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.

Saturday 11 March 2023

Your AI companion maybe all ears but don't ask him for a hand?

For AI, Human Hands Are Exceptional…For Now

Peter Biles

AI image generators like Midjourney or DALL-E are generally adept at capturing the accuracy of the human form. The concerns over copyright, job infringement, and general degradation of the visual arts via such AI are ongoing concerns for many artists and practitioners. However, a new New Yorker article by Kyle Chayka identifies a noticeable flaw in AI artwork: human hands.

Missing the Big Picture

Chayka recalls an art class where he was asked to draw his own hand. It’s an assignment for beginners, and as behooves a novice, tempts the artist to focus more on the specific contours of the hand instead of the overall structure and form. The forest gets lost in the trees, so to speak. AI is guilty of a similar flaw. In many artificially contrived images, the hands come up gnarled, disfigured, or otherwise anatomically incorrect. Some of them are minor yet noticeable mistakes upon investigation. Others are repulsive, looking alien and mutant. Chayka writes,

A generator can compute that hands have fingers, but it’s harder to train it to know that there should be only five, or that the digits have more or less set lengths in relation to one another. After all, hands look very different from different angles. Looking down at my own pair as I type this on my laptop keyboard, my fingers are foreshortened and half obscured by my palms; an observer wouldn’t be able to determine their exact X-ray structure from a static image.

KYLE CHAYKA, THE UNCANNY FAILURE OF A.I.-GENERATED HANDS | THE NEW YORKER

Hands are hard for computers to replicate given the many angles they can rest in and their general complexity. The result isn’t pretty.

Chayka thinks that someday we will look back on this flaw with wistful nostalgia. Eventually, AI will learn the form of the human hand and no longer be a novice in Art 101. We will then wish for the days when it produced a bad hand and could remember how a real person could do it more justice. For now, though, AI’s failure in this arena shows a gap in its capacities and highlights an area in the arts still best left to human creators.

Art and Human Bonding

This week, professor of economics Gary Smith wrote on the importance of critical thinking and writing skills for students. ChatGPT, he says, tempts students to outsource their cognitive brainpower to the machine, but notes that this is setting kids up for failure. In addition, ChatGPT will fail to perform complex written tasks that are best left to humans. He also notes that “writing bonds us,” commenting,

When I tell you what I think, you learn more about me. When you respond, I learn more about you. We learn about our similarities and differences and, if done politely, become closer. All of that is lost if our written communication becomes my LLM chatting with your LLM.

GARY SMITH, LEARNING TO COMMUNICATE | MIND MATTERS

I wonder if Smith’s wonderful observations here might translate into the issue of AI “art.” Both writing and drawing depend acutely on observation. We have to pay attention to the world around us before we can link together a coherent sentence or draw a glass vase sitting on the kitchen counter. In addition, what if art, like writing, “bonds” us? Isn’t that, after all, one of art’s

principal purposes? Even if Midjourney and DALL-E master the human hand and its images become indistinguishable from the best digital art done by humans, it lacks a human genesis. It fails to “speak” to us.

Communicating with a Live Intelligence

The essayist Becca Rothfeld frames the problem in terms of whether ChatGPT could write a novel, writing brilliantly in this piece from The Point,

Indeed, we read novels, rather than textbooks or user’s manuals, because we are not in the business of extracting propositions but in the business of effecting intimacy with another live intelligence. Literature is not (only) a conveyer of information but a locus of communication, and we cannot communicate with an inanimate mechanism, whirring its insensate way through text it does not even comprehend. For this reason, we could only ever really care about words that have been deliberately placed on a page by another person. Books, the German Romantic novelist Jean Paul once wrote, are “thick letters to friends.” Who would want to correspond with the void?

BECCA ROTHFELD, WHAT CHATBOTS CAN’T DO | THE POINT MAGAZINE

In Rothfeld’s estimation, the technical abilities of AI don’t lay a foundation for its artistic and linguistic value. We don’t go to books and art to ingest information formulated by “the void,” but, as she so eloquently puts it, to commune “with another live intelligence.” The more we value literature and art created by humans, for humans, the more we can discern AI’s proper use and purpose.

Before victory,there must be trials and testings.

Scammed by the crown?

The warmth of solitude?

On the missing mass: Molecular biology edition?

Richard Sternberg on the Trail of the Immaterial Genome

Evolution news

On a classic episode of ID the Future, Dr. Richard Sternberg, research fellow at Biologic Institute, speaks on his mathematical/logical work showing the difficulty of identifying genes purely with material phenomena, and that DNA doesn’t have all that’s needed to direct the development of organisms. The math, he says, is even showing gaps in the computability of what happens in the cell, which could help shed light on how machine-like organisms are or are not, how evolvable they are, and whether artificial life is possible. Download the podcast or listen to it here

All noise no signal?

What the Big Bang Theory Tells Us About Creation

Rob Sheldon

Writing at Big Think, University of Rochester astrophysicist Adam Frank informs us, “The Big Bang says nothing about the creation of the cosmos.”

We are often told that the Big Bang is a theory of cosmic creation — that it tells us how the Universe was created out of nothing and went on to evolve into all the galaxies, stars, and planets. The problem with that characterization is that only the second part of it is true. Yes, what we call the Big Bang is a theory of cosmic evolution. But the Inflationary Universe standard model that guides cosmology says nothing about cosmic origins. The birth of space, time, matter, and energy is simply not there.

While strictly true, that is a bit misleading. It’s like saying that evolution has nothing to say about the origin of life (OOL). That’s what Ernst Mayr said anyway. But it does. Evolution says that the first life began with a very, very simple cell. And everything evolved from there. The theory of evolution does not say that life came from a primeval pair of humans, for example. Simply by accepting the theory, one excludes many, many creation myths about origins.

In the same way, simply by accepting the Big Bang, many origin stories are excluded. The universe did not begin with a cosmic snow globe, or an accident at the CERN accelerator. It had to begin with Georges Lemaître’s “Cosmic Egg.”

If one thinks that OOL is constrained by being forced into an evolutionary theory, then one could at least argue that the origin of the universe is constrained by being fitted into a Big Bang theory.

Friday 10 March 2023

scams as WMD?

A paper fortress falls?

Transcending biology?

Canadian masters athletics ratifies first national record by a trans female.

Running Magazine Canada

In February 2022, at an indoor meet at Toronto’s York University, Tiffany Newell of Welland, Ont., ran 18:02.30 over 5,000m, breaking the Canadian W45-49 record by six seconds. That record was recently ratified by Canadian Masters Athletics (CMA), under the rules and regulations of World Masters Athletics (WMA); it’s the first time a Canadian record was set on the track by a trans woman.

Newell, a former soccer player and triathlete, began her transition in 2017, but did not begin competing until she completed her transition in 2020 and her testosterone levels matched World Athletics’ current transgender athlete’s policies (WMA follows the rules of the sport set by its worldwide governing body, World Athletics).

The World Athletics policy states that to be eligible for female competition, transgender athletes must follow three guidelines:

1) provide a written and signed declaration, in a form satisfactory to WA Medical Manager, confirming their gender identity is now female; however, athletes need not have sought or obtained legal recognition of their gender identity or changed the sex marker on official identification (i.e. passports or drivers license).

2) demonstrate to the satisfaction of WA officials “on the balance of probabilities” that the concentration of testosterone in their blood serum has been less than 5 mol/L continuously for a period of at least 12 months (WA’s average range for serum testosterone in males is 7.7-29.4 mol/L; the average for females is 0.2-1.68 mol/L).

3) transgender athletes must keep their serum testosterone concentration below 5 mol/L to maintain eligibility and compete in the female category.

Newell has had some success in her past two seasons. She won a silver medal at the 2021 Canadian XC Championships in the masters 8K and finished second at the 2022 Hamilton Marathon (2:55:57).

Athletics Ontario and Athletics Canada currently offer two gender choices on their annual membership application (male or female), and they do not check the selection unless there is a national record application involved. The member lines up and competes in the gender category that they select.

The inclusion of transgender athletes in sports became a public debate when U.S. collegiate swimmer Lia Thomas began to break NCAA records. Thomas competed on the University of Pennsylvania’s men’s swim team from 2017 to 2020 and the women’s swim team from 2021 to 2022. In March 2022, she became the first openly transgender athlete to win an NCAA Division I national championship in any sport, winning the women’s 500-yard freestyle event.

As a result of Thomas’ success, swimming’s world governing body World Aquatics (known as FINA), voted to restrict the participation of transgender athletes in elite women’s competitions and is working to establish an ‘open’ category in some events as part of its new policy.

World Athletics announced shortly after FINA’s decision that it would review its transgender eligibility policies after swimming passed new rules that restrict transgender participation in women’s events in June 2022.

World Athletics president Sebastian Coe said to Insider that when it comes to transgender athletes, he believes in prioritizing fairness over inclusion. “If you pushed me and said I had to choose between fairness or inclusion, I will always lean towards fairness, because that’s what sports have to be based on.”

Newell thinks there are pros and cons to the open category: “The policy makes sense for non-binary athletes, but I don’t feel comfortable racing against men. It categorizes me in the sex I am not identified as. I am a woman, and I feel most comfortable racing against women or other transgender women. I believe an open category can work if athletes can continue to race against athletes of the same gender.”

Waiting for Darwinism?

Fossil Friday: A Waiting Time Problem for Feathers

Gunter Bechly

This Fossil Friday features a beautiful fossil feather from the Lower Cretaceous Crato limestones of northeast Brazil, which are about 115 million years old. I photographed this fossil at a German trader collection in July 2008. The feather with preserved color pattern could have belonged to a primitive bird or a feathered theropod dinosaur, which coexisted at this time in Earth history. Actually, the origin of pennaceous feathers represents another striking example of the waiting time problem as an obstacle to neo-Darwinian evolution. The rich fossil record of the dinosaur-bird transition shows that there are only a few million years available for the transformation of hair-like dino-fuzz into real bird feathers. This window of time corresponds to only about the average longevity of a single species, but has to accommodate the origin and fixation of multiple coordinated mutations to allow for the formation of vaned feathers, which are considered the most complex integumental structures in the animal kingdom.

Mathematical calculations based on mainstream population genetics strongly suggest that this time interval is much too short for such a transition to be plausibly explained with a blind process of natural selection acting on random mutations. Birds may well have descended from small bipedal dinosaurs, but this transition arguably required the input of very specific new genetic information that had to come from somewhere. Wherever you look in the history of life you stumble upon overwhelming evidence for design.

The highest cliffs in natural history's fitness landscape?

New book: New proteins evolve very easily.

Cornelius G Hunter

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.

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Sunday 12 March 2023

Massive RNA Editing and the octopus.

New evolution book reviewed by Hans Madueme.

Saturday 11 March 2023

For AI, Human Hands Are Exceptional…For Now

Richard Sternberg on the Trail of the Immaterial Genome

What the Big Bang Theory Tells Us About Creation

Friday 10 March 2023

Fossil Friday: A Waiting Time Problem for Feathers

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

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