Michael J. Behe's Blog, page 436

September 3, 2019

Is Nature needlessly annoying Dan Graur, the champion of junk DNA?

File:DNA simple.svg



A friend asks, on reading this:





Far from being junk DNA, the pervasive retrotransposons that populate the genome have a powerful capacity to influence genes and chromatin. A new study demonstrates how the transcription of one such element, HERV-H, can modify the higher-order 3D structure of chromatin during early primate development.

Michael I. Robson & Stefan Mundlos, “Jumping retroviruses nudge TADs apart” at Nature Genetics, volume 51, pages1304–1305 (2019)








Graur has been so convinced of junk DNA that he — last we heard — stopped even doing politeness on the subject any more.





Hmmm. Does someone have Miss Manners’ private e-mail or some other discreet means to get in touch with her, perhaps through a friend? Possibly Dr. Graur might wish to consider luncheon at some point. She is his guest, of course…

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Published on September 03, 2019 12:36

September 2, 2019

Rational Religion’s conversations with Darwin skeptic David Berlinski

Philosopher and novelist David Berlinski is an early and interesting Darwin skeptic. His iconic 1996 Commentary essay, The Deniable Darwin, set thousands of people thinking.





Anyway, hat tip to Philip Cunningham:











1:16 – Berlinski’s background





2:17 – Does Materialism makes sense?





3:47 – What are the Laws of Nature





10:01 – What is consciousness?





15:47 – Is Artificial Intelligence a threat?





19:36 – Is Darwinian Evolution on its way out?





23:28 – How did language originate?





35:03 – Does religion poison human morality? 37:35 – Can science teach us morality? 40:49 – How influential has New Atheism been? 41:24 – Spiritual but not religious/ are we just bodies? 42:52 – Can religious ideas make a comeback in the west?





35:03 – Does religion poison human morality?





37:35 – Can science teach us morality?





40:49 – How influential has New Atheism been?





41:24 – Spiritual but not religious/ are we just bodies?





42:52 – Can religious ideas make a comeback in the west?














See also: Hoover Institution interview with David Berlinski





David Berlinski with Mark Levin: The Link Between Evolution, Science And Progressivism





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Published on September 02, 2019 15:20

Intelligent design? Ray Kurzweil’s AI-driven Singularity would make the whole universe intelligent

If computers got that smart. At the COSM meet, Ray Kurzweil will offer, by video link, a glimpse of his foreseen Singularity where we merge with superintelligent computers:





He believes that the merger will eventually make the whole universe intelligent. Kurzweil’s critics believe that the superintelligent computers he needs can’t exist. If the critics are correct, we have misread the AI revolution.

Even Kurzweil’s friend George Gilder questions the underlying basis of the transhumanist vision and points out that information is precisely what is not determined by a machine and is therefore the source of creativity.

Kurzweil has little use for such quibbles. He responds that “the entire universe will become saturated with our intelligence. This is the destiny of the universe.” As Marks notes, “His predictions are often so far in the future that they escape any immediate scrutiny.”

That doesn’t mean that such predictions do not answer a need. The definite religious undertones attract seekers. Nearly as many young Americans believe in ET as in God, religion prof Diana Pasulka reports, from her research. In a recent interview with Sean Illing at Vox, she tells him, “Technology defines our world and culture; it’s our new god…”

With what consequences, we shall see.

Will we become mere apps of our smart machines?” at Mind Matters News








See also: Tales of an invented god





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Published on September 02, 2019 14:45

Rob Sheldon on why statisticians are in a panic

Yes, recently, we learned from a highly official source that statisticians are in some kind of a panic:





While the crisis of statistics has made it to the headlines, that of mathematical modelling hasn’t. Something can be learned comparing the two, and looking at other instances of production of numbers.Sociology of quantification and post-normal science can help.

While statistical and mathematical modelling share important features, they don’t seem to share the same sense of crisis. Statisticians appear mired in an academic and mediatic debate where even the concept of significance appears challenged, while more sedate tones prevail in the various communities of mathematical modelling. This is perhaps because, unlike statistics, mathematical modelling is not a discipline. It cannot discuss possible fixes in disciplinary fora under the supervision of recognised leaders. It cannot issue authoritative statements of concern from relevant institutions such as e.g., the American Statistical Association or the columns of Nature.

Andrea Saltelli, “A short comment on statistical versus mathematical modelling” at Nature








So what’s going on? Our physics color commentator Rob Sheldon offers,









The author of this article is contrasting the growing sense of panic in statisticians, with the complacency of modelers.





The panic in sociology, psychology, nutrition science, and pharmacology has been growing as >70% papers with “p-values” smaller than 0.05 are discovered to be unrepeatable.





Since the “p-value” is a statistical quantity invented by Ronald Fisher and is tied to “frequentist” statistics, the competing “Bayesian” statisticians have claimed that the method is deeply flawed. That battle is not new, having been fought since the year that Fisher introduced his p-value, but until recently, had been won by the frequentists. Today, Bayesian methods are not just widely popular, but have replaced frequentists in many niche fields, so that the “irreproducibility” crisis is not simply pointing the finger at a few fraudulent bad apples, but at an entire educational system that promoted p-hacking.





By contrast, modellers have been growing in prestige and fame year upon year. For example, in 2018, nine Neanderthal genomes had been sequenced, and one Denisovan genome.





Yet we have a news item this week, typical of recent news items, which claims that Neanderthals carry 1% of their genes from previous encounters with modern humans.




The Long Ascent: Genesis 1â 11 in Science & Myth, Volume 1 by [Sheldon, Robert]




How do they figure this out? Especially since we have zero genomes from Modern humans that predate Neanderthals?





Models.





But how do we know, asks Andrea Saltelli, if our models are valid? Can we run calibration tests on them with known answers? How about simple consistency checks? What about stating all our assumptions up front?





Nope, nope, and double nope. Modellers get a free pass, while statisticians get the bright lights in their eyes and the grilling from unseen questioners, with the threat of retracted papers and tenure-destroying expulsion.





Saltelli then goes on to show a rather disturbing plot. The more complicated our model becomes, the more ability it has to match our actual data. If you have only two data points, a model needs only two free parameters, and it can find a line through both those points. If you have 3 points, you can find a curve, a quadratic polynomial that will go through them. As long as you have as many free parameters as there are data points, there is always a curve that goes directly through all the points.





But is this increasingly complex mathematical model valid?





The way to test it, is to find one additional point, and see if the curve for n-1 points matches this last point. And weirdly enough, when the model has too many free parameters, it gets more and more “unstable”, more and more “wiggly” as it strains to perfectly match the previous data, with less and less likelihood of matching new data. This is what Saltelli’s disturbing plot shows, that the model error is minimized somewhere in the middle of the “complexity” axis.





So rather than complimenting our modellers (think global climate models) for matching past data perfectly by adding in adjustable variables (aerosols, feedback), we should be suspicious that they are actually making their predictions worse by overcomplicating them.





And it isn’t just Neanderthal genetics and global climate models. This is true for every area of science, from cosmology to particle physics to cladistics and AI. This is why IBM is abandoning “Deep Mind.” The problem wasn’t fixed by throwing more complexity at it.





So rather than being complacent, modellers ought to be in an equal state of panic as statisticians. Saltelli is not abandoning modelling, he just wants it to be ethical. From his concluding paragraph: “While this vision is gaining new traction [sociology of modelers working with suppliers of data and users of models] more could be done. A new ethics of quantification must be nurtured.”





Perhaps this is all part of the Paley renaissance, recognizing that the days of coddled dogmatics and their supporting cast of modellers are coming to an end.









See also: Confirmed: Deep Mind’s deepest mind is on leave. The chess champ computer system just never made money





Note:Rob Sheldon is the author of Genesis: The Long Ascent





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Published on September 02, 2019 09:36

One of the biggest problems with Darwin’s theory may now be his supporters

Their unreflective belligerence advertises all the other problems.





MercatorNet has reprinted leading Canadian columnist Barbara Kay’s column on David Gelernter’s rejection of Darwinism (as understood by hordes of trolls):





Time has proven unkind to Freud’s and Marx’s theories, but very kind to Darwinism. Why? Shhh. If you dare to ask, you invite ridicule. Because the minute one expresses doubt about Darwin’s basic premise that all life-forms, including humans, descend from a common ancestor through the simple processes of random, heritable variation and natural selection, one admits the possibility of a counter-theory — Intelligent Design — that is considered anathema to the intelligentsia, since it implies, you know, the G-word.

David Gelernter, a conservative Yale professor of computer science, is suffering extreme ridicule and worse from colleagues for having just published an article in the Claremont Review, “Giving up Darwin.” The title is misleading, because Gelernter does not reject Darwin completely. He says there is no doubt that Darwin “successfully explained the small adjustments by which an organism adapts to local circumstances” through fur density or beak shape or wing style changes.

It’s the big thing Gelernter now believes Darwin got wrong: humans.

There are intractable problems with Darwin’s “beautiful” theory.

Barbara Kay, “Daring to question Darwin ” at MercatorNet








As our title implies, the biggest problem now is the difficulty of discussing the problems honestly. Everyone expects that the Darwinator will bang the gavel down hard and make some pronouncement that “solves” them. Trolls love that kind of thing. They can emote and call it thinking.





The fact that nothing can refute Darwinism—because it is implicit in so many people’s basic assumptions about life—should tell us what we need to know.





Note: It sounds as though Kay has discovered Trollus darwiniensis, the Darwin troll. This type are mainly dangerous to those in academic life. But they are deadly serious, with good reason, for the same reasons as other cult members are.









See also: Maybe the best defence of Darwinism is now ignorance of the problems. They said things like, “I don’t need to read this to know it’s ignorant.” Which is a fine way to expose their own ignorance: They had no idea what they were talking about, and acted proud of it!





But WHY are they abandoning Darwinism? And note, these are NOT the raging Woke who would pull down Darwin’s statue because he is dead, white, and male. These are thoughtful people. They can see that he might be reasonable but wrong.





Meanwhile, other engaged brains have been getting restless too:





At First Things, They Are Also Getting Over Darwinism





Another Think Tank Now Openly Questions Darwinism So Power Line is interviewing J. Scott Turner, author of Purpose and Desire: What Makes Something “Alive” and Why Modern Darwinism Has Failed to Explain It. He’s not an “ID guy” but that doesn’t matter. His book’s title tells you what you need to know. He understands that something is wrong. And his insights into insects’ hive mind are a piece in the puzzle.





Hoover Institution interview with David Berlinski





Mathematicians challenge Darwinian Evolution





The College Fix LISTENS TO David Gelernter on Darwin! It’s almost as though people are “getting it” that Darwinism now functions as an intolerant secular religion. Evolution rolls on oblivious but here and there heads are getting cracked, so to speak, over the differences between what really happens and what Darwinians insist must happen.





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Published on September 02, 2019 04:33

September 1, 2019

Late stage materialism?: Panpsychism (your coffee mug is conscious) sounds crazy but…

A philosopher of consciousness says, it is probably true. Just so you know what you are up against:





No doubt the willingness of many to accept special relativity, natural selection and quantum mechanics, despite their strangeness from the point of view of pre-theoretical common sense, is a reflection of their respect for the scientific method. We are prepared to modify our view of the world if we take there to be good scientific reason to do so. But in the absence of hard experimental proof, people are reluctant to attribute consciousness to electrons…

In fact, the only thing we know about the intrinsic nature of matter is that some of it – the stuff in brains – involves experience. We now face a theoretical choice. We either suppose that the intrinsic nature of fundamental particles involves experience or we suppose that they have some entirely unknown intrinsic nature. On the former supposition, the nature of macroscopic things is continuous with the nature of microscopic things. The latter supposition leads us to complexity, discontinuity and mystery. The theoretical imperative to form as simple and unified a view as is consistent with the data leads us quite straightforwardly in the direction of panpsychism.


Philip Goff, “Panpsychism is crazy, but it’s also most probably true” at Aeon




Right. If you believe that nature is all there is and you can’t otherwise explain the mind, the mind must be part of nature and therefore electrons are conscious. Unless you want to say that the mind is an illusion.





See also: Further reading on panpsychism, the Next Big Thing:





Why some scientists believe that the universe is conscious. They’re not mystics. But materialism is not giving good answers so they are looking around





No materialist theory of consciousness is plausible. All such theories either deny the very thing they are trying to explain, result in absurd scenarios, or end up requiring an immaterial intervention. (Eric Holloway)





Panpsychism: You are conscious but so is your coffee mug Materialists have a solution to the problem of consciousness, and it may startle you





and





How can consciousness be a material thing? Maybe it can’t. But materialist philosophers face starkly limited choices in how to view consciousness.





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Published on September 01, 2019 13:30

Computers’ stupidity makes them dangerous

Not their intelligence. Statistician Gary Smith thinks the real danger today is not that computers are smarter than us, but that we think computers are smarter than us.





I made up some household spending data for 1,000 imaginary people, of whom half had suffered heart attacks and half had not. For each such person, I used a random number generator to create fictitious data in 100 spending categories.


These data were entirely random. There were no real people, no real spending, and no real heart attacks. It was just a bunch of random numbers. But the thing about random numbers is that coincidental patterns inevitably appear.


In 10 flips of a fair coin, there is a 46% chance of a streak of four or more heads in a row or four or more tails in a row. If that does not happen, heads and tails might alternate several times in a row. Or there might be two heads and a tail, followed by two more heads and a tail. In any event, some pattern will appear and it will be absolutely meaningless.


In the same way, some coincidental patterns were bound to turn up in my random spending numbers. As it turned out, by luck alone, the imaginary people who had not suffered heart attacks “spent” more money on small appliances and also on household paper products.


When we see these results, we should scoff and recognize that the patterns are meaningless coincidences. How could small appliances and household paper products prevent heart attacks?


A computer, by contrast, would take the results seriously because a computer has no idea what heart attacks, small appliances, and household paper products are. If the computer algorithm is hidden inside a black box, where we do not know how the result was attained, we would not have an opportunity to scoff.
Gary Smith, “Computers’ stupditiy makes them dangerous” at Mind Matters News





Think what that means for all the stuff we hear in the media about what computer-based analyses have supposedly shown.









More from Smith, at your own risk of knowing more than you want to about what’s in the sausage of the information presented to us from approved sources:





The Paradox of luck and skill: If four work friends play a round of golf and one player is much better than the others, the winner is determined mostly by ability. If four of the top golfers in the world play a round of golf, the winner is determined mostly by luck.





We see the pattern!—but is it real? Patterns are not always a source of information. Often, they are a meaningless coincidence like the 7-11 babies this summer.





Podcasts: Catch Gary Smith discussing with Bradley Center director Robert J. Marks what AI can and can’t do:





Why was IBM Watson a flop in medicine? Last year, the IBM Health Initiative laid off a number of people, seemingly due to market disillusionment with the product.





Why an AI pioneer thinks Watson is a “fraud.” The famous Jeopardy contest in 2011 worked around the fact that Watson could not grasp the meaning of anything.





Can AI combat misleading medical research? No, because AI doesn’t address the “Texas Sharpshooter Fallacies” that produce the bad data.





AI delusions: A statistics expert sets us straight. We learn why Watson’s programmers did not want certain Jeopardy questions asked.





and





The US 2016 election: Why Big Data failed. Economics professor Gary Smith sheds light on the surprise result.





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Published on September 01, 2019 12:35

Once More from the Top on “Mechanism”

We often get some variation of “Until ID proposes a ‘mechanism’
for how the design is accomplished, it cannot be taken seriously as an
explanation for origins.”





Here is an example from frequent commenter Bob O’H (who, after years of participation on this site should know better):





If ID is correct, then the design has to have happened somehow, so a “how” theory has to exist.





OK, Bob, once more from the top:





Suppose someone printed your post on a piece of paper and
handed it to an investigator.  We’ll call
him Johnny.  The object of the
investigation is to determine whether the text on the paper was produced by an intelligent
agent or a random letter generator. 





Johnny, using standard design detection techniques, concludes that the text exhibits CSI at greater than 500 bits, and reaches the screamingly obvious conclusion that it was designed and not the product of a random letter generator.





“Ha!” the skeptic says. 
“Johnny did not propose a mechanism by which someone designed the
text.  Therefore his design inference is
invalid.  If his design inference is
correct, then the design has to have happened somehow, so a ‘how’ theory has to
exist.”





Bob, is the objection to Johnny’s conclusion valid?


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Published on September 01, 2019 08:02

August 31, 2019

A Logical Misunderstanding About Design Arguments

Many materialists are confused about the obsession of ID’ers with Darwinian evolution. They believe that our targeting of Darwin is misguided for the simple reason that showing that Darwin is wrong doesn’t make us correct. On the simple face of it that is correct—showing that X is false doesn’t make Y true.


However, the story of Darwin and design is deeper than that, and to understand why ID’ers target Darwin you have to understand more of the story. For the next two paragraphs, if you are a Darwinist, set that to the side for a moment to at least understand where the ID’er is coming from.


To and ID’er, the biological world screams design. That is, nearly every thing in our bodies and in the world serves some purpose. If there is an organ, you can bet it is there to serve a purpose. Organisms themselves serve purposes in the larger environment. Everything in biology is endowed with purposive intent. In fact, even the problems make the purpose stand out more clearly. We can tell that cancer is bad because it does not line up with the purposes of our body. We can see and understand everything in terms of purpose.


Additionally, these purposes are carried out utilizing stunning machinery at every level. You can see it in the gross anatomy. Organisms are built with logically distinct systems serving the organisms purpose. You can see it all the way down to the molecular biology. Each cell comes equipped with tiny organelles which work together to keep the cell running, and each of these are very precise machines.


This is the starting point—the starting evidence. It is true that it is not quantitative. However, most observations that you can make about an organism screams for purpose and design. While there are many intricate, purposive systems built by intelligent agents, we have never seen it occur in the absence of agency. Therefore, being surrounded by intricate, purposive systems, we infer that there is some sort of agent behind it. So why don’t people believe in design in biology?


It used to be that design was the default assumption in biology, for these very reasons. The innovation that Darwin had was that there was another way to account for all of this purpose and design in biology. Darwin proposed natural selection as a way to get purpose and design entirely through purposeless, material causes.


So, abstractly, the old argument was like this:


Y can only be caused by X; we see Y, therefore X.


The Darwinian logic was:


Oh, wait a minute there, Y can also be caused by Q; therefore, when we see Y, it *might* by X, but it could also be Q.


Further along intellectual history, X was ruled out as a possible cause. This made the logic become:


Y can be caused by either Q or X. However, we are not allowed to consider X. Therefore, we see Y, and can only conclude Q.


So, hopefully you can now see why ID focuses on the defeat of Q. The entirety of the living world already gives evidence of X. We could add more (as Behe has often done), but it is largely unnecessary, simply because of the overwhelming evidence of X. If Q is shown to be wrong, then the methodological assertion against X is shown to be ridiculous, and people can return to concluding X from the massive amount of evidence that is simply everywhere we look.

This is why Dawkins said, “Darwin made it possible to be an intellectually fulfilled atheist.” He provided a defeater for the obvious conclusion. If the defeater is out of the way, then making the obvious conclusion is, well, obvious.


Additional note – some may wonder about the many purported “other mechanisms” of evolution. I have found that pretty much all suggested mechanisms fall into two categories. (1) a Darwinian mechanism, but which is more specific. That is, some may talk about all sorts of potential mutations, and categorize them. For example, Allen McNeil has such a list. As far as I’m aware, McNeil suggests no teleological or teleonomic directionality in any of these mechanisms, which is precisely what is meant by “random mutation” – mutations lacking in directionality. Therefore, this post (and any post on random mutation and natural selection) applies equivalently to these mechanisms. (2) Non-Darwinian mechanisms. These are mechanisms where either (a) the organism has sufficient knowledge/agency to construct its own destination (i.e., Natural Genetic Engineering or the Implicit Genome), or (b) evolution presupposes a huge amount of existing information in the genome ahead-of-time (evo-devo). These can be wrapped up in the broader term evolutionary teleonomy. These mechanisms, like all the other biological mechanisms, are expressions of purpose. While they may or may not undermine specific views of natural *history*, they do nothing at all to undermine the general view of purpose and design in nature. They merely move the design back, which, mathematically, makes the amount of design required bigger, not smaller.


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Published on August 31, 2019 20:37

Maybe the best defence of Darwinism is now ignorance of the problems

Ably discussed at The Stream:





Last week, Rachel Alexander wrote about Yale professor David Gelernter’s “leaving Darwinism.” The article has garnered almost 400 comments already. I encourage you to read through them. It’s entertaining, at least — especially if you know anything about the history of this debate. Especially the online version.

Because — how shall I say this nicely? — people who defend Darwin online typically don’t know what they’re talking about. They’re terribly sure of themselves, though, and they don’t mind spewing insults to tell you so. And that’s not just bias speaking on my part. I’ve got data to back it up, as you’ll see shortly…

Ten years ago Stephen C. Meyer, head of the Discovery Institute’s Center for Science and Culture, published his first book, Signature in the Cell: DNA and the Evidence for Intelligent Design. A few months later I analyzed its 200-plus reviews so far on Amazon. (Full data detailed here.) I found that three quarters of the book’s one-star reviews came from people who stated outright they hadn’t read the book. Three-quarters! They said things like, “I don’t need to read this to know it’s ignorant.” Which is a fine way to expose their own ignorance: They had no idea what they were talking about, and acted proud of it!

Tom Gilson, “Intelligent Design Opponents Don’t Know What They’re Talking About, But Love Telling You ID is Stupid Anyway” at The Stream 1114




Here are the comments to which Gilson refers. Read the Darwinspouting for laughs.





Note: Amazon, to its credit, has been trying to crack down on those sorts of non-reviews (= “I’m proud to say I haven’t read it and neither should you!”) But hey, that’s not a risky business decision for Amazon. It’s hard to make a business case for just plain wasting prospective customers’ time by making them wade through the remarks of people who have chosen to waste their own time and take up space in that way.





Hat tip: Ken Francis, co-author with Theodore Dalrymple of The Terror of Existence: From Ecclesiastes to Theatre of the Absurd





See also: But WHY are they abandoning Darwinism? And note, these are NOT the raging Woke who would pull down Darwin’s statue because he is dead, white, and male. These are thoughtful people. They can see that he might be reasonable but wrong.





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Published on August 31, 2019 17:14

Michael J. Behe's Blog

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