Evo-Info: Publication delayed, supporting materials online

Introduction to Evolutionary Informatics, by Robert J. Marks II, the “Charles Darwin of Intelligent Design”; William A. Dembski, the “Isaac Newton of Information Theory”; and Winston Ewert, the “Charles Ingram of Active Information.” World Scientific, 350 pages. Jan 31 May 1, 2017.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.

I cannot tell you exactly what will be in the forthcoming book by Marks, Dembski, and Ewert. I made it clear in Evo-Info 1 and Evo-Info 2 that I was responding primarily to technical papers on which the book is based. With publication delayed once again, I worry that the authors will revise the manuscript to deflect my criticisms. Thus I’m going to focus for a while on the recent contributions to the “evolutionary informatics” strain of creationism by George D. Montañez, a former advisee of Marks who is presently a doctoral candidate in machine learning at Carnegie Mellon University (advisor: Cosma Shalizi). My advice for George is that if he wants not to taken for a duck, then he had better not walk like a duck and swim like a duck and quack like a duck.

Interestingly, young-earth creationist Jonathan Bartlett did an Amazon “customer review” of Introduction to Evolutionary Informatics in late January, after World Scientific had changed its online announcement to indicate that the book would be published in May. When I let the folks at Amazon headquarters know that they were misrepresenting the book as available for purchase, they went above and beyond the call of duty to correct the mistake. I’m interested in hearing from Jonathan whether he removed his “customer review” voluntarily. Of course, I’d like to know also what led him to post it in the first place.

I’ll hazard to suggest that the book will be much like the supporting materials, which were revised extensively in January. The presentations on the Weasel, ev, and Avida models of evolution are self-contained. And they cast doubt on the advertising claim:

Built on the foundation of a series of peer-reviewed papers published by the authors, the book is written at a level easily understandable to readers with knowledge of rudimentary high school math.

Click on the “Mathematics” tab here, and you will see that the math — the easy stuff, as it happens — is something that almost everyone will skip. It’s there to impress, not to enlighten, the general reader. As I’ve said before, I would love to address the math, and not the rhetoric that the authors attach to it. Things would be much easier for me if the authors turned out to have magical teaching powers. But we have evidence now, and the evidence says no magic.

201 thoughts on “Evo-Info: Publication delayed, supporting materials online

  1. Thank you Allan and Dazz for your comments even if you all disagree.

    Related to Tom English’s crusade against CSI and active information, Minnich’s work actually gives some reason to criticize the tractability of active information.

    Clearly Minnich had a better search function than Lenski’s. Lenski wasn’t looking, but Minnich was, and Minnich had specialized knowledge of the search space. His search using selection was 2750 times more effective then Lenski’s and millions of time better than what happens in nature. So what is the active information in Minnich’s search? How is it calculated? And even if calculated, what does it prove beyond the obvious? For these reasons I’ve been indifferent to negative on the notions of CSI and active information. They can be nice academic exercises, but even in simple cases like evaluating the active information in Minnich’s experiment to evolve Cit+ vs. Lenski’s accidental discovery, it doesn’t seem so straight forward! So supposing we could calculate the active information by Minnich’s search, so what?

  2. keiths: Again, why would I waste time tweaking a script that’s designed to be run once, in the background, and doesn’t take that long anyway?

    Not tweaking. You want to iterate over permutations? Then you Google to find out what’s available in Python to do that for you. Standard practice.

    I did not post a tweak above. Again, I took a terribly simpleminded approach, and simply did not build in the inefficiencies that you did.

    When you force the operators to be binary, it’s quite easy to generate only valid expressions. So there’s no reason, actually, to take the simpleminded approach. Not that it’s the right thing to do, but it’s not too hard to think of permuting the digits, then generating 4-permutations of the 8 positions separating digits, and inserting the operators into those positions. If I’m not mistaken, you actually don’t need to permute the (binary) operators when you’re permuting the digits.

    Writing one-use code does not mean you don’t use your brain in advance. I mean, you’re trying to do a brute-force solution, so it’s pretty fucking stupid not to avoid obvious inefficiencies. And don’t tell me that your solution was simple. It was considerably more complicated than it needed to be, because you didn’t use an iterator.

  3. colewd,

    Good point.What was the intended ROI (investment return) on the 4 million spent?

    Yeah. Did it lead any souls to Jesus?

  4. stcordova: Clearly Minnich had a better search function than Lenski’s

    Why do you keep ignoring the fact that Lenski and Blount had already performed reply experiments and got some results in even less generations than Minnich? And that was BEFORE Minnich published his paper!

  5. Tom English: Not that it’s the right thing to do, but it’s not too hard to think of permuting the digits, then generating 4-permutations of the 8 positions separating digits, and inserting the operators into those positions. If I’m not mistaken, you actually don’t need to permute the (binary) operators when you’re permuting the digits.

    Not sure I understand, but wouldn’t this leave out valid expressions like “2/+3” with more than one consecutive operator?

  6. Tom:

    Writing one-use code does not mean you don’t use your brain in advance. I mean, you’re trying to do a brute-force solution, so it’s pretty fucking stupid not to avoid obvious inefficiencies.

    Who cares about the inefficiencies in a one-off script that is already fast enough?

    You crack me up, Tom. Is this a repeat of the ‘weasel envy’ episode? Is it really that important to you to be able to say “My code is better than Keith’s one-off script”?

    If that’s your goal, then maybe the tweaking is worth it to you. To me, it’s a waste of time.

  7. D:\projects\tsz>ruby rth0a.rb
    87_178_291_200

    That’s a lot of permutations without running out of memory. And all while simultaneously running two other programs generating an even greater number of permutations.

  8. Mung:
    D:projectstsz>ruby rth0a.rb
    87_178_291_200

    That’s a lot of permutations without running out of memory. And all while simultaneously running two other programs generating an even greater number of permutations.

    running which algo exactly?

  9. dazz: running which algo exactly?

    I’m simply cycling through all the permutations. That’s all. keiths admitted he was wrong, but for some reason still seems committed to claiming that I was lying when I said my program does not run out of memory after running x number of permutations.

  10. Mung,

    keiths admitted he was wrong, but for some reason still seems committed to claiming that I was lying when I said my program does not run out of memory after running x number of permutations.

    It couldn’t be simpler. I claim that you lied because you actually did lie:

    Mung, then:

    Well, my program eventually stopped due to running out of memory after more than 1.685B permutations. Guess maybe the built-in permutation function isn’t the way to go.

    Mung, now:

    It doesn’t run out of memory after 1.685 billion permutations. That’s just you refusing to see the evidence that is before your eyes.

    If you find it unpleasant to have your lying pointed out, there’s a simple solution: stop lying.

  11. Entirely germane to this post, I just published an article that shows the flaws in one of type of information argument against evolution. I’d be curious your thoughts everyone. If possible, some one put this in its own thread?

    I wonder if studies like this will be important given the “information” turn of ID of late. A positive reception from you might encourage me to do more.

    http://www.biorxiv.org/content/early/2017/03/06/114132

  12. swamidass:

    If possible, some one put this in its own thread?

    Hi Joshua,

    One of the moderators can give you posting privileges if you don’t already have them.

    To write a new OP, just click on “+ New” in the toolbar at the top of the browser window and select “Post”.

  13. Dr. Swamidass!

    You got published in Cold Spring Harbor Press. Congratulations!

    FWIW, although I’m an ID proponent, I’ve gone on record as saying I’m somewhat negative to ID proponents using information arguments. I look forward to the discussion on your paper. Thanks for dropping in.

  14. keiths: It couldn’t be simpler. I claim that you lied because you actually did lie:

    You misinterpreted what I wrote. That’s not me lying to you, that’s you lying to yourself.

    Mung: It doesn’t run out of memory after 1.685 billion permutations.

    It doesn’t run out of memory after 87_178_291_200 permutations either. The number of permutations was not the issue.

  15. Swamidass:

    The fantastic rarity of functional proteins computed by this approach emboldens some to argue that evolution is impossible.

    LoL. What utter garbage. Even Young Earth Creationists accept that evolution is possible. So who is Swamidass talking about here?

  16. swamidass: the “information” turn of ID of late

    Marks, Dembski, and Ewert are, of late, putting a question mark after “information.” They seem to be saying, “Hey, we have our ideas about information, and you have yours.” Of course, that’s not how things work. I’ll show in Evo-Info 4 that the rationale of Marks et al., and also of Montanez, for regarding “active information” as information applies to a host of measures that obviously are not information measures.

  17. [Matlock and] Swamidass: The fantastic rarity of functional proteins computed by this approach emboldens some to argue that evolution is impossible.

    Mung: LoL. What utter garbage. Even Young Earth Creationists accept that evolution is possible. So who is Swamidass talking about here?

    Like, um, maybe Axe and Gauger?

  18. Mung: LoL. What utter garbage. Even Young Earth Creationists accept that evolution is possible. So who is Swamidass talking about here?

    Maybe try reading the article. In the refs and the supplementary data it is 100% clear who I am talking about.

  19. keiths:
    One of the moderators can give you posting privileges if you don’t already have them.

    To write a new OP, just click on “+ New” in the toolbar at the top of the browser window and select “Post”.

    Sweet. I just posted it and it is waiting to be approved.

  20. dazz: Not sure I understand, but wouldn’t this leave out valid expressions like “2/+3” with more than one consecutive operator?

    keiths forced the operators to be binary with is_legal. If you reread my comment, you’ll see that I emphasize “binary.” As for the ordering of operators, what obviously holds is that the multiplication and the division are done before the addition and the subtraction. It’s a no-brainer that the permutations of the operators can be limited to [/ | /] [+- | -+]. That’s 4 instead of 24 permutations — a factor-of-6 reduction in the number of expressions evaluated.

    When I won the student programming competition at Mississippi State, I completed 5 problems in 2.5 hours (30 minutes apiece), and the second-place finisher (a very bright computer engineering student, and a friend of mine) completed 3 of those 5 problems in 3 hours (60 minutes apiece). Put simply, I completed problems twice as fast as the guy who came in second. I have a vivid memory of the sound of others pounding away at keyboards, while I was working out designs on paper. I subsequently competed in a team, with the other top finishers, and found that they indeed thought that there was not enough time to bother with design. That’s simply not true. It’s actually much faster to think carefully about what you’re going to do than to jump into implementation.

  21. Tom,

    That’s more than a little sad. Is it really that hard to accept that you’re not the only smart guy here?

  22. Tom English: Sad to say, I get an error when I click on the link to Patrick’s stuff.

    Damn bitrot. I won’t have time to fix it until the weekend. If I can figure out how to access the database behind TSZ, perhaps I’ll add in some new training material.

  23. Tom,

    I think you’re a smart guy, and I’ll bet others here do, too. Why isn’t that enough for you?

    This happened during the Weasel discussion, and it happened here. I published a program, and you felt the need to show, somehow, that you could do it better, even though it was pointless to do so.

    It isn’t a crisis when someone else writes a program that does what it was intended to do, or when their program gets more attention than your competing version does. You don’t have to outdo them or bring up old college programming contests, complete with results.

    Let it go. Life can be good even if you don’t always feel that you’re being recognized as the smartest guy in the (virtual) room.

  24. keiths: Is it really that hard to accept that you’re not the only smart guy here?

    Tom English: You’ve just highlighted the greatest of your defects.

    Rather than say again what you find it convenient to say I’m saying, why don’t you take a shot at listing the sensible readings of my remark.

  25. Tom English: It’s a no-brainer that the permutations of the operators can be limited to [/ | /] [+- | -+]. That’s 4 instead of 24 permutations — a factor-of-6 reduction in the number of expressions evaluated.

    Come on, keiths. I’ve given you a chance to show how smart you are, and how dumb I am — twice now. Want to say something about commutativity? The expression tree, perhaps? You’re ignoring substance.

  26. Come on, keiths. I’ve given you a chance to show how smart you are, and how dumb I am — twice now.

    I don’t think you’re dumb, Tom. Just very insecure.

  27. stcordova: It took Lenski 33,000 generations over 15 years to get 1 success, it only took Minnich’s lab about 100 generations in a matter of weeks to get 46 independent successes.

    Lenski made it look like the change was soooooo inaccessible when it wasn’t. Like it was a necessary long trail of trials and errors to finally achieve success. It wasn’t.

    This is somewhat like saying, “hey, I got antibiotic resistance to evolve in 15 years when others have gotten to do it in a matter of weeks. I should be in the headlines for this. I found something so rare since it takes 15 years to achieve.” That’s what Lenski did, and he gets elected to the National Academy of Science for this.

    sigh
    Sal, you’re not an IDiot, so stop behaving like an idiot.

    https://telliamedrevisited.wordpress.com/2016/02/20/on-the-evolution-of-citrate-use/

    “Rapid evolution of citrate utilization”

    In the title of their paper and throughout, Van Hofwegen et al. emphasize that, in their experiments, E. coli evolved the ability to grow aerobically on citrate much faster than the 30,000 generations and ~15 years that it took in the LTEE. That’s true, but it also obscures three points. First, we already demonstrated in replay experiments that, in the right genetic background and by plating on minimal-citrate agar, Cit+ mutants sometimes arose in a matter of weeks (Blount et al. 2008). Second, rapid evolution of citrate utilization—or any evolution of that function—was not a goal of the LTEE. So while it is interesting that Van Hofwegen et al. have identified genetic contexts and ecological conditions that accelerate the emergence of citrate utilization (as did Blount et al., 2008), that in no way undermines the slowness and rarity of the evolution of this function in the context of the LTEE (or, for that matter, the rarity of Cit+ E. coli in nature and in the lab prior to our work). Third, the fastest time that Van Hofwegen et al. saw for the Cit+ function to emerge was 19 days (from their Table 1), and in most cases it took a month or two. While that’s a lot faster than 15 years, it’s still much longer than typical “direct selections” used by microbiologists where a readily accessible mutation might confer, for example, resistance to an antibiotic after a day or two.

    So while we commend the authors’ patience, we do not think the fact that their experiments produced Cit+ bacteria faster than did the LTEE is particularly important, especially since that was not a goal of the LTEE (and since we also produced them much faster in replay experiments). However, in a manner that again suggests an ulterior nonscientific motive, they try to undermine the LTEE as an exemplar of evolution. The final sentence of their paper reads: “A more accurate, albeit controversial, interpretation of the LTEE is that E. coli’s capacity to evolve is more limited than currently assumed.” Alas, their conclusion makes no logical sense. If under the right circumstances the evolution of citrate utilization is more rapid than it is in the LTEE, then that means that E. coli’s capacity to evolve is more powerful—not more limited—than assumed.

  28. stcordova: Lenski’s experiments are not RM+NS they are RM+Un-Natural Selection since the environment was unnatural.

    That the environment is artificial doesn’t mean the selective pressures are “unnatural”. That’s really just a meaningless sematic categorization.
    It’s still an example of selection. Selection in a constant and unchanging flask-environment. Specifically, because of the synthetic and constant nature of the flask environment, the main selection pressure is replication speed. One of the easiest ways to increase replication speed is genome size reduction, so many of the mutations fixed are deletions.

    What happens naturally in an artificial environment isn’t what happens naturally in a natural environment. You’re equivocating the meaning of “natural”. It’s highly misleading.

    No, you are equivocating on the meaning of natural. Actually you’re oddly focused on that word as if what the hell kind of label you use to describe the selective pressures in operation is important.

    So Lenski’s crowing about how he can evolve new function 2,750 times slower than Minnich, and millions of times slower (if ever) than what happens naturally in nature what happens un-natrually through un-natural evolution experiments like his LTEE.

    He is? Where? Let’s be clear, Lenski isn’t crowing about anything like that dumb shit at all.

    And this proves Darwinian evolution how?

    No single experiment has ever been hailed as “proving Darwinian evolution” you fucking gimp. What does that even mean?

    Are you talking about proving that evolution happens?
    That the evolution that happens is primarily, or exclusively Darwinian (adaptive, as opposed to neutral)?
    That all species share common descent?

    The experiment has never been hailed as “proving Darwinian evolution”.

    What it does demonstrated, is ASPECTS OF the evolutionary process. Besides showing that in fact, evolution takes place. For example, divergence of independent lineages even in a constant and identical environment, from an original clonal population, is something that happens. As in it proves that divergence from the ancestral type and from each other, even in identical and unchanging environments, happen. It also shows there is effectively no limit to fitness, yet it slows down over time and that it follows a power law. That’s some of the things it shows. It also shows that irreducibly complex functions can and do evolve.

    It shows the blindwatchmaker isn’t as capable as directed-goal-oriented evolution of complexity through directed selection.

    Well fuck me, this was thought to be otherwise by… whom? That’s right, nobody. In other news, the experiment also failed to prove General Relativity, Ohm’s Law and Newton’s laws of motion. All of which was expected to be proven in this experiment by… no fucking person ever.

    After 33,000 generations, we have something not much different than what was started with.

    How different is “not much different” and how much different was it predicted to be to be that knock-down case for Darwinian evolution you’re trying to insinuate it should be?

    You’re just blathering vapid rhetoric here.

    If that is extrapolated to human evolution, that’s not much change in a million years, like say developing lactose tolerance, not much else.

    A lot of things have changed for these bacteria (morphologically, behaviorally, genetically) besides their ability to transport citrate under aerobic conditions. And each lineage is different.

  29. Moved a comment to guano. The noyau thread is available for flaming. In other threads, accusations of lying are against the rules.

  30. D:\projects\tsz>ruby rth0b.rb
    1_307_674_368_000

    That’s impossible. No way could I generate that many permutations without running out of memory.

  31. Rumraket:

    Well fuck me, this was thought to be otherwise by… whom? That’s right, nobody. In other news, the experiment also failed to prove General Relativity, Ohm’s Law and Newton’s laws of motion. All of which was expected to be proven in this experiment by… no fucking person ever.

    But there was a point for me mentioning that goal-directed engineering exceeds blindwatchmakers. Humans are hard pressed to construct enzymes from scratch that perform as amazingly well as the enzymes in the biological world. So if real natural selection (not Darwin’s fantasized selection), are less capable than human engineering, and humans are hard pressed to make enzymes from scratch, why should anyone think as a matter of principle natural selection can make such amazing enzymes? It’s just assumed as an article of faith with no proof.

    There are 145 unique proteins to a spliceosome. Does anyone believe humans could build something so complex from scratch? So if humans outperform natural selection but can build a spliceosome, why would you think natural selection built a spliceosome?

    Since Larry thinks spliceosomal introns are junk, why didn’t the first eukaryote with spliceosomal introns not just die in the absence of spliceosomes? Why should selection create such a monstrosity of junk, if indeed it is junk, and equally monstrous molecular machines like the spliceosome to chop introns out?

    I’m just pointing out some of the reasons the evolutionary story goes against probability and why we might not expect natural selection to act as advertised by Darwin.

    But back to the OP, I see little reason to throw information theory upon these considerations. I wish IDists talked more about biochem and molecular biology than esoteric concepts like active information.

  32. stcordova: There are 145 unique proteins to a spliceosome. Does anyone believe humans could build something so complex from scratch? So if humans outperform natural selection but can build a spliceosome, why would you think natural selection built a spliceosome?

    Probably the impressive homologies between them, both of protein families within single organisms, and across taxa as well.

    Or is that just more amazing engineering, not only are they very functional, they’re even arranged as if they evolved, just to impress (and maybe test) us?

    But ignore all of that, Sal. You always do. Who needs to follow the evidence when you can slavishly cling to one “explanation” over the one that actually explains?

    Glen Davidson

  33. I said:

    It [Minnich’s experiment] shows the blindwatchmaker isn’t as capable as directed-goal-oriented evolution of complexity through [intelligently] directed selection

    To which:

    Rumraket said:

    Well fuck me, this was thought to be otherwise by… whom? That’s right, nobody

    In contrast:

    “Evolution is cleverer than you are.”

    Leslie Orgel

    Oops. Looks like somebody thinks [godless, mindless] evolution can outwit humans.

  34. keiths: Afterwards, you got caught lying about the fact that the program ran out of memory.

    This is false.

    Dazz and I diagnosed the problem, and I fixed your program for you. Now it works.

    False again.

    Wrong three times before and now wrong a fourth time.

  35. Moved comments to guano. It should hardly be necessary to remind regular contributors that accusations of lying are against the rules. Noyau is available for flaming.

  36. So, keiths, just how is it that you fixed my program for me. Do tell. I missed something, somewhere.

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