Thursday 16 March 2023

Darwinism is the fittest? III

Peer-Reviewed Paper Cites Stephen Meyer to Critique Darwinian Evolution

In an article yesterday I noted that a peer-reviewed paper published last year in Progress in Biophysics and Molecular Biology, titled “Neo-Darwinism Must Mutate to survive,” offered potent probability arguments against the Darwinian evolution of a complex molecular pathway. These arguments, presented by authors Olen R. Brown and David A. Hullender, in many respects resemble intelligent design probability arguments.

Importantly, the authors seem aware that intelligent design offers similar arguments, and they appear to agree that these hold some merit:

Probability reasoning has been applied to the evolution alternative known as intelligent design by Elliott Sober who argued that ‘Darwinian gradualism’ and ‘random genetic drift’ are reasonable ‘evolutionary processes’ to overcome weaknesses in natural selection by survival of the fittest (Sober, 2007). We challenge these assumptions. Stephen Gould, and Niles Eldredge initiated a controversy described in the book Punctuated Equilibrium (Gould, 2007). Their proposal was widely ridiculed but the problem they addressed was real and continues today e survival of the fittest is not a satisfactory explanation for macroevolution.

Indeed, the authors cite Stephen Meyer’s 2013 book Darwin’s Doubt and his arguments about “the combinational problem of the Cambrian explosion”:

There is much published evidence that Darwinian and Neo-Darwinian evolutionary theories are probabilistically extremely improbable. Stephen Meyer in his book Darwin’s Doubt (S. C. Meyer, n.d.) has intelligently examined the meaning of the rapid expansion of life forms that appeared in what is known as the Cambrian explosion. Many life forms with essentially new body types appeared quickly and without precursors in the Burgess Shale discovered in Canada’s Kicking Horse Valley in British Columbia in the 1880s.

Mainstream biologists have maintained that up to 20 million years was provided during this ‘explosion’ which they maintain is adequate for the presumed process of change with selection to have accounted for Neo-Darwinian Evolution as typified in a critique of Meyer’s book published in 2013 in the New Yorker (Cook, n.d.). Myer also has spoken about the combinational problem of the Cambrian explosion, including: “… the mystery of how the neo-Darwinian mechanisms of natural selection and random mutation [emphasis added] could have given rise to all these fundamentally new forms of animal life.” (S. Meyer, n.d.).

In this perspective, we seek to promote a sea change in mainstream biology to follow the evidence. We do not propose that probability alone is a solution, but that it is a useful initiative for redirecting prior efforts that have too often been met, unfortunately, with a mental shrug and the statement ‘we are here’.

The authors seem to have appreciated Meyer’s message — namely that some factor other than standard evolutionary mechanisms is needed to produce life’s complex features.

Others Calling for New Models

The paper further notes that many sources are calling for new models of evolution, as it quotes Corning (2020) stating that there is no valid replacement paradigm for the Modern Synthesis:

Many theorists in recent years have been calling for evolutionary biology to move beyond the Modern Synthesis — the paradigm that has long provided the theoretical backbone for the discipline. Terms like ‘postmodern synthesis’, ‘integrative synthesis’, and ‘extended evolutionary synthesis’ have been invoked by various critics in connection with the many recent developments that pose deep challenges — even contradictions — to the traditional model and underscore the need for an update, or makeover. However, none of these critics, to this author’s knowledge, has to date offered an explicit alternative that could provide a unifying theoretical paradigm for our vastly increased knowledge about living systems and the history of life on earth.

Similarly they quote Noble (2021)

[T]he illusions of the modern synthesis … something has gone deeply wrong in biology … [there is] the difficulty of trying to ‘break out of its attractive simplicity’ as it is still routinely taught in schools and universities … This is a serious and unnecessary situation that urgently needs rectifying … We have reached a critical turning point in evolutionary biology.

On the origin of life, the authors note that key problems are unsolved, quoting Mariscal et al. (2019) who offer a forceful critique of the state of the field of origin of life research:

[W]e provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open.

Opposition from Mainstream Biology

They know these are serious challenges, that they are in for some tough sledding, and that their claims may not be well received. So the introduction to the paper contains a pre-emptive statement expressing their awareness of the “opposition” their claims will face:

The central thesis of this perspective is that reasonable scientific challenges to evolutionary theories, like other theories in science, should be explored. We focus on assessing the weaknesses of survival of the fittest, evaluating alternatives, and proposing new ideas. Mainstream biology remains opposed to any opposition to the central concepts of evolution.

It’s quite striking to see a mainstream scientific journal acknowledging that “Mainstream biology remains opposed to any opposition to the central concepts of evolution.” They further state that they “are critical of accepting without question Darwinian evolution and Neo-Darwinism including what is generally referred to as the modern synthesis”— the implication being that many accept it uncritically. But they haven’t given up on mainstream biology, and thus attempt to remind readers of the scientific virtues of humility and openness to new ideas:

[T]he Templeton Foundation on its website in January 2022 described the ‘Joy of being wrong’ and said that Saint Augustine called humility the foundation of all other virtues. “Psychologists and philosophers are working to tease apart the ways we respond to new ideas and information — and the possible benefits of intellectual humility … a mindset that guides our intellectual conduct … it involves recognizing and owning our intellectual limitations in the service of pursuing deeper knowledge, truth, and understanding.”

Again, I had not heard of these authors prior to the publication of this paper — but their courage and boldness inspire confidence that there are still people within the scientific community willing to follow the evidence where it leads.

Darwinism is the fittest? II

Peer-Reviewed Paper: “Neo-Darwinism Must Mutate to Survive”

Casey Luskin

A peer-reviewed paper published towards the end of last year in the Elsevier journal Progress in Biophysics and Molecular Biology has a provocative title: “Neo-Darwinism Must Mutate to survive ” The paper’s abstract opens with points that few would dispute:

Darwinian evolution is a nineteenth century descriptive concept that itself has evolved. Selection by survival of the fittest was a captivating idea. Microevolution was biologically and empirically verified by discovery of mutations.

However, there then comes a major “but”:

There has been limited progress to the modern synthesis. The central focus of this perspective is to provide evidence to document that selection based on survival of the fittest is insufficient for other than microevolution.

And according to authors Olen R. Brown and David A. Hullender, just what is the basis for saying this? It’s calculations showing that the likelihood of microevolutionary processes adding up to macroevolutionary changes is highly improbable:

Realistic probability calculations based on probabilities associated with microevolution are presented. However, macroevolution (required for all speciation events and the complexifications appearing in the Cambrian explosion) are shown to be probabilistically highly implausible (on the order of 10-50) when based on selection by survival of the fittest. We conclude that macroevolution via survival of the fittest is not salvageable by arguments for random genetic drift and other proposed mechanisms.

They go on to state, “We are critical, as previously explained, of the position that macroevolution is sufficiently explained by the processes useful for microevolution — in particular that mutations and survival of the fittest are adequate to the task,” and argue that “Microevolution does not explain speciation — only smaller changes.”

A Familiar Critique

Prior to the publication of this paper I was not familiar with these authors (though Olen R. Brown contributed an article to Evolution News while I was in South Africa completing my PhD). But clearly they share a critical perspective on neo-Darwinism that is very similar to that of the intelligent design community. Consider this striking passage:

Survival of the fittest is adequate to select for such changes (gains) which occur within one genome primarily by single fixed mutations (and perhaps sometimes by horizontal gene transfer). Macroevolution, however, requires major changes necessitating multiple changes that logically most frequently occur in multiple genomes. Therefore, the concept survival of the fittest is inadequate to conserve individual changes in multiple genomes where the individual changes generate no increased fitness. … Thus, survival of the fittest is illogical when proposed as adequate for selecting the origination of all complex, major, new body-types and metabolic functions because the multiple changes in multiple genomes that are required have intermediate stages without advantage; selection would not reasonably occur, and disadvantage or death would logically prevail.

What they are saying is that when some feature requires multiple changes before providing an increase in fitness, the changes cannot be produced by mutation and selection alone. Their subsequent comments, read carefully, almost sound like an implicit endorsement of intelligent design:

It is our perspective that the burden is too great for survival of the fittest to select evolutionary changes that accomplish all evolutionary novelty. Thus, evolution lacks a sufficient mechanism for multifactorial selections because a process that looks forward, is nonrandom, deterministic, or occurs by an unknown biological process, is required. The position of mainstream biologists regarding this aspect of evolution is that nature is always non-purposeful and, therefore, the proposed selection (process, force, tendency), could not possibly be natural (scientific). However, our perspective is that this is a supposition of necessity rather than an established principle. Logic demands that it be open to investigation. This first requires an openness to ideas and science must be open to new ideas.

They thus propose that evolution is only possible if it is “nonrandom, deterministic, or occurs by an unknown biological process” — something that some would reluctantly conclude “could not possibly be natural.” They continue:

Darwin wrote in On the Origin of Species… : “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.” Today, Darwin’s missing cases are abundant including each complex transition to a new body type, metabolic cycle, or metabolic chain. Multi-step processes are routinely required at every evolutionary step.

They then perform a probability calculation which shows that the likelihood of producing a necessary pathway would require such multi-step processes leading to probabilities below the plausibility bound they had previously set.

Origin of the Krebs Cycle

They use a case study of the origin of the Krebs cycle — a metabolic pathway involving 12 enzymes that is necessary for life. They believe that this is a useful test for evolution. They assume that the genome is “ripe” to produce each enzyme where a minimal number of mutations is needed for a gene to suddenly become functional. They therefore choose an incredibly generous value of 0.00001 as the probability that a given enzyme can be created by a single mutation.

They calculate the likelihood of producing all 12 enzymes needed to produce a selectable function as 10-51. They note this is below 10-50, a probability that was called “negligible” by Émile Borel, the French mathematician, who stated “this process of evolution involves certain properties of living matter that prevent us from asserting that the process was accomplished in accordance with the laws of chance.”

They also reject co-option and exaptation as possible explanations for the origin of the Krebs cycle:

The idea that the complete, functioning Krebs cycle arose by purloining each intermediate step from other uses (Meléndez-Hevia, 1996) lacks empirical support. The discoveries that genes can be switched on and off, that codes read forward and backward, gene duplication, and the homeobox, are helpful but inadequate to save evolutionary theory without modification.

In the end, producing a complex feature like the Krebs cycle is just too improbable because “Selection based on survival of the fittest, for anything beyond single mutational changes in a genome, is insufficient scientifically and biologically.” They conclude, “there is something besides mutations and survival of the fittest needed to explain evolution.”

The Junk DNA trope further exposed as Junk science.

More Jobs for “Junk” DNA

Paul Nelson

It turns out the mouse endogenous retrovirus L (MERVL) is essential for embryogenesis, according to a recently published article in Nature Genetics. From the Discussion

We provided functional evidence that transcriptional activation of MERVL is essential for progression of development in mouse preimplantation embryos. Depletion of MERVL transcripts results in embryonic lethality with profound defects in development and is associated with dysregulation of MERVL including their adjacent transcripts, and retaining two-cell-like transcriptome and chromatin state (Fig. 6i). These findings suggest the possibility that MERVL transcription in totipotent cells may act as a switch for the transition from totipotency to pluripotency and is responsible for the onset of differentiation and ontogeny.

For more, see “Transcription of MERVL retrotransposons is required for preimplantation embryo development” (open access).

Biology's lexicon and the design inference.

Mapping the Pleiotropic Network of Human Cells

Paul Nelson

If you think about how you use English words, you quickly realize that words are polyfunctional. “House,” for instance, can be a noun, a verb, or an adjective (“house music,” “house money,” etc.).

Thus, if you imagine eliminating the word “house” from your daily-use lexicon, a wide range of different propositions would be affected, many having no apparent semantic relation to each other.

Genes and proteins are remarkably similar to natural-language words in this polyfunctional respect. For many decades, “pleiotropy” has been the term describing the multiple-system consequences of genetic mutations to a single locus, where the functional consequences can be wide-ranging, and often surprising in their diversity.

For more on the subject, here is an open access article at Nature Genetics: “Network expansion of genetic associations defines a Pleiotropy map of human cell biology.”

Wednesday 15 March 2023

The beast stirs?

Zelenskiy: Ukraine seeks 'spiritual independence', acts against church

Reuters

March 12 (Reuters) - Ukraine's punitive actions against a branch of the Orthodox church linked to Russia are part of a drive to achieve "spiritual independence," President Volodymyr Zelenskiy said on Sunday.

Zelenskiy and other Ukrainian leaders have accused the long-established Ukrainian Orthodox Church (UOC) of undermining Ukrainian unity and collaborating with Moscow.

Authorities ordered the church last Friday to leave its base in the 980-year-old Pechersk Lavra monastery complex, prompting Russian Orthodox Patriarch Kirill to ask Pope Francis and other religious leaders to help stop the crackdown.

"One more step towards strengthening our spiritual independence was taken this week," Zelenskiy said in his nightly video address, without referring directly to the order.

Ukrainians, he said, had reacted positively.

"We will continue this movement," he said. "We will not allow the terrorist state any opportunity to manipulate the spiritual life of our people, to destroy Ukrainian shrines - our Lavras - or to steal values from them."

Kirill has strongly supported Russia's invasion of Ukraine. In his appeal, he urged religious leaders and international organisations to "make every effort to prevent the forced closure of the monastery".

The Security Service of Ukraine has since October carried out searches at UOC churches, imposed sanctions on its bishops and financial backers, and opened criminal cases against dozens of clergymen.

Church officials say it and its millions of worshippers are victims of a witch-hunt.

Orthodoxy is the primary faith in Ukraine and the Moscow-linked church has been in competition for worshippers with an independent Orthodox Church, founded after the Soviet collapse in 1991 but only recognised by church hierarchy in 2018.

The independent church has been gaining in size and following since the invasion.

The Ukrainian culture ministry says the Moscow-linked church has until March 29 to leave the Pechersk Lavra monastery complex.

Ps. The Russian Church is complicit in the stripping of the rights of JEHOVAH'S servants in Russia so this could be viewed as a reaping of what they've sown.

Welcome to our world.

A financial pandemic? II

Pay their fair share?

Why good intentions are never enough.

Tuesday 14 March 2023

Rules for aspiring titans.

Darwinism simple beginning is more than a phantom? Pros and cons.

Rise of the planet of the monkeys?

Monkey-Made “Tools” Cast Doubt on High Intelligence in Early Hominids

Casey Luskin

A new paper in Science Advances, titled “Wild macaques challenge the origin of intentional tool production,” is making headlines. Macaque monkeys from Lobi Bay, Thailand, have been observed “unintentionally” producing stone tools that are “almost indistinguishable” from some very old stone artifacts typically attributed to our supposed evolutionary ancestors. Gizmodo reports, “Uh-Oh: Monkeys Make Stone Flakes That Look a Lot Like Human Tools.” According to The Hill, “New study on monkeys using stone tools raises questions about evolution.” The reason for the “Uh-Oh” and the “questions” is that if living monkeys can produce tools resembling those supposedly produced by our intelligent hominid ancestors, then many tools currently ascribed to our purported ancestors may be no such thing. From Gizmodo:

Researchers studying macaques in one of Thailand’s national parks made a surprising discovery: While cracking nuts, the monkeys make stone flakes that look an awful lot like the flakes that scientists have attributed to ancient human. The finding means that some of the material held up as the earliest evidence of hominin tool use may have actually come from monkeys and not our ancestors.

The Hill elaborates:

The Thai monkeys produced stone artifacts “indistinguishable from what we see at the beginning of the [human] archeological record — what we see as the onset of being human,” said Lydia Luncz of the Max Planck Institute for Evolutionary Anthropology, a co-author on the study.

The monkeys — long-tailed macaques — seem to have made their artifacts by accident, not by design. But in many ways, that only makes the finding more disruptive.

[…]

Ancient humans used knapping to break apart rocks to create an incredibly flexible set of tools — the earliest forms of which cannot be distinguished from the ones macaques made by accident.

That points to a possibility that could throw a wrench into the established narrative, Luncz said: that “all the conoidal flakes we find in the archaeological record — deemed to be intentionally made — could be unintentional byproducts.”

Doubts About Our “Ancestors”

Similarly Inverse reports, “Because the macaques created stone flakes by accident, Luncz and colleagues wondered if some ancient primates may have done the same — creating objects that researchers today might interpret as intentional tools.” It continues:

For the new study, the researchers compared more than 1,000 stone flakes made by macaques to ancient flakes dating back 1.3 to 3.3 million years ago. Samples came from several excavated sites in Tanzania, Kenya, and Ethiopia.

Looking at the shape, size, and markings on each flake, the researchers determined that there were very few physical differences between the samples from today and those made by human ancestors from millions of years ago.

That leads the researchers to believe it’s possible that some ancient stone flakes may have been misinterpreted as intentionally-made tools, since the macaques make such similar ones without even trying.

“Given these similarities, it may be that some flakes and flaked stones from Plio-Pleistocene contexts are derived as a by-product of percussive behaviors and may be easily misidentified as intentional products,” they write.

“All of the Same Characteristics”

Just how similar are these “tools” to the stone tools we find in the archaeological record? The technical paper reports “morphological overlap between unintentionally produced (macaque) material and those interpreted as intentional (Oldowan and Lomekwian),” and concludes, “These results show that between 30 and 70% of an Oldowan assemblage can be replaced by macaque flakes before significantly changing the central tendency of the morphological and technological parameters of the original assemblage.” A press release from the authors of the technical paper states:

[M]any of these artefacts bear all of the same characteristics that are commonly used to identify intentionally made stone tools in some of the earliest archaeological sites in East Africa.

This evidence has apparently not been well received, as The Hill reports:

That idea remains controversial in the field, however.

“You will not believe the fights we had to fight,” Luncz said.

Even calling the macaque-produced stone flakes “artifacts” was controversial because some scientists felt it implied an overlap between tool use by Homo sapiens and other primates that wasn’t justified.

‘Artifacts,’ after all, shares its root with ‘art’ and ‘artifice’ — words that suggest intention, planning and humanity.

“People were not happy with monkeys being able to create those artifacts,” she added. “And somewhere in the records of macaque and early hominid tools, there must be a difference. But right now, the diagnostic criteria we’re using can’t find one.”

A Word of Caution

But the paper offers a potential way forward:

Our results suggest that larger, more elongated flakes, with high cutting edge–to–mass ratios and more platform preparation are attributes associated with intentional flake production. However, measures such as external platform angle and platform dimensions, flake scar frequency, flake scar directionality and cortical coverage on flakes, as well as exploitation strategies and number of exploited surfaces on flaked pieces do not differ between nut cracking and intentionally produced assemblages.

But the paper offers a caution at the end, noting that previously used criteria also turned out to wrongly infer “intentional” activity:

Previous studies have relied on the aforementioned co-occurring attributes to infer intentional hominin tool production. Building on previous studies of primate flaked stone assemblages, this study shows that these criteria now occur repeatedly within multiple phylogenetically and geographically diverse nonhuman primate lineages.

This study is a potential gamechanger. As they conclude, “The results of this study demonstrate that a fundamental reassessment of how we define and identify this uniquely hominin behavior in the archaeological record is still needed.” If current criteria for inferring intelligent tool production can be wrong, it raises the specter that future studies could show monkeys and apes are capable of “unintentionally” producing other complex tools still ascribed to our supposed hominid ancestors. This could mean that a sacred evolutionary icon — apelike species acting smart and making tools — could potentially be axed (pun intended!).

To make a long story short re: Darwinism's "simple beginning"

James Tour on why the OOL is the linchpin of the design argument.

How the giraffe got its neck? :with apologies to Rudyard Kipling.

Evolution’s Tall Tale — The Giraffe Neck

Jonathan Witt

The giraffe’s neck has long been a beloved icon of evolutionary theory. According to the story, one of the giraffe’s short-necked ancestors had a slightly longer neck, which helped him reach leaves the other animals on the savannah couldn’t. This gave him a survival advantage he passed on to his offspring. Or maybe the female giraffes really dug his slightly longer neck, giving him a reproductive advantage. Same result. He passed his slightly longer neck on to his offspring. Rinse and repeat a few thousand times, and voila, the lineage ends up with 600-pound, six-foot long giraffe necks.

But the devil is in the details. An article in the journal Nature frankly characterizes the evolution of the giraffe’s cartoonishly long neck as “a puzzle”:

There should be a good reason for the extraordinary length, because it causes hardship. A giraffe’s heart needs to pump blood 2 metres up to the head, which requires a high blood pressure and management to avoid fainting or stroke. “It’s beautifully adapted to this, but it’s a big cost,” says Rob Simmons, a behavioural ecologist at the University of Cape Town in South Africa, who was not involved in the study.

One prevailing theory is that giraffes evolved longer necks to reach higher trees for food. “This is widely believed; it’s really entrenched,” says Simmons…. [But] research has shown that giraffes tend to eat from lower levels, and tall giraffes aren’t more likely to survive drought, when food competition is highest. Another idea is that giraffes evolved longer necks for sexual competition, with male giraffes engaging in violent neck-swinging fights and longer necks attracting mates…. [But] males don’t have longer necks than females.1

Fossil Phantasms

Fossils aren’t much help either. German geneticist Wolf-Ekkehard Lönnig surveyed the literature on fossils and giraffe evolution and reports that there is an abundance of fossils from giraffes and creatures said to be either giraffe ancestors or closely related to those ancestors, but what remains stubbornly absent is a smooth series of transitional fossils from short-necked to long-necked. He writes:

No continuous series of fossil links leads to the Giraffa or Okapia. “The giraffe and the okapi of the Congo rain forest are considered as sister groups, the origins of which are still not known” (Devillers and Chaline 1993, p. 247). Similarly Starck (1995, p. 999) remarks: “The ancestry of Giraffidae is disputed.” Wesson (1991, pp. 238-239) agrees with these statements about giraffe fossils, as follows: “The evolving giraffe line left no middling branches on the way, and there is nothing, living or fossil, between the moderate neck of the okapi and the greatly elongated giraffe. The several varieties of giraffe are all about the same height.”

An okapi, keep in mind, is an extant even-toed ungulate that looks not dramatically different from a large deer. Between it and the giraffe there stretches a great morphological gulf.

There was a much-ballyhooed fossil find reported in 2015 purporting to bridge that great gulf. A Live Science article, “7-Million-Year-Old Fossils Show How the Giraffe Got Its Long Neck,” promised the moon, and the lead researcher, Nikos Solounias, was only slightly more restrained. “We actually have an animal whose neck is intermediate [in length] — it’s a real missing link,” he said. But as the evolutionists behind the study later concede, they don’t even think the creature, Samotherium major, is a direct ancestor of the giraffe.

Stretching the Truth

More fundamentally, as researchers learn more and more about giraffe physiology, it’s increasingly clear that hundreds, maybe even thousands, of genetic changes would be needed to arrive at a functioning giraffe; many of the changes would need to arrive simultaneously for the creature to survive; and such big-jump changes would need to occur numerous times over millions of years.

Yes, natural selection could jump in to preserve these coordinated mutation freak events if they ever occurred, but first the freak-event mutations would have to occur.

Oxford biologist Richard Dawkins, famous for his many books defending atheism and evolutionary theory, characterizes the difference between a giraffe’s neck and that of its short-necked ancestor as relatively “slight.” Dawkins writes: “The giraffe’s neck has the same complicated arrangement of parts as the okapi (and presumably as the giraffe’s own short-necked ancestor). There is the same sequence of seven vertebrae [Lönnig contests this], each with its associated blood vessels, nerves, ligaments, and blocks of muscle. The difference is that each vertebra is a lot longer, and all its associated parts are stretched or spaced out in proportion.”2

So, how hard could it be to evolve?

Dawkins’s characterization is one a Darwin disciple could love, but never an attentive engineer, or any biologist with a working familiarity with giraffe physiology. As Lönnig puts it, Dawkins “simplifies the biological problems to a degree that is tolerable for evolutionary theory, but not realistic with regard to the biological facts.”

Giraffe Spectacular

Lönnig describes several things that must be either engineered or reengineered to arrive at a functional giraffe from a short-necked ancestor. First, giraffes, like cows and many other grazing animals, are ruminants, meaning they regurgitate a half-digested cud and chew on it before swallowing the food a second time, helping them digest tough fibrous grass and leaves. But to pull off this trick, a giraffe, with its neck as tall as a man, needs “a special muscular esophagus,” Lönnig explains. So that’s one reengineering challenge.

Lönnig gives so many more that there isn’t room for them all here. His book debunking giraffe evolution, The Evolution of the Long-Necked Giraffe, is dense and thorough. But he helpfully quotes Gordon Rattray Taylor, who concisely summarized several of the reengineering challenges in his book The Great Evolution Mystery:

Nineteenth-century observers assumed that the giraffe had only to develop a longer neck and legs to be able to reach the leaves which other animals could not. But in fact such growth created severe problems. The giraffe had to pump blood up about eight feet to its head. The solution it reached was to have a heart which beats faster than average and a high blood pressure. When the giraffe puts his head down to drink, he suffers a rush of blood to the head, so a special pressure-reducing mechanism, the rete mirabile, had to be provided to deal with this. However, much more intractable are the problems of breathing through an eight-foot tube. If a man tried to do so, he would die — not from lack of oxygen so much as poisoning by his own carbon dioxide. For the tube would fill with his expired, deoxygenated breath, and he would keep reinhaling it. Furthermore, one study group found that the blood in a giraffe’s legs would be under such pressure that it would force its way out of the capillaries. How was this being prevented? It turned out that the intercellular spaces are filled with fluid, also under pressure — which in turn necessitates the giraffe having a strong, impermeable skin. To all these changes one could add the need for new postural reflexes and for new strategies of escape from predators. It is evident that the giraffe’s long neck necessitated not just one mutation but many — and these perfectly coordinated.3

Percival Davis and Dean Kenyon cogently tease out the significance of all this:

In short, the giraffe represents not a mere collection of individual traits but a package of interrelated adaptations. It is put together according to an overall design that integrates all parts into a single pattern. Where did such an adaptational package come from? According to Darwinian theory, the giraffe evolved to its present form by the accumulation of individual, random changes preserved by natural selection. But it is difficult to explain how a random process could offer to natural selection an integrated package of adaptations, even over time. Random mutations might adequately explain change in a relatively isolated trait, such as color. But major changes, like the macroevolution of the giraffe from some other animal, would require an extensive suite of coordinated adaptations.4

A Lottery-Winning Fiend

This means that if we hold to the evolutionary story for the giraffe neck, we must go from believing that the giraffe lineage won a series of longshot lotteries over millions of years to believing that the various ancestors in the lineage each won numerous longshot lotteries simultaneously and managed to do this over and over.

To grasp the enormous difference, imagine that the President of the United States takes a winding summer trip through the American heartland and buys a state lottery ticket in each of those 45 states that has a state lottery. (Not all do.) Later that summer it emerges that every one of the lottery tickets the President bought was a jackpot winner. The President’s handlers attribute this to “dumb luck,” but you can bet that 45 state lottery commissioners will smell a rat and, if brave enough, launch an investigation. They will reasonably infer that all those wins were somehow gamed in the President’s favor — that is, were intelligently designed. There are long odds, and then there are odds so long, and so beneficial to someone, that reasonable people begin to look for other explanations.

In the giraffe’s case, a bit of reasoning goes a long way. Blind evolution doesn’t look ahead and coordinate a group of changes for some future advantage. It’s blind and must proceed by one small useful step at a time. No evolutionist, for instance, believes that a small number of mega-mutations turned a land mammal into a whale.

But what if loads of changes are needed simultaneously to successfully make a biological transition, or even just a significant step in a larger transition? We know of only type of cause with the demonstrated ability to meet such a challenge, and it isn’t dumb luck and natural selection. The engineering marvel that is the giraffe, long neck and all, was intelligently designed.

On humanity's privileged homeworld.

The Problem of Earth Privilege: It’s Getting Worse

Evolution News

On a new episode of ID the Future, astrobiologist Guillermo Gonzalez, co-author of The Privileged Planet, provides a rapid survey of some of the growing evidence that Earth is finely tuned in numerous ways to allow for life. He draws a helpful distinction between local fine-tuning and universal fine-tuning. And he tells us about the many extra-solar planets astronomers have discovered in recent years and how all that new data continues to undermine the misguided assumption (encouraged by the misnamed “Copernican Principle”) that Earth is just a humdrum planet. Far from it, Gonzalez argues. Download the podcast or listen to it here

The mind of a slave with the power of a king?

Russia's man of steel: then and now.

Why we will always have the poor with us?

Monday 13 March 2023

Yet more on separating artificial from actual intelligence.

Depths of Design: Moving Pixels

Nathan Jacobson

Editor’s note: This is Part II of a series. Look here for Part I. Cross-posted from Mind Matters News.

As with traditional art, computer animation has followed a similar trajectory toward realism. Early animations were as crude as rock carvings, limited as they were by relatively weak CPU’s, as yet undeveloped rendering engines, and a lack of digital artists. The monochromatic Space Invaders was endlessly playable, as were the whirling, 8-bit dervishes of Centipede and the bubble-gumless, three-dimensional spaces of Duke Nukem. But the graphics were a million pixels from virtual reality.

Now decades and countless iterations in, with enormous human capital and ingenuity invested in motion graphics and GPUs, the optics are indeed seductive, convincing, and engrossing. Head phones on and eyes glued to the screen, it’s easy to get lost in the sprawling world and epic narrative of Mass Effect, or to feel that you are attacking the Ludendorff Bridge at Remagen with an M1 Garand rifle, your rag-tag squad assisting. With each iteration, game developers make strides in simulating the unique recoil of each gun model, the aural pattern of explosions near versus far, the game physics of spilt blood and bent grass underfoot, and the fraying edges of a soldier’s ribbon bars, specific to rank and nation.

Bravo! Charlie!

It’s amazing. It’s an adrenaline rush. And it’s all artifice. These animations are becoming ever more realistic, but not in the least bit more the kind of real thing which they represent.

In addition to cosmetic advances, motion capture technology has progressed by leaps and bounds. Painstaking attention to plotting our distinctive expressions and gaits has greatly increased the appearance of natural movement. Ever since Andy Serkis so convincingly gave life to Gollum, recordings of humans in motion have supplied the scaffolding for countless characters.

In animation … everything is fabricated. … Every moment. Every scratch and look. Everything is a discussion. There are no gifts. There are no happy accidents … It was useful having the live action performance reference. We’d pull them up in front of the animators and say, look at what’s happening here. Little twitches underneath the eyelid, little things that are involuntary became very important.

GORE VERBINSKI, “RANGO BEHIND THE SCENES: BREAKING THE RULES”

One of the joys as a viewer is having that dawning recognition of a familiar actor who has been reincarnated as Puss in Boots, Shrek the ogre, or Mator the tow truck. The idiosyncrasies and tics of the human originals are prized source material for the animators. So, Kristen Bell’s signature phrase — “Wait, what?” — and her habit of biting her lip is mirrored in Anna of Arendelle. Dwayne “The Rock” Johnson’s brow wave personalizes Maui. Although these beloved characters are singing and dancing and joking along, like Mona Lisa, the image is a mirror image. It has no life of its own.

No Breaths, No Sacrifices

Though we are moved by these pixels on the screen, our digital allies and enemies breathe no breaths, make no sacrifices, feel no lonely deaths. Whether crying, dying, or respawning, they are as lifeless as a dead pixel and vacuous as a wireframe.

Because the textures that skin them and algorithms that animate them are more sophisticated, it is tempting to think that the ducking and evading Juvies, Pouncers, and Swarmaks of Gears of War are more intelligent than Pac Man’s nemeses: Blinky, Pinky, Inky, and Clyde. One might think that whereas the ghosts that haunted Pac Man had a wisp of personality, the villainous grunts of a modern first-person shooter have a measure more. Surely, in some future game, they’ll reach self-realization. Game AI will continue on this trajectory and surpass human intelligence, just as Watson bested Kasparov. But the truth is, none of these avatars possess any inherent intelligence whatsoever. Every human instinct therein is an extension of a game developer’s forethought. The characters are thoughtless.

We’ve erected this elaborate system of gears and pulleys using electronic nodes. The number of these levers that we can fit on a circuit is mind boggling. At the push of a button and the tilt of a joystick, these systems are able to reenact remarkable routines that the human programmers have strung together. But as the less exhaustively routinized NPCs (Non-Playable Characters) in the game betray, if the programmer hasn’t yet written the routine, the character will be left kicking blindly into a wall.

A financial pandemic?

Iron vs. Bronze?

File under "well said." XCII

"There are some ideas so absurd that only an intellectual could believe them."

George orwell

Photosynthesis and Darwinism's quest for a simple beginning

Brand new study on the evolution of photosynthesis.

Cornelius G Hunter

How exactly is evolution a fact when, as the number two science journal in the world put it, “How and when Cyanobacteria evolved the ability to produce oxygen through photosynthesis is poorly understood”? Or as evolutionist Robert Blankenship admitted, “The whole question of the origin of cyanobacteria has long been a mystery because they kind of just appeared out of the tree of life with this very advanced capability to do oxygenic photosynthesis without any apparent forebears.”

If the cyanobacteria that do photosynthesis “just appeared” with this “very advanced capability” and “without any apparent forebears,” and if how and when they evolved photosynthesis “is poorly understood,” then just how is it that evolutionists are so certain that evolution is a fact?

What am I missing here?

It is not as though photosynthesis is a tangential capability or a minor event in the so-called “evolutionary history” of life. As the leading science writer Charles Q. Choi put it, “One of the most pivotal moments in Earth’s history was the evolution of the photosynthetic life that suffused air with the oxygen on which virtually all complex life on the planet now depends.”

Nor is it as though photosynthesis is a simple capability, in no need of explanation for how it possibly could have arisen by random mutations. Anyone who has studied photosynthesis even superficially knows it is incredibly complex. And for those who have studied in greater detail, it only gets worse. The molecular machines and their exquisite, finely-tuned, functions are truly amazing. It doesn’t “just happen.”

Even evolutionists, who are always trying to explain how easy it would be for biology’s wonders to arise by happenstance, admit to the complexity of photosynthesis. As Blankenship put it, photosynthesis is a “very advanced capability.” Similarly, Woodward Fischer agreed that the evolution of photosynthesis would be “very challenging”:

It took a substantial unfolding of evolutionary time before oxygenic photosynthesis developed, perhaps because, as we know, it was a very challenging biochemistry to develop.

Nor is it as though the evidence we do have suggests any kind of a straightforward evolutionary development of photosynthesis.

If evolution is true, then we must fire up fresh rounds of evolution’s fake news, including incredible convergences and massive horizontal, or lateral, gene transfer and fusion. Round up the usual suspects:

The phylogenetic relationships of these prokaryotes suggest that the evolution of aerobic respiration likely occurred multiple times. This, along with evidence that the modern photosynthetic system apparently arose through the lateral gene transfer and fusion of two photosynthetic systems

This is absurd. Convergence, horizontal gene transfer, and fusion are all made up mechanisms to fix the problem that the scientific evidence contradicts evolutionary theory. This isn’t making sense.

But it gets worse.

Not only are evolutionists forced to draw from their army of phony explanatory mechanisms, but they are left with the proverbial “missing link.” The problem is, from where did the photosynthesis come? It couldn’t have come from the purported common ancestor via descent, and it “just appeared” with this “very advanced capability.” So evolutionists have to usher in their horizontal gene transfer story.

But from where?

From where did the incredible battery of genes—that would just happen to team up and create the all-time incredible capability of photosynthesis—come? Conveniently for evolutionists—and here’s one of the beauties of being an evolutionist—they can never know. Like Flew’s gardener, evolutionists are certain that some “missing link” organism somehow had photosynthesis up and running, or just happened to have the crucial genes just lying around, but we likely will never observe that organism because it has long since become extinct.

Oh how convenient. Some mysterious organism did it. We’ll never know just how photosynthesis evolved because the organism where it happened has long since gone extinct, billions of years ago. Since then, it just luckily passed the technology around for other organisms to have, such as the cyanobacteria. Choi and Fischer explain:

The fact that Oxyphotobacteria possess the complex apparatus for oxygenic photosynthesis while their closest relatives do not suggests that Oxyphotobacteria may have imported the genes for photosynthesis from another organism via a process known as lateral gene transfer. It remains a mystery what the source of these genes was, “and because it happened long ago, it's pretty likely that the group may actually have gone extinct,” Fischer said.

Can I be an evolutionist too?

Photosynthesis is crucial to life and incredibly complex, evolutionists haven’t a clue how it could have evolved, it doesn’t fit the evolutionary common descent model and “just appeared” without a hint of where it came from, evolutionists are forced to make up a long just-so story to try to explain it, their story can’t be falsified because the origin of photosynthesis has long since disappeared, and on top of all this, evolutionists insist their theory is a fact, beyond all reasonable doubt.

This is hilarious. It is like something out of a Monte Python skit. Evolution loses every battle, but manages to win the war because, after all, it’s right.

How the U.S went from king George to president George.

Sunday 12 March 2023

Molecular biology and the edge of Darwinism.

Darwinism's metaphysics?

Octopuses troll Darwinism,?

Massive RNA Editing and the octopus.

Cornelius G Hunter

Click the video to see an octopus mimic algae. Octopuses have an amazing ability to sense and mimic the coloration, shape, and texture of their surroundings. They literally “blend in” as the video illustrates. Note how the audience appropriately responds at the end of the video. You can read more about this amazing ability here. The idea that such mimicry evolved is unlikely. The problem is that evolution’s random mutations are not up to the task. Too many of them are required. And no, natural selection doesn’t make it happen. Selection cannot coax, cajole, persuade or otherwise sweet talk mutations into happening. Selection is simply a label for what happens afterwards: in a word, harmful mutations are eliminated. Indeed, evolution co-founder Alfred Wallace thought the term “natural selection” should be dropped altogether, because it really doesn’t do anything and so is misleading. According to evolutionary theory, selection can have no forward influence on mutations. It cannot cause helpful mutations to occur—no teleology. But helpful mutations are what is needed, and in spades. The octopuses amazing mimicry needs both to sense the surrounding environment, and then to perform its amazing blending ability. Sensing without blending is useless. And blending without sensing is useless. You need both, and that is beyond the reach of random mutations. It isn’t going to happen. In fact, this same problem applies to both sensing and to blending, taken individually. This is because a large number of mutations are required to construct either one. And to add insult to injury, research at the molecular level is just making things worse.

Evolution is supposed to be caused by random mutations in the genome. Mutations in segments of the DNA where genes reside may change the gene product, such as a protein. But organisms have a way of creating such genetic changes on the fly, and it is called RNA editing. After a gene is transcribed, the RNA copy can be edited, for example by altering a single nucleotide. This RNA editing, or recoding, is done by a protein machine.

RNA editing is typically not very common. But in recent years, high levels of recoding have been found in the octopus, and new research is adding to the story. In the octopus and allied species, the majority of RNA transcripts are found to have an edited nucleotide and, importantly, they are often conserved across the species.

In other words, whereas in most species that have been studied there is relatively little RNA editing, in the octopus and its closest neighboring species there is extensive RNA editing and the recoding sites are often conserved across these neighboring species. Also the DNA flanking sequences, on either side of the recoding sites, tend to be conserved across these neighboring species.

This evidence demolishes evolution. Here are seven reasons why.

First, why would these few species suddenly have such an escalation of RNA editing? Evolution has no explanation why this mechanism would suddenly take on such importance in this small group of species. As one evolutionist admitted, “Most organisms have very few functional [editing] sites in coding regions. This is why we find it so unusual and surprising that in squid, octopus, and cuttlefish, we see exactly the opposite.”

Second, the flanking sequences are difficult to evolve. These consist of hundreds of nucleotides, and once transcribed they need to form RNA secondary structures which the RNA editing protein recognizes. These sequences can be highly specific. In some cases even a single nucleotide substitution can abolish RNA editing. In other words, evolution’s random mutations must somehow luckily find these specific sequences. Without the right secondary structure, RNA editing is greatly slowed. But at the start of the search evolution is most likely nowhere close to having a sequence that will form the right secondary structure. And it would be unlikely for a random mutation to make the difference. In other words, multiple mutations are required before even a hint of success is obtained. And of course this all must occur while not disrupting any preexisting messages the sequence carries. This is highly unlikely. And yet this must occur not just once, but twice, on both sides of the recoding site. And furthermore, this must occur not just twice but, err, hundreds of thousands of times, at the many different recoding sites. It’s not going to happen.

Third, these long conserved flanking sequences, hundreds of nucleotides long on either side of the recoding sites, imply evolution loses the ability to evolve.

Fourth, according to evolutionary theory the fact that these recoding sites are conserved across different species means that they are adaptive. In other words, they improve fitness. This massive RNA editing is a feature, not a bug. But given that there are many thousands of these recoding sites, evolution faces a combinatorial explosion. Not only is there an astronomical number of different combinations of RNA editing actions, but for any given gene there is the question of which RNA transcripts to recode? Unless a very simple solution is found, this combinatorial explosion is way beyond the meager resources of evolution’s random mutations.

Fifth, undoubtedly RNA editing is used to respond to changing conditions. Recoding has been shown, for example, to affect potassium channel function. But if RNA editing is a mechanism for response to changing conditions, then there must be signaling instructions that tell the RNA editing protein when and where to perform its editing. But the origin of that signaling system would require a great many mutations. Again, that likely would be beyond evolution’s resources.

Sixth, this massive RNA editing capability will not function properly without its many components in place. You need the recoding site, the flanking sequences, the RNA editing protein, and the signaling system. It will do no good to have the proper DNA sequences without the editing protein, or both of those without the signaling system, or the signaling system without the flanking sequences. In other words, there are multiple, interdependent components which all need to be in place for this RNA editing capability to function.

Seventh, it is silly to think evolution could find the right recoding sites. The problem is that, even if this RNA editing capability could evolve and all the different interdependent components could fall into place, it would not likely pick the right recoding site. Simply put, each evolutionary experiment would require a monumental effort and time span before the needed feedback could be obtained about whether or not the recoding site was a good one. Evolution would need to evolve the recoding site and the flanking sequences before natural selection could act. Undoubtedly most recoding sites would not help. They might be neutral, or they might be harmful. But they would not help to construct the adaptive RNA editing capability we find in the octopus. Therefore this evolution search problem is astronomically difficult. It needs to search through a large number of mostly useless candidate recoding sites, and each try would require an eternity. But it gets worse, for it is likely that any single recoding site isn’t going to accomplish much all by itself. There are many thousands of these recoding sites, and undoubtedly multiple recoding sites are needed to work together. So even if evolution could somehow accomplish the search for a single recoding site, which is astronomically difficult, it likely would not improve fitness by itself.

One look at the video above and anyone can see evolution is not a good theory. This is just common sense. Not surprisingly, the science confirms this common sense. In fact, the science doubles down, many times over.

There simply is no excuse for continuing to thinking evolution created the species. There are just too many contradictions, too many absurdities, too many ridiculous examples showing evolution to be a complete failure.

So it shouldn’t be too surprising that all of this leaves evolutionists a bit shell-shocked. They can manage little more than the usual Aristotelian teleology. As one headline explained, “ ‘Smart’ cephalopods trade off genome evolution for prolific RNA editing.” Trade off genome evolution for prolific RNA editing? That is teleological. Likewise, an evolutionist explained, “Mutation is usually thought of as the currency of natural selection, and these animals are suppressing that to maintain recoding flexibility at the RNA level.” Again, more teleology. The infinitive form tells all.

The research paper explains that these species “invented” the massive recoding. Invented? The paper also turns these species into intelligent agents:

..... Why would the coleoids choose to alter genetic information within RNA rather than hardwire the change in DNA?

Choose to?

This is absurd.

Evolution has been demolished by science. We are far, far beyond any kind of controversy. While evolutionists want to claim they do legitimate science, the empirical evidence has long since left the station. Evolution has been utterly demolished.

Yet more on Darwinism as secular superstitition

New evolution book reviewed by Hans Madueme.

Cornelius G Hunter

If you want to understand evolutionary thought just read the literature. Charles Darwin accurately characterized his 1859 book on evolution as “one long argument.” That argument was based on several popular religious beliefs leading to faulty science. For example, throughout the volume Darwin’s ideas rely on a popular religious doctrine called utilitarianism, and in Chapter Six Darwin explicitly states that his theory would absolutely fail without it.

Ever since Darwin, little has changed. One after the other, evolutionists have attempted to explain and prove Darwin’s idea. And one after the other, they have simply confirmed that evolutionary thought is not a scientific theory in the normal sense but rather is, at its core, a religious idea with little regard for the science. It really is nothing more than the ancient Epicureanism, inserted into modern science. Consider the latest entry, Adam and the Genome, a brand new Brazos Press title authored by Dennis Venema and Scot McKnight.

In the tradition of the evolution literature, the first part of the book presents a long list of arguments for why we should believe the biological world arose by evolution—a combination of chance and natural law. The second part of the book, as the title suggests, addresses the question of Adam and Eve. Simply put, the book argues that Scripture, read rightly, never did point to a historical Adam in the first place. This makes Scripture consistent with evolution’s call for humanity to begin as a relatively large population.

But this reading of Scripture is influenced by evolution. As McKnight explains, his approach accepts “the reality of genetic evidence supporting a theory of evolution”. [173] But, in fact, there is no such “reality.” The genetic evidence does not support evolution—quite the opposite.

Religious beliefs mandating evolution are what led to today’s theory of evolution, not empirical scientific findings. And now, new scientific observations (such as genetics) are interpreted according to evolution. The observations are theory-laden. Furthermore, with the broad acceptance of evolution, theologians such as McKnight are telling us we need to adjust our religious understandings in light of the “reality” of the scientific evidence.

This is what computer scientists refer to as Garbage-In, Garbage-Out (GIGO). It is little wonder McKnight and many others are calling for this “new” understanding of Scripture, for that “new” understanding is centuries old, and is what mandated evolution in the first place. What goes around comes around.

Unfortunately the myth that evolution is a scientific no-brainer, a given, a fact, and on par with gravity and the round Earth, is difficult to dispel. The powerful religious ideas mandating evolution have led to the myth that evolution is legitimate and compelling science.

For example, in his review of Adam and the Genome, Hans Madueme rightly explains that the history of science should give us pause regarding evolution. Too often scientists have had high confidence in ideas that later would be discarded. Madueme accurately detects such high confidence in evolutionary thought, as exemplified in Adam and the Genome.

Unfortunately Madueme also gives high marks to the science presented in the book. According to Madueme, it “unpacks the genomic evidence for evolution and common ancestry,” and even “skeptical readers will come away impressed at the deep explanatory power of evolutionary theory.” Impressed?

And what exactly is this “deep explanatory power of evolutionary theory” to which Madueme refers? Well, err, Madueme fails to mention any for he “skipped over most of the details.” But it is precisely in those details where the evidences and arguments fall apart. We have already seen that the book makes erroneous arguments that the fossil evidence and echolocation support evolution (here and here). In fact, as we saw, both these evidences and arguments, once stripped of the religion, far from supporting evolution, severely contradict the theory.

In my next post I will look at another one of the book’s arguments involving pseudogenes. What we will find, again, is not “deep explanatory power of evolutionary theory” but exactly the opposite.

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Thursday 16 March 2023

Peer-Reviewed Paper Cites Stephen Meyer to Critique Darwinian Evolution

Peer-Reviewed Paper: “Neo-Darwinism Must Mutate to Survive”

More Jobs for “Junk” DNA

Mapping the Pleiotropic Network of Human Cells

Wednesday 15 March 2023

Tuesday 14 March 2023

Monkey-Made “Tools” Cast Doubt on High Intelligence in Early Hominids

Evolution’s Tall Tale — The Giraffe Neck

The Problem of Earth Privilege: It’s Getting Worse

Monday 13 March 2023

Depths of Design: Moving Pixels

Brand new study on the evolution of photosynthesis.

Sunday 12 March 2023

Massive RNA Editing and the octopus.

New evolution book reviewed by Hans Madueme.

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