a probability is greater than 1.0. I don’t know what he was thinking.

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This sounds like a criticism, but calling the authors numerologists does not disprove their claims. Perhaps ID might want to distance themselves from authors that PZ Myers doesn’t like, but I don’t see a reason here to retract a statement that the paper is an example of CSI. Prima facie it seems to be, but if it turns out it is easy to get these special numbers given enough different operators then there could be a problem. At any rate, hard to tell whether the paper really is flawed or not based on this exposition.

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I agree!

It would be great to see hear if DI agrees that this article is appropriate application of CSI or not. It would be great to hear that from you too. As it is, it really does look like numerology. I suppose that label is pejorative, and I can avoid it. If paper is consistent with with the best ID theories out their, I’d like to help explain it to people.

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