A functional protein ab initio would necessitate a miracle?

 To Create Functional Proteins, Evolution Would Need a Miracle

Brian Miller

Theologian Rope Kojonen claims that God designed the laws of nature, which then gave rise to “fine-tuned” preconditions and smooth fitness landscapes. He says, among other things, that these conditions allow proteins to evolve by natural processes. Is he right?

At Evolution News, philosopher Stephen Dilley has already written two articles in a series (here) introducing an evaluation of Kojonen’s argument. Dilley summarized his contribution to a review article he wrote with Casey Luskin, Emily Reeves, and myself titled “On the Relationship Between Design and Evolution,” in the peer-reviewed journal Religions. In the article we critique Kojonen’s book The Compatibility of Evolution and Design, which argues that evolutionary theory can be reconciled with the belief that life demonstrates evidence of design. Dilley commended the book for the sophistication and comprehensiveness of its philosophical arguments. 

However, Dilley noted that the viability of Kojonen’s thesis depends on the scientific details. Even though the proposal is primarily a philosophical analysis, its strength or weakness hinges largely upon empirical evidence. As we state in our article:

It is true that KEBDA [Kojonen’s evolution-friendly biological design argument] is a philosophical argument. And, of course, the conceptual and epistemological elements of the argument are important. But some philosophical arguments also depend in part upon scientific evidence. In this case, much depends on whether there is a good case for fine-tuned preconditions and suitable fitness landscapes (as Kojonen envisions them). Indeed, Kojonen situates design precisely in those fine-tuned preconditions which yield smooth fitness landscapes that allow evolution to succeed. His case for marrying design with evolution therefore depends on the existence of this fine-tuning. So, it is crucial to assess whether this fine-tuning is real. And this question can be assessed scientifically: are fitness landscapes smooth? Are there open pathways between functional proteins, for example? Or are there impassible barriers between such proteins?

Thus, to assess Kojonen’s conception of design (and its compatibility with evolution) involves careful empirical analysis of “preconditions” and fitness landscapes. We examine Kojonen’s account of these phenomena, especially his claim that preconditions and landscapes are set up to allow proteins to evolve.

Kojonen’s Argument

We summarize Kojonen’s argument as follows:

To his credit, Kojonen acknowledges that the weight of empirical evidence affirms that functional proteins are often exceptionally rare — an exceedingly small percentage of amino acid sequences in sequence space fold into complex three-dimensional structures that can perform biological tasks (Kojonen 2021, pp. 119–20). (Sequence space is the multidimensional map of all possible amino acid sequences.) Finding a viable protein sequence is akin to finding a needle in a haystack. Yet Kojonen then argues that protein rarity is not a barrier for evolution because functional proteins are sufficiently close to each other in sequence space such that one protein could plausibly transform into another. He argues that, because of the fine-tuning of natural laws, there are otherwise unexpected functional pathways through sequence space to link up functional amino acid sequences such that one protein sequence could traverse to another through sequence-space via evolutionary mechanisms. Proteins might be rare, but they are not isolated. There is a proverbial cluster of needles lumped together in the haystack: when one is found, another is close at hand.

Andreas Wagner’s Contribution

Kojonen justifies this assertion by citing the research of Andreas Wagner and his team. Wagner claims to have demonstrated that every protein can evolve into another protein through a limited number of mutations. In addition, every protein in biology is interconnected through a continuous series of traversable steps.

We respond as follows:

Yet Wagner’s research is significantly limited. In particular, Wagner never directly studied the feasibility of one protein evolving into another. Instead, he compared the metabolic pathways of different organisms and identified enzymes (a type of protein) that are present in multiple pathways, and he also identified enzymes that are missing (Rodrigues and Wagner 2009). In addition, Wagner studied how mutations can change the regulatory regions of proteins to alter when (and to what extent) proteins are expressed (Aguilar-Rodríguez et al. 2017, 2018). Wagner argued that such changes could direct proteins to enter or leave metabolic pathways. But he did not study the more fundamental question of the plausibility (or implausibility) of the evolutionary origin of proteins in the first place. 

To be sure, Wagner has performed notable research that bears some (limited) relevance on protein evolvability. For example, in addition to the studies above, he surveyed numerous proteins’ relative locations in sequence space (Ferrada and Wagner 2010). He identified which proteins with the same structures perform different functions and which functions could be performed by proteins with different structures. He also tallied the functions performed by proteins in pairs of local regions in sequence space, noting these regions’ specific sizes and distances from each other. In addition, he mapped the percentage of functions performed in paired local regions as a function of the regions’ size and separation (i.e., amino acid differences). Based on this analysis, Wagner extrapolated the conclusion that mutations could change a protein (with a particular function) into another protein (with a different function) in the same region. In Wagner’s view, this allowed proteins to evolve in organic history. Yet again, he did not actually empirically demonstrate that such transformations were ever possible. Instead, he simply mapped interesting correlations between protein sequences, functions, and structures.

In fact, Wagner’s own research suggests that protein evolution is exceedingly difficult. He acknowledged, for example, that many proteins correspond to extremely rare sequences. Moreover, he identified highly separated regions of sequence space where the proteins in the different regions possessed different structures and performed different functions. This observation suggests that many proteins are not simply rare but also isolated — they are strikingly different from all other proteins in distant regions of sequence space. Wagner did not demonstrate that a series of short steps (or smooth evolutionary pathways) connect these distinct types of proteins. Even if mutations might transform some proteins into other close-at-hand proteins — which Wagner did not show — his own data strongly indicate impassable chasms between many other types of proteins. To borrow Wagner’s metaphor: many proteins appear to be separated from each other like stars in the universe.

The State of the Field

We then describe how research by leading experts in the field of protein evolution reinforces the view that distinct proteins are so isolated from each other that one could never evolve into another. From an article referencing the late Dan Tawfik:

“Once you have identified an enzyme that has some weak, promiscuous activity for your target reaction, it’s fairly clear that, if you have mutations at random, you can select and improve this activity by several orders of magnitude”, says Dan Tawfik at the Weizmann Institute in Israel. “What we lack is a hypothesis for the earlier stages, where you don’t have this spectrum of enzymatic activities, active sites, and folds from which selection can identify starting points. Evolution has this catch-22: Nothing evolves unless it already exists.” (Mukhopadhyay 2013)

We also reference a lecture by Tawfik where he states that proteins can only be modified to the point where their structure does not significantly change. He describes how different protein structures appear completely isolated from each other, and biologists have zero knowledge of how they emerged. The vast preponderance of the evidence indicates that novel complex proteins could never have evolved through an undirected process. This conclusion completely overturns Kojonen’s thesis about the compatibility of evolution and design. 

So, Kojonen’s model of design is empirically testable: are preconditions fine-tuned and fitness landscapes smooth such that proteins can readily evolve? Or does the empirical data indicate that fitness landscapes are not smooth and that distinct proteins are isolated from each other? As we show in our article, there is good evidence for the latter view. If we are correct, then Kojonen’s account of design is mistaken. This severely damages his attempt to harmonize “design” with “evolution.”

How about we just stick to the plain reading of the text?

 1John ch.4:12NIV"No one has ever seen God; but if we love one another, God lives in us and his love is made complete in us."

John Ch.6:46NIV"No one has seen the Father except the one who is from God; only he has seen the Father."

Exodus Ch.33:20NIV"But,” he said, “you cannot see my face, for no one may see me and live.”"

Colossians Ch.1:15NIV"The Son is the image of the INVISIBLE God(Not merely father), the firstborn over all creation. "

An interlude X

 

The epigenome:The kingmaker?

 Epigenetics: Performing the Genome

David Coppedge

Epigenetics has been rising in esteem contemporaneously with the decline of the Central Dogma of genetics (that DNA is the master control in the cell). Just as the pianist gets the applause and not the piano, the epigenome is now being considered the artist behind the instrument. It’s not that the genome has lost any of its aura, but it cannot do anything without a performer.

Frank Gannon wrote a most interesting essay in the journal EMBO Reports, titled, “The piano and the pianist.” Gannon, an Australian who was the former director of a medical research institute in Brisbane, was not writing about the performing arts. He wanted to introduce a new analogy to overcome “the ubiquitous ‘DNA is the blueprint of life’ interpretation of biology,” repeated by some who downplay the elements in the cell that give an organism its dynamic responsiveness to the environment.

The image of inevitability and of a rigorous design plan, and the notion of the dominating importance of DNA are misleading messages, however, that do not represent reality.

I suggest that the piano and the pianist is a better analogy as to how our lives and our health unfold.

Gannon denies that our health is genetically determined: i.e., if we have a certain genetic defect, we will get the disease. That is not entirely true, he says as he details the analogy.

The function of each piano is defined by its 88 keys, but different pianos have different tones and timbres.Some pianos have defects that distort some notes. These could be at the little-used periphery of the keyboard or they could be more central. If the middle C was out of tune, it could be very jarring for the listener in a solo lyrical piece but it may be more subtle if it is part of complex chords. More importantly, though, it is the way the pianist plays the piano that will define the outcome as a pleasure or as discordant. Each pianist selects the tempo and the mood and may even compensate for a dud note.

How Does the Analogy Relate to Biology? 

Writes Gannon, “If the keyboard is the genetic code, the piano is the epigenetic context that interprets the blueprint of life and varies the outcome.” He discusses specific ways cells “perform” the genome. DNA is wrapped in chromatin made of histone proteins that can be tagged with markers like methyl or acetyl groups. Parts can be phosphorylated or tagged with ubiquitin proteins. A host of accessory proteins switch genes on and off, responding to cues from the environment. Indeed, “a growing number of regulatory RNAs create a bewildering combination of possibilities that define the performance of the cell and ultimately of the individual.” 

No analogy is perfect, and one must understand that most of these regulatory agents are coded in DNA themselves. In music, we don’t see pianists emerging from the keys of a piano. Still, the “defining role of epigenetics” deserves more attention, Gannon argues. We are not slaves of our genes. Lifestyle choices, such as diet, exercise, and mental habits, can improve the quality of the performances played on our genetic instruments. 

Most of Gannon’s one-page essay deals with epigenetic targets for treating genetic diseases. While surprised at the lack of attention given to epigenetics, he understands the difficulties involved. “Compared to the neat linearity of the genome,” he notes, “epigenetic regulation is a mess that is hard to reduce into a defined sequence.” Targeting the correct epigenetic regulator is correspondingly difficult. If the dud note is middle C, a carelessly targeted drug might inadvertently put a different note out of tune.

In biology, additional factors other than the genome and epigenome come into play, such as the microbiome — all those microbial and viral partners in and on the organism. These, in turn, respond to the habits of the organism in its habitat. Gannon ends with a cadenza and coda:

As we analyze the beneficial effects of a healthy microbiome and lifestyle, we are looking for answers to why these work. What does the microbiome in the gut provide the organism with to improve health? What are the molecular consequences of exercise such that the total organism and not just the muscles work better? How does diet modify the health of individuals? How does excess fat impact functions in other tissues? More results and more insights will inevitably highlight the crucial role of the epigenome as the connection between the environment and the genome. The piano remains important, but the pianist will finally move into the limelight.

Other Epigenetic News

Researchers at the John Innes Centre explored “intricate mechanisms of epigenetic silencing” (the suppression of gene activity) that impact vernalization in plants. Researchers identified several accessory proteins that trigger epigenetic switches when Arabidopsis plants feel the cold snap that indicates the time for flowering is coming. The switch turns off the floral repressor gene FLC, allowing the genes for bud formation to activate.

At the University of Georgia, researchers investigated the ticking of epigenetic clocks that are biomarkers for aging. “While these clocks work accurately from birth until death,” the press release says, “they are set back to zero in each new generation.” The team confirmed that such epigenetic clocks work in plants, including Arabidopsis and poplar trees, and that these clocks “keep ticking accurately over many generations.”

Remember “Intelligent Design at High Altitudes”? Another paper in Current Biology examined genetic changes in 2,252 Tibetan women who live at high elevations. The authors claim the gene modifications show evidence of positive natural selection. It appears though, that instead of finding new adaptive genes, they found existing genes that were downregulated — i.e., epigenetic responses to the low oxygen atmosphere rather than naturally selected mutations. 

Putting Life Back into Performance

Gannon’s piano analogy suggests opportunities for design theorists. If the genome is like the piano keyboard, it cannot be that the epigenome is as static and determined as the sheet music on the stand. There is dynamic responsiveness in the performance. The pianist (if by that we mean the organism) might have to play the same piece as another individual within its species, but can alter the tempo and quality of the performance depending on the occasion: the audience, the venue, the number of broken keys, the amount of stress on the player, the player’s age and experience, and other factors. 

Every zebra, zebra finch, or zebrafish may resemble its conspecifics, but no two individuals will follow the exact same path. A plains zebra in South Africa may face fewer predators than one in the Serengeti but will endure wider swings in seasonal temperatures. Many individual organisms, such as snowshoe hares, change their appearance from summer to winter. Deciduous trees cycling through seasonal changes offer another example. Epigenetic responses in different tissues of the body will also behave according to local conditions despite having the same genome. The epigenome tunes each performance using its built-in mechanisms to detect the conditions in the environment. It switches on internal controls that adapt cell processes appropriately to the conditions they are sensing. Design theorists are keen on elucidating the mechanisms by which organisms track the environment and actively switch on applicable responses.

Beyond Histones

If epigenetics plays the genome, who plays the epigenome? What tells the epigenome to add a methyl group to a particular histone on a particular gene? Is epigenetics just another layer of information written in matter, cycling mindlessly, amenable to philosophical naturalism? What breathes fire into a piano piece, putting the soul into a rendition by Van Cliburn or Vladimir Horowitz? Even a paper roll with dots on it, running through a mechanical player piano, had to be originally performed by a live pianist. The same is true with digital recording: the soul of the performance is not in the bumps on a CD or the bits in an MP3 file.

If scientists were ever to put together all the parts of a cell, I’m not convinced it would come alive. Information by itself is sterile. All the codes and epi-codes for all the parts could be present, but they would exist as mere fancy arrangements of dumb matter without an additional spark. A spark-discharge apparatus wouldn’t do it. Dr. Frankenstein’s Tesla-coil bolts wouldn’t make his monster sit up except in the movies. To be or not to be is a metaphysical question, but the animating factor that switches on life itself — whether in microbe or man — appears to be an endowment from the ultimate Mind

Why 536c.e would scoff at 2023c.e's idea of a climate catastrophe.

 

On why the physical universe cannot be its own God

 

The speed of light demystified(?)

 

Why the coming apocalypse is the best news

 Genesis Ch.8:21NIV"The LORD smelled the pleasing aroma and said in his heart: “NEVER again will I curse the ground because of humans, even though a every inclination of the human heart is evil from childhood. And NEVER again will I destroy all living creatures, as I have done."

The Lord JEHOVAH Will never destroy (nor will he permit anyone to destroy) his earthly Creation. Especially the human race. JEHOVAH'S Messiah the Lord Jesus Christ will return to usher in a glorious millennium in which the promise of peace on earth announced by Holy Angels at his birth will be fulfilled.

Luke Ch.2:12-14NIV"“Today in the town of David a Savior has been born to you; he is the Messiah, the Lord. 12This will be a sign to you: You will find a baby wrapped in cloths and lying in a manger.”

13Suddenly a great company of the heavenly host appeared with the angel, praising God and saying,Glory to God in the highest heaven,

and on earth PEACE to those on whom his favor rests.”"

This peace is not the enforced quiet that passes for peace in the less unfortunate parts of our global civilisation. JEHOVAH Has higher standards than that.

Isaiah Ch.55:8,9NIV"“For my thoughts are not your thoughts,

neither are your ways my ways,”

declares the LORD.

9“As the heavens are higher than the earth,

so are my ways higher than your ways

and my thoughts than your thoughts."

The coming kingdom of JEHOVAH is not going to be a police state  characterized by a peace maintained by the threat of armed violence.

The examiner of hearts himself will be the guarantor of humanity's enduring peace and security.

Psalms Ch.37:7-11ASV"Rest in JEHOVAH, and wait patiently for him: Fret not thyself because of him who prospereth in his way, Because of the man who bringeth wicked devices to pass.

8Cease from anger, and forsake wrath: Fret not thyself, it tendeth only to evil-doing.

9For evil-doers shall be cut off; But those that wait for JEHOVAH they shall inherit the land.

10For yet a little while, and the wicked shall not be: Yea, thou shalt diligently consider his place, and he shall not be.

11But the meek shall inherit the land, And shall delight themselves in the abundance of peace."

Politics cannot bring about this promised peace. The only "peace" the politicians and political activists can give us is the temporary quiet while they restock their arms and ammunition. 

So even if our anger is justified JEHOVAH urges us to patiently wait on him rather than look to the politicians of the present age and their enablers. How many "revolutions" have proved to be nothing more than an exchanging of one tyrant for another. Indeed the exchanging of one tyrant for several tyrants.

But the faith we place in JEHOVAH is not mere credulity . It is indeed no different from the faith we put in any other trusted companion or counselor. We become acquainted with the character and expertise of said person and our confidence is a fruit of that acquaintance. So too with our Lord JEHOVAH We can let others make up our mind for us or we can choose to investigate for ourselves.

Acts ch.17:26,27ASV"and he made of one every nation of men to dwell on all the face of the earth, having determined their appointed seasons, and the bounds of their habitation; 27that they should seek God, if haply they might feel after him and find him, though he is not far from each one of us:"

Try our free bible course

Why no amount of Chance and necessity is sufficient.

 Dembski and Tour: Why Chance Doesn’t Have a Chance

Andrew McDiarmid

Are life and the universe products of chance, necessity, or design? In anticipation of a new updated second edition of his seminal book The Design Inference, out this coming week, ID the Future features Rice University synthetic organic chemist James Tour and intelligent design pioneer William Dembski concluding a discussion about the origin and role of information in living things. Here in Part 2, Dr. Dembski tackles questions from Dr. Tour’s audience on topics like information theory, probability theory, the origin of life, evolution, the multiverse hypothesis, and Dembski’s contributions to the theory of intelligent design. 

Proponents of an evolutionary explanation for life and the universe often credit natural processes with a seemingly unlimited amount of time and boundless creativity. But the discovery in the 20th century that the universe had a beginning showed that evolution does not have unlimited resources. Dembski has calculated a universal probability bound — the finite limit of available resources and opportunities in the history of the universe — and argues that the complexity of the living cell, the foundational unit of all life on Earth, is leaps and bounds beyond the reach of chance. Download the podcast or listen to it here.

ID is still in the fight?

 

ITimothy Chapter 6 New International Version

 

6.1All who are under the yoke of slavery should consider their masters worthy of full respect, so that God’s name and our teaching may not be slandered. 2Those who have believing masters should not show them disrespect just because they are fellow believers. Instead, they should serve them even better because their masters are dear to them as fellow believers and are devoted to the welfare a of their slaves.

These are the things you are to teach and insist on. 3If anyone teaches otherwise and does not agree to the sound instruction of our Lord Jesus Christ and to godly teaching, 4they are conceited and understand nothing. They have an unhealthy interest in controversies and quarrels about words that result in envy, strife, malicious talk, evil suspicions 5and constant friction between people of corrupt mind, who have been robbed of the truth and who think that godliness is a means to financial gain.

6But godliness with contentment is great gain. 7For we brought nothing into the world, and we can take nothing out of it. 8But if we have food and clothing, we will be content with that. 9Those who want to get rich fall into temptation and a trap and into many foolish and harmful desires that plunge people into ruin and destruction. 10For the love of money is a root of all kinds of evil. Some people, eager for money, have wandered from the faith and pierced themselves with many griefs.

11But you, man of God, flee from all this, and pursue righteousness, godliness, faith, love, endurance and gentleness. 12Fight the good fight of the faith. Take hold of the eternal life to which you were called when you made your good confession in the presence of many witnesses. 13In the sight of God, who gives life to everything, and of Christ Jesus, who while testifying before Pontius Pilate made the good confession, I charge you 14to keep this command without spot or blame until the appearing of our Lord Jesus Christ, 15which God will bring about in his own time—God, the blessed and only Ruler, the King of kings and Lord of lords, 16who alone is immortal and who lives in unapproachable light, whom no one has seen or can see. To him be honor and might forever. Amen.

17Command those who are rich in this present world not to be arrogant nor to put their hope in wealth, which is so uncertain, but to put their hope in God, who richly provides us with everything for our enjoyment. 18Command them to do good, to be rich in good deeds, and to be generous and willing to share. 19In this way they will lay up treasure for themselves as a firm foundation for the coming age, so that they may take hold of the life that is truly life.

20Timothy, guard what has been entrusted to your care. Turn away from godless chatter and the opposing ideas of what is falsely called knowledge, 21which some have professed and in so doing have departed from the faith.

Grace be with you all.

On why artificial intelligence will remain subordinate to actual intelligence.

 Must AI Inevitably Degenerate into Nonsense, through “Model Collapse”?

Casey Luskin

Discovery Institute’s recent COSM 2023 conference hosted a panel on “The Quintessential Limits and Possibilities of AI,” addressing one of the fundamental questions that COSM seeks to investigate: “Is artificial intelligence ‘generative’ or degenerative?” If these experts are right, AI might be doomed to eventually degenerate into nonsense.

George Montañez, Assistant Professor of Computer Science at Harvey Mudd College, opened the session by explaining how AI works. Modern AIs and their “large language models” (LLMs) are trained on huge sets of real-world data — namely text and images generated by humans. Panelist William Dembski, a mathematician and philosopher, pointed out that these LLMs “require a lot of input data and training” in order to work. For example, he notes that it took an immense amount of data, time, money, and collateral damage to humans, to train AI to recognize and reject pornography. Similarly, software engineer Walter Myers noted on the panel that ChatGPT had to train on millions of images of cats and dogs before it could reliably recognize them. In contrast, Montañez points out that a human child can see a few pictures of an animal and they’re immediately able to recognize that species as life.

Montañez further explained that after enough training, AI can interpret data “beyond the things it’s seeing” — but this is only due to “biases and assumptions” provided by humans who program AI with these capabilities. This means that “human fingerprints are all over” the capabilities of AI, and “as impressive as these systems are,” they are “highly parasitic on human rationality and creativity.” Montañez gave the example of an AI that remixes rap with Shakespeare. You “might think it’s amazing” but the reality is “it’s all based upon human programming.”

Model Collapse

But there’s a pitfall to training AI on large datasets — something Denyse O’Leary recently wrote about — called “model collapse.” In short, AI works because humans are real creative beings, and AIs are built using gigantic amounts of diverse and creative datasets made by humans on which they can train and start to think and reason like a human. Until now, this has been possible because human beings have created almost everything we see on the Internet. As AIs scour the entire Internet, they can trust that virtually everything they find was originally made by intelligent and creative beings (i.e., humans). Train AI on that stuff, and it begins to appear intelligent and creative (even if it really isn’t).

But what will happen as humans become more reliant on AI, and more and more of the Internet becomes populated with AI-generated material? If AI continues to train on whatever it finds on the Internet, but the web is increasingly an AI-generated landscape, then AI will end up training on itself. We know what happens when AIs train on themselves rather than the products of real intelligent humans — and it isn’t pretty. This is model collapse.

Enter Robert J. Marks, Distinguished Professor of Electrical and Computer Engineering at Baylor University. He noted that on the first day of COSM 23, computer scientist and AI pioneer Stephen Wolfram warned that we’re at the edge of available training data for AI — essentially we’re hitting the limits of what we can feed AI to make it smart. Once AI runs out of training data, what will it do — train itself?

After taking the audience through a brief history of computing and the development of AI, Marks noted that “each jump [in computing ability] was done by humans, not AI. Each jump in AI happened due to human ingenuity.” But when AI runs out of human ingenuity to train on, will it itself hit a limit — i.e., model collapse? As Montañez put it, “After we’ve scraped the web of all human training data” then “it starts to scrape AI-generated data” because “that’s all you have.” That’s when you get model collapse, and we might be getting close to it.

Marks cited a newly posted study at Arxiv.org, “The Curse of Recursion: Training on Generated Data Makes Models Forget,” which shows model collapse in action. An initial “generation” of AI is trained directly on human-created data and its output generally makes sense. But after multiple generations of AI training on itself, the result is gibberish that’s obsessed with nonsensically colored jackrabbits:

A similar phenomenon happens with images. Marks showed how an AI trained to creatively make variations of the Mona Lisa painting initially provides some interesting if perhaps disturbing images. But eventually, as it trains on its own material, you end up not with art but with nonsensical lines and smudges.

Digital Inbreeding

The problem of model collapse is not entirely unlike human genetics, where siblings or cousins are warned never to marry because they both carry the same deleterious mutations which, when combined, will yield malformed offspring. Better to marry someone outside your immediate gene pool, because they will likely have “fresh genetic material” that can be combined with yours to make healthy children.

In a similar way, AI training on itself needs fresh creative material on which to train or else the algorithms will end up feeding on themselves in recursive cycles that degenerate into nonsense. As Popular Mechanics put it recently, AI will end up “eating its own tail.” 

To mix metaphors, the threat of model collapse is akin to digital inbreeding, and it guarantees that without humans constantly providing fresh creative material for AIs to train on, AIs are doomed to deteriorate. Their creativity may therefore be limited by the human datasets they’re given, meaning there are basic limits to what AI can do. AI will never surpass humans in fundamental ways, and will always be limited by what they can learn from us.

The antiZionism faction of evangelicalism's civil war(s)?

 

There are no good guys V

 

MAGA : South Africa edition?

 

Darwinists can't show their work because the caterpillar ate it?

 Fossil Friday: How the Caterpillar Got Its Legs, or Not

Gunter Bechly

This Fossil Friday features a caterpillar trapped in 45-million-year-old tree resin of Eocene Baltic amber. A caterpillar of course looks very much different from the butterfly into which it eventually develops. The wonderful metamorphosis of caterpillars into butterflies was first discovered by the British physician William Harvey (1651) and Dutch biologist Jan Swammerdam (1669), and famously featured in paintings by the pioneer entomologist Maria Sybilla Merian in her book Metamorphosis insectorum Surinamensium (Merian 1705).

The more primitive groups of insects like roaches, locusts, cicadas, and bugs have a so-called hemimetabolous development, where the nymph is similar in body plan to the adult insect, and with each molting grows in size and especially in length of the wing sheaths. However, most insect species, and indeed most animals on our planet, belong to Holometabola, the clade of insects with complete metamorphosis, which includes lace wings, beetles, bees and wasps, mosquitoes and flies, scorpionflies and fleas, as well as caddisflies and butterflies. In these insects the larva has a very different body plan from the adult insect. After the final larval stage there is a resting stage called pupa or chrysalis, in which the larval body is mostly dissolved into a kind of cell soup and rearranged into the adult body plan. This miraculous development was featured in the Illustra Media documentary Metamorphosis (Illustra Media 2011, Klinghoffer 2011) and poses a considerable conundrum for evolutionary biologists.

The Nature of the Conundrum

Only three hypotheses for the evolution of metamorphosis in insects have been presented: one, which suggests that the holometabolan larva is equivalent to the hemimetabolan nymph, fell out of favor decades ago. Another hypothesis suggested that the holometabolan caterpillar originated from a weird hybridization event of an insect with a velvet worm (Williamson 2009), which is generally considered as preposterous nonsense (Giribet 2009; also see Evolution News 2011). The currently preferred hypothesis is based on very old ideas of Harvey (1651) and Berlese (1913), which were further developed and elaborated by Truman & Riddiford (1999, 2002, 2019, 2022). Their so-called pronymph hypothesis suggests that the juvenile stages of hemimetabolous and holometabolous insects are not homologous, but that only the hemimetabolan pronymph is equivalent to the caterpillar larva, and the multiple nymphal instars are all equivalent to the pupal stage (also see Grimaldi & Engel 2005). However this hypothesis faces two formidable challenges:

The proymph is a non-feeding final embryonic stage, lacking functional mouth parts, which hatches from the egg and immediately molts into the first nymphal instar. The caterpillar larva is a pure feeding stage, basically a gut with legs. How could one evolve into the other with functional and advantageous intermediate forms?

Likewise, how could a single pupal stage, in which the complete body plan is dissolved and rearranged (including even the brain, see Truman et al. 2023 and Saplakoglu 2023), evolve via viable transitional forms from a normal series of nymphal instars that gradually transform into the adult with each molting? This appears to be not just unlikely but inconceivable and virtually impossible. Therefore, this hypothesis is controversial even among mainstream biologists, who have raised many objections to the interpretation of the pupa as only nymphal stage (e.g., DuPorte 1958). All that evolutionists have to offer are vague speculations such as this: “Perhaps 280 million years ago, through a chance mutation, some pro-nymphs failed to absorb all the yolk in their eggs, leaving a precious resource unused. In response to this unfavorable situation, some pro-nymphs gained a new talent: the ability to actively feed” (Jabr 2012). Easy peasy.

Anyway, we should expect that such a marvellous mode of development evolved from normal nymphal stages, if at all, after hundreds of millions of years of gradual change. However, that is not at all what the fossil record shows.

Actually, the first holometabolan insects are recorded from the same Pennsylvanian period as the first flying insects. Molecular clock data even suggest that Holometabola are at least as ancient (about 328-318 mya) as the earliest fossil record of flying insects (Labandeira 2011), or place “the origin of Holometabola in the Carboniferous (355 Ma), a date significantly older than previous paleontological and morphological phylogenetic reconstructions” (Wiegmann et al. 2009a, 2009b, Misof et al. 2014). My dear colleague and frequent co-author André Nel (2019) recently commented that “the late Carboniferous was also the time of the oldest known holometabolous insects, with complete metamorphosis (wasps, beetles, scorpionflies).” Indeed, fossils from larval and adult holometabolous insects of different orders have been found in late Carboniferous layers (see Kukalová-Peck 1997, Nel et al. 2007, 2013, Béthoux 2009, Kirejtshuk & Nel 2013, Kirejtshuk et al. 2014).

Early and Abrupt Appearance

This very early and abrupt appearance of the highly complex holometabolan metamorphosis represents one of the many examples of the waiting time problem, because it certainly required many coordinated mutations, which again required orders of magnitude more time to originate and spread than was available.

But any theory for the origin of the caterpillar larva needs to explain a lot more than that. While hemimetabolan nymphs and all adult winged insects have only three pairs of thoracic legs, the caterpillar larvae of butterflies and plant wasps additionally possess several pairs of chubby abdominal leglets called prolegs. “These prolegs pose an evolutionary mystery, and scientists have long grappled over how and why they got them” (Pallardy 2023). Where did those prolegs come from? There are three alternative hypotheses on the table:

Prolegs are serially homologous with thoracic legs, and thus derived from reactivated abdominal legs of crustaceans. This alternative was challenged and arguably refuted by previous evo-devo studies like Yue & Hua (2010) and Oka et al. (2010).

Prolegs are novel adaptations without immediate precursor structures.

Prolegs are derived from endites, internally facing structures of the crustacean limbs (e.g., Oka et al. 2010).

Now, a new study by Matsuoka et al. (2023) tested these three hypotheses with evo-devo data. The authors suggest that prolegs are novel traits, but based on the re-activation of pre-existing endite genes. The press release makes it very clear: prolegs “seem to be modified endites. As crustaceans evolved into insects, endites were largely lost. But in butterflies and moths, the gene for them got reactivated, providing caterpillars with their prolegs.” (Pallardy 2023).

To evaluate the feasibility of this hypothesis we first have to look at the distribution of prolegs within holometabolan insects, because this character is not hierarchically distributed as would be predicted by Darwinism, but instead is very incongruent (homoplastic): prolegs occur in the larvae of plant wasps, scorpionflies and fleas, caddisflies and butterflies, and some families of flies, but are absent in all other holometabolan groups. This incongruent pattern implies that prolegs were either reduced multiple times, or instead originated independently as a convergence, which is also suggested by developmental data (Suzuki & Palopoli 2001). Actually, Hinton (1955) proposed an independent origin of prolegs 27 times within Diptera. This alone is a grandiose empirical failure of Darwinian theory, because the unique anatomical similarity does not seem to be plausibly based on inheritance from a common ancestor. For the sake of the argument we will let this pass and just look at the new study.

Assessing the new study

As we have seen above, Darwinists now explain the origin of caterpillar leglets with the reactivation of a crustacean gene, that was dormant for maybe 100 million years. Seriously? After such a long period without function and without adaptive pressure to eliminate deleterious mutations, this gene should still have remained functional instead of been degraded by random genetic noise? This would be akin to a genuine miracle and arguably would violate an assumed law of evolution known as Dollo’s Law, which is based on the simple fact that history does not repeat itself (Gould 1970). Could this law be broken on some realistic time scale?

As shown by Rana (2017), there were several studies that evaluated the time frame in which the function of a gene is degraded and lost, so that it cannot be reactivated:

The study by Marshall et al. (1994) suggested that reactivation is reasonable over time scales of 0.5-6 million years. The authors concluded that “the reactivation of long (>10 million years)-unexpressed genes and dormant developmental pathways is not possible unless function is maintained by other selective constraints.”

Lynch & Conery (2000) showed that duplicated genes lose function by stochastic silencing within a few million years. Rana (2017) mentions that such duplicated genes can serve as proxy for dormant genes, because they are no longer under the influence of selection. Lynch and Conery found a half-life of 4 million years, which implies that function is lost after 16-24 million years.

Protas et al. (2007) showed that such a loss of function happens much more quickly, in about 1 million years, if it is advantageous and thus influenced by selection.

Horne (2010) studied the reactivation of eye sight in blind ostracods and commented that “there appear to be several well-documented examples of the reactivation of dormant genes, allowing the reappearance of ‘lost’ characters, in some cases after several [my emphasis] million years.” 

So, we have a realistic time frame of roughly 1-24 million years for the reactivation of a dormant gene. Indeed, short term reversals can be observed in lab experiments, e.g., concerning drug resistance among germs (Gouda et al. 2019). Anything longer than the mentioned time constraint is prohibited by Dollo’s Law of irreversibility (Gould 1970, Bull & Charnov 1985). Any apparent reactivation on longer time frames (see examples mentioned by Fryer 1999, Dingle 2003, Cruickshank & Paterson 2006, Horne 2010, and Rana 2017) cannot be reasonably explained with Darwinian processes, but requires intelligent design as more plausible and causally adequate explanation. Rana (2017) correctly emphasized that “it is not unusual for engineers to reuse the same design or to revisit a previously used design feature in a new prototype.”

But There Might Be a Loophole

Lynch (2022) recently found that “the long half‐life of enhancers, transcription factor binding sites, and protein−protein interaction motifs suggest that evolutionary reversals are possible after much longer periods of loss than previously suspected.” He concluded that “these data indicate that reactivation of these smaller functional units is possible after many millions of years and suggest that re-evolution of complex traits may occur through their loss and regain. Thus these data suggest that organisms need not surmount “the sheer statistical improbability … of evolution ever arriving at the same complex genic end‐result twice” (Müller in Gould 1970), rather “organisms might only need to retrace a single step such as the reacquisition of a transcription factor binding site in a cis‐regulatory element of a protein−protein interaction motif.”

However, there is a caveat, because the longer half-life does not apply to silenced protein coding genes, which would degrade much faster. Lynch (2022) explicitly admitted that “it seems unlikely that the genetic information for the development and function of the character can be maintained for long periods of time in the absence of the character (Bull & Charnov, 1985).” This could only be avoided in cases of serially homologous characters, when at least one instance of expression of this character would remain, so that selection could work against the deterioration of function by random copy errors. Therefore, Lynch (2022) suggested as a loophole for the violation of Dollo’s law “that the developmental programs required for the establishment of serially homologous characters may never really be lost so long as a single instance of the character remains.”

How Would Darwinists Argue?

So, let’s have a look at the possibility that this loophole could allow for the reactivation of the endite gene in caterpillars as suggested in the new study by Matsuoka et al. (2023). Probably, Darwinists would argue as follows: putative homologs of abdominal leg endites are present as pairs of eversible vesicles on the abdomen in some primitive wingless insects (apterygotes) like diplurans, bristletails, and silverfish that are known from (controversial) Devonian and Carboniferous fossils. Such vesicles are absent in all known winged insects and thus were reduced in the stem species of crown group pterygotes, which lived at least 323 million years ago in the earliest Pennsylvanian (Namurian) period according to the oldest fossil record (Brauckmann et al. 1994, Brauckmann & Schneider 1996, Prokop et al. 2005, Prokop & Hörnschemeyer 2016, Wolfe et al. 2016), and 410 million years ago in the Late Devonian period according to molecular clock estimates (Wiegmann et al. 2009b, Misof et al. 2014). This is 10 million years prior to the oldest fossil record of holometabolans (313.7 mya, Wolfe et al. 2016) and 60 million years prior to molecular clock estimates of their origin (350 mya, Wiegmann et al. 2009a, 2009b, Misof et al. 2014 / 328-318 mya according to Labandeira 2011). Therefore, the transformation would have occurred after 60-10 million years of gene suppression if the prolegs would belong to the ground plan of holometabolan insects. This would still reach or exceed the above mentioned limits imposed by Dollo’s law.

But it gets much worse for the evolutionist hypothesis. As we have seen above, larval prolegs do not belong to the ground plan of holometabolan insects (Peters et al. 2014), but developed independently multiple times in several crown groups among them. Therefore, we have to look at the age of those crown groups and not the age of Holometabola as a whole to evaluate the available window of time. Let’s be maximally generous and assume that larval prolegs are at least homologous in caddisflies (Trichoptera) and butterflies (Lepidoptera), so that they could belong to the ground plan of their common amphiesmenopteran ancestor. According to The Timetree of Life (Wiegmann et al. 2009a, 2009b) the relevant crown groups originated in Permian and Triassic periods: Lepidoptera, for example, about 230 million years ago and Amphiesmenoptera (the clade of Trichoptera+Lepidoptera) 282 million years ago. This molecular dating roughly agrees with the early fossil record of these groups. This implies that the reactivation of the dormant gene would have occurred after 128-41 million years (410/323-282 mya) of absence of any instantiated serially homologous character, which is simply impossible according to the limits proposed by mainstream evolutionary biology itself.

Is This Hard Science? Really?

Of course, such inconvenient facts do not bother evolutionary biologists at all, because the law obviously must have been broken, because we know it happened. Apparently laws do not mean much in evolutionary biology and can be suspended whenever a just-so story requires it. Sounds like hard science — not!

Why is it that you cannot find such simple calculations as we just made above anywhere in the mainstream scientific literature, to check if a scenario is plausible and compatible with other claims of evolutionary theory? Are the scientists really interested in testing their hypotheses and eventually finding out that they don’t hold water? It certainly doesn’t look like that to me. In spite of all the scientific efforts by Darwinists, the origin of complete metamorphosis in holometabolan insects remains an unsolved mystery, which is much better and causally more adequately explained by intelligent design.

As crooked as it gets?

 

Design is wrong by definition?

 

It's complicated? IV

 

The third horseman picks up his pace?

 

North America's last king?

 

File under "Well said" CII

 "In war, truth is the first casualty."

       Aeschylus

It's complicated? III

 

It's complicated? II

 

It's complicated?

 

Psalms chapter 9 American Standard Version

 I will give thanks unto JEHOVAH with my whole heart; I will show forth all thy marvellous works.

2I will be glad and exult in thee; I will sing praise to thy name, O thou Most High.

3When mine enemies turn back, They stumble and perish at thy presence.

4For thou hast maintained my right and my cause; Thou sittest in the throne judging righteously.

5Thou hast rebuked the nations, thou hast destroyed the wicked; Thou hast blotted out their name for ever and ever.

6The enemy are come to an end, they are desolate for ever; And the cities which thou hast overthrown, The very remembrance of them is perished.

7But JEHOVAH sitteth as king for ever: He hath prepared his throne for judgment;

8And he will judge the world in righteousness, He will minister judgment to the peoples in uprightness.

9JEHOVAH also will be a high tower for the oppressed, A high tower in times of trouble;

10And they that know thy name will put their trust in thee; For thou, JEHOVAH, hast not forsaken them that seek thee.

11Sing praises to JEHOVAH, who dwelleth in Zion: Declare among the people his doings.

12For he that maketh inquisition for blood remembereth them; He forgetteth not the cry of the poor.

13Have mercy upon me, O JEHOVAH; Behold my affliction which I suffer of them that hate me, Thou that liftest me up from the gates of death;

14That I may show forth all thy praise. In the gates of the daughter of Zion I will rejoice in thy salvation.

15The nations are sunk down in the pit that they made: In the net which they hid is their own foot taken.

16Jehovah hath made himself known, he hath executed judgment: The wicked is snared in the work of his own hands. Higgaion. Selah

17The wicked shall be turned back unto Sheol, Even all the nations that forget God.

18For the needy shall not alway be forgotten, Nor the expectation of the poor perish for ever.

19Arise, O JEHOVAH; let not man prevail: Let the nations be judged in thy sight.

20Put them in fear, O JEHOVAH: Let the nations know themselves to be but men. Selah

There is no preDarwinian Darwinism?

 

On the primeval AI of earth's Flora

 The Superior Programming that Makes Plants Look Smart

David Coppedge

Wesley Smith has warned more than once against anthropomorphizing plants and ascribing intelligence — even personhood — to flowers and trees. But like responsive robots, plants can have smarts programmed into them. “So sure, investigate how plants interact with their environment,” he advises. “But use proper, non-personal language. They are plants.” Let’s do that, and look at some of the superior programming that makes plants look smart because their design is smart

Leaf Recycling

Science Magazine notes that “leaf recycling is a two-step process.” Leaves don’t just curl up and die on a cold day. That algorithm would be too simplistic, and potentially harmful to the tree if warm sunny days follow. Actually, two signaling molecules — strigolactone and ethylene — can work independently to begin the process of leaf senescence (pictured above), but together, they work in synergy. “This multistep process probably preserves leaves when possible, only carrying through to leaf senescence when the stress becomes too much

Nitrogen Fixing

Separating molecular nitrogen’s triple bond requires a lot of energy and pressure when humans do it, but some plants do it with ease, utilizing the capabilities of nitrogen-fixing bacteria. These bacteria have an enzyme called nitrogenase that so far has defied our attempts to understand it or duplicate it. Even though legumes outsource the work, they regulate their symbiotic partners’ activity depending on nitrogen availability in the soil, according to researchers at Chapman University. This does not require plants to be sentient. We are all familiar with machines like thermostats, rheostats, and governors that can adjust their work depending on environmental conditions

Climbing

Some plants and animals produce tentacles (in plants, tendrils) that can grab things. At Iowa State University, scientists are attempting to create (so far with only partial success) artificial tentacles that can wrap around delicate objects. The tendrils in ivy and other climbing plants are touch-sensitive. Contact changes the concentration of hormones in the tendril so that growth is accelerated on the far side, producing curvature. As a result, the tendril wraps around the object so that the plant can anchor itself to something firm. Time-lapse photos of ivy growing up a wall might look like the action of an intelligent agent. We see from Iowa State’s biomimetic experiments, though, that the intelligence is imposed by the agent. It’s a matter of programming with the right materials.

Watching the Clock

Every living thing keeps time, and plants are no exception. In fact, they have two clocks, says Duke University:

Time management isn’t just important for busy people — it’s critical for plants, too. A Duke University study shows how two biological clocks work together to help plants deal with intermittent demands such as fungal infections, while maintaining an already-packed daily schedule of activities like growth.

The anthropomorphic language might make it seem that plants are like people, but time management regulation can be programmed, as we know from our own machines that contain timers or sun sensors. Researchers at Duke showed this by chemically altering the circadian rhythms in Arabidopsis plants to see how the “morning” clock and the “evening” clock interacted. In the process, they identified a regulating gene named NPR1 that links the two clocks. Their work is published in Nature:

Mathematical modelling and subsequent experiments show that NPR1 reinforces the circadian clock without changing the period by regulating both the morning and the evening clock genes. This balanced network architecture helps plants gate their immune responses towards the morning and minimize costs on growth at night. Our study demonstrates how a sensitive redox rhythm interacts with a robust circadian clock to ensure proper responsiveness to environmental stimuli without compromising fitness of the organism.

Separating Behavior from Intelligence

Intelligent agents can exhibit behavior, but not all behaving entities are intelligent agents. For example, the Curiosity rover on Mars might look to an alien visitor like a sentient being acting autonomously. Its behavior, however, has been programmed into it. Some of that behavior runs from embedded instructions in its software; some of its actions are controlled by sentient beings millions of miles away. It would be fallacious to call Curiosity “intelligent” or a “person.”

This is the fallacy Adrian Barnett toyed with in his book review for New Scientist that Wesley Smith wrote about. Barnett stated that “plants are smart” as if they conjured up their intelligence by themselves; it’s only our “serious parochialism” that makes us unable to appreciate “intelligence not as we know it.”

Another reviewer in Nature, Ian T. Baldwin commits the same fallacy, though in a more nuanced way. A plant scientist, Baldwin reviewed three new books on plant behavior, including the one by Richard Karban that Barnett reviewed in New Scientist. 

The food writer Michael Pollan, author of The Omnivore’s Dilemma (Penguin, 2006) among others, wrote an article in The New Yorker in 2013 exploring why terms such as intelligence, memory and even behaviour have been contentious for plant scientists.His thesis boils down to a divide in biology that allows zoologists to use anthropomorphic terms, but denies the privilege to plant scientists. Pollan allies himself with a small band of intrepid researchers crusading against the “cerebrocentric” view that permits behaviour only to organisms with brains. He tells of collateral damage from sensationalist treatments that exaggerate plant-science findings, and of glimmers of a new sensitivity towards all life.

Pollan identifies an interesting story about the development of an emerging scientific field, and the baggage that scientists bring to their work. The idea that plants are ‘smarter’ than their immobility suggests is now supported by rigorous experimentation and fieldwork that are uncovering the genes and chemicals that mediate plants’ environmental intelligence. We know now that much of a plant’s rich behavioural repertoire is hard to observe because it is played out in a chemical arena. Plants overcome the constraints of immobility mainly by harnessing their prowess as synthetic organic chemists. For instance, floral scents contain compounds that attract pollinating animals and repel flower-eating ones. Nectar is a brew of nutrients and toxins that optimize the behaviour of pollinators. Much of the relevant literature is now synthesized in three books by leading researchers in the field: Edward Farmer’s Leaf Defence, Anthony Trewavas’s Plant Behaviour and Intelligence and Richard Karban’s Plant Sensing and Communication.

The fallacy is obvious when you imagine him writing a similar exaltation of “rover intelligence” after observing Curiosity’s behavior. Would it make any sense to praise Curiosity’s “prowess as a synthetic organic chemist”? 

Baldwin gave the three books varying degrees of commendation. Excited as he is by the resurgence of interest in plant behavior, he understands that these “phytomorphic” activities must be understood mechanistically and biochemically.

The root of the fallacy, though, is Darwinian thinking. It allows no room for human exceptionalism. To the evolutionist, humans differ not in kind but in degree. Animal and plant intelligence is just as self-generated as that “emerging” from our physical brains. While they can partially see how anthropomorphism is misleading, they cannot draw a divide between us and them. That’s why Baldwin praises Trewavas for thinking like a plant and avoiding animal envy:

Trewavas, by contrast, moves effortlessly from mechanistic research to invigorating insights into real-world plant behaviour. Plant Behaviour and Intelligence is a wild ride, covering ground from the origins of life to intelligent nutrient-foraging behaviour in the roots of higher plants. Trewavas’s five decades of research into plants’ molecular biology and physiology, and their evolution as self-organizing systems, make him fully ‘phytomorphized’. He thinks like a plant, effortlessly calling on specific traits to look at how plants solve problems in similar ways to social insects — from siphonogamy (in which pollen tubes carry sperm cells to egg cells) to highly dispersed sensory systems. He celebrates behaviour in plants while avoiding “animal envy”.

Darwinian thinking unravels, though, when you see it cannot be sustained logically. For one thing, Baldwin and Barnett use their own sentience, including conscious purposeful choice, to ascribe it to plants and animals. This would be like Curiosity coming into contact with Opportunity and deciding it was an independent, autonomous, intelligent being that emerged from the Martian soil like itself. 

For another logical short-circuit, Darwinians routinely ascribe motives and goals to plants and animals, even when they deny this is possible. The unguided neo-Darwinian mechanism cannot see a distant target and move toward it. Baldwin says that plant defenses “evolved primarily to thwart herbivores.” He says “leaves evolved to have particular traits.” Nothing in Darwinism allows the phrase “evolve to” in foresight or in hindsight. Such language is just as misleading as anthropomorphism.

The only logically self-consistent position is to see plants and animals as possessing design impressed on them by an outside intelligent cause. In this way, we can appreciate and study the rational design in plants that makes their behaviors so interesting (and often worth imitating). Our physical bodies and brains also carry the imprint of design, but we humans have the additional gift of conscious self-awareness that allows us to choose our behaviors. This sets us apart from the rest of the living world. It’s the reason we use reason to study plants, but plants do not study us.

Homology=Common Ancestry?

 

In the beginning there was information?

 

Phillipians chapter 3 verses 1 through 9 New international Version.

 1Further, my brothers and sisters, rejoice in the Lord! It is no trouble for me to write the same things to you again, and it is a safeguard for you. 2Watch out for those dogs, those evildoers, those mutilators of the flesh. 3For it is we who are the circumcision, we who serve GOD by his Spirit, who boast in Christ Jesus, and who put no confidence in the flesh— 4though I myself have reasons for such confidence.

If someone else thinks they have reasons to put confidence in the flesh, I have more: 5circumcised on the eighth day, of the people of Israel, of the tribe of Benjamin, a Hebrew of Hebrews; in regard to the law, a Pharisee; 6as for zeal, persecuting the church; as for righteousness based on the law, faultless.

7But whatever were gains to me I now consider loss for the sake of Christ. 8What is more, I consider everything a loss because of the surpassing worth of knowing Christ Jesus my Lord, for whose sake I have lost all things. I consider them garbage, that I may gain Christ 9and be found in him, not having a righteousness of my own that comes from the law, but that which is through faith in a Christ—the righteousness that comes from GOD on the basis of faith. 

The idolising of necessity and chance is the real science stopper?

 The Best and Worst Heuristics for Biological Discovery

Paul Nelson

The bad news first. What’s the worst possible heuristic for making biological discoveries?

We don’t know what this structure does, so it probably does nothing. Remember, evolution produces a lot of non-functional debris.

What’s the best heuristic?

We don’t know what this does. Let’s find out.

Here’s a case in point at Cell. It’s open access and incredibly cool and interesting:

“Mammalian oocytes store proteins for the early embryo on cytoplasmic lattices”

According to the Summary section:

Mammalian oocytes are filled with poorly understood structures called cytoplasmic lattices. First discovered in the 1960s and speculated to correspond to mammalian yolk, ribosomal arrays, or intermediate filaments, their function has remained enigmatic to date. Here, we show that cytoplasmic lattices are sites where oocytes store essential proteins for early embryonic development. Using super-resolution light microscopy and cryoelectron tomography, we show that cytoplasmic lattices are composed of filaments with a high surface area, which contain PADI6 and subcortical maternal complex proteins. The lattices associate with many proteins critical for embryonic development, including proteins that control epigenetic reprogramming of the preimplantation embryo. Loss of cytoplasmic lattices by knocking out PADI6 or the subcortical maternal complex prevents the accumulation of these proteins and results in early embryonic arrest. Our work suggests that cytoplasmic lattices enrich maternally provided proteins to prevent their premature degradation and cellular activity, thereby enabling early mammalian development.

Kraken released?

 Fossil Friday: Triassic Kraken Hypothesis Provoked Scornful Darwinist Revenge

Gunter Bechly

Professor Mark McMenamin is a maverick paleontologist and critic of neo-Darwinism, who is known for very interesting but controversial hypotheses like Hypersea (McMenamin & Schulte McMenamin 1993, 1994, Zimmer 1995), The Garden of Ediacara (McMenamin 1986, 1998), Paleotorus (McMenamin 2009), and the Triassic Kraken (McMenamin & Schulte McMenamin 2011, 2013, McMenamin 2023). The latter hypothesis has met with particularly scornful skepticism from his peers (Simpson 2011, Switek 2011, Than 2011, DNews 2013, Pappas 2013, Viegas 2016, HourDark 2020), and of course from the usual suspects, i.e., activists of the Darwinian thought police like P. Z. Myers (2011) and Donald Prothero (2011, 2013). It has even been called a “dangerous speculation” (Dresow 2022).

An Admittedly Bold Hypothesis

McMenamin’s kraken hypothesis has never been published in a peer-reviewed journal but was only proposed in two congress abstracts (McMenamin & Schulte McMenamin 2011, 2013), a magazine article (McMenamin 2012), and a book chapter (McMenamin 2016). It was also covered by numerous sensationalist press releases and media reports (Bryner 2011, Flatow 2011, GSA 2011, Herald Sun 2011, IB Times 2011, Leach 2011, Praetorius 2011, Wang 2011). The admittedly bold hypothesis claims that a gigantic 100-foot Triassic cephalopod killed large ichthyosaurs and arranged their bones in a self-portrait-like pattern. The main evidence is a curious biserial pattern of ichthyosaur vertebrae at the Berlin-Ichthyosaur State Park in Nevada, which mimics the pattern of suckers on a cephalopod tentacle. Meanwhile, a second locality with this pattern was discovered in Switzerland (Sander et al. 2022). Just this year, McMenamin described a large cephalopod beak from the same Triassic layers in Nevada, which could directly confirm the actual existence of the postulated “kraken” (McMenamin 2023, also see Pappas 2013).

Nevertheless, instead of a reasonable and fair scientific debate, McMenamin’s hypothesis has been ridiculed by other scientists and science journalists. Of course, this was totally unrelated (irony warning) to the fact that McMenamin is an outspoken critic of neo-Darwinism and has dared to write a positive review for an ID documentary based on Stephen Meyer’s book Darwin’s Doubt at Amazon (McMenamin 2010), just a year before the publication of his kraken hypothesis. He was even accused by vicious activists in the skeptic movement (Prothero 2013) of being a “creationist” himself, even though a fair reading of his review clearly shows that he is not. Others were not beneath abusing McMenamin with the insulting nick name McMinimal (Simpson 2011).

An Inconvenient Thinker

To be clear: There are some good scientific arguments against McMenamin’s interpretation (e.g., the fact that basal fossil coleoids from the Mesozoic all had uniserial suckers; see Anonymous 2020, Greenfield 2021), and his kraken hypothesis may very well be wrong. However, the way he and his hypothesis were treated by the scientific community is far from impartial. It is clearly driven by the desire to marginalize and ostracize an inconvenient thinker — who made the big mistake of showing sympathy for the ID movement — as a foolish crackpot who should be ignored. McMenamin is lucky to have a tenured position as college professor, because his opponents would not shy away from destroying his career as they tried or successfully did with other dissidents who think outside the box. I can tell you a thing or two about that myself. So much for objective science and academic freedom.

An interlude IX

 

No laughing matter?

 

The bitter fruit of the imperium?

 

File under "Well said" CI

 "He will guard the feet of his faithful servants,

but the wicked will be silenced in the place of darkness.

“It is not by strength that one prevails;"

1Samuel chapter 2 verse 9 New International Version.

High noon for OOL Science's gatekeepers.

 On Origin of Life, Chemist James Tour Has Successfully Called These Researchers’ Bluff

Brian Miller

David Klinghoffer and Tova Forman previously wrote about Rice University chemist James Tour’s 60-day challenge to leading origin-of-life researchers to demonstrate that the field had substantively advanced in the past seventy years (here,here). Tour offered to remove all his videos on the topic if three leading experts agreed that any of five fundamental problems had been solved:

Linking of amino acids into chains (aka polypeptides)

Linking of nucleotides into RNA molecules

Linking of simple sugars (aka monosaccharides) into chains known as polysaccharides 

Origin of biological information

Assembly of components into a cell

Tour issued this challenge in response to the many false claims made by YouTubers, such as Dave Farina, about how these hurdles to life’s origin had been fully addressed. The deadline has expired, and no one has presented solutions to any of the problems. 

The Rules

For the first three problems, Tour allowed origin-of-life researchers to assume a chemical mixture started with amino acids, nucleotides, or sugars with the same handedness (aka enantiomerically pure). For instance, all the amino acids were left-handed as required in modern proteins. For the first problem, participants needed to detail how chains of just two amino acids — aspartic acid and lysine — could have formed with the correct bonds. For the second problem, proposed solutions needed to describe how nucleotides could have linked into chains with less than 2 percent of the wrong linkages. And for the third, proposals needed to explain how molecules of the simple sugar glucose could have properly joined in high yields. 

For the fourth problem, researchers could assume that the first three challenges had been solved. They only needed to explain how amino acids, nucleotides, or simple sugars could have linked together in the correct order to contain the required functional information to perform some biologically relevant task. For the fifth problem, researchers could assume that all cellular components were available in abundance. They only needed to explain how the biological building blocks could have assembled into a functional cell. Proposed solutions for all the problems had to rely only on chemistry that could have occurred on the early Earth. 

The implications of failure

The failure of any origin-of-life expert to propose a solution to even one of the five problems has dire implications for the field. Tour allowed origins researchers to assume unrealistically favorable starting conditions. The hurdles are collosal for life’s constituent molecules to form in sufficiently high concentrations and purities to allow for even the slightest possibility of their linking into proteins, RNA, or complex polysaccharides (here, here). In addition, any cellular component that formed on the early Earth would have decomposed long before finding its way to the staging ground for an aspiring cell. Consequently, even if every problem were fully solved, life’s genesis would still face the insurmountable hurdle of transporting the components of life to the same microscopic environment. 

YouTubers and other defenders of the secular faith of scientific materialism have confidently asserted that scientists are steadily unraveling the mystery of life’s origin. Yet Tour called on leading experts to demonstrate whether they had achieved any real progress in answering any of the most fundamental questions. None could rise to the challenge. 

At some point, both the scientific community and the public will need to recognize that the lack of progress cannot be explained by a lack of serious effort by highly competent scientists but by the philosophical assumptions blinding them from seeing the truth staring them in the face. The answer to life’s origin does not reside in the fields of physics and chemistry but in the mind behind our universe. 

Time for the OOL Establishment to throw down?

 

Against Calvin again.

 

Following the science re: the God hypothesis.