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.
It’s amazing how nature pretends not to know what it’s supposed to do.
Like natural selection can’t hear phoodoo lecturing on the direction it’s supposed to take.
Technically that’s among the fastest-dividing bacteria known, which is the E coli in Lenski’s experiment. There are very few species that divide that fast. Many more species of bacteria are much slower than this, having generation times ranging from multiple hours, through several days, to years and even decades.
For really short generation times, viruses are king. But one problem faced by viruses is that if they overwhelm the host, the host dies before it can transmit the virus to other hosts, in turn rendering themselves extinct. And now you should at least begin to see how the problem you correctly perceive, still has solutions.
Rumraket,
Why doesn’t nylon eating bacteria spread throughout the globe and digest the entire world’s supply of polyester?
Among other reasons because they don’t actually “eat nylon”, they eat a byproduct of nylon-manufacture.
Dunno, maybe the Designer is not comfy with cotton undies
Once again, what we have is people on one side endlessly presenting empirical data, and people on the other side endlessly repeating policy positions. The data people seem to consider actual reality to be dispositive, and cannot seem to grasp that policy positions are not based on reality, they are based on emotional preference. And the policy position people can’t understand why the reality people continue to insist on what they recognize as Bad Religion, basically wrong preferences due to faulty beliefs.
We get these silly threads because otherwise intelligent people can’t understand that faith and reality are mutually irrelevant. Ships in the night.
Well, among other reasons, because nylon is a polyamide, not a polyester. Also (as noted by Rumraket), nylon eating bacteria eat linear dimers of 6-aminohexanoate. Finally, even if they did eat nylon, they would need some way of being carried from one food source to the next. One could just as well ask “Why don’t [micoorganism of your choice] spread throughout the globe and digest the entire world’s supply of sugar?
In other news, the bacteria inside your gut are generally helping you out, not trying to kill you. Furthermore, they are limited by the food that is available to them, and the fact that they will get egested after about a day and a half.
You are welcome to see what happens if you recycle them, phoodoo!
BS as usual. Alleles do not “dominate”. They coexist. And Darwin’s retard idea of “natural selection” never had anything to do with alleles.
There was an “evolutionary reason” based on which mankind’s doom was falsely predicted.
BS again. What is your freaking “fitness” then? How come none of you can reply with your “fitness” function?
You don’t even understand the comment. Let alone the fact it was not addressed to you.
They can’t gain a mutation that would enable them to eat any nylon they like? They can’t become airborne?
There are all sorts of ways that bacteria could mutate to dominate the entire planet, without being so friendly to it, like they are to your gut.
With 39 trillion chances per hour, I reckon they could do a lot. And yet…
No what he said was a fact.
If one is more numerous than another, it dominates over it in terms of relative numbers.
One may still numerically dominate over another despite their continued coexistence. The terms “coexist” and “dominate” are not mutually contradictory.
Look, most of what you write is nonsense and it’s tiresome having to “debunk” your posts at the level of reading comprehension. It’s not so much that your regurgitations represent actual logical or rational arguments against evolution, it’s that what you write is almost exclusively logically incoherent or grammatically nonsensical.
You should learn to think before you attempt to communicate, and once you’ve learned to think, proceed to learn to communicate too. Then and only then may you consider returning to argue with people around here. Should you finally have learned to do that one day, you will return on the other side of this “debate”.
Darwin didn’t know what alleles were because the physical basis and mechanisms of inheritance were unknown to him. Even so, Darwin’s “retard idea” of natural selection actually makes complete sense when combined with Mendelian genetics.
Is there?
It doesn’t contain information, using your own standard.
We can directly observe nature conserving function. It’s called natural selection and mutation.
Can you show me one observation of an intelligent designer who is involved in two snails reproducing? Please show us videos of this third party.
Have you never heard of natural selection?
Not in the experiment I just described. The population can move from a 50/50 split between two alleles to 100% one allele. It would also be helpful if you could show us the natural process that prevents alleles from disappearing within a population.
Reference? Who predicted it, and when?
I did give you the fitness function. It has its own wiki page, for crying out loud. Does Google not work where you are?
https://en.wikipedia.org/wiki/Fitness_(biology)
Someone seemed to have forgotten that the host evolves, too. They also seemed to have ignored other obvious pathways, such as commensalism. People who don’t know about the existence of immune systems shouldn’t be commenting on the accuracy of theories in biology.
You missed a few points, try to keep up.
The score is 39 trillion to one. How does the one keep up with the 39 trillion.
But again, 39 trillion, we jest of course.
Again, study immunology. A human is made up of more than one cell, and there are non-cellular innate immunological systems that also kill pathogens, such as the complement pathway. Do you know what a macrophage is? What about an immunoglobulin? Toll-like receptors?
There used to be an apocryphal story of how scientists proved the bumblebee couldn’t fly. I see phoodoo has simply omitted the reference to scientists, and simply SAID that the bumblebee can’t fly (or, actually, that people cannot survive a planet full of bacteria).
I’m presuming here the argument goes:
1) It is stone obvious that bacteria render people impossible due to relative reproductive rates.
2) However, it’s obvious even to phoodoo that he exists.
3) Therefore, there must be some magical agency protecting his existence.
But I speculate that phoodoo’s actual argument inverts this:
1) A magical agency exists because phoodoo SAYS so.
2) With sufficient mendacity, it’s possible to deploy unsupportable claims about biology, which are true because phoodoo SAYS they are true.
3) By extension, phoodoo’s magical agency is proved by lying about anything.
T_aquaticus,
I respectfully disagree. The sequence is certainly meaningful as it describes a functional protein. You appear to be intentionally misrepresenting me but correct me if I am wrong. I get the fact that you have no model to support your claim. Natural selection is meaningless until you show how it works by model and can generate information. I gave you an out to use any mechanism you want to generate information so please get creative 🙂
There is probably is very little natural selection going on with a protein that is so highly preserved. It is probable that mutation is very rarely making it out of embryo development as not a single mutation is getting fixed in the population over 50 million years.
Design best explains the origin of such a highly preserved group of sequences.
We all get the fact you have no hesitation in lying for your beliefs as you’ve been shown models dozens of times.
Bill’s “a disembodied mind used magic to POOF the sequences into existence”, Episode 12,486.
A “mutation very rarely making it out of embryo development” IS natural selection, so there has been a lot of it going on. In this thread you have consistently relied on evolutionary concepts like homology of proteins and purifying selection and claimed them as successes of Intelligent Design. That is false. The likely reason for the conservation of the ubiquitin-conjugating enzyme E2 D3 or the alpha actin protein is that any mutations that were introduced negatively impacted viability, survival and/or fertility. This reduced (or blocked) the efficiency of transmission of these alleles into successive generations, i.e. you are making an implicit appeal to that “vague” thing called fitness.
I would appreciate it if you conceded that strong sequence conservation is a demonstration of the power of natural selection, NOT intelligent design. Natural (purifying) selection is, by your own admission, capable of preserving a functional sequence (and hence the information associated with it). Therefore, natural selection MUST be capable of discriminating sequences that differ in the amount of whatever you call “information”; We don’t need any regular check-ups from intelligent minds servicing our genomes.
One drawback of this paper is that it does not describe a mechanism for selection; instead, it works directly with the “frequency of each type after selection”.
I suspect Eric will require that a mechanism for selection be specified in order to apply Levin’s results on non-increase of AMI or Eric’s claimed results on conservation of (expected) ACS.
Given this mechanism, I predict the exchange will then stalemate, as always, on one of the following issues:
– the mechanism requires a non-natural component, such as a halting oracle, and hence requires intelligence
– the mechanism requires that information be built in from the outside, eg built into a target or into a search space
– as Tom documents in OP, the purported AMI or ACS limitations on NS derived from the algorithm or model will be applied directly to NS operating in reality, eg by assuming that reality is computational or that reality is fundamentally constrained by the armchair mathematical constraints that ID proponents presume in their derivations
I love this. “See, see, a bunch of scientists were totally wrong about flight, so….trust the scientists more would ya!”
Thanks for that.
The story is apocryphal. The point is that scientists never actually said that, it is a folk-myth that they said that, and that you’re mindlessly regurgitating a story while having done no work at all to determine if it’s true.
You’re welcome.
That has already been shown in the paper I referenced. It’s a functional protein, hence it’s “meaningful” and constitutes information in your view. So evolution can in fact generate information. It’s been observed in real time, not just modeled. Observed..
The other way around. Natural selection is the reason why some proteins are prevented from changing on very long timescales. The less they change, the stronger selection is against change, because the protein sits on some local optimum where mutations to it are strongly deleterious.
Haha…
Did you just wake up?
Maybe get some coffee before you say something so stupid.
Try a Google search for “Bumblebees can’t fly”. A myth, in the sense that some early calculations making oversimplified assumptions did show that, but that was over 80 years ago. Even Snopes calls this a myth.
Corneel,
You have made an interesting point here until you rely on assertion for your conclusion,
It is actually not false. You need design to explain the origin of homology or what Eric calls mutual information. The observation that any change is causing system failure is very strong evidence of design as it supports Behe’s irreducibly complexity concept.
It supports both. It also supports the power of the cellular reproductive cycle. We would not see this without optimized system design such as the ubiquitin system which is a component of the cellular reproductive cycle. This is showing you a problem that natural selection and purifying selection has supporting evolution. It is reducing variation and preserving the status quo of the population.
You need to explain the origin of your disembodied mind and the magic mechanism it used to POOF biological life into existence.
The final nail in evolution’s coffin, the remarkable insight that will finally make “the entire rodden edifice come crashing down“, the “taliban-style collapse” was instigated and delivered by none other than phoodoo in December 2019:
“39 trillion > 1”.
How is the field to ever recover?
Common descent. They’re identical because they were inherited as-such from a common ancestor.
Bill’s ignorance of biology is on display again.
Yes there are some genes which are highly conserved across all life because they are critical for survival. But there are many other genes which can tolerate a wide range of mutations, even break, without harm to the species. A good example is the GLO gene (also known as GULO) which is part of vitamin C synthesis. In humans the gene is broken but humans still survive by getting external sources of vitamin C. In other species the gene has mutated and still partially performs the function.
The Genetics of Vitamin C Loss in Vertebrates
Hey Bill, what is your Magic Designer explanation for the wide range of GLO variants seen in vertebrates?
Rumraket,
Explain the origin of common descent by sexual reproduction.
Damn Bill, read a basic Biology 101 textbook. You constant mewling “I DON’T BELIEVE IT!!” is way past its sell-by date.
What?
Rumraket,
This is what is required to explain the origin of the mutual information that Eric is talking about. At this point ID is unavoidable in biology. At some point science hits the wall. The interesting discussion is there are so many points of novel mutual information appearing over evolutionary time.
In reality common descent only explains the copier of the information. The copier itself, however, is quite a sophisticated mechanism.
That would be a pickle indeed, but as far as I know it has never been demonstrated that ANY change causes system failure. Nor is such result likely to come forth, because most species sport an enormous amount of genetic variation. You are trying to “prove a negative” again.
No, it does not. You are confusing the origin of the protein sequence with its conservation. You cannot use the conservation of complex functional protein sequences as evidence of their Design.
Which would be somewhat more plausible if ALL proteins remained perfectly conserved, but most of them are diverging between separated lineages.
No, you aren’t getting it. It’s you who insisted on getting a very particular sentence from a model without a target, and thus it’s you who’s misrepresenting both what the model does, and what natural selection, as a phenomenon, should or should not do. Your overemphasis on a sentence is what lead to people exaggerating your supposed point, your deep misunderstanding, to try and see if such reductio ad absurdum, of your own claims, would get the message home.
Nope. Natural selection is meaningful as soon as the idea behind it is understood. With the idea understood, it becomes clear that natural selection cannot but “generate” information. The models serve as demonstrations about how far, or how quickly, or how slowly, it can go given predefined circumstances, or about the effects of one or another parameter in how quickly the information increases/decreases, etc.
However, there’s models demonstrating the principle. The real problem is that you don’t really pay much attention. Joe has presented some models demonstrating the “generation” of information by processes involving random mutations and selection. I reckon that you prefer to ignore them because you don’t actually understand them, and because you rather accept models produced by ID deceivers, that you don’t understand either, just because you prefer their conclusions.
You didn’t give anybody a way out. You’re demanding people to generate a particular sentence w/o a target as if anybody were claiming that evolution does such a thing. This is why they’re reducing your demand to absurdity Bill, to try and see if you get that evolution is not about producing particular protein sequences. It works by survival, and it would produce functional proteins, not particular sequences. That a protein gets “frozen in time” doesn’t mean that it was the only possible functional protein at the outset.
Preservation indicates negative selection, and negative selection is also natural. There’s no need for a ghost to keep mutant sequences out of the genetic “pool.”
Things like these are called negative selection, and they’re natural Bill.
No, it doesn’t. Proposing that a function acquired outmost importance as evolutionary history developed doesn’t require anybody to break basic philosophical principles. After all, there’s paths that could lead to the “freezing” of particular protein versions. Proposing design, on the other hand, breaks philosophical principles at the very foundation. It’s absurdly circular and lazy to the point of ridicule.
Corneel,
Based on what?
Materialist: You cannot use that evidence.
Why?
Because its devastating to my worldview 🙂
Entropy,
With all due respect this is nonsense. This is an assertion to support materialist ideology.
The design argument has been around a while. It will not die because you assert it is false based on some illogical philosophy you cite.
On the fact that high conservation doesn’t mean design, it just indicates strong negative selection, thus that the sequence might be too “involved” for it to change. That the sequence is too involved doesn’t mean that it was always too involved, or that it’s the only protein that could have done the job at the outset. It just indicates its current state, not its original state.
Has Corneel declared to be a materialist?
Because it doesn’t follow, and understanding why it’s a non-sequitur doesn’t require anybody to be a materialist.
I didn’t know that materialism, as a worldview, demanded the rejection of non-sequiturs to survive.
What does that have to do with “the origin of common descent by sexual reproduction”? That sentence was incoherent.
Also, we’ve been over this information stuff already. Novel proteins can evolve de novo from non-coding DNA.
Entropy,
It is very strong evidence of design or mind as an explanation of the observed sequences having extremely high mutual information.
With all due respect, your ignorance of basic philosophy doesn’t make it nonsense. I have explained this to you ad nauseam. The “design inference” is supposed to be founded on what designers, we humans, can do. It conveniently ignores everything needed by us in order to be able to produce any designs whatsoever. I don’t ignore any of that and thus notice the foundational problem with the “inference.” If the “design inference” is really about gods, then stop saying that it’s based on such a particular human ability, and call it apologetics, rather than “inference,” and stop pretending that it is scientific.
It would be great if you could point to the illogical parts, because it’s very clear to me that the “design inference” fails at the very foundation. For example, show me that our designs don’t require anything else but our minds. Show me that we don’t require ubiquitin or every other of our highly involved proteins, just to survive and thus be able to design. Show me that we don’t need tools. Show me what’s illogical of we needing to be alive to produce designs. Long etc.
Very importantly, show me that it is illogical to keep looking for answers in nature, when nature is right here, while your “designers,” at best, are nebulous absurd concepts lacking an explanation themselves.
Rumraket,
What is the origin of the non coding DNA that is only a few mutations away from function?
No it isn’t. It would be helpful if you to tried and read the rest of what I wrote. For comprehension please.
Entropy,
The design inference is tested by human designers as gravity has been tested using large mass and measurement tools.
It is absolutely scientific as it is a mechanistic explanation of the data.
You should be trying to falsify design by looking for natural explanations. This is what makes science work. In reality falsification comes from models that are repeatably tested. This is what the grand claims of evolutionary theory lacks.
In general science struggles explaining origin events without design. Biology is a difficult area for science because there are lots of origin events.
So no illogical parts to point out Bill? I thought so. Now:
You’re deflecting. Testing and inferring are not the same things Bill. There could be no “design inference” out of the blue. What’s the supposed foundation for the “inference” Bill?
No, it isn’t. It doesn’t show us any designers that could have performed such tasks, or their tools, or their sources of energy, or their plans, or anything that allows designs to be produced. Starting with the designers themselves.
It’s falsified from the very foundation by being absurd philosophically and scientifically.
Don’t be absurd Bill. Design cannot be the default position. It doesn’t make sense since designers have an origin themselves, and the nature supporting designers comes before designers. It cannot be any other way. We depend on the nature that supports and conforms us, not the other way around. You put cart-before-the-horse Bill!
It sure is. Getting closer and closer to actual answers, even if by tiny bits, makes it a very exiting and challenging scientific area of research.
No, that really is incorrect.
ID says that ‘certain features in Nature are best explained by Design’. That doesn’t rule out that both design and evolution are true, so finding natural explanations for certain features still doesn’t rule out a design inference for others. Therefore, this is not the way to falsify ID.
The real, scientific, way to falsify design is to test its unique predictions (the ones that differ from the predictions of evolutionary theory) and show them to be false.
What testable predictions does ID make that differ from evolutionary theory? Please be specific, and demonstrate how and why these predictions are unique to ID and follow logically from its tenets.
If this kind of falsification isn’t possible it doesn’t mean that ID is necessarily wrong, but it does mean that ID is non-scientific.
1. Holloway most definitely has not begun with a conceptual model. He has made a cosmic principle of a theorem due to Leonid Levin. When asked to show how the theorem applies to evolution, Holloway had no choice but to provide a mathematical model of evolution. It is impossible to apply the theorem to an informal model.
2. Mathematical models are conceptual models. For people who have gained facility with mathematical concepts, much of conceptualization is mathematical conceptualization. It is not the case that all mathematical models are based on informal conceptual models.
If you’re talking about evolutionary biology, I agree. Joe Felsenstein isn’t bothered by the term target, but I think that the use of it contributes hugely to misunderstanding.