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.
Many different sources. Excessive and unneeded gene duplicates that suffer deleterious mutations become non-coding. Retrotransposons, pseudogenes, retroviral elements, microsatellite and other types of repetitive DNA.
Bill thinks a disembodied mind used magic to POOF biological life into existence.
Bill doesn’t need any of that evidence stuff. Bill BELIEVES!
We don’t need to falsify “design” in biological life since “design” was never established in the first place. Should science be trying to falsify the idea invisible gravity pixies are responsible for the force of gravity?
False.
dominate
[ˈdäməˌnāt]
VERB
have a commanding influence on; exercise control over.
“the company dominates the market for operating system software”
synonyms:
control · influence · exercise control over · be in control of · command · be in command of · be in charge of · rule · govern · direct · be the boss of · preside over · [more]
be the most important or conspicuous person or thing in.
“the race was dominated by the 1992 champion”
(of something tall or high) have a commanding position over; overlook.
“a picturesque city dominated by the cathedral tower”
synonyms:
overlook · command · tower above · tower over · stand over · project over · jut over · hang over · loom over · dwarf · overtop · overshadow · overhang · bestride · span · straddle · extend across
How can it? How come “natural selection” doesn’t select one allele and instead they all coexist in equilibrium as Mendel shows?!?
It is retard to try to adopt as ally someone that clearly cancels all your stupid claims.
First of many search results. And in fact you need no references if you truly believe your own stupid theory.
https://prepperbits.com/antibiotic-doomsday/
I asked for YOUR fitness function, not more BS.
Your link only shows more baseless modeling of unreal fluff.
I am worried about “target” if it implies that evolution has a target. I agree it can “contribute hugely to misunderstanding”. But mathematical models that have a target can be useful as long as you don’t take the targetness too seriously.
I am a little taken aback by how insistent creationists-and-ID-advocates are that evolution has to have a target. I guess it’s part of thinking of the world as fundamentally teleological. So therefore evolution has to have badly wanted to have wombats.
Some are deleterious, others are beneficial, it comes in degrees. That’s how.
You are asserting a demonstrable falsehood. They don’t all “coexist in equilibrium”. There are alleles that simply don’t exist, because if the mutation were to happen that would create them, the organism would die.
What’s “retard” is to make assertions in demonstrable conflict with observational reality, so please stop doing that.
Another problem with arguing with you is that you are full of mere assertions but we never get to see any coherent arguments or evidence. You just declare things but never support them. It’s a complete waste of time.
It’s part of their “it’s too improbable” deceptive strategy. The can’t even begin to talk about probability unless they have a specific target as the goal.
I understood that, but not this:
I gladly stand corrected.
Rumraket,
There is an apocryphal story that if you drop a penny off the Empire State Building it would go so fast it would kill someone.
See, no wonder you don’t understand evolution. Geez, get a clue.
Entropy already answered it, but just to drive the point home: It doesn’t follow that conserved protein sequences are necessarily designed. Evolved sequences sitting at a fitness peak will also be conserved, for the same reasons.
The reason I commented is because you claimed that fitness was a “vague” concept, whereas you displayed a correct understanding of fitness whenever you were talking about purifying selection. Deleterious alleles will be purged because they reduce the efficiency of the transmission of genetic material. This is especially easy to see with embryonic lethals: they just don’t make it into the next generation.
This in itself demonstrates that natural selection has discriminative power with regard to function, and by extension to biological information. So there is no need to call fitness a vague concept: you already grasped its essentials.
Corneel,
Alpha Actin is not an enzyme with fitness peaks. It is part of an irreducible complex structure called a muscle cell or formally myocyte. Along with myosin and titan it functions to allow muscles to contract. It is the surface area that myosin moves along.
Additional data that supports the design argument here is that there is a slightly different version for the heart muscle (vs skeletal muscle) which substitutes 4 amino acids. This also has no alignment differences among several mammals including rodents and humans. The four substituted amino acids are the same. A remarkable demonstration of mutual information inside living organisms.
What is the design argument for the choice of going with slightly different versions?
newton,
The design argument does not deal with choice as far as I know. You pose an interesting question.
Nope. It’s a protein with fitness peaks.
Stop with this “mutual information” misdirection. Mutual information, here, is just a measure of similarity. You’re just saying that the sequences are highly conserved. Calling conservation “mutual information” doesn’t make your design “inference” any better. It remains as absurd as always.
So, As I said before:
Negative selection and purifying selection are synonyms.
ETA: People write full explanations to you, yet you choose one sentence to “answer” as if there was nothing else explaining what you have missed. I’d read a bit more carefully if I were you. That way you’d avoid making the same mistakes time and again. You might even learn something.
TRANSLATION: “Oops, my omnipotent disembodied mind magic POOF hypothesis is directly contradicted by the empirical evidence. I’d better spew some squid ink and rapidly swim away until the question scrolls off the board”. 🙂
It won’t happen. Bill Cole has decided learning about the science he attacks isn’t in his Warrior For Jesus job description. 🙂
Entropy,
Can you describe how you think these fitness peaks work?
Entropy,
The post is about Eric’s mathematical ideas. Mutual information information is one of his ideas so why not show how it exists in biology?
Adapa,
It is interesting that you think I am attacking science. How would you support this claim? Is everyone who is skeptical about a single scientific theory attacking science?
Or is it only the theories that if falsified put atheism in doubt?
You are right: this is interesting.
First up, Adapa did not claim that you were attacking “science” in general; he noted your reluctance to learn about the science [that] you attack, as opposed to, say, inorganic chemistry, which I suspect leaves you unmoved.
So it is you, Bill, who is making the claim that there is only a “single scientific theory” that you are skeptical about. Furthermore, it is you, Bill, who is describing that theory as the one that, if falsified, would put atheism in doubt.
Science, as a methodology, cares nothing for the theological consequences of its research. Thus your attempt to separate theories on that basis is, in and of itself, an attack on “science”, big picture.
You also implied (unintentionally, I’m sure) that evolution needs to be falsified in order to put atheism “in doubt”. That’s quite the theological motivation and lack of faith that you are displaying there, mate.
Patently false again.
This discussion was about Mendel vs. Darwin and your desire to “merge” them. There’s nothing in Mendel’s work about mutations (at least not in his popular experiments). Hence Mendel simply doesn’t support Darwin at all. Aside from the fact that Darwin was clueless about mutations too (“blended inheritance” and other retardedness).
Also, the idea of “beneficial” mutation is wrong and this was discussed at length: “Survival of descendants is the ONLY thing out there, not “fit”, not “best adapted”, not “selection”, not “beneficial mutations”. To see this, imagine an experiment where you want to determine one of those four without any information whatsoever about survival of descendants. Can you? No way! “
They do in Mendel’s experiments which doesn’t deal with mutations at all. Have you seen one inheritance table? Do you understand them? They’re quite basic.
Au contraire, amigo. Unsupported assertions is what I face all the time. Like this one right here – that Mendel supports Darwin. No, he doesn’t as explained with facts.
Your turn to name one unsupported assertion.
Quick question, Nonlin.org,
Do you think it would be possible to detect a “deleterious” mutation without any information whatsoever about survival of descendants. ?
Asking for a friend.
I think you are evaluating the quality of scientific theories on theological rather than evidential grounds. Only a few scientific theories are regarded by certain religious faiths as incompatible with those faiths, and those holding such faiths invariably question the science rather than their faith. Without exception, scientific theories not regarded as antithetical to one’s faith are accepted as probably accurate, despite perhaps far less experimental or evidential basis.
So, in a backwards way, I think you have nailed it. You doubt ONLY those theories that threaten your faith, and ONLY because they threaten your faith. And quite clearly, your sole criterion absolves you of any need to understand ANY scientific theory in scientific terms.
How about a mutation that prevents an organism from having any descendants at all?
Did you even try and understand what I wrote Bill? If so try harder. Let’s start with the simplest part: mutual information, in the context where you’re using it, is but a measure of similarity. Got it now? Because if you got it, then you’d understand, among other things, that Eric did not invent it, and that you’re using a common measure of similarity for no other reason that it contains the word “information.”
Let me give you an example that shows why your use of the concept is merely a misdirection (even if not intended by you, even if by ignorance): If loads and loads of rocks fell on sand, the sand they’re resting on, and the face of the rocks resting on the sand, would have enormous amounts of mutual information (they’d have shapes looking a lot like molds of each other). It is silly to think that the word “information,” let alone “mutual information,” makes everything a designed product.
You mean like a mutation that makes someone want to be a bachelor, something like that?
Like the Michael Fassbender mutation. Very unfit!
No. Not according to the definition of deleterious and fit that evolution uses.
What deleterious mutation does Betty White have? Being too rich and living too long?
Entropy,
I understand that mutual information did not originate with Eric. Better stated that he uses the concept with his arguments. What do you think the mutual information is of two identical bit strings?
Bachelors have been known to leave descendants.
I see you can’t read for comprehension. You attack anything connected to the evolutionary sciences for the only reason the scientific findings contradict your religious beliefs. Sadly those beliefs and fear of evolutionary sciences have turned you into a compulsive liar. It’s pretty much a standing joke on the web now how you will ask the same stupid question 100X and ignore every last answer you are given. You make willful ignorance into an art form. Congratulations Bill, you’re in Joe Gallien / Sal Cordova / Jorge Fernandez territory. Not something to be proud of.
Only fit ones.
There you go, a definition for fitness.
Isn’t the point of intelligent design is that the intelligence has a wider range of choices in the design assuming ,as intelligent design must , that there exists a designer who chooses to do something and that designer has the knowledge and capabilities to physically manifest those choices?s
So it seems to me , the essence of intelligent design argument is intelligence equals choice.Certainly not the how something becomes manifest.
newton,
The intelligent design argument is about the capability of a mind as a mechanism. What we are observing in cells are long functionally constrained linear sequences and parts that appear arranged for a purpose. Matter and its properties appear to not have the capability to explain the origin of what we are observing in evolution as complexity has increased over time requiring lots of new origin events. The cell itself also does not seem powerful enough to explain these changes on its own.
Bill back with his disembodied mind magic POOF hypothesis. 🙂
They appear and seem that way only to the willfully scientifically ignorant like yourself Bill.
Adapa,
The straw-man kid strikes again. 🙂
The compulsive liar dodges questions about his claims once again! 🙂
Adapa,
The disembodied mind is your claim. You have not shown a single ID person make this claim so if your honorable you should retract it. Again Merry Christmas. 🙂
I’l ask again: if the mind you speak of is not disembodied then what body does it reside in and how was that determined?
You’re now make your usual lame excuse and scuttle off with no answer to the questions. Once a coward always a coward Bill.
Back to repeating the same lie again I see.
Bill Cole at PS: “It would validate that a mind is a mechanism that can build a complex biological trait”
Lying for Jesus won’t get you into Heaven Bill.
Can we try to keep to the topic?
Thanks.
Neil Rickert,
Geez Neil, its like Adapa can’t even call Bill an ignorant liar without you warning Bill to keep it on topic.
Why so hard on Adapa?
I see I should have included phoodoo on that list. Look how jealous he got! 😀
Then it seems the focus of intelligent design argument should be how the mind as a mechanism works. What are the necessary elements required, limitations , how the mind interfaces with the external world, manipulates the external.
So a design argument is those sequences appear to be chosen/ selected by something. Evolutionary theory posits a physical mechanism. ID , the mechanism is a designer’s choice. How that choice is made or becomes physically manifested is of little interest.
Then my question is ,what is the relation of designer’s mind and matter and its properties? You seem to dismiss Adapta’s claim that ID requires a disembodied mind, but minds that we are aware of, seem complex, and they seem affected by matter and its properties. Same issues that are problematic for evolution.
Wouldn’t ID require, a certain type of mind that does not require or is affected by the properties of matter and maybe even lacking complexity and like evolution, an explanation of its origin event of the mind?
Goose and gander.
Isn’t the environment the cell resides also be part of the equation, for evolution or design?
Wouldn’t the mind have to have some ability to forecast the unexpected events or at least manipulate the environment in order to hit its target. Another option might be a constant tweaking of design over the long stretch of time, which brings up another issue concerning the longevity of a designer’s mind or the choice of that mechanism.
Just saying, a lot of focus on evolution when the bare bones of design could use some fleshing out.
I agree with the first statement but not the second. In science we need to work with what is available to us. The designer and his attributes are more of a theological question. What we have is the human mind as a test vehicle. We can use human design as a model to compare what we are observing in biology. Winston Ewert is working on this.
Sure but this mind is not available for us to test. Human minds are.
Maybe a little but the evidence shows species live together in very diverse environments.
Gpuccio’s work shows evidence of this “tweaking” over time. How this is occurring I don’t know but I cannot rule out common descent contributing to these changes.
Bill continues to vomit up his logical fallacy, that since humans designed things therefore his disembodied magic mind must have designed biological life.
Lying for Jesus is a full time job for Bill Cole it seems.
I don’t just think. I know how to calculate it. It depends on the strings. Two identical strings of zeroes would have zero MI. Two identical strings of 1s, same thing. One of just 1s, the other of just 0s same thing. It depends on the number of symbols within each string, and whether the two strings have correspondences beyond random expectations. As I said, and you keep failing to read: in the context where you’re using it, MI is but a measure of similarity. If two sequences are identical or close-to-identical, saying that they have high mutual information is redundant, since it just means that they look alike beyond random expectations. We know they’re close to identical, or identical, because of common ancestry, so you gain nothing by using that terminology.
Clear now?
Nah. The disembodied mind is YOUR claim. This is why the ID community and yourself don’t want to confront the enormous philosophical problems with ID. they’d have to admit that they’re talking about religion, rather than science.
Look at yourself:
See? A disembodied mind after all. Your claim all along.
Entropy,
Whenever an evolutionist says anything whatsoever about ID, i think the only appropriate answer is, “That’s a caricature, no one believes that!” since this is their defense anytime someone tells them why their theory is bollocks.
That’s funny. The reason people respond that way to you is that you’re not really telling us why the theory is bollocks, you’re simply rendering aspects of the theory in language you appear to feel makes it difficult to accept. But you’re never establishing that the theory should not be accepted.
Just to pick one example, you keep describing mutations in this emotively colorful language as “happy accidents” as if that was some sort of argument. As if the label you choose for some idea or concept somehow was a rationally compelling reason to accept or reject that idea. It is not. Drawing a caricature of someone does not make that someone into the caricature. The argument from ridicule is logically fallacious.
It simply does not follow that there’s something objectionable about accepting that “happy accidents” can have beneficial results.
As such, you never truly argue against the reality of evolution, or against acceptance of it. All you ever do, when it comes down to it, is to describe it in a different and emotive language. You are making it clear that you disapprove of and reject it, but you never show that anyone should do so.
Simply stated, the entirety of your output on this question is rationally impotent.