Stark incompetence

David Nemati and Eric Holloway, “Expected Algorithmic Specified Complexity.” Bio-Complexity 2019 (2):1-10. doi:10.5048/BIO-C.2019.2. Editor: William Basener. Editor-in-Chief: Robert J. Marks II.

Let us start by examining a part of the article that everyone can see is horrendous. When I supply proofs, in a future post, that other parts of the article are wrong, few of you will follow the details. But even the mathematically uninclined should understand, after reading what follows, that

  1. the authors of a grotesque mangling of lower-level mathematics are unlikely to get higher-level mathematics correct, and
  2. the reviewers and editors who approved the mangling are unlikely to have given the rest of the article adequate scrutiny.

Before proceeding, you must resolve not to panic at the sight of Greek letters and squiggly marks in the passage displayed below. Note that although the authors attempt to define a term, you need not know the meaning of the term to see that their “definition” is fubar. First, look over the passage (reading \zeta as “zeta” and \epsilon as “epsilon”), and get what you can from it. Then move on to my explanation of the errors. Finally, review the passage.

This is just the beginning of a tour de farce. I encourage readers who have studied random variables to read Section 4.1, and post comments on the errors that they find.
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Non-conservation of algorithmic specified complexity…

… proved without reference to infinity and the empty string.

Some readers have objected to my simple proof that computable transformation f(x) of a binary string x can result in an infinite increase of algorithmic specified complexity (ASC). Here I give a less-simple proof that there is no upper bound on the difference in ASC of f(x) and x. To put it more correctly, I show that the difference can be any positive real number.

Updated 12/8/2019: The assumptions of my theorem were unnecessarily restrictive. I have relaxed the assumptions, without changing the proof.
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Evo-Info 4 addendum

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, 332 pages.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.

In “Evo-Info 4: Non-Conservation of Algorithmic Specified Complexity,” I neglected to explain that algorithmic mutual information is essentially a special case of algorithmic specified complexity. This leads immediately to two important points:

  1. Marks et al. claim that algorithmic specified complexity is a measure of meaning. If this is so, then algorithmic mutual information is also a measure of meaning. Yet no one working in the field of information theory has ever regarded it as such. Thus Marks et al. bear the burden of explaining how they have gotten the interpretation of algorithmic mutual information right, and how everyone else has gotten it wrong.
  2. It should not come as a shock that the “law of information conservation (nongrowth)” for algorithmic mutual information, a special case of algorithmic specified complexity, does not hold for algorithmic specified complexity in general.

My formal demonstration of unbounded growth of algorithmic specified complexity (ASC) in data processing also serves to counter the notion that ASC is a measure of meaning. I did not explain this in Evo-Info 4, and will do so here, suppressing as much mathematical detail as I can. You need to know that a binary string is a finite sequence of 0s and 1s, and that the empty (length-zero) string is denoted \lambda. The particular data processing that I considered was erasure: on input of any binary string x, the output \mathtt{erased}(x) is the empty string. I chose erasure because it rather obviously does not make data more meaningful. However, part of the definition of ASC is an assignment of probabilities to all binary strings. The ASC of a binary string is infinite if and only if its probability is zero. If the empty string is assigned probability zero, and all other binary strings are assigned probabilities greater than zero, then the erasure of a nonempty binary string results in an infinite increase in ASC. In simplified notation, the growth in ASC is

    \[A(\mathtt{erased}(x)) - A(x) = \underbrace{A(\lambda)}_\text{infinite} - \underbrace{A(x)}_\text{finite} = \infty\]

for all nonempty binary strings x. Thus Marks et al. are telling us that erasure of data can produce an infinite increase in meaning.

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Number of Unique Commentators

For The Panda’s Thumb’s After the Bar Closes thread on Uncommon Descent, I created a graph of the number of unique commentators at UD:

Here, for each day from Apr 2005 until Nov 2019, I gave the number of different people who commented at UD at least once during the previous 365 days. The colors indicate the number of contributions such a commentator has made over this period of time.

Obviously, the same can be done for “The Skeptical Zone”:

Enjoy!

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Behe and Co. in Canada

This past Friday, I bumped into Dr. Michael Behe, and again on Saturday, along with Drs. Brian Miller (DI), Research Coordinator CSC, and Robert Larmer (UNB), currently President of the Canadian Society of (Evangelical) Christian Philosophers. Venue: local apologetics conference (https://www.diganddelve.ca/). The topic of the event “Science vs. Atheism: Is Modern Science Making Atheism Improbable?” makes it relevant here at TSZ, where there are more atheists & agnostics among ‘skeptics’ than average.

On the positive side, I would encourage folks who visit this site to go to such events for learning/teaching purposes. Whether for the ID speakers or not; good conversations are available among people honestly wrestling with and questioning the relationship between science, philosophy and theology/worldview, including on issues related to evolution, creation, and intelligence in the universe or on Earth. Don’t go to such events expecting miracles for your personal worldview in conversation with others, credibility in scientific publications or in the classroom, if you are using ‘science’ as a worldview weapon against ‘religion’ or ‘theology’. That argument just won’t fly anymore and the Discovery Institute, to their credit, has played a role, of whatever size may still be difficult to tell, in making this shift happen.

A question arises: what would be the first question you would ask or thing you would say to Michael Behe if you bumped into him on the street?

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Does Paul Nelson really teach both ‘design theory’ & ‘Intelligent Design’ theory?

He sure made it sound that way. I’m guessing he actually doesn’t. It may be just a bluff or a semantic game. And then, given Paul Nelson seems to be a man who enjoys good jokes, we’ll laugh together and return to the ‘other’ conversation that respectfully doesn’t accept double-talking between these terms.

Gladly and thankfully, I’m open and ready for Paul to prove me wrong and to show us (people on the internet) his great balancing act. I really don’t think he teaches what I’m talking about when he professes ‘Intelligent Design’ theory. I would willingly admit and concede to being wrong, if he were to outline more clearly his views showing how he teaches ‘design theory’, ‘design thinking’, ‘design thinkers’ & ‘design studies,’ and not actually just IDism (which he calls IDT), which is what I suspect.

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The Demise of Intelligent Design

At last?

Back in 2007, I predicted that the idea of “Intelligent Design” would soon fade into obscurity. I wrote:

My initial assessment of ID in my earliest encounter with an ID proponent* was that ID would be forgotten within five years, and that now looks to me an over-generous estimate.

*August, 2005

I was wrong. Whilst the interest in “Intelligent Design” (ID) as a fruitful line of scientific enquiry has declined from the heady days of 2005 (or perhaps was never really there) there remain diehard enthusiasts who maintain the claim that ID has merit and is simply being held back by the dark forces of scientism. William Dembski; the “high priest” of ID has largely withdrawn from the fray but his ideas have been promoted and developed by Robert Marks and Winston Ewert. In 2017 (with Dembski as a co-author) they published Introduction to Evolutionary Informatics, which was heralded as a new development in the ID blogosphere. However, the claim that this represents progress has been met with scepticism.

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Swamidass vs. Nelson – trying to find a “Common Narrative with ID on MN”?

I’ll intervene on this conversation started by S. Joshua Swamidass as my guess is he’s going to mangle terms & then claim mastery over them, as he has done in the past on the topic of ‘methodological naturalism’ (MN). Paul Nelson (of micro-/macro- distinction) has posted here in the past & has done a fine job of staying more neutral, scholarly and welcoming to discussion than most IDists at the DI. It would be welcome for Nelson to clarify, re-iterate or to add any points here that Swamidass might not wish to address at PS, or in case the naive scientism cum MN lobby grows too loud there.

This is one of those topics where in my view Swamidass scores quite low in credibility and coherency (much like I score in biology! = P). This makes sense because he has little training and doesn’t seem to have done much personal reading in philosophy, social sciences or humanities. Paul Nelson, on the other hand, did a PhD in the philosophy of biology. So if Swamidass starts to try to out-philosophize Nelson, things could get hilarious quickly, as they have in the past, e.g. with Jonathan Burke, who discovered predecessors to GA -> GAE that Swamidass missed & had to add at the last minute.

Let’s see if Swamidass is ready to learn if the term ‘methodological naturalism’ is really a sword he wants to fall on or not. So far, it has been. Nelson, as do I, rejects MNism, & not just as a misnomer.

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Behe vs Swamidass: Why?

According to Joshua Swamidass Michael Behe and him have a lot in common… Swamidass has even publicly defended Behe on his blog by demanding a fair hearing.

Not only that, Swamidass agrees with Behe on many evolutionary/ID issues, such as guided evolution…

So, why would Behe and Swamidass square off at Texas A & M University in 2020?
What are they going to discuss? Not the polar bear evolution/devolution fiasco, right?

What do you think?

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No cloning theorem: the double edge sword

Essentially, there are 2 types of cloning…

Biological cloning leading to clones such as identical twins who share exactly the same DNA.

Or artificial, genetically engineered cloning leading to such clones as plants whose DNA is also identical.

But there exists a more precise kind of cloning in physics that reaches all the way to the subatomic level of particles. Everything in the universe is made up of elementary quantum particles and the forces by which they interact, including DNA and us. This kind of cloning is more detailed because it involves the superposition of subatomic particles; their relative positions (particles can be in more than 1 position or state at the time), momenta and energy levels of every particle and all of their bonds and interactions are exactly the same in the copy (clone) as the original.

This kind of perfect cloning is impossible. It has been proven mathematically and formulated into the no cloning theorem, which states:

“In physics, the no-cloning theorem states that it is impossible to create an identical copy of an arbitrary unknown quantum state.”

How those two types of cloning apply to life systems, such as us, our DNA and so forth?

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Echo Chambers & Epistemic Bubbles

This article might help some people make better sense of what goes on around here. https://aeon.co/essays/why-its-as-hard-to-escape-an-echo-chamber-as-it-is-to-flee-a-cult

Unarguably, young earth creationism (YECism) was & still is an echo chamber. It’s a shock to YECists when then get out of their common circles to hear statistically higher educated Christians than they are speaking about how compatible accepting limited biological evolutionary theories with their religious faith actually is. So when they get out of their echo chamber and realize that learning and research hasn’t stopped but rather continues, even among their fellow religious, that they didn’t know existed, it can have a chilling or liberating effect.

The Intelligent Design movement with its Intelligent Design theory/ideology (IDism) was & still is an echo chamber, based, governed & funded in Seattle, USA. I’d welcome an open conversation with Stephen C. Meyer & John G. West about this. Indoctrination going one way is all they’ve focused on, while indoctrination going the other way is an elephant in the room that IDists will eventually need to come around to address.

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Evolution affirms the Consequent

  1. Affirming the Consequent is a logical fallacy that takes a known true statement [if P then Q] and invalidly concludes its converse [if Q then P]:
    1. If Bill Gates owns Fort Knox, then Bill Gates is rich. Bill Gates is rich. Therefore, Bill Gates owns Fort Knox. False!
    2. If an animal is a dog, then it has four legs. My cat has four legs. Therefore, my cat is a dog. False!
    3. If it’s raining, then the streets are wet. The streets are wet. Therefore it’s raining. False! It could be raining or it could be something else. The “therefore” claim is false.
  2. How does ‘Affirming the consequent’ apply to evolution? We have not observed “evolution”. No one has, and no one will, despite the effort (see LTEE). What was observed is Resemblance, the Birth Mechanism, Variability and Adaptability. Neither of these (even combined) can logically be extrapolated to “evolution”, namely the hypothesized transmutation of one type of organism into another. Proofs of “evolution” always take the form: If “evolution” is true, then XYZ is true. XYZ is true. Therefore “evolution” is true. This is a classical Affirming the Consequent logical fallacy.
  3. Let’s see some concrete examples of “proof of evolution” fallacies:
    • If “evolution” is true, some fossils are ancestors of and therefore resemble existing organisms. Fossils resemble one another and existing organisms. Therefore “evolution” is true. This argument fails because there will always be some resemblance between two or more entities (even chairs and cats have four legs in general). Also, a fossil can always be from an unrelated branch of the “tree of life” which circularly presupposes “evolution” anyway.
    • If “evolution” is true, organisms are genetically similar. Organisms are genetically similar. Therefore “evolution” is true. This argument is false because other hypotheses such as common design account for genetic similarities just as well.
    • If “evolution” is true, one might expect common embryology. Similar organisms have similar embryology. Therefore “evolution” is true. This fails because embryology is expected to match genetics and morphology, hence the previous counterargument applies.
    • If “evolution” is true, one might expect vestigial organs. What looks like vestigial organs can be observed. Therefore “evolution” is true. This fails because what if those organs are useful rather that “vestigial”? And why would “evolution” not do away with “vestigial” organs as soon as they become useless? In sum, why can’t these organs have another reason or origin than “evolution”?
    • If “evolution” is true, one expects adaptability such as antibiotic resistance. Antibiotic resistance is observed. Therefore “evolution” is true. This fails because adaptabilities such as antibiotic resistance are compatible with other hypotheses, not just “evolution”. In addition, antibiotic resistance is ubiquitous, limited, reversible, and never observed to result in organism transmutation aka “evolution”.
  4. How can “proofs of evolution” avoid the ‘Affirming the Consequent’ logical fallacy? Direct confirmation of “evolution” is unlikely as shown by the LTEE study. Alternatively, an observation that is true for “evolution” and only for “evolution” might also work. In other words, what’s missing from all the examples above is a true statement of the kind: “only if evolution is true, then XYZ”. Of course, excluding all alternatives to “evolution” is an impossible task therefore, given that Intelligent Design is the main rival, proponents of “evolution” need only add a true statement of the kind: “if Intelligent Design is true, then XYZ is not true” to turn their invalid arguments into valid ones. But even this lower bar cannot be met by “evolution” proponents, thus making all “proofs of evolution” invalid.
  5. Isn’t then all science ‘Affirming the Consequent’? For example, “if Newtonian physics is true, a ball thrown at angle Theta and speed V will land D meters away. The experiment is carried out, and we find that the ball landed distance D away. Therefor physics is true.” No! This is not a fallacy because it meets the “if and only if” requirement and is limited to “everything else equal” cases. Rockets do not disprove this claim because everything else is not equal between them and thrown inactive projectiles. In addition, no one claims a single experiment confirms all Newtonian Mechanics the way “proofs of evolution” are presented. In this case, multiple combinations of Angles and Speed result in the same Distance without violating Newtonian Mechanics because this experiment proves only portions of the theory.

Links:

https://en.wikipedia.org/wiki/Affirming_the_consequent

https://www.amazon.com/Biblical-Wisdom-Literature-Joseph-Koterski/dp/1598035258

http://myxo.css.msu.edu/ecoli/

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ID journal silently revises article

The online intelligent-design journal, BIO-Complexity (Robert J. Marks II, editor-in-chief; Douglas Axe, managing editor), has revised at least one of its published articles without giving any indication of change. “A Unified Model of Complex Specified Information,” by George D. Montañez, states that it was published on December 14, 2018, and makes no note of having been revised since. However, the article presently has two more entries in the reference list than it did on December 17, 2018, when I downloaded it. The announcments page of the journal says nothing about the change.

BIO-Complexity claims to be an archival publication. Thus the content should not change at all once it is released. The editors have given us reason to wonder how much of journal has silently morphed over the years. They should have required the author to submit an erratum or an addendum, no matter how benign the changes he wanted to make to the article.

I suspect, but cannot be sure, that Montañez changed the article merely to give credit to A. Milosavljević for a theorem, after learning of it from my post “Evo-Info 4: Non-Conservation of Algorithmic Specified Complexity.” If that is the case, then Montañez should have submitted an addendum explaining that he had learned of the theorem from me after his article was published. Changes to supposedly archival material are wrong even when announced, and are doubly wrong when unannounced.

It now behooves the editors of BIO-Complexity to make an announcement detailing the changes to Montañez’s article, and indicating whether any other articles have been modified since publication. If they have any sense at all, then they will announce also that they will never again change material that they represent as archival.

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Giving Evolutionary Biologists the Finger!

Evolution of KRAB Zinc Finger Proteins vs. the Law of Large Numbers

There are patterns in biology that violate the law of large numbers, and thus suggests Intelligent Design or at the very least statistical miracles. The pattern involves KRAB-ZnF proteins that have multiple zinc finger domains side by side that are inexact copies of each other and would require a scenario of co-evolution of their DNA binding partners with every additional zinc-finger insertion — a scenario indistinguishable from a miracle.

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Darwin’s God-The Omnipotent Natural Selection?

Darwinists are not much different than their God-fearing counterparts when it comes to their belief system. Theists believe in the omnipotent God, or Creator and yet Darwinists believe in the omnipotent, creative powers of natural selection.. In short, the belief systems are fundamentally the same, except that Darwinists supplanted the omnipotent God for another god-the omnipotent natural selection
Therefore, due to this widespread belief in the omnipotence of natural selection among great number of evolutionary biologists everything and anything in evolution can be explained by inserting the omnipotence of natural selection when scientific evidence is lacking… 

I call it the 1+1=3 (or any number you wish it to equal ) the first commandment of evolutionary theory, which includes that irreducible complexity coined by Behe, the chicken and egg paradoxes in the origins of life and life systems-the indispensable components need to be present for the life system to function, the miraculous appearance of genes in the supposedly evolved organisms and many, many more…
The most interesting, and hilarious at the same time, is that this believe is not consistent among all the Darwinists as it should, because there are so called errors (Lents) or imperfections, that at least seem to contradict the omnipotence of natural selection…However, what is consistent about it is that the omnipotence of natural selection is often applied when it is called upon… or what I call the natural selection of the gaps… 
One of the rebels, or misinformed Darwinists about the omnipotence of natural selection, is professor Losos… He seems to strongly believe that natural selection, while powerful in its creative works, is not really omnipotent, but works with the materials it has available…which implies what?

Here is his assay:

2017 : WHAT SCIENTIFIC TERM OR CONCEPT OUGHT TO BE MORE WIDELY KNOWN?

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Paging Dr. Holloway!

TSZ member Eric Holloway is the latest rising star of the “Intelligent Design” movement. Such a meteoric rise is bound to attract attention and it has indeed caught the eye of veteran biologist Professor Joseph Felsentein who noticed a comment young Eric posted here at TSZ and remarks


Eric Holloway just made a dramatic announcement on The Skeptical Zone, in Dieb’s thread on the number of posts at the ID site Uncommon Descent. In this comment he concludes “At least in my personal interactions with people, it seems like ID has won the debate”.

Professor Felsenstein has a few questions for Eric and hopes he may find the time to respond. I’m just helping out in case Eric has missed Joe’s post at the Panda’s Thumb.

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Help Dr. Lenski to Design Real LTEE

[Admin edit: This thread is, with the agreement of the thread author, a rule-free thread.]

As most TSZ readers already know, Dr. Lenski has been growing bacteria for 31 years now… Unlike the 99.99% of evolutionary biologist, who spend most of their time speculating about evolution, he set out to test evolutionary capabilities, or that what most of us thought he had, by laboratory experiments……

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Darwinism Kill-Bear by Behe

As some already are aware many, even the most biased Darwinists, have abandoned their belief in Darwinism, especially recently…

So, one might rightly ask: Why do we still need to review Behe’s book if Darwinism is dead? Why did Behe even need to write the book in the first place?

Well some, while few left, still believe that Darwinism, although dead, could be kept on life-support for at least a little while, or another 31 years, as Lenski, one of the three musketeers, hopes for…

Why? I will try to cover this in one of my upcoming OPs…

Few facts about Behe before we get to the kill-bear:

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Plants evolved the sophisticated math abilities?

In the retrospect of the publicity over Behe’s Devolution book, which exposes Darwinian evolution as the devourer rather than the builder of novelty in life systems, the sophisticated arithmetic calculation done by plants provide proof that, at the very least, if this ability evolved, it couldn’t have been by any know evolutionary mechanism today….

“Plants do complex arithmetic calculations to make sure they have enough food to get them through the night, new research published in journal eLife shows. Scientists at Britain’s John Innes Centre said plants adjust their rate of starch consumption to prevent starvation during the night when they are unable to feed themselves with energy from the sun. They can even compensate for an unexpected early night. here

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