Sunday, 15 January 2023
On the origins of our natural satellite.
The new science of moon formation.
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Friday, 13 January 2023
Wednesday, 11 January 2023
Darwinism's narrative re:mitochondria takes it on the chin?
Rewrite the Textbooks (Again), Origin of Mitochondria Blown Up
Cornelius G Hunter
There You Go Again
Why are evolutionists always wrong? And why are they always so sure of themselves? With the inexorable march of science, the predictions of evolution, which evolutionists were certain of, just keep on turning out false. This week’s failure is the much celebrated notion that the eukaryote’s power plant—the mitochondria—shares a common ancestor with the alphaproteobacteria. A long time ago, as the story goes, that bacterial common ancestor merged with an early eukaryote cell. And these two entities, as luck would have it, just happened to need each other. Evolution had just happened to create that early bacterium, and that early eukaryote, in such a way that they needed, and greatly benefited from, each other. And, as luck would have it again, these two entities worked together. The bacterium would just happen to produce the chemical energy needed by the eukaryote, and the eukaryote would just happen to provide needed supplies. It paved the way for multicellular life with all of its fantastic designs. There was only one problem: the story turned out to be false.
The story that mitochondria evolved from the alphaproteobacteria lineage has been told with great conviction. Consider the Michael Gray 2012 paper which boldly begins with the unambiguous truth claim that “Viewed through the lens of the genome it contains, the mitochondrion is of unquestioned bacterial ancestry, originating from within the bacterial phylum α-Proteobacteria (Alphaproteobacteria).”
There was no question about it. Gray was following classic evolutionary thinking: similarities mandate common origin. That is the common descent model. Evolutionists say that once one looks at biology through the lens of common descent everything falls into place.
Except that it doesn’t.
Over and over evolutionists have to rewrite their theory. Similarities once thought to have arisen from a common ancestor turn out to contradict the common descent model. Evolutionists are left having to say the similarities must have arisen independently.
And big differences, once thought to show up only in distant species, keep on showing up in allied species.
Biology, it turns out, is full of one-offs, special cases, and anomalies. The evolutionary tree model doesn’t work.
Now, a new Paper out this week has shown that the mitochondria and alphaproteobacteria don’t line up the way originally thought. That “unquestioned bacterial ancestry” turns out to be, err, wrong.
The paper finds that mitochondria did not evolve from the currently hypothesized alphaproteobacterial ancestor, or from “any other currently recognized alphaproteobacterial lineage.”
The paper does, however, make a rather startling claim. The authors write:
our analyses indicate that mitochondria evolved from a proteobacterial lineage that branched off before the divergence of all sampled alphaproteobacteria.
That is a startling claim because, well, simply put there is no evidence for it. The lack of evidence is exceeded only by the evolutionist’s confidence. Note the wording: “indicate.”
The evolutionist’s analyses indicate this new truth.
How can the evolutionists be so sure of themselves in the absence of literally any evidence?
The answer is, because they are evolutionists. They are completely certain that evolution is true. And since evolution must be true, the mitochondria had to have evolved from somewhere. And the same is true for the alphaproteobacteria. They must have evolved from somewhere.
And in both cases, that somewhere must be the earlier proteobacterial lineage. There are no other good evolutionary candidates.
Fortunately this new claim cannot be tested (and therefore cannot be falsified), because the “proteobacterial lineage” is nothing more than an evolutionary construct. Evolutionists can search for possible extant species for hints of a common ancestor with the mitochondria, but failure to find anything can always be ascribed to extinction of the common ancestor.
This is where evolutionary theory often ends up: failures ultimately lead to unfalsifiable truth claims. Because heaven forbid we should question the theory itself.
Planet of the monkeys?
Monkeys, Not Humans, Likely Made Ancient Brazilian Tools
Evolution News
There’s a danger in looking too hard for evidence of our ancient ancestors. Sometimes we could be seeing things that aren’t there. One group of stone tools from 50,000 years ago could, it is now suggested, have been made by monkeys:
Excavations at Pedra Furada, a group of 800 archaeological sites in the state of Piauí, Brazil, have turned up stone shards believed to be examples of simple stone tools. Made from quartzite and quartz cobbles, the oldest ones appear to be up to 50,000 years old, which would put them among the earliest evidence of human habitation in the Western Hemisphere.
However, the tools also bear a striking resemblance to the stone tools currently made by the capuchin monkeys at Brazil’s Serra da Capivara National Park.
SARAH CASCONE, “ANCIENT STONE TOOLS ONCE THOUGHT TO BE MADE BY HUMANS WERE ACTUALLY CRAFTED BY MONKEYS, SAY ARCHAEOLOGISTS” AT ARTNET (JANUARY 3, 2023) THE PAPER IS OPEN ACCESS.
But there’s a twist. Back in 2016, a similar point was raised at Nature:
In January, archaeologist Tomos Proffitt was examining a set of stone artefacts that his colleague Michael Haslam had brought to him. Some of the quartz pieces looked like sharpened stone tools made by human relatives in eastern Africa, some 2–3 million years ago.
But Haslam told Proffitt that the artefacts had been made the previous year by capuchin monkeys in Brazil. “I was pretty gobsmacked,” he says. “I did my PhD looking at hominin stone tools. I’ve learnt how to make these things. I was looking at this material, and it looked like it had been made by humans.” …
The capuchins make the fragments unintentionally while bashing rocks into dust, the researchers find. Some scientists say that the results call into question whether some stone tools have been incorrectly attributed to hominins — including 3.3-million-year-old artefacts from Kenya that are the oldest on record.
EWEN CALLAWAY, “MONKEY TOOLS RAISE QUESTIONS OVER HUMAN ARCHAEOLOGICAL RECORD ” AT NATURE (OCTOBER 19, 2016) THE PAPER REQUIRES A FEE OR SUBSCRIPTION.
Not Even Tools
The twist is that those artifacts were not even tools. The monkeys were producing them accidentally…
Many life forms shape and use objects as tools: These include crows, dolphins, octopuses, alligators, and ants.
The casualty in this case is the contention — attractive to many researchers, of course — that humans were living in the Americas 50,000 years ago based on the presence of what are thought to be tools:
Coupled with the lack of other evidence of human habitation from 50,000 years ago, such as concrete traces of dietary remains or hearths — charcoal at the site could have originated from naturally occurring fires — the tools’ resemblance to rock fragments created by monkeys calls into question the likelihood that humans were responsible for their creation.
The new findings could have a major impact on our understanding of when the first humans arrived in the Americas.
SARAH CASCONE, “ANCIENT STONE TOOLS ONCE THOUGHT TO BE MADE BY HUMANS WERE ACTUALLY CRAFTED BY MONKEYS, SAY ARCHAEOLOGISTS” AT ARTNET (JANUARY 3, 2023) THE PAPER IS OPEN ACCESS.
A Calendar in the Mix?
We need to be clear about what part of the archeological record is under question. Another current dispute, for example, turns on whether the dots that accompany many Ice Age paintings from 20,000 years ago are evidence of a lunar calendar. It’s quite likely that the series of dots and symbols represent some form of record-keeping or communication. There may or may not be a lunar calendar in the mix but there is no possibility that these artworks were created by monkeys. We know that we are in a human world here. We just aren’t sure what its inhabitants were trying to say.
If we are going to offer theories about ancient humans, it is best to be on ground as sure as that.
Darwinism's quest for a simple beginning rolls on.
Centrobin Found to be Important in Sperm Development
Cornelius G Hunter
Numerous, Successive, Slight Modifications
Proteins are a problem for theories of spontaneous origins for many reasons. They consist of dozens, or often hundreds, or even thousands of amino acids in a linear sequence, and while many different sequences will do the job, that number is tiny compared to the total number of sequences that are possible. It is a proverbial needle-in-the-haystack problem, far beyond the reach of blind searches. To make matters worse, many proteins are overlapping, with portions of their genes occupying the same region of DNA. The same set of mutations would have to result in not one, but two proteins, making the search problem that much more tricky. Furthermore, many proteins perform multiple functions. Random mutations somehow would have to find those very special proteins that can perform double duty in the cell. And finally, many proteins perform crucial roles within a complex environment. Without these proteins the cell sustains a significant fitness degradation. One protein that fits this description is centrobin, and now a new study shows it to be even more important than previously understood.
Centrobin is a massive protein of almost a thousand amino acids. Its importance in the division of animal cells has been known for more than ten years. An important player in animal cell division is the centrosome organelle which organizes the many microtubules—long tubes which are part of the cell’s cytoskeleton. Centrobin is one of the many proteins that helps the centrosome do its job. Centrobin depletion causes "strong disorganization of the microtubule network" and Impaired cell division .
Now, a New study shows just how important centrobin is in the development of the sperm tail. Without centrobin, the tail, or flagellum, development is “severely compromised.” And once the sperm is formed, centrobin is important for its structural integrity. As the paper concludes:
Our results underpin the multifunctional nature of [centrobin] that plays different roles in different cell types in Drosophila, and they identify [centrobin] as an essential component for C-tubule assembly and flagellum development in Drosophila spermatogenesis.
Clearly centrobin is an important protein. Without it such fundamental functions as cell division and organism reproduction are severely impaired.
And yet how did centrobin evolve?
Not only is centrobin a massive protein, but there are no obvious candidate intermediate structures. It is not as though we have that “long series of gradations in complexity” that Darwin called for:
Although the belief that an organ so perfect as the eye could have been formed by natural selection, is enough to stagger any one; yet in the case of any organ, if we know of a long series of gradations in complexity, each good for its possessor, then, under changing conditions of life, there is no logical impossibility in the acquirement of any conceivable degree of perfection through natural selection.
Unfortunately, in the case of centrobin, we do not know of such a series. In fact, centrobin would seem to be a perfectly good example of precisely how Darwin said his theory could be falsified:
If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.
Darwin could “find out no such case,” but he didn’t know about centrobin. Darwin required “a long series of gradations,” formed by “numerous, successive, slight modifications.”
With centrobin we are nowhere close to fulfilling these requirements. In other words, today’s science falsifies evolution. This, according to Darwin’s own words.
Let there be light
The wave nature of light
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Tuesday, 10 January 2023
These cavemen were men of letters?
Possible Cave “Proto-Writing” Challenges Slow Evolution of Human Consciousness
Denyse o'Leary
London-based wood carving conservator Ben Bacon has, with academic colleagues, shaken up Ice Age paleontology by demonstrating that the marks on the 20,000-year-old cave paintings of animals found across Europe could be interpreted as a lunar calendar timing reproductive cycles:
Prof Paul Pettitt, of Durham University, said he was “glad he took it seriously” when Mr Bacon contacted him.
“The results show that Ice Age hunter-gatherers were the first to use a systemic calendar and marks to record information about major ecological events within that calendar.”
NEWS, “LONDONER SOLVES 20,000-YEAR ICE AGE DRAWINGS MYSTERY” AT BBC (JANUARY 5, 2023) THE PAPER IS OPEN ACCESS.
Bacon had spent many hours both on the Internet and in the British Library, studying the paintings, looking for repetitive numerical patterns — something we would expect to find more often in a calendar than in other types of record-keeping. A collaboration took place among Bacon, two Durham University profs, and one from University College London then working out birth cycles for similar animals today. Thus, the BBC reports, “they deduced that the number of marks on the cave paintings was a record, by lunar month, of the animals’ mating seasons.”
Of the 800 sequences of dots analyzed, no sequence contained more than 13 dots, which suggested to the researchers the 13 months of the lunar year. They also “found strong correlations between the number of marks and the lunar months in which the specific animal is known to mate.” (Live Science) The frequent “Y” sign was, they believe, connected to giving birth:
A Statistical Analysis
After conducting a statistical analysis of the database, Bacon and his colleagues were amazed to find that their lunar calendar seems to hold up well with the patterns.
“Overall, there is a remarkable degree of correlation between the numbers of lines/dots in sequences with and without Y and the position of Y and the mating and birthing behaviors of our analytical taxa,” the researchers said in the study. “Our data do not explain everything, but even taking imprecision and regional variability into account, the degree of support for our hypothesis is striking.”
BECKY FERREIRA, “A TOTAL AMATEUR MAY HAVE JUST REWRITTEN HUMAN HISTORY WITH BOMBSHELL DISCOVERY” AT VICE (JANUARY 5, 2023)
Other researchers are not convinced, however:
Melanie Chang, a paleoanthropologist at Portland State University who was not involved in the study, told Live Science in an email that she agrees with the researchers’ assessment that “Upper Palaeolithic people had the cognitive capacity to write and to keep records of time.” However, she cautioned that the researchers’ “hypotheses are not well-supported by their results, and they also do not address alternative interpretations of the marks they analyzed.”
KRISTINA KILLGROVE, “20,000-YEAR-OLD CAVE PAINTING ‘DOTS’ ARE THE EARLIEST WRITTEN LANGUAGE, STUDY CLAIMS. BUT NOT EVERYONE AGREES.” AT LIVE SCIENCE (DECEMBER 5, 2022)
The Big News
No doubt the paleontology community will be debating the exact significance of the marks for some time. For now, the big news is the fact that such ancient humans were apparently communicating via symbolic record-keeping as well as art ten thousands or more years earlier than we have thought:
It would be hard to overstate the magnitude of this discovery, assuming it passes muster in the wider archaeological community. It would rewrite the origins of, well, writing, which is one of the most important developments in human history. Moreover, if these tantalizing symbols represent an early calendar, they offer a glimpse of how these hunter-gatherers synchronized their lives with the natural cycles of animals and the Moon.
In short, if the new hypothesis is accurate, it shows that our Paleolithic ancestors “were almost certainly as cognitively advanced as we are” and “that they are fully modern humans,” Bacon told Motherboard. It also means “that their society achieved great art, use of numbers, and writing” and “that reading more of their writing system may allow us to gain an insight into their beliefs and cultural values,” he concluded.
BECKY FERREIRA, “A TOTAL AMATEUR MAY HAVE JUST REWRITTEN HUMAN HISTORY WITH BOMBSHELL DISCOVERY” AT VICE (JANUARY 5, 2023)
The researchers, who plan further publications in this area, are careful to call their find “proto-writing” rather than “writing” because it simply marks seasonal patterns. If they or others were to find inscriptions or apparent histories, that would be an even more significant development.
The find certainly challenges the idea that human consciousness underwent a long, slow evolution in recent millennia. It was mainly the technology that evolved, it seems.
You may also wish to read: Why is Neanderthal art considered controversial? It makes sense that whenever humans started to wonder about life, we started to create art that helps us think about it. Science writer Michael Marshall reports that some researchers are accused of banning others from taking samples that would prove a Neanderthal was the artist.
An architectural icon examined.
The Chrysler building
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Lamarck's revenge?
On Lamarck
Cornelius G Hunter
In the twentieth century Lamarckian Inheritance was an anathema for evolutionists. Careers were ruined and every evolutionist knew the inheritance of acquired characteristics sat right along the flat earth and geocentrism in the history of ideas. The damning of Lamarck, however, was driven by dogma rather than data, and today the evidence has finally overcome evolutionary theory.
Indeed there is much contemporary discussion, observations and critical analysis consistent with this position led by Corrado Spadafora, Yongsheng Liu, Denis Noble, John Mattick and others, that developments such as Lamarckian Inheritance processes (both direct DNA modifications and indirect, viz. epigenetic, transmissions) in evolutionary biology and adjacent fields now necessitate a complete revision of the standard neo-Darwinian theory of evolution or “New Synthesis " that emerged from the 1930s and 1940s.
Indeed, we now know of a “plethora of adaptive Lamarckian-like inheritance mechanisms.
””
Samuel Clarke on the trinity.
Stanford Encycloedia
In his lifetime, Clarke was infamous for his view of the trinity, and he sparked a vociferous debate (Ferguson 1974, 59–149; Pfizenmaier 1997, 179–216). Clarke was not officially censured (but nearly so), but it surely prevented his rising to higher office. Clarke’s writing on the trinity are relevant for understanding his other metaphysical positions, especially his identification of “person” with intelligent, acting agent rather than with a particular substance, which has not been sufficiently reconciled with his account of personal identity as wrapped up with an immaterial soul.
In Christian theology, God is represented as tripartite—three persons but one God. In the 1662 Book of Common Prayer, in use in England during Clarke’s lifetime, one of the liturgies draws from the Athanasian Creed, which includes the following discussion of the Trinity: “For there is one Person of the Father, another of the Son: and another of the Holy Ghost. But the Godhead of the Father, of the Son, and of the Holy Ghost, is all one… So the Father is God, the Son is God : and the Holy Ghost is God. And yet they are not three Gods: but one God.” In his position as a cleric, Clarke was required to subscribe to this formulation. In 1712, against the advice of his friends, he published The Scripture-Doctrine of the Trinity, in which he diverged from what his opponents considered the plain sense of this formulation. The Scripture-Doctrine of the Trinity begins by collecting all the passages of the New Testament that relate to the Trinity. It then sets out a series of 55 propositions regarding the Trinity, each supported by references to the texts collected in the first section and writings from the early Christian church. However, the biblical texts do not primarily discuss God’s metaphysical attributes, according to Clarke, but ascribe dominion to God (W 4.150; Snobelen 2004, 265–275). The third section relates these propositions to the Anglican liturgy. This approach reflects Clarke’s general expectation that the correct theological doctrines are found in the Bible, are endorsed by the early church, and are compatible with reason. Through hundreds of years of what he considered bad metaphysics, the correct and intelligible doctrine of the trinity had become obscured, and Clarke hoped to return to a pre-Athanasian understanding of the trinity.
Clarke’s position in The Scripture-Doctrine of the Trinity was labeled by his opponents as “Arian,” “Socinian,” and “Sabellian.” Although they were commonly used as abusive terms for anyone holding non-traditional or anti-trinitarian views, they also have more precise meanings. An Arian holds that the Son (the second person of the Trinity) is divine but not eternal; he was created by God the Father out of nothing before the beginning of the world. A Socinian holds that the Son is merely human and was created at or after the conception of Jesus. A Sabellian holds that the Son is a mode of God. In the precise use of the terms, Clarke is none of these. Unlike the Arians, Clarke affirmed that the Son is co-eternal with the Father and not created (W 4.141). (Pfizenmaier 1997 provides further textual and historical arguments that Clarke should not be classified as an Arian.) From this it also follows that, contra the Socinians, the Son existed before the conception of Jesus. Unlike the Sabellians, Clarke denied that the Son was a mode of the Father. (This would have been very problematic given that he sometimes claimed that space is a mode of God.) Clarke’s claimed ignorance about substance made him reluctant to declare that the Father and the Son were the same divine substance, but the Son is endowed by the Father with all of the power and authority of the Father. He also called the manner of the Son’s generation from the father “ineffable.” So while Clarke denied that the trinity was a “mystery,” he did believe that the manner in which the Father’s power is communicated to the Son is “after a manner to us unknown” (Proposition 35; 4.159).
Clarke affirms that each member of the trinity is a person, but only the Father is self-existent, which means that the Father by essence (rather than by “office”) has a property that the Son does not. His views are best described as subordinationist but he could also be called a unitarian, in at least some senses of the term (Tuggy 2014; 204–205). See especially Prop. 25 (W 4.150); Prop. 27 (W 4.151); and Prop. 34 (“The Son, whatever his metaphysical essence of substance be, and whatever divine greatness and dignity is ascribed to him in scripture; yet in this he is evidently subordinate to the Father, that he derives his being, attributes, and powers, from the Father, and the Father nothing from him”; 4.155). To the Father alone are ascribed “independence and supreme authority” (Proposition 27; 4.151). Every other attribute and power that can be ascribed to the Father can also be ascribed to the Son, “but the titles ascribed to the Son, must always carry along with them the idea of being communicated or derived” (4.153).
Monday, 9 January 2023
David Berlinski :Ace Darwin Skeptic on Darwinism v. Maths
David Berlinski on Darwinism.
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Darwinism's fall of Rome moment at hand?
Will an Engineering Paradigm Supplant Darwinism?
David Coppedge
The heyday of Darwinism may be coming to an end. Its summer of dominance after neo-Darwinism arose and conquered every field of biology led to an autumn of colorful just-so stories, and now a Narnian rule, where it is always winter and never Christmas. Evolutionary biologists repeat the old dogmas with less and less creative insight, as if cranking out expected boilerplate in a spirit of drudgery. But like a waft of a slightly less-cold breeze, with a slightly higher sun in the sky, hints of a new paradigm may be signaling that biology is about to turn over a new leaf.
One such tender shoot of greenery appeared in Science Magazine, where Maria Clara Zanellati and Sarah Cohen wrote a perspective piece titled, “The endosome as engineer.” It’s an example of an ever-so-slight tendency in mainstream journals — perhaps too early to call a trend — that ignores Darwinism completely while warming up to the engineering paradigm. It is often done without voicing the name of the Enemy, intelligent design.
A hallmark of eukaryotic cells is that they are compartmentalized into membrane-bound organelles. This allows for the spatial separation of biochemically incompatible processes. Nevertheless, organelles must work together for the cell to function. There has been increasing interest in organelle communication at membrane contact sites — where two organelles are anchored in close apposition by “tether” proteins. These contact sites allow the exchange of materials and information between cellular compartments. Intriguingly, organelles can also influence one another’s abundance and morphology. Most studies have focused on the role of the endoplasmic reticulum (ER) in shaping other organelles. However, on page 1188 of this issue, Jang et al. show that the endosome can reengineer ER shape in response to changing nutrient levels, which in turn affects the morphology and function of additional organelles.
The word “engineering” appears briefly in the above-referenced paper by Jang et al., but only in regard to the scientists who engineered the cell lines and their genomes. Still, significantly, evolution was notable for its absence, while engineering terms were used to describe what the endosome is doing: rewiring, signaling, orchestration, function, program, coordination, and regulation.
It’s Logical
Another paper, in Science Advances, is almost comical in its dissing of Darwinism. The paper is all about logic, using the word 18 times. Authors Sun and Horrigan from Baylor College of Medicine describe “A gating lever and molecular logic gate that couple voltage and calcium sensor activation to opening in BK potassium channels.” Sounds like what an IT engineer might do. Here’s their only mention of evolution:
The logic gate–like integration of V and Ca2+ signaling by the YFF pathway is a potentially unique mechanismthat raises many interesting questions regarding its physiological role and evolution. While we cannot speculate about the latter, the most obvious role of the mechanism is to enhance both V- and Ca2+-dependent coupling, and it may also act paradoxically to simplify the physiological response to V and Ca2+, as discussed below.
Forward they proceed into engineering language, leaving Darwinism behind, mumbling in his beard about what “seems to me.” Sun and Horrigan are more interested in couplings and sensors:
In conclusion, our results suggest that coupling mechanisms can be indirect and distributed and that resolving these mechanisms requires structure-function analysis that can distinguish changes in coupling from changes in sensor or gate equilibria, as well as structural information in different states to distinguish static and dynamic interactions.
Nature Feeling the Warmth, Too?
Norman Lockyer founded the journal Nature in the days of the X Club to promote Darwinism. The first issue had a frontispiece by Thomas Huxley, and in the first year there were half a dozen articles “urging Darwin’s scheme, two of which were written by Darwin himself” (Browne, p. 248). That was in 1869. As everyone knows, the Nature Publishing empire proceeded to dominate the journal business and continues its “polemic purpose” in support of materialist science.
Recently, however, at Scientific Reports, one of Nature’s open-access journals, three scientists wrote a Darwin-free editorial on “3D Genome Organization.” Like the paper described above, this editorial portrays biological engineering without using the word. More importantly, it promotes interdisciplinary research focused on how genomes achieve structure-function relationships from a linear sequence. This opens doors for engineering-based research that scientists weary of Darwinism might find attractive.
We are still a long way from understanding how 3D genome organization is linked precisely to genome function. A concerted multi-disciplinary effort is needed to develop new tools and computational prediction methods, multi-target chromatin imaging techniques in live-cells, and efficient manipulation methods for 3D genome structures. These efforts should be accompanied by the collection of 3D genome data from different diseased and healthy cells and tissues in humans, as well as a range of model organisms. Our increased knowledge of 3D folding of the genome will lead to a better appreciation of the regulatory potential of the linear genetic sequence. 3D genome organization emerges as a cell type specific epigenetic mechanism and gives us clues about the regulatory effect of the non-coding genome in the 3D context. This understanding will allow for enhanced interpretation of genetic variants and their potential phenotypic effects. Finally, such studies will bring new 3D insights into diagnostics and therapies for different conditions including cancer, developmental diseases, ageing, and related disorders.
One can almost sense the excitement at the potential of looking at genomics with an engineer’s eyes.
Disruptors Needed
Nature complained this month that “‘Disruptive’ science has declined — and no one knows why.” Max Kozlov explained, “The proportion of publications that send a field in a new direction has plummeted over the last half-century.” Kozlov gropes for reasons for it. A related paper by Park, Leahey and Funk in the same issue likewise comes to no firm conclusion. All they can suggest are possible ways to stir the embers and ignite something exciting.
Understanding the decline in disruptive science and technology more fully permits a much-needed rethinking of strategies for organizing the production of science and technology in the future.
One factor they ignore is the stupor of consensus. In biology, the aging Darwinian consensus has stifled fresh, disruptive thinking outside the box. Many scientists have contented themselves with describing whatever complex phenomenon is under investigation by saying with a ho-hum that it “evolved” to do what it does. To this day, though, nobody has witnessed a new organ or programmed system come into being by Darwin’s mutation/selection “mechanism” (as if “mechanism” can properly be applied to products of mindless processes).
People do, by contrast, witness new products coming from engineers. Intelligent minds possess foresight and creativity that can find elegant solutions to problems. That’s what life does. The engineering paradigm is explicitly and effectively applied within the intelligent design community, such as in the new book Your Designed Body by an engineer and an MD. Their interdisciplinary collaboration achieves credible understanding: the body looks designed because it is designed in ways that would make human engineers envious.
Discovery Institute leads the world in design-based initiatives, events, and publications. If the engineering paradigm succeeds in bringing a new leaf to biology after the long Darwinian winter, DI may not get the credit it deserves. It is still hard for scientists to overtly embrace intelligent design because the Darwin empire’s punishment of all who stray from the consensus is legendary. But if, after a century of Darwin’s reign of terror, with its racism, eugenics, meaninglessness, ugliness, and censorship, an engineering-theoretic paradigm offers a new way of doing research, it promises to bring not only superior understanding of how life works, but with it untold practical benefits to the whole world — not the least of which might be great pleasure and satisfaction at rediscovering purpose at the root of life.
On origin of life science's spectacular fail re:design denial.
The mystery of life's origin.
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On the prehuman singularity.
Cosmologist Frank Tipler on the Singularity Atheists Try To Evade
Evolution news
On a classic ID the Future episode we hear commentary on the singularity from distinguished cosmologist Frank Tipler, co-author of The Anthropic Cosmological Principle. The singularity in question isn’t the supposed future singularity imagined by transhumanists, but the evidentially well-supported singularity at the foundation of the Big Bang. The equations are clear, says Tipler, as are their implications: among its many arresting features, the Big Bang singularity had an existence outside of space and time, was intrinsically infinite, and was not subject to any laws of physics. Atheists today still resist this conclusion, Tipler says, but only this conclusion has experimental support, and the negative implications for atheism are hard to miss.Download the podcast or listen to it here.
Sunday, 8 January 2023
On the zombies prowling Darwinism's badlands.
Icons of evolution
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On Darwinism's gradualism(or lack thereof) problem.
Diversity of Life
Cornelius G Hunter
But the origin of life is just the beginning of evolution’s problems. For science now suggests evolution is incapable of creating the diversity of life and all of its designs:
Before the extensive sequencing of DNA became available it would have been reasonable to speculate that random copying errors in a gene sequence could, over time, lead to the emergence of new traits, body plans and new physiologies that could explain the whole of evolution. However the data we have reviewed here challenge this point of view. It suggests that the Cambrian Explosion of multicellular life that occurred 0.54 billion years ago led to a sudden emergence of essentially all the genes that subsequently came to be rearranged into an exceedingly wide range of multi-celled life forms - Tardigrades, the Squid, Octopus, fruit flies, humans – to name but a few.
As one of the authors writes, “the complexity and sophistication of life cannot originate (from non-biological) matter under any scenario, over any expanse of space and time, however vast.” As an example, consider the octopus.
Octopus
First, the octopus is an example of novel, complex features, rapidly appearing and a vast array of genes without an apparent ancestry:
Its large brain and sophisticated nervous system, camera-like eyes, flexible bodies, instantaneous camouflage via the ability to switch colour and shape are just a few of the striking features that appear suddenly on the evolutionary scene. The transformative genes leading from the consensus ancestral Nautilus (e.g., Nautilus pompilius) to the common Cuttlefish (Sepia officinalis) to Squid (Loligo vulgaris) to the common Octopus (Octopus vulgaris) are not easily to be found in any pre-existing life form.
But it gets worse. As Darwin’s God has explained, The Cephalopods demonstrate a highly unique level of adenosine to inosine mRNA editing. It is yet another striking example of lineage-specific design that utterly contradicts macroevolution:
These data demonstrate extensive evolutionary conserved adenosine to inosine (A-to-I) mRNA editing sites in almost every single protein-coding gene in the behaviorally complex coleoid Cephalopods (Octopus in particular), but not in nautilus. This enormous qualitative difference in Cephalopod protein recoding A-to-I mRNA editing compared to nautilus and other invertebrate and vertebrate animals is striking. Thus in transcriptome-wide screens only 1–3% of Drosophila and human protein coding mRNAs harbour an A-to-I recoding site; and there only about 25 human mRNA messages which contain a conserved A-to-I recoding site across mammals. In Drosophila lineages there are about 65 conserved A-sites in protein coding genes and only a few identified in C. elegans which support the hypothesis that A-to-I RNA editing recoding is mostly either neutral, detrimental, or rarely adaptive. Yet in Squid and particularly Octopus it is the norm, with almost every protein coding gene having an evolutionary conserved A-to-I mRNA editing site isoform, resulting in a nonsynonymous amino acid change. This is a virtual qualitative jump in molecular genetic strategy in a supposed smooth and incremental evolutionary lineage - a type of sudden “great leap forward”. Unless all the new genes expressed in the squid/octopus lineages arose from simple mutations of existing genes in either the squid or in other organisms sharing the same habitat, there is surely no way by which this large qualitative transition in A-to-I mRNA editing can be explained by conventional neo-Darwinian processes, even if horizontal gene transfer is allowed.
Another look at Darwinism '" simple beginning" issues.
Origin of Life
Cornelius G Hunter
Regarding origin of life studies, which try to explain how living cells could somehow have arisen in an ancient, inorganic, Earth, the paper explains that this idea should have long since been rejected, but instead it has fueled “sophisticated conjectures with little or no evidential support.”
the dominant biological paradigm - abiogenesis in a primordial soup. The latter idea was developed at a time when the earliest living cells were considered to be exceedingly simple structures that could subsequently evolve in a Darwinian way. These ideas should of course have been critically examined and rejected after the discovery of the exceedingly complex molecular structures involved in proteins and in DNA. But this did not happen. Modern ideas of abiogenesis in hydrothermal vents or elsewhere on the primitive Earth have developed into sophisticated conjectures with little or no evidential support.
In fact, abiogenesis has “no empirical support.”
independent abiogenesis on the cosmologically diminutive scale of oceans, lakes or hydrothermal vents remains a hypothesis with no empirical support
One problem, of many, is that the early Earth would not have supported such monumental evolution to occur:
The conditions that would most likely to have prevailed near the impact-riddled Earth's surface 4.1–4.23 billion years ago were too hot even for simple organic molecules to survive let alone evolve into living complexity
In fact, the whole idea strains credibility “beyond the limit.”
The requirement now, on the basis of orthodox abiogenic thinking, is that an essentially instantaneous transformation of non-living organic matter to bacterial life occurs, an assumption we consider strains credibility of Earth-bound abiogenesis beyond the limit.
All laboratory experiments have ended in “dismal failure.” The information hurdle is of “superastronomical proportions” and simply could not have been overcome without a miracle.
The transformation of an ensemble of appropriately chosen biological monomers (e.g. amino acids, nucleotides) into a primitive living cell capable of further evolution appears to require overcoming an information hurdle of superastronomical proportions, an event that could not have happened within the time frame of the Earth except, we believe, as a miracle. All laboratory experiments attempting to simulate such an event have so far led to dismal failure.
Saturday, 7 January 2023
The question of the millennium: Can we talk about this?
Listen: Dr. Jay Bhattacharya on COVID-19 as One of the Most Divisive Events in American History
Evolution news
The COVID-19 pandemic has been one of the most politically and culturally divisive events in American history. Which seems odd. Usually, a universal external threat unites societies and rallies populations to focus on the common foe. Instead, American society fractured into different tribes, which often coincided with our preexisting political factionalism.
Adding to our woes, the proper approach to scientific inquiry and policy makers’ relationship with the expert class became badly skewed. Once an orthodoxy was declared by the World Health Organization or the Center for Disease Control, government leaders, the mainstream media, and Big Tech circled the wagons to prevent dissenting views from being aired — and even seeking to punish those with differing opinions.
And we now know that action was taken to suppress heterodox voices. On a new episode of the Humanize podcast, Wesley Smith’s guest is one of those caught in this cultural oppression. Dr. Jay Bhattacharya, making his second appearance on the podcast, is a Professor of Health Policy at Stanford University and a research associate at the National Bureau of Economics Research. He directs Stanford’s Center for Demography and Economics of Health and Aging. Download or listen to the podcast here
Copernicus redux?
paper demonstrates superiority of the design heuristic
Did you know Mars is going backwards? For the past few weeks, and for several weeks to come, Mars is in its retrograde motion phase. If you chart its position each night against the background stars, you will see it pause, reverse direction, pause again, and then get going again in its normal direction. And did you further know that retrograde motion helped to cause a revolution? Two millennia ago, Aristotelian physics dictated that the Earth was at the center of the universe. Aristarchus’ heliocentric model, which put the Sun at the center, fell out of favor. But what Aristotle’s geocentrism failed to explain was retrograde motion. If the planets are revolving about the Earth, then why do they sometimes pause, and reverse direction? That problem fell to Ptolemy, and the lessons learned are still important today.
Ptolemy explained anomalies such as retrograde motion with additional mechanisms, such as epicycles, while maintaining the circular motion that, as everyone knew, must be the basis of all motion in the cosmos. With less than a hundred epicycles, he was able to model, and predict accurately the motions of the cosmos. But that accuracy came at a cost—a highly complicated model.
In the Middle Ages William of Occam pointed out that scientific theories ought to strive for simplicity, or parsimony. This may have been one of the factors that drove Copernicus to resurrect Aristarchus’ heliocentric model. Copernicus preserved the required circular motion, but by switching to a sun-centered model, he was able to reduce greatly the number of additional mechanisms, such as epicycles.
Both Ptolemy’s and Copernicus’ models accurately forecast celestial motion. But Copernicus was more parsimonious. A better model had been found.
Kepler proposed ellipses, and showed that the heliocentric model could become even simpler. It was not well accepted though because, as everyone knew, celestial bodies travel in circles. How foolish to think they would travel along elliptical paths. That next step toward greater parsimony would have to wait for the likes of Newton, who showed that Kepler’s ellipses were dictated by his new, highly parsimonious, physics. Newton described a simple, universal, gravitational law. Newton’s gravitational force would produce an acceleration, which could maintain orbital motion in the cosmos.
But was there really a gravitational force? It was proportional to the mass of the object which was then cancelled out to compute the acceleration. Why not have gravity cause an acceleration straightaway?
Centuries later Einstein reported on a man in Berlin who fell out of a window. The man didn’t feel anything until he hit the ground! Einstein removed the gravitational force and made the physics even simpler yet.
The point here is that the accuracy of a scientific theory, by itself, means very little. It must be considered along with parsimony. This lesson is important today in this age of Big Data. Analysts know that a model can always be made more accurate by adding more terms. But are those additional terms meaningful, or are they merely epicycles? It looks good to drive the modeling error down to zero by adding terms, but when used to make future forecasts, such models perform worse.
There is a very real penalty for adding terms and violating Occam’s Razor, and today advanced algorithms are available for weighing the tradeoff between model accuracy and model parsimony.
This brings us to common descent, a popular theory for modeling relationships between the species. As we have discussed many times here, common descent fails to model the species, and a great many additional mechanisms—biological epicycles—are required to fit the data.
And just as cosmology has seen a stream of ever improving models, the biological models can also improve. This week a very important model has been proposed in a new paper, authored by Winston Ewert, in the Bio-Complexity journal.
Inspired by computer software, Ewert’s approach models the species as sharing modules which are related by a dependency graph. This useful model in computer science also works well in modeling the species. To evaluate this hypothesis, Ewert uses three types of data, and evaluates how probable they are (accounting for parsimony as well as fit accuracy) using three models.
Ewert’s three types of data are: (i) Sample computer software, (ii) simulated species data generated from evolutionary / common descent computer algorithms, and (iii) actual, real species data.
Ewert’s three models are: (i) A null model in which entails no relationships between
any species, (ii) an evolutionary / common descent model, and (iii) a dependency graph model.
Ewert’s results are a Copernican Revolution moment. First, for the sample computer software data, not surprisingly the null model performed poorly. Computer software is highly organized, and there are relationships between different computer programs, and how they draw from foundational software libraries. But comparing the common descent and dependency graph models, the latter performs far better at modeling the software “species.” In other words, the design and development of computer software is far better described and modeled by a dependency graph than by a common descent tree.
Second, for the simulated species data generated with a common descent algorithm, it is not surprising that the common descent model was far superior to the dependency graph. That would be true by definition, and serves to validate Ewert’s approach. Common descent is the best model for the data generated by a common descent process.
Third, for the actual, real species data, the dependency graph model is astronomically superior compared to the common descent model.
Let me repeat that in case the point did not sink in. Where it counted, common descent failed compared to the dependency graph model. The other data types served as useful checks, but for the data that mattered—the actual, real, biological species data—the results were unambiguous.
Ewert amassed a total of nine massive genetic databases. In every single one, without exception, the dependency graph model surpassed common descent.
Darwin could never have even dreamt of a test on such a massive scale.
Darwin also could never have dreamt of the sheer magnitude of the failure of his theory. Because you see, Ewert’s results do not reveal two competitive models with one model edging out the other.
We are not talking about a few decimal points difference. For one of the data sets (HomoloGene), the dependency graph model was superior to common descent by a factor of 10,064. The comparison of the two models yielded a preference for the dependency graph model of greater than ten thousand.
Ten thousand is a big number.
But it gets worse, much worse.
Ewert used Bayesian model selection which compares the probability of the data set given the hypothetical models. In other words, given the model (dependency graph or common descent), what is the probability of this particular data set? Bayesian model selection compares the two models by dividing these two conditional probabilities. The so-called Bayes factor is the quotient yielded by this division.
The problem is that the common descent model is so incredibly inferior to the dependency graph model that the Bayes factor cannot be typed out. In other words, the probability of the data set given the dependency graph model, is so much greater than the probability of the data set given the common descent model, that we cannot type the quotient of their division.
Instead, Ewert reports the logarithm of the number. Remember logarithms? Remember how 2 really means 100, 3 means 1,000, and so forth?
Unbelievably, the 10,064 value is the logarithm (base value of 2) of the quotient! In other words, the probability of the data on the dependency graph model is so much greater than that given the common descent model, we need logarithms even to type it out. If you tried to type out the plain number, you would have to type a 1 followed by more than 3,000 zeros!
That’s the ratio of how probable the data are on these two models!
By using a base value of 2 in the logarithm we express the Bayes factor in bits. So the conditional probability for the dependency graph model has a 10,064 advantage of that of common descent.
10,064 bits is far, far from the range in which one might actually consider the lesser model. See, for example, the Bayes factor Wikipedia page, which explains that a Bayes factor of 3.3 bits provides “substantial” evidence for a model, 5.0 bits provides “strong” evidence, and 6.6 bits provides “decisive” evidence.
This is ridiculous. 6.6 bits is considered to provide “decisive” evidence, and when the dependency graph model case is compared to comment descent case, we get 10,064 bits.
But it gets worse.
The problem with all of this is that the Bayes factor of 10,064 bits for the HomoloGene data set is the very best case for common descent. For the other eight data sets, the Bayes factors range from 40,967 to 515,450.
In other words, while 6.6 bits would be considered to provide “decisive” evidence for the dependency graph model, the actual, real, biological data provide Bayes factors of 10,064 on up to 515,450.
We have known for a long time that common descent has failed hard. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data.
Friday, 6 January 2023
A heavenly witness against design deniers?
Animals Tune Behavior by Lunar Cycle; but How?
David Coppedge
Tonight’s moon will be full, so here is a timely question. Many unrelated animals tune their behavior by the lunar cycle. How do they do it, given that sunlight overpowers moonlight?
Researchers in Austria think they have found a clue: a cryptochrome protein that appears to respond to the lunar cycle. Cryptochrome proteins are also implicated in the geomagnetic sense in birds. Whatever they found, it surely must represent only a piece of a biological puzzle. Let them explain in this from the University of Wien:
Many marine organisms, including brown algae, fish, corals, turtles and bristle worms, synchronize their behavior and reproduction with the lunar cycle. For some species, such as the bristle worm Platynereiis dumerilii, lab experiments have shown that moonlight exerts its timing function by entraining an inner monthly calendar, also called circalunar clock. Under these laboratory conditions, mimicking the duration of the full moon is sufficient to entrain these circalunar clocks. However, in natural habitats light conditions can vary considerably. Even the regular interplay of sun- and moon creates highly complex patterns. Organisms using the lunar light for their timing thus need to discriminate between specific moon phases and between sun and moonlight. This ability is not well understood.
The first statement should alarm evolutionists. Circalunar clocks are found in very unrelated animals (evolutionarily speaking): vertebrates like fish and turtles and invertebrates like worms and corals. Each of these must have hit upon lunar tuning independently.
The researcher’s paper in Nature Communications points out that we humans have connections to the lunar cycle, too:
In addition, lunar timing effects have also been documented outside the marine environment, and recently uncovered correlations of human sleep and menstrual cycle properties with moon phases have re-initiated the discussion of an impact of the moon even on human biology. As recently documented for corals, desynchronization of these reproductively critical rhythms by anthropogenic impacts poses a threat to species survival.
The Bristle Worm as a Test Case
P. dumerilii, the so-called bristle worm is a polychaete (“much-haired) worm in phylum Annelida. Smithsonian Magazine lists 14 Fun Facts about these polychaetes, an “amazingly diverse family” of marine organisms:
Unbeknownst to most landlubbers, polychaetes rule the seas. There are at least 10,000 species of these swimming bristly worms, some of which pop with brilliant colors or light up with a bioluminescent glow. They’ve adapted to every imaginable marine habitat, from deep hydrothermal vents to crowded coral reefs to the open ocean—and many have found ways to survive that are definitely bizarre.
Interested readers can browse through Smithsonian’s list of facts and look at the pictures. A short horror movie shows a lionfish learning too late not to mess with a bobbit worm (Eunice aphroditois), a different species of bristle worm in the Atlantic. It’s a creature of nightmares, so be forewarned. The poisonous lionfish can’t use its defensive weapons against this lightning-fast monster: a worm! It’s a terrifying creature right out of the movie Tremors. More about bobbit worms can be found at ARCReef.com. Do not read this: some bobbit worms grow up to ten feet long! Fortunately, attacks on humans are rare, limited to “nasty bites” (Daily Mail).
Evolutionary Challenges
Back to P. dumerilii, a much more benign polychaete only 2-4 cm long. A type of ragworm, this species is found worldwide. Wikipedia calls it a living fossil. Although it’s an invertebrate, “it has an axochord, a paired longitudinal muscle that displays striking similarities to the notochord regarding position, developmental origin, and expression profile.” It swims with a coordinated system of cilia on its surface. “Whole-body coordination of ciliary locomotion is performed by a ‘stop-and-go pacemaker system’,” the article says. That’s not the only pacemaker in this amazing little worm. Despite having “a pair of the simplest eyes in the animal kingdom,” it can “see” the phases of the moon. Those little eyes do not help the evolutionary story:
The ciliary photoreceptor cells are located in the deep brain of the larva. They are not shaded by pigment and thus perceive non-directional light. The ciliary photoreceptor cells resemble molecularly and morphologically the rods and cones of the human eye. Additional [sic], they express an ciliary opsin that is more similar to the visual ciliary opsins of vertebrate rods and cones than to the visual rhabdomeric opsins of invertebrates.
The bristle worm’s genome also challenges Darwinism:
The genome of Platynereis dumerilii … contains approximately 1 Gbp (giga base pairs) or 109 base pairs. This genome size is close to the average observed for other animals. However, compared to many classical invertebrate molecular model organisms, this genome size is rather large and therefore it is a challenge to identify gene regulatory elements that can be far away from the corresponding promoter. But it is intron rich unlike those of Drosophila melanogaster and Caenorhabditis elegans and thus closer to vertebrate genomes including the human genome.
Wikipedia prudently abstains from speculating on how these worms evolved.
Possible Lunar Oscillator Found in P. dumerilii
In the introduction to the paper, the authors say, “Despite the importance and widespread occurrence of lunar rhythms, functional mechanistic insight is lacking.” They found a cryptochome protein they call L-Cry that appears to keep time to the full moon. Its asymmetric dimer appears to have two monomers with very different light sensitivities, which “provides the molecular basis to sense and interpret light intensities across five orders of magnitude.”
This is important because full sunlight swamps moonlight, so the worm brain must be able to discriminate the smaller peaks of illumination from larger ones. Additionally, L-Cry must be able to avoid being tricked by artificial light that can also outshine full moonlight. It must also be robust against darkness on cloudy full-moon nights and by “natural acute light disturbances, such as lightning.”
Experiments in the “worm room” under controlled simulations of sun and moon illumination cycles demonstrated this ability. “L-Cry’s major role could be that of a gatekeeper controlling which ambient light is interpreted as full-moonlight stimulus for circalunar clock entrainment,” they say. If an organism can set its lunar clock to a full moon, it can also discriminate other lunar phases.
The full moon is unique in having the longest duration of light at night, followed by sunrise. A circalunar clock presupposes, therefore, the ability to measure the duration as well as intensity of light. L-Cry may do this with a ratchet mechanism: as the protein accumulates photons, it reaches higher quantum levels that photoreduce parts of the low-sensitivity monomer. The authors also observed L-Cry accumulating in the nucleus and diminishing in the cytoplasm during the simulated moonlight exposure time. “This suggests that different cellular compartments convey the different light messages to different downstream pathways.”
Even so, this cryptochrome discovery only delivers “the first molecular entry point into the mechanisms underlying a moonlight-entrained monthly oscillator.” The photoreceptor for L-Cry is unknown. Additionally, L-Cry must cooperate with the circadian clock genes, adding to the regulatory complexity. How these proteins signal a cascade of physiological behaviors when it’s time to spawn remains curious. “Certainly, more extensive mechanistic studies are required to further verify our models.”
Convergent Functionality
Finally, an evolutionary consideration: Monthly synchronization by the moon has been documented for a wide range of organisms– including brown and green algae, corals, crustaceans, worms, but also vertebrates… Furthermore, recent reports also provide increasing evidence that the lunar cycle influences human behavior… Are the lunar effects mediated by conserved or different mechanisms?
Since L-Cry is not known in these other species, the authors speculate that either conservation of other proteins will be discovered, or that other proteins with analogous functions will be found.
Last, but not least the molecular mechanisms underlying the circalunar oscillator also await identification, and it is possible that conservation exists on this level. Examples are known from circadian biology and it will now require further work to reach a similar level of understanding for moon-controlled monthly rhythms and clocks.
Surely, though, conservation of function using entirely different molecular mechanisms poses a severe challenge to Darwinism. It would seem to require entirely different sets of mutations to be selected for a common function. In design theory, intelligence starts with the concept and can use different instruments to play the same tune.
The Palolo Worm
We end with a spectacular case of circalunar time tuning. Another polychaete, the Palolo Worm of the South Pacific, undergoes a remarkable reproductive cycle timed to both lunar and annual cycles. Britannica explains its life cycle:
The palolo worm of the South Pacific (Palolo siciliensis [P. viridis or Eunice viridis]) inhabits crevices and cavities in coral reefs. As the breeding season approaches, the tail end of the body undergoes a radical change.The muscles and most of the organs degenerate, and the reproductive organs rapidly increase in size. The limbs on the posterior segment become more paddlelike. After the animal backs part way out of its tubelike burrow, the posterior section breaks free and swims to the surface as a separate animal, complete with eyes. The anterior end, still attached to its tube, regenerates a new posterior end.
The free-swimming half-worms contains sperm and eggs. Tens of thousands of these half-worms swim to the surface as if on cue, and release their reproductive cells always at the same time of year and at a particular phase of the moon.
The free-swimming section always makes its appearance in the early morning for two days during the last quarter of the Moon in October. Twenty-eight days later, it appears in even greater numbers in the final quarter of the November Moon. At the surface of the sea the sperm and eggs are discharged, and fertilization occurs. Palolo tails, considered a delicacy by the Polynesians, are gathered in vast numbers during swarming.
Worms. Such simple, lowly creatures. But what wonders await the biologists who delve into their mechanisms. Like everything else in biology, design-inspired awe explodes in the details.
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