Navigators of the ant kingdom v. Darwin.

Ant Navigation Fascinates Engineers

David Coppedge  

Watching ants optimize their search strategies is fun, and motivates biomimicry, but few are the biologists who consider what design requirements make it possible. 

Research teams from two universities recently observed navigation strategies for different ants that live in very different habitats. Both were amazed at their skills and thought the findings would be helpful for robotics engineers. Both, however, simply did a lateral pass to Darwin to explain what they observed. It “evolved,” they said dismissively, thinking the explanatory work was done. Design theorists know better. They understand the hardware and software requirements to optimize a search algorithm.

                 

Tree Ants

The first team, harking from Stanford and publishing in PNAS, studied arboreal ants. The arboreal turtle ant (Cephalotes goniodontus), common in Mexico’s subtropics, can solve the “shortest path problem” while navigating on the limbs of trees and bushes, these authors say. Finding the shortest path is a tricky problem facing service providers who deliver goods. The University of Texas explains the “Chinese Postman Problem” —

                 It is the problem that the Chinese Postman faces: he wishes to travel along every road in a city in order to deliver letters, with the least possible distance. The problem is how to find a shortest closed walk of the graph in which each edge is traversed at least once, rather than exactly once.

            In a tree, limbs can be considered “edges” and branching points can be considered “vertices.” Think of the complexity of branches going this way and that, with food sources at unknown distances from the nest. How do the ants minimize the energy cost of foraging, locating, and retrieving their food? And what do they do when obstacles are in the path?

            Here, we investigate how the trail networks of the arboreal turtle ant (Cephalotes goniodontus) can solve variants of the shortest path problem, a basic optimization problem on graphs. Textbook algorithms for this problem find optimum solutions using knowledge of the entire network. Turtle ants nest and forage in the tree canopy of the tropical forest; their trail network is constrained to lie on a natural graph formed by tangled branches and vines (Fig. 1), and no ant has any global information about the network. Observations of turtle ants in the field show that a colony’s trail network approximately minimizes the number of vertices.

                With no roadmap, each individual ant must somehow participate in the solution. The research team found, first, that the ants drop pheromones at each vertex and along edges. The strength of pheromones decays with time, giving them data about how recently another ant visited. The scientists noticed that two other data sources help the ants find the shortest path: (1) the bidirectional flow rate at a vertex, and (2) the “leakage” of ants as some leave the path to explore. The dynamics of these inputs helps the ants quickly converge on the shortest path. 

                   In summary, our model for how ant trails change over time contributes to the synergistic exchange between biology and computer science, providing a plausible explanation for how turtle ant colonies can find paths that minimize the number of vertices, and suggesting a surprising algorithm for the shortest path discovery, by increasing the flow rate, applicable to distributed engineering systems.

                    How do they explain this surprising algorithm? “Evolution has led to natural algorithms that regulate collective behavior in many biological systems.” Enough said?

Rock Ants

Another team from the University of Arizona investigated a different kind of ant: a tiny species that inhabits rock crevices. “The ants go marching … methodically,” they say. Their work overturned an assumption about ant navigation: it’s more methodical than previously thought. Using a familiar analogy, they begin,

               When strolling through an unfamiliar grocery store, you may find yourself methodically walking down each aisle to ensure you find everything you need without crossing the same path twice. At times, you’ll stray from this orderly process, such as when you see a vibrant “for sale” sign from across the store or realize that you forgot something. According to a study led by researchers at the University of Arizona, some ants go about their search for food and shelter in a similar manner.

         Stefan Popp and Anna Dornhaus collected rock ants (Temnothorax rugatulus) near Tucson and set up an experiment in their lab where they could watch their movements with cameras and tracking software. This species does not form the familiar ant trails we find in our homes; rather, the individuals forage on their own.

             Anecdotal evidence suggests they mostly forage on small living or dead arthropods and opportunistically lick up sugary liquids. Individuals can discriminate their own pheromone from that of other ants and are not attracted to or follow the trails of nestmates toward food. Their traits of foraging individually, having a relatively small range compared to other ant species, and small colony size make these ants a good study species to investigate search efficiency of Central Place Foragers.

                  Contrary to expectations, the individual ants did not move about in a random manner but instead walked in a back-and-forth motion as they explored. Hunters often train their dogs to catch scents using a similar method. The dog may need guidance from the hunter when blocked by an obstacle. These little ants, though, when faced with an obstacle, will switch to random mode to continue. How does this navigation strategy succeed in optimizing the path?

                “Until now, the widespread assumption was that free-searching animals are incapable of searching for new resources methodically,” Popp said. “Most of the previous research on search behavior only focused on situations where the animal is already familiar with where it’s going, such as going back to the nest entrance or going back to a memorable food source.”

“Based on these results, many animals may be using complex combinations of random and systematic search that optimize efficiency and robustness in real and complex habitats,” Dornhaus said. “This discovery opens up a whole new way of looking at all animal movement.“

             As in the previous research, this team believes what they discovered will help robot designers and other problem solvers. The ants’ strategy also “has the potential to unify different fields of science” and to provide “applications for real environments where a completely systematic search would fail when faced with an obstacle.”

So how does this team explain the origin of this robust, adaptable search strategy? It evolved. It evolved all over the world! “According to the researchers, the evolutionary advantage of meandering found in these rock ants could have possibly evolved in other species of insects and animals as well.”

                     

Ant What It Used to Be

Is  it helpful in science to toss the explanation for a complex ability to some unaccounted-for series of mistakes in the past? Can anyone really imagine some pre-ant without these abilities achieving the spectacular innovations that make their navigational skills so attractive?

Both teams realize, of course, that engineers who will use their findings to build robots or optimize search algorithms will have to apply their intelligent minds diligently to succeed as well as these tiny ants have. Undoubtedly, the engineers would have to draw up a set of requirements before creating a successful application. Are the evolutionary biologists overlooking the requirements for ant navigation?

In his excellent book Animal Algorithms, pp. 62-65, Eric Cassell shares additional astounding capabilities of ants. He mentions that an ant brain is one fourth the size of a bee brain, with about 250,000 neurons. Within that tiny brain, elegant software operates that can do landmark recognition, vector analysis, and path integration, using multiple sensory inputs: a sun compass, pheromones, and polarized light. The brain, furthermore, requires at minimum enough memory to store and retrieve the information, an odometer for measuring path length, and decision algorithms for chemotaxis. These all must be under central control to enable path integration. Without these requirements being met in each individual, the ants could not perform the wonders scientists admire. Cassell asks at the end of this discussion, “How did these complex programmed behaviors originate?” The question deserves a better answer than, “They evolved.”

An oracle re:the spawn of amoral science?

On channeling your inner secret agent?

Darwin and the evolution of homo politicus?

 Nancy Pearcey on the Politics of Darwinism, Then and Now

Evolution News

On a classic episode of ID the Future, Nancy Pearcey, professor and scholar in residence at Houston Baptist University, tells some of the political history of Darwinism, and explains how the same troubling issues persist today. Darwin was one of the first to say, if it isn’t purely naturalistic, it isn’t science. Others, then and now, have suggested that we can keep Darwinian evolution and just trust that God is at work behind the scenes. Pearcey, co-author of The Soul of Science: Christian Faith and Natural Philosophy, says that the problem with this tactic of wedding Darwinism and theism is that ultimately it turns one’s understanding of God into something that is largely private and subjective. Download the podcast or listen to it here.

Just another blind alley in Darwinism labrynth?

A Remarkably Candid Statement About an Unsolved Evolutionary Puzzle

Paul Nelson 

According to current systematic theory, everyone reading this right now belongs to the taxonomic category Deuterostomia. This refers to the “second opening”: the group was originally defined with respect to the embryological appearance of the anus (first opening) versus mouth (second opening), a trait no longer considered diagnostic. Deuterostomia is still around as a systematic grouping, however, and it is showing signs of strain. At present, three phyla belong to Deuterostomia: chordates (that’s you), echinoderms (e.g., sea urchins), and hemichordates (acorn worms).

A Long-Standing Mystery

The origins of Deuterostomia represent a long-standing mystery:

                   Deuterostomes are the major division of animal life which includes sea stars, acorn worms, and humans, among a wide variety of ecologically and morphologically disparate taxa. However, their early evolution is poorly understood, due in part to their disparity, which makes identifying commonalities difficult, as well as their relatively poor early fossil record.

                    A new review article, from a team at Harvard, the Smithsonian, and the University of Oklahoma, carefully evaluates the conflicting evidence about deuterostome affinities. See Karma Nanglu et al., “Worms and gills, plates and spines: the evolutionary origins and incredible disparities of deuterostomes revealed by fossils, genes, and development,” Biological Reviews 98 (2023): 316-351.

              Leaving a Muddle

Their message is — no clarity, many possibilities, leaving a muddle. What really struck me was this paragraph:

                In many ways, despite hundreds of years of zoological effort and two decades since the publication of the new animal phylogeny (Halanych et al., 1995; Aguinaldo et al., 1997), we remain in an intellectual wild west with regard to deuterostome origins. No hypothesis, no matter how far-fetched it may seem, can be entirely discarded. No theory, no matter how enticingly logical, can claim to have emerged victorious among its competitors. The deuterostomes continue to elude a single, clean narrative to describe their early evolution, a state that is both fascinating and frustrating in equal measure.

          The philosopher in me then asks — at what point does the category Deuterostomia become unreal? That is, become a term without a corresponding referent out there in nature; something whose origins no one should spend any more time trying to explain, because there is actually nothing there to explain.

When does an unsolved problem morph into a non-problem? Turn around, and walk out of that alley. There’s a brick wall at the end.

Collateral damage in the war on woke?

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If not JEHOVAH'S thumb print whose?

 The Other Intelligent Designer(s)?

Geoffrey Simmons 

It is readily apparent that life itself, and human beings in particular, were designed by an intelligent mind. The digital information system found in every person’s genome, and all of the ramifications, are evidence enough. All of our complexities upon complexities upon complexities, portrayed vertically and laterally on graphs, could not have come about by accident over 4.54 billion years. And, notably everything reflects forethought. To say otherwise is to believe that the Emperor was wearing clothes. 

                 

So, Who Did It? 

Who thought of a clotting cascade just in case there’s bleeding? Who thought of an antibody system? Besides God, one can only consider extraterrestrials. That is, even remotely. The latter group would need to have been technically more advanced than we are, by far. Perhaps, by a measure of a million or more years. Since the universe is known to be 13.6 billion years old, there might have been enough time for this to have happened. These ET individuals might reside on one of the six (“newest”) oldest galaxies recently discovered by the James Webb Space Telescope and discussed last month in the journal Nature. These galaxies came about 500-700 million years after the Big Bang.

If a very advanced civilization actually did create us, one might ask: Why bother? Was it for fun? Was it like climbing Mount Everest, because it’s there? Or, maybe we’re an experiment like watching elephants and snakes breed in a zoo. Might we live in a giant terrarium that was prepped with water, top soil, oxygen, and gravity? 

           

“To Serve Man”

My favorite explanation comes from a famous short story, “To Serve Man,” written in 1950 by Damon Knight (a deceased, famous, and good friend). Well known, it is one of the most memorable stories that ever appeared on Rod Serling’s Twilight Zone. Nine-foot-tall, humanoid pig aliens, called Kanamits, arrive by rocket and address the United Nations by mental telepathy. They came to help us and they gave us a very thick book titled To Serve Man. They claimed to have achieved cheap unlimited power, boundless supplies of food, and a device which disables all modern armies. Their book will help us achieve similar goals. This appeared to be one of the best things that ever happened to the human race.

As the story goes on, a scientist strives to decipher this book. She eventually figures out that the book was actually abounding with recipes. These were instructions on how to serve human beings, such as to bake, boil, or fry them, with or without garnishments. Visibly stressed, and knowing that time is very tight, she races off to stop a huge delegation of dignitaries from leaving Earth on a ten-year excursion to visit the Kanamits’ planet. But, she arrives one second after the nick of time.

Other questions might include: If we have alien creators, why haven’t they shown themselves to us? Without disguises, might they be too hideous for the steeliest of us to handle. Or, too smelly? Perhaps, they remain out of sight because of their huge size, like the Nephilim of the Bible? That, too, might be very scary. Or, perhaps they stay out of sight because they are so tiny and we might step on them. Might they be exquisitely sensitive to our bacteria as proposed in H. G. Wells’s classic sci-fi novel? All of these are plausible to science-fiction writers. Much less so to true scientists.

                           

Already Among Us?

On the other hand, perhaps, they look and act like us, and they already live among us. Maybe they love beer and like to watch sports on the weekends. They may even vote. No way to tell for which party’s candidates, however.

Might they be watching our progress from UFOs or UAPs? In the year 2022 the Pentagon’s new office devoted to studying the subject received hundreds of reports of UFO sightings. Most were ultimately explained, but they are focusing on 171 cases which “appear to have demonstrated unusual flight characteristics or performance capabilities, and require further analysis.” 

Might they be our “parents,” or does this belong in the rubbish bin with the theory of evolution? If they should fly overhead, I have decided not to wave.

What could go wrong? With apologies to Dr Frankenstein.

Commonsense resurgent?

In U.S. and Europe, Gender Ideology as “Settled Science” Is Crumbling

Wesley Smith  

The cultural hegemony of the gender ideologists is crumbling. Europe is hitting the brakes on potentially harmful interventions for gender-dysphoric children such as puberty blocking, cross-hormone administration, and surgeries. In the U.S., an increasing number of states are passing laws or medical guidelines to protect children from potentially irreversible and life-shattering outcomes that the “detransitioners” are increasingly exposing. Lawsuits are being filed for the harm allegedly done to minors put on “gender-affirming” medical care.

                      

A Controversial Field

Now, the British Medical Journal reports that the entire field remains controversial from medical and scientific perspectives. And just in the nick of time. Identifying as transgender is a social contagion that is consuming an increasing number of American youth:

                 More adolescents with no history of gender dysphoria — predominantly birth registered females — are presenting at gender clinics. A recent analysis of insurance claims by Komodo Health found that nearly 18 000 US minors began taking puberty blockers or hormones from 2017 to 2021, the number rising each year. Surveys aiming to measure prevalence have found that about 2% of high school aged teens identify as “transgender.” These young people are also more likely than their cisgender peers to have concurrent mental health and neurodiverse conditions including depression, anxiety, attention deficit disorders, and autism.

In the US, although Medicaid coverage varies by state and by treatment, the Biden administration has warned states that not covering care is in violation of federal law prohibiting discrimination. Meanwhile, the number of private clinics that focus on providing hormones and surgeries has grown from just a few a decade ago to more than 100 today.

              As we have discussed repeatedly, teenage girls who identify as boys are having their breasts removed, facial-reconstruction surgeries on boys and girls who are still maturing are being performed, and even the occasional genital-reconstruction operation that results in life-long sterilization and sexual dysfunction are occurring. Rather than “life-saving individualized care,” as the ideologues call it, a good argument can be made that great harm is being done to these children — especially since many will cease being gender dysphoric by the time they reach maturity.

                     

Radical, Not Settled

The story clearly indicates that this radical approach is not “settled science.” Many European countries are backing off from early medicalized care, as is New Zealand.

Independent research is showing that the “guidelines” for treating these children, for example, published by the Endocrine Society, are poorly supported by evidence:

                 The Endocrine Society commissioned two systematic reviews for its clinical practice guideline, Endocrine Treatment of Gender-Dysphoric/Gender-Incongruent Persons: one on the effects of sex steroids on lipids and cardiovascular outcomes, the other on their effects on bone health.3233 To indicate the quality of evidence underpinning its various guidelines, the Endocrine Society employed the GRADE system (grading of recommendations assessment, development, and evaluation) and judged the quality of evidence for all recommendations on adolescents as “low” or “very low.”

        The article notes that the affirmation recommendations raced ahead of the actual data:

                Robert Garofalo, chief of adolescent medicine at the Lurie Children’s Hospital in Chicago and one of four principal investigators, told a podcast interviewer in May 2022 that the evidence base remained “a challenge . . . it is a discipline where the evidence base is now being assembled” and that “it’s truly lagging behind [clinical practice], I think, in some ways.” That care, he explained, was “being done safely. But only now, I think, are we really beginning to do the type of research where we’re looking at short, medium, and long term outcomes of the care that we are providing in a way that I think hopefully will be either reassuring to institutions and families and patients or also will shed a light on things that we can be doing better.”

                          

An Important Development

There is also a problem with informed consent:

                   Without an objective diagnostic test [to diagnose gender dysphoria], however, others remain concerned. The demand for services has led to a “perfunctory informed consent process,” wrote two clinicians and a researcher in a recent issue of the Journal of Sex and Marital Therapy, in spite of two key uncertainties: the long term impacts of treatment and whether a young person will persist in their gender identity. And the widespread impression of medical consensus doesn’t help. “Unfortunately, gender specialists are frequently unfamiliar with, or discount the significance of, the research in support of these two concepts,” they wrote. “As a result, the informed consent process rarely adequately discloses this information to patients and their families.”

                    This is an important development. The BMJ is a very mainstream medical publication — which is why its story admitting that this field remains controversial matters to the debate. Those who oppose mutilating gender-dysphoric children now have a new and powerful argument against the kind of mandatory gender-affirming-care approach that political, cultural, and media organs favor imposing.

                       

The war on truth?

On the journey to zero re:temperature.

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Man: an "also ran" in the longevity stakes?

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A Divided Christ?

 Welby not longer recognized as Anglican Communion leader by Global South

Faith on View 

The Global South Fellowship of Anglicans has refused to recognize Justin Welby, the Archbishop of Canterbury, as the global leader and has overturned the traditional Instruments of Communion through a seven-point plan. GSFA leaders have appealed to the Provinces to take into account the deviation of the Church of England from the faith based on the Apostles and that it has severed ties with the faithful provinces and thus has lost the qualification of being the leader of the Communion. In accepting this, Justin Welby is no longer recognized as being “first among equals” and thus it results in the overturning of the first Instrument of Communion.

                           

Christian Today reports

Change is afoot in the Anglican Communion after the Global South Fellowship of Anglicans today published a seven-point plan, overturning the traditional Instruments of Communion and ousting the Archbishop of Canterbury, Justin Welby, from any position of global leadership.

The leaders of the GSFA have called Provinces to acknowledge that the Church of England has “departed from the historic faith passed down from the Apostles,” “broken communion with those province that remain faithful” and “disqualified herself from leading the Communion.”

If this is accepted, it follows that they will no longer recognise the present Archbishop of Canterbury as ‘first among equals’. And so, the first Instrument of Communion topples.

In, “forfeiting [his] leadership role of the global Communion,” the Archbishop of Canterbury no longer has the authority to call either the Primates Meetings or a future Lambeth Conference.

Instead, they intend to collaborate with other faithful Anglicans to “work out the shape and nature of [their] common life together.” Bang go the next two Instruments of Communion.

That leaves the Anglican Consultative Council (ACC) as the last Instrument standing – but this is also dismissed, with the leadership of the GSFA stating firmly that they can no longer “walk together” in the way that last week’s ACC-18 meeting in Ghana proposed.

The GSFA are not interested in another decade-long talking-shop with revisionist provinces.

Having removed the Instruments of Communion from power they recognise “the responsibility falls to the remaining orthodox Primates,” to take the lead.

         Read the full article here

Homology=common ancestry except when it doesn't?

 

The Astonishing Examples of Repeated Evolution

Cornelius G Hunter 

According to evolution the species arose as a consequence of random events, such as mutations. Yet the biological world is full of repeated designs. These so-called convergences are ubiquitous. And while a fundamental tenet of evolutionary theory is that similarity implies common ancestry, convergences are similarities found in more distant species—they cannot have arisen from a common ancestor. This falsifies the fundamental tenet that similarity implies common ancestry. This tension can be further amplified by complexity and multiplicity. Similarities in different species which are highly complex can be difficult to explain how they evolved once, let alone twice in independent lineages. Add to this similarities which are found not twice, but a multiplicity of times, and you have what the press release of a new study out of Germany on the evolution of jawed vertebrates called “astonishing examples of repeated evolution.”

Why "junk DNA"=junk science.

 In “Junk DNA,” Here Are Benefits of Seeking Function

David Coppedge 

“Junk DNA” is so 1972. Why is it hard to shed worn-out phrases? One bad stain can wear out dozens of wipes. Fortunately, we don’t have to do all the wiping. Science reporters have been getting better at helping clean up this genomic blemish.

An example is a paper in PNAS summarized on Eurekalert!. The paper doesn’t refer to junk DNA, but the news item does. “Punctuating messages encoded in human genome with transposable elements” is the title:

The vast majority of the human genome (~98% of the total genetic information) is not dedicated to encoding proteins, and this non-coding sequence was initially designated as “junk DNA” to underscore its lack of apparent function. Much of the so-called junk DNA in our genomes has accumulated over evolutionary time due to the activity of retrotransposable elements (RTEs), which are capable of moving (transposing) from one location to another in the genome and make copies of themselves when they do so. These elements have been considered as genomic parasites that exist by virtue of their ability to replicate themselves to high numbers within genomes without providing any beneficial function for the hosts in which they reside. However

   , recent studies on RTEs have shown that they can in fact encode important functions, and much of their functional activity turns out to be related to how genomes are regulated. RTEs have been linked to stem cell function, tissue differentiation, cancer progression and ultimately to aging and age-related pathologies. 

                        Although this statement credits evolution with the accumulation of RTEs, the original paper is loaded with the word “function” and says nothing of significance about evolution. It also never claims that “cancer progression” or “aging” constitute functions for RTEs.

A Design Prediction

Instead, the paper offers a design prediction and finds it largely true. Wang et al. predicted that RTEs act as “insulators” that “help to organize eukaryotic chromatin via enhancer-blocking and chromatin barrier activity.” Of the 1,178 mammalian-wide interspersed repeats (MIRs, a form of RTE) they predicted would be functional, they found that 58 percent of them do, indeed, function as insulators (the rest may have so-far-unknown functions). The news item calls them a form of “punctuation”:

                   “We randomly picked a hand full of the MIR sequences predicted to serve as boundary elements by the Jordan lab and experimentally validated their activity in mouse cell lines and, with help of our Spanish collaborators, in Zebrafish upon embryonic development,” Dr. [Victoria] Lunyak said. “This testing revealed that MIR sequences can serve as punctuation markswithin our genome that enable cells to correctly read and comprehend the messagetransmitted by the genomic sequences.”

“One thing that is particularly striking is the fact that these punctuation marks, as Victoria calls them, play a role that is deeply evolutionary conserved,” said Dr. [King] Jordan. “The same exact MIR sequences were able to function as boundaries in human CD4+ lymphocytes, in mouse cell models and in Zebrafish.”

            You wouldn’t toss out all the punctuation in a book as “junk ABC” now, would you? Punctuation has a function — an important one. It came late in human written language (try reading ancient Greek). Human intelligent agents recognized that punctuation could help the understanding of texts. If it took intelligence to design punctuation, why would we credit genetic punctuation to blind processes? The fact that it is deeply conserved in unrelated animals argues against its being randomly accumulated for no purpose.

                 

Another Function

Here’s another function for these MIR sequences: tissue-specific regulation of gene expression. This helps explain why cell types can differ dramatically even though they all contain the same genetic library:

             Boundary elements are epigenetic regulatory sequences that separate transcriptionally active regions of the human genome from transcriptionally silent regions in a cell-type specific manner. In so doing, these critical regulatory elements help to provide distinct identities to different cell types, although they all contain identical sets of information. The regulatory programs that underlie these cell- and tissue-specific functions and identities are based largely on genome packaging. Genes that should not be expressed in a given cell or tissue are located in tightly packaged regions of the genome and inaccessible to the transcription factors that would otherwise turn them on. These boundary elements help to establish the geography of genome packaging by delineating the margins between silent regions in which genes are not expressed and active regions in which they are. In this critical role, boundary elements help to control the timing and extent of gene expression across the entire genome. As a result, defects in the organization of the genome by boundary elements are highly relevant for physiological and pathological processes.

                         Another benefit of looking for design instead of junk lies in gaining knowledge that has positive applications. Dr. Lunyak comments, “This is an important discovery because the understanding of how RTEs punctuate messages encoded in the human genome can help researchers to develop treatments for a wide variety of human diseases, including aging.” You have to understand punctuation in order to fix it. Would the “junk DNA” concept have led to this productive line of inquiry? Incidentally, we can thank the ENCODE Project for motivating Dr. Jordan’s project.

                    

Functional Transfer-RNA “Litter”

Another example is this research from UC Santa Cruz. The announcement doesn’t mention junk DNA, but it shows the benefit of looking for function. All geneticists know the well-characterized functions of transfer RNA (tRNA), but the research team wondered why the nucleus is “littered” with pieces of tRNA. Notice the focus on function:

                Transfer RNA was characterized decades ago and plays a well-defined role, together with messenger RNA and ribosomal RNA, in translating the genetic instructions encoded in DNA into proteins. The discovery of RNA interference and genetic regulation by microRNA, however, revolutionized scientists’ understanding of RNA’s role in gene regulation and other cellular functions. Since then, a bewildering abundance and variety of small RNA molecules has been found in cells, and scientists are still struggling to sort out what they all do.

               One doesn’t struggle to find out what junk does. The search for function is a good motivation for research. It inquires: these pieces must be there for a reason. As for the “Transfer RNA fragments,” the search for function is only in the early stages, but an important one was found:

                          “In the past five years, we’re starting to see that transfer RNAs are not just translatinggenes into proteins, they are being chopped up into fragments that do other things in the cell,” Lowe said. “Just recently, a subset of these fragments was found to suppress breast cancer progression.”

           Many women can be relieved these UCSC researchers didn’t give up on “litter” they didn’t understand.

        

Endogenous Retroviruses

As Casey Luskin has Explained, endogenous retroviruses (ERVs) also have functions and are not junk. Current Biology published a “Quick Guide” to ERVs. The authors seem ambivalent about these former poster children for useless, selfish invaders in our genome. On one hand, they point to examples that appear invasive and parasitic. On the other, they show examples of function, where ERVs are expressed purposefully by the “host”:

                 At each end of the ERV genome are long terminal repeats (LTRs), which contain regulatory sequences that can alter the expression, splicing, and polyadenylation of those host genes located near the ERV insertion site. LTRs regulate the cell type that the virus replicates in by controlling its expression, and so can be co-opted by their hosts as alternative promoters, resulting in tissue-specific expression of host genes. Often, solitary LTRs have been generated by homologous recombination between the two LTRs present in a single ERV, resulting in loss of the internal sequence. Consequently, host genomes are peppered with solo LTRs of potential regulatory significance.

                   The best evolutionary story the authors come up with is that the host learns to “co-opt” its ERVs and turn them into benefits. However, a search for design of ERVs would be more productive. Why must we always view viruses as destructive invaders? Many are neutral or beneficial. Why not look at ERVs as functional at the ecological level, instead of portraying them in the Dawkins selfish-gene way? The latter would motivate scientists to want to eliminate them, overlooking their potential benefits. It certainly is not helpful to ascribe mental planning to evolution, as the authors say in conclusion:

                          Taken together, the evidence suggests that sequences sequestered from ERVs have had a considerable influence on the evolution of their vertebrate hosts. So, not only is evolution a tinkerer, but it is also a conscientious recycler.

                   That word “recycler” represents a tacit admission that there was function there in the first place.

The Future of Genomics

PLOS Biology published a collection of short essays under the title, “Where Next for Genetics and Genomics?” Gil McVean looked back at the revolution in understanding when geneticists turned their attention from junk to gems:

The study of genetic variation has, over the last decade, been turned from a polite discipline focused on the finer points of evolutionary modelling to a fast, exhilarating, and sometimes messy hunt for gems hiding within the mines of genome-wide, population-scale datasets, most of which have been from humans. The coming years will only see the data rush grow: bigger samples, new species, extinct species, data linked to phenotype, temporal data, and so on. What, in this great whirlwind, am I most excited by?

Data are at their most fun when they bring to light things you would never have imagined.

                   Although he thinks the future will revisit “some of those big questions in evolution that never went away,” like “How does adaptation actually work?” (You mean that after 156 years they don’t know?), one thing is clear: focusing on “the finer points of evolutionary modelling” is passé. What’s “exhilarating” now is “the hunt for gems.” Things evolutionists “would never have imagined” — like finding functions in assumed junk — have been the “most fun.”

            

Death of a Meme

The demise of the “junk DNA” meme is a powerful reminder of the positive benefit of design thinking. “Junk DNA” was a science stopper, relegating non-coding sequences in the genome to the trash basket. Many years of fruitful research were lost because of it. Had scientists been focused on design and function back in the 1970s, who knows how much further along we would be?

Here is a challenge to all researchers to look at nature with a different focus. When something in a cell or organism appears useless, learn to think: It must be there for a reason. History has shown that approach often leads to fundamental new insights into the design of life, yielding practical applications for health and understanding.

Uberman v. Unterman: courtesy of Darwin

 When Darwinism Came to Africa, Horrors Ensued

Evolution News 

On a new episode of ID the Future, hear a Nigerian voice-actor reading from the opening pages of Nigerian scholar Olufemi Oluniyi’s new book, Darwin Comes to Africa. In this section from the preface, Oluniyi explores the relationship of Darwinism to Social Darwinism, and some of the ways Social Darwinism fueled and justified horrific ideas and actions among European thinkers and colonizers. Oluniyi tells the story of Russian scientist Ilya Ivanovich Ivanov (pictured above), who, guided by Social Darwinist thinking, “sought to produce a race of super-soldiers for Stalin’s army by impregnating French Guinea women with the sperm of a dead chimpanzee — black African women, mind you, who were presumed to be less highly evolved and thus closer to chimpanzees than were white European women.” As Oluniyi further notes, this scientist was far from a “lone gunman…. Colonial authorities approved the plan, and the Russian found support amongst both the French and American scientists.” As horrifying as this plan is, it and other horrors make sense under the false and twisted logic of social Darwinism, Oluniyi explains. Download the podcast or listen to it here . Buy the eye-opening book here

JEHOVAH'S masterclass on supply chain operation.

How the Earth Operates Supply Chains for Life

David Coppedge  

The “supply chain crisis” in the news underscores the need for complex systems to have access to the parts they need in time. Breakdowns in the supply chain for one system can cause ripple effects with other systems.

During World War II, the science of Operations Research, a branch of engineering dealing with time and space efficiency, was founded to optimize interconnected systems. With new diagrams like Pert charts, efficiency experts identified nodes where supply breakdowns could slow or halt production of complex systems like aircraft or ships. Some nodes can be worked on in parallel; others cannot. For instance, if parts for a subsystem are plentiful at the Norfolk shipyard but specific widgets must be shipped from Peoria on unreliable transports, laborers could find themselves being paid for idle time waiting for the parts to arrive. Tracing a project’s critical path through these nodes allows managers to estimate the time required to complete a project, and then look for ways to eliminate showstoppers or inefficiencies. Advances in Operations Research led to innovations like buffering and Just-in-time delivery.

             As with engineering, so with life. For one example, I’ve reported on how toxic heme molecules, essential for many life processes, are synthesized, stored, and buffered for just-in-time delivery without endangering the cell. See here as well for three other examples.

          

Elemental Abundance vs. Availability

The most abundant elements in our bodies (carbon, hydrogen, oxygen, and nitrogen, comprising 96 percent) are available plentifully in the crust and atmosphere. Proximity, though, does not equate to availability. As we saw here and here, nitrogen is a tough nut to crack despite being the most abundant gas in the atmosphere, and oxygen is highly toxic to cells unless handled carefully. Similarly, carbon and hydrogen come in many molecular forms that are not directly useful to cells. The supply chain problem, therefore, depends not only on proximity but on packaging. Essential ingredients are not helpful if locked in a metal box without a key. 

         The Earth is blessed with a crust and an atmosphere that provide essential elements for life. But it’s no help having the elements in the Earth’s crust if they can’t get where the organisms need them. One of the most fascinating aspects of Michael Denton’s Privileged Species series of books, especially The Miracle of Man (2022), concerns the synergy between geology and biology that satisfies life’s supply chain requirements. Let’s look at some new discoveries about getting chemical elements where they are needed, on time.

The Geological Supply Chain

Denton spoke of the combined benefits of glaciers and the unique properties of water for grinding down rocks to expose minerals. The process works like sandpaper, he says (The Miracle of Man, pp. 37-38), creating “rock flour” that brings elements to soils and clays usable by plants.

From Penn today, we learn that “Biogeochemist Jon Hawkings of the School of Arts & Sciences and his lab study glaciers to understand the cycling of elements through Earth’s waters, soils, and air in its coldest regions, with implications for climate change, ecosystem health, and more.” Collecting freezing water in Greenland without contamination is not glamorous work, Hawkings says, but is leading his colleagues at the University of Pennsylvania to appreciate the rivers of ice as habitats for algae and bacteria.

                In addition to harboring life, glaciers also move, albeit fairly slowly, says Hawkings. They are sometimes referred to as “ice rivers.” As they flow, the ice can act like sandpaper, grinding up the bedrock upon which they sit. “Anything that’s in that bedrock can become mobilized and, if it’s reactive, will dissolve into water,” he says.

          The team’s work on “elemental mobilization and global systems” has only been possible in the past decade, Hawkings says. 

The geological supply chain also includes volcanoes, which enrich soils with nutrients. One “striking” non-biological supplier is lightning, which can break N2’s triple bonds and create nitrates usable by organisms. Many planetary scientists, furthermore, believe that other essential elements, like zinc (Imperial College London), and perhaps Earth’s ocean water, were delivered air mail: via meteorites and comets. Micrometeoroids deliver a steady rain of Elements that include biological essentials like manganese, iron, magnesium, calcium, phosphorus, and even chromium. Some of these are also supplied by volcanoes.

                 Chromium (Cr, atomic number 24) is another essential trace Element not just for shiny bicycle handlebars and stainless steel kitchenware but also for insulin utilization. Though it is toxic in excess, our metabolism depends on it. We usually get sufficient chromium in a variety of foods. A paper by Bertinotto and Griffin in PLOS one reported that “A low chromium diet increases body fat, energy intake and circulating triglycerides and insulin in male and female rats fed a moderately high-fat, high-sucrose diet from peripuberty to young adult age.” Without the volcanic and meteoritic supply chains, there might not be sufficient chromium on the surface. That could be true of other trace elements needed by organisms, including rare earth Elements.

                  

The Biological Supply Chain

As stated above, lightning can make atmospheric nitrogen available, but most biologically available nitrogen is “fixed” by microbes containing the nitrogenase enzyme. These biological marvels are located in root nodules of legumes and other plants that have symbiotic relationships with the microbes. It’s more irreducibly complex than a mousetrap, but if you could build a mimic of nitrogenase the world would beat a path to your door.

Another interesting case of microbial delivery concerns cobalt. Many do not think of this shiny metal in their diet, but Co (element 27) is incorporated in the active site of Vitamin b12, essential for the synthesis of nucleic acids and for cellular metabolism. The vitamin is also involved in the synthesis of fatty acids for the myelin sheath that supercharges neurons. Watanabe and Bito (2017) describe how we obtain vitamin B12 with its cobalt ion in the center:

           Vitamin B12 is synthesized only by certain bacteria and archaeon, but not by plants. The synthesized vitamin B12 is transferred and accumulates in animal tissues, which can occur in certain plant and mushroom species through microbial interaction. In particular, the meat and milk of herbivorous ruminant animals (e.g. cattle and sheep) are good sources of vitamin B12 for humans. Ruminants acquire vitamin B12, which is considered an essential nutrient, through a symbiotic relationship with the bacteria present in their stomachs. In aquatic environments, most phytoplankton acquire vitamin B12 through a symbiotic relationship with bacteria, and they become food for larval fish and bivalves. Edible plants and mushrooms rarely contain a considerable amount of vitamin B12, mainly due to concomitant bacteria in soil and/or their aerial surfaces. Thus, humans acquire vitamin B12 formed by microbial interaction via mainly ruminants and fish (or shellfish) as food sources.

                From volcano to ore to microbe to cow to lunchtime hamburger, this unexpected metal makes its appearance through both geological and biological supply chains. (The role of the ruminant forestomach I discussed here. You can listen to the episode on ID the Future.)

         

Limiting Factor?

Of the essential elements for life, phosphorus (P, atomic number 15) may be a limiting factor. See “The Problem of Phosphorous” and “Is There Enough Phosphorus for Us?” Those articles gave circumstantial evidence that P availability has been adequate through the history of life on Earth, and noted that microbes and plants are good recyclers of phosphorus, able to implement pre-programmed remediation measures under P starvation.

Phosphorus shortages have become a global concern (Auburn University). Nature Communications is worried that soil warming may decrease phosphorus availability. There may be better supply chain strategies at work in the biosphere than we realize. The Chinese Academy of Sciences reported via Phys.org that phosphorus availability is enhanced in some cases by — of all things — termites.

           Termites are social insects of the infraorder Isoptera and are widely distributed across tropical and subtropical ecosystems. These insects are the most important soil bioturbators and have been called “soil engineers.”Phosphorus concentrations are usually low in highly weathered tropical acid soils, but termite nests form bioaggregates that serve as carriers for P protection and stabilization.

                 As this is a new finding, it is reasonable to expect other biological processes will be found working to maintain just-in-time delivery of phosphorus in other ecosystems.

A Hidden Hand

One hopes these glimpses into Earth’s “operations research” solutions help give us confidence that life will continue to thrive as it has since the beginning. And maybe the success of the biosphere will point to a hidden hand of engineering that knew all about critical paths and just-in-time delivery.

James Gates on our becoming a spacefaring civilisation.

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The militant vegans are coming.

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David Berlinski has got agreeing to disagree down to a science?

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The fall of college?

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The new Rome? II

 

The gene dethroned?

 New Study: Transgenerational Epigenetics Can Have a Profound Impact

Cornelius G Hunter 

The Third Rail of Evolution

In the spring of 2006 I gave a talk on the campus of Cornell University and afterwards was joined by then Cornell professors Richard Harrison and Kern Reeve for a sort of panel discussion or debate about biological evidences and origins. I presented a dozen or so interesting and important evidences that I felt needed to be recognized in any discussion of origins. The evidences falsified key predictions of evolution and so needed to be acknowledged and reckoned with, one way or another. One of the items on my list was the so-called directed adaptation mechanisms which, broadly construed, can include everything from non random, directed, mutations to transgenerational epigenetic inheritance. But I was in for a big surprise when Harrison and Reeve gave their response.

Directed adaptation is reminiscent of Lamarckism. Rather than natural selection acting over long time periods on biological variation which is random with respect to need, directed adaptation mechanisms provide rapid biological change in response to environmental challenges. Like physiological responses, directed adaptation can help an organism adjust to shifts in the environment. But those adaptations can then be inherited by later generations. Stresses which your grandparents were subjected to may be playing out in your own cells.

In the twentieth century evolutionists had strongly rejected any such capability. Lamarckism was the third rail in evolutionary circles. And for good reason, for it would falsify evolutionary theory. But empirical evidence had long since pointed toward the unthinkable, and by the twenty first century the evidence was rapidly mounting.

While there was of course still much to learn in 2006 about directed adaptation (as there still is today for that matter), it could no longer be denied, and needed to be addressed. At least, that is what I thought.

I was shocked when Harrison and Reeve flatly denied the whole story. Rick waved it off as nothing more than some overblown and essentially discredited work done by Barry Hall and John Cairns, back in the 1970s and 80s (for example here).

But there was a body of work that had gone far beyond the work of Hall and Cairns. Incredulously I responded that entire books had been written on the subject. Rick was quick to respond that “entire books are written about all kinds of discredited things.”

True enough. It was me versus two professors on their home turf with a sympathetic audience, and there was no way that I was going to disabuse them of what they were convinced of.

Confirmation testing and theory-laden evidence are not merely philosophical notions. They are very real problems. I’m reminded of all this every time a new study adds yet more confirmation to the directed adaptation story, such as the recent Paper out of Nicola Iovino’s lab on transgenerational epigenetic inheritance in house flies, which states:

Gametes carry parental genetic material to the next generation. Stress-induced epigenetic changes in the germ line can be inherited and can have a profound impact on offspring development.

The Press release gives little indication of the controversy as it admits that these findings were once considered impossible:

It has long been thought that these epigenetic modifications never cross the border of generations. Scientists assumed that epigenetic memory accumulated throughout life is entirely cleared during the development of sperms and egg cells

It is hard enough to see how organisms can respond intra-lifetime to environmental challenges, but how can it be inherited as well? For epigenetic changes that occur in somatic cells, that information must also enter into the germ line as well. Somehow it must be incorporated into the sperm and/or egg cells.

It is an enormous problem to explain how such capabilities evolved. Not only are a large number of mutations required to make this capability work, it would not be selected for until the particular environmental condition occurred. That means that, under evolution, it would be not preserved, even if it could somehow arise by chance.

Prophet of the master race and his apostles.

 Cambridge UP Book Airbrushes Darwin’s Contribution to Scientific Racism

Evolution News 

On a new episode of ID the future historian Richard Weikart (Cal State Stanislaus) dissects a recent Cambridge University Press book on Social Darwinism by Jeffrey O’Connell and Michael Ruse. Weikart, author of Hitler’s Ethic, From Darwin to Hitler, Hitler’s Religion, and The death of humanity, says a major shortcoming of the book is the authors’ attempt to put as much distance as possible between Darwin and eugenics thinking, and between Darwin and Hitler. The new book paints Darwin follower Herbert Spencer as the eugenics-championing bad guy and contends that Darwin and Darwinism had little or no influence on Hitler’s warped master-race ethic. Weikart patiently highlights some key evidence to the contrary, including statements front and center in Hitler’s writing. Did Darwin cause Hitler? No. Would Darwin have approved of Hitler? Almost certainly not. But according to Weikart, Darwin’s own racist and pro-eugenics thinking, combined with some implications of his theory that he himself explicitly expressed, manifestly did lay the groundwork for Hitler’s diabolical outlook on war, “the master race,” “the struggle for life,” and eugenics.

More on why no rise of the machines.

Are you tired of hearing about ChatGPT yet — “basically high-tech plagiarism,” as Noam Chomsky has said? Dr. Robert J. Marks, director of Discovery Institute’s Walter Bradley Center, appeared on a segment of The Agenda recently to examine the hype surrounding artificial intelligence and ChatGPT. He was joined by Melanie Mitchell of the Sante Fe Institute and MIT’s Max Tegmark. Hosted by Steve Paikin, the three discussed the benefits and drawbacks of artificial intelligence and what it means to be human in a technological age, as well as the perennial question of consciousness. You can watch the entire conversation on YouTube:

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Dr. Marks had the opportunity to talk about some of the key themes he discusses in his book Non-computable you: What You Do That Artificial Intelligence Never Will, contending that AI, while it has benefits, does not, and never will, have the creativity, empathy, and personal consciousness unique to human beings. 

 

On distinguishing between natural and artificial selection.

 Robot Evolution? How the Trick Is Done

David Coppedge 

It’s been decades since Richard Dawkins committed the Weasel Blunder and since Tim Berra committed Berra’s Blunder, but some evolutionists still don’t get it. You can’t design something for a purpose and call it Darwinism. Even if some randomness is thrown in, once a goal is specified in advance, that’s not evolution; it’s intelligent design.

An example comes from PLOS ONE: “Morphological Evolution of Physical Robots through Model-Free Phenotype Development,” by Brodbeck, Hauser, and Iida. Look for the evidence of guidance by the investigators:

Artificial evolution of physical systems is a stochastic optimization method in which physical machines are iteratively adapted to a target function. The key for a meaningful design optimization is the capability to build variations of physical machines through the course of the evolutionary process. The optimization in turn no longer relies on complex physics models that are prone to the reality gap, a mismatch between simulated and real-world behavior. We report model-free development and evaluation of phenotypes in the artificial evolution of physical systems, in which a mother robot autonomously designs and assembles locomotion agents. The locomotion agents are automatically placed in the testing environment and their locomotion behavior is analyzed in the real world.This feedback is used for the design of the next iteration. Through experiments with a total of 500 autonomously built locomotion agents, this article shows diversification of morphology and behavior of physical robots for the improvement of functionality with limited resources. 

Stamped by Design

These researchers from Switzerland carefully crafted a “mother robot” that could assemble pre-fab parts into blocks that could perform some simplified locomotion. The algorithm was set to reward “offspring” that performed faster. Despite employing Darwinian words like “fitness” and “selection,” their work has “design” stamped all over it. Reporters, though, went ape attributing this to Darwinian evolution. 

At Phys.Org, Sarah Collins titled her report, “On the origin of (robot) species” in tribute to the Great Bearded Guru. She’s like a viewer of a magic show unaware of how the trick is done:

For each robot child, there is a unique ‘genome’ made up of a combination of between one and five different genes, which contains all of the information about the child’s shape, construction and motor commands. As in nature, evolution in robots takes place through ‘mutation’, where components of one gene are modified or single genes are added or deleted, and ‘crossover’, where a new genome is formed by merging genes from two individuals.

In order for the mother to determine which children were the fittest, each child was tested on how far it travelled from its starting position in a given amount of time. The most successful individuals in each generation remained unchanged in the next generation in order to preserve their abilities, while mutation and crossover were introduced in the less successful children.

In all fairness, Collins points out some differences between robots and natural organisms. Still, nowhere does she explain how the experiment clearly requires design instead of natural selection. She thinks the “mother” robot did the designing. And she takes on faith the opinion of one of the authors that they were watching Darwinian evolution happen before their eyes:

“Natural selection is basically reproduction, assessment, reproduction, assessment and so on,” said lead researcher Dr Fumiya Iida of Cambridge’s Department of Engineering, who worked in collaboration with researchers at ETH Zurich. “That’s essentially what this robot is doing — we can actually watch the improvement and diversification of the species.“

“Learning to Evolve”

At the BBC News, evolution reporter Pallab Ghosh titled his coverage, “Robots learn to evolve and improve.” It’s not clear how one could “learn to evolve” if evolution is an unguided natural process, but that’s not the only conundrum in his article. Like Collins, he fails to make any distinction between intelligently designed robots and natural processes. 

Engineers have developed a robotic system that can evolve and improve its performance.

A robot arm builds “babies” that get progressively better at moving without any human intervention.

The ultimate aim of the research project is to develop robots that adapt to their surroundings.

There’s a second conundrum: if human minds are developing robots that evolve, isn’t Ghosh making a case for intelligent design?

What the designers and reporters all seem to be missing is the fact that goals were determined from the outset. “Improvement” was defined as the ability to move faster. Yet in nature, not every successful animal is the speediest (consider the sloth, or the fabled tortoise and hare). Darwinian evolution cannot work toward a distant target. As Paul Nelson remarks in the film Living Waters, “Any evolutionary process you consider, any materialistic process you can consider has no foresight. It can’t see five years, five seconds, five milliseconds into the future. For that, you need a mind.”

An Aim and an Approach

The paper actually makes a powerful if unintended case for intelligent design when you think about it. Ghosh reports that Dr. Iida got into robotics because the ones he saw in real life were not as good as the ones he enjoyed in movies like Star Trek and Star Wars. “His aim was to change that,” Ghosh says, “and his approach was to draw lessons from the natural world to improve the efficiency and flexibility of traditional robotic systems.” He had an aim. He had an approach. He wanted to gain knowledge, or information. So he looked at the efficiency and flexibility of natural solutions, where he found efficient designs worth copying. In other words, he was motivated by biomimicry — an approach saturated with design thinking.

But he used an evolutionary algorithm, someone might complain. True, but it wasn’t evolutionary in the Darwinian sense. There’s no such thing as a Darwinian “algorithm” despite the use of familiar lingo like mutation, selection, and fitness in the paper. Algorithms are intelligently designed for function. Once an algorithm is defined, a mindless mechanism like a computer program or robot can use it, applying inputs and monitoring outputs, as in this case. But those mechanisms were also predesigned to implement the predetermined goal.

Animal and plant breeders use “evolutionary algorithms” of a sort; they know what they want; they use algorithms of sexual reproduction, and they monitor the output to decide what offspring get to breed in the next iteration. All this is under the guiding hand of the intelligent agent (the breeder). Artificial selection is intelligent design, not Darwinism.

                  If the authors and reporters really wanted to see materialistic Darwinian processes in action, they should have taken their hands off the equipment, shut the door, and let nature take its course. Most likely, nothing more interesting would happen than rust.

Two Blunders in One

Dawkins set a goal of generating Shakespeare’s phrase “Methinks it is like a weasel.” Berra watched cars “evolve” but missed the role of designers. The designers of these robots (and their Darwin-friendly reporters) committed both blunders. They had a target, designed a way to reach it, yet presumed after the fact that their carefully engineered “mother robot” resembled a mindless, material entity working by Darwinian natural selection. We can at least thank them for providing another opportunity to show why they really made the case for design.