Conserving function from root to branches of a "tree of life"

 Quiz: Is This a Prediction from the Tree of Life?

Paul Nelson

The three-domain Tree of Life (TOL) geometry below is textbook orthodoxy, due largely to the work of the late Carl Woese on patterns in 16S rRNA.

Okay — here’s a quiz:

On the basis of this TOL geometry, what would you predict as the genome content for the Last Bacterial Common Ancestor (LCBA) — the hypothetical entity occupying the branch near the red circle?

Or, to turn the puzzle around — this is the actual quiz question — if the LCBA existed, what would you expect to find in the “core genomes” of bacterial groups at the tips of the branches within the domain Bacteria? Should every bacterial group conserve the same core set of orthologous genes?

Give your answer, then read on…

Now refer to a new article in Genome Biology, “Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome” (open access). From the article:

core genomes differed greatly at the gene-level, with no single OG [orthologous group] observed in all 183 core genomes, consistent with previous observations that biochemical functions rather than individual genes tend to be conserved.”

Conservation of function, but not genes, can be understood with an analogy to natural language. Consider two sentences:

The hulking great lorry skirted round an enormous chasm in the roadway.

The massive truck dodged a huge pothole in the street.

The individual words in these sentences — e.g., “lorry” vs. “truck” — are functional synonyms, but not direct variants of each other (such as “color” and “colour”). Varying “lorry” letter by letter will take a LONG way to get to “truck,” with nearly all of the intermediate character strings not referring to large commercial vehicles.

Is conservation of function, without conservation of genes, a TOL prediction? It would seem not.

Physicists still on the quest for JEHOVAH'S Mind?

 Barbieri’s Dilemma: Biological Information without Intelligence

Denyse O Leary

Last week, we looked at a most interesting paper, by University of Ferrara theoretical biologist Marcello Barbieri. He was discussing the discomfort biologists feel with the vast amount of information in life forms, which — in the view of many — “does not really belong in science.” The divide, he says, is between biologists who insist that life is chemistry only and those who, like him, see it as chemistry plus information. The problem is obvious: Information is by its nature immaterial. It is measured in bits, not kilograms or joules. It is understood in terms that invoke mathematics and probability more than chemistry and physics.

A physicalist biologist ignores or discounts the role of information. Barbieri wants to show that information is fully compatible with current assumptions in biology. So, in his 2016 paper, he tries his hand at incorporating it into a materialist origin-of-life story:

It comes from the idea that life is artefact-making, that genes and proteins are molecular artefacts manufactured by molecular machines and that artefacts necessarily require sequences and coding rules in addition to the quantities of physics and chemistry. More precisely, it is shown that the production of artefacts requires new observables that are referred to as nominable entities because they can be described only by naming their components in their natural order. From an ontological point of view, in conclusion, information is a nominable entity, a fundamental but not-computable observable.

BARBIERI MARCELLO 2016 WHAT IS INFORMATION? PHIL. TRANS. R. SOC. A.3742015006020150060

HTTP://DOI.ORG/10.1098/RSTA.2015.0060, 13 MARCH 2016

Wait. Artifacts, are made by intelligent, purposeful agents. Almost all artifacts are, of course, developed by humans, using abstract thinking. Some other animals use artifacts in the form of simple tools. But these life forms are not prebiotic chemistry; they are already highly developed life forms.

That Raises a Question

If the James Webb Space Telescope required many human intelligent agents, why should we simply accept that the development of early cells, also complex, could be managed by chemistry alone — when such a development has never happened in nature since? That is, there is no spontaneous generation, as far as know.

Barbieri uses terms like “manufactured” and “naming” freely but they are only meaningful if we suppose intelligent agents. Some may blame the limits of human language for that. But there is a reason why language features those limits: When writing for a serious purpose, we don’t attribute decisions that clearly require intelligence to non-intelligent agents.

A Speculative History

Barbieri sketches a speculative history of the molecular machines that, he argues, preceded life:

The origin of protein life, on the other hand, was a much more complex affair, because proteins cannot be copied and their reproduction required molecular machines that employ a code, machines that have been referred to as codemakers. The evolution of the molecular machines, in short, started with bondmakers, went on to copymakers and finally gave origin to codemakers.

BARBIERI, 2016

It’s an interesting story. It sounds a bit like the history of a human industry. Which again raises the problem: If these makers were themselves unintelligent and non-purposeful, some other entity must have been using them as instruments. Complex, specified artefacts don’t just “happen” to get built. When Barbieri tells us that “The divide between life and matter is real because matter is made of spontaneous objects whereas life is made of manufactured objects,” he sounds like an intelligent design theorist. Unpopular but right.

The resemblance becomes even clearer when he offers,

Both the sequence of nucleotides in a gene and the sequence of letters in a book are carrying information: hereditary information in genes and syntactic information in language. In both cases, the information is digital (because it is made of discrete units) and linear (because the units are arranged in a linear order).

A book? Yes. He cites photos and music as well. Then, “Finally, we can represent letters, numbers, pixels, musical notes and many other symbols with the characters of computer language… ”

Indeed We Can!

Immaterial ideas can be represented in any number of ways. But now, as to the origin of immaterial ideas…

Barbieri, of course, would not want to associate himself with intelligent design theory! Instead, he cites in his defense eminent biologist Ernst Mayr (1904–2005): “There is nothing in the inanimate world that has a genetic program which stores information with a history of three thousand million years!” Also, information theorist Hubert Yockey (1916–2016) who “tirelessly pointed out that no amount of chemical evolution can cross the barrier that divides the analogue world of chemistry from the digital world of life, and concluded from this that the origin of life cannot have been the result of chemical evolution.”

He senses that there is something missing from Yockey’s summation:

At this point, one would expect to hear from Yockey how did linear and digital sequences appear on Earth, but he did not face that issue. He claimed instead that the origin of life is unknowable, in the same sense that there are propositions of logic that are undecidable. This amounts to saying that we do not know how linear and digital entities came into being; all we can say is that they were not the result of spontaneous chemical reactions. The information paradigm, in other words, has not been able to prove its ontological claim, and that is why the chemical paradigm has not been abandoned.

BARBIERI, 2016

Exposing the Problem

In doing so, Barbieri exposes the problem: “Life is chemistry” is an accepted dogmatic proposition that flies in the face of the evidence of large amounts of information in life that did not get there only by chemistry.

But defenders of the evidence for information, like Barbieri, are stymied. Complex, specified information does not originate without underlying intelligence. But the defenders do not wish to acknowledge that intelligence and anyway, they wouldn’t be allowed to. They would be speaking an unspeakable truth and would lose their membership in the establishment. 

Therefore, it is said, they have not proved their case. Either the information does not exist or anyway, it can be treated as if it did not. And all is well.

Note: As it happens, intelligent design theorists consider Yockey’s work a “primary contribution to the ID movement,” though an unintentional one, to be sure.

Next and last in this three-part series: Can information be separated from intelligence? Barbieri’s dilemma seems to be that he can’t give information its rightful place in life without acknowledging truths he cannot afford.

On physicists' search for the mind of God.

 John Horgan on the Madness of “Scientific Omniscience”

Paul Nelson 

I only saw physics Nobel laureate Steven Weinberg in person once — at Baylor University, in April 2000, at the big conference on “The Nature of Nature” organized by Bill Dembski and Bruce Gordon before the Polanyi Center ran into problems. Weinberg (third from left in the photo above) had the supreme self-confidence of a scientific Alpha Male, leaning on the speaker’s lectern from the side and dismissing design with ill-concealed contempt, except when he got onto the topic of the mysterious value of the cosmological constant. Then he paced the stage from one end to the other, not looking at the audience, muttering to himself and staring at his feet. The cosmological constant definitely bothered him.

Puzzles and Mysteries

Nonetheless, as science writer John Horgan explains in an article, Weinberg was one of the leading promoters of a “final theory” — the bedrock scientific account which would once and for all drive away all the remaining puzzles and mysteries. From, “The Delusion of Scientific Omniscience”:

Does anyone still think science can explain, well, everything? This belief was ascendant in the 1980s, when my career began. Bigshot scientists proclaimed they were solving the riddle of existence. They would explain why our universe exists and takes the form it does, and why we exist and are what we are. …

Stephen Hawking was the most influential know-it-all. In his 1988 mega-bestseller A Brief History of Time, Hawking predicted that physicists would soon find an “ultimate theory” that would explain how our cosmos came into being. He compared this achievement to knowing “the mind of God.” This statement was ironic. Hawking, an atheist, wanted science to eliminate the need for a divine creator.

I suspect Hawking, who had a wicked sense of humor, was goofing when he riffed on the ultimate theory. The success of Brief History nonetheless inspired copycat books by physicists, including Theories of Everything by John Barrow (1991), The Mind of God by Paul Davies (1992) and Dreams of a Final Theory (1993) by Nobel laureate Steven Weinberg.

Weinberg, a deadly serious man, was definitely not kidding when he envisioned a final theory. He argued that with the help of a new “supercollider” in Texas (which ended up being canceled), physicists might soon “bring to an end a certain kind of science, the ancient search for those principles that cannot be explained in terms of deeper principles.” Like Hawking, Weinberg hoped the final theory would crush, once and for all, our superstitious faith in an all-powerful, beneficent deity. “It would be wonderful to find in the laws of nature a plan, prepared by a concerned creator in which human being played some special role,” Weinberg wrote. “I find sadness in doubting that they will.”

Physicists were not the only scientists bewitched by the dream of omniscience.

As examples of “bewitched” scientists, Horgan mentions Peter Atkins, Francis Crick, and Richard Dawkins. Of note, he writes: “As for life, Dawkins’s claim that it is no longer a mystery is absurd. We still don’t have a clue how life began, or whether it exists elsewhere in the cosmos. We don’t know whether our emergence was likely or a once-in-eternity fluke.” Horgan himself bought into the final theory idea, at least for a time. Now he regards the notion as a species of insanity.

The edge of spacetime?

 

And still yet more on the business of war

 

Matthew's gospel according to the King James Version.

 

Science: the one enterprise that is better than those administering it?

 Science Is Self-Correcting? Time for a Reality Check

Denyse O Leary

Many of us grew up with the claim “Science — unlike religion — is self-correcting!” Why so many science boosters dragged religion into it was never clear to me. It sounded too much like saying “The chemistry department, unlike the (stupid) philosophy department, is self-correcting!”

Oh? Well, Let’s See Then

Self-absorbed nonsense often followed, which only heightened suspicion. 

The recent resignation of neuroscientist Marc Tessier-Lavigne, president of Stanford University, over yet another peer-reviewed research scandal has forced science thinkers to accept a, perhaps unaccustomed, moment of serious self-reflection. Here’s a sampling from recent news, first from veteran whistleblower Ivan Oransky:

You may have thought, given the voluminous coverage of this case, that Tessier-Lavigne’s defenestration demonstrates such failures are highly unusual and typically lead to significant sanctions.

Neither is true. If — and given the history of such episodes, that’s a big if — journals end up retracting the three papers Tessier-Lavigne has said he has agreed to retract (two in Science and one in Cell), the number will represent less than a tenth of a percent of the retractions we expect to see this year. We at Retraction Watch, which tracks retracted papers, estimate that figure to be about 5,000 — a tiny fraction of how many retractions should happen but don’t. And the careers of most researchers whose names are on the retractions that do happen haven’t suffered a scratch. The ones whose papers haven’t been retracted have even fewer worries.

IVAN ORANSKY, “SCIENCE CORRECTS ITSELF, RIGHT? A SCANDAL AT STANFORD SAYS IT DOESN’T,“ SCIENTIFIC AMERICAN, AUGUST 1, 2023.

Oransky reasonably wonders, why do prestigious journals suffer no loss of reputation as these incidents multiply? You know they are having problems in this area when, as he reports, it is often volunteer sleuths whose efforts bring down questionable papers. Tessier-Lavigne was brought down by student journalist Theo Baker.

But It’s Worse than That

As he and fellow Retraction Watch whistleblower Adam Marcus note at The Guardian, journals passively enable flawed work:

Journals and publishers also fail to do their part, finding ways to ignore criticism of what they have published, leaving fatally flawed work unflagged. They let foxes guard the henhouse, by limiting critics to brief letters to the editor that must be approved by the authors of the work being criticized. Other times, they delay corrections and retractions for years, or never get to them at all.

IVAN ORANSKY AND ADAM MARCUS, “THERE’S FAR MORE SCIENTIFIC FRAUD THAN ANYONE WANTS TO ADMIT, THE GUARDIAN, AUGUST 9, 2023.

Veteran science journalist Matt Ridley surveys the scene:

Gloriously, in June this year, a study of honesty itself was accused of being dishonest. Professor Francesca Gino of Harvard Business School had claimed that people who signed truthfulness declarations relating to tax or insurance at the top of a page were more honest than those who signed at the bottom of a page. Her co-author says he has been shown ‘compelling evidence’ of data falsification. Gino denies the accusation and filed a lawsuit against Harvard last week.

MATT RIDLEY, “SCIENCE FICTION: THE CRISIS IN RESEARCH,” SPECTATOR, 12 AUGUST 2023.

Yes, That’s Another Factor

Increasingly, researchers facing retraction and possible consequences have begun resorting to lawsuits. Their chances of winning may be small but if accusers must run up a big legal bill defending themselves, they may well back off and let the whole matter drop. 

Flawed but accepted research has even attracted a parody paper, a Sokal hoax-style entry that attempted to test just how bad the situation really is:

In 2015 John Bohannon published a deliberately misleading study showing that chocolate could cause weight loss and submitted it to multiple journals from a fake institute to see how many would publish it. It was a real study but its design, with a small sample size and a large number of variables tested, was a ‘recipe for false positives’. It was accepted within 24 hours by a journal that boasts that it ‘reviews all papers in a rigorous way’ and published unchanged. With the help of a press release, it was soon all over the media, for which any diet story is irresistible clickbait.

MATT RIDLEY, “SCIENCE FICTION: THE CRISIS IN RESEARCH,” SPECTATOR, 12 AUGUST 2023 HERE’S MORE ON THAT PAPER. 

Reading about proposed remedies in Times Higher Education is dispiriting (i.e, when the ship is on fire, rearrange the deck chairs). It’s as if Top People don’t understand how serious the problem is.

Here’s How Serious It Is

Stanford statistician John Ioannidis pointed out in 2005, “most published research findings are false.” And not much has changed. Spurious correlations, data mining, and data torturing, etc. go on as before because there is no true incentive to tackle the problem at the root. The incentive is simply to slap the wrists of the worst offenders. For example, Tessier-Lavigne is expected to remain a tenured professor at Stanford.

Here’s what may be changing though. Decades ago, it was the better informed people who trusted ongoing science research. Less well-informed people relied on unexamined truisms, folk beliefs, etc. Today, especially in the wake of utter debacles like the official response to COVID-19, “Trust the Science!” is becoming, in many places, a jibe — and for good reason.

Time will tell if the problem is even fixable in a world of philosophical and political wars on math and wars on science. Stay tuned.

The caste system is impeding the rise of India?

 

A blow for the right to repair?

 

Building a Cathedral to chance and necessity?

 Is the Cosmos One Big Happy Accident?

David Klinghoffer

And are science and religion mortal enemies? On a classic episode of ID the Future, Casey Luskin talks with Discovery Institute Senior Fellow Jay Richards about distortions and outright falsehoods presented in Neil deGrasse Tyson’s reboot of the Cosmos TV series. Dr. Richards discusses how Cosmos: A Spacetime Odyssey presents science and religion as enemies by misrepresenting the lives of key figures in the history of modern science. “If you’re going to tell that story of the warfare between Christianity and science, you absolutely have to have a martyr,” says Richards. Both Copernicus and Galileo died peacefully, so the show spends an unusual amount of time animating the story of Dominican friar and mystic Giordano Bruno and his persecution by the Catholic Church. The problem? Bruno isn’t a central character in the story of modern science, and he was executed for alleged theological crimes, not scientific ones. Richards goes on to discuss the show’s misrepresentation of scientific giant Isaac Newton and even of the monotheistic ideas of the ancient Chinese philosopher Mozi. “What you get is the sense that religion and Christianity were either an enemy of science or at best they were incidental beliefs to early modern science that made no difference to scientific discovery. It’s just not true.” Download the podcast or listen to it here.

A house more divided than ever?

 Right-wing Catholics interrupt Mass for LGBTQ World Youth Day pilgrims

Christopher White

The same day Pope Francis told half a million Catholics gathered in the Portuguese capital for a major youth festival that the church must be a home for everyone, ultra-traditionalist Catholics interrupted a Mass for LGBTQ pilgrims in protest of the organizer's efforts to put the pope's message into action. 

When some two dozen Catholics gathered for Mass on Aug. 3 at the Church of Our Lady of the Incarnation here in Lisbon, a group of protesters began to chant "a reparatory prayer" in an effort to disrupt the gathering. 

According to noted British theologian Fr. James Alison, an openly gay priest who was one of three concelebrants of the Mass, the group of a dozen protesters wore long mantillas and held crucifixes and increasingly raised their voices in an effort to drown out the priests and congregants during Mass. 

Police who had already been notified of a potential disturbance were soon on the scene to escort the protesters out of the church, and the Mass continued without further incident. Alison told NCR that the interruption highlights the challenges that LGBTQ Catholics face in trying to practice their faith. 

Those roadblocks began several days earlier, when the organizers of the Mass, the Global Network of Rainbow Catholics and a local Portuguese LGBTQ Catholic group, had to scramble to find a new location to hold the Mass after their original hosts grew anxious after calls for protests began to circulate online. 

Much of the protesters' motivation, Alison said, was their mistaken belief that Jesuit Fr. James Martin would concelebrate the Mass. While Martin — a prominent LGBTQ Catholic advocate — had been in Portugal for Jesuit-related events ahead of World Youth Day, he had already left the country. 

Despite the forced change of venue and the interruption, Alison said that he has no ill will toward the protesters. 

"I was terribly sorry to see these people who have been led to this terrible ideology of hatred," he said. "They live in a weird, alienated world and did not look happy. We were principally sad for them." 

"I don't blame them," Alison added. "I blame the intellectual authors who seem to bear the responsibility for this." 

Alison said that the fact that the protest occurred on the same days that Francis — who arrived in Portugal Aug. 2 for a five-day visit for World Youth Day — used three speeches to repeatedly emphasize that everyone has a home in the Catholic Church, showed that the Mass for LGBTQ Catholics was "clearly in line with the Holy Father's message." 

Since the start of his pontificate in 2013, Francis has walked a tightrope on LGBTQ issues — continuing to uphold traditional church teaching, which prohibits gay relations, while repeatedly offering calls for everyone to be welcomed in the church and personally befriending a number of openly gay Catholics. 

On Aug. 4, the Spanish Catholic news weekly, Vida Nueva, published an interview with Francis, in which the pope reflected on his meetings with transgender people.

"The first time a group of transsexuals came to the Vatican and they saw me, they came out crying, saying that I had given them a hand, a kiss … as if I had done something exceptional with them," he told the magazine. "But they are DAUGHTERS(?) of God!"

An ancient superpower remembered.

 

On the dark arts of branding

 

In search of mindless information?

 Is Life Just Chemistry, or Chemistry Plus Information?

Denyse O Leary

In 2016, University of Ferrara theoretical biologist Marcello Barbieri wrote a rather interesting open access paper on a key philosophical conflict in biology: Is life only chemistry or is it chemistry plus information? In it, he says that many biologists see information in life forms — biological information — as something that “does not really belong to science.” 

How did they get there from here?

Author of Code Biology: A New Science of Life (Springer, 2015), Barbieri offers a history, a critique, and a proposed solution. In this and two upcoming articles, I will look at all three elements.

First, the History

Molecular biology understands genes as transferring linear sequences of information to proteins that carry out instructions. That’s information as it is generally understood. But some biologists, surveying the vast, complex, specified structures it builds, appear spooked by the thought:

This implies that there is an ontological difference between information and chemistry, a difference which is often expressed by saying that information-based processes like heredity and natural selection simply do not exist in the world of chemistry. Against this conclusion, the supporters of the chemical paradigm have argued that the concept of information is only a linguistic metaphor, a word that summarizes the result of countless underlying chemical reactions. The supporters of the information paradigm insist that information is a real and fundamental component of the living world, but have not been able to prove this point. As a result, the chemical view has not been abandoned and the two paradigms both coexist today.

BARBIERI MARCELLO 2016 WHAT IS INFORMATION? PHIL. TRANS. R. SOC. A.3742015006020150060 HTTP://DOI.ORG/10.1098/RSTA.2015.0060, 13 MARCH 2016

Barbieri offers a solution, which we will look at later. But for now, note the nature of the conflict: “Information can’t be real if chemistry doesn’t completely subsume it” versus “information is real, apart from chemistry.”

He points to origin of life researcher Günter Wächtershäuser as a leading exponent of the first view: “If we could ever trace the historic process backwards far enough in time, we would wind up with an origin of life in purely chemical processes.” The physicalism that Wächtershäuser espouses here may cause us to overlook the fact that we really have no idea how to trace the “historic process” that far back in time. His claim is simple but not easily researchable. And in these times, that fact alone gives his chemical paradigm a certain weight. A dominant idea that cannot be proved can also not be disproved.

Of course, as Barbieri notes, Watson and Crick’s discovery of the double helix suggested the image of life forms as “information-processing machines.” That image was not welcomed in many places:

This is one of the most deeply dividing issues of modern science. Many biologists are convinced that biological information and the genetic code are real and fundamental components of life, but physicalists insist that they are real only in a very superficial sense and that there is nothing fundamental about them because they must be reducible, in principle, to physical quantities.

BARBIERI MARCELLO 2016 WHAT IS INFORMATION? PHIL. TRANS. R. SOC. A.3742015006020150060

HTTP://DOI.ORG/10.1098/RSTA.2015.0060, 13 MARCH 2016

He realizes that conventional biologists’ most serious intellectual commitment is to Darwin’s theory of evolution by natural selection acting on random mutation — a commitment he appears to support. So he reassures readers that Wächtershäuser’s “life is just chemistry” approach doesn’t really accord with Darwinism after all because “natural selection, the cornerstone of Darwinian evolution, does not exist in inanimate matter.” He does not seem to grasp that the two theories get on very well precisely because both purport to explain how bewilderingly complex and highly specific life forms can come to exist in a universe that is devoid of intelligence.

So What Type of Material Substance Is Information?

The problem he does not address is that information, unlike chemistry, is fundamentally immaterial. A USB stick that contains vital information weighs the same as one that contains nothing or strings of random numbers. And the content, meaningful or not, is measured using concepts like bits and bytes, not physical attributes like kilograms and joules. And, unlike other quantities, information can convey meaning.

Meaning is a term Barbieri uses a good deal:

The existence of meaning in the organic world may seem strange, at first, but in reality it is no more strange than the existence of a code, because they are the two sides of the same coin. To say that a code establishes a correspondence between two entities is equivalent to saying that one entity is the meaning of the other, so we cannot have codes without meaning or meaning without codes. All we need to keep in mind is that meaning is a mental entity when the code is between mental objects, but it is an organic entity when the code is between organic molecules.

BARBIERI MARCELLO 2016 WHAT IS INFORMATION? PHIL. TRANS. R. SOC. A.3742015006020150060

HTTP://DOI.ORG/10.1098/RSTA.2015.0060, 13 MARCH 2016

No, actually. Meaning is an aspect of conveying information to an intelligent being, as in “The meaning of James’s earlier actions became clear to us when he suddenly switched sides.” If anything in life forms has a meaning, an intelligent agent will be needed to recognize it. 

And if the chemistry-only faction is at all consistent, it should have no truck whatever with the idea that “meaning is a mental entity when the code is between mental objects.” True physicalism denies that there are any mental objects. The mind is an illusion generated in the brain via natural selection, one that happens to further human survival. Meaning is merely a part of that illusion.

Barbieri seems to want biology to combine physicalism with an acceptance of information — information that is stripped of its relationship to intelligence and thus somehow belongs to science after all. But, as we shall see, it can’t be done.

Next: Can information be separated from intelligence? Barbieri tries for an origin of life theory that allows for information but tries to separate it from intelligence. Does he succeed? I will consider that question in a subsequent post.

Yet another Battle Royale of Titans.

 

On Darwinian apologists' "what Cambrian explosion" defence

 Fossil Friday: Did the Cambrian Explosion Really Happen?

Gunter Bechly

When confronted with the argument from the sudden appearance of animal body plans in the Cambrian Explosion about 540-515 million years ago (e.g., early arthropods like the featured trilobite Redlichia), the newest fad among anti-ID activists and hardcore Darwinists is to boldly deny that this event ever happened. A good example is the silly rant by YouTuber Dave Farina against Stephen Meyer’s book Darwin’s Doubt. These deniers of the well-established scientific consensus rest their argument on the recent publications of a few maverick paleontologists, who indeed made similar claims about the Cambrian Explosion and the Great Ordovician Biodiversification Event being nothing but a mirage, i.e., an artifact of incomplete preservation, undersampling, and sampling bias. I have already responded to several such claims in previous articles (e.g., Bechly 2022a, 2022b) and have shown why they are unconvincing and based on obfuscating language and ambiguous redefinition of common terms.

No Reasonable Doubt

I also established in my articles with numerous quotes from up-to-date peer-reviewed scientific literature that there is no reasonable doubt about the reality of the Cambrian Explosion and its status as a fatal problem for Darwinism (also see these articles by Luskin 2013, Luskin 2023 and Coppedge 2023).

Now, a new study by the above-mentioned team of maverick authors (Servais et al. 2023) has regurgitated the revisionist views, and this was of course accompanied by sensational press releases with catchy headlines like “Did the Cambrian explosion really happen?” (Heidt 2023). The main claims of this paper are:

The early Palaeozoic accommodated a single long-term radiation.

Continental fragmentation exerted a first-order control on this long-term radiation.

The Cambrian biodiversification was not a sudden burst (“explosion”) of diversity.

The Great Ordovician Biodiversification “Event” was not a single “event.”

Terms such as “radiation” or “biodiversification” are more suitable terms.

The general fallacy of this paper is the conflation of the traditional understanding of the Cambrian Explosion as the sudden appearance of animal body plan disparity with the mere rate of biodiversification in terms of species diversity more or less continuously increasing from the Cambrian to the Ordovician. In other words: They are knocking down straw men.

But It Get’s Worse

In  fact, the real data do not support their main point at all. What the scientists did in this study is simply screen two large paleontological databases, which collectively contain about 2 million entries about fossil biodiversity. Based on these data, which actually contradict their thesis, “the authors assert that these resources aren’t truly global …” and claim that “Were they to put the same effort into studying this period, the existence of two individual events would likely melt away” (Servais quoted in Heidt 2023). This is of course nothing but ad hoc special pleading and mere speculation about potential biases to explain away the inconvenient actual data. It is fishy indeed and suggests that the whole point of this endeavor is the protection of Darwinian evolution against empirical evidence. It certainly isn’t solid science!

So, it is hardly suprising that other experts remain utterly unconvinced and object that “there is actually quite good evidence that there was a Cambrian explosion, as we would typically call it” (Nanglu quoted in Heidt 2023). This will of course not prevent our dear opponents from misrepresenting the new paper as alleged proof that science has shown that the Cambrian Explosion never happened. Cherry picking and confirmation bias anyone?

References

Bechly G 2022a. Untangling “Professor Dave’s” Confusion about the Cambrian Explosion. Evolution News November 29, 2022. https://evolutionnews.org/2022/11/untangling-professor-daves-confusion-about-the-cambrian-explosion/

Bechly G 2022b. Dave Farina Criticizes Intelligent Design but Doesn’t Understand It. Evolution News December 5, 2022. https://evolutionnews.org/2022/12/dave-farina-criticizes-intelligent-design-but-doesnt-understand-it/

Coppedge D 2023. Evolutionists Spin the Cambrian Explosion — But Alas, All in Vain. Evolution News July 26, 2023. https://evolutionnews.org/2023/07/evolutionists-spin-the-cambrian-explosion-but-alas-all-in-vain/ (originally published 2015)

Heidt A 2023. Did the Cambrian explosion really happen? LiveScience July 8, 2023. https://www.livescience.com/planet-earth/evolution/did-the-cambrian-explosion-really-happen

Luskin C 2013. How “Sudden” Was the Cambrian Explosion? Evolution News July 16, 2013. https://evolutionnews.org/2013/07/how_sudden_was_/

Luskin C 2023. FAQ: The Cambrian Explosion Is Real, and It Is a Problem for Evolution. Evolution News May 19, 2023. https://evolutionnews.org/2023/05/faq-the-cambrian-explosion-is-real-and-it-is-a-problem-for-evolution/

Servais T, Cascales-Miñana B, Harper DAT, Lefebvre B, Munnecke A, Wang W & Zhang Y 2023. No (Cambrian) explosion and no (Ordovician) event: A single long-term radiation in the early Palaeozoic. Palaeogeography, Palaeoclimatology, Palaeoecology 623(9):111592

DOI: https://doi.org/10.1016/j.palaeo.J.Palaeo.2023.111592

On matter's evil twin?

 

The UBS is superior to the TR? Pros and Cons.

 

The Umayyad dynasty a brief history.

 

The spectre of homochirality continues to loom over OOL science.

 Origin of Life: The Challenge of Achieving Homochirality in a Prebiotic World

Carl Linnaeus

 It's  a challenge crucial for research on the origin of life. Among the many obstacles to generating biologically relevant polymers abiotically, achieving homochirality is perhaps the most difficult impediment to overcome. What is homochirality? Well, all macromolecules in life are composed of building blocks that exist as mirror images. The analogy of left and right hands is most commonly used to convey this chemical concept. With very few exceptions, life only uses one of these forms. 

The chemical properties of mirror imaged compounds are equivalent for all practical purposes. The production of these building blocks in a prebiotic world, using very simple compounds as starting material, would therefore be expected to result in a racemic mixture, or 50/50 distribution, of these building blocks. This has already been confirmed from analysis of organic compounds retrieved from an asteroid, as I wrote here back in May. 

Producing polymers consisting of only one configuration from this mixture is obligatory if a prebiotic origin of life on Earth is be convincingly explained to the scientific community. Proposing chemical schemes that produce polypeptides (proteins) or RNA using homochiral building blocks is the task at hand. Performing such a feat in solution appears unfeasible, so the prebiotic soup approach has been abandoned by many origin of life (OOL) scientists. A better alternative, widely investigated, is the use of mineral surfaces where adsorption of organic chemicals could theoretically select preferentially one configuration of a pair of chiral molecules. 

Here I will briefly discuss this experimental approach, noting where the relevant studies have led. I’ll first consider polymerization of amino acids to form proteins, followed by attempts to achieve this feat using RNA precursors.

From Racemic Amino Acids to Homochiral Proteins

Among studies showing efficacy in obtaining short lengths of amino acids to form oligopeptides, one of earliest was reported in 1978 (Lahav N., White D., and Chang S. (1978) Science 201: 67-69). The system employed, to facilitate the condensation reaction to form peptide bonds between amino acids, was the use of clay minerals (kaolinite and bentonite). Repeated cycles of heating, evaporation, and rehydration were invoked, which are conditions likely present on a prebiotic Earth. Using the simplest amino acid, glycine (having no chiral center), diglycine was found to be produced at low levels with progressively lower amounts up to pentapeptide lengths. Notably the heating-drying phase of this cycle apparently facilitates the condensation reaction, enabling peptide bond formation. 

A Long Way from the Goal

was a start, but still a long way from producing polypeptide lengths of any biological relevance. Small proteins should reach at a minimum 100-200 amino acids to effectively contribute to biological function. After this initial glimmer of hope, many other laboratories undertook similar approaches, testing out different mineral surfaces and a variety of reaction conditions. The highest achievers managed to produce polypeptides up to decamers. It became clear from these studies that the longer the polypeptide produced, the harder it was to retrieve it from the mineral surface, as it was tightly bound via a multitude of chemical bonding forces spread over a long chain of amino acids. Success at making long polypeptides seemingly dooms the polymer to remain fixed to the surface instead of being released into solution as needed by life.

A major flaw with the studies described above is that they did not attempt to account for how homochiral selectivity could be enforced by this route. Synthesizing polypeptides with a racemic mixture of amino acids offers prebiotic life nothing in terms of functionality. For proteins to assume specific and reproducible structures, a homochiral set of amino acids must be used. With this goal in mind, one laboratory reported that enantiomeric pairs of aspartic acid preferentially adsorb to opposing faces with mirror symmetry of calcite (calcium carbonate). It was proposed that aspartic acid, having three functional groups (two carboxylic acids and one amine group), orients itself with homochiral selectivity to the exposed chemical groups of calcite. This follows logically to account for the ~90 percent chiral enrichment observed. 

It works for aspartic acid in this case, but what about glutamic acid? It has the same functional groups but they are spaced apart a little differently. There is no guarantee that the corresponding chiral glutamic acid also binds selectively to the same surface. Sadly, this was not reported. Among the 20 amino acids, only 11 possess at least three functional groups required for appropriate spatial positioning to the mineral interface. The remaining nine have only two, one carboxyl and one amine group. This leaves little room for attaining homochirality for all amino acids as needed to construct proteins. 

To give this laboratory credit, they did mention that alanine, valine, and lysine do not exhibit chiral selection on calcite. The lack of data for most remaining amino acids leads one to believe minerals in general are another dead end for the homochirality problem that OOL protein researchers are trying to solve. In contrast to the conclusions I draw from these observations, the authors were not dissuaded from making bold claims about how this model might help account for homochiral polymerization of amino acids on mineral surfaces in general.

Mineral Models to Select Ribose for RNA

The carbohydrate ribose, required to make RNA, presents a highly problematic situation. Ribose has four chiral centers, unlike amino acids with just one. Therefore, D-ribose found in RNA has seven other chemical partners differing in their spatial arrangement of atoms. Ribose has one advantage to assist the OOL researchers. It most often exists as six- or five-membered ring structures where the functional hydroxyl groups are positioned geometrically to one side of this chemical framework. Minerals such as rutile can accommodate hydrogen bonding, presenting an opportunity to preferentially bind ribose over its other carbohydrate competitors. Such a model has been proposed with the caveat that a third dimensional force must be applied to effect separation of ribose from the other sugars. 

The first two dimensions are accounted for by quasi-planar interactions of sugar rings to the mineral interface. In simpler terms, this mineral needs to be applied to a separation technique called chromatography. The tighter binding of ribose, by virtue of its hydroxyl groups all pointing to the mineral surface, would permit tighter retention where the other sugars would proceed more rapidly through this chromatographic separation. 

There are several problems with this innovative proposal. Setting up a chromatographic separation does not happen naturally. It requires a specific design where all molecules must enter the chromatographic medium simultaneously. In other words, an external agent is required to carry out this exercise. Assuming that chromatography proceeds as hoped, the last 5-carbon sugar eluting from the chromatographic medium will be D- and L-ribose. There is still a racemic mixture of ribose that must be contended with. Finally, as discussed in my earlier article, appropriately linking a nucleobase and finally phosphate to D-ribose is an extremely difficult task without the use of specifically engineered catalysts, e.g., enzymes. This is highly unlikely to happen in a prebiotic scenario. 

The Task at Hand

I have addressed here the potential minerals proposed by OOL researchers to abiotically synthesize the first functional biopolymers. Simple principles discounting these proposals can be applied to other comparable scenarios in this area, but that would require a much longer and more technical article. Suffice it to say there are sound counterarguments to the plethora of schemes that OOL researchers devise in trying to account for how life could have emerged abiotically. Critically examining these schemes is the job with which scientists on the other side of the field are tasked.

Science as one party state?

 Andrew Klavan, Casey Luskin: Displaced Authority and Progressive Censorship

Andrew Mcdiarmid

On  a new episode of ID the Future, we’re pleased to share Daily Wire host Andrew Klavan’s recent interview with Dr. Casey Luskin. Klavan loves science, but he smells a rat when famous scientists like Richard Dawkins use displaced authority to make proclamations about science’s relationship with religion. So after reading Luskin’s recent Daily Wire article about progressives and their long history of banning intelligent design from the classroom, Klavan invited Luskin on his show to help his viewers better understand the theory of intelligent design and the reality of the evolutionary paradigm. 

Luskin starts with the meanings of evolution and the questions that guide intelligent design researchers. He cites plenty of examples of design from biology and cosmology. Klavan asks how badly people get censored for considering design perspectives in their work. Luskin explains, using the case of physicist Eric Hedin and his treatment at Ball State University as an example. Luskin rounds out the conversation by explaining how intelligent design uses the scientific method to detect the hallmarks of design in both living systems and the universe at large. “Science never gives us, under any conditions, absolute certainty,” Luskin notes. “What it can allow us to do, though, is use the methods of historical sciences to infer the best explanation for a given situation given what we know about how the world works.” Download the podcast or listen to it here.

On Darwin's unresolved doubt?

 In Resolving Darwin’s Doubt, These Cambrian Fossils Are No Help

David Coppedge

More complexity in the earliest multicellular animals has only intensified what Stephen Meyer calls “Darwin’s Doubt.” Some examples follow.

Euarthropods

A paper in Current Biology comes closest to demonstrating “the deep homology between exoskeletal features in an evolutionary continuum of taxa with distinct types of body organization.” Author Javier Ortega-Hernández takes on “the euarthropod head problem” by finding similarities between two specimens from the Burgess Shale (Middle Cambrian). His analysis, though, only compares positions of complex tissues, not how they originated. Amid various controversies, he focuses on a relatively simple structure, the anterior sclerite (a front plate of cuticle) within one phylum, the true arthropods.

Despite its ubiquitous nature, the significance of the anterior sclerite remains controversial, as there is little agreement on the correspondence of this structure among stem- and crown-group euarthropods. 

His attempt at finding phylogenetic relationships, given such a trifling structure in a narrow range of animals, is less than convincing. Worse, he ignores the weightier matters of the explosive origin of the complex body plans of these animals.

Collinsium

Science media were excited to report on a “spiky monster worm” from China, named Collinsium ciliosum (original paper is in PNAS). If this is supposedly an ancestor of modern velvet worms, as researchers at the University of Cambridge claim, it was already complex, with spikes, a mouth with teeth, antennae, and filter feeding appendages. Its 72 spikes in rows down its back are particularly noteworthy. If anything, it looks more complex than “Today’s 180 or so species of velvet worms [that] all look and act pretty much the same” (Science Magazine). “This isn’t the first time that an ancestral group has displayed more diversity than its modern-day relatives,” Live Science comments. If this is evolution, it’s going backwards.

The critter is one of the first known animals on Earth to develop protective armor and to sport specialized limbs that likely helped it catch food, the researchers said. This newfound species lived during the Cambrian explosion, a time of rapid evolutionary development, they said.

Abrupt appearance? Rapid development? How this helps the evolutionary story is not clear. The Cambridge news item offers word salad as a distraction from the issues raised by Dr. Meyer, which they simply ignore.

Animals during the Cambrian were incredibly diverse, with lots of interesting behaviours and modes of living,” said Ortega-Hernández. “The Chinese Collins’ Monster was one of these evolutionary ‘experiments’ — one which ultimately failed as they have no living direct ancestors — but it’s amazing to see how specialised many animals were hundreds of millions of years ago. At its core, the study of the fossil record seeks answers about the evolution of life on Earth that can only be found in deep time. All the major biological events responsible for shaping the world we inhabit, such as the origin of life, the early diversification of animals, or the establishment of the modern biosphere, are intimately linked to the complex geological history of our planet.” 

Anomalocaris

The apex predator Anomalocaris was mentioned in connection with a more recently discovered member of its family. This one, a giant named Aegirocassis benmoulae, was found in Morocco, indicating the global extent of the anomalocaridids. Unlike its more famous relative, “this anomalocaridid from the Ordovician exposes a second set of body flaps and reopens the question of how the two branches of arthropod legs evolved,” Gregory Edgecombe notes in Current Biology. The authors of the paper in Nature are not much help to Darwin, having to invoke “convergent evolution” again:

Among arthropods, the size of A. benmoulae (over 2 m in length) is paralleled only by some pterygotid eurypterids and terrestrial arthropleurids. The evolution of gigantic filter-feeders within clades of nektic macrophagous predators is well documented in Mesozoic pachycormid fish and Cenozoic sharks and whales. The huge size of A. benmoulaerepresents a much earlier example of a filter-feeding lifestyle correlating to gigantism. The abundance of gigantic anomalocaridid filter-feeders in the high palaeolatitude Fezouata Biota points to a complex planktic ecosystem. Early Cambrian anomalocaridid filter-feeders also fed on zooplankton, but they remained relatively small. Although the Cambrian Explosion saw the establishment of the first complex planktic ecosystems, the convergent (Supplementary Text) rise of giant filter-feeding anomalocaridids during the Ordovician followed an increase in the abundance and diversity of phytoplankton and a consequent zooplankton radiation as part of the Great Ordovician Biodiversification Event.

Once again: abrupt appearance of complex body plans, complex ecosystems, and convergent evolution. None of this helps the evolutionary story or answers the key issue: where did the genetic information come from to build complex body plans with hierarchical structures and functional organs composed of new tissues and cell types? 

Hallucigenia

When Hallucigenia (pictured above) was first found in the Burgess Shale a century ago, paleontologists couldn’t tell top from bottom or front from back. The bizarre creature with paired spines pointing away from its paired legs was missing an important part: its head. Since then, the head has been found. It’s complex, with a pair of eyes and rows of teeth. This requires explaining more cell types and tissue types than before, exacerbating the problem Stephen Meyer identifies.

Martin R. Smith from Cambridge, with Jean-Bernard Caron from the Toronto Museum of Natural History, announced the discovery in Nature. Other sites, like Phys.prg and New Scientist, picked up the story and showcased the new artwork. For BBC News, Smith described his initial reaction:

By delicately chipping away at the rock, scientists found a spoon-shaped head with some surprising features.

“When we put it into the electron microscope, we were delighted to see not just a tiny pair of eyes looking back at us, but also beneath them a really cheeky semi-circular smile.

“It was as if the fossil was grinning at us at the secrets it had been hiding,” explained Dr Smith.

Inside the creature’s mouth, the researchers found a ring of teeth and then another set of teeth running from its throat down towards its stomach. 

Most of the chatter is preoccupied with where to put this creature in a Darwinian phylogenetic tree. For a long time, animals were lumped together by their type of body cavity (coelom). That’s changed; in 1997, Aguinaldo invented the category “ecdysozoa” (“molting animals”) based on ribosomal RNA comparisons. This lumped together everything from butterflies to roundworms, from tardigrades (“water bears”) to centipedes, from velvet worms to spiders. But is such a clade meaningful? “These disparate phyla are united by their means of molting, but otherwise share few morphological characters — none of which has a meaningful fossilization potential.” Smith and Caron note. “As such, the early evolutionary history of the group as a whole is largely uncharted.” 

The purpose of the grouping was to try to unite all the creatures that supposedly had a common ancestor. A more meaningful designation would account for the complexity and unique features of each animal, without forcing it into preconceived notions of common ancestry. Hallucigenia is a prime example. This creature had eyes, a mouth, teeth, a throat, a foregut, a stomach, and an anus. It had appendages that could reach its mouth. It had seven pairs of spines, each emerging from “a buttress of soft tissue,” arranged with curvatures from front to back, protecting the entire animal. It had claws on the ends of the legs. 

It’s not just the cell types that need to be explained, but their arrangement into functional structures. These structures, moreover, need to be integrated into a functional animal in its ecosystem. And, they need software in some central nervous system that allowed the animal to use all of it. This is hierarchical organization, none of which is seen in the Precambrian layers beneath.

Just-So Storytelling

Live Science has a nice gallery of these and other Cambrian critters. Interesting animals, but nothing new here. More of the same complexity. More of the same just-so storytelling that assumes undirected evolution. More distraction from the main question: what is the source of complex specified information to build a complex animal? How could it emerge from a blind, unguided process?

John Locke on the Logos of the gospel

 

A brief history of the triune God?

 

Continuing to rethink the unrethinkable

 

The technology of life.

 Listen: The Innovative Cellular Engineering That Keeps Us Alive

Andrew Mcdiarmid

When left to their own devices, the laws of nature tend toward death, not life. So what does it take for life to exist? On a new episode of ID the Future, host Eric Anderson talks with physician Howard Glicksman about some of the remarkable engineering challenges that have to be solved to produce and maintain living organisms such as ourselves. Glicksman is co-author with systems engineer Steve Laufmann of the recent book Your Designed Body, an exploration of the extraordinary system of systems that encompasses thousands of ingenious and interdependent engineering solutions to keep us alive and ticking. In the “just so” stories of the Darwinian narrative, these engineering solutions simply evolved. They emerged and got conserved. Voila! But in this chat, Anderson and Glicksman explain that it takes more than the laws of nature to keep us from dying. “Chemicals on their own don’t have any desire or tendency to turn into living organisms,” says Anderson. “They tend to degrade, they tend to break down, they tend to go back to their basic constituents.” Glicksman and Anderson discuss examples, including how the human body handles friction, heat transfer, and the crucial task of maintaining chemical balance at the cellular level. And where does all this essential innovation come from? Glicksman points to an intelligent cause that transcends matter and energy. Download the podcast or listen to it here.

Luke's gospel on Rich and Poor.

 Luke ch.6:20-26KJV"20And he lifted up his eyes on his disciples, and said, Blessed be ye poor: for yours is the kingdom of God. 21Blessed are ye that hunger now: for ye shall be filled. Blessed are ye that weep now: for ye shall laugh. 22Blessed are ye, when men shall hate you, and when they shall separate you from their company, and shall reproach you, and cast out your name as evil, for the Son of man's sake. 23Rejoice ye in that day, and leap for joy: for, behold, your reward is great in heaven: for in the like manner did their fathers unto the prophets.

24But woe unto you that are rich! for ye have received your consolation. 25Woe unto you that are full! for ye shall hunger. Woe unto you that laugh now! for ye shall mourn and weep. 26Woe unto you, when all men shall speak well of you! for so did their fathers to the false prophets."

Here is strong's on the word rendered "poor": 

4434. ptóchos ►

Strong's Exhaustive Concordance

beggar, poor.

From ptosso (to crouch); akin to ptoeo and the alternate of pipto); a beggar (as cringing), i.e. Pauper (strictly denoting absolute or public mendicancy, although also used in a qualified or relative sense; whereas penes properly means only straitened circumstances in private), literally (often as noun) or figuratively (distressed) -- beggar(-ly), poor.:

Taken literally Jesus said happy/ blessed are you beggars. There were certainly no literal beggars among the twelve apostles that He had just chosen. So what kind of beggar does JEHOVAH bless ,the parallel account of Matthew is helpful. 

Matthew ch.5:3NIV"“Blessed are the poor in(Beggars for the) spirit,

for theirs is the kingdom of heaven."

The simple fact of the matter is that when it comes to the spiritual we are all poor. Some are aware of that critical poverty in their own particular case and are eagerly pursuing the one source that can alleviate it, our Lord promises that all such are due for a blessing.

Others imagine themselves to be "rich" but Paul warns that our evaluation of ourselves is of no consequence

1Corinthians ch.4:4NIV"My conscience is clear, but that does not make me innocent. It is the Lord who judges me."

So the "rich" are "poor" in JEHOVAH'S eyes and the "poor" are "rich" in JEHOVAH'S eyes.

How Wikipedia became the Borg.

 

Our AI overlords will finally bring the revolution?

 

Actual design not merely apparent design.

No, Intelligent Design Doesn’t Reason by Analogy; Here’s Why

Evolution News

It's  time again to address some misunderstandings of intelligent design. First, is the inference to design in biology based on a mere analogy to other forms of design, by humans? 

Let’s consider the question. To start, let’s ask: Why can we make this inference in the first place? It’s because natural systems contain the type of information and complexity that in our experience come only from intelligence. This is not merely an “analogy” but derives instead from the sequence-based specified complexity that we see in living systems (e.g., DNA), which is precisely the same, at the mathematical level, as we see in written language. Hubert Yockey makes this clear:

               It is important to understand that we are not reasoning by analogy. The sequence hypothesis [that the exact order of symbols records the information] applies directly to the protein and the genetic text as well as to written language and therefore the treatment is mathematically identical.

HUBERT P. YOCKEY, “SELF ORGANIZATION ORIGIN OF LIFE SCENARIOS AND INFORMATION THEORY,” JOURNAL OF THEORETICAL BIOLOGY, VOL. 91:13-31 (1981).

                     So what we see in living systems has mathematical and informational properties that are identical to written language.

Aligned with Mainstream Science

We also see machines in living systems. That’s not to say that cells or living systems on the whole are “machines,” but they do contain machines. It’s not a stretch to say that calling these things a machine is more than an analogy — it’s an identity. This is because you see the same design logic in molecular machines within cells that you see in human-designed machines.

The classic example would be ATP synthase where you find a stator, a rotor, an energy source, and you are converting one form of energy into another (with ATP synthase you are converting the electrical potential of proton flow into mechanical energy and that mechanical energy is then converted into the chemical energy of ATP). You’d be hard pressed not to call these things machines, and the idea is not unaligned with mainstream science. As former President of the U.S. National Academy of Sciences Bruce Alberts stated:

                         The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines…. Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts. 

BRUCE ALBERTS, “THE CELL AS A COLLECTION OF PROTEIN MACHINES: PREPARING THE NEXT GENERATION OF MOLECULAR BIOLOGISTS,” CELL, VOL. 92:291 (FEBRUARY 6, 1998).

                                        Likewise, in 2000, Marco Piccolini wrote in Nature Reviews Molecular Cell Biology that “extraordinary biological machines realize the dream of the seventeenth-century scientists … that ‘machines will be eventually found not only unknown to us but also unimaginable by our mind.’” He notes that modern biological machines “surpass the expectations of the early life scientists.” (Marco Piccolino, “Biological machines: from mills to molecules,” Nature Reviews Molecular Cell Biology, Vol. 1:149-153 (November, 2000).)

So, is it just an analogy or is it an identity? Or perhaps both? When we look at the mathematics and physics behind what is going on, the similarities between biological machines and biological information and written language and human-designed machines go beyond mere analogy and become an identity. If it’s an identity then it’s more than just an analogy. 

                            

How Things Become Themselves

Other people (or sometimes the same people) label arguments for intelligent design as “theology” or “metaphysics.” Are they right?

Now science is in the business of explaining how things originate and form. This is done through the historical sciences. A historical science starts by observing causes at work in the world around us. Some of those causes include:

Random mutation

Natural selection

Intelligent agency

We can observe each of these causes and understand the kind of information and complexity they are capable of generating. Because we have observation-based experience with these causes we know what they can and cannot do. Because we can observe, study, and understand the causal powers of these causes in real time, they are therefore proper subjects of scientific study and are causes that we can potentially invoke to explain things in nature. Full stop.

And here is what some of those observations reveal, in simple terms:

Random mutation and/or natural selection does NOT generate high levels of complex and specified information.

Intelligent agency DOES generate high levels of complex and specified information.

Random mutation and/or natural selection does NOT generate machines.

Intelligent agency DOES generate machines.

In all of our experience, high levels of complex and specified information and machines have only one known source: intelligence. We know that intelligence can produce these things due to our experience-based observations of intelligent agents in the world around us. Thus, we have empirical grounds for inferring that an intelligent cause was at work.

So, it’s true that some label these arguments metaphysics or theology, or call it a “distortion” to say this type of reasoning is science. But no, everything above is based the methods of science. That’s all there is to it