I was short with Joe Felsenstein in the comments section of “Stark Incompetence,” a post in which I address, well, um, the stark incompetence on display in a recent publication of Eric Holloway. I have apologized to Joe, and promised to make amends with a brief post on the topic that he wants to address. Now, the topic is a putative model that Eric introduced in “Mutual Algorithmic Information, Information Non-growth, and Allele Frequency” (or perhaps an improved version of the model). Here is a remark that I addressed to Joe:
Tom English: As you know, if a putative model is logically inconsistent, then it is not a model of anything. I claim that that EricMH’s putative model is logically inconsistent. You had better prove that it is consistent, or turn it into something that you can prove is consistent, before going on to discuss its biological relevance.
I will not have to go far into Eric’s post to identify inconsistencies. After explaining the inconsistencies, which I doubt can be eliminated, I will remark on why the “model” is not worth salvaging. The gist is that Eric’s attempted analysis puts a halting, output-generating simulator of a non-halting, non-output-generating evolutionary process in place of the process itself. An analysis of the simulator would not, in any case, be an analysis of the simuland.
Inconsistency
In the following passage from his post, Eric describes a randomized procedure, dubs it an evolutionary algorithm, and then asserts the existence of a halting program that implements the procedure.
The alleles are 1s and 0s, and the gene G a bitstring of N bits. A gene’s fitness is based on how many 1s it has, so fitness(G) = sum(G). The population consists of a single gene, and evolution proceeds by randomly flipping one bit, and if fitness is improved, it keeps that gene, otherwise it keeps the original. Once fitness(G) = N, the evolutionary algorithm stops and outputs G, which consists of N 1s. The bitstring that is N 1s will be denoted Y. We will denote the evolutionary algorithm E, and it is prefixed on an input bitstring X of length N that will be turned into the bitstring of N 1s, so executing the pair on a universal Turing machine outputs the bitstring of 1s: U(E,X) = Y.
The first thing to note is that the randomized procedure is not an algorithm: it halts with probability less than one. That is, by a simple inductive argument, for all natural numbers 
the probability is less than one that the procedure halts after 
or fewer bit flips. Indeed, the probability is greater than zero that the procedure performs bit flips without improving fitness. Thus if you were to turn the procedure into an algorithm by stipulating that it performs at most 
bit flips, there would be a nonzero probability that gene 
remains equal to input 
when the algorithm halts, no matter how large you make 
The problem is not the particular randomized procedure that Eric has chosen. Evolutionary procedures do not converge surely to local fitness maxima in discrete spaces (except in trivial cases).
It is gobsmacking for me, though probably not for you (I labored over “Stark Incompetence” in hope that everyone would be as astonished by something coming from Eric as I am by many of his claims), to see Eric flatly assert that the randomized “algorithm” is a program for a deterministic computer. To put it plainly, a universal Turing machine cannot flip bits randomly. Eric’s “model” is inconsistent, and thus is not a model. To get randomness, Eric must
- draw the deterministic bit-flipping program
randomly, or - endow the deterministic bit-flipping program with a pseudo-random number generator, and supply the program with a random seed as input (along with
).
).However, this will not produce consistency, because Eric has predicated, with the expression 
that the program surely halts with an output that is maximal in fitness — no ifs, ands, or buts. His subsequent argument requires it. But his prior specification of the random bit-flipping procedure does not allow it.
The map is not the territory
Computer programs used by scientists to model evolutionary processes commonly signal the occurrence of events of interest to the scientists, and halt when the scientists are uninterested in gathering further data. An exceedingly naive response, most prominently on display in the “evolutionary informatics” of Marks, Dembski, and Ewert, is to analyze a program, and claim that the analysis applies to the modeled process — as though the evolutionary process itself signals the occurrence of events and halts.
I am not going to dig into Eric Holloway’s attempt at analysis. You should be able to see for yourself, if you have any business discussing what he has done, that it is literally the program 
that enters into the analysis, and not the evolutionary process that is simulated by the program. It ought to be obvious that an evolutionary process does not “know” when fitness is maximized, let alone announce the genome for which fitness is maximal. The part of the program that detects and announces the event in which fitness is maximized, and subsequently halts, is not part of the (simulation of the) evolutionary process. It is a monitor of the simulated process, and can be decoupled from the simulation per se, even though it is usually tightly coupled with the simulation in practice. I advise against struggling to make Eric’s inconsistent “model” into one that is internally consistent, because the result would be a bogus, though consistent, “model” that mistakes the simulation software for the evolutionary process itself.
Right, happy accidents.
Why are you calling it different language? You just agreed that’s what the theory claims.
You just hate that I spell it out so clearly. I can certainly understand why.
Here’s a number of examples of phoodoo appearing to confuse his ability to declare something to be ridiculous or unacceptable, with it actually being unacceptable.
No arguments here, just a couple of blind assertions and then the statement of your disapproval. It’s not “very convincing” (what you find convincing isn’t an argument for or against anything). It’s “a whack theory” in your view, but you never show there’s anything wrong with it.
Here you’re not even stating that it’s wrong or somehow misguided to accept evolution, you’re just sort of implying it by acting out a person in a state of disbelief.
This one is of course a literal caricature.
Mutations are accidents, which you appear to think nobody could possibly accept. The ridicule is implied. No argument is actually made.
Here you laugh at the folly, which you find delusional. But there’s no argument there, you never establish that it is follow. You just state that you think so. Congratulations.
Again you laugh at labels for things. Random lucky accidents is something you laugh at. You definitely don’t believe it. You don’t establish that someone shouldn’t, you just state that you don’t.
Again here putting on the act of being suprised anyone would believe in “accident”. No argument of any kind is made.
And so on and so forth. A never ending stream of rationally vacuous, emotive statements and ridicule. No arguments are ever made from you, it’s just various fanciful ways you have of acting out your disapproval and disbelief. That appears to be all you really have, your ability to state over and over again that you disapprove and find it ridiculous.
Nobody is under any obligation to refute your incredulous stare.
No actually the problem is that you are NOT spelling it out at all. All you have are different labels that you appear to think establish that evolution must be wrong and should not be believed. But you don’t ever show this to be the case.
Can you try to explain why one should not accept a theory of “random lucky happy accidents”?
It seems to me that “random lucky happy accidents” is a fully fleshed out theory compared to, well, nothing at all which is what phoodoo actually has on offer.
So, as a starting point “random lucky happy accidents” sounds great to me. Shall we take it from there? Unless, of course, anyone has anything better to suggest?
I refuse to accept modern physics. It uses happy accidents to explain why particles diffuse in a solution. They call it “Brownian Motion”, but I am not fooled, it is just a theory of happy accidents.
phoodoo,
Most of arguments I see used against ID are straw-man arguments because the mechanism (mind) does the job and so far no cellular mechanism has been identified that we can test or even model.
OMagain,
You assert; nothing at all. The mechanism (mind) does the job at least for generating functional information. Yes it has limitations but the straw-man arguments are a result that the grand claims of evolution are not supported by any natural mechanism so far. Get to work and find a mechanism that really explains life’s diversity.
FFS Bill learn a new song. Your “magic mind did it” stupidity is way too stale and boring
It does? What limitations?
Corneel,
It does? What limitations?
Like the claim that something is random. Now what do you do with it?
I don’t understand. The creations of “mind” are not random but intentional and purposeful. So what are the limitations?
Bill doesn’t have any idea. He’s making up this shit as he goes along.
Oh good. That saves us the trouble of having to erect strawmen.
Nope. Is your “friend” a fish-brain? This has been discussed.
“Natural Selection fails since survival is not directly tied to phenotype and “survival of the best adapted” is tautological. In a small farm, only organisms closely related to their wild cousins survive, but agribusinesses select for chickens with oversize breasts and research labs select for populations with specific genetic mutations requiring tight environments to survive. As shown, all these different organisms may or may not survive regardless of their phenotype. The only measure of “selection” is survival – we only know if an organism was selected if it survives and reproduces. “Best adapted” is also unknowable separate from survival.”
If they’re selecting for oversized chest muscles, then only those with the most amount of chest muscles get to breed. Hence their reproductive success (not merely “survival”) is directly tied to their phenotype.
Fail again.
Fail indeed to comprehend. When do we know? “Post facto”.
IOW, is “oversized chest muscles” deleterious or beneficial? IT DEPENDS!
Survival and reproduction . A genotype can have higher fitness even if its probability of survival is lower, provided the expected number of offspring the surviving individuals have is enough higher. Any evolutionary biologist knows that. But don’t expect nuance like this from Mr. Loudmouth.
Joe Felsenstein,
And the niche!
And the niche!
Alan approved.
Probability of survival is not a real concept Joe. Fitness is a measurement of offspring.
Care to take Jock’s little school exam-Do you think it would be possible to detect a “deleterious” mutation without any information whatsoever about survival of descendants?
My, thank you for the unequivocal response.
You are, of course, unequivocally wrong.
By way of example, I offer you the following mutation.
The 24th nucleotide of the coding region of human FVIII (under NC_000023.11 Chromosome X Reference Sequence GRCh38.p13 Primary Assembly, that’s nucleotide #155,022,529 on the other strand) is mutated from C to A.
This is deleterious.
I know this is deleterious without any information about the survival of descendants.
I could offer up other similar mutations that we know have occurred, but you might complain that I had information about the survival of the descendants. You’d be wrong, but that really does not seem to inhibit you at all.
(My mutation of choice leads to a very premature stop codon in the FVIII gene. These are the types of patients who develop inhibitors when treated with recombinant FVIII…)
Spectacularly wrong. Biologists do before-and-after observations all the time and calculate probabilities of survival for different phenotypes. Most of these observations don’t look at offspring at all.
Corneel,
The limitation is what do you do after you conclude design. The same issue is what do you do when you conclude the data is random.
The only thing left is to falsify your conclusion as you have hit a wall science cannot go through.
DNA_Jock,
What’s the definition of deleterious?
If it’s reduced organismal fitness, and the definition of fitness is the number of offspring (which we have been over a hundred times, and it always comes back to that, no matter how much you guys try to dance around it), then sorry, you don’t get to claim others are wrong.
Before and after observations of what? Not offspring?
Told you he was making up this shit as he goes along. 🙂
phoodoo,
expected number of offspring, phoodoo.
Learn the difference.
So nonlin is unequivocally wrong.
As are you.
To put it in terms you might understand: nonlin claimed that it was impossible to ever be able to predict survival and fecundity. I provided a counterexample.
You think that the fact that super-awesome specimens sometimes meet untimely deaths disproves evolution. It doesn’t.
How does one even make sense of your statement?
Of course one can determine a probability of survival for all sorts of circumstances, such as when sea turtle eggs hatch and the offspring have to make their way back to the ocean. There is obviously some fraction of them that gets killed, hence we can calculate an average probability of any one of them surviving.
And we can compare the preponderance of certain alleles between survivors and the dead.
You have quite a task ahead, Eric:
Tom English: As you know, if a putative model is logically inconsistent, then it is not a model of anything. I claim that that EricMH’s putative model is logically inconsistent. You had better prove that it is consistent, or turn it into something that you can prove is consistent, before going on to discuss its biological relevance.
Since you already have a clue what’s going to happen just in case you get your math right:
In other words, as soon as you fix your math, Tom and Joe will question whether your math applies to biology (They claim their math applies to biology because of …you know…fitness). But, if need be, they sure will use the super-natural selection to fill any mathematical gaps in their theory, as they should, as the true worshippers of super-natural selection…
How do you feel about this predicament, Eric?
BTW: I personally feel that the classical information theory doesn’t have much application to biology, if at all. At some point, one would have to apply the information theory to DNA and then Shannon entropy and Von Neumann entropy would have to be considered. In other words, quantum information supersedes classical information, if applied to biology, such as in case of DNA.
On what basis do you scientifically conclude design ? You said the approach to the attributes of the designer is a theological question. You conclude that something beyond scientific knowing did something , somehow, for some reason therefore a large majority of biologists are incorrect
Bold talk for a one-eyed fat man , metaphorically speaking.
Throwing two dice is random, but seven comes up more often. That hardly seems the same issue as what are necessary attributes of the designer’s mind and explain in a step by step manner how the designer with this mind , manipulates matter.
When you hit a wall you just keep searching . Left ,right ,up ,or under.
Is curiosity unknown among intelligent designists?
Oh can you now? Then after the survivors are dead do you count them in the dead column or do they stay in the survival column?
The answer is, of course, no you can’t.
Tell me something, this should be easy, is tall fitter or is short fitter? Can we just count?
DNA_Jock,
Jock, I have made a model that shows in one hundred years from now, there will be more poodles than any other dog breed. Because of my prediction, according to your definition, the poodle is the most fit dog in the world.
Definitions are hard to live with sometimes Jock. Platypus, also very fit. My model says so.
They carefully miss the point, but I’m still planning to address their take on things. Plus, though my proof is invalid as stands due to my sloppiness, it is easily correctable.
Now regarding Felsensteins question, dealing with runtime is a bit trickier when it comes to AIT, since normal AIT deals with any computation that halts, regardless of how long it runs. But, there are still some straightforward identities. E.g. any time bound AIT is going to require more information than traditional unbounded AIT. So any problem posed by traditional AIT becomes even more difficult when we have a time bound.
What mathematically distinguishes quantum info from Shannon?
I had difficulty trying to understand what the hell phoodoo was on about here, but I tracked back and realized that he was having trouble with the expected in ‘expected number of offspring’. He interpreted the word as meaning “expected” in the colloquial sense, under some model that he would be free to invent.
No, phoodoo, the expected number of progeny is simply the sum of xi.p(xi) over all xi.
It’s a math term. There’s no requirement for a model. Particularly not to predict that on average a male hemophiliac with a null mutation will have fewer progeny than those with a regular FVIII gene. Something which you and nonlin claim it is not possible to predict.
Um, from, say, newborns to adults who have survived long enough to be getting ready to reproduce. You can look at shifts in genotype frequencies and from them get estimates of relative fitness.
Any survivors who are dead at the second time point are, by definition, not survivors.
For a phenotype like height, we have to be careful because it is changing over the course of individuals’ lives.
For a short time period, say a snowstorm hitting a flock of sparrows, we may be able to observe survivors as well as dead ones, and compare the distributions of characters among them. Here is exactly such a study, with all of its data available. It is Hermon Bumpus’s pioneering and classic 1898 study on sparrows knocked down by a storm. He actually publishes a table showing all of his data. Have fun. Analyze the data yourself.
EricMH,
You have made the mistake of assuming that JMac is putting forward a coherent position on something-or-other. I think you must not have read his past comments.
Quite right. Let me add that, if ever the handiwork of “mind” will be scientifically confirmed, scientists can and will investigate further. What would stop them from learning about the methods used, motivations for, chronology of, etc, etc of Designed entities?
So this “limitation” seems self imposed, right?
Perhaps, but it intrigues me. Bill is not the only IDer that is reluctant to investigate or even speculate on [mind/Intelligence/Designer] itself. All IDers desperately crave scientific confirmation of the existence of God, but at the same time they all refuse to investigate Him. I don’t understand that. If you don’t like the idea of scientists poking into His business, then why insist that ID creationism is science?
ETA: less mangled grammar
I have discussed purifying selection on devastating genetic diseases with both phoodoo and Nonlin before. At those times, phoodoo accepted that it occurs but denied that it is relevant for non-disease traits. Nonlin, of course, went into full denial mode.
Oh is that so? How tall is the male hemophiliac? Big schloong or small? Does he have good lung capacity? What’s his face symmetry like? Does he have a great singing voice? What if he looks like Brad Pitt, does that matter?
You are going to pick apart EVERY aspect of his genome and factor that in as well, or can we just pick and choose the factors we think are most relevant?
Yes, definitely.
If they die in the window of time when you count, they are not survivors. Obviously.
But you can. For example, mortality and fecundity rates are real things. We do it for humans too, we look at the mortality of people in different income groups, different educational backgrounds, immigrants vs natives, different states, different cities, different countries. How many children they have and so on.
And yes, they basically just count. Literally just add up each individual case.
You can in fact do that, and it is really being done. Counting is a real thing.
Yes we can just count. You have learned to count right? Are you truly this blasted or merely pretending?
Define your limits (at what height does it change from short to tall?), then count(for example) the mortality and fecundity of both cohorts over some finite period of time, and compare them. Simple.
Eric,
I’m not a mathematician, so I’m going to pretend.
Perhaps this will answer your question:
https://www.quora.com/What-is-the-difference-between-Shannon-entropy-and-Von-Neumann-entropy
Keep in mind that on quantum level DNA is all about quantum states: the information about quantum correlations. For information in DNA to increase, quantum information about quantum correlations would have to increase. This is not possible due to the conservation law even though Joe claims super-natural selection can do anything and everything…
Yes. Supernatural selection is omnipotent is your most coherent answer. Who can argue with that? Why would anybody argue with that? It’s the best argument-the supernatural selection of the gaps…
EricMH,
What’s your email address? I’d like to email you something interesting, if you wish.
Jmac
God. J-Mac. I missed your comments so much.
newton,
On the basis of what you observe is explained by a mind. Biologists are not all incorrect. Many realize we don’t have a good mechanistic explanation for the diversity of life.
Throwing two dice is not random. It is a stochastic process with a predictable distribution. You are trying to invoke a straw-man argument.
Science should continue to try and falsify the design argument. The falsification however requires a tested hypothesis.
Corneel,
The discussion of the identity of the designer is a diversion and has nothing to do with whether the theory is scientific. The theory is required to keep evolutionary theory from being a collection of “just so stories” and untested assumptions.
IDiots first need to make a coherent argument for “design” and support it with some positive evidence. Science doesn’t need to falsify what has never been demonstrated in the first place.
We’d ask you for ID’s tested hypotheses but we know that question always sends you whimpering and running for the door.
Just like the “Magic Pixies Pushing Rocks Around” idea is required to keep geology from being a collection of “just so stories” and untested assumptions. Right Bill?
Well, phoodoo, for many deleterious alleles, we can pick the factors that we think are most relevant. Here’s another SNP — A to G in the Iduronidate-2-sulfatase gene.
But suppose that, instead of a G, the base mutated to a T.
Again, that would be introducing a premature stop codon early in the transcript. Boys who are I2S null do not survive to adulthood. I could go on. And on.
It is rather sad that Corneel walked you through this over two years ago, yet you remain proudly ignorant, still singing the same old song.