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Wednesday 8 March 2023

The thumb print of JEHOVAH :Molecular biology edition.

 

Subcellular Map of the Human Proteome Reveals “Highly Complex Architecture”



 High Degree of Regulation and 
Control

New research is using antibodies to map out the spatio-temporal locations of 12,003 different proteins in human cells. The results are another example of how, as Bruce Alberts put it in 1998: “We have always underestimated cells.” Alberts explained how cells were once naively viewed as something of a random affair, where molecules “were thought to diffuse freely, randomly colliding.” The new research reveals the “the highly complex architecture of the human cell” and adds more detail to the fact that the workings of the cell are far from random:

A total of 12,003 proteins targeted by 13,993 antibodies were classified into one or several of 30 cellular compartments and substructures, altogether defining the proteomes of 13 major organelles.

Although evolutionists “thought the cell was so simple ,” this research is showing that the “cellular proteome is compartmentalized and spatiotemporally regulated to a high degree.” In fact “[m]ore than half of these 12,003 proteins localize in more than one compartment at the same time.” This is consistent with the fact that most proteins are capable of performing multiple functions, and is another indicator of high complexity:

Moreover, proteins that localize to more than one compartment may have context-specific functions, increasing the functionality of the proteome. The fact that proteins “moonlight” in different parts of the cell is now well accepted. … The more complex a system is, the greater the number of parts that must be sustained in their proper place, and the lesser the tolerance for errors; therefore, a high degree of regulation and control is required.

Indeed, the degree of regulation and control required for this system is not only enormous, but contrary to evolutionary expectations.

Consciousness?

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Tuesday 7 March 2023

The edge of physics II.

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The edge of physics?

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Mind will ever govern matter?

Marks: Human Exceptionalism in a World of AI


Dr. Robert J. Marks directs Discovery Institute’s Bradley Center for Natural and Artificial Intelligence. His book Non-computable You: What You Do that Artificial Intelligence Never Will got a shout-out and a well-written review over at The Federalist. David Weinberger writes:
               Ever wonder whether computers will one day be capable of doing everything that human beings can? If so, pick up the recent book by engineer and computer scientist Dr. Robert J. Marks, Non-Computable You: What You Do That Artificial Intelligence Never Will. Marks explains what makes human beings unique, and therefore why no computer will ever match all [our] human capabilities. To be sure, computers excel humans at many tasks — but only tasks that are “algorithmic,” or that entail step-by-step instructions to complete, such as calculating probabilities, retrieving information, or executing functions.

DAVID WEINBERGER, “WHY ARTIFICIAL INTELLIGENCE CAN NEVER OUTPACE HUMANS” (Thefederalist.com)
               You can read the rest of the excellent write-up here, and be sure to purchase the book to learn more about the unique exceptional place of human beings in a world of artificial intelligence.

Evolution by design?

Jonathan Bartlett on the Growing Evidence of Designed Mutations


On a new episode of ID the Future, host and evolutionary biologist Jonathan McLatchie sits down with software R&D engineer Jonathan Bartlett to discuss Bartlett’s work on the question of when genetic mutations are random versus directed. Bartlett explains that the issue isn’t an all-or-nothing affair. Often a given biological system dramatically limits the search space of possible mutations in useful ways, and then within that much more limited set of possible mutations, random processes are at play. He gives the example of antibody mutations. He argues that many biological systems show considerable evidence of having been beneficially designed for directed mutations. Why, then, are many mutations deleterious? He also has an answer for that. Tune in to learn more. Download the podcast or listen to it here.

Why we should really fear the machines?

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On spaceship earth's forcefield.

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On the decline of entrepreneurship


Darwinism the fittest?

 Natural Selection: The Evolution of a Mirage


American scientific educator John A. Moore has pointed out that one of the most ironic episodes in intellectual history occurred when Darwin drew on the very database of knowledge accumulated by natural theologians to support his evolutionary ideas:
                         The beautiful adaptations [of Nature] could not be denied, all that was required was to switch the explanatory hypothesis from divine will to natural causes.1
                     The purely material hypothesis began to resonate better with a secularizing age, as David Handke observed:
                           One reason for this is the manner in which Natural Selection slipped seamlessly into the place of the Creator as the acceptable new face of the creative Designer.2
                  Needless to say, not all minds in democratic societies could be changed by would-be intellectual fiats issued by Darwin or by anybody else.3 Darwin’s theory that life on Earth could have evolved unplanned and undirected, due to some wondrously benign concatenation of mutational flukes followed by the supposedly “selective” ministrations of Mother Nature, has never ceased to appear improbable to many persons not bent on conjuring up a materialist explanation for all things (at whatever cost to logic and probability). Even Darwin himself developed doubts over time as he came to ask himself: could natural selection really have exerted the vast transformative powers he had claimed for it? This late failure of nerve might well account for his later flirtation with a form of “supplementary” Lamarckism and even go some way to explain the famous peroration of Origin to the effect that evolution had come about by dint of “laws impressed upon matter by the Creator.”

The latter statement can scarcely be glossed as anything other than what is now termed theistic Darwinism since it is plainly discrepant with exclusively natural processes. Darwin’s shifting ideas made it easy for those of his peers with more traditional (Anglican) opinions to infer that ultimately everything owed its existence to a power transcending the natural order.4 It may even be possible to speculate that Darwin’s two-decade-long procrastination over publication of Origin owed something to his difficulties in convincing himself of some ideas which, on the advice of colleagues and critics, he was driven to modify quite considerably over his five later revisions of Origin.
                        
Darwin at the Literal Level

Summarized at the literal level, the Origin of Species aspires to supply us with a fresh, materialist myth to explain the development of earth’s numerous species. That messaging is, however, undermined by interference from an apparently ineradicable subtext arising from Darwin’s deeper intuitions and spiritual promptings. This factor bids us revisit the precise ontological and definitional status of “natural selection” — that ubiquitous metaphor which, in the verdict both of Alfred Russel Wallace and many other of Darwin’s expert peers, had led Darwin so seriously astray.

Conceptual interferences arising from strained metaphors, distant analogies, and widely dispersed narrative patterns with deep roots in people’s imaginations have long been discussed across the whole range of human cultures.5 Even in the context of scientific reporting Misia Landau has detected some surprising interferences from folklore and myth,6 warning that scientists should be aware of the capacity of preexistent narrative structures to exert a subconscious influence on the way they present supposedly objective data. In a similar vein, Andrew Reynolds more recently drew attention to the large role played by analogical reasoning in Darwin’s thinking — a factor which did not always contribute to clarity of thought:
                 This analogical reasoning was in turn reliant on several key metaphors. One was the Tree of Life to represent the thesis of the community of descent or shared ancestry of all species. The other concerned his hypothesized mechanism for species transmutation, which he called natural selection, a choice of terminology based on an analogy with the process of artificial selection practised by humans in the production of domesticated plants and animals.7
                            
An Important Tool

The fact is that metaphorical and analogical thinking is an important tool for human beings to verbalize their conceptions of reality, so it is not surprising that Darwin and neo-Darwinians have been drawn to it. However, it is not an intrinsically analytical or even descriptive way of approaching the world, something recognized as early as 1666 by Samuel Parker, an eminent member of the Royal Society, who described metaphors in the following terms:
                Wanton and luxuriant phantasies climbing up into the Bed of Reason, [that] do not only defile it by unchast and illegitimate Embraces, but instead of real conceptions and notices of things impregnate the mind with nothing but Ayeries and Subventaneous [= borne on the wind] Phantasmes.8
                        Parker clearly saw metaphorical thinking as leading to false and illusory analogies, opposing “real conceptions” to unnatural (“unchast and illegitimate”) associations of ideas arising from unfocused and unbridled imaginations. The numerous objections of colleagues who pointed out to Darwin that there was simply no comparison between what animal breeders did purposefully and by the use of human ingenuity and how mindless Nature herself acted clearly had a long pedigree.

Nevertheless, Darwin initially persisted in claiming a close analogy between the artificial breeding methods of such persons as pigeon-fanciers and the claimed “selection” performed by Nature herself. He was explicit about this claim, stating that he favored the term “natural selection” in order to mark its relation to man’s power of selection. Perhaps drawing auxiliary strength from ancient ideas of an active and directive Nature — this being a logic which we have now lost but a conception which achieved its late flowering by the middle of the 19th century9 — Darwin deposed that Nature, with limitless millennia at her disposal, could do a more comprehensive job of bringing about major physiological changes (and eventually new species) than could human breeders, an idea to which he gave lyrical expression in a famous passage in his Origin of Species:
                It may metaphorically be said that natural selection is daily and hourly scrutinising, throughout the world, every variation. Even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life. We see nothing of these slow changes in progress, until the hand of time has marked the long lapse of ages, and then so imperfect is our view into long past geological ages, that we only see that the forms of life are now different from what they formerly were.10
                 It should be noted in the above that the word “metaphorically” was not present in the first edition of 1859. Darwin later added the expression defensively to protect himself from sundry colleagues’ criticisms that he was advancing a covertly theistic conception of the evolutionary process. Not without reason was Darwin’s metaphor of natural selection recently decoded as “an anthropomorphic but superhuman agency, ‘daily and hourly scrutinizing’ all variation, and making intelligent and benevolent decisions like a Paleyan Designer.”11 Or as Jerry Fodor and Massimo Piattelli-Palmarini more pointedly observed, Darwin strove to exorcize all “ghosts in the machine” such as God, selfish genes, or a World Spirit, yet “Mother Nature and other pseudo-agents got away scot free.”12
                
The Climb-Down

Hence although the Origin purports to offer humankind a fresh, materialist myth to explain the development of earth’s numerous species, that project is subverted by interference from a subtext springing from Darwin’s well-documented cognitive dissonance concerning material and spiritual domains.13 Such an interference explains his boundless faith in what he stated were the directive powers of a process which others could see only as being unfathomable and wholly unpredictable (such having been the original meaning of natural selection coined by breeders whose sense was so radically altered by Darwin). For Darwin the powers of natural selection transcended human intelligence to such a degree that he came exceedingly close to imputing to it the capacity for intelligent design. It was only belatedly that he succumbed to colleagues’ numerous objections, conceding in a letter to Charles Lyell,
              Talking of “Natural Selection,” if I had to commence de novo, I would have used natural preservation.14
                          This was an emendation with enormous consequences. One can understand why Darwin was minded to hold out as long as possible and why he eventually capitulated only under protest. For the letter to Lyell involved a truly fatal concession which, had it been analyzed dispassionately at the time, could (and arguably should) have halted the onward march of Darwinism there and then in the Fall of 1860. As a host of recent studies make clear, the term to which Darwin eventually acquiesced, natural preservation, can by definition only be passive rather than actively productive in the formation of new body parts (let alone whole new species). The Darwinian theory of an advance from organic simplicity to complexity — from microbes to man — must inevitably fall after such a major semantic retreat.

Wanted: A Theory of the Generative

As Steve Laufmann and Howard Glicksman and others have recently pointed out, neo-Darwinism simply has no theory of the generative and therefore no innovative capacity: nothing in Darwin’s theory can account for nontrivial innovations15and Darwin’s rowing back on that point was fatal to any macromutational claims. As Professor Nick Lane has recently explained, 
                     It is generally assumed that once simple life has emerged, it gradually evolves into more complex forms, given the right conditions. But that’s not what happens on Earth (…) If simple cells had evolved slowly into more complex ones over billions of years, all kinds of intermediate forms would have existed and some still should. But there are none (…) This means that there is no inevitable trajectory from simple to complex life. Never-ending natural selection, operating on infinite populations of bacteria over millions of years, may never give rise to complexity. Bacteria simply do not have the right architecture.16
                              So how did speciation occur then? Competent scientists are thrown back on the placeholder terms “fate” or “chance,” such being all too plainly a cover for complete ignorance.17 Fodor and Piatelli-Palmarini are more refreshingly candid:
               “So if Darwin got it wrong, what do you guys think is the mechanism of evolution?” Short answer: we don’t know what the mechanism of evolution is. Nor did Darwin and nor (as far as we can tell) does anybody else.18
                    The bottom line today appears to be that 
                     Speciation still remains one of the biggest mysteries in evolutionary biology and the unexamined view of natural selection leading to large-scale innovations is not true.19
                          
No Longer Beyond Question

Such new findings mean that aspects of the Darwinian narrative once accepted as veridical and beyond question can no longer provide the solid pillars of scientific consensus we had once assumed them to constitute. Which does not mean that some über-Darwinians will not attempt to cling to old certainties. “Evolutionary psychologist” Steve Stewart-Williams reaffirmed the notion that micromutation can result in macromutation given a superabundance of time:
                              If natural selection can produce small-scale change in the short term, why could it not produce large-scale change in the long term? Unless a compelling example can be found, a sensible default assumption would be that it could and does. And let’s not forget all the indirect evidence (the fossil record, etc.) suggests that species do indeed evolve from other species.20
                    Both the “sensible default assumption” to which Stewart-Williams refers and the corroborative fossil evidence are without basis in fact.21 Even the considerably less doctrinaire John A. Moore, despite his attempts to play honest broker between evolutionism and other competing theories, can come up with some eminently contestable verdicts when comparing the relative merits of the two sides:
                Whereas the natural theologians began with the answer — divine creation — and then used the data they had gathered from nature to support the answer they had already decided was true, Darwin began with the data of adaptation and followed them wherever they led.22
                   That statement is surely incorrect on two counts. As to the point about natural theology, Moore places the cart before the horse since for natural theologians the commitment to a belief in God represents the inference to the best explanation provided by Nature itself (not the other way round). As to Darwin following the data in the direction the data prompted, this too is very wide of the mark (pace Darwin’s virtue-signaling protestations to be working on “Baconian principles”). From the start Darwin hoped that the natural selection postulate would revive the flailing evolutionary project initiated by his grandfather, Erasmus Darwin, by supplying it with some semblance of empirical, properly quantifiable support. He experienced his Eureka moment on reading demographer Thomas Malthus on populations because, hallowed as it was by notions of social-science testability, it was seized upon as a confirmation of the grandpaternal program. Natural selection became a veritable deus ex machina to provide a (claimed) mechanism or vera causa to justify the idea of evolution developed by Erasmus alongside sundry 18th-century French “transmutationists.”
             
The Forging of a Secular
 Myth

Had not Charles come to the rescue, there are grounds for supposing that the grandfather’s ideas might have withered on the vine for lack of support and so fallen into neglect in later 19th-century Europe. That which Erasmus termed the transmutation of species was a subject which had already exercised a group of 18th-century French thinkers to whom history refers collectively as “les philosophes.” This group had toyed with the idea of animal types, over vast tracts of time, being liable to experience change in their physical morphology. Julien Offray de la Mettrie, in his L’Homme Machine (1747), argued that all animal forms had emerged from previous forms, so that the earthworm might be expected to transmute in time to become a considerably larger and more complex animal. Often such speculations became airy (even Charles complained that Erasmus’s speculations were without empirical foundation) and could even tend towards the physiologically illiterate. Such was the case when Denis Diderot, mooting in his D’Alembert’s Dream (1769) the possibility of a creature evolving through habitual functioning into another form of life altogether, toyed with the bizarre idea that those humans not required to perform manual labor might eventually become just heads. Not surprisingly, such fantasies were destined to become mal vu, even in France.
                    In the midst of what others not unreasonably saw as the eccentric musings of a small, self-referential côterie, it became clear that what was required was the identification of a causal underpinning or mechanism which might prove the somewhat counterintuitive phenomenon of physiological evolution alleged by the group. Since that theory had been greeted with considerable skepticism by the generality of people, it was vital to be able to point to the supposed “scientific” credentials of natural selection. Only in that way would it be possible to rescue the idea of evolution from the scorn and ultimately the oblivion to which it was heading before 1859. Hence for Darwin the postulate of natural selection had to be true if he were to keep faith with and support the great evolutionary project initiated by his brilliant grandfather, Erasmus. It was anything but the case of his dispassionately following the evidence in the direction it led him. Rather, the analogical thinking that that had encouraged Darwin to map the biological domain onto that of sociology led to an intellectual mirage masking his theory’s dearth of data-based foundations.

Only time will tell whether the idea of evolution itself, which natural selection was meant to support, will endure now that so many scientists are “coming out” to express doubts about natural selection as traditionally glossed. As Michael Ruse recently pointed out, natural selection cannot actually select and is better understood as a score-recording statistic than as a “true cause”:
                          Natural selection is simply keeping score, as does the Dow Jones [Industrial] Average. The Dow Jones does not make things (cause things to) happen. It is just statistics about what did happen.23
                            Natural selection reveals itself as not just a metaphor but a mixed one: Nature being dumb but nevertheless capable of discrimination. It is a poetic concept rather than a scientific one, appealing more to emotional and aesthetic sensibilities than to reason. Denuded of the “cover” provided by natural selection as the motive factor to explain evolution, the broader subject of evolution itself once again becomes as enigmatic to us as it was to our Victorian forbears. Now as in 1858 evolution remains the “mystery of mysteries.” 

Edward Feser on why matter matters?

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The religious left's push to take the lead in their race with the religious right toward tyranny?

 Canadian Catholic student suspended for speaking on Biblical perspectives on gender


Josh Alexander (16), a junior at Ontario’s St. Joseph’s Catholic High School, was suspended from school last November for the rest of the year, over comments he made opposing transgender ideology. James Kitchen, an attorney from Liberty Coalition Canada (LLC), a Christian law firm, who is representation Alexander, warns that freedom in Canada is rapidly decaying. Alexander, who describes himself as a born-again Christian, has reported that the comments for which he was suspended were made during a discussion in his class about gender. He commented that only two genders exist, male and female, while the discussion revolved around male students using female restrooms, male breastfeeding, gender dysphoria, etc.

CBN News reports:
                                     The attorney representing a Canadian student who was reportedly kicked out of school for the rest of the year for opposing transgender ideology at his Catholic high school is warning freedom in America’s neighbor to the north is quickly decaying.

“I think it’s representative of where the culture is at, where society is at, and where our government institutions are at up here,” attorney James Kitchen with the nonprofit Christian law firm Liberty Coalition Canada (LCC) told Fox News concerning the case against his client.

The young man, 16-year-old Josh Alexander, has described himself to several outlets as a born-again Christian.

Alexander, a junior at St. Joseph’s Catholic High School in Renfrew, Ontario, was suspended from school last November over comments he made during a class discussion that included the teacher. He was told by school officials he couldn’t return to school unless he recanted.

When he returned to the Catholic high school for the start of the second semester, he was promptly met by the vice-principal, arrested by two local police officers, and charged with trespassing, The Toronto Sun reported.

During an interview with the National Post, Alexander said the comments that got him into trouble were made during a class discussion about gender.

“It was about male students using female washrooms, gender dysphoria, and male breastfeeding. Everyone was sharing their opinions on it, any student who wanted to was participating, including the teacher,” Alexander said.

“I said there were only two genders, and you were born either a male or a female, and that got me into trouble. And then I said that gender doesn’t trump biology,” he recalled. 

How Darwin made it possible to be an intellectually fulfilled 'wolf'

 Darwin’s Contribution to Racial Extermination



Editor’s note: The following article by the late Dr. Olufemi Oluniyi is adapted from chapter one of his recently released book, Darwin Comes to Africa: Social Darwinism and British Imperialism in Northern Nigeria (DI Press, 2023). 

Charles Darwin elevated race as a factor in the struggle for survival. 

Twelve years after the publication of On the Origin of Species, in 1871, Darwin published The Descent of Man and Selection in Relation to Sex, a highly impactful book as far as Europe’s attitudes to Africa. Professor Frank Besag observes that in Darwin’s first book, he used “race” and “species” interchangeably. In other words, at that time “for Darwin, there was a human race but not a black race.” Or at least Darwin chose, in his earlier book, not to explicitly bring up such a controversial idea. The implications, however, were clear; thus Rutledge M. Dennis notes that “the philosophical and political underpinnings of ideas associated with racial superiority and inferiority were first given scientific legitimacy and credence with the publication of Charles Darwin’s (1859) revolutionary book, The Origin of Species.”

In his second book, however, Darwin not only made references to races among humans, but he further distinguished between “the lowest savages” and “the lowest barbarians” on the one hand, and the “highly civilised nations,” including “the Western nations of Europe, who… stand at the summit of civilisation” on the other. 
             
Clarification on Two Points

Two points of clarification are here required. First, while at times Darwin used the terms “savages” and “barbarians” to refer to the modern human’s ancient forebears, at other times he used those derogatory terms to speak of his contemporaries in distant lands, as when he writes, “At the present day civilised nations are everywhere supplanting barbarous nations, excepting where the climate opposes a deadly barrier; and they succeed mainly, though not exclusively, through their arts, which are the products of the intellect. It is, therefore, highly probable that with mankind the intellectual faculties have been gradually perfected through natural selection.”

Second, as has been most indisputably and thoroughly documented elsewhere, Darwin’s letters and other writings clearly demonstrate that by “barbarous,” “inferior,” or “lower” peoples he usually meant dark-skinned people. The terms “highly civilised” or “superior” he applied to Caucasians. For example, in The Descent of Man Darwin states that the black man is closer than the white man to apes, and speaks of “the Negro” who “differs more… from the other races of man than do the mammals of the same continents from those of the other provinces.” There can be no doubt that Darwin thought dark-skinned peoples were less highly evolved than light-skinned peoples. 

Racism (the dividing of humans on the supposed basis of race) did of course exist before Darwin. By 1779 German physiologist Johann Friedrich Blumenbach had divided humankind into five races based on cranial features, while by 1759 Swedish botanist Carl Linnaeus had classified human beings into four categories based on the four known continents (European white, American reddish, Asian tawny, African black). The Frenchman Joseph Arthur de Gobineau classified humans into three racial groups by 1855 (black, white, and yellow).
                           
Darwin’s “Scientific” Basis for Racism

Nevertheless, what the classifications lacked was a more credible scientific basis, which Darwin ostensibly provided. (Later we shall speak more of these foolish and harmful divisions and show that they have no basis in reality, but that rather there is only one human race, of which we are all a part.) 

In the aftermath of Darwin’s books, as Gregory Claeys notes, Social Darwinism redefined fitness as intelligence, and intelligence as white — and let it be noted that “Darwin accepted the application… with others following suit, crafting a language of exclusion… [and] racial conflict.” In short, within a few years of Darwin’s books, “much of the language of ethnicity which would come to haunt the next century was now in place.”

Thus we see, summarizes historian Richard Weikart, the biologist Wilhelm Roux (1850–1924) describing the Darwinian “struggle within organisms as analogous to the struggle within society.” Similarly, writes Weikart, paleontologist Friedrich Rolle (1827–1887) argued that “population pressure naturally precipitates wars and violent conflicts between peoples and races” and that “the physically and mentally superior races suppress and exterminate the lower races, bringing progress and benefit to the whole of mankind.”

The Importance of War

Likewise the biologist Heinrich Ziegler (1891–1918) advocated that “according to Darwin’s theory, war has constantly been of the greatest importance for the general progress of the human race” and that “the physically weaker, the less intelligent, the morally inferior or morally degenerate peoples must clear out and make room for the stronger and better developed” in the interest of the general progress of the human race. 

According to Weikart, Darwin’s disciple Ernst Haeckel differentiated “between ten races of humanity, with the Caucasian race the most highly developed,” following which he fervently “condoned the extermination of” so-called primitive races. Similarly, zoologist Oscar Schmidt (1823–1886), zoologist Richard Hertwig (1850–1937), biologist Richard Semon (1859–1918), and biologist Ernst Krause (1839–1903) all advocated “the extermination of human races as a natural and inevitable part of the process of natural selection.”

You see what we have here. These men and likewise many others argued that the logical extrapolation of Darwin’s theory was the extermination of their fellow humans in the name of evolutionary progress! 





On the math resistant nature of Darwinism.

A Good Example of Evolutionary Use of Extremely Small Probability Singularities


Bill Dembski was asking recently about probability estimates in evolutionary biology, ranging from effectively 1.0 to effectively 0.0. Given the importance of evidentially grounded probabilities to the overall argument of The Design Inference (which Bill and Winston Ewert are revising for a 25th anniversary second edition), this is an important area about which to have clarity.

In reply, I pointed out that evolutionary theory makes abundant use of extremely small probability singularities while reconstructing the history of life on Earth. Postulating such events is widely seen NOT as an inferential defect, but in fact a positive and biologically realistic aspect of the theory.

This Article illustrates my point: “Key steps in evolution on Earth tell us how likely intelligent life is anywhere else.” Adam Frank writes:
             A hard step is an evolutionary change that has only occurred once in the entire history of the planet.
                            
Chordates and Company

Examples include the origin of life itself, the origin of eukaryotes, the origin of any metazoan phylum (e.g., Chordata, Arthropoda), or the origin of language. I don’t have time today to spell out the full structure of these inferences, but phylogenetic reasoning SEARCHES for singularities, as these enable one to tie together (into a monophyletic clade) what are otherwise very different species. How can you be certain, for instance, that you, horned lizards, and brook trout share a common chordate ancestor?

Chordates arose only once.
                     
The Signal Weakens

But as the probability of an evolutionary transition moves away from effectively 0.0 (a singularity) towards 1.0 (bound to happen), the historical signal of monophyly correspondingly weakens. This goes some way towards explaining the paradox that evolutionary theorists such as Jacques Monod, or Richard Dawkins, are quite happy (eager) to say that the antecedent probability of the natural origin of life on Earth was indistinguishable from zero. As Monod famously put it:
              The present structure of the biosphere far from excludes the possibility that the decisive event occurred only once. Which would mean that its a priori probability was virtually zero.
          If abiogenesis represents a singularity, the Biogenetic Law (omne vivum ex vivo) gives one — for free, so to speak — universal common descent, or Darwin’s Tree of Life. I’d take that deal in a heartbeat, if what I really wanted was a single Tree of Life, without much, or any, further explanatory effort.

Politics without polarisation?


Monday 6 March 2023

In the history of life missing links are the rule not the exception.

 Human evolution: missing link still missing


The evolution of humans is, in many ways, similar to evolutionary theory on the whole. As Colin Barras reveals in his recent article at the BBC, There are conflicting evidences, a lack of details, opposing hypotheses held with great confidence, and a wide range of explanatory mechanisms that are routinely used as needed. That much is obvious. What is a bit more subtle, and arguably even more important, is the absence of a serious evaluation of the theories at hand.


Barras’ article is a good summary, from TH Huxley and Darwin up to today, of how evolutionists have viewed human evolution. What is humanity’s phylogenetic neighbor, our so-called sister species, and what is our most recent common ancestor?

Following Huxley, gorillas or chimpanzees were typically held by early evolutionists as both our sister species and representative of the common ancestor, which swung from branch to branch and rambled along on all fours. But some evolutionists held that monkey’s were our closest evolutionary neighbor.

With the rise of molecular biology came genetic comparisons and the firm conclusion that chimpanzees and bonobos are our sister species. Huxley, it seemed, was right. Students were told, in no uncertain terms, that the chimp was our sister species—after all, we shared something like 99% of our DNA in common.

But then new evidences arose, questioning this seemingly incontrovertible truth. Subtle differences between gorillas and chimps suggested independent evolution, rather than inheritance via a common ancestor, of certain traits. Furthermore, a new fossil species, Ardipithecus ramidus, as well as anatomical and behavioral comparisons, called into question the accepted human-chimp relationship.

All of this leaves evolutionists today contemplating a range of explanations for human evolution. One common theme of all the different explanations, however, is their lack of detail. The explanations do not provide any sort of detailed account of the rise of the many unique traits and capabilities in humans.

And where detailed evidence does exist, such as in the chimp, gorilla, and human DNA data, it makes little sense (see here, here, and here, for example).

The theoretical problems and lack of detail with human evolution, and evolution in general, raise the question of how good these theories are. Evolutionists repeatedly state that evolution is a fact, just as much as gravity, heliocentrism, and the roundness of the Earth are facts. There is no question about it.

But the science does not support this claim. What we need is a legitimate, serious evaluation of the theories at hand.

Phillip of Macedon: master diplomat?

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On extraordinary claims and extraordinary evidence.

Yes, Extraordinary Claims Require Extraordinary Evidence — Let’s Hear Some for Darwinian Evolution


Carl Sagan famously said on his TV series Cosmos, “I believe that the extraordinary should be pursued. But extraordinary claims require Extraordinary evidence " I agree. You shouldn’t change the entire direction of science based on a few isolated pieces of evidence.

Intelligent design (ID) proponents make an extraordinary claim, that the origin and evolution of life cannot be explained without postulating a guiding intelligence. If this idea becomes generally accepted it will be a huge change in the direction of science, so the scientific establishment is justified in dragging its feet. But the evidence for intelligent design does not consist of a few missing fossils or a few examples of irreducible complexity, which could eventually be shown to be reducible. ID advocates believe we have long ago passed the threshold of evidence required to accept this extraordinary claim and that every new discovery in biology and biochemistry pushes us farther beyond the threshold. Evolution News readers are exposed to this evidence daily.
                
Another Extraordinary Claim

But less noticed is that ID opponents also make an extraordinary claim. They believe that they have found, or at least will eventually find, natural, unintelligent, causes capable of creating things which in our uniform experience are known to be created only by intelligence. 

I have often argued (most recently here) that to attribute to natural selection the ability to create spectacular order out of disorder is to attribute to it, alone among all unintelligent forces in the universe, the ability to defy the more general statements of the second law of thermodynamics, or at least the general principle behind this law. But it is not really necessary to appeal to the second law because everyone can see that Darwin’s claim to have discovered an unintelligent force capable of creating all the magnificent species in the living world, and even human brains, was quite an extraordinary claim. It credits natural selection with creative powers far beyond those claimed for any other natural causes. (Origin-of-life researchers’ claim that chance chemical processes could have created the first self-replicators, when human engineered self-replicating machines are still far beyond current technologies, could also be considered to be an extraordinary claim.)

And where do we stand with regard to evidence for the Darwinists’ extraordinary claim? Have we passed the threshold of evidence required to accept their claim? Hardly. The ongoing debate between Michael Behe and his critics is over whether or not there is evidence that natural selection of random mutations can be credited with any evolutionary changes that would not be considered “devolution” and do not simply “promote the loss of genetic information.” And evolutionists now openly wonder if they need an entirely new theory. While the evidence for the extraordinary claim made by design theorists continually increases, the evidence for the Darwinists’ claim seems to be shrinking.

“Why Evolution Is Different”

In my 2020 video “Why Evolution Is different” I imagine watching a tornado running backward and trying to come up with a scientific explanation for what we are seeing. It concludes: 
                                Anyone who claims to have a scientific explanation for how unintelligent agents might be able to turn rubble into houses and cars would be expected to produce some very powerful evidence if they want their theory to be taken seriously. The burden of proof should be equally heavy on those who claim to have a scientific explanation for how a few unintelligent forces of physics alone could rearrange the basic particles of physics into computers and encyclopedias and Apple iPhones — and there is no evidence that natural selection of random mutations can explain anything other than very minor adaptations.
                         Some observers of the ID-Darwinism debate feel that the Darwinian point of view is the default so that the burden of proof is on us. But it is extraordinary that we are here at all, so any ideas about how we got here should require extraordinary evidence. 

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Saturday 4 March 2023

Frenemies?

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A realistic evaluation of the expertocracy.

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The search for Darwin's "simple beginning" yet another wild goose chase?

Why High School Biology Made Me Angry (And Why I Like It So Much Better Now)


I didn’t like biology in high school. It made me angry, actually. That’s ironic, looking back now. Besides writing here at The Stream, I’ve edited almost all of Discovery Institute’s last 400 to 500 podcasts on Intelligent Design theory, with a lot of biology included in them. Needless to say, I’ve come around since school days.

It was bad then, though. Mr. V., my high school biology teacher, was definitely part of the problem. He spent six class periods teaching us Charles Darwin’s life story. Don’t jump to conclusions here, now. It’s not that it took him six hours to get through all his material. No such luck. He delivered exactly the same story. One class period long. Beginning to end. All six times.

Maybe he didn’t realize he’d already done it once (twice? three times? four or five times?) before. Whatever the reason, it was certifiably bad teaching. But Mr V. wasn’t my biggest issue with biology, and it wasn’t Mr. V. who made me angry, either.

Angry? Yes.

And now some of you will jump to conclusions again. I’m a conservative Christian, so the problem was evolution, right?

Wrong. Way wrong.

How Does It Know the Difference?

An old joke tells the problem nicely.

There’s this company that wants to hire a genius, you see, and the hiring manager has it down to three candidates. They’re all sitting in the room together with him, and he asks them, “What would you say is the most amazing technology in the world today?”

The first person says, “It’s the internet, no doubt about it. Look at all the information! Look at all the communication!”The hiring manager nods appreciatively.

The second says, “No, it’s medicine. Can you even believe how many lives we’re saving these days?” Another appreciative nod.

The third guy says, “No, no, you’re both wrong. It’s the Thermos bottle!” No nod this time.

Everyone turns and stares. Finally, someone asks the question. “The Thermos bottle???”

“Yes, the Thermos bottle! Just look: It keeps hot things hot, and cold things cold. How does it know the difference?”

Glossing Over the Question

I had a problem like that with what they taught me about the living cell. It had a cell wall (plants) or cell membrane (everything else). That membrane or wall let oxygen in, along with hydrogen and nitrogen and calcium and phosphorus and sodium and everything else the cell needed. It put other chemicals out, like garbage on trash day. How does it know the difference? 

This time, unlike the Thermos bottle, something really incredible was going on. And our the textbook glossed over it like no problem at all. That’s what bugged me.

The Darwin Connection

Interestingly enough, it turns out there’s a connection here with Charles Darwin — not that he had the same problem, actually. What’s interesting is that he didn’t. As far he knew — as far as anyone knew in his day — the living cell was a featureless little blob. It had its cell wall or cell membrane, and all it had inside was a boring glob of goo. This goo had a name, or would soon enough. While Darwin was publishing his Origin and Descent, other scientists were publishing things like, “All living cells are made of a living substance called protoplasm.”

Note how they called it “a substance,” as in, just one thing. What did they mean by that? Well, I’ve got another weird story for you.

Many years ago, I read a comic that explained Lex Luthor’s hostility to Superman. (There have been lots of Lex Luthor myths.) Luthor had just invented protoplasm in his lab. He had manufactured life! The real thing! But then the lab caught on fire. And Superboy (they were both teens at the time) came along and put the fire out with his super-breath. In the process the chemicals got mixed up, and Luthor’s grand invention, life itself in the form of protoplasm, was ruined. He blamed it on Superboy, and the rest is comic and movie history.

No, I didn’t turn to comic books to fill in for my disappointing biology classes. The authors were years behind on the science themselves. Still, it helps illustrate what science thought for several decades. Life’s secret ingredient, the thing that made life different from non-life, was a substance, something you could imagine a mad scientist cooking up in a beaker.

Boy, were they wrong.

Discovering How It Knows the Difference

It was the best they could see with early microscopy, but it was way too simple. (Even the way I said that was way too simple.) That apparent simplicity was one reason Darwin could think evolution could easily produce all of life’s grand variety. Darwin didn’t know what we know.

Anyway, when I was in high school (if I recall correctly — it has been a while) they were still talking about protoplasm. By then, though, they’d also found out there was other stuff in the cell besides: the nucleus, mitochondria, organelles, and other organelles. They also knew the cell membrane pulled the right chemicals in and pushed the right stuff out. As for how that membrane knew the difference, though, my textbook just ignored the question.

I didn’t buy it. I figured something was up — something they weren’t telling us. Maybe I was too hard on them. Scientists really had not much clue at the time, at least compared to what’s known now. Again, it wasn’t their fault; it has taken decades of advances to get us where we’ve come since then. Still it bothered me how the textbook just ignored the problem — bothered me enough I remember it to this day.

Maybe with a better teacher I’d have been inspired to go study and help find out. Others did, and I’m glad. I’m glad, too, that I get to help bring some of their work to the public. Because scientists have a clue now, and it’s more amazing than I’d ever dreamed. Way more amazing.

Astonishing Machinery

Someone at church asked me not long ago, “Just how complex is a simple cell? Is it as complex as a computer?” I gave him the answer I’d learned lately. Take a simple cell like a bacterium, and you’re not looking at complexity on the level of a computer. Not even close. Cells are more on the level of a large city, computers included.

I can only imagine how different school might have been if we’d had videos like this one from Veritasium. Ever heard of molecular machines? This’ll blow your mind.

(I’m a great fan of Veritasium, by the way.)

Derek Muller, the host, raises an intriguing question at the end: Will humans someday be able to design nanomachines like these, to insert in our bodies and help heal diseases? Maybe? I won’t say no, but I’m skeptical. This much is certain: It could only happen with years of intense study, extraordinary technology, enormous insight, and a healthy dose of creativity. Muller would undoubtedly agree.

Taking the Complexity Seriously

I seriously doubt he’s taking the problem seriously enough, though. Your own body has something like 30 trillion cells in it. That’s 30 trillion large cities’ worth of complexity, with thousands of nanomachines powering and doing the work inside each and every one.

That’s only a glimmer of it. All that complexity gets multiplied exponentially by what it takes for those trillions of “cities” to work together as tissues, organs, and systems, keeping you alive, moving, thinking, communicating, working, loving, and everything else you do. It raises the question: How did all this happen in the first place? How did all those nanomachines develop? How did they come to work together so effectively? Can naturalistic evolution explain this? Seriously?

There was a time — maybe when I was in high school — when evolutionists would have answered, “Just hold on. We’ll learn more, and we’ll get that solved for you.” They would have been wrong. Science is going the other direction instead. The problem now is much harder than they ever thought it was.

This isn’t “God of the gaps,” or some silly rush to say “God did it,” when with a little more patience, we could hold on for answers from science. No, this is, “Science keeps running into greater and greater problems for evolutionary theory.”

A Better Paradigm

Meanwhile, the Intelligent Design paradigm keeps fitting better and better. In one of those podcasts I edited, Dr. Howard Glicksman tells part of the story. I wish someone could have taught me in high school: how the cell membrane “knows the difference.” It’s stunning. And as he explains, it’s pretty hard to give unguided evolution credit for accomplishing it. (If you prefer video, go for “The Design Inference,” the series on “A Theory of Biological Design,” or “Unlocking the Mystery of Life.”)

That’s why I like biology better now. Someone is taking the questions seriously. They always were, but we have more detailed answers now, they’re astonishingly interesting answers, and it’s easier find access to those answers. I have to wonder, though: What are they teaching in your children’s high school?

The theory of everything and its opposite?

Casey Luskin Debunks a Museum’s Evolutionary Propaganda


On a new episode of ID the Future, geologist Casey Luskin continues to discuss his recently published essay directed against the view that humans evolved from ape-like ancestors via blind Darwinian processes. In this episode he shares his experience of walking into the fossil hall at South Africa’s famous Maropeng Museum and immediately being confronted by a piece of shameless materialist propaganda, a Richard Dawkins quotation prominently displayed as part of a floor-to-ceiling display. The quotation insists that humans are essentially just DNA survival machines. Luskin says, not so fast, and points out the various ways such a view fails to explain important aspects of human behavior, including altruistic behavior toward non-kin. Luskin and host Eric Anderson also call evolutionary theory to task for being overly supple, with its adherents regularly employing vague just-so stories to explain virtually any behavior or feature AND its opposite. Download the podcast or listen to it here
                 To read Luskin’s essay on the subject, get the new free online ID book from South Africa, Science and Faith in Dialogue, with contributions from Luskin, Stephen Meyer, Hugh Ross, Guillermo Gonzalez, James Tour, Fazale Rana, Marcos Eberlin, and others. Find Part 1 in this Anderson/Luskin

Conspiracy theorist extraordinare?

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On the rise of Russia's man of steel.


Friday 3 March 2023

Why actual intelligence will continue to rule artificial intelligence.

Will AI “Own the World”? Robert J. Marks Talks with Laura Ingraham


Robert J. Marks directs Discovery Institute’s Bradley Center for Natural & Artificial Intelligence. He recently appeared on a podcast episode with Fox News host Laura Ingraham to talk about artificial intelligence, tech, and Dr. Marks’s book Non-Computable You: What You Do That AI Never Will. 

Ingraham prefaced the conversation with some thoughts on the rapidly evolving technological world we find ourselves in, and the changes such developments are inflicting on society. In response to the futurism and unbounded optimism about AI systems like ChatGPT that many modern figures hold, Marks said that what computers do is strictly algorithmic:
                       This leads us to the idea of whether or not there are non-computable characteristics of human beings, and I think there is growing evidence that there are. I would give the simple examples of happiness, joy, empathy. I think less obvious are the operations of sentience, creativity, and understanding. I believe that probably these are not algorithmic either. Again, we’re starting to have scientific evidence that this is indeed the case. So, you’re not allowed to build your own religion and speculate. We see this a lot in artificial intelligence. 
           
To “Own the World”

Ingraham brought up an ominous remark from Klaus Schwab, founder of the World Economic Forum, in which he said that in the future, whoever owns artificial intelligence will “own the world.” Schwab thinks this revolution of the world order, brought about in large part by advances in AI, is just a decade away at most. Marks, however, responded by appealing to the history of exaggerated, utopian (or dystopian) visions for humanity: 
                   I think we only have to look at history and see a lot of these other incredibly hyperbolic claims that have come out. I was old enough to remember the Y2K scare, which was supposed to dissolve the world into all sorts of problems. Deepfakes are going to disrupt political discourse. Self-driving cars are going to cause all truck drivers to lose their jobs. No, that hasn’t happened. Maybe it will happen someday, but we’re on a much slower path to that. Here’s my prophecy: in ten to twenty years we are going to recognize the limits of artificial intelligence (which we are starting to do, especially these chat models like ChatGPT and LaMDA) and we’re going to find out the limitations of them. And we’re going to incorporate this into our society. Is it going to make a difference? Yes. But is it going to become sentient and take over the world? No. Artificial intelligence isn’t going to do that. 
                       Marks emphasized that AI is a tool and that it can be used for either good or evil. 

Ingraham and Marks went on to talk about the guardrails computer engineers have made for ChatGPT, the state of higher education, and the legacy of Walter Bradley, the namesake of the Walter Bradley Center. 

You can find the link to the full conversation here but will need to get 7-day free trial for full access

The Fossil record's equilibrium continues to rebut Darwin

Fossil Friday: Evolutionary Stasis in Fossil Damselflies Challenges Darwinism


This Fossil Friday features a beautiful fossil damselfly from the Upper Jurassic limestone of Painten in Bavaria, Germany, which is about 152 million years old. I acquired this remarkable fossil for the collection of the Natural History Museum in Stuttgart in 2012 (no. SMNS 70154) and scientifically described it as a new genus and species, Jurahemiphlebia haeckeli, a few years later (Bechly 2015, 2019). It represents the oldest fossil record of crown group Zygoptera and belongs to the damselfly family Hemiphlebiidae.

For a lay person it would hardly be distinguishable from its living relative Hemiphlebia mirabilis from Australia, even sharing the tiny size of just 11 mm wing length and the characteristic wing venation. Such cases of evolutionary stasis present a conundrum and challenge for neo-Darwinism, which can only be explained away with ad hoc hypotheses like stabilizing selection under unchanging ecological conditions. However, the profound changes in geography, climate, and vegetation since the Late Jurassic make the assumption of a stable habitat quite implausible. Also, it looks like natural selection is considered as a “magic wand” that can be highly creative and transformative or highly conservative and stabilizing.

How convenient. Sounds like the old saying: If the cockerel crows from his favorite spot, the weather may change or again it may not. In the hard sciences such universal explanations that can explain everything and rule out no possible observations are usually considered empirically empty and worthless. Not so in modern evolutionary biology, which tells a lot about its dubious status as a “hard science.” It is instead an unfalsifiable assemblage of fancy just-so stories and ad hoc explanations, a kind of meta-narrative for a naturalistic worldview but not a serious science on par with physics or chemistry.

Sources

Bechly G 2015. [Chapter] Insekten (Hexapoda). pp. 239-270 in: Arratia G, Schultze HP, Tischlinger H & Viohl G (eds). Solnhofen – Ein Fenster in die Jurazeit. 2 vols. Pfeil Verlag, Munich (DE), 620 pp.
Bechly G 2019. New fossil Odonata from the Upper Jurassic of Bavaria with a new fossil calibration point for Zygoptera. Palaeoentomology 2(6), 618-632. DOI: https://doi.org/10.11646

Comparing our patch of real estate to the fixer uppers(?) around the galaxy.

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On the empire of the atom?

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Let there be light?


An answer looking for a question?

 The philosophy naturalism.


Last time we saw that by wholeheartedly embracing and promoting Theodosius Dobzhansky’s famous phrase, “Nothing in Biology Makes Sense Except in the Light of Evolution,” evolutionists have backed themselves into a corner from which they cannot escape. As we saw, there is much to say about this evolutionary rallying cry, but at the top of the list is that it is false. Unequivocally false. This is not an opinion or a pushback. I’m not trying to pick a debate—because there is no debate. We may as well debate whether bachelors are male. Dobzhansky’s phrase, with all due respect, is “not even wrong,” as physicists like to say. It is silly, and yet there it is—all over the literature. The phrase is approvingly recited even in peer-reviewed technical journal papers. It is the mantra that evolutionists will not stop repeating, all the while revealing that this isn’t about science. Evolutionists will never repeal and recant, because there simply is too much at stake here. As we discussed, this isn’t like admitting that a particular prediction went wrong. Dobzhansky’s phrase was not merely a prediction, it was meta-prediction—the aphorism of an entire world view—and walking it back would be to reveal the man behind the curtain. Suddenly all those epistemological claims, such as that evolution is as much a fact as is gravity, heliocentrism and the round shape of the earth, would be left hanging, open to scrutiny and with a long, long way to fall. But Dobzhansky’s famous phrase is not the only way evolutionists have self-destructed. They have made other nonnegotiable and important claims that are equally corrosive. One is that evolution is both confirmed and required.

The National Association of Biology Teachers’ official position statement on the teaching of evolution states that evolution is (i) confirmed by the scientific evidence and (ii) a necessary going in position in order for science to function properly. Here is what the NABT says about the confirmation of evolution:
                               Scientists who have carefully evaluated the evidence overwhelmingly support the conclusion that both the principle of evolution itself and its mechanisms best explain what has caused the variety of organisms alive now and in the past. … The patterns of similarity and diversity in extant and fossil organisms, combined with evidence and explanations provided by molecular biology, developmental biology, systematics, and geology provide extensive examples of and powerful support for evolution.
                 And here is what the NABT says about the necessity of evolution:
                    Evolutionary biology rests on the same scientific methodologies the rest of science uses, appealing only to natural events and processes to describe and explain phenomena in the natural world. Science teachers must reject calls to account for the diversity of life or describe the mechanisms of evolution by invoking non-naturalistic or supernatural notions … Ideas such as these are outside the scope of science and should not be presented as part of the science curriculum. These notions do not adhere to the shared scientific standards of evidence gathering and interpretation.
                      There you have it, evolutionary theory is both confirmed and required. And the National Association of Biology Teachers is by no means alone here. The dual epistemological and philosophical claims, respectively, are broadly held by evolutionists and go back centuries.

Do you see the problem?
This philosophical position that evolutionists have staked themselves to is circular. To understand this, imagine for a moment that you witness a miracle, involving “non-naturalistic or supernatural” causes. According to evolutionists, such an event is “outside the scope of science.”

Does that imply the event was necessarily not real?

No, the fact that something falls outside of one’s definition of science does not rule it out of existence. The event does not automatically become necessarily impossible. Something can be not amenable to scientific investigation yet real.

The standard claim of evolutionists that evolution is necessary for proper science reflects a particular philosophy of science called naturalism. They present it as though it were a fact, but that is false. There are many philosophies of science, and none are facts. They are rules of the road for those who declare them to follow.

That’s it.So evolutionists have committed themselves to yet another false statement. But that’s not the main problem. The main problem is that if one insists and is committed to naturalism, then naturalistic, evolutionary, explanations is what they will find.

So of course evolution is confirmed by the science. It has to be. For evolutionists, the question is not whether evolution is confirmed by the science, the only question is what are the particulars.

This explains why evolutionists interpret the evidence the way they do. It explains how contradictory evidence can be sustained over and over and over. It also explains why, so long as you stick to naturalism, anything and everything is allowed. Natural selection, gradualism, mutations, common descent, drift, saltationism, and all the rest are up for grabs. They all may be forfeited. Any kind of theory, not matter how at odds with the empirical data, can be contemplated.

What cannot be contemplated in evolutionary science is creationism. There must be no miracles.

This means that evidence will be interpreted, filtered, analyzed, and processed according to the rules. Non cooperative evidence will be set aside and viewed as “grounds for further research.” Or it will be ground up and recast until it can be made to work right.

Cooperative evidence, on the other hand, will be viewed a normative, and ready for incorporation into proper scientific theories.

When evolutionists insist that science must be strictly naturalistic they show their hand. The flip side of their claim, that evolution is confirmed, is not a theory-neutral, objective finding. It is driven by the philosophy. It is circular—the conclusion was assumed in the first place. If your going-in position is that naturalism is required, then your results will adhere to naturalism.
Evolution is not a scientific finding, it is a philosophical mandate.

A clash of titans (again)

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