Invited responses to my nylonase research and the question of “New Proteins Without God’s Help”

Susumo Ohno (who coined the term “junkDNA”) published a paper in 1984 through the National Academy of Sciences that was used by the NCSE, Ken Miller and Dennis Venema to claim “proteins can evolve without God’s help”. At the request of John Sanford, a courtesy associate research professor at Cornell, I was recruited to write a paper to refute Ohno’s evolutionary hypothesis on nylonases. I wrote it under John’s guidance based on his intuitions about genetics, his life-long specialty of 40 years and for which he became famous as attested by the fact he is one of the few geneticists who had their work featured in the Smithsonian National Museum of American History.

The actual paper is now in review, but it is not intended to be published in any journal, but will be released in a variety of channels shortly. It is hoped the material can be used by others to actually create papers that enter peer review. The motivation for releasing the paper in this way is to counter Venema’s book while it is still hot off the press.
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Free Speech, pseudonymity and the Web

Where to draw the line between the right to say what we sincerely believe and the right of others not to be insulted, belittled, threatened? Where to draw the line on protecting those who post pseudonymously on the internet?

The Internet has created opportunity. The opportunity for those living under repressive regimes to communicate, to organise, to advertise the fact of their oppression internationally. But also the opportunity for oppressive regimes to trace and document this activity and track down dissidents. And the opportunity for groups with extreme views to advertise and organise racist rallies.

I’m conflicted. My conflict is between ensuring the right of anyone to speak their mind and the responsibility of owning up to those views.

Where to draw the line?

Save them, smash them, relocate them or critique them?

I’m not going to write about the tragic events in Charlottesville in this post. I think the VICE News video says it all. It should be obvious that in this particular march, the violence that occurred came overwhelmingly from the alt-right, many of whom came to the march armed with pepper spray and hidden assault weapons (see the end of the video), although I note for the record that a few protesters on the Left did as well. I am frankly mystified by President Trump’s reluctance to condemn the white nationalist marchers en masse and by his bizarre assertion that there were some people “protesting very quietly” at the torchlight march on the night before the rally (which has been debunked by Paul Blake of the BBC), but I doubt whether racism is his underlying motivation: after all, the marchers shouted Nazi slogans against the Jews, and the President’s own daughter and son-in-law are Jewish. Perhaps the man is morally timid, and reluctant to condemn even bad people who might vote for him. Or perhaps the President views racism as self-evidently absurd, requiring no further comment in the 21st century. Or perhaps he fears that by demonizing the 500 or so marchers who took part in the alt-right rally in Charlottesville, he will only succeed in making them look more appealing to alienated juvenile delinquents, thereby consolidating their base of support. I don’t know. In any case, this is not a post about Trump, whose White House seems to be facing a meltdown of its own making.

Instead, what I’d like to write about in this post is the question of what Americans should do with the 718 monuments and statues (709, according to the BBC) situated on public property throughout the country, mostly in the South, although there are also a few in former Union States, including Iowa, Kansas and Pennyslvania, and there’s even one in Massachusetts. The Southern Poverty Law Center has published a paper calling for their removal, and a summary of their responses to counter-arguments can be found on pages 38 to 39.

I’d like to begin by asking viewers how they feel about this video, showing a statue of a Confederate soldier being pulled down in Durham, North Carolina, on Monday (courtesy of World Viral Videos):

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Working out a gentleman’s agreement between TSZ and my publishing activities

As much as the TSZ regulars may have sharp disagreement with many of my views, I actually have a vested interest in seeing TSZ survive and prosper and attract participation with talent and brains. TSZ is valuable because of the quality of the participants, namely, professors (like Joe Felsenstein, Jeff Shallit), textbook authors (like Larry Moran), specialists (Tom English, John Harshman, Mark Frank, Mike Elzinga, etc.), academics, practicing scientists, etc. I suspect JohnnyB and VJTorley might have comparable reasons for their participation at TSZ.

The purpose of me posting here is to see what sort of INFORMAL gentleman’s agreement can be worked out to the mutual benefit of TSZ and my publishing efforts.
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Betting on the Weasel

… with Mung.   In a recent comment Mung asserted that

If Darwinists had to put up their hard earned money they would soon go broke and Darwinism would be long dead. I have a standing $10,000 challenge here at TSZ that no one has ever taken me up on.

Now, I don’t have $10,000 to bet on anything, but it is worth exploring what bet Mung was making. Perhaps a bet of a lower amount could be negotiated, so it is worth trying to figure out what the issue was.

Mung’s original challenge will be found here.  It was in a thread in which I had proposed a bet of $100 that a Weasel program would do much better than random sampling.  When people there started talking about whether enough money could be found to take Mung up on the bet, they assumed that it was a simple raising of the stake for my bet.  But Mung said here:

You want to wager over something that was never in dispute?

Why not offer a meaningful wager?

So apparently Mung was offering a bet on something else.

I think I have a little insight on what was the “meaningful wager”, or at least on what issue.  It would lead us to a rather extraordinary bet.  Let me explain below the fold …

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There are only two sides, and you are on one or the other of them

We condemn in the strongest possible terms this egregious display of hatred, bigotry and violence on many sides, on many sides.

— Donald J. Trump

He who passively accepts evil is as much involved in it as he who helps to perpetrate it. He who accepts evil without protesting against it is really cooperating with it.

— Martin Luther King, Jr.

I condemn, in the strongest possible terms, the involvement of President of the United States in the evil of racism. The counter-protesters in Charlottesville lapsed into evil, to be sure. Meeting violence with violence, they handed their adversaries a huge victory. But their error does not make them the moral equivalent of white nationalists, neo-Nazis, and Klansmen. Seizing on their error to construct such an equivalence, as Donald Trump has done, is positively obscene. “Grab them by the pussy” pales in comparison.

Determining Probability

There’s been some debate here at TSZ recently about probability and the interpretation of probability.

I took some flak (my personal subjective opinion) for attempting to distinguish between calculating probabilities and estimating probabilities.

Yet in recent reading I came across this bit of text:

How do you determine the probability that a given event will occur? There are two ways: You can calculate it theoretically, or you can estimate it experimentally by performing a large number of trials.

– Probability: For the Enthusiastic Beginning. p. 335

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A Reason To Doubt Design In Nature

I’ve never found the ID arguments for the design of biological organisms all that compelling for a number of reasons. The dubious math, the fallacious arguments, the disingenuous bait and switch to Christian apologetics, and so forth. But even beyond that, there was something about objects in nature – organisms themselves – that just don’t seem designed to me. There is something different about them compared to man-made objects, but for the longest time I just could not put my finger on what I felt the difference was. And then it hit me last night: replaceable parts.

All man-made objects – every single one – is either designed specifically to be discarded or has components that are designed specifically to be replaced. Why? Because tool users learn really quick that tools and/or certain parts of tools wear out. So as designers, we <i>anticipate the need for maintenance</i>.

No such anticipation or planning for maintenance can be found in nature. None. If something breaks in an organism, either that organism learns to live without it or it dies. Or, in the case of humans, that part gets replaced by human designed or human configured replacements (as in my case). But even in the later case, humans have to create a work-around, because biological parts actual <i>resist</i> being replaced. You can’t just replace human parts with other human parts willy-nilly. In most cases, the new parts just won’t work, or worse, they’ll be rejected by the body’s immune system. But of particular note, there’s no surplus of replacement parts anywhere; no storage unit somewhere with a bunch of eyes or hearts or toes or hair or kidneys or…anything. Not even bark or leaves or antennae or scales. Nothing. There’s replacement part supply or even creation in nature.

Of course, this makes perfect sense given evolution and other similar natural processes. It makes no sense if there were an actual biological designer behind it all.

The Mysteries of Evolution: 4. How did we get here…

…from: “having been originally breathed by the Creator into a few forms or into one”?

Welcome all after vacation!

I have been reviewing many different articles recently and it hit me like a bolt of lighting: How did materialist who promote the Darwinian theory of evolution get to spontaneous emergence of life from what Darwin himself wrote in the Origin of Species:

“There is grandeur in this [natural selection] view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved”

One would think that scientific, experimental evidence convinced Darwinists to change their mind… Unfortunately, just like many of my posts and comments have revealed, no such evidence has emerged…. So, my question is: what prompted the Darwiwnists to change the fundamental idea about the origins of life originally written by Darwin himself, if no evidence for such a change exists?

Why Gradualism?

In Why Evolution is True, Jerry Coyne writes that gradualism is one of the six tenets of “the modern theory of evolution” (which he equates with Darwinism – see page 3).

Eugene Koonin writes that the tenet of gradualism is known to be false (The Logic of Chance p. 398).

Yet gradualism is obviously still quite popular here in “The Skeptical Zone.”

Surely gradualism is not a logical requirement or entailment of the theory of evolution. Neither is it supported by the evidence.

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Granville Sewell’s argument for Intelligent Design

Over at Evolution News, mathematician Granville Sewell has written an article titled, From Barren Planet to Civilization — Four Simple Steps (July 27, 2017). My intention in writing this post is not to critique Dr. Sewell’s latest argument, but to clarify its premises. Sewell’s own comments reveal that it is ultimately a philosophical argument, rather than a scientific one. Although I agree with Dr. Sewell’s key intuition, I contend that his argument hinges on two assumptions: that unguided processes have a snowball’s chance in hell of giving rise to factories, and that mental states do not supervene upon physical states.

The bulk of this post will be devoted to what Dr. Sewell has written in his latest Evolution News article. At the end of my post, I will briefly comment on the thermodynamic arguments in his accompanying video, which I see as peripheral to Sewell’s main point.

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Eye Mock Stupidity

I’m all in favor of mocking stupidity, and here’s something definitely worth mocking.

In arguing for evolution, author Alan R. Rogers appeals to the Nilsson and Pelger paper on how simple it is to evolve an eye. He writes:

If eyes evolve, they must do so often and easily. Could it really be so easy?

Dan-Eric Nilsson and Susanne Pelger have answered this question. They constructed an evolutionary story much like the one that I told above.

– The Evidence for Evolution. p. 42.

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How ENV muddies the waters on the evidence for human evolution

Recently, Evolution News and Views published an article titled, The Human-Ape Missing Link — Still Missing (July 18, 2017), which attempts to cast doubt on human evolution by quoting from a recent BBC article which highlighted the massive uncertainties that still remain over the identity, appearance and date of the last common ancestor (LCA) of human beings and chimpanzees, and which even questions whether the chimpanzee is our closest relative, after all. The Evolution News and Views (ENV) article also revives the myth of an unbridgeable gap between Australopithecus and Homo.

Here’s my two-sentence rebuttal: uncertainty as to who the last common ancestor of humans and chimps was, what it looked like, and when it lived, in no way diminishes scientists’ certainty that it existed. And while the fossil record of human ancestors is very meager and patchy until about 4.4 million years ago, from that time onward, we have a veritable hodgepodge of hominins – and no unbridgeable gaps.

Well, that was quick, wasn’t it? Now for a more detailed rebuttal.

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Suffer the children

During the past few days, there has been much discussion of philosophy professor Gary Comstock’s spirited defense of infanticide, in the case of a severely handicapped newborn baby who is likely to die (New York Times, July 12, 2017). Such an infant, argues Comstock, lacks “the things that make a life: thoughts, wants, desires, interests, memories, a future.” And if did have thoughts, its dominant thought about being kept alive on a respirator would surely be: “This hurts. Can’t someone help it stop?”

Bioethicist Wesley Smith has pointed out that the case described by Comstock (who is not a doctor), of an infant suffering excruciating pain as its life is needlessly prolonged, is totally fictitious: “When life support is removed, doctors do not just let patients twist choking in the wind. They palliate — as necessary to alleviate pain and agitation.” The testimony of palliative care physician Ira Byock (whom Smith mentions in his article) is well worth citing: “In more than 35 years of practice I have never once had to kill a patient to alleviate the person’s suffering. When other measures fail, palliative sedation for alleviation of physical suffering is reliably effective. Alleviating suffering is different than eliminating the sufferer.” (Maryland Medicine vol. 17, no. 4; January 2017.) And Dr. Michael Egnor, commenting on Comstock’s article for Evolution News and Views, writes: “The notion that handicapped children intractably suffer is a lie. I’ve treated thousands of these kids. Most of the conditions that cause severe neurological impairment aren’t painful and don’t inherently cause physical suffering. Spina bifida, holoprosencephaly, various trisomies and anencephaly don’t ‘hurt,’ and in fact the children afflicted are often quite content babies. They are loved by their families, and they can enjoy life in accordance with their physical limitations.”

Wesley Smith and Michael Egnor point out that infanticide is a crime against humanity, for which doctors were hanged at Nuremberg. Some of these doctors had euthanized handicapped children. Both authors make a telling point; nevertheless, the question needs to be addressed: exactly why is infanticide wrong?

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Evolution is not design

This is a continuation of an earlier OP. Design by Evolution

When we think of design, it is usually in the context of solving some sort of problem, … To be effective, the design must address a purpose to be achieved. … Thus, effective design requires some feedback mechanism to the designer.

But perhaps we can fit the square peg of purposeless blind watchmaker evolution into the round hole of purposeful intelligent design.

Some people here at TSZ seem to think that no one ever claimed that evolution is a designer. So let’s remind them.

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Evo-Info 3: Evolution is not search

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.

Marks, Dembski, and Ewert open Chapter 3 by stating the central fallacy of evolutionary informatics: “Evolution is often modeled by as [sic] a search process.” The long and the short of it is that they do not understand the models, and consequently mistake what a modeler does for what an engineer might do when searching for a solution to a given problem. What I hope to convey in this post, primarily by means of graphics, is that fine-tuning a model of evolution, and thereby obtaining an evolutionary process in which a maximally fit individual emerges rapidly, is nothing like informing evolution to search for the best solution to a problem. We consider, specifically, a simulation model presented by Christian apologist David Glass in a paper challenging evolutionary gradualism à la Dawkins. The behavior on exhibit below is qualitatively similar to that of various biological models of evolution.

Animation 1. Parental populations in the first 2000 generations of a run of the Glass model, with parameters (mutation rate .005, population size 500) tuned to speed the first occurrence of maximum fitness (1857 generations, on average), are shown in orange. Offspring are generated in pairs by recombination and mutation of heritable traits of randomly mated parents. The fitness of an individual in the parental population is, loosely, the number of pairs of offspring it is expected to leave. In each generation, the parental population is replaced by surviving offspring. Which of the offspring die is arbitrary. When the model is modified to begin with a maximally fit population, the long-term regime of the resulting process (blue) is the same as for the original process. Rather than seek out maximum fitness, the two evolutionary processes settle into statistical equilibrium.

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Introduction to Evolutionary Informatics

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.1

Yes, Tom English was right to warn us not to buy the book until the authors establish that their mathematical analysis of search applies to models of evolution.

But some of us have bought (or borrowed) the book nevertheless. As Denyse O’Leary said: It is surprisingly easy to read. I suppose she is right, as long as you do not try to follow their conclusions, but accept it as Gospel truth.

In the thread Who thinks Introduction to Evolutionary Informatics should be on your summer reading list? at Uncommon Descent, there is a list of endorsements – and I have to wonder if everyone who endorsed the book actually read it. “Rigorous and humorous”? Really?

Dembski, Marks, and Ewert will never explain how their work applies to models of evolution. But why not create at list of things which are problematic (or at least strange) with the book itself? Here is a start (partly copied from UD):
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