Casey Luskin: ID as fruitful approach to science

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May 13, 2022

Intelligent Design

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Intelligent Design}

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In his Kitzmiller v. Dover testimony, biologist Kenneth Miller referred to intelligent design as a “science stopper.” Similarly, in his book Only a Theory, Miller stated, “The hypothesis of design is compatible with any conceivable data, makes no testable predictions, and suggests no new avenues for research. As such, it’s a literal dead end…”
Casey Luskin, “Science Stopper? Intelligent Design as a Fruitful Scientific Paradigm” at Evolution News (May 9, 2022)

Luskin offers a number of examples of areas where ID is a fruitful approach, including

Evolutionary computation: ID produces theoretical research into the information-generative powers of Darwinian searches, leading to the discovery that the search abilities of Darwinian processes are limited, which has practical implications for the viability of using genetic algorithms to solve problems.
Anatomy and physiology: ID predicts function for allegedly “vestigial” organs, structures, or systems whereas evolution has made many faulty predictions of nonfunction.
Bioinformatics: ID has helped scientists develop proper measures of biological information, leading to concepts like complex and specified information or functional sequence complexity. This allows us to better quantify complexity and understand what features are, or are not, within the reach of Darwinian evolution.
Casey Luskin, “Science Stopper? Intelligent Design as a Fruitful Scientific Paradigm” at Evolution News (May 9, 2022)

The trouble is, many people would just as soon that research into evolutionary computation anatomy and physiology, and bioinformatics, however fruitful, not be done if it undermines a comfortable Darwinism.

This is the 12th and final entry in Casey Luskin’s series, which is a modified excerpt from The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos (2021).

Incidentally, here are two hilarious vids about fake COVID news from Shanghai. Couldn’t think where to put it but wouldn’t want you to miss out.

Note: The content is available. The warning is part of the joke.

Comments

Can we retire the term “junk DNA” since it essentially is a meaningless term. Why it is brought up I don’t know. Some here think it will show something but it doesn’t. Some previously thought excess DNA has been shown to have function. Big Deal! Some previously thought excess DNA appears to have no function. Big Deal! Let’s ignore comments or parts of comments that mention “junk DNA.”jerry_{May 16, 2022
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Relatd/49 Jerry Coyne is a secular Jew and emeritus professor of biology at UChicago--why would he be a spokesperson for the Catholic position on evolution? You are perhaps confusing him with the late George V. Coyne, a Jesuit priest and former chief astronomer for the Vatican and Director of the Vatican Observatory, who I quoted as critical of ID. Coyne received his PhD in astrophysics from Georgetown and spent his entire career harmonizing science and Catholicism. He has also been critical of Schoenborn for his affiliations with the ID movement.chuckdarwin_{May 16, 2022
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Bob O'H:
I’m sorry, is this the ID junk concept, or the actual one used by biologists, and referenced almost 100 times in Nature since 2004? Including 9 times in 2021.
Please tell us blind and mindless processes knew to produce histone octamers to spool up and organize the junk so that the junk-laden genome would be functional. Or admit that you just don't know how much of the genome is junk.ET_{May 16, 2022
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JHolo:
But it cannot be called a scientific endeavour until it starts researching the designer and the mechanisms used to realize the design.
That is complete and total ignorance. ID is not about the who or the how. You are obviously just an ignorant trollET_{May 16, 2022
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Jerry: People are getting hung up on ID being science. ID adds to science definitely. But it is not science.
I tend to agree with this. At most it is a tool that can be used by science, much like a microscope, a spectrophotometer or statistics. But it cannot be called a scientific endeavour until it starts researching the designer and the mechanisms used to realize the design.JHolo_{May 16, 2022
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Sandy @ 101 -
Have you searched newer articles than 2004 in the same Nature journal? I guess not because you would have found that the junk concept is discarded and can’t be defended anymore.
I'm sorry, is this the ID junk concept, or the actual one used by biologists, and referenced almost 100 times in Nature since 2004? Including 9 times in 2021.Bob O'H_{May 16, 2022
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Technology sometimes uses redundant systems. The extra systems can be removed without affecting the function. Those removed systems were not junk.ET_{May 16, 2022
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People are getting hung up on ID being science. ID adds to science definitely. But it is not science. ID is better thought of a layer added to science that provides a better explanation for physical phenomena. So it is not in the game of making predictions, but mainly making better conclusions of physical events. It does not mean ID cannot make some predictions like the one I pointed to above. But that’s not what it’s mainly about. There’s also the obvious prediction Kf makes all the time that no natural processes can produce complex specified functional information. That underlies the predictions about new proteins and DNA itself. ID is Science+ A great way to see ID in action is to read Denton’s new book which takes hundreds of unrelated physical phenomena and show how they all must be present for complex life to exist.jerry_{May 16, 2022
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Fred Hickson:
My purpose (heh) is not to defend evolutionary theory and convince you and others here that it is a useful working model that won’t be discarded until a better one turns up.
There isn't any scientific theory of evolution. And there isn't any useful models for evolution by means of blind and mindless processes. Fred is just a dishonest and clueless tool.ET_{May 16, 2022
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Again, anyone claiming that the majority of any genome is junk has to tell us how blind and mindless processes produced histone octamers to spool and organize the genomes into something functional. Absent that all you have is your ignorance.ET_{May 16, 2022
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Fred Hickson:
A penguin flipper’s ancestry is an adaptation to flight.
Propaganda isn't science. It's beyond pathetic when Fred uses question-begging as actual arguments.ET_{May 16, 2022
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@Fred Hickson: have you even read the article linked by BobO'Hara?
"Knowles cautions that the study doesn't prove that non-coding DNA has no function. "Those mice were alive, that's what we know about them," she says. "We don't know if they have abnormalities that we don't test for."
Have you searched newer articles than 2004 in the same Nature journal? I guess not because you would have found that the junk concept is discarded and can't be defended anymore. The advanced scientific methods unavailable a decade ago start to clear the mysticism of darwinists . We can see better in the "black box" of genetics and darwin is obsolete.Sandy_{May 16, 2022
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Fred Hickson:
I just feel the need to point out that people here in general are attacking a strawman when they should be thinking about proposing a genuine, testable, scientific ID hypothesis ...
You couldn't defend your claim of a strawman as you don't even understand evolutionary concepts. And ID has scientific hypotheses, unlike evolution by means of blind and mindless processes which only has liars.ET_{May 16, 2022
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the best “prediction” ID can come up with
Actually a much better prediction is that gene sequences producing proteins arising from natural processes are extremely rare or non existent. So far as I still know, a valid prediction.jerry_{May 16, 2022
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The onion test is a way of assessing the validity of an argument for a functional role for non-coding DNA, sometimes called "junk DNA"... Proof that Wikipedia isn't a reliable source. :)Fred Hickson_{May 16, 2022
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PS, the notion, widely circulated 10+ years ago was that non coding DNA was, overwhelmingly junk. ID theorists and thinkers at the time proposed that this was a gross error induced by a bad paradigm, and that much DNA would in fact be useful. It was of course pooh pooed, only to increasingly be vindicated. So, the successful risky prediction is now being dismissed.
Scientific knowledge advances on a broad front daily. You are welcome to argue who said and thought what and when. The simple fact is there is "junk" DNA in the human genome (not under selective pressure) because it has been identified, as Bob O'H confirms. How much and whether some DNA that we cannot the moment assign any role may turn out to have some function is a subject that scientific research will continue to elucidate. On the other hand, I don't see how the percentage of junk DNA in a genome (which is hugely variable across species - see The Onion Test) relates to "Intelligent Design". Maybe someone could put a few dates and declarations out for discussion.Fred Hickson_{May 16, 2022
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@ Bob O'H, Let's hope Querius listens to you, being a professional.Fred Hickson_{May 16, 2022
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FH, that multi-part functionality is dependent on well matched, properly arranged, oriented and coupled entities, is a massive fact of observation, of technology, of life, of thought, of text in language, of mathematics, of computing etc. That you wish to pour scorn on it as a painting the target after the fact fallacy or the like, speaks volumes by way of confession by projection. Remember, the issue pivots here, on there being a credible degree of complex organisation to achieve a functional cell, well established fact. Further, the mere fact of vital organs and functional systems in living creatures, shows the same for body plans, which must unfold from a single cell, e.g. the zygote. KFkairosfocus_{May 16, 2022
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FH, your attempt to hyperskeptically dismiss by alleged disanalogy, fails. Do I have to remind you how for example DNA has actually been used as a general purpose memory storing digital information, therefore accessible to storing data and instructions, or that it has been artificially chemically extended etc? As for configuration spaces, WLOG, any 3-d functional entity may be described by a chain of bits in some description language (cf. AutoCAD etc) and so can be located in a virtual space that is cut down from phase space [position-momentum] to position only. The pattern of islands of function in such a space holds for protein fold domains in AA sequence space, it holds for sex determination systems and for functionally coherent complex structures in general, system integration is a big deal in engineering to the point where systems engineering is a discipline. For that matter, this extends to cosmological fine tuning. The tree of life analogy -- actually, metaphor -- is of course Darwin's sole illustration in Origin, but of course is a commonplace data related structure, e.g. it is reflected in taxonomy of life forms and other systems as Berra mistakenly suggested for vehicles. It definitely has a root at OoL, and implies gradualistic incremental change without limit. Of course, I summarised the frame of the theory and showed that differential reproductive success . . . "preservation of favoured races" is in the subtitle of Origin . . . aka natural selection . . . is not the source of novel information. That is chance variation and the problem you are ducking is the scale of increments for first cell based life and for novel body plans. KF PS, the notion, widely circulated 10+ years ago was that non coding DNA was, overwhelmingly junk. ID theorists and thinkers at the time proposed that this was a gross error induced by a bad paradigm, and that much DNA would in fact be useful. It was of course pooh pooed, only to increasingly be vindicated. So, the successful risky prediction is now being dismissed. Just as, the design thinking view of deep order and intelligible organisation of cosmos, biological life etc was a suspect notion, only to be vindicated by the way modern science grew in such soil and has succeeded. Only, we now hear, how dare you point to the Logos principle and linked theology. The pattern of hyperskepticism is plain.kairosfocus_{May 16, 2022
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Querius @ 82 -
Junk DNA, now renamed to non-protein coding DNA is not useless “junk” as Susumu Ohno suggested, but actually has an undiscovered function.
Oh no! Ohno didn't suggest "junk" DNA was useless. I guess it's par for the course that the best "prediction" ID can come up with is based on ignorance, and predicting something after the fact. We know that some non-coding DNA is vital (start at centromeres and telomeres), but other non-coding DNA can be safely removed. How do we know? Because we've done it. So, we know (and have known for a long time) that some "junk" DNA has a purpose, but others don't (how else would you explain the difference in genome size between wheat and rice, for example?). This makes me wonder what your "prediction" actually is: is it that all junk DNA has a function, or that only some junk DNA has a function?Bob O'H_{May 16, 2022
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Just one point on "islands of function". This is a version of the Texas sharpshooter fallacy. I've seen Keefe and Szostak's work mentioned before here by ID skeptics. Random protein sequences can and do show function (K & S only looked at ATP affinity). Evolution, the accumulation of small changes which selection of proteins with "improved" function is not a one in gazillion all-at-once process. It's gradual. Yes, I am aware selection acts on whole phenotypes.Fred Hickson_{May 16, 2022
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@ Querius My purpose (heh) is not to defend evolutionary theory and convince you and others here that it is a useful working model that won't be discarded until a better one turns up. I just feel the need to point out that people here in general are attacking a strawman when they should be thinking about proposing a genuine, testable, scientific ID hypothesis while I'm waiting for Upright Biped to turn up.Fred Hickson_{May 16, 2022
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It would help if you checked your fallacious baloney before posting it or at least try to provide references before just making stuff up.
Read more carefully. I don't dispute drift happens. It can be significant in small populations.Fred Hickson_{May 15, 2022
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KF, You continue to speak in bad analogies. If your model doesn't fit reality, you should discard it and look for one that is closer to reality. Well, you can do what you want but if your intent is to convince anyone...Fred Hickson_{May 15, 2022
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Querius:
Dr. Ohno made no such distinction as you have. The fact is that the amount of so-called “junk” DNA keeps shrinking...
Prior to 1953, scientists did not have a structure for DNA. Models improve with knowledge. Yes, we will continue to find function in some sequences but we already confirm some DNA really is "junk". The broken human GULOP gene is an example that fails your hypothesis.Fred Hickson_{May 15, 2022
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FH, 65
Monkeys on typewriters! It’s never going to sink in, is it? No matter how many times I point out there is a non-random element to evolution, everyone here will continue to blather on about blind chance.
Your refusal to acknowledge our addressing of a point does not entail that we have failed to address the point, actually many times. All it does is it exposes your fundamental hyperskeptical dismissiveness. However, for record: 1: Darwin's proposal is in effect predicated on a tree of life branching incrementally across a continent of viable configurations, but this is already questionable. 2; That is, complex multi part function depending on matched, organised coupled parts and tuning of parameters is observed instead to come in deeply isolated islands of function in large configuration spaces, so even if we ignore the question of ruggedness within islands, the dominant problem is to find shorelines of functional configuration amidst seas of nonfunction. With relatively speaking negligible search resources and time once the 500 to 1,000 bit threshold is on the table. 3: The first key issue is to create C-chem, aqueous medium, encapsulated, smart gated, metabolising process-flow network cell based life that uses codes, algorithms and molecular, polymer based nanotech. This is the root of tree of life problem and it is a natural part of the problem, 4: In short playing datum line games that beg the biggest question, root, imply failure at the outset. The evidence is, such come from and reflect signs of design. 5: Design is at the root, it is available everywhere thereafter so In this context, it is question begging to impose thereafter a lockout of design under various guises and excuses. 6: Given the above, we may summarise Darwin et al:
chance variation [CV] + differential reproductive success [DRS] --> descent with unlimited modification [DWUM] DWUM + time, space, ecological circumstances --> branching tree of life pattern, BTOL and origin of diverse body plans [OoBP] BTOL + OoBP --> life forms in fossil record and today in macroevolutionary, incrementalist patterns [ME]
7: At outset, DRS subtracts less successive variants at a given time, it has no foresight. It therefore is not the SOURCE of variation, which leaves only chance variation, and the hope of a smoothly varying BTOL pattern to lead to a branching walk. 8: However, the implied continent of function is implausible, islands of function are plausible due to organisation, matching etc required for complex configuration based function. In WW2, it was discovered that parts built to the same blueprints and dimensions were incompatible because of small differences of units between US, UK, Australia. 9: The islands of function issue starts with deep isolation of several thousand protein fold domains in AA sequence space. Significance can be seen from misfolded prions and presence of chaperonin structures to foster correct folding. It continues up to things like diversity of sex determination systems. It is reflected in systematic gaps among fossils where 1/4 million species in museums and billions of fossils seen in the ground remove appeals to sparse sampling. 10: In addition, we can reasonably estimate that novel body plans require 10 - 100+ mn base pairs of new genetic information. The blind chance + mechanical necessity dynamic lacks power to discover shorelines of function. 11: Intelligently directed configuration, as observed, readily does so. Where we exemplify we do not exhaust possibilities. KFkairosfocus_{May 15, 2022
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Fred Hickson @84,
Huge error here. Junk DNA is DNA that performs no function for the host organism (viral elements, the broken GULOP gene in primates). Non-coding DNA is functional DNA that does not get translated into proteins. Anyway, you say that an ID hypothesis is that all DNA sequences in all organisms are essential to those organisms? Well, that fails.
Huge error on your part! Dr. Ohno made no such distinction as you have. The fact is that the amount of so-called "junk" DNA keeps shrinking just as happened to the list of "vestigial organs" (what they were originally called) that kept shrinking, while Darwinists pretended they had known this all along. I provided you with two (2) testable hypotheses, but I'm aware that Darwinists keep moving their goal posts or redefining their terms as new discoveries come to light that falsify their outdated, racist theory as elaborated in Darwin's 1871 travesty, The Descent of Man, which he wrote to justify the uncounted brutalities against brown people. Didn't you read the link I provided for the definition of Genetic Drift indicating that it was random? According to Darwin's theory, genetic drift is one of the primary mechanisms of evolution despite your pretending that it doesn't apply to your previous claims. Since you won't believe me, here's a link to a resource page published by the University of California at Berkeley on the topic of genetic drift and evolution: https://evolution.berkeley.edu/evolution-101/mechanisms-the-processes-of-evolution/genetic-drift/ Here's how it starts out:
Genetic drift is one of the basic mechanisms of evolution. In each generation, some individuals may, just by chance, leave behind a few more descendants (and genes, of course!) than other individuals. The genes and other genetic elements of the next generation will be those of the “lucky” individuals, not necessarily the healthier or “better” individuals. That, in a nutshell, is genetic drift. It happens to ALL populations — there’s no avoiding the vagaries of chance.
It would help if you checked your fallacious baloney before posting it or at least try to provide references before just making stuff up. -QQuerius_{May 15, 2022
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I haven't mentioned genetic drift. It happens that in small populations over time will lose diversity as alleles competing at a locus not under selection are lost are lost to fixation. But I don't find the phenomenon of drift signifiant except to make space for new variation. Prediction fails.Fred Hickson_{May 15, 2022
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Q
So called “vestigial” organs are not useless vestiges of evolution, but rather appear to be designed to serve important biological functions.
I think it better to refer to vestigial structures. You are confusing function and ancestry. A penguin flipper's ancestry is an adaptation to flight. It's function has changed (exaptation) to swimming. Design by the niche. Evolutionary theory does not say vestigial structures are useless but they no longer function as their ancestral purpose. Your hypothesis fails.Fred Hickson_{May 15, 2022
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Junk DNA, now renamed to non-protein coding DNA is not useless “junk” as Susumu Ohno suggested, but actually has an undiscovered function.
Huge error here. Junk DNA is DNA that performs no function for the host organism (viral elements, the broken GULOP gene in primates). Non-coding DNA is functional DNA that does not get translated into proteins. Anyway, you say that an ID hypothesis is that all DNA sequences in all organisms are essential to those organisms? Well, that fails.Fred Hickson_{May 15, 2022
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