Friday, 10 March 2023

The highest cliffs in natural history's fitness landscape?

New book: New proteins evolve very easily.

We have seen that a new evolution book co-authored by evolutionist Dennis Venema and Scot McKnight is influenced by the mythical Warfare Thesis (here and here) and makes erroneous arguments that the fossils, echolocation, and pseudogenes support evolution (here, here and here). We now move on to another topic: protein evolution. Proteins are composed of a linear string of amino acids, often hundreds in length, and perform all sorts of important tasks in the cell. They could not have evolved by any stretch of the imagination, and so pose a rather difficult problem for evolutionists. Our new book on evolution attempts to resolve this problem with a claim that has long since been understood to be false. In fact, the claim, properly understood, provides yet more scientific evidence against evolution.

The problem of protein evolution

For evolution to work biology must be chocked full of structures that can arise via long, gradual evolutionary pathways. Mutations must be able to slowly accumulate, gradually improving the structure. In other words, the “fitness landscape” must be smooth and gradual, not rugged or precipitous.

That evolutionary expectation has been found to be false many times, and proteins are no exception. It is now clear that for a given protein, only a few changes to its amino acid sequence can be sustained before the protein function is all but eliminated. Here is how one paper explained it:

The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability—the ability of proteins to acquire changes in sequence and function

In other words, protein function precipitously drops off with only a tiny fraction of its amino acids altered. It is not a gradual fitness landscape. Another paper described the protein fitness landscape as rugged.

Therefore it is not surprising that various studies on evolving proteins have failed to show a viable mechanism. One study concluded that 10^63 attempts would be required to evolve a relatively short protein. And a similar result (10^65 attempts required) was obtained by comparing protein sequences. Another study found that 10^64 to 10^77 attempts are required, and another study concluded that 10^70 attempts would be required.

So something like 10^70 attempts are required yet evolutionists estimate that only 10^43 attempts are possible. In other words, there is a shortfall of 27 orders of magnitude.

But it gets worse. The estimate that 10^43 attempts are possible is utterly unrealistic. For it assumes billions of years are available, and that for that entire time the Earth is covered with bacteria, constantly churning out mutations and new protein experiments. Aside from the fact that these assumptions are entirely unrealistic, the estimate also suffers from the rather inconvenient fact that those bacteria are, err, full of proteins. In other word, for evolution to evolve proteins, they must already exist in the first place.

This is absurd. And yet, even with these overly optimistic assumptions, evolution falls short by 27 orders of magnitude.

The numbers don’t add up. Proteins reveal scientific problems for evolution. What is interesting is how evolutionists react to these problems.

The “solution” to protein evolution

A common solution cited by evolutionists for the problem of protein evolution is the case of nylonases—enzymes that rapidly arose in bacteria, in the last century, and are able to breakdown byproducts of the nylon manufacturing process. The idea here is that these byproducts of the nylon manufacturing process were present in the bacteria’s environment for the first time. The bacteria had never been exposed to such chemicals, and yet in an evolutionary blink of an eye, were able to produce proteins to metabolize the new chemicals. Does this not demonstrate that the chance origin of a protein-coding genes is not a problem? Proteins could have evolved with no problem, after all, we just witnessed it occur with the origin of nylonases. As the new book explains, protein evolution “appears to be trivial for evolution to achieve.” [86]

Unfortunately this icon of evolution is an enormous misrepresentation of the science.

The science

The evolutionary claim that the nylonases demonstrate how easy protein evolution is non scientific for several reasons. Indicators of this include that fact that the nylonases evolved so rapidly—in an entirely unrealistic time frame under evolution, and that they arose in bacteria with thousands of preexisting proteins. Again, this evolutionary claim of how proteins evolve is circular, it requires the preexistence of proteins.

None of this is feasible given the problems of protein evolution discussed above. The scientific inference would be that the bacteria developed the nylonases because those chemicals they metabolize were present in the environment. In other words, directed adaptation.

Indeed, this is precisely what researchers in the field have concluded. They hypothesize that the new metabolism capability is a stress response, an adaptation to a challenging environment. In other words, the environment influenced the adaptation. This is not a case of evolutionary change. The nylonase enzymes did not arise from a random search over sequence space until the right enzymes were luckily found and could be selected for. That would have required eons of time, and is far beyond evolution’s capability, as we have seen. Instead, cellular structures rapidly formed new enzymes, due to the environmental change.

Indeed, such adaptation to nylon manufacture byproducts has been repeated in laboratory experiments. In a matter of months bacteria acquire the ability to digest the unforeseen chemical. Researchers speculate that mechanisms responding to environmental stress are involved in inducing adaptive mutations.

This does not demonstrate protein evolution. In fact it refutes evolution. Evolution does not have the resources to have created directed adaptation mechanisms. And even if it did, such mechanisms would not have been selected for because they provide no immediate fitness improvement.

This is not evidence that protein-coding genes can evolve by chance. A new gene, arising within a modern cell responding to an environmental challenge, is not analogous to chance origin. Unfortunately evolutionists have a long history of inappropriately claiming otherwise (for example, see here and here).

We have seen that this new evolution book makes erroneous arguments that the fossils, echolocation, and pseudogenes support evolution. We now see another erroneous argument for protein evolution.

All these arguments and evidences are typical. They are icons of evolution, and it is astonishing how durable they are in the evolution literature given their complete failure.

If evolution was indicated by the science I would be the first to sign up. But in fact it is an age-old religious idea that makes no sense on the science. And likewise this new book is an utter disaster. The confection immediately crumbles under even a little probing.

From savage 'wolf' to civilised 'wolf'?

When Darwinian Racism Came to Africa, and to the West

Evolution News

A new episode of ID the Future features another reading from scholar Olufemi Oluniyi’s new book, Darwin comes to Africa. In this excerpt we learn how Darwin himself laid much of the groundwork for social Darwinist ideas, primarily in his book The Descent of Man, and how those ideas were energetically developed in the ensuing decades by various mainstream scientists. Oluniyi further details how their work fueled pseudo-scientific racism against Africans and other indigenous peoples outside the West. Download the podcast or listen to it here. To learn more about this neglected corner of modern Western history, and for the good news that the flow of evidence has turned against Darwinism and, with it, social Darwinist principles, pick up Oluniyi’s book here.

Dr. Frankenstein's Children?

Mice Born with No Mother, Two Fathers: What Next?

Wesley Smith

Biotechnologists keep pushing the borders of what is possible in procreation. Mice pups have now been born with no mother and two fathers.

It was done, apparently, by transforming skin cells from male mice into pluripotent stem cells and thence into egg cells with XX chromosomes. From the Guardian story:

Male skin cells were reprogrammed into a stem cell-like state to create so-called induced pluripotent stem (iPS) cells. The Y-chromosome of these cells was then deleted and replaced by an X chromosome “borrowed” from another cell to produce iPS cells with two identical X chromosomes.

“The trick of this, the biggest trick, is the duplication of the X chromosome,” said Hayashi. “We really tried to establish a system to duplicate the X chromosome.”

Finally, the cells were cultivated in an ovary organoid, a culture system designed to replicate the conditions inside a mouse ovary. When the eggs were fertilised with normal sperm, the scientists obtained about 600 embryos, which were implanted into surrogate mice, resulting in the birth of seven mouse pups.

Why Do Such a Thing?

Ostensibly the purpose would be to help with rare forms of infertility in women. But these are dual-edged technologies. This, I believe, is the real aim behind such experiments:

“Purely in terms of technology, it will be possible [in humans] even in 10 years,” he said, adding that he personally would be in favour of the technology being used clinically to allow two men to have a baby if it were shown to be safe.

Why? What is the urgency in that?

And What About the Baby?

There is no assurance that the baby would not be harmed by such biological manipulation. Or, is that a secondary concern to the great contemporary maw of “I want”?

But Wesley, what if it really is “safe”? How would we know without unethical human experimentation? Humans are much more complex organisms than mice. The only way such procreative manipulation could “be shown to be safe” in humans would require repeated experiments — that would almost surely involve repeated abortions, stillbirths, or babies born with birth defects — to perfect techniques. It would also require surrogate mothers or artificial gestation chambers to bring the babies to term, which would pose other ethical issues.

Because we might be able to figure out how to twist nature into a knot doesn’t mean that we should. The time is long past due to legally regulate human experiments in this field of biotechnology before it is too late.

The sausage factory?

Thursday, 9 March 2023

Why some anamolies are more equal than others.

A convenient convergence?

Convergence? One-Celled Creature Has an Eye!

David Coppedge

They thought it was a joke. A century ago, biologists could not believe that a one-celled creature had an eye. But since the warnowiid dinoflagellate was difficult to find and grow in the lab, detailed research was rare, until now. A team from the University of British Columbia gathered specimens off the coast of BC and Japan for a closer look. They found that the structure, called an ocelloid, has structures that mimic the complex eye of higher animals. Phys.Org says:

In fact, the ‘ocelloid’ within the planktonic predator looks so much like a complex eye that it was originally mistaken for the eye of an animal that the plankton had eaten.

“It’s an amazingly complex structure for a single-celled organism to have evolved,” said lead author Greg Gavelis, a zoology PhD student at UBC. “It contains a collection of sub-cellular organelles that look very much like the lens, cornea, iris and retina of multicellular eyes found in humans and other larger animals.”

Astonishment to Share

New Scientists shares the astonishment:

It is perhaps the most extraordinary eye in the living world — so extraordinary that no one believed the biologist who first described it more than a century ago.

Now it appears that the tiny owner of this eye uses it to catch invisible prey by detecting polarised light. This suggestion is also likely to be greeted with disbelief, for the eye belongs to a single-celled organism called Erythropsidinium. It has no nerves, let alone a brain. So how could it “see” its prey?

The “retina” of this eye, a curved array of chromosomes, appears arranged to filter polarized light. The news item from the Canadian Institute for Advanced Research quotes Brian Leander, co-supervisor of the project:

“The internal organization of the retinal body is reminiscent of the polarizing filters on the lenses of cameras and sunglasses,” Leander says. “Hundreds of closely packed membranes lined up in parallel.”

And that’s not all this wonder of the sea has in its toolkit. It also has a piston and a harpoon:

Scientists still don’t know exactly how warnowiids use the eye-like structure, but clues about the way they live have fuelled compelling speculation. warnowiids hunt other dinoflagellates, many of which are transparent. They have large nematocysts, which Leander describes as “little harpoons,” for catching prey. And some have a piston — a tentacle that can extend and retract very quickly — with an unknown function that might be used for escape or feeding.

Did This Eye Evolve?

Lest anyone think the dinoflagellate’s eye presents an easy evolutionary stepping stone to more complex eyes, the data reveal several problems. The paper in Nature claims that the ocelloids are built from “different endosymbiotically acquired components” such as mitochondria and plastids. “As such, the ocelloid is a chimaeric structure, incorporating organelles with different endosymbiotic histories.” We can treat endosymbiosis as a separate issue. For now, we can ask if this complex structure is explainable by unguided natural selection.

The authors did not think this is a clear evolutionary story. “The ocelloid is among the most complex subcellular structures known, but its function and evolutionary relationship to other organelles remain unclear,” they say. Never in the paper do they explain how organelles with different histories came together into a functioning eye. Most of the paper is descriptive of the parts and how they function individually, or where they might have been derived by endosymbiosis. To explain the eye’s origin as a functioning whole, they make up a phrase, “evolutionary plasticity” —

Nevertheless, the genomic and detailed ultrastructural data presented here have resolved the basic components of the ocelloid and their origins, and demonstrate how evolutionary plasticity of mitochondria and plastids can generate an extreme level of subcellular complexity.

Other than that, they have very little to say about evolution, and nothing about natural selection.

Reviewing the paper

In the same issue of Nature, Richards and Gomes review the paper. They list other microbes including algae and fungi that have light-sensitive spots. Some have the rhodopsin proteins used in the rods and cones of multicellular animals. But instead of tracing eye evolution by common ancestry, they attribute all these innovations to convergence:

These examples demonstrate the wealth of subcellular structures and associated light-receptor proteins across diverse microbial groups. Indeed, all of these examples represent distinct evolutionary branches in separate major groups of eukaryotes. Even the plastid-associated eyespots are unlikely to be the product of direct vertical evolution, because the Chlamydomonas plastid is derived from a primary endosymbiosis and assimilation of a cyanobacterium, whereas the Guillardia plastid is derived from a secondary endosymbiosis in which the plastid was acquired ‘second-hand’ by intracellular incorporation of a red alga. Using gene sequences recovered from the warnowiid retinal body, Gavelis et al. investigated the ancestry of this organelle by building phylogenetic trees for the plastid-derived genes. Their analysis demonstrated that this modified plastid is also of secondary endosymbiotic origin from a red alga.

Although derived independently, there are common themes in the evolution of these eye-like structures. Many of them involve the reconfiguration of cellular membrane systems to produce an opaque body proximal to a sensory surface, a surface that in four of the five examples probably involves type 1 rhodopsins. Given the evolutionary derivation of these systems, this represents a complex case of convergent evolution, in which photo-responsive subcellular systems are built up separately from similar components to achieve similar functions. The ocelloid example is striking because it demonstrates a peak in subcellular complexity achieved through repurposing multiple components. Collectively, these findings show that evolution has stumbled on similar solutions to perceiving light time and time again.

But is convergence just a word masquerading as an explanation? We read:

The work sheds shed new light on how very different organisms can evolve similar traits in response to their environments, a process known as convergent evolution.Eye-like structures have evolved independently many times in different kinds of animals and algae with varying abilities to detect the intensity of light, its direction, or objects.

“When we see such similar structural complexity at fundamentally different levels of organization in lineages that are very distantly related to each other, in this case warnowiids and animals, then you get a much deeper understanding of convergence,” Leander says.

A Post-Hoc Observation

But “convergent evolution” is not a process. It is a post-hoc observation based on evolutionary assumptions. An environment has no power to force an organism to respond to it with a complex function. Light exists, whether or not an organism sees it. Magnetism exists, too; does it contain the power to nudge fish, turtles, and butterflies to employ it for navigation?

If it is highly improbable for a complex solution to evolve once, “convergent evolution” only exacerbates the improbability. In Illustra Media’s new film Living Waters , Timothy Standish explains why “convergent evolution” is not a plausible explanation for unrelated similarities. “Evolution is blind,” he says. It doesn’t know that another organism has an elegant solution to a problem. It cannot drive a different animal to converge on a similar solution. What we do know, Standish continues, is that intelligence can take a solution to a problem and apply it in different circumstances over and over again.

It makes sense that a designer would understand optics and electromagnetic waves. A mind can take parts and arrange them into corneas, lenses, and receptors appropriate for the needs and sizes of disparate organisms. Unguided selection cannot do that. The environment cannot do that. From our uniform experience, the only cause we know that can organize parts into a functioning whole is intelligence. This is positive evidence for design. The alternative theory could be dubbed, “Convergence of the Gaps.”

Wednesday, 8 March 2023

Some more on secular humanism's civil war.

On our expertocracy's messiah complex?

Why the trinity is a mystery?: Positive edition.

Positive mysterianism

Stanford University

In contrast, the positive mysterian holds that the trinitarian doctrine can’t be understood because of an abundance of content. That is, the doctrine seems to contain explicit or implicit contradictions. So while we grasp the meaning of its individual claims, taken together they seem inconsistent, and so the conjunction of them is not understandable, in the sense explained above. The positive mysterian holds that the human mind is adequate to understand many truths about God, although it breaks down at a certain stage, when the most profound divinely revealed truths are entertained. Sometimes an analogy with recent physics is offered; if we find mysteries (i.e., apparent contradictions) there, such as light appearing to be both a particle and a wave, why should we be shocked to find them in theology (van Inwagen 1995, 224–7)?

The best-developed positive mysterian theory is that of James Anderson (2005, 2007), who develops Alvin Plantinga’s epistemology so that beliefs in mysteries (merely apparent contradictions) may be rational, warranted, justified, and known. Orthodox belief about the Trinity, Anderson holds, involves believing, for example, that Jesus is identical to God, the Father is identical to God, and that Jesus and the Father are not identical. Similarly, one must believe that the Son is omniscient, but lacks knowledge about at least one matter. These, he grants, are apparent contradictions, but for the believer they are strongly warranted and justified by the divine testimony of scripture. He argues that numerous attempts by recent theologians and philosophers to interpret one of the apparently contradictory pairs in a way that makes the pair consistent always result in a lapse of orthodoxy (2007, 11–59). He argues that the Christian should take these trinitarian mysteries to be “MACRUEs”, merely apparent contradictions resulting from unarticulated equivocations, and he gives plausible non-theological examples of these (220–5).

It is plausible that if a claim appears contradictory to someone, she thereby by has a strong epistemic “defeater” for that belief, i.e., a further belief or other mental state which robs the first belief of rational justification and/or warrant. A stock example is a man viewing apparently red objects. The man then learns that a red light is shining on them. In learning this, he acquires a defeater for his belief that the items before him are red. Thus with the Trinity, if the believer discovers an apparent contradiction in her Trinity theory, doesn’t that defeat her belief in that theory? Anderson argues that it does not, at least, if she reflects properly on the situation. The above thought, Anderson argues, should be countered with the doctrine of divine incomprehensibility, which says that we don’t know all there is to know about God. Given this truth, the believer should not be surprised to find herself in the above epistemic situation, and so, the believer’s trinitarian belief is either insulated from defeat, or if it’s already been defeated, that defeat is undone by the preceding realization (2007, 209–54).

Dale Tuggy (2011a) argues that Anderson’s doctrine of divine incomprehensibility is true but trivial, and not obviously relevant to the rationality of belief in apparent contradictions about God. The probability of our being stuck with such beliefs is a function not only of God’s greatness in comparison to humans’ cognitive powers, but also of what and how much God chooses to reveal about himself. Nor is it clear that God would be motivated to pay the costs of inflicting apparently contradictory divine revelations on us. Moreover, Anderson has not ruled out that the apparent contradictions come not from the texts alone, but also from our theories or pre-existing beliefs. Finally, he argues that due to the comparative strength of “seemings”, a believer committed to paradoxes like those cited above will, sooner or later, acquire an epistemic defeater for her beliefs.

In a reply, Anderson (2018) denies that divine incomprehensibility is trivial, while agreeing that many things other than God are incomprehensible (297). While Tuggy had attacked his suggestions about why God would want to afflict us with apparent contradictions, Anderson clarifies that

…my theory doesn’t require me to identify positive reasons for God permitting or inducing MACRUEs. For even if I concede Tuggy’s point that “the prior probability of God inducing MACRUEs in us is either low or inscrutable,” the doctrine of [divine] incomprehensibility can still serve as…an undercutting defeater for the inference from D appears to be logically inconsistent to D is false. (298–9)

The defense doesn’t require, Anderson argues, any more than that MACRUEs are “not very improbable given theism” (299). As to whether these apparent contradictions result from the texts rightly understood, or whether they result from the texts together with mistaken assumptions we bring to them, this is a question only biblical exegesis can decide, not any a priori considerations (300). As to Tuggy’s charge that a believer in theological paradoxes will inevitably acquire an undefeated defeater for her beliefs, Anderson argues that this has not been shown, and that Tuggy overlooks how a believer may reasonably add a relevant belief to her seemingly inconsistent set of beliefs, such as that the apparently conflicting claims P and Q are only approximately true, or that “P and Q are the best way for her to conceptualize matters given the information available to her, but they don’t represent the whole story” (304).

Anderson’s central idea is that the alleged contradictions of Christian doctrine will turn out to be merely apparent. In contrast, some theologians have held that doctrines including the Trinity imply not merely apparent but also real contradictions, but are nonetheless true. Such hold that there are exceptions to the law of non-contradiction. While some philosophers have argued on mostly non-religious grounds for dialetheism, the claim that there can be true (genuine, not merely apparent) contradictions, this position has for the most part not been taken seriously by analytic theologians (Anderson 2007, 117–26) (For a recent exception, see Beall 2019.)

Why the trinity is a mystery?: Negative edition.

Negative mysterianism

Stanford University

The negative mysterian holds that the true doctrine of the Trinity is not understandable because it is too poor in intelligible content for it to positively seem either consistent or inconsistent to us. In the late fourth-century pro-Nicene consensus this takes the form of refusing to state in literal language what there are three of in God, how they’re related to God or to the divine essence, and how they’re related to each other. (See section 3.3 in the supplementary document on the history of Trinity theories.) The Persons of the Trinity, in this way of thinking, are somewhat like three men, but also somewhat like a mind, its thought, and its will, and also somewhat like a root, a tree, and a branch. Multiple incongruous analogies are given, the idea being that a minimal content of the doctrine is thereby expressed, though we remain unable to convert the non-literal claims to literal ones, and may even be unable to express in what respects the analogies do and don’t fit. Negative mysterianism goes hand in hand with the doctrines of divine incomprehensibility (that God or God’s essence can’t be understood completely, at all, or adequately) and divine ineffability (that no human concept, or at least none of some subset of these, applies literally to God). Some recent studies have emphasized the centrality of negative mysterianism to the pro-Nicene tradition of trinitarian thought, chastising recent theorists who seem to feel unconstrained by it (Ayres 2004; Coakley 1999; Dixon 2003).

The practical upshot of this is being content to merely repeat the approved trinitarian sentences. Thus, after considering and rejecting as inadequate multiple analogies for the Trinity, Gregory of Nazianzus concludes,

So, in the end, I resolved that it was best to say “goodbye” to images and shadows, deceptive and utterly inadequate as they are to express that reality. I resolved to keep close to the more truly religious view and rest content with some few words, taking the Spirit as my guide and, in his company and in partnership with him, safeguarding to the end the genuine illumination I had received from him, as I strike out a path through this world. To the best of my powers I will persuade all men to worship Father, Son, and Holy Spirit as the single Godhead and power, because to him belong all glory, honor, and might forever and ever. Amen. (Nazianzus, Oration 31, 143.)

Opponents of this sort of mysterianism object to it as misdirection, special pleading, neglect of common sense, or even deliberate obfuscation. They emphasize that trinitarian theories are human constructs, and a desideratum of any theory is clarity. We literally can’t believe what is expressed in trinitarian language, if we don’t grasp the meaning of it, and to the extent that we don’t understand a doctrine, it can’t guide our other theological beliefs, our actions, or our worship (Cartwright 1987; Dixon 2003, 125–31; Nye 1691b, 47; Tuggy 2003a, 176–80). Negative mysterians reply that it is well-grounded in tradition, and that those who are not naively overconfident in human reason expect some unclarity in the content of this doctrine.

The arrival of fittest?

The foundation of the mind?

Make way for our AI overlords?

The thumb print of JEHOVAH :Molecular biology edition.

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

Cornelius G Hunter

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?

Tuesday, 7 March 2023

The edge of physics II.

The edge of physics?

Mind will ever govern matter?

Marks: Human Exceptionalism in a World of AI

Evolution News

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

Evolution News

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?

On spaceship earth's forcefield.

On the decline of entrepreneurship

Darwinism the fittest?

Natural Selection: The Evolution of a Mirage

Neil Thomas

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?

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

Faith on view

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

Olufemi Oluniyi

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

Paul Nelson

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.

Pages

Search This Blog

Friday, 10 March 2023

New book: New proteins evolve very easily.

When Darwinian Racism Came to Africa, and to the West

Mice Born with No Mother, Two Fathers: What Next?

Thursday, 9 March 2023

Convergence? One-Celled Creature Has an Eye!

Wednesday, 8 March 2023

Positive mysterianism

Negative mysterianism

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

Tuesday, 7 March 2023

Marks: Human Exceptionalism in a World of AI

Jonathan Bartlett on the Growing Evidence of Designed Mutations

Natural Selection: The Evolution of a Mirage

Canadian Catholic student suspended for speaking on Biblical perspectives on gender

Darwin’s Contribution to Racial Extermination

A Good Example of Evolutionary Use of Extremely Small Probability Singularities

Pageviews last month