Less simple than ever?

 Walking Cells and Other Surprises Among Protists — An Evolutionary Challenge

David Coppedge

The world of protists is expanding at a fast clip. New eukaryotic microbes are being discovered, some with little or no known connection to identified species. Taxonomists are not sure how to classify them. Some are even willing to create new phyla, supergroups, or kingdoms to house them. Three commentators in Current Biology expressed the surprise:

Probably more scientists study sparrows than all the free-living microbial eukaryotes (protists) combined. This is quite unfortunate, not because the former are unworthy, but because the latter not only contribute substantially to planetary health, but they also represent the majority of functional and evolutionary eukaryotic diversity on Earth. This fact usually comes as a surprise to people studying macroscopic eukaryotes, yet the diversity of protists is bound to grow even further, as implied by the fact that 50% of eukaryotic genes expressed in the ocean do not have any match in public databases and/or lack any reliable phylogenetic affiliation. 

Let’s examine two new species identified recently. Imagine protists that walk on legs like bugs, or paddle with arms. How do they do it? Where did they come from? And must the commentators beg the question of evolution in the phrase “evolutionary eukaryotic diversity” instead of just describing “eukaryotic diversity”? These two protists possess only distant morphological similarities to other members of their taxa, so imagining a phylogeny between them seems strained. For now, behold and wonder!

Meteora sporadica: The Paddling Hunter

This creature is so weird, you have to watch it in motion to believe it. The cell body is slightly elongated, and from the major axis two long filaments extend twice its body length forward and backward. This is the axis along which it glides with cilia. But now, picture “arms” extending out to the sides that paddle back and forth, one sweeping forward while the opposite arm sweeps backward.

It’s rare to find the word “incredible” in a formal scientific paper’s title, but Eglit et al., writing in the same issue of Current Biology, must have been astonished when they announced this creature as “a protist with incredible cell architecture.” 

“Kingdom-level” branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down. Some are completely new discoveries, whereas others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19th century but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted. Meteora sporadica is a protist with a unique morphology; cells glide over substrates along a long axis of anterior and posterior projections while a pair of lateral “arms” swing back and forth, a motility system without any obvious parallels.

For those without access to the paper with its videos of this protist, the only YouTube video I could find is a short one with very loud music, so you might want to quiet your device before viewing this otherwise good look at M. sporadica in action. 

This creature’s motility suggests more complexity under the hood. The authors say it has the most gene-rich mitochondrial genome among protists. The “arms” that swing back and forth are made of bundles of microtubules, which grow from unique subnuclear microtubule organizing centers (MTOCs) that are unlike the more familiar axonemes of cilia. Surprisingly, this protist can move without the “arms” but gets along faster with them. 

Bumps are visible along the lateral arms; what are those? They are called extrusomes. These granules can move up and down along the arms and can be “fired” at bacterial prey. Once it surrounds the target, the extrusome delivers the bacterial burrito to a food vacuole where it is phagocytosed (digested).

Like all other eukaryotes, M. sporadica is equipped with organelles: a nucleus, mitochondria, longitudinal bundles of microtubules, and molecular motors like dyneins to animate the microtubules. Of course, it also contains all the machinery for metabolism, mitosis, DNA storage, transcription, and translation, in addition to motility. This is no simple animal. 

Euplotes, a Microbial Cockroach

Seen from the side, this protist looks like a cockroach or pill bug scooting along the floor, but it is much tinier. Insects have legs made of cells. This protist is a single cell. How can it sprout legs and walk? Take a look at it under the microscope on this YouTube video (again, the music contributes little). The side view at 1:08 shows its resemblance to a walking bug. Investigators Laeverenz-Schlogelhofer and Wan, writing in the same issue of Current Biology, are amazed at the uncanny similarity to animal behavior on a vastly different scale.

Diverse animal species exhibit highly stereotyped behavioral actions and locomotor sequences as they explore their natural environments. In many such cases, the neural basis of behavior is well established, where dedicated neural circuitry contributes to the initiation and regulation of certain response sequences. At the microscopic scale, single-celled eukaryotes (protists) also exhibit remarkably complex behaviors and yet are completely devoid of nervous systems. Here, to address the question of how single cells control behavior, we study locomotor patterning in the exemplary hypotrich ciliate Euplotes, a highly polarized cell, which actuates a large number of leg-like appendages called cirri (each a bundle of ∼25–50 cilia) to swim in fluids or walk on surfaces.

The paper describes the coordination between the cirri (sing. cirrus) when the protist moves. There are 10 frontoventral cirri and 5 transverse cirri arranged in an asymmetrical pattern, plus 4 caudal cirri at the tail end. “Distinct cirri are involved in generating distinct gaits,” the authors observe. Each cirrus moves with a power stroke and recovery stroke, like a swimmer. The cilia that line our airways move in a similar fashion, but in Euplotes they stroke in large bundles. Like other ciliates, these protists are well equipped with numerous other individual cilia that control the movement of food to their vacuoles. “These organisms are among the most morphologically complex and differentiated groups of ciliates,” remark Laeverenz-Schlogelhofer and Wan.

The authors identified three stereotypical movements performed by Euplotes with their cirri: the swim, the forward walk, and the sidestep reaction (SSR). The first two strategies allow the protist to move forward. The SSR allows it to quickly back up and turn. While swimming, the asymmetrical pattern of cirri makes it rotate in a helical fashion. But while walking on a surface (like the cover slip of a microscope slide), it scoots along like a cockroach. The authors notice the functional purpose of cirri when they describe them as “compound leg-like structures comprising many cilia.”

In higher animals, movement is powered by muscles in response to neural signals. The “legs” of these microbes are electrically powered. Specifically, calcium ions flowing through channels in the membrane create cycles of polarization and depolarization about every half second. A slight delayed response shows the cirri decelerating during depolarization and speeding up during polarization. Overall, though, the motion is fairly uniform and rapid. High speed videography allowed the researchers to monitor the actions in slow motion; otherwise the pauses would hardly be noticeable.

Implications

It’s exciting to ponder that the world is filled with examples of cellular motility beyond the iconic bacterial flagellum — and we probably don’t know even half of what exists. While ciliates such as Vorticella, Stentor, and Paramecium have been well known since Van Leeuwenhoek wrote about the “wee beasties” that he saw “very prettily a-moving” under his crude microscopes, many more remain to be identified. These two examples were found in shallow marine sediments. Some of the newly discovered microbes are common in our own backyards, in soil or puddles. The fact that many of them show no clear phylogenetic connection with other microbes, and may contain unique morphological structures, poses a severe challenge to Darwinism. The more isolated diversity, the weaker the argument for common ancestry. 

We intuitively appreciate the form and function of legs in Euplotes and arms in Meteora even though they are profoundly smaller than ours. A “leg” on Euplotes differs in size by six orders of magnitude from the leg of Brachiosaurus, yet both perform the function of motility. Each limb’s design, further, is suited for its habitat and for the physical forces required. The more unique purposeful motion is discovered, the more the evidence that the biosphere has been engineered for action.

Darwinist are just following the science?

 Does Darwinism Meet the Tests of a True Theory?

Eric Hedin

Commenting on the philosophical implications of quantum mechanics, physicist Richard Feynman said, “It is not true that we can pursue science completely by using only those concepts which are directly subject to experiment….The basis of a science is its ability to predict.” (The Feynman Lectures on Physics, Vol. III, pp. 2-9)

We can appreciate this statement by contrasting it with the popular view, where science is a matter of measuring and experimenting with observable reality. Feynman points out that with the advent of quantum mechanics, the scientific reality of nature is no longer directly observable, even in principle. Probabilistic predictions are actually all that quantum theory allows. 

However, while predictive accuracy is a necessary attribute of a scientific theory, it is by no means a sufficient indicator of the theory’s truth. A theory may predict well enough, but we need to ascertain if its assumptions are true. In other words, do the assumptions of the theory correspond to reality? The concept of reality means an accurate description of nature that is consistent with experimental observations and established laws of physics. Such tests can tell us if an idea counts as a true scientific theory.

Let’s illustrate these requirements by considering several cases from the history of science — including Darwinian theory. But first, let us look further back to attempts to develop a theory that explained the motions of the celestial sphere — the astronomical realm thought to contain the stars and planets visible from Earth. 

The Geocentric Model

Readers will be familiar with the geocentric model of the solar system, most often associated with Ptolemy (second century CE). This model, embellished with planetary epicycles, gave reasonable predictions of the trajectories of the five visible planets, including their periodic episodes of retrograde motion. It also comported with the prevailing Aristotelean philosophy of the cosmos and agreed with everyday observations, in which all heavenly bodies appear to revolve around a stationary Earth. Nonetheless, the geocentric model was completely wrong.

Clues supporting the correct heliocentric model remained below the level of observational resolution until the advent of the telescope. 

Galileo was the first to use a crude telescope to obtain observational data that proved inconsistent with the geocentric model. His observations showed sunspots, which disappointed those who held to celestial perfection….Galileo also detected a full set of phases of the planet Venus, which was inconsistent with geocentricism. In sum, Galileo’s more accurate observations showed that this long-standing theory of how the solar system worked was incompatible with several aspects of physical reality. 

CANCELED SCIENCE, P. 178

The heliocentric model, first published by Copernicus in 1543 (21 years before Galileo’s birth), although conceptually simpler and cleaner than the Ptolemaic model, initially failed to make better predictions. That was because Copernicus assumed perfect circles for the planetary orbits. In the early 1600s, Kepler analyzed detailed naked-eye observations of the planets to deduce the correct elliptical shape of their orbits around the sun, allowing for more accurate predictions. 

The point is that successful predictions of a theory do not prove its correctness. With technological developments in observational astronomy, evidence unequivocally demonstrated the foundational errors in the assumptions of the geocentric model. Ptolemy’s Earth-centered model is now taught only as an interesting phase in the history of astronomy. 

Spontaneous Generation

Another example of a now-discarded theory is that of spontaneous generation, a hypothetical process of living organisms developing from nonliving matter. The theory made accurate predictions, such as “maggots will appear in rotting meat,” but Pasteur’s experiments proved that the underlying assumption of the theory was false. We might ponder the significance of the timing of this example. Pasteur’s experiments, disproving the ancient belief in the spontaneous generation of life, coincided with the publication of Darwin’s On the Origin of Species in 1859.

Darwinian evolution as a theory of the development of life on Earth makes predictions that overlap with various lines of observational evidence, such as shared genetic and morphological traits among numerous species, both living and extinct. Given some predictive successes, along with observations of the mechanism of natural selection, extended assumptions of the theory have been presumed true. However, many shortcomings remain, both with the predictions and assumptions of Darwinian evolution. In a classic article, Casey Luskin details numerous failed predictions of Darwinism.

In Darwin’s day, the deep and interconnected functional biocomplexity of every living cell lay beneath the observational resolution available to science. Even so, as Robert Shedinger remarks in Darwin’s Bluff, Darwin “base[d] his continued confidence in his theory on the grounds that it, ‘explains so many facts.’” However, Shedinger adds, as we have already discussed, “this does not prove that a particular theory is correct.” (p. 57)

In Need of Restraint

The Bohr model of the hydrogen atom yielded a stunningly precise prediction of the wavelengths of the spectral lines of hydrogen. Yet a closer look involving quantum theory showed that fundamental assumptions of the Bohr model were incorrect. It is very tempting, especially for the inventor of a theory, to believe that the theory must be correct if it produces predictions that overlap with reality. But utmost restraint needs to be employed not to conflate successful predictions of a theory with the truth of the theory’s assumptions.

An assumption of evolution is that natural processes suffice to have produced the vast information required for cellular reproduction and function. This represents an increase in information by natural processes over the passage of time, in disagreement with established laws of theoretical physics.

Meanwhile it has turned out that the predictions of the theory of Darwinian evolution have an overall accuracy that is arguably worse than that of the long-entrenched geocentric theory of the solar system. With ongoing scientific advances, the assumptions of Darwinism, both those on which it is based, and other assumptions extrapolated from the theory’s presumptive truth, have come under increasingly critical scrutiny. Darwin’s original theory and modern syntheses of it thus fail to satisfy the requirements of a valid scientific theory: Several of its predictions don’t adequately match reality, while its fundamental assumption, of life in all its forms arising without a designer, conflicts with established laws of physics. 

The influence of evolutionary thought arises as an outgrowth of uncritical acceptance of its assumptions, but the theory deflates like a punctured balloon when those assumptions are exposed as falsehoods. Rather than its continuing to dominate scientific thought, the curtain has been pulled back on Darwinian evolution. As evidence continues to accumulate contrary to the predictions and assumptions of evolution, its place on the shelf of discarded theories in the history of science is already being prepared.

In search of the ultimate rube Goldberg.

 

Darwinism is atheism's creation myth? Pros and Cons.

 

Darwin's hoped for simple beginning is still nowhere in sight?

 

Fake it till you make it?

 Fossil Friday: Piltdown Lizard Was Too Good to Check

Gunter Bechly

This Fossil Friday features Tridentinosaurus antiquus, which was discovered in 1931 and described by Leonardi (1959) from the Early Permian (ca. 280 million years old) sandstone of the Italian Alps. The 10-foot-long fossil animal looks like a dark imprint of an Anolis lizard. It was attributed by Dalla Veccia (1997) to the extinct Protorosauria (= Prolacertiformes) and considered to be “one of the oldest fossil reptiles and one of the very few skeletal specimens with evidence of soft tissue preservation” (Rossi et al. 2024), interpreted as carbonized skin showing the whole body outline like a photograph. Only the bones of the hind limbs were clearly visible.

The 90-year-old fossil find remained unique, as nothing similar was ever discovered again in the Permian of the Italian Alps (Starr 2024). This should have raised some red flags. However, why question a fossil that was “thought to be an important specimen for understanding early reptile evolution” (University College Cork 2024)? As journalists would say, it was too good to check. Instead the find was “celebrated in articles and books but never studied in detail” (University College Cork 2024).

Bombshell and Headlines

Now a new study (Rossi et al. 2024) of the famous fossil has turned out to be a bombshell, making global media headlines (University College Cork 2024). The scientists used sophisticated methods including ultraviolet light photography, 3D surface modeling, scanning electronic microscopy, and Fourier transformed infrared spectroscopy to analyze the apparent soft tissue of the fossil reptile. To their great surprise they discovered that “the material forming the body outline is not fossilized soft tissues but a manufactured pigment indicating that the body outline is a forgery,” which of course also throws into doubt the “validity of this enigmatic taxon.”

The study concludes that “The putative soft tissues of T. antiquus, one of the oldest known reptiles from the Alps, are fake and thus this specimen is not an exceptionally preserved fossil. Despite this, the poorly preserved long bones of the hindlimbs seem to be genuine.” But in the absence of novel information about the preserved skeleton, the authors “suggest caution in using T. antiquus in phylogenetic studies.”

Bombshell and Headlines

Now a new study (Rossi et al. 2024) of the famous fossil has turned out to be a bombshell, making global media headlines (University College Cork 2024). The scientists used sophisticated methods including ultraviolet light photography, 3D surface modeling, scanning electronic microscopy, and Fourier transformed infrared spectroscopy to analyze the apparent soft tissue of the fossil reptile. To their great surprise they discovered that “the material forming the body outline is not fossilized soft tissues but a manufactured pigment indicating that the body outline is a forgery,” which of course also throws into doubt the “validity of this enigmatic taxon.”

The study concludes that “The putative soft tissues of T. antiquus, one of the oldest known reptiles from the Alps, are fake and thus this specimen is not an exceptionally preserved fossil. Despite this, the poorly preserved long bones of the hindlimbs seem to be genuine.” But in the absence of novel information about the preserved skeleton, the authors “suggest caution in using T. antiquus in phylogenetic studies.”

Who Did It, and Why?

It is not known who perpetrated the forgery or why, but probably it was just a way to embellish the poor remains of the leg bones with some fancy painting (Starr 2024), coating it with varnish as a protective layer to hide the forgery from easy discovery (University College Cork 2024).

Italian paleontologist Valentina Rossi, the lead scientist of the study that uncovered the forgery, said in an article at The Conversation (Rossi 2024a) that “fake fossils are among us, passing almost undetected under the eye of experts all over the world. This is a serious problem — counterfeited specimens can mislead palaeontologists into studying an ancient past that never existed.” The reprinted article in Scientific American (Rossi 2024b) even admits in the subtitle, “Paleontology is rife with fake fossils that are made to cash in on illegal trade but end up interfering with science.” Let that sink in, and remember it when Darwinists try to ridicule Darwin critics, who bring up forgeries such as Piltdown Man or Archaeoraptor. Don’t let them get away with (despite knowing better) claiming that such forgeries are not a real problem in evolutionary biology.

Therefore, in loving memory of the Piltdown Man forgery, and the Piltdown Fly (Bechly 2022), we may in the future call this specimen the Piltdown Lizard.

There is nothing simple about this beginning? II

 Brian Miller: Rarity and Isolation of Proteins in Sequence Space

Andrew McDiarmid

Was the universe designed to evolve through natural processes? In a recent book, theologian Rope Kojonen has argued that evolutionary mechanisms work in harmony with intelligent design to produce the diversity of life we see on Earth. But can these fundamentally different processes really work together? On a new episode of ID the Future, host Casey Luskin speaks with physicist Dr. Brian Miller to explore why Kojonen’s theory fails on scientific grounds.

In this episode, Dr. Miller delves into the rarity and isolation of proteins in sequence space. Kojonen takes mainstream evolutionary mechanisms for granted, positing that the laws of nature are specially designed to allow every protein in nature to evolve through standard natural processes. But Miller shows that the limits of protein evolution are very real and very problematic for Kojonen’s model. He explains in detail multiple lines of evidence that show how unlikely it is that protein sequences occur naturally or by chance in sequence space. Miller reports on research showing that the probability of a protein continuing to work after each mutation drops precipitously. He also explains that even the most similar proteins are about 80 percent different from each other. It all adds up to a headache for evolutionary theory, and the headache doesn’t go away when you marry mainstream evolutionary theory with intelligent design.

Download the podcast or listen to it here

James Tour wants to see a manager re:OOL Research

 Apparently there is a problem with his prebiotic soup.

The Origin of Life remains darwinism's achilles heel?

 On the Origin of Life, a Measure of Intelligent Design’s Impact on Mainstream Science

David Klinghoffer

Don’t let anyone tell you that intelligent design isn’t having an impact on the way mainstream scientists are thinking about problems like the origin of life (OOL). David Coppedge points out the “devastating assessment” of OOL that was just published in Nature, the world’s most prestigious science journal. The authors are Nick Lane and Joana Xavier. The latter is a chemist at Imperial College London. As Coppedge notes, she’s been frank in comments about intelligent design and specifically Stephen Meyer’s Signature in the cell.

“One of the Best Books I’ve Read”

From a 2022 conversation with Perry Marshall:

But about intelligent design, let me tell you, Perry, I read Signature in the Cell by Stephen Meyer…And I must tell you, I found it one of the best books I’ve read, in terms of really putting the finger on the questions. What I didn’t like was the final answer, of course. But I actually tell everyone I can, “Listen, read that book. Let’s not put intelligent design on a spike and burn it. Let’s understand what they’re saying and engage.” It’s a really good book that really exposes a lot of the questions that people try to sweep under the carpet….I think we must have a more naturalistic answer to these processes. There must be. Otherwise, I’ll be out of a job.

That is a remarkable statement. Paul Nelson first Noted it at Evolution News. 

Under the Carpet

Dr. Xavier rejects ID, which is fair enough, but recommends an ID book by Dr. Meyer to “everyone I can” because “it really exposes a lot of the questions that people try to sweep under the carpet.” In the book, Meyer finds that, in addressing the origin-of-life puzzle, all current materialist solutions fail. He has a politer way of saying what chemist James Tour does on the same subject.

So that’s September 2022. Now a year and a half later, Xavier is back in the pages of Nature exposing weaknesses in the OOL field as currently constituted. She still holds out for a “more naturalistic answer.” But do you think, in writing about those “questions that people try to sweep under the carpet,” she didn’t have Meyer’s book in the back of her mind? I’m no mind reader, but to me, the question seems self-answering.

The odd couple? II

 Can Evolution and Intelligent Design Work Together in Harmony?

Andrew McDiarmid

Or is that wishful thinking? On a new episode of ID the Future, host Casey Luskin concludes his conversation with philosopher Stephen Dilley about a recent proposal to marry mainstream evolutionary theory with a case for intelligent design. Dr. Dilley is lead author of a comprehensive critique of Kojonen’s model co-authored with Luskin, Brian Miller, and Emily Reeves and published in the journal Religions.

In the second half of their discussion, Luskin and Dilley explain key scientific problems with Kojonen’s theistic evolutionary model. First up is Kojonen’s acceptance of both convergent evolution and common ancestry, two methods used by evolutionary biologists to explain common design features among different organisms. But if the design can be explained through natural processes, there is little need to invoke intelligent design. After all, the whole point of mainstream evolutionary theory is to render any need for design superfluous.

Dr. Dilley also explains why Kojonen’s model contradicts our natural intuition to detect design. If we look at a hummingbird under Kojonen’s proposal, we are still required to see unguided natural processes at work, the appearance of design without actual intelligent design. Yet we are also supposed to acknowledge that an intelligent designer front-loaded the evolutionary process with the creative power it needs to produce the hummingbird. So is it intelligently designed or isn’t it? The theist on the street is left scratching his or her head.

Download the podcast or listen to it here

There is nothing simple about this beginning?

 Getting It Together: Tethers, Handshakes, and Multitaskers in the Cell

David Coppedge

Running a cell requires coordination. How do molecules moving in the dark interior of a cell know how and when to connect? Protein tethers offer new clues, according to research at Philipps University in Marburg, Germany.

The ways that organelles and proteins connect at the right place and time are coming to light. One method is to encapsulate interacting molecules within compartments called condensates, droplets, and speckles. Like offices or cubicles where employees can talk without excess noise, these temporary spaces allow molecules to interact in peace (see “Caltech Finds Amazing Role for Noncoding DNA”). 

Another method for coordination of moving parts involves tethers. Certain molecular machines use “two hands” to bring other molecules or organelles together. Visualize a person taking a stranger’s hand and using her other hand to grasp a doorknob, leading the stranger to the place he needs to be. Many protein machines have a critical binding site for their targets, but these “dual affinity” tethering machines contain two different recognition sites on different domains that recognize separate targets needing to come together. Such multitasking machines are marvelously designed to promote fellowship for effective interactions in the cellular city.

A similar phenomenon has long been known in DNA translation. A set of molecules called aminoacyl-tRNA synthetases brings dissimilar molecules together. One synthetase feels the anticodon on its matching transfer RNA (tRNA) and then puts the corresponding amino acid on the opposite end. Like a language translator, each synthetase needs to know two languages — the DNA code and the protein code — to equip the tRNA with the correct amino acid. As the activated tRNA enters the ribosome, its anticodon base pairs with the complementary codon on the messenger RNA at one end, and its amino acid fits onto the growing polypeptide chain on the other end. This is a spectacular example of double duty, multitasking know-how. But is it the only one?

Another Example of Double Duty

A team of 15 researchers publishing in PLOS Biology under lead author Elena Bittner, also from Philipps University, and colleagues at Berkeley and Howard Hughes, has just reported a case of a multitasking machine that bridges dissimilar targets — in this case, peroxisomes with mitochondria or the endoplasmic reticulum (ER). It may not be the only case of “Proteins that carry dual targeting signals [that] can act as tethers between” organelles, they say:

Peroxisomes are organelles with crucial functions in oxidative metabolism. To correctly target to peroxisomes, proteins require specialized targeting signals. A mystery in the field is the sorting of proteins that carry a targeting signal for peroxisomes and as well as for other organelles, such as mitochondria or the endoplasmic reticulum (ER). Exploring several of these proteins in fungal model systems, we observed that they can act as tethers bridging organelles together to create contact sites. 

Take note that they found this in yeast, the simplest of eukaryotes.

We show that in Saccharomyces cerevisiae this mode of tethering involves the peroxisome import machinery, the ER–mitochondria encounter structure (ERMES) at mitochondria and the guided entry of tail-anchored proteins (GET) pathway at the ER. 

Why is this significant? 

Our findings introduce a previously unexplored concept of how dual affinity proteins can regulate organelle attachment and communication.

Previously unexplored: this sounds like a game changer. How does this “tethering” system work? After all the biochemistry work by the team is shown, demonstrating the dual-targeting capability, they illustrated it with a simplified diagram in Figure 10 in their open-access paper. As usual, even in simplified form, the system involves numerous other factors. The upshot is described as follows:

We have found that distinct proteins with targeting signals for 2 organelles can affect proximity of these organelles. This conclusion is supported by the notion that different types of dual affinity proteins can act as contact-inducing proteins (Fig 10) … Although dual affinity proteins are a challenge for maintaining organelle identity, they are ideally suited to support organelle interactions by binding to targeting factors and membrane-bound translocation machinery of different organelles. Dually targeted proteins appear to concentrate in regions of organelle contact, which may coincide with regions of reduced identity.

Within the mitochondria, we already met TIM and TOM, the channel guards who check the credentials of proteins entering the organelle’s outer and inner membranes. (The authors note that these translocase proteins are “evolutionarily conserved.”) But outside the mitochondrion, proteins needing to enter or exit have to find their way to the guards. That’s where the “dual affinity proteins” operate. 

What Do the Tethers Look Like?

Ptc5 is one of these tethering proteins, one of many that “contain targeting signals for mitochondria and peroxisomes at opposite termini.” Its Peroxisome Targeting Signal (PTS) recognizes the peroxisome at one end, and its Mitochondrial Targeting Signal (MTS) recognizes TOM at the mitochondrial channel. Experimenting with mutant strains of this and associated proteins and chaperones, the researchers confirmed that Ptc5 does tether peroxisomes to mitochondria. Moreover, its activity is dependent on need. “In aggregate,” they write, these data show that tethering via dual affinity proteins is a regulated process and depends on the metabolic state of the cell.” This implies the additional capability of sensing the fluctuating metabolic need.

The authors didn’t have much to say about evolution. As usual, it involved copious amounts of speculation.

While many peroxisomal membrane proteins can target peroxisomes without transitioning through the ER, several peroxisomal membrane proteins have evolved to be synthesized in vicinity to the ER and may translocate from it.

Other than TOM and TIM being “evolutionarily conserved,” that was all they had to offer Darwin.

A New Class of Activity Coordinators

What Bittner et al. have identified is probably the trigger for a paradigm shift concerning methods that cells use to get components together.

We conclude that dually targeted cargo includes a diverse and unexpected group of tethers, which are likely to maintain contact as long as they remain accessible for targeting factors at partner organelles. Coupling of protein and membrane trafficking is a common principle in the secretory pathway and it might also occur for peroxisomes at different contact sites.

And so, what lies ahead? Design proponents in biochemistry and molecular biology, play tetherball! Here is a potentially fruitful area for new discoveries.

How dually targeted proteins and their rerouting affect the flux of molecules other than proteins, e.g., membrane lipids remains a topic for future research. 

The odd couple?

 Can Evolution and Intelligent Design Be Happily Wedded?

Andrew McDiarmid

On a new episode of ID the Future, host Casey Luskin kicks off a series of interviews responding to theologian Dr. Rope Kojonen’s proposal that front-loaded intelligent design and a full-blooded evolutionary process worked together in harmony to produce the diversity of life we find on Earth. Here, Dr. Luskin interviews Dr. Stephen Dilley, lead author of a comprehensive critique of Kojonen’s model, co-authored with Luskin, Brian Miller, and Emily Reeves and published in the journal Religions.

In the first half of a conversation, Luskin and Dilley describe Dr. Kojonen’s proposal in a nutshell, providing the philosophical framing needed to grasp Kojonen’s elegant but flawed argument. Kojonen’s idea is the ultimate front-loaded design model, allowing for evolutionary mechanisms to work themselves out, but within a careful and purposeful arrangement of finely tuned preconditions and laws of form. Seemingly, t’s the best of both worlds: empirically detectable design within a fully natural evolutionary process. 

But there’s a problem. The fine-tuning Kojonen claims is baked into evolutionary processes is actually not there. The sequence space for amino acids to come together to form functional proteins has been found to be exceedingly rare as well as isolated. We don’t find evidence of fine-tuning within the mutation/selection mechanism. Instead, we find a process limited in its creative power that cannot have produced the complexity and information-rich innovation necessary to bring about life’s biological diversity. As Luskin puts it, “He [Kojonen] is arguing that God had to stack the deck in favor of evolution in order to get it to work.” It’s an interesting thesis, and Kojonen is serious and scholarly in his approach to the problem. But in the end, it fails on scientific grounds.

Download the podcast or listen to it here.

Yet more confirming of the humanity of ancient humans.

 Burials Reveal Prehistoric Cultures Valued Children with Down Syndrome

Denyse O Leary

We’ve all probably heard from one pundit or another that prehistoric humans discarded children with disabilities, just as animals might. Well, recently, researchers screened the DNA of 10,000 ancient humans (historic and prehistoric) for evidence of genetically detectible syndromes like Down sydrome. According to their report in Nature, “We find clear genetic evidence for six cases of trisomy 21 (Down syndrome) and one case of trisomy 18 (Edwards syndrome), and all cases are present in infant or perinatal burials.”

Clearly, people with significant genetic disorders could not expect a long life back then. But the researchers were surprised by the respect shown to the deceased children: “Notably, the care with which the burials were conducted, and the items found with these individuals indicate that ancient societies likely acknowledged these individuals with trisomy 18 and 21 as members of their communities, from the perspective of burial practice.”

The five prehistoric burials were all located within settlements and in some cases accompanied by special items such as colored bead necklaces, bronze rings or sea-shells. “These burials seem to show us that these individuals were cared for and appreciated as part of their ancient societies,” says [Adam] Rohrlach, the lead author of the study.

MAX PLANCK SOCIETY, “ANCIENT GENOMES REVEAL DOWN SYNDROME IN PAST SOCIETIES,” PHYS.ORG, FEBRUARY 20, 2024 > THE PAPER IS OPEN ACCESS VIA A SHAREIT TOKEN

Down syndrome (an extra whole or partial copy of the 21st chromosome, hence trisomy 21 ) is comparatively common (1/1,000 births). Edwards syndrome — three copies of chromosome 18 — occurs in 1/3,000 births.

Five of these burials of children with Down syndrome date to between 5,000 and 2,500 years before the present, in settled communities. An interesting feature is that the infants were buried inside houses:

“At the moment, we cannot say why we find so many cases at these sites,” says Roberto Risch, an archaeologist of the Universitat Autònoma de Barcelona working on intramural funerary rites, “but we know that they belonged to the few children who received the privilege to be buried inside the houses after death. This already is a hint that they were perceived as special babies.”

MAX PLANCK SOCIETY, “IN PAST SOCIETIES“

“A Surprise to Us”

In an article at The Conversation, researchers Adam “Ben” Rohrlach and Kay Prüfer comment,

The fact that three cases of Down syndrome and the one case of Edwards syndrome were found in just two contemporaneous and nearby settlements was a surprise to us.

“We don’t know why this happened,” says our co-author Roberto Risch, an archaeologist from The Autonomous University of Barcelona. “But it appears as if these people were purposefully choosing these infants for special burials.” “

ANCIENT DNA REVEALS CHILDREN WITH DOWN SYNDROME IN PAST SOCIETIES. WHAT CAN THEIR BURIALS TELL US ABOUT THEIR LIVES?,” FEBRUARY 20, 2024

Generally, when people are buried inside a home (floor burials), they are thought to be good, not bad, in some way. The sixth such burial was in a church graveyard in Finland, dated to the 17th–18th century

Why Were the Researchers So Surprised?

The researchers may be startled that the children were treated as members of the community because today considerable effort is made to identify children with Down syndrome prenatally — and most of them are aborted.

But perhaps Wayne Gretzky (in hockey, the legendary Great One) would be less surprised. In 1981, he met and developed a friendship with teenage Joey Moss (1963–2020) who had Down syndrome. In 1984, he got him a job as a locker room attendant with the Edmonton Oilers. Moss took to League life very well. An ardent fan and great favorite, he was inducted into the Alberta Sports Hall of Fame in 2003. He also received the National Hockey League Alumni Association’s Seventh Man award that year, for those “whose behind-the-scenes efforts make a difference in the lives of others.

A YouTube commenter writes, “I still tear up when I think of what we lost in Joey. He totally changed the way I deal with handicapped people. Clearly, his name must be in the rafters.”

Gretzky told People Magazine in 2016, “The people of Edmonton have accepted Joey as an everyday person without any sort of handicap and that’s what’s really special about his story.” Meanwhile, Gretzky himself raised money through golf tournaments to build more group homes for people who live with Down syndrome as adults — something that, of course, didn’t happen much in remote antiquity when almost all life expectancies were short.

If we don’t give people like Joey a chance, perhaps we haven’t advanced beyond our ancestors as much as we think, apart from our better living conditions.

Yet another of the fossil record's explosions.

 Fossil Friday: The Big Bang of Tertiary Birds and a Phylogenetic Mess

Gunter Bechly

This Fossil Friday we look into the abrupt origin of birds, which is just one of the many discontinuities in the fossil record of life on Earth. The image features a fossil bird of the genus Rhychaetites from the famous Eocene Messel pit in Germany. It is similar and also related to modern ibises.

While feathered dinosaurs and primitive toothed birds were abundant during the Cretaceous period, only the chicken and duck clade (Galloanserae) appeared in the Late Cretaceous (Field et al. 2020), while all the other groups of modern birds (Neoaves) appeared suddenly and with great diversity in the Lower Tertiary (today called Paleogene). Indeed, modern crown group birds appear and diversify so abruptly that it has been called a “Big Bang of Tertiary birds” by some paleo-ornithologists (Feduccia 1995, 2003a, 2014, Ksepka et al. 2017). Some of their colleagues did not like such an explosive view for obvious reasons (e.g. Dyke 2003, van Tuinen et al. 2003), but Alan Feduccia addressed and rebutted all critics (Feduccia 2003b), and emphasized that “a rapid, explosive Tertiary radiation best explains why resolving phylogenetic relationships of modern orders remains intractable.” James (2005) reviewed the Paleogene fossil record of birds and found that

before the Paleogene, fossils of putative neornithine birds are sparse and fragmentary (Hope 2002), and their phylogenetic placement is all the more equivocal. … The weak molecular genetic signal found so far for relationships among many higher-level taxa of birds could be explained if there was an early, explosive radiation of birds into diverse ecological niches. … Perhaps the greatest unsolved problem in avian systematics is the evolutionary relationships among modern higher-level taxa.

Rocks vs Clocks

Molecular clock studies, which suggested that modern birds might have originated more early in the Cretaceous, were thoroughly rejected as incompatible with the fossil record (Benton 1999), which could rather suggest that the molecular clock is running faster during the phases of rapid diversification in the major radiations. Nevertheless, van Tuinen (2009) estimated for the Timetree of Life that Neoaves initially diversified already 95 million years ago, followed by another diversification 87-75 million years ago and in the Tertiary (van Tuinen 2009). The author hoped that “more Cretaceous and Paleocene fossil material” may resolve the conflict but admitted that “phylogenetic resolution among the main divergences within Neoaves continues to remain a major hurdle, with most neoavian orders appearing to have diverged in close succession … indicating a rapid evolutionary radiation.” Six years later new fossil discoveries did not come to rescue yet: A fossil calibrated time line of animal evolutionary history (Benton et al. 2015; also see Fossil Calibration Database) suggested an age 86.8-60.2 million years for crown group Neoaves, even though the authors explicitly acknowledged the Paleocene penguin Waimanu from New Zealand as oldest unequivocal neoavian fossil record. Clearly, the molecular clock studies still do not agree with the empirical data of paleontological research.

A few scientists claimed that the problem can be resolved, such as the study by Ericson et al. (2006), which presented “the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils.” According to these authors their results “do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.” However, their result was quickly critiqued and refuted by Brown et al. (2007), who found that “nuclear DNA does not reconcile ‘rocks’ and ‘clocks’ in Neoaves”. They mentioned that “the discrepancy between fossil- and molecular-based age estimates for the diversification of modern birds has persisted despite increasingly large datasets on both sides”, and their reanalysis of Ericson’s data documented “that there is no reliable molecular evidence against an extensive pre-Tertiary radiation of Neoaves.” In the same year Zhang (2007) confirmed that “paleontological studies showed that modern avian groups probably first appeared in the Paleocene and experienced an explosive radiation in the early Cenozoic.”Brown et al. (2008) called this problem the “rock-clock gap” and said that “determining an absolute timescale for avian evolutionary history has proven contentious. The two sources of information available, paleontological data and inference from extant molecular genetic sequences (colloquially, ‘rocks’ and ‘clocks’), have appeared irreconcilable; … These two sources of data therefore appear to support fundamentally different models of avian evolution.” Their own study of mitochondrial DNA did “fail to reconcile molecular genetic divergence time estimates with dates taken from the fossil record; instead, we find strong support for an ancient origin of modern bird lineages.” Thus, the problem turned out to be quite stubborn and refused to go away with more data. On the contrary, each new study reenforced the problem. For example, the attempt by Pratt et al. (2008) to resolve the deep phylogeny of Neoaves produced molecular datings from mitochondrial genomes that “support a major diversification of at least 12 neoavian lineages in the Late Cretaceous.” Another example is the study by Pacheco et al. (2011), who used several molecular dating approaches and conservative calibration points, but still “found time estimates slightly younger than those reported by others, most of the major orders originated prior to the K/T boundary.” But even more interestingly, these authors revealed the secret reason why so many evolutionary biologists do not like the Big Bang model: “proponents of this hypothesis do not provide viable genetic mechanisms for those changes” (Pacheco et al. 2011). In other words, if there were such Big Bangs then Darwinism cannot plausibly explain them. This is why these abrupt appearances in the history of life fascinate me and will be subject of my book project called “The Big Bangs of Life.”

Phylogenomics vs Clocks

But it gets worse. Not just that rocks and clocks conflicted, but phylogenomic studies increasingly supported the Big Bang of Tertiary birds so that now molecular trees conflicted with molecular clocks. The Big Bang view was most strongly confirmed by the seminal study of Jarvis et al. (2014), a genome scale phylogenetic analysis by more than 100 authors (!), who found that “even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.” This result was widely reported by the popular science media with sensational headlines about the mapping of the “‘Big Bang’ of Bird Evolution” (AMNH 2014, Duke University 2014, BGI Shenzen 2014, Smithsonian Insider 2014), or as Time Magazine titled “There was a Big Bang for Birds” (Kluger 2014), or “Rapid bird evolution after the age of dinosaurs unprecedented, study confirms” (University of Sydney 2014). Casey Luskin (2014) then also reported for Evolution News how this “massive genetic study confirms birds arose in Big Bang-type of explosion.”

Another comprehensive phylogenetic study more recently again confirmed such an extremely rapid “major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction” (Prum et al. 2015; also see Wink et al. 2023 for a perfect visualization of Prum’s results). Claramunt & Cracraft (2015) “combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes” and concluded that “it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world.” Brusatte et al. (2015) concluded in their review article on the origin and diversification of birds that “after the mass extinction, modern birds (members of the avian crown group) explosively diversified, culminating in more than 10,000 species distributed worldwide today.” Braun et al. (2019) still acknowledged that Neoaves “appears to have undergone a rapid radiation near the end Cretaceous mass extinction (the K-Pg boundary).” Looks like a solid scientific consensus, but not so fast. After all, we are dealing with evolutionary biology, where almost anything can happen.

A New Study

Indeed, this month a new paper by Wu et al. (2024) came to a totally different result from the consensus of virtually all previous studies. The press release (Yirka 2024) says that this “new study suggests birds began diversifying long before dinosaurs went extinct” and “the research team found evidence that the Neoaves divergence path began long before the asteroid struck.” The team of mainly Chinese authors analyzed the genomes of hundreds of species of birds and arrived at a new tree of Neoaves. The authors concluded that “the evolution of modern birds followed a slow process of gradualism rather than a rapid process of punctuated equilibrium, with limited interruption by the KPg catastrophe”. They dated the common ancestor of Neoaves to 130 million years ago in the Early Cretaceous and their diversification to the Late Cretaceous, even though there exists not a single Cretaceous fossil of this group, which had already led the worlds foremost expert on the fossil record, Michael Benton (1999), to strongly reject such hypotheses as impossible.

Unsurprisingly, other experts are not convinced either, and said that “if the new study was right, there should be fossils of all major groups of living birds from well before the asteroid impact. But almost none have been found. The signal from the fossil record is not ambiguous” (Berv quoted in Zimmer 2024 for the New York Times). Likewise another comment in the prestigious journal Science said that “if major bird groups really did emerge before the asteroid impact, then why have almost no ancient bird fossils from that time period been found?” (Jacobs 2024). Spot on, but still we have a conflict between molecular evidence and the fossil record, which should agree if Darwinism is correct.

Conflicting Trees

However, the conflicts are by no means restricted to the timing of bird evolution. Even though Darwinism would predict that all different sources of data should point to one true tree of life, there is fundamental conflict in the various attempts to reconstruct the tree of birds in the 20th and 21st century. This conflict is visible in the results of three general methodological approaches (DNA-DNA-hybridization, morphological cladistics, and phylogenomics), as well as between morphological and molecular data and even between different sets of molecular genetic data.

DNA-DNA-Hybridization

In the 1970s and 1980s the American ornithologists and molecular biologists Charles Sibley and Jon Edward Ahlquist conducted DNA-DNA-hybridization studies of numerous species of modern birds (Sibley & Ahlquist 1990, Sibley 1994; also see Wikipedia). Their revolutionary great tree of 1,100 species of living birds was called “the tapestry” and introduced a major revision of avian classification.

Sibley and Ahlquist’s used the melting temperatures of hybridized strands of DNA of two species as proxy for their overall similarity. Their methods were strongly critiqued as flawed and phenetic (Houde 1987, Lanyon 1992, Harshman 1994, Marks 2011), but even John Harshman found that “the data in Sibley and Ahlquist (1990), properly analyzed, have a strong phylogenetic signal.” Nevertheless, only few of the supraordinal groups from their tree survived later studies, mainly the basal split between Galloanserae and Neoaves.

It is of course a cheap point to say today that the method of DNA-DNA-hybidization is obsolete and was just a short-lived and misguided fad in the early days of phylogenetics, but was it? Think about it. Instead of just comparing arbitrarily selected and arbitrarily defined morphological characters, or instead of just looking into selected sequenced genes, this method compared the overall similarity between complete genomes, the whole shebang of DNA. If anything, it is this very method, which should have recovered the echo of evolutionary history and common descent. That its results failed to agree with the more modern cladistic and phylogenomic studies is basically evidence for the total bankruptcy of Darwinism.

Hennigian Phylogenetics (Cladistics)

Another school of phylogenetic methodology that dominated the pre-phylogenomic era was Hennigian phylogenetic systematics, also known as cladistics. It was mainly based on data from comparative morphology and used only shared derived similarities (called synapomorphies) for the reconstruction of the most parsimonious tree topology. In bird phylogenetics the most prominent representative was certainly the American paleo-ornithologist Joel Cracraft, who was the curator for birds at the American Museum of Natural History in New York (Cracraft 1981, Cracraft & Clarke 2001, Cracraft et al. 2004). Even though Cracraft’s work was not without criticism even from fellow cladists (e.g., Olson 1982), it arguably represents the culmination of traditional cladistic studies on avian phylogeny. Other important cladistic studies based on bird morphology were contributed by Livezey & Zusi (2001, 2006, 2007) and many other works on particular neoavian subgroups. The results differed from each other, from Sibley & Ahlquist’s “tapestry,” and from more modern phylogenomic trees.

By the way: Cracraft (2001) also looked into the rocks vs clocks problem. He acknowledged that “the fossil record has been used to support the origin and radiation of modern birds (Neornithes) in Laurasia after the Cretaceous-Tertiary mass extinction event, whereas molecular clocks have suggested a Cretaceous origin for most avian orders.” He looked into the vicariance biogeography of birds as new source of data to resolve the problem and concluded “that neornithines arose in Gondwana prior to the Cretaceous-Tertiary extinction event.” However, this is fully consistent with the Big Bang hypothesis, which is about the radiation of Neoaves, not of Neornithes. After all, we do have a late Cretaceous fossil record of fowl (Galloanserae). Fifteen years later Claramunt & Cracraft (2015) clarified, as already mentioned above, “that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world.”

Phylogenomics

In the 21st century the era of phylogenomics came to dominate the field of bird phylogenetics, which mainly uses maximum likelihood and Bayesian methods for tree reconstruction from DNA sequence data. Within a few years several very extensive phylogenomic studies appeared (e.g., Ericson et al. 2006, Hackett et al. 2008, Pratt et al. 2008, Pacheco et al. 2011, McCormack et al. 2013, Jarvis et al. 2014, Zhang et al. 2014, Prum et al. 2015, Reddy et al. 2017, Houde et al. 2019, Kimball et al. 2019, Braun & Kimball 2021, Kuhl et al. 2021, Yu et al. 2021, Wu et al. 2024; also see the Bird Phylogeny website), which not just conflicted with the previous phylogenies but also with each other (Mayr 2011, Matzke et al. 2012, Braun et al. 2019). This led some experts, such as Poe & Chubb (2004) and Suh (2016), to rather propose a hard polytomy (called “neoavian comb” by Cracraft et al. 2004) based on an explosive evolution, which brings us right back to the Big Bang of birds, because as Feduccia (2014) said: “our continued inability to produce a veracious phylogeny of higher avian taxa is likely related to a Paleogene explosive burst or ‘big bang’ evolution of bird and mammal evolution, resulting in short ordinal internodes.” The resolution of this polytomy has been called “the greatest current challenge of avian systematics” and “last frontier” which “is still elusive” (Pratt et al. 2008). The numerous phylogenomic studies only agree on a few higher clades that were called the “magnificent seven” by Reddy et al. (2017), which already indicates how rare such agreement is, but even those few clades conflict with the older trees based on DNA-DNA-hybridization and morphological cladistics (but see Mayr 2007, 2008 for a few exceptions).

Collapsing Trees

The above-described phylogenetic conflict and incongruent trees of birds exactly confirm a point that I recently made in two other Evolution News articles for Fossil Friday on the phylogeny of arachnids (Bechly 2023) and of insectivore mammals (Bechly 2024): When you look at the numerous published phylogenetic trees of a certain group of organisms and then calculate a strict consensus tree as a kind of common denominator, the result generally tends to be an unresolved polytomy, with basically only the pre-Darwinian Linnean classification of phyla, classes, orders, and families surviving this collapse of phylogenies. This is highly unexpected under Darwinian assumptions but very much resonates with the views of Darwin critics.

This is even implicitly and a bit cryptically acknowledged in mainstream findings like that of Gordon et al. (2021) who said:

Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals.

Maybe non-history (in the sense of uncommon descent) is the simple reason for a non-historical signal.

Braun et al. (2019) concluded in their review of the phylogenomic era in avian phylogenetics:

Reconstructing relationships among extant birds (Neornithes) has been one of the most difficult problems in phylogenetics, and, despite intensive effort, the avian tree of life remains (at least partially) unresolved. Thus far, the most difficult problem is the relationship among the orders of Neoaves, the major clade that includes the most (~95%) named bird species.

Explaining Away Conflicting Evidence

Of course, this is all reflecting the substantial conflicting data that do not align with an unambiguous nested hierarchy, contrary to the predictions of neo-Darwinism and the bold (and false) claims of its modern popularizers like Richard Dawkins. Something is way off, and mainstream evolutionary biologists simply ignore it and happily produce one conflicting tree after the other without ever questioning the underlying assumptions or even the general Darwinian paradigm. Conflicting evidence is explained away with inexpensive ad hoc hypotheses like convergence, ghost lineages, or incomplete lineage sorting. Torres & Van Tuinen (2013) said “rampant phylogenetic conflict at the ordinal level in modern birds can be explained by ordinal diversification taking place over a short time interval.” However, this is not the explanation of the problem but the description of the problem!

We can conclude that fossil and molecular data conflict in terms of the question when and how quickly modern birds originated, and molecular and morphological data conflict in terms of the reconstruction of the assumed bird tree of life. Why is there such a stark conflict, when Darwinism would naturally predict that different lines of evidence should converge towards one true evolutionary history of birds. Again, a quite obvious explanation could be that there just was no such history, or at least that totally different causal mechanism were at work.

Abrupt Origins

The most important take home message from this article is this: in spite of the new study by Wu et al. (2024), there is overwhelming evidence, recognized by the vast majority of mainstream experts, that there was an explosive diversification of modern birds (Neoaves) in the Lower Tertiary (Paleogene). There was an abrupt origin, a burst of biological creativity with a genuine Big Bang of modern birds, which is best explained by an infusion of new information from an intelligent agent outside the system. What do evolutionary biologists suggest instead? They say that the global collapse of forest ecosystems after the end-Cretaceous impact killed off all arboreal bird lineages and the remaining ground-dwelling ancestors of modern birds experienced a rapid diversification afterwards (Field et al. 2018). Yet another description of the problem, rather than an explanation, which seems to be a recurring theme in evolutionary biology.

Not an argument from silence.

 Atheist Philosopher Explains Why Intelligent Design Is Not a “God of the Gaps” Argument

Jonathan McLatchie

Jeffrey Jay Lowder is an atheist philosopher and author, whom I would rate as among the top tier of intellectual critics of theistic belief (you can watch him debate Frank Turek here). Not only is he an extremely balanced and nuanced thinker, but he is also quite amicable. I consider him a friend, and we have met for dinner or drinks a couple of times. On Twitter (I refrain from calling it by its hideous new name, “X”), he goes by the handle “Secular Outpost.” Recently Lowder posted the following remark:

Unpopular opinion (among nontheists): the arguments for intelligent design defended by the likes of Moreland, Craig, and Meyer are NOT god of the gaps arguments.

My colleague David Klinghoffer asked Lowder to clarify his thinking on this. In response, Lowder linked to two blog posts he had written addressing the subject. The first, published in 2016, responds to Victor Reppert, who had asked whether there is “any theistic argument [from/in natural theology] that can’t be accused of being a god-of-the-gaps argument,” and if this rejoinder may serve as “an all-purpose reply to all natural theology.” Lowder answers the first of those questions in the affirmative and the second in the negative. 

Why Intelligent Design Is Not a “God of the Gaps’ Argument

(1) There is some puzzling phenomenon P which science cannot at present explain. 

(2) Theism does explain P. 

Therefore, 

(3) P is more likely on the assumption that God exists than on the assumption God does not exist.

I have no issues with Lowder’s reconstruction of a god-of-the-gaps argument. As he explains, “The key feature of this argument — and what makes it a ‘God-of-the-gaps’ argument — is premise (1). The focus is on science’s present inability to explain P.” How might one construct an argument that is not vulnerable to the god-of-the-gaps critique? Suppose you want to advance an argument for theism based on the existence of consciousness. Lowder proposes that the following formulation of the argument (where E is the existence of human consciousness, T is theism, and N is naturalism) evades this charge:

(1) E is known to be true, i.e. Pr(E) is close to 1.

(2) N is not intrinsically much more probable than T, i.e., Pr(|N|) is not much greater than Pr(|T|).

(3) Pr(E | T & B) > Pr(E | N & B).

(4) Other evidence held equal, N is probably false, i.e., Pr(N | B & E) < 1/2.

Put into straightforward English, the argument is as follows:

(1) The existence of human consciousness is known to be true.

(2) Naturalism is not intrinsically much more probable than theism.

(3) The probability of the existence of human consciousness given theism and the background information is greater than the probability of the existence of human consciousness given naturalism and the background information.

(4) Other evidence held equal, naturalism is probably false (i.e., the probability of naturalism given the background and the evidence is less than 50 percent).

Lowder concludes that “Whatever problems may exist within that argument, being a God-of-the-gaps argument clearly isn’t one of them.” I completely agree with Lowder’s assessment. Intelligent design makes the argument that various specific features of life and the universe — in particular, the informational properties of DNA, and the irreducibly complex nature of molecular systems — are rendered vastly more probable than they would otherwise be by the supposition that a conscious mind was involved in their origins. Thus, they are positively confirmatory of design. Since confirmations of design in the universe are significantly less surprising (or, more probable) given the hypothesis of theism than on its falsehood, the evidence of design also translates into positive evidence of the existence of God. Perhaps there are vulnerabilities in this argument structure — but, whatever may be wrong with it, it is certainly not wrong by virtue of being a god-of-the-gaps argument. I would like to commend Lowder for his intellectual integrity in pointing this out, despite our disagreements on the larger question of whether intelligent design is in fact true.

Jeff Lowder Reviews Signature in the Cell

The second article linked by Lowder is a critical review of Stephen Meyer’s book, Signature in the Cell: DNA and the Evidence for Intelligent Design. I had more disagreements with this article than with the first. Lowder remarks that “We are fortunate that Meyer explicitly provides the logical form of his argument,” which he quotes as follows:

Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information. 

Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information. 

Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.

Lowder, again to his credit, notes, “I agree with Meyer that it would be a mistake to dismiss his argument as an argument from ignorance.” Furthermore, “We should consider the possibility that the origin of life is a source of potential evidence for intelligent design (and for theism).” What, then, is Lowder’s principle objection to Meyer’s argument? He writes,

The objection I have in mind is this: the design hypothesis is not an explanation because, well, it doesn’t explain. Regarding the origin of biological information, it still isn’t clear to me what Meyers [sic] believes the design explanation is. I don’t find in the book a description of how an intelligent designer created / designed / programmed — not sure what the right verb is — the first biological information. In order to explain biological information, it’s not enough to posit the existence of an intelligent designer as a potential cause of biological information. In addition, it seems to me that a design explanation must also include a description of the mechanism used by the designer to design and build the thing. In other words, in order for design to explain something, we have to know how the designer designed it. If we don’t know or even have a clue about how the designer did it, then we don’t have a design explanation.

However, this seems to me to be mistaken. For example, suppose that future scientists are able to capture high resolution images of Alpha Centauri, the closest star to our sun, and were to discover that a vehicle resembling a Volkswagen Beetle were orbiting a planet there. Presumably, we could justifiably infer design if we had no idea what equipment or processes were used to assemble the vehicle, and even if we could not identity the agent responsible. Those are interesting downstream questions, to be sure. But our inability to answer them does not negate our ability to infer design as an explanation of how the Beetle came to be there. 

Moreover, we all believe that our conscious minds interact with the material world, even though we lack an understanding of how consciousness works. Thus, to postulate that a conscious mind is responsible for complex and functionally specific information content, or an engineered system, is a legitimate explanation, even though we currently cannot give an adequate account of how our minds animate our bodies to accomplish engineering tasks.

Theism and Explanation

Lowder quotes Gregory Dawes’s Theism and Explanation, in which he asserts, objecting to Richard Swinburne’s argument for theism,

It is only when you have specified the divine intention in question that we can test your explanation, by asking what else would follow if God did indeed have this intention. And as we have seen, it will not do merely to substitute the explanandum for the posited goal… As we have already seen, this would be a spurious kind of explanation, seriously lacking in empirical content. 

P. 119

However, to make a compelling argument for theism, it is not necessary to posit that there is a high probability of God having a particular motivation or intention for creating, for example, complex life. It is enough to posit that it is not immensely implausible that God would have such a purpose for creating. Suppose, for example, that God’s purpose in creating a world containing complex embodied creatures is that they might participate in an arena of moral choice, providing them opportunities to mold and shape their character, developing in morally significant ways. In such a scenario, for actions to have predictable consequences, the universe would have to be governed by fixed natural laws. And it is being physically embodied — in a world of pushes and pulls — that accentuates our ability to engage in moral decision-making. I think most readers can see that such a scenario is not at all wildly implausible on the supposition of classical theism. However, the existence of such a world is rendered absurdly improbable if we assume the falsehood of theism. Therefore, the world we observe constitutes strong (I would say, overwhelming) evidence in favor of theism.

Despite our many disagreements, I sincerely appreciate Lowder’s spirit and intellectual honesty. I hope the next generation of secular thinkers follow his lead.