Bacteria: The real world savers?

 “Bacteria Are Incredible” — Here Are More Illustrations

David Coppedge

In his latest “Secrets of the Cell” video, biochemist Michael Behe tells about wonderful bacteria that eat organic waste, remove smells from mud by conducting electricity, recycle plastic, aid our digestion, and more. “Folks, you can’t make this stuff up!” he exclaims. “Bacteria are incredible.”

That is true, and I provided some illustrations yesterday. Here are more. 

Think of man’s worst environmental disasters. The Deepwater Horizon oil spill and the Chernobyl nuclear accident probably take priority on the list. The American Chemical Society posted a video showing how bacteria are good at cleaning up oil spills, radioactive waste and toxic chemicals — not that this fact gives humans license to damage the planet, but it’s interesting. The narrator, who demonstrates a controlled experiment with oil-eating bacteria in her kitchen, was surprised that the microbes that flock to oil spills need no genetic engineering. They get to work on their own and seem to enjoy it. “How cool is it that genetic tinkering is not always needed?” she comments. Much of our plastic debris, however, accumulates in the oceans where it collects in huge revolving garbage patches on the surface called gyres. How many people faithfully recycle plastic bottles only to find in news reports that China no longer accepts the West’s barges of compressed plastic, and so it ends up in the ocean anyway? It’s depressing. Some have remarked that recycling might do more damage than throwing it in the regular trash. For those trying to be environmentally conscious, that’s really depressing.

Environmental engineers fret as plastic waste accumulates and circulates in those gyres. But a few decades ago, scientists began to discover that these garbage patches are not lifeless deserts. They are teeming with a class of organisms collectively known as “neuston.” New Scientist reports:

Neuston are organisms that float on the ocean surface. They encompass a wide range of species, including blue sea dragons (Glaucus atlanticus), violet snails (Janthina janthina), blue button jellyfish (Porpita porpita) and by-the-wind sailors (Velella velella).

Rebecca Helm at the University of North Carolina at Asheville and colleagues found that there are more neuston in the center of the North Pacific Garbage Patch than at the edges. This is probably true worldwide, as similar garbage patches are found in the South Pacific, South Atlantic, and Indian oceans. At least some life forms are making a living on our trash! Some of the organisms are quite beautiful.

So now, Helm is worried that cleanup efforts could endanger these thriving communities of organisms. Another worry is that fish and whales could imbibe plastic by feeding on the neuston. There is a race against time to give the plastic-degrading bacteria time to work while the higher organisms enjoy their merry-go-round ride on artificial boats. There’s a research project: to what extent does the neuston ecosystem contribute to the breakdown of floating plastic?

If environmental engineers can find ways to accelerate bacteria’s good work, it may prove to be a much more cost-effective way to recycle plastic than packing it on barges. Maybe biodegradation could be started earlier in the process. Either way, it appears that the food chain, with microbes at the base, has the power to degrade all that plastic eventually if a true circular economy comes to fruition and the accumulation in the gyres ceases.

A Food Chain of Recyclers

Alice Klein’s article in New Scientist doesn’t mention the food chain, but earlier reports have found that microbes contribute to the breakdown of ocean garbage and even larger artificial junk. We know that organisms recycle our shipwrecks in the deep sea. If you want to visit the Titanic by submarine, you had better hurry; it could vanish by 2037. The EE Times explained why:

The iconic ocean liner is, in fact, disintegrating where it lies; as well as animals and plants, its inhabitants include bacteria, which are eating their home at a staggering rate. One type of bacteria transforms dissolved iron into insoluble iron oxide to create rusticles — like icicles, but made of rust. Other types of the dozen or so microbes present effectively eat the rusticles.

And so the evidence of man’s grandiose projects — elegant ballrooms under chandeliers on a doomed “unsinkable” ship — vanishes into memory, as the ocean reclaims its own. But there’s a happy side to some of our shipwrecks. Multitudes of fish and other sea creatures have taken up residence in and around battleships from the South Pacific, even those sunk by nuclear bomb tests. Considering this discovery, some ships have been submerged on purpose to provide havens for fish and scuba divers. Microbes and viruses are sure to be key players in those thriving ecosystems.

Don’t Dismiss Bacteria

Instead of dismissing bacteria as primitive remnants of early evolution, design-thinking scientists can help our planet’s tiny ecosystem engineers solve some of the most pressing problems facing us today. By looking at microbes as the intelligently designed systems they are — having shown their benefits in many ways — ID advocates can partner with them. Like the first ranchers, they can bridle and saddle up these tiny workhorses that come equipped to tackle planet-sized loads.

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What unbelievers need to believe.

 Three Realities Chance Can’t Explain That Intelligent Design Can.

Granville Sewell

The scientific establishment is slowly beginning to allow scientists who believe in intelligent design to have a platform. Why? It may be because the theory that the universe was crafted intentionally explains many realities that theories based on chance do not.

Perhaps the simplest and best argument for intelligent design is to clearly state what you have to believe to not believe in intelligent design, as I did in my book, In the Beginning and Other Essays on Intelligent Design. Peter Urone, in his physics text College Physics, writes, “One of the most remarkable simplifications in physics is that only four distinct forces account for all known phenomena.”

This is what you have to believe to not believe in intelligent design: that the origin and evolution of life, and the evolution of human consciousness and intelligence, are due entirely to a few unintelligent forces of physics. Thus you must believe that a few unintelligent forces of physics alone could have rearranged the fundamental particles of physics into computers and science texts and jet airplanes and nuclear power plants and Apple iPhones.    

These four unintelligent forces of physics may indeed explain everything that has happened on other planets, but let us look at three essential elements of our human existence and examine whether the currently believed origin theory can explain them.

1. The Origin of Life

To appreciate that we still have no idea how the first living things arose, you only have to realize that with all our advanced technology we are still not close to designing any type of self-replicating machine; that is still pure science fiction. We can only create machines that create other machines, but no machine that can make a copy of itself. 

When we add technology to such a machine, to bring it closer to the goal of reproduction, we only move the goalposts because now we have a more complicated machine to reproduce. So how could we imagine that such a machine could have arisen by pure chance?

Maybe human engineers will someday construct a self-replicating machine. But if they do, I’m sure it will not happen until long after I am gone, and it will not show that life could have arisen through natural processes. It will only have shown that it could have arisen through design. 

2. The Origin of Advanced Life Forms

Furthermore, imagine that we did somehow manage to design, say, a fleet of cars with fully automated car-building factories inside, able to produce new cars — and not just normal new cars, but new cars with fully automated car-building factories inside them. Who could seriously believe that if we left these cars alone for a long time, the accumulation of duplication errors made as they reproduced themselves would result in anything other than devolution, and eventually could even be organized by selective forces into more advanced automobile models?  

No, we could confidently predict that the whole process would grind to a halt after a few generations without intelligent humans around to fix the mechanical problems that would inevitably arise, long before we saw duplication errors that held any promise of advances. 

The idea that it could even be remotely plausible that random mutations could produce major improvements relies completely on the observed but inexplicable fact that, while they are awaiting rare favorable mutations, living species are able to preserve their complex structures and pass them on to their descendants without significant degradation. We are so used to seeing this happen that we don’t appreciate how astonishing it really is.  

But perhaps trying to imagine designing self-replicating cars, and trying to imagine that these cars could make progress through the accumulation of duplication errors, may help us realize that we really have no idea how living things are able to pass their current complex structures on to their descendants, generation after generation — much less how they evolve even more complex structures.

Lehigh University biochemist Michael Behe, in his 2019 book Darwin Devolves, writes:

Darwinian evolution proceeds mainly by damaging or breaking genes, which, counterintuitively, sometimes helps survival. In other words, the mechanism is powerfully de-volutionary. It promotes the rapid loss of genetic information. Laboratory experiments, field research, and theoretical studies all forcefully indicate that, as a result, random mutation and natural selection make evolution self-limiting. … Darwin’s mechanism works chiefly by squandering genetic information for short-term gain.

So, according to Behe, duplication errors, even when organized by selective forces, have the same effect on living species as we would expect them to have on self-replicating cars: only devolution and degradation.

Also, here we have not even discussed what is generally considered to be the main problem with Darwinism: its inability to explain the appearance of major new, irreducibly complex features that consistently appear suddenly in the fossil record. (I discussed this problem in my article “A Mathematician’s View of Evolution,” and in the second part of my video “Why Evolution is Different.”)

3. The Origin of Human Intelligence and Consciousness

Trying to imagine that the accumulation of duplication errors made by our fleet of self-replicating cars could eventually result in conscious, intelligent machines might help us to realize that the evolution of intelligent beings, capable of designing computers, science texts, jet airplanes, and Apple iPhones, is an especially monumental and unsolved problem. 

In my video “A Summary of the Evidence for Intelligent Design,” I began my fifth point with a picture of three children in the 1950s. One of them is me, the other two are not. I saw the world from inside one of these children. I saw every picture that entered through his eyes, I heard every sound that entered through his ears, and when he fell on the sidewalk, I felt his pain. How did I end up inside one of these children? 

This is a question that rarely seems to trouble evolutionists. They talk about human evolution as if they were outside observers and never seem to wonder how they got inside one of the animals they are studying. They consider that human brains are just complicated computers, and so to explain how we got here they just have to explain how these mechanical brains evolved. 

But even if they could explain how animals with mechanical brains evolved out of the primeval slime, that would leave the most important question — the one evolutionists never seem to even wonder about — still unsolved: How did I get inside one of these animals?

The argument for intelligent design could not be simpler or clearer: Unintelligent forces alone cannot rearrange atoms into computers and airplanes and nuclear power plants and smartphones, and any attempt to explain how they can must fail somewhere because they obviously can’t. Perhaps this is the best way to understand why explanations without design will never work, and why science may finally be starting to recognize this.

Cross-posted from The Federalist with permission of the author.

Could one man(not God-man) really save humanity from sin.

 1Corinthians15:21ASV"For since by man came death, by man came also the resurrection of the dead. "

The first human sinner did not inherit his sinful state he chose it. Unlike his descendants he had a choice in the matter.

1Timothy2:14KJV"And Adam was not deceived, but the woman being deceived was in the transgression."

Now what if humanity's founding father had made the moral choice. Would it not be the case that he would be our savior? So then that is all that is required to save mankind. A father who choses aright.

Can this tree be replanted? III

 More Turbulence at the Base of the Tree of Life

Evolution News @DiscoveryCSC

Here is a new open-access paper, published in Frontiers in Microbiology, that is instructive: “Eukaryogenesis: The Rise of an Emergent Superorganism.” Author Philip J. L. Bell begins:

Although it is widely taught that all modern life descended via modification from a last universal common ancestor (LUCA), this dominant paradigm is yet to provide a generally accepted explanation for the chasm in design between prokaryotic and eukaryotic cells. Counter to this dominant paradigm, the viral eukaryogenesis (VE) hypothesis proposes that the eukaryotes originated as an emergent superorganism and thus did not evolve from LUCA via descent with incremental modification. [Emphasis added.]

The “chasm in design”? For a theory (i.e., the universal Tree of Life, rooted in LUCA — universal common descent, or UCD) whose empirical strength is so great that it cannot be doubted, UCD certainly is doubted a lot.

Doubted by biologists, in fact, with no known interest in intelligent design.

On the anternet.

 Yes, Ants Think — Like Computers

Denyse O'Leary

Navigation expert Eric Cassell, whose recent book is Animal Algorithms: Evolution and the Mysterious Origin of Ingenious Instincts, offers some insights into how ants organize themselves by using what amount to algorithms, without any central command:

Ants are remarkably consistent in their lifestyle. All of the roughly 11,000 species of ants live in groups, large or small. There are no known solitary ants. 

Living in groups, they have developed a social lifestyle that includes “agriculture, territorial wars, slavery, division of labor, castes, consensus-building, cities, and a symbolic language.” (p. 85) How is this managed by ants with very small brains (200,000 to 250,000 neurons) and very limited individuality?

For comparison, among mammals, the agouti has roughly 857 million neurons, the capybara has 1.60 billion, and the capuchin monkey, 3.690 billion. Humans have roughly 85 billion neurons. It seems that the ant is doing something that does not rely on individual problem-solving skills.

Cassell points out that the ants’ complex colony organization where one queen or several queens lay all the eggs and the other females do all the work is almost exclusively the domain of life forms with very small brains. The naked mole rat is the only mammal that follows this pattern. Incidentally, the naked mole rat has fewer neurons in a smaller brain than expected for its body size, relative to other rodents.

Such colonies are sometimes called “superorganisms” because the individual organisms work for the survival of the colony as a whole. Take these leafcutter ants in Brazil:

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What Are Some of the Ant Colony’s Methods?

We don’t know exactly how the ant “algorithm” works out divisions of labor but one study found that young ants typically tend to the eggs, larvae, and pupae while older ants forage outside the nest. Foraging is a much more dangerous activity than tending the young, so if the older ants forage, fewer days of ant life are lost to the colony (pp. 89–90). Some ant species have castes of workers with specially shaped heads, best suited to specific purposes like attacking other ants or blocking a tunnel (pp. 95–96). In that case, they might naturally gravitate to the task without having to think about it. They just find it easier than the differently structured ants would.

Ants communicate mainly by pheromones, scents that provide information. In their book The Superorganism: The Beauty, Elegance, and Strangeness of Insect Societies (2008), Bert Hölldobler and E. O. Wilson (1929–2021) identified 12 areas of communication mediated by pheromones, including “alarm, attraction, recruitment, grooming, feeding, exchange of fluids and solid particles, group effect, recognition of nestmates, caste determination, control of other individuals competing for reproduction, territoriality, and sexual communication” (p. 90).

What makes pheromones a complex communication system is that most emissions are of several pheromones mingled rather than only one. Some signals are recognized by all ants in the vicinity, others only by the ant’s own species, and others are specific to the ant’s colony. 

One evolutionary biologist describes the processing of pheromones as equivalent to AND gates and STOP in a computer system. (p. 91). The ant is not so much deciding what to do as responding to an AI-like signal.

Computer programmers have adapted ant algorithms to the computer:

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Welcome to the Anternet!

Stanford’s Deborah M. Gordon, a specialist in ant behavior, thinks of the complex algorithms ants use to communicate without personal understanding as the “anternet”:

Ant colonies use dynamic networks of brief interactions to adjust to changing conditions. No individual ant knows what’s going on. Each ant just keeps track of its recent experience meeting other ants, either in one-on-one encounters when ants touch antennae, or when an ant encounters a chemical deposited by another.

DEBORAH GORDON, “WHAT DO ANTS KNOW THAT WE DON’T?” AT WIRED

Read the rest at Mind Matters News, published by Discovery Institute’s Bradley Center for Natural and Artificial Intelligence.

Pseudoscience vs. actual science.

 Listen: Mendel vs. Darwin

Evolution News @DiscoveryCSC

On a classic episode of ID the Future, geneticist Wolf-Ekkehard Lönnig, former research scientist at the Max Planck Institute for Plant Breeding Research, talks with host Casey Luskin about Gregor Mendel’s laws of inheritance, how they clashed with the thinking of Charles Darwin, and how acceptance of Darwinism hindered acceptance of Mendel’s great insights. Listen in as Dr. Lönnig explains Mendel’s laws and why they’re still relevant for biology, and particularly genetics. Download the podcast or listen to it here.

Can this forest be replanted?

 Study: “Most of Our Evolutionary Trees Could Be Wrong”

Günter Bechly

From Phys.org:

Study suggests that most of our evolutionary trees could be wrong

New research led by scientists at the Milner Centre for Evolution at the University of Bath suggests that determining evolutionary trees of organisms by comparing anatomy rather than gene sequences is misleading. The study, published in Communications Biology, shows that we often need to overturn centuries of scholarly work that classified living things according to how they look.

In other words: often anatomical similarities are not based on common descent and different lines of evidence (anatomy versus genetics) conflict and thus do not converge on one true tree of life! This refutes one of the favorite talking points of popularizers of Darwinism like Richard Dawkins.

Darwinists continue to invoke I.D to refute I.D.

 Rosenhouse’s Blunder: Another Nonsensical Mathematical Argument Against Intelligent Design

Michael Egnor

Darwinist mathematician Jason Rosenhouse is back. He has a recently published book from Cambridge University Press, The Failures of Mathematical Anti-Evolutionism, and an article in Skeptical Inquirer in which he claims to debunk mathematical arguments that point to intelligent design in biology. A core argument for ID is that living things contain molecules, cells, tissues, organs, and physiological processes displaying complex and specified information, which rules out the possibility that they “evolved” via unintelligent processes. The presence of a language code in DNA, the astonishing nanotechnology underlying every cellular process, the elegant integration of cellular activity into tissues and organs, and the orchestration of these countless highly specified processes into a living organism is so far beyond the capacity of dumb “chance and necessity” that it is fair to call Darwinian explanations ludicrous fairytales posing as science. Intelligence is undeniable — it permeates living things. 

Despite this massive evidence for design, Darwinists like Rosenhouse cling to their ideological myth — atheism’s creation myth — rather than acknowledge the irrefutable scientific evidence of design in nature and particularly the evidence for design that permeates all life. 

Self-Refuting Arguments

The Darwinist arguments against design are all self-refuting, because all arguments against design in biology depend on formal and teleological (i.e., designed) causes in life. Darwinists necessarily invoke highly specific physical laws (e.g., quantum mechanics) and undeniable purposes (e.g., a purpose of DNA is to encode protein structure), and the only known source of a specific law or purpose is a mind. In other words, Darwinist arguments against intelligent design always invoke design — there are no Darwinist arguments from mere chaos and there cannot be such arguments (because even chaos presupposes order against which chaos is defined). 

ID scientists point out that the specified complexity of protein structure necessary for life precludes spontaneous “evolution” without intelligent agency. Proteins may be hundreds of amino acids long, and the correct and precise placement of amino acids (not to mention the as-yet unexplained precision of protein-folding, the organization of innumerable proteins into complex enzymatic pathways, etc.) is inexplicable except as a consequence of a guiding Intelligence. 

No Intelligence Needed?

Rosenhouse denies that intelligence is needed to explain the remarkably precise and specific structure of proteins — he asserts that the Darwinian process of mindless random heritable mutations and survival of survivors (i.e., “natural selection”) explains it all. He uses the analogy of a coin toss to defend the Darwinian explanation:

However, this [design] argument is premised on the notion that genes and proteins evolve through a process analogous to tossing a coin multiple times. This is untrue because there is nothing analogous to natural selection when you are tossing coins. Natural selection is a non-random process, and this fundamentally affects the probability of evolving a particular gene.

To see why, suppose we toss 100 coins in the hopes of obtaining 100 heads. One approach is to throw all 100 coins at once, repeatedly, until all 100 happen to land heads at the same time. Of course, this is exceedingly unlikely to occur. An alternative approach is to flip all 100 coins, leave the ones that landed heads as they are, and then toss again only those that landed tails. We continue in this manner until all 100 coins show heads, which, under this procedure, will happen before too long. The creationist argument assumes that evolution must proceed in a manner comparable to the first approach, when really it has far more in common with the second.

Everything in Rosenhouse’s coin-toss analogy to natural selection manifests intelligent design. The coin is intelligently designed, the person who tosses the coin is intelligent, and the choice by the coin-tosser to re-toss only the coins that land on tails is intelligent selection.  

For Rosenhouse’s analogy to point to unintelligent causes — to Darwinian natural selection — he would have to invoke the analogy that we leave a block of silver on a table by itself and wait for it to (by erosion and wind) sculpt itself into 100 coins, each of which would then spontaneously fall off the table, and the coins that landed tails up would then spontaneously (perhaps by earthquakes!) jump back up onto the table and spontaneously fall again, with this mindless but amazingly specific cycle repeating itself until all 100 coins lay heads-up on the floor (and the floor would first have to assemble itself!). This is a fine model of Darwinian natural selection — i.e., a preposterous fairytale.  

A Deeper Design in Nature

And of course, Rosenhouse misses the even deeper design in nature that forms the framework for the coin-toss analogy. The physical constants and forces that make silver and coins and gravity and space and time all point to intelligent agency (cf. Aquinas’ Fifth Way). Even Darwinian jumping coins need the law of gravitation and laws of electromagnetism and quantum mechanics and innumerable finely tuned physical constants to self-construct and spontaneously jump off the table and self-sort. Design is everywhere in nature.

Darwinian “chance” and “natural selection” exist in an ocean of design — from space-time to physical laws and fine-tuned constants to complex specified biochemical and physiological processes to intelligent observers who flip coins and make hypotheses about evolution. Rosenhouse’s risible analogy of coin-tossing is akin to Berra’s Blunder — a similarly self-refuting analogy proposed by Darwinist biologist Tim Berra, who explained that mindless Darwinian evolution is like designs in automobiles that change with time (notwithstanding that cars are intelligently designed). 

Even Darwinist arguments for natural selection in biology depend on intelligent design. All scientific evidence in cosmology, physics, and biology points to a Mind as the source and the continuing basis of the natural world.  

H/t Jerry Coyne.

Hail the Lord JEHOVAH: The liberator!

Psalms146 American Standard Version.

1Praise ye Jehovah. Praise Jehovah, O my soul.

2While I live will I praise Jehovah: I will sing praises unto my God while I have any being.

3Put not your trust in princes, Nor in the son of man, in whom there is no help.

4His breath goeth forth, he returneth to his earth; In that very day his thoughts perish.

5Happy is he that hath the God of Jacob for his help, Whose hope is in Jehovah his God:

6Who made heaven and earth, The sea, and all that in them is; Who keepeth truth for ever;

7Who executeth justice for the oppressed; Who giveth food to the hungry. Jehovah looseth the prisoners;

8Jehovah openeth the eyes of the blind; Jehovah raiseth up them that are bowed down; Jehovah loveth the righteous;

9Jehovah preserveth the sojourners; He upholdeth the fatherless and widow; But the way of the wicked he turneth upside down.

10Jehovah will reign for ever, Thy God, O Zion, unto all generations. Praise ye Jehovah.

The recipe for reality?

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Can this tree be replanted? II

 

Troubles with the Tree of Life

Mike Keas

Paul Nelson

Claims to know that an evolutionary Tree of Life (TOL) existed are increasingly problematic. The TOL is a picturesque way of imagining a branching pattern of universal common descent (UCD) — the alleged evolution of all current life by descent with modification from earlier life forms on earth, with all organisms tracing back to the Last Universal Common Ancestor (abbreviated as LUCA). We will update you on TOL troubles by analyzing a new paper authored by a group of biologists associated with the largest university in Latin America: the National Autonomous University of Mexico. 

Amadeo Estrada and his colleagues show how the huge literature devoted to constructing the TOL by means of large data sets of molecular sequencing (including many complete genomes of many organisms) is fraught with debilitating problems. Following up on earlier stern warnings from top TOL critics such as W. Ford Doolittle, Estrada et al. survey a wide field of molecular-based phylogenetic chaos — a bunch of mutually inconsistent accounts of the alleged branching pattern of evolution. They observe: “The strictly statistical approach [to molecular-based phylogenetic studies] … has resulted in divergent and even contradictory evolutionary hypotheses unsupported by independent evidence, between different research groups, and at times in single research groups.”1 Put more plainly, such studies have produced a large number of deeply inconsistent pictures of UCD, which undermines confidence about UCD itself. 

How Deep? How Severe?

Just how deep are these inconsistencies in the popular story of UCD? Molecular studies have produced radically different answers to what lies near the base of the TOL — that is, these studies have created confusion about LUCA. To grasp the severity of the situation, consider the wildly divergent range of recent opinion about LUCA; in the words of Estrada et al.(their key points numbered by us, with minor edits to English):

The LUCA has been characterized as

1. close to the origin of life (Koonin 2003; Weiss et al. 2016a), or as being far away from the origin of life (Mirkin et al. 2003; Delaye et al. 2005)
2. having a small genome (Koonin 2003), or as having a genome similar in size to many free living bacteria today (Kyrpides et al. 1999; Harris et al. 2003; Mirkin et al. 2003; Delaye et al. 2005; Yang et al. 2005; Ouzounis et al. 2006; Ranea et al. 2006; Becerra et al. 2014)
3. being autotrophic (Martin et al. 2008; Weiss et al. 2016a), or as being heterotrophic (Delaye et al. 2005; Becerra et al 2014, Muñoz-Velasco et al. 2018)
4. being hyperthermophilic (Woese 1987; Weiss et al. 2016a); or as being mesophilic (Galtier et al. 1999; Groussin et al. 2013; Cantine and Fournier 2018)
5. constituted by an RNA genome (Mushegian and Koonin 1996; Koonin 2003), or as having a DNA genome (Ouzounis et al. 2006; Delaye et al. 2005; Becerra et al. 2014)
6. being a simple cell (Koonin 2003), or as having a complex cell, similar to today’s bacteria (Kyrpides et al. 1999; Harris et al. 2003; Mirkin et al. 2003; Delaye et al. 2005; Yang et al. 2005; Ouzounis et al. 2006; Ranea et al. 2006; Becerra et al. 2014).2

Obviously, the evolution of the TOL could not have occurred in all of these mutually inconsistent ways (contradictory inferred stages of evolution near the base of the TOL). These evolutionary inferences are all over the biological map.Nonetheless, Estrada et al. do not extend their skepticism to the entire TOL-UCD paradigm. However, they do note:

New findings and changes in what we think about certain subjects are common in science. Nevertheless, we think that these extreme divergences between and even inside some researchers’ characterizations of the LCA are linked to the fact of relying on statistical approaches only without other kinds of data outside the sequence comparisons methods. In doing so, researchers can become subjects of contradictory algorithm results.3

As they hint here, Estrada et al. (building on Doolittle and others) propose their own way out of this mess, but admit that even their revised approach has its own additional troubles — though these are lesser troubles in their estimation (more on that below).

Scaling Back Claims

This research group recommends making estimations of LUCA that are less detail-rich, by scaling back claims of what we can legitimately know from molecular studies. They also urge fellow evolutionists to take into account more data beyond the confines of comparative molecular sequencing. Let’s explore the first prong of their dual revisionist research program first. 

On the one hand, they acknowledge that without molecular (especially genetic) sequence data, “there is no possibility of phylogenetic [TOL] reconstruction.” On the other hand, they point out the “serious epistemic disadvantages” of these studies “for the reconstruction of early forms of life, despite being rewarded in scientific practice.”4 Put bluntly, many scientists have advanced their careers by churning out shiploads of TOL claims. The relative ease these days of molecular sequencing and computer-aided statistical analysis make this bioinformatics research program hard to resist. When, however, this results in “contradictory hypotheses even within the same team and in consecutive publications, with no recognition of their divergent conclusions,”5 the internal coherence and logical consistency of the TOL / LUCA model inevitably suffer.

As Estrada et al. observe, over the past two decades Doolittle and others have attributed some of the molecular phylogenetic confusion to lateral (horizontal) gene transfer (LGT). By multiplying the possible modes of genetic transmission beyond so-called “vertical” inheritance, LGT greatly complicates tracing organismal lineages through subsequent generations. But most evolutionists do not think that LGT severely downgrades the historical signals that they use to determine the shape of the TOL. But, Estrada et al. note, “the problem is that there are major difficulties to measure LGT, not the least because the statistical criteria and bioinformatic tools used to estimate it share the same methodological constraints that plague phylogenetic reconstructions (Cortez et al. 2009).”6

A Candid Confession

That is a refreshingly candid confession. LGT is often cited as part of the reason why we get very differently shaped candidate TOLs (and different candidate LUCAs). But we should not doubt the overall TOL-UCD story in the face of such conflicting TOL reconstructions, we are told, because LGT is partly to blame for this situation.

This does not solve, however, the severe LUCA retrodictive inconsistencies that the authors bemoan in the large block quote above, listing six major evolutionary contradictions. Why? Because LGT estimates themselves depend upon, and are epistemically limited by, the “same methodological constraints that plague phylogenetic [TOL] reconstructions.”

We now turn to the second prong of this Mexican research group’s revisionist recommendations: the call to take into account more data beyond the confines of comparative molecular sequencing. “Any hypothesis of the LCA must be confronted with current empirical knowledge from the Earth sciences, as well as what scientists know about biochemistry and metabolic pathways….” This sounds wise, but then they immediately admit the severe limitations of this recommendation due to the “scarcity of biochemical and geochemical knowledge surrounding the early stages of life,” which “poses a severe epistemic constraint” on LCA theories.7

In an attempt to remedy this situation, they advocate scaling back LUCA retrodictions to what they call “a slimmer LCA.” This means that phylogenetic reconstructions should be “aiming at a lower resolution” — claiming we know a lot less — so that our claims are less likely to be contradictory or to be falsified by stubborn data. A skeptical philosopher of science could have said this about many branches of evolutionary biology. 

Kuhn’s Diagnosis

Sixty years ago, the historian and philosopher of science Thomas Kuhn listed what he described as the “symptoms” of a research field undergoing destabilizing change. Kuhn’s diagnosis stands as acutely relevant today as when he first offered it — especially the first symptom, which we have set in bold:

The proliferation of competing articulations, the willingness to try anything, the expression of explicit discontent, the recourse to philosophy and to debate over fundamentals, all these are symptoms of a transition from normal to extraordinary research.8

There is only one true history of life. (If you doubt this, ask yourself if you have, somewhere, an unknown set of biological parents with an equally valid claim to being your actual physical ancestors, when compared with the familiar names on your birth certificate.) Estrada et al. identify the competing historical articulations, only one of which can be the case, now current in evolutionary theory. A mature science converges on a single answer. A science in trouble? Not so much.

Notes

1. Amadeo  Estrada, Edna Suarez-Diaz, and Arturo Becerra, “Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges.” Acta Biotheoretica 70, no. 2 (2022): 1-18, p. 3.
2. Ibid., 3.
3. Ibid., 3.
4. Ibid., 4.
5. Ibid., 9.
6. Ibid., 6.
7. Ibid., 10.
8. T. S. Kuhn, The Structure of Scientific Revolutions (Chicago: University of Chicago Press, 2nd ed., 1970), p. 91.

The design is intelligent, the explaining away, not so much.

 

Yawn: Atheist YouTuber “Professor Dave” Rants about Intelligent Design

Günter Bechly 

Dave Farina is an atheist American YouTuber who runs a channel called Professor Dave Explains with almost two million subscribers. According to his channel he has “a knack for explaining stuff and … want[s] to share some knowledge.” Although he calls himself “Professor Dave,” Farina is not a college professor nor does he have a PhD. He has a Master’s in Science Education. He says he chose “Professor Dave” as his persona “without much thought. It was kind of tongue-in-cheek to be honest.”

Farina mainly produces science videos addressing high school and undergraduate students. Some of his stuff might even be decent edutainment. Unfortunately, he undermines his credibility by ranting about and misrepresenting various people he disagrees with. His latest target for abuse? Proponents of intelligent design associated with Discovery Institute. 

Pardon me while I stifle a yawn. The clichés and misrepresentations Farina recycles about intelligent design are beyond tired. Still, those new to the debate might find it helpful to see Farina’s false claims debunked.

The Scientist Who Made Farina Blink

First, some background: Farina previously targeted Professor James Tour, who ranks among the ten most cited chemists in the world (Berger 2010). Tour does not advocate the theory of intelligent design, but he is a scientific skeptic of unguided chemical and biological evolution. And he has dared to publicly share his expert critique of the hapless field of origin of life research. 

Farina produced three YouTube videos (1, 2, and 3) attacking Tour, which he boasted presented “a demolition of… Tour and his anti-science antics in the realm of origin of life research.” Decide for yourself who was really engaging in “anti-science” antics by watching Professor Tour’s exhaustive 13-part response to Farina and others. Tour cordially invited Farina to participate in a one-on-one public discussion about the issues Farina raised. Farina did not accept. Maybe he feared his claims against Tour couldn’t withstand critical scrutiny?

Instead of manning up to defend his critique of Professor Tour, Farina moved on in search of new targets to denounce. And what could be better than those eeevil intelligent design proponents from the super-villainous Discovery Institute? Accordingly, Farina has begun to produce a series titled Exposing the Discovery Institute, which promises to go after intelligent design proponents “one clown at a time.” Part 1 of the series attacks intelligent design, Discovery Institute, and Dr. Casey Luskin and his appearance in the Science Uprising episode on human evolution.

The ad hominem flavor of Farina’s video series can be seen from its official description on YouTube, which accuses Discovery Institute of “propaganda,” “dishonesty,” “slander,” and “fraudulent activity.” Serious intellectual discussion is not Farina’s forte. Neither is accuracy.

Farina starts his introductory video by calling Discovery Institute “an evangelical propaganda mill.” Of course, he presents no evidence for this assertion. Farina next claims that Discovery Institute is nothing but an “effort to push for creation science or intelligent design to be taught in schools alongside evolutionary biology.” You could hardly pack more falsehoods into a single sentence.

A False Stereotype

First of all, it is an absolutely false stereotype to equate intelligent design theory with creation science. This equation has been refuted so often that nobody can plausibly claim to be ignorant about it. Google is your friend. Here are two classic articles by John West (2002) and by Stephen C. Meyer (2006) explaining why intelligent design is not creationism. I can add a very personal reason: I became an intelligent design proponent when I was still committed to Whiteheadian process metaphysics, long before I became a theist or a Christian. I had no religious reasons at all for supporting ID and still don’t have them. I reject literalist readings of Scripture as some kind of science textbook. Like most ID proponents I accept an old Earth, and like many prominent ID proponents (e.g., Michael Behe, Michael Denton, Richard Sternberg), I also accept common descent. But in the fanciful imagination of someone like Farina, we must still be Bible-thumping creationists. 

Farina seems more interested in caricaturing those he disagrees with than understanding them. That’s too bad. If he were more open-minded, he would learn that intelligent design, in the sense of infusions of information from outside the system, does not necessarily imply any commitment to miraculous divine interventions. After all, the simulation hypothesis, which is now so popular among some physicists and IT engineers (e.g., John Barrow, Nick Bostrom, Michio Kaku, Ray Kurzweil, Marvin Minsky, Elon Musk, Martin Rees, and Neil deGrasse Tyson), is nothing but an intelligent design argument. My own preferred hypothesis of teleological evolution as quantum computation (Raatz & Bechly 2019, also see my website) is another example that has no “God diddit” or “Here a miracle occurs” in the equation.

What about Farina’s second point, that Discovery Institute allegedly pushes the teaching of intelligent design in schools? This is yet another demonstrably false claim. Discovery Institute’s Science Education Policy could hardly be clearer: “As a matter of public policy, Discovery Institute opposes any effort to require the teaching of intelligent design by school districts or state boards of education” (Discovery Institute 2002; also see here). Which part of “Discovery Institute opposes” did Farina not understand? Even before the famous Dover trial, Discovery Institute had strongly advised the Dover school board not to push ID into the curriculum, but they unfortunately did not listen (West 2005). All these facts can be googled in a few minutes. Seemingly, that was too much of an effort for Farina.

Three Major Problems 

Farina also thinks that intelligent design theory “cannot be validated as real science because it does not explain or predict anything.” Here are three major problems with this statement:

1. Who defines what qualifies as “real science”? It is certainly not Dave Farina. It is not judges in court rooms. And it is not even the scientists themselves who define “science.” Reasonably, it is philosophers of science who address this question. But Farina seems to be totally ignorant of the fact that there is no consensus among philosophers of science about a demarcation criterion that could reliably distinguish science from non-science. Any criterion yet suggested, including Karl Popper’s criterion of falsifiability, either excludes too much (e.g., scientific fields like string theory or evolutionary biology) or includes too much (e.g., homeopathy or parapsychology).
2. Of course, intelligent design has explanatory power. Otherwise, we could not even explain the existence of Romeo and Juliet by the intelligent agency of William Shakespeare. There is no doubt that the designing activity of an intelligent agent is a perfectly valid explanation for complex specified patterns. The only question under debate is whether such patterns are confined to the realm of human cultural artifacts or if they are also found in nature. But this question should not be decided by dogmatic a priori restrictions of certain worldviews that do not allow for design explanations whatever the evidence might be, but should rather follow the evidence wherever it leads. It is an empirical question to be decided by the data.
3. It is simply false that intelligent design does not predict anything. Indeed, this is yet another common stereotype that has been refuted so many times by ID proponents that any further use of this argument can be based only on a total ignorance of the facts (or perhaps deliberate lying, but I prefer not to apply that interpretation). Stephen Meyer (2009) included in his book Signature in the Cell a whole chapter with a dozen predictions inspired by intelligent design theory. These are often very precise and easily falsifiable, for example: “No undirected process will demonstrate the capacity to generate 500 bits of new [specified] information starting from a nonbiological source.” Just write a computer simulation that achieves this, without smuggling the information in through a backdoor, and you can claim victory over a core prediction of intelligent design.

Oh No — Theocracy!!!

Toward the end of his dreadful video, Farina raises the hackneyed threat of intelligent design leading to a totalitarian theocracy comparable to the Ayatollah regime in Iran or the dystopian Handmaid’s Tale. No, I’m not kidding. 

We’re supposed to believe that prominent Discovery Institute Fellows like the Jewish agnostic David Berlinski or the deist Michael Denton have nothing else in mind than establishing a theocracy to burn some witches. And these non-believing Fellows apparently agree with their Catholic (DI co-founder Bruce Chapman, Michael Behe, Ann Gauger, Jay Richards, and myself, even though I joined the ID movement when I was still neither a Christian nor even a theist), Jewish (David Klinghoffer), Orthodox (Richard Sternberg), and Protestant (Douglas Axe, William Dembski, Stephen Meyer, Paul Nelson) colleagues on the kind of theocracy they want to impose. 

Didn’t Farina bother to do any genuine research before making such ridiculous claims? And he has the chutzpah to accuse others of slander? Where is his evidence for such an agenda, apart from wild and unsubstantiated assertions? 

Discovery Institute does indeed have an agenda, and it is no secret at all (Crowther 2005; Discovery Institute 2019): it is an agenda directed against the hijacking of modern science by the nihilistic worldview of materialism and atheism. I am proud to contribute to this noble task, because science should be free to “follow the evidence wherever it leads,” which has become the unofficial motto of Discovery Institute and the ID movement. The agenda is not about pushing religion onto society but about freedom of thought and freedom of research. That sounds evil and dangerous, doesn’t it?

Farina’s Metaphysics Is Showing

Farina’s next blunder is another howler. He says that “science is inherently materialistic” and that “science IS materialism.” He then boldly claims that “anyone who says otherwise does not know what science is.” Well, it’s clearly he who doesn’t understand what science is, because science is neither inherently nor actually materialism. Materialism is a metaphysical and not a scientific position. It is the view that all that exists is matter, energy, space, and time. Science can only study this spatiotemporal realm but it cannot say if it is all that exists. Science is just a methodology. Science is silent about metaphysics, which is why the latter is called METAphysics and not physics. Science is perfectly compatible with many different metaphysical positions, from materialism to Platonism, idealism, and theism. 

Many modern scientists are explicitly not materialists. I am not just speaking about the many Christian scientists and Nobel laureates, but, for example, cosmologist Max Tegmark (2008, 2014), who suggests that all that exists is mathematics and that matter does not even exist, or Nobel laureate Roger Penrose (Murphy 2020), who is one of the many Platonists who think that there is a separate realm of math and forms additional to the material universe, or eminent quantum physicists like Anton Zeilinger (NZZ 2008) who reject materialism and endorse some version of idealism instead. Actually, the growing consensus in modern physics (endorsed by world class physicists like Sean Carroll, Brian Greene, Nima Arkani-Hamed, Leonard Susskind, Max Tegmark, and Erik Verlinde) — that spacetime (and thus also matter and energy) is not fundamental but emergent from an immaterial and atemporal realm of entangled quantum information — has thoroughly debunked materialism as an obsolete 19th-century paradigm. New results from modern experimental physics inspire headlines like “Quantum physics says goodbye to reality” (Physics World 2007), “Reality doesn’t exist until we measure it, quantum experiment confirms” (MacDonald 2015), and “A quantum experiment suggests there’s no such thing as objective reality” (MIT 2019). Many more findings that refute naïve materialism — such as the experimental violations of the inequalities of Bell, Leggett, and Leggett & Garg, as well as the experimental confirmation of the Kochen-Specker theorem — are cited in my article on quantum idealism, for those who are interested and can read German (Raatz & Bechly 2019). Even if some may still disagree with certain interpretations of these results, they at least prove that modern science by no means entails materialism. Quite the contrary! 

“Prediction Prior to Investigation”

Farina further claims that evolution is science but intelligent design is not, because only the former follows the rule of “prediction prior to investigation.” That again is nonsense on many levels. The theory of evolution and its predictions did not precede investigation but is a consequence of investigation. Charles Darwin explicitly made a cumulative empirical case and derived his theory by interpreting data which pre-existed the development of his theory. Of course, the theory then makes predictions that can be empirically tested. For example, it predicts a gradualistic pattern where small changes slowly accumulated into big differences over long periods of time. When this prediction was contradicted by the fossil evidence, numerous ad hoc explanations were forged to explain away the conflicting evidence, such as the artifact hypothesis or punctuated equilibria, etc. The same happened with the vast amount of conflicting evidence (homoplasy) in phylogenetic studies, likewise explained away with ad hoc hypotheses like ghost lineages and incomplete lineage sorting, etc. This is not per se a bad thing. No good theory is given up only because of minor anomalies. However, it is a problem when the anomalies become so massive that a paradigm shift is warranted, which is what ID proponents aim to demonstrate. 

What about intelligent design theory and its predictions? Intelligent design predicts, for example, that changes in the history of life came about abruptly by pulses or infusions of new information from outside the system. That is strongly corroborated by paleontological research and the ubiquitous discontinuities in the fossil record that can no longer be explained away by reference to incompleteness or undersampling (Bechly & Meyer 2017; Bechly 2021). Here is another successful prediction that was made prior to investigation: ID proponent Richard Sternberg predicted in 2005 (Shapiro & Sternberg 2005) that junk DNA would turn out not be junk after all. That was later confirmed by the findings of the ENCODE project (Axe 2012). Above, I mentioned the 12 predictions listed by Meyer (2009). Thus, intelligent design theory does make testable predictions just like evolutionary theory does, which is why even atheist thinkers like philosopher Thomas Nagel (Nagel 2012) and physicist Bradley Monton (Monton 2009) have acknowledged the scientific status of ID theory. It is comical when anti ID-activists claim that intelligent design is not science because it is not falsifiable, and a sentence later say that it has been debunked (i.e., falsified), without recognizing the deep inconsistency of such claims.

Missing the Target

In the end, Farina’s potshots against intelligent design and Discovery Institute completely miss their targets. “Professor Dave” needs to do more than recycle past discredited claims if he wants to be taken seriously by anyone genuinely interested in pursuing the truth. 

Farina makes additional false or misleading statements in his video, and I will be reviewing them in the future. Next up will be his claim that the term “Darwinism” is obsolete and only used by “creationists.” After that, I will address his specific charges about Casey Luskin and the fossil evidence for human evolution. 

Man redeprivileged? II

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Who needs Dr. Doolittle?

 

These Animals Know How to Self-Medicate

Denyse O'Leary

It turns out that many animals know how to alleviate some of their common health problems and we are only beginning to (officially) learn about it. Dolphins, for example:

Indo-Pacific bottlenose dolphins get skin conditions, too, but they come about their medication by queuing up nose-to-tail to rub themselves against corals. In the journal iScience on May 19, researchers show that these corals have medicinal properties, suggesting that the dolphins are using the marine invertebrates to medicate skin conditions.

Thirteen years ago, co-lead author Angela Ziltener (@DWAORG), a wildlife biologist at the University of Zurich, Switzerland, first observed dolphins rubbing against coral in the Northern Red Sea, off the coast of Egypt. She and her team noticed that the dolphins were selective about which corals they rubbed against, and they wanted to understand why. “I hadn’t seen this coral rubbing behavior described before, and it was clear that the dolphins knew exactly which coral they wanted to use,” says Ziltener. “I thought, ‘There must be a reason.’” 

CELL PRESS, “WATCH DOLPHINS LINE UP TO SELF-MEDICATE SKIN AILMENTS AT CORAL ‘CLINICS’” AT EUREKALERT (MAY 19, 2022) THE PAPER IS OPEN ACCESS.

There was indeed a reason: The dolphins were stirring up the coral polyps which then released mucus which may help the dolphins with skin health and with treating infections: “It’s almost like they are showering, cleaning themselves before they go to sleep or get up for the day,” says study researcher Angela Ziltener, who dived down to where the dolphins hang out to find out what was going on.

Natural Healing, the Chimp Way

In one of many other such observations, a chimp mother was recently seen using an insect to ease a bite wound on her offspring:

For the first time, researchers observed chimpanzees in Gabon, West Africa applying insects to their wounds and the wounds of others…

“In the video, you can see that Suzee is first looking at the foot of her son, and then it’s as if she is thinking, ‘What could I do?’ and then she looks up, sees the insect, and catches it for her son,’” Mascaro says. The Ozouga team started to monitor the chimpanzees for this type of wound-tending behavior, and over the next 15 months documented 76 cases of the group applying insects to wounds on themselves and others. 

CELL PRESS, “CHIMPANZEE MOTHER SEEN APPLYING AN INSECT TO A WOUND ON HER SON” AT SCIENCEDAILY (FEBRUARY 7, 2022).

Just what the insect does for the chimp’s wound is unclear but cognitive biologist Simone Pika notes, “There have been studies showing that insects can have antibiotic, antiviral, and anthelmintic functions.” That may be but perhaps the main outcome will turn out to be pain/itch relief.

Learning from Elephants

Elephants have been observed to use plants for medicinal purposes too. Researchers interviewed mahouts (work elephant riders) as to what the elephants did on their own that they had adopted as part of a care routine:

114 species [of plants] were recorded as being consumed by elephants during interviews with mahouts and forest outings with them to collect samples. Twenty species were identified as used by elephants in particular pathological conditions or physiological states. According to interviewed mahouts, the consumption of certain plants improves the health of the elephant. We observed clear convergences between the observations interpreted by the mahouts as self-medication behaviour from elephants and their own medicinal practices (for human and veterinary purposes). 

DUBOST JM, LAMXAY V, KRIEF S, FALSHAW M, MANITHIP C, DEHARO E. FROM PLANT SELECTION BY ELEPHANTS TO HUMAN AND VETERINARY PHARMACOPEIA OF MAHOUTS IN LAOS. J ETHNOPHARMACOL. 2019 NOV 15.

Similarly, dogs self-medicate:

Anyone who has seen a dog eat grass during a walk has witnessed self-medication. The dog probably has an upset stomach or a parasite. The grass helps them vomit up the problem or eliminate it with the feces.

JOEL SHURKIN, “ANIMALS THAT SELF-MEDICATE” AT PROC NATL ACAD SCI U S A. 2014 DEC 9; 111(49): 17339–17341.

So do cats, likely for the same reasons.

Read the rest at Mind Matters News, published by Discovery Institute’s Bradley Center for Natural and Artificial Intelligence.