Search This Blog

Saturday, 4 March 2023

Frenemies?


A realistic evaluation of the expertocracy.

<iframe width="932" height="524" src="https://www.youtube.com/embed/JyufeHJlodE" title="Thomas Sowell on the second edition of Intellectuals and Society" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe> 

The search for Darwin's "simple beginning" yet another wild goose chase?

Why High School Biology Made Me Angry (And Why I Like It So Much Better Now)


I didn’t like biology in high school. It made me angry, actually. That’s ironic, looking back now. Besides writing here at The Stream, I’ve edited almost all of Discovery Institute’s last 400 to 500 podcasts on Intelligent Design theory, with a lot of biology included in them. Needless to say, I’ve come around since school days.

It was bad then, though. Mr. V., my high school biology teacher, was definitely part of the problem. He spent six class periods teaching us Charles Darwin’s life story. Don’t jump to conclusions here, now. It’s not that it took him six hours to get through all his material. No such luck. He delivered exactly the same story. One class period long. Beginning to end. All six times.

Maybe he didn’t realize he’d already done it once (twice? three times? four or five times?) before. Whatever the reason, it was certifiably bad teaching. But Mr V. wasn’t my biggest issue with biology, and it wasn’t Mr. V. who made me angry, either.

Angry? Yes.

And now some of you will jump to conclusions again. I’m a conservative Christian, so the problem was evolution, right?

Wrong. Way wrong.

How Does It Know the Difference?

An old joke tells the problem nicely.

There’s this company that wants to hire a genius, you see, and the hiring manager has it down to three candidates. They’re all sitting in the room together with him, and he asks them, “What would you say is the most amazing technology in the world today?”

The first person says, “It’s the internet, no doubt about it. Look at all the information! Look at all the communication!”The hiring manager nods appreciatively.

The second says, “No, it’s medicine. Can you even believe how many lives we’re saving these days?” Another appreciative nod.

The third guy says, “No, no, you’re both wrong. It’s the Thermos bottle!” No nod this time.

Everyone turns and stares. Finally, someone asks the question. “The Thermos bottle???”

“Yes, the Thermos bottle! Just look: It keeps hot things hot, and cold things cold. How does it know the difference?”

Glossing Over the Question

I had a problem like that with what they taught me about the living cell. It had a cell wall (plants) or cell membrane (everything else). That membrane or wall let oxygen in, along with hydrogen and nitrogen and calcium and phosphorus and sodium and everything else the cell needed. It put other chemicals out, like garbage on trash day. How does it know the difference? 

This time, unlike the Thermos bottle, something really incredible was going on. And our the textbook glossed over it like no problem at all. That’s what bugged me.

The Darwin Connection

Interestingly enough, it turns out there’s a connection here with Charles Darwin — not that he had the same problem, actually. What’s interesting is that he didn’t. As far he knew — as far as anyone knew in his day — the living cell was a featureless little blob. It had its cell wall or cell membrane, and all it had inside was a boring glob of goo. This goo had a name, or would soon enough. While Darwin was publishing his Origin and Descent, other scientists were publishing things like, “All living cells are made of a living substance called protoplasm.”

Note how they called it “a substance,” as in, just one thing. What did they mean by that? Well, I’ve got another weird story for you.

Many years ago, I read a comic that explained Lex Luthor’s hostility to Superman. (There have been lots of Lex Luthor myths.) Luthor had just invented protoplasm in his lab. He had manufactured life! The real thing! But then the lab caught on fire. And Superboy (they were both teens at the time) came along and put the fire out with his super-breath. In the process the chemicals got mixed up, and Luthor’s grand invention, life itself in the form of protoplasm, was ruined. He blamed it on Superboy, and the rest is comic and movie history.

No, I didn’t turn to comic books to fill in for my disappointing biology classes. The authors were years behind on the science themselves. Still, it helps illustrate what science thought for several decades. Life’s secret ingredient, the thing that made life different from non-life, was a substance, something you could imagine a mad scientist cooking up in a beaker.

Boy, were they wrong.

Discovering How It Knows the Difference

It was the best they could see with early microscopy, but it was way too simple. (Even the way I said that was way too simple.) That apparent simplicity was one reason Darwin could think evolution could easily produce all of life’s grand variety. Darwin didn’t know what we know.

Anyway, when I was in high school (if I recall correctly — it has been a while) they were still talking about protoplasm. By then, though, they’d also found out there was other stuff in the cell besides: the nucleus, mitochondria, organelles, and other organelles. They also knew the cell membrane pulled the right chemicals in and pushed the right stuff out. As for how that membrane knew the difference, though, my textbook just ignored the question.

I didn’t buy it. I figured something was up — something they weren’t telling us. Maybe I was too hard on them. Scientists really had not much clue at the time, at least compared to what’s known now. Again, it wasn’t their fault; it has taken decades of advances to get us where we’ve come since then. Still it bothered me how the textbook just ignored the problem — bothered me enough I remember it to this day.

Maybe with a better teacher I’d have been inspired to go study and help find out. Others did, and I’m glad. I’m glad, too, that I get to help bring some of their work to the public. Because scientists have a clue now, and it’s more amazing than I’d ever dreamed. Way more amazing.

Astonishing Machinery

Someone at church asked me not long ago, “Just how complex is a simple cell? Is it as complex as a computer?” I gave him the answer I’d learned lately. Take a simple cell like a bacterium, and you’re not looking at complexity on the level of a computer. Not even close. Cells are more on the level of a large city, computers included.

I can only imagine how different school might have been if we’d had videos like this one from Veritasium. Ever heard of molecular machines? This’ll blow your mind.

(I’m a great fan of Veritasium, by the way.)

Derek Muller, the host, raises an intriguing question at the end: Will humans someday be able to design nanomachines like these, to insert in our bodies and help heal diseases? Maybe? I won’t say no, but I’m skeptical. This much is certain: It could only happen with years of intense study, extraordinary technology, enormous insight, and a healthy dose of creativity. Muller would undoubtedly agree.

Taking the Complexity Seriously

I seriously doubt he’s taking the problem seriously enough, though. Your own body has something like 30 trillion cells in it. That’s 30 trillion large cities’ worth of complexity, with thousands of nanomachines powering and doing the work inside each and every one.

That’s only a glimmer of it. All that complexity gets multiplied exponentially by what it takes for those trillions of “cities” to work together as tissues, organs, and systems, keeping you alive, moving, thinking, communicating, working, loving, and everything else you do. It raises the question: How did all this happen in the first place? How did all those nanomachines develop? How did they come to work together so effectively? Can naturalistic evolution explain this? Seriously?

There was a time — maybe when I was in high school — when evolutionists would have answered, “Just hold on. We’ll learn more, and we’ll get that solved for you.” They would have been wrong. Science is going the other direction instead. The problem now is much harder than they ever thought it was.

This isn’t “God of the gaps,” or some silly rush to say “God did it,” when with a little more patience, we could hold on for answers from science. No, this is, “Science keeps running into greater and greater problems for evolutionary theory.”

A Better Paradigm

Meanwhile, the Intelligent Design paradigm keeps fitting better and better. In one of those podcasts I edited, Dr. Howard Glicksman tells part of the story. I wish someone could have taught me in high school: how the cell membrane “knows the difference.” It’s stunning. And as he explains, it’s pretty hard to give unguided evolution credit for accomplishing it. (If you prefer video, go for “The Design Inference,” the series on “A Theory of Biological Design,” or “Unlocking the Mystery of Life.”)

That’s why I like biology better now. Someone is taking the questions seriously. They always were, but we have more detailed answers now, they’re astonishingly interesting answers, and it’s easier find access to those answers. I have to wonder, though: What are they teaching in your children’s high school?

The theory of everything and its opposite?

Casey Luskin Debunks a Museum’s Evolutionary Propaganda


On a new episode of ID the Future, geologist Casey Luskin continues to discuss his recently published essay directed against the view that humans evolved from ape-like ancestors via blind Darwinian processes. In this episode he shares his experience of walking into the fossil hall at South Africa’s famous Maropeng Museum and immediately being confronted by a piece of shameless materialist propaganda, a Richard Dawkins quotation prominently displayed as part of a floor-to-ceiling display. The quotation insists that humans are essentially just DNA survival machines. Luskin says, not so fast, and points out the various ways such a view fails to explain important aspects of human behavior, including altruistic behavior toward non-kin. Luskin and host Eric Anderson also call evolutionary theory to task for being overly supple, with its adherents regularly employing vague just-so stories to explain virtually any behavior or feature AND its opposite. Download the podcast or listen to it here
                 To read Luskin’s essay on the subject, get the new free online ID book from South Africa, Science and Faith in Dialogue, with contributions from Luskin, Stephen Meyer, Hugh Ross, Guillermo Gonzalez, James Tour, Fazale Rana, Marcos Eberlin, and others. Find Part 1 in this Anderson/Luskin

Conspiracy theorist extraordinare?

<iframe width="932" height="524" src="https://www.youtube.com/embed/56GWPcazLsU" title="Joe McCarthy: The Original Conspiracy Theorist" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe> 

On the rise of Russia's man of steel.


Friday, 3 March 2023

Why actual intelligence will continue to rule artificial intelligence.

Will AI “Own the World”? Robert J. Marks Talks with Laura Ingraham


Robert J. Marks directs Discovery Institute’s Bradley Center for Natural & Artificial Intelligence. He recently appeared on a podcast episode with Fox News host Laura Ingraham to talk about artificial intelligence, tech, and Dr. Marks’s book Non-Computable You: What You Do That AI Never Will. 

Ingraham prefaced the conversation with some thoughts on the rapidly evolving technological world we find ourselves in, and the changes such developments are inflicting on society. In response to the futurism and unbounded optimism about AI systems like ChatGPT that many modern figures hold, Marks said that what computers do is strictly algorithmic:
                       This leads us to the idea of whether or not there are non-computable characteristics of human beings, and I think there is growing evidence that there are. I would give the simple examples of happiness, joy, empathy. I think less obvious are the operations of sentience, creativity, and understanding. I believe that probably these are not algorithmic either. Again, we’re starting to have scientific evidence that this is indeed the case. So, you’re not allowed to build your own religion and speculate. We see this a lot in artificial intelligence. 
           
To “Own the World”

Ingraham brought up an ominous remark from Klaus Schwab, founder of the World Economic Forum, in which he said that in the future, whoever owns artificial intelligence will “own the world.” Schwab thinks this revolution of the world order, brought about in large part by advances in AI, is just a decade away at most. Marks, however, responded by appealing to the history of exaggerated, utopian (or dystopian) visions for humanity: 
                   I think we only have to look at history and see a lot of these other incredibly hyperbolic claims that have come out. I was old enough to remember the Y2K scare, which was supposed to dissolve the world into all sorts of problems. Deepfakes are going to disrupt political discourse. Self-driving cars are going to cause all truck drivers to lose their jobs. No, that hasn’t happened. Maybe it will happen someday, but we’re on a much slower path to that. Here’s my prophecy: in ten to twenty years we are going to recognize the limits of artificial intelligence (which we are starting to do, especially these chat models like ChatGPT and LaMDA) and we’re going to find out the limitations of them. And we’re going to incorporate this into our society. Is it going to make a difference? Yes. But is it going to become sentient and take over the world? No. Artificial intelligence isn’t going to do that. 
                       Marks emphasized that AI is a tool and that it can be used for either good or evil. 

Ingraham and Marks went on to talk about the guardrails computer engineers have made for ChatGPT, the state of higher education, and the legacy of Walter Bradley, the namesake of the Walter Bradley Center. 

You can find the link to the full conversation here but will need to get 7-day free trial for full access

The Fossil record's equilibrium continues to rebut Darwin

Fossil Friday: Evolutionary Stasis in Fossil Damselflies Challenges Darwinism


This Fossil Friday features a beautiful fossil damselfly from the Upper Jurassic limestone of Painten in Bavaria, Germany, which is about 152 million years old. I acquired this remarkable fossil for the collection of the Natural History Museum in Stuttgart in 2012 (no. SMNS 70154) and scientifically described it as a new genus and species, Jurahemiphlebia haeckeli, a few years later (Bechly 2015, 2019). It represents the oldest fossil record of crown group Zygoptera and belongs to the damselfly family Hemiphlebiidae.

For a lay person it would hardly be distinguishable from its living relative Hemiphlebia mirabilis from Australia, even sharing the tiny size of just 11 mm wing length and the characteristic wing venation. Such cases of evolutionary stasis present a conundrum and challenge for neo-Darwinism, which can only be explained away with ad hoc hypotheses like stabilizing selection under unchanging ecological conditions. However, the profound changes in geography, climate, and vegetation since the Late Jurassic make the assumption of a stable habitat quite implausible. Also, it looks like natural selection is considered as a “magic wand” that can be highly creative and transformative or highly conservative and stabilizing.

How convenient. Sounds like the old saying: If the cockerel crows from his favorite spot, the weather may change or again it may not. In the hard sciences such universal explanations that can explain everything and rule out no possible observations are usually considered empirically empty and worthless. Not so in modern evolutionary biology, which tells a lot about its dubious status as a “hard science.” It is instead an unfalsifiable assemblage of fancy just-so stories and ad hoc explanations, a kind of meta-narrative for a naturalistic worldview but not a serious science on par with physics or chemistry.

Sources

Bechly G 2015. [Chapter] Insekten (Hexapoda). pp. 239-270 in: Arratia G, Schultze HP, Tischlinger H & Viohl G (eds). Solnhofen – Ein Fenster in die Jurazeit. 2 vols. Pfeil Verlag, Munich (DE), 620 pp.
Bechly G 2019. New fossil Odonata from the Upper Jurassic of Bavaria with a new fossil calibration point for Zygoptera. Palaeoentomology 2(6), 618-632. DOI: https://doi.org/10.11646

Comparing our patch of real estate to the fixer uppers(?) around the galaxy.

<iframe width="932" height="524" src="https://www.youtube.com/embed/l77o_36xd_I" title="NASA&#39;s Telescope Just Found An Object That Defies All Logic" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe> 

On the empire of the atom?

<iframe width="932" height="524" src="https://www.youtube.com/embed/ae36scLdCsE" title="Why Is Everything Made Of Atoms?" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe> 

Let there be light?


An answer looking for a question?

 The philosophy naturalism.


Last time we saw that by wholeheartedly embracing and promoting Theodosius Dobzhansky’s famous phrase, “Nothing in Biology Makes Sense Except in the Light of Evolution,” evolutionists have backed themselves into a corner from which they cannot escape. As we saw, there is much to say about this evolutionary rallying cry, but at the top of the list is that it is false. Unequivocally false. This is not an opinion or a pushback. I’m not trying to pick a debate—because there is no debate. We may as well debate whether bachelors are male. Dobzhansky’s phrase, with all due respect, is “not even wrong,” as physicists like to say. It is silly, and yet there it is—all over the literature. The phrase is approvingly recited even in peer-reviewed technical journal papers. It is the mantra that evolutionists will not stop repeating, all the while revealing that this isn’t about science. Evolutionists will never repeal and recant, because there simply is too much at stake here. As we discussed, this isn’t like admitting that a particular prediction went wrong. Dobzhansky’s phrase was not merely a prediction, it was meta-prediction—the aphorism of an entire world view—and walking it back would be to reveal the man behind the curtain. Suddenly all those epistemological claims, such as that evolution is as much a fact as is gravity, heliocentrism and the round shape of the earth, would be left hanging, open to scrutiny and with a long, long way to fall. But Dobzhansky’s famous phrase is not the only way evolutionists have self-destructed. They have made other nonnegotiable and important claims that are equally corrosive. One is that evolution is both confirmed and required.

The National Association of Biology Teachers’ official position statement on the teaching of evolution states that evolution is (i) confirmed by the scientific evidence and (ii) a necessary going in position in order for science to function properly. Here is what the NABT says about the confirmation of evolution:
                               Scientists who have carefully evaluated the evidence overwhelmingly support the conclusion that both the principle of evolution itself and its mechanisms best explain what has caused the variety of organisms alive now and in the past. … The patterns of similarity and diversity in extant and fossil organisms, combined with evidence and explanations provided by molecular biology, developmental biology, systematics, and geology provide extensive examples of and powerful support for evolution.
                 And here is what the NABT says about the necessity of evolution:
                    Evolutionary biology rests on the same scientific methodologies the rest of science uses, appealing only to natural events and processes to describe and explain phenomena in the natural world. Science teachers must reject calls to account for the diversity of life or describe the mechanisms of evolution by invoking non-naturalistic or supernatural notions … Ideas such as these are outside the scope of science and should not be presented as part of the science curriculum. These notions do not adhere to the shared scientific standards of evidence gathering and interpretation.
                      There you have it, evolutionary theory is both confirmed and required. And the National Association of Biology Teachers is by no means alone here. The dual epistemological and philosophical claims, respectively, are broadly held by evolutionists and go back centuries.

Do you see the problem?
This philosophical position that evolutionists have staked themselves to is circular. To understand this, imagine for a moment that you witness a miracle, involving “non-naturalistic or supernatural” causes. According to evolutionists, such an event is “outside the scope of science.”

Does that imply the event was necessarily not real?

No, the fact that something falls outside of one’s definition of science does not rule it out of existence. The event does not automatically become necessarily impossible. Something can be not amenable to scientific investigation yet real.

The standard claim of evolutionists that evolution is necessary for proper science reflects a particular philosophy of science called naturalism. They present it as though it were a fact, but that is false. There are many philosophies of science, and none are facts. They are rules of the road for those who declare them to follow.

That’s it.So evolutionists have committed themselves to yet another false statement. But that’s not the main problem. The main problem is that if one insists and is committed to naturalism, then naturalistic, evolutionary, explanations is what they will find.

So of course evolution is confirmed by the science. It has to be. For evolutionists, the question is not whether evolution is confirmed by the science, the only question is what are the particulars.

This explains why evolutionists interpret the evidence the way they do. It explains how contradictory evidence can be sustained over and over and over. It also explains why, so long as you stick to naturalism, anything and everything is allowed. Natural selection, gradualism, mutations, common descent, drift, saltationism, and all the rest are up for grabs. They all may be forfeited. Any kind of theory, not matter how at odds with the empirical data, can be contemplated.

What cannot be contemplated in evolutionary science is creationism. There must be no miracles.

This means that evidence will be interpreted, filtered, analyzed, and processed according to the rules. Non cooperative evidence will be set aside and viewed as “grounds for further research.” Or it will be ground up and recast until it can be made to work right.

Cooperative evidence, on the other hand, will be viewed a normative, and ready for incorporation into proper scientific theories.

When evolutionists insist that science must be strictly naturalistic they show their hand. The flip side of their claim, that evolution is confirmed, is not a theory-neutral, objective finding. It is driven by the philosophy. It is circular—the conclusion was assumed in the first place. If your going-in position is that naturalism is required, then your results will adhere to naturalism.
Evolution is not a scientific finding, it is a philosophical mandate.

A clash of titans (again)

 <iframe width="932" height="583" src="https://www.youtube.com/embed/hsAeXyRidag" title="Magnus Against Youngest Grandmaster Ever" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>

Commonsense resurgent? II

 Medical Malpractice Lawsuits to the Rescue


I believe that one day the transgender moral panic will come crashing down. But not before thousands of minors are harmed by having their natural puberties blocked, breasts removed, and even worse. Indeed, “de-transitioners” — people who realize they really are the sex they were born — are already appearing and complaining about how they were abandoned or pressured by medical professionals to engage in medical or surgical “affirming care” as it is incorrectly called. Some, like Chloe Cole, are planning to sue.

The problem is that many medical-malpractice statutes of limitations are relatively short — two or three years. By the time the adult so treated as a child realizes the harm done, the allowable time to sue may have elapsed.

An Example from Arkansas

Several state legislatures are considering bills to remedy that problem by lengthening their statute of limitations for such lawsuits when the procedures were done on minors. Here’s the one from Arkansas that lengthens the statute of limitations to “15 years after the date on which the minor turned 18.” I have read it, and it seems well considered. First, the definitions:
          “Gender transition procedure” means any medical or surgical service, including without limitation physician’s services, inpatient and outpatient hospital services, or prescribed drugs related to gender transition that seeks to: (i) Alter or remove physical or anatomical characteristics or features that are typical for the individual’s biological sex; or ii) Instill or create physiological or anatomical characteristics that resemble a sex different from the individual’s biological sex, including without limitation medical services that provide puberty-blocking drugs, cross-sex hormones, or other mechanisms to promote the development of feminizing or masculinizing features in the opposite biological sex, or genital or nongenital gender reassignment surgery performed for the purpose of assisting an individual with a gender transition.
                       That’s good specificity and it doesn’t include non-body altering interventions like pronoun use.

The bill also properly excludes interventions such as treating someone born with “ambiguous” external sex characteristics and treatment of side effects caused by gender-transition surgeries.

And it offers safe harbor if the child was followed for two years before medical interventions and
              At least two (2) healthcare professionals, including at least one (1) mental health professional, certified in writing that the minor suffered from no other mental health concerns, including without limitation depression, eating disorders, autism, attention deficit hyperactivity disorder, intellectual disability, or psychotic disorders.
                    This is most wise because we have seen autistic children and others with mental-health issues hustled onto the trans train.
           
Supplying Information

The bill also specifies the information that must be supplied to the child and parents to qualify as informed consent. For example:
                     The use of cross-sex hormones in males is associated with numerous health risks, such as thromboembolic disease, including without limitation blood clots; cholelithiasis, including gallstones; coronary artery disease, including without limitation heart attacks; macroprolactinoma, which:
1 is a tumor of the pituitary gland; cerebrovascular disease, including without
2 limitation strokes; hypertriglyceridemia, which is an elevated level of
3 triglycerides in the blood; breast cancer; and irreversible infertility.
             The bill also protects medical conscience:
                State law shall not require, or be construed to require, a healthcare professional to perform a gender transition procedure.
                    Clearly, the point of this bill is designed to chill the eagerness and speed at which some youth with gender dysphoria are medically transitioned and better ensure that legal remedies will be available for those harmed thereby. Chloe Cole, for example, says she was put onto the tran assembly line at 12, given puberty blockers after her parents where threatened by doctors that she would commit suicide, and had a double mastectomy at age 15.

The gender ideologues will howl. Some will create transgender sanctuary states — as California has Already done. But if many states pass responsible legislation like this, countless children will be protected from irreversible harm.

Thursday, 2 March 2023

Navigators of the ant kingdom v. Darwin.

Ant Navigation Fascinates Engineers


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


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.

Wednesday, 1 March 2023

Just another blind alley in Darwinism labrynth?

A Remarkably Candid Statement About an Unsolved Evolutionary Puzzle


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?

 <iframe width="932" height="524" src="https://www.youtube.com/embed/x0O6CSMcbPE" title="Ron DeSantis&#39; War on Wokeness with Kmele Foster, Chloé Valdary and David Bernstein" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>

If not JEHOVAH'S thumb print whose?

 The Other Intelligent Designer(s)?


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


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.

<iframe width="932" height="524" src="https://www.youtube.com/embed/IAXY8cX9_ss" title="Why is There Absolute Zero Temperature? Why is There a Limit?" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe> 

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

<iframe width="532" height="324" src="https://www.youtube.com/embed/un9DGdlK-7k" title="Some of the World&#39;s Most Interesting Ancient Organisms" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe> 

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


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


“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.