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Sunday 20 November 2016

Long live the nanny state?:Pros and cons

On skepticism and pretensions of skepticism.

I Told You So
David Berlinski 

From the introduction to The Deniable Darwin:

My own view, repeated in virtually all of my essays, is that the sense of skepticism engendered by the sciences would be far more appropriately directed toward the sciences than toward anything else. It is not a view that has engendered wide-spread approval. The sciences require no criticism, many scientists say, because the sciences comprise a uniquely self-critical institution, with questionable theories and theoreticians passing constantly before stern appellate review. Judgment is unrelenting. And impartial. Individual scientists may make mistakes, but like the Communist Party under Lenin, science is infallible because its judgments are collective. Critics are not only unwelcome, they are unneeded. The biologist Paul Gross has made himself the master of this attitude and invokes it on every conceivable occasion.
Now no one doubts that scientists are sometimes critical of themselves. Among astrophysicists, backbiting often leads to backstabbing. The bloodletting that ensues is on occasion salutary. But the process of peer review by which grants are funded and papers assigned to scientific journals, is, by its very nature, an undertaking in which a court reviews its own decisions and generally finds them good. It serves the useful purpose of settling various scores, but it does not -- and it cannot -- achieve the ends that criticism is intended to serve.

If the scientific critic finds himself needed wherever he goes, like a hanging judge he finds himself unwelcome wherever he appears, all the more reason, it seems to me, that he really should get around as much as possible.


I told you so.

On distinguishing the hypothetically possible from the plausible.

New Peer-Reviewed Paper Demolishes Fallacious Objection: "Aren't There Vast Eons of Time for Evolution?"
Casey Luskin 

When debating intelligent design (ID), there are countless times I've heard the old objection, "But aren't there millions of years for Darwinian evolution?" Perhaps there are, but that doesn't mean the Darwinian mechanism has sufficient opportunities to produce the observed complexity found in life. Darwin put forward a falsifiable theory, stating that his mechanism must work by "numerous successive slight modifications." Michael Behe took Darwin at his word, and argued in Darwin's Black Box that irreducible complexity refuted Darwinian evolution because there exist complex structures that cannot be built in such a stepwise manner. Darwin's latter day defenders responded to Behe by effectively putting Darwinism into an unfalsifiable position: they put forth wildly speculative and unlikely appeals to indirect evolution. Largely based upon "exaptation," these scenarios required that complex biological systems be built by spontaneously "co-opting" or borrowing multiple parts within the cell to suddenly to perform wholly different functions in an entirely new system. The only evidence for such speculative scenarios is typically "protein homology," or sequence similarity between one part and another. The mere remote possibility of such a story is said to salvage evolution from falsification by Behe's arguments.

But is "mere possibility" sufficient justification to assert "scientific plausibility"? A new peer-reviewed article in Theoretical Biology and Medical Modelling asks just this question. The abstract states:

Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, "Yes." A method of objectively measuring the plausibility of any chance hypothesis (The Universal Plausibility Metric [UPM]) is presented. A numerical inequality is also provided whereby any chance hypothesis can be definitively falsified when its UPM metric of ξ is < 1 (The Universal Plausibility Principle [UPP]). Both UPM and UPP pre-exist and are independent of any experimental design and data set.
(David L. Abel, "The Universal Plausibility Metric (UPM) & Principle (UPP)," Theoretical Biology and Medical Modelling, Vol. 6:27 (Dec. 3, 2009).)

It's not just prominent proponents of intelligent design who are publishing peer-reviewed articles that support ID arguments. Other scientists are doing the same--and this article by Abel in fact cites to the work of Douglas Axe, Stephen Meyer and William Dembski, eloquently explaining why the progress of science depends on our rejecting falsified theories and not retaining highly unlikely explanations:

But at some point our reluctance to exclude any possibility becomes stultifying to operational science. Falsification is critical to narrowing down the list of serious possibilities. Almost all hypotheses are possible. Few of them wind up being helpful and scientific ally productive. Just because a hypothesis is possible should not grant that hypothesis scientific respectability. More attention to the concept of "infeasibility" has been suggested. Millions of dollars in astrobiology grant money have been wasted on scenarios that are possible, but plausibly bankrupt. The question for scientific methodology should not be, "Is this scenario possible?" The question should be, "Is this possibility a plausible scientific hypothesis?" One chance in 10200 is theoretically possible, but given maximum cosmic probabilistic resources, such a possibility is hardly plausible. With funding resources rapidly drying up, science needs a foundational principle by which to falsify a myriad of theoretical possibilities that are not worthy of serious scientific consideration and modeling.
(David L. Abel, "The Universal Plausibility Metric (UPM) & Principle (UPP)," Theoretical Biology and Medical Modelling, Vol. 6:27 (Dec. 3, 2009).

The willingness of modern evolutionists to tolerate highly unlikely explanations in order to avoid the design inference has always reminded me of the great scene from "Dumb and Dumber" when Jim Carrey, who plays a socially awkward buffoon named "Lloyd," asks his secret crush Mary about the odds that she will return his love. As the exchange goes:
LLOYD: I'm gonna ask you something flat out and I want you to answer me honestly: What do you think the chances are of a girl like you and a guy like me ending up together?
MARY: Lloyd, that's difficult to say. I mean we hardly--

LLOYD: --I asked you to be honest, Mary.

MARY: But Lloyd, I really can't--

LLOYD: --Come on, give it to me straight. I drove a long way to see you, the least you can do is level with me. What are my chances?

MARY: Not good.

LLOYD: You mean not good, like one out of a hundred?

MARY; I'd say more like one out of a million.

LLOYD: So you're telling me there's a chance?

Only an illogical emotional infatuation for Mary kept Lloyd hoping she would return his love. But if Lloyd understood how the world works, he would have realized Mary just told him that his chances of ending up with her are effectively zero, short of a miracle. Lloyd's hopes of getting the girl should have been falsified.
Michael Behe responded to his critics by noting that like Lloyd, they need to learn when it's time to acknowledge they're not gonna get the girl. He thus writes:

[O]ne needs to relax Darwin's criterion from this: "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." to something like this:
If a complex organ exists which seems very unlikely to have been produced by numerous, successive, slight modifications, and if no experiments have shown that it or comparable structures can be so produced, then maybe we are barking up the wrong tree. So, LET'S BREAK SOME RULES!
Of course people will differ on the point at which they decide to break rules. But at least with the realistic criterion there could be evidence against the unfalsifiable. At least then people like Doolittle and Miller would run a risk when they cite an experiment that shows the opposite of what they had thought. At least then science would have a way to escape from the rut of unfalsifiability and think new thoughts.

(Michael Behe, "Answering Scientific Criticisms of Intelligent Design," Science and Evidence for Design in the Universe, Proceedings of the Wethersfield Institute, Vol 9:146-147 (Ignatius Press, 2000))

Behe's arguments are echoed by Abel's new paper:
The same standard should apply in falsifying ridiculously implausible life-origin assertions. Combinatorial imaginings and hypothetical scenarios can be endlessly argued simply on the grounds that they are theoretically possible. But there is a point beyond which arguing the plausibility of an absurdly low probability becomes operationally counterproductive. That point can actually be quantified for universal application to all fields of science, not just astrobiology. Quantification of a UPM and application of the UPP inequality test to that specific UPM provides for definitive, unequivocal falsification of scientifically unhelpful and functionally useless hypotheses. When the UPP is violated, declaring falsification of that highly implausible notion is just as justified as the firm commitment we make to any mathematical axiom or physical "law" of motion.
(David L. Abel, "The Universal Plausibility Metric (UPM) & Principle (UPP)," Theoretical Biology and Medical Modelling, Vol. 6:27 (Dec. 3, 2009).

Abel then calculates the universal probability bounds wherein we are able to "falsify not just highly improbable, but ridiculously implausible scenarios." According to Abel's calculations, the probability bounds for various environments are as follows:
cΩu = Universe = 1013 reactions/sec X 1017 secs X 1078 atoms = 10108
cΩg = Galaxy = 1013 X 1017 X 1066 = 1096

cΩs = Solar System = 1013 X 1017 X 1055 = 1085

cΩe = Earth = 1013 X 1017 X 1040 = 1070

Thus, even though there are billions of years available in the universe, that does not imply that there are unlimited probabilistic resources. By calculating the maximum number of chemical reactions given the available time, Abel ably calculates the probabilistic resources. He concludes:
The application of The Universal Plausibility Principle (UPP) precludes the inclusion in scientific literature of wild metaphysical conjectures that conveniently ignore or illegitimately inflate probabilistic resources to beyond the limits of observational science. The UPM and UPP together prevent rapidly shrinking funding and labor resources from being wasted on preposterous notions that have no legitimate place in science. At best, notions with ξ < 1 should be considered not only operationally falsified hypotheses, but bad metaphysics on a plane equivalent to blind faith and superstition.
(David L. Abel, "The Universal Plausibility Metric (UPM) & Principle (UPP)," Theoretical Biology and Medical Modelling, Vol. 6:27 (Dec. 3, 2009).


Such clarity of thought will undoubtedly be bitterly opposed by the evolutionary scientific community.

The case for mind re:The Origin of Life

Information Runs The Show -- The Understatement of the Century!
Jonathan M.

An interesting paper published in Nature by . Evgenia et al. documents the ability of the DNA double helix to exist in a functional alternative form for 1% of the time, called an "excited state." What does this mean for neo-Darwinism?

What is particularly remarkable is that the base-pairs present in these alternative forms show the ability to break apart and come together again to form stable structures which are non-characteristic of Watson-Crick base-pairing (called "Hoogsteen base pairs"). While these Hoogsteen base pairs have been observed before in instances where DNA has been subjected to damage or bound to drugs, this is the first time where such Hoogsteen base pairs have been observed under normal circumstances.

The authors report in the paper's abstract,
Sequence-directed variations in the canonical DNA double helix structure that retain Watson-Crick base-pairing have important roles in DNA recognition, topology and nucleosome positioning. By using nuclear magnetic resonance relaxation dispersion spectroscopy in concert with steered molecular dynamics simulations, we have observed transient sequence-specific excursions away from Watson-Crick base-pairing at CA and TA steps inside canonical duplex DNA towards low-populated and short-lived A�T and G�C Hoogsteen base pairs. The observation of Hoogsteen base pairs in DNA duplexes specifically bound to transcription factors and in damaged DNA sites implies that the DNA double helix intrinsically codes for excited state Hoogsteen base pairs as a means of expanding its structural complexity beyond that which can be achieved based on Watson-Crick base-pairing. The methods presented here provide a new route for characterizing transient low-populated nucleic acid structures, which we predict will be abundant in the genome and constitute a second transient layer of the genetic code. [Emphasis mine]
The researchers used NMR to study the structure of the alternative form, and they concluded that the observed chemical shifts were characteristic of a structural orientation in which particular base-pairs are flipped 180 degrees to form a "Hoogsteen base pair." This was further corroborated by computer modelling.

As the papers' authors suggest, those results may imply that the DNA molecule is responsible for coding for excited state Hoogsteen base pairs as a means by which it can expand its structural complexity beyond that which it is able to achieve through classical Watson-Crick base-pairing.


If this prediction is correct, then it succeeds in adding a whole additional layer to the information enigma. This, of course, raises the pertinent issue of whether this discovery sits more comfortably with a neo-Darwinian paradigm or with an ID paradigm. Since neo-Darwinism, to date, may be considered to be demonstrably impotent to account for that specific property of living systems -- namely, information -- I would be inclined to significantly favour the latter.

See no evil,hear no evil,speak no evil.

Who Is James Le Fanu? Part V: Darwin's Three Monkeys
David Klinghoffer

Anyone who raises doubts about evolution in public discussions with non-scientists knows the automatic response you always get from the Three Monkeys crowd. Hands wrapped tightly over eyes, ears, and mouth, they chant: See no evil, hear no evil, speak no evil -- about Darwin!

That's not exactly how it comes out. People will say things more like: But science has spoken! Scientists say! Science wins! Which sounds reasonable at first, until you reflect that it's a little like a Roman Catholic fending off some challenge to his faith by pointing out that 98 percent of Catholic priests agree with Catholic doctrine, and who knows more about Catholicism than Catholic priests? So it must be true. (Or substitute rabbis and Jewish doctrine, pastors and Protestant belief, etc.) As James Le Fanu smartly notes in his new book Why Us? How Science Rediscovered the Mystery of Ourselves  (Pantheon), there is a similar circularity to the "Scientists say!" case for Darwinian dogma:

The commitment to Darwin's materialist explanation of the living world would, in time, become a qualification requirement for all who aspired to pursue a career in biology -- where to express doubt (at least publicly) was tantamount to confessing to being of unsound (or at least unscientific) mind.
I've been writing this week in praise of Dr. Le Fanu's extremely lucid, readable, and unapologetic narration of Darwinism's increasingly obvious failure to account for the evidence of science, with an emphasis on recent advances in our knowledge about the brain and the genome. Then why is the meaning of these advances ignored, greeted with a great, booming silence?
Scientists themselves, apart from being qualified for the priesthood on the condition of their voicing no doubts about Darwin, are caught in a conflict of interest. Their professional standing is predicated on explaining a purely physical reality:

Scientists cannot acknowledge the possibility of there being a 'dual' nature of reality, with both a material and a non-material realm, for that would be to subvert their exclusive claims to understand how the world 'works.' Hence the silence. Scientists cannot 'see' the significance of the findings of the recent past because they cannot stand outside their materialist view and conceive of forms of understanding different from those in which they have been trained....
The dual nature of reality has, in short, been censored, written out of the script as being of historical interest only, a relic of the superstitious ways of thinking of the distant past.

So you find that the case against Darwin is made by a brave band of professional scientist dissenters, a vocal minority in the scholarly community, but more so by those outside the academic scientific cathedral. Like James Le Fanu, a physician and peer-reviewed writer of medical journal essays, but not the picture of a lab-coated scientist that the Three Monkeys insist on hearing from.
The loss is all of ours. Le Fanu describes the cost of Darwinism: "We have lost that sense of living in an enchanted world" that was taken for granted 150 years ago. As Richard Dawkins himself puts it, in his world there is "no design, no purpose, no evil and no good -- nothing but blind, pitiless indifference." Or as Isaiah Berlin bizarrely remarked, "As for the meaning of life, I do not believe it has any -- and [that] is a source of great comfort."


The situation is not irreversible, though: "It cannot be long before a proper appreciation of the true significance of the findings of the recent past begins to sow doubts in inquisitive minds." If as many people read Le Fanu's book as it deserves, the time of that hoped for outcome will have been advanced at least a little.