Wednesday, 22 March 2023

Yet more evidence of technology all the way down.

A Biochemical Icon of Intelligent Design, ATP Synthase Does More than Spin

The biochemical icon of rotary machines, ATP synthase, remains in the news with new discoveries. Now that cryo-electron microscopy is widely used, biophysicists are looking at the function of individual subunits of the engine and figuring out what they do. The fact that molecular machines exhibit more functional elegance the closer one looks indicates that intelligent design is the best explanation.

Automatic Brake

Animals and plants both contain these vital rotary engines that supply their energy needs in ATP. In animals, they are found in mitochondria. In plants and other photosynthetic organisms, they are found in chloroplasts. Photosynthesis, being dependent on light, has a problem: when it’s dark, their rotary engines might start running in reverse, risking “a wasteful ATP hydrolysis reaction.”

Working with the green alga Chlamydomonas reinhardtii (pictured above) as a “model organism,” a team of eight Japanese scientists took a closer look at the γ subunit in chloroplast ATP synthase (this is the “camshaft” part of the engine that drives the synthesis of ATP in the F1 domain). They found that two specific domains in the γ subunit act as an automatic brake in the dark. They wrote in PNAS in January,

Among the FoF1-ATP synthase complexes of all organisms, chloroplast FoF1 (CFoCF1) is a unique enzyme with a redox regulation mechanism; however, the underlying mechanism of redox regulation of the adenosine triphosphate (ATP) synthesis reaction in CFoCF1 has not been fully elucidated. By taking advantage of the powerful genetics of Chlamydomonas reinhardtii as a model organism for photosynthesis, we conducted a comprehensive biochemical analysis of the CFoCF1 molecule. Here we identify structural determinants for the kinetics of the intracellular redox response and demonstrate that the redox regulation of ATP synthesis is accomplished by the cooperative interaction of two γ subunit domains of CFoCF1 that are unique to photosynthetic organisms.

Figure 6 in the article (reproduced by Phys.org) shows how the two domains act like a

stopper:

The tight conformation weakens the interaction between the redox loop and the β-hairpin. Consequently, the β-hairpin remains stuck in the cavity between the α and β subunit, like a stopper, and inhibits the rotation of the central stalk (γεc-ring). In a reduced form, the redox loop recovers flexibility to interact with the β-hairpin. The redox loop interacts to pull out the β-hairpin from the cavity and thus accelerates the central stalk, like a cooperative regulator.

Watching the Snap

Another Japanese team, this one from the University of Tokyo, looked closer at the “catalytic dwell” in the F1 domain of the ATP synthase engine where ADP is converted to ATP with the addition of a phosphate. The F1 domain has 3 pairs of α, β subunits arranged like petals of a flower, each pair in a different phase of activity: insertion of ingredients, catalysis, and ejection of ATP. The γ subunit, like a camshaft, activates each α, β pair in turn as it rotates a full 360°. Dividing by three, each α, β pair feels the force of the camshaft during the catalysis stage (ADP + P yielding ATP) within 120° at each full turn of the crankshaft. At the other times, the pair is either receiving the ingredients or ejecting the finished ATP. When running in reverse, the F1 motor becomes an ATP cleaver, hydrolyzing ATP to yield ADP and P, ejecting protons in the process. In hydrolysis, then, ATP becomes the fuel to make the motor run in reverse.

During normal operation, the motor catalyzes ATP. Biophysicists have long suspected that the camshaft (the γ subunit) exerts pressure on the incoming ADP and P to snap them together. If 0° represents the moment ATP is catalyzed, previous studies have found a short pause stage at 80° and a longer dwell at the subsequent 40° of rotation, representing the “chemomechanical coupling scheme,” as their Paper calls it.

In the reverse reaction, though, the angle for cleavage of ATP was unclarified. The team made a hybrid ATP synthase that ran extremely slowly so that they could observe “the world’s

smallest rotary biological molecule motor” running in reverse. Their hybrid allowed them to measure the angle at which ATP cleavage occurs.

As a result, the new hybrid F1 showed two pausing angles that are separated by 200°. They are attributable to two slowed reaction steps in the mutated β, thus providing the direct evidence that ATP cleavage occurs at 200° rather than 80° subsequent to ATP binding at 0°. This scenario resolves the long-standing unclarified issue in the chemomechanical coupling scheme and gives insights into the mechanism of driving unidirectional rotation.

See the “Graphical Abstract” in the paper that illustrates this “extremely long dwell” they measured. The finding reveals that in both directions, ATP synthase is finely tuned for its work. The reverse direction (hydrolysis) is not just like a motor leaking fuel. Its parts act with precision to cleave ATP in a specific way.

Insights into a Related Rotary Motor

There’s a cousin to ATP synthase. It’s a proton pump called V-ATPase (vacuolar-type adenosine triphosphatase), and its catalytic parts are labeled V1Vo instead of F1Fo. Like its counterpart, V-ATPase runs with a rotary action but spends ATP to pump protons into organelles. Its job is to acidify vacuoles and other organelles or intracellular compartments that need a lower pH to work. The Vo part pumps the protons (H+ ions) into the vacuole, increasing its acidity. A little thought shows that such a motor could be dangerous. Would you want an acid-generating motor running loose?

Scientists from a Toronto hospital, publishing in PNAS, were curious to figure out how these acid pumps get built without causing harm to the cell. The Vo complex is assembled in the endoplasmic reticulum (ER) and then transported to the Golgi apparatus to be combined with V1. What quality control mechanism keeps the domains inactivated until they are fully assembled and ready for action?

Using cryo-electron microscopy, the team imaged three proteins (Vma12p, Vma22p, and Vma21p) that must work together to achieve the quality control for safely handling the acid pumps during assembly. “The resulting structures,” they found, “show how a sequence of coordinated interactions and conformational changes ensures that only properly assembled Vo leaves the ER and proton pumping into the neutral ER is avoided.” Spilling acid into the ER could be bad! “Unsurprisingly,” they remark, “owing to their importance for Vo assembly, mutations in the human homologues of Vma12p, Vma22p, and Vma21p have been linked to disease.” So how do these three essential proteins perform quality control? Do you really want to know?

The structures described above suggest the sequence of events that occur during Vo assembly in the ER membrane and subsequent binding of V1 in the Golgi…. The c ring assembles around Voa1p, with binding of subunit d to the c8c′c″Voa1p ring masking the ER-retrieval motif of Voa1p. The Vo∆aef:Vma12-22p structure indicates that the Vma12-22p complex binds this fully assembled ring prior to interaction with subunits a, e, and f (Fig. 4A). Vma12-22p helps recruit and secure the interaction of subunit a with the c ring through interaction of Vma12p with subunits a and d….

Their Final Sentence

OK, OK. Suffice it to say that a complicated set of interactions takes place to ensure V-ATPase assembly is safe! Biochemists may wish to labor through the details. Fortunately, the authors provided diagrams and animations to illustrate the dynamics of all these working parts. Note their final sentence: “Importantly, the structures illustrate how Vma21p and Vma12-22p play central roles in both V-ATPase assembly and quality control.”

Quality control: it’s an engineering concept that permeates all three of these studies. Without quality control, these nanoscopic rotary engines, on which all life depends, would never last — indeed, would never emerge in the first place. Quality control belongs in the working vocabulary of intelligent design and engineering. It is not found in Darwin’s dictionary.

Junk DNA trope continues to be exposed as Junk science?

More Jobs for “Junk” DNA (Cont.)

Paul Nelson

If “junk” DNA goes toxic, does that suggest it had an original normal function? See the conclusion of this new paper, “Native functions of short tandem repeats”

Historically, repetitive elements within human genomes have been viewed as mostly unregulated ‘junk DNA’ that is not under selective evolutionary pressure. As such expansions of these repetitive elements are unfortunate accidents which become apparent and important only when they elicit highly penetrant and syndromic human diseases. Consistent with this line of reasoning, the field of REDs [Repetitive Element Diseases] has largely focused on emergent toxic mechanisms as drivers of disease only in the setting of large STR [Short Tandem Repeats] expansions rather than considering their pathology as alterations in the native functions played by these repeats in their normal genomic contexts. Here, we propose re-framing the discussion around repetitive elements in general — and STRs in particular — within human genomes. For each STR, we suggest first considering whether the STRs associated with a human disease have any native functions at their ‘normal’ size. If a native function exists, then expansion of these STRs can be viewed primarily as an aberrancy of that native function with coincident predictable impacts on gene expression dysregulation above certain repeat lengths. This reframing aligns with the approach typically taken in studying gain-of-function and loss-of-function mutations in disease associated single amino acid mutations and better ties the native functions of STRs to their pathology. It also suggests that shared regulatory rules will likely apply across REDs.

The article by Shannon E. Wright and Peter K. Todd is open access at eLife. Of course, lots of so-called “junk” has turned out to be functional. For another recent example, see Here

The real ocean master?

When man leapt to the moon.

The central nervous system of the warmachine?

The boogaloo begins?

Indoctrination makes science boring?

Gilson: How a Teacher Wrecked Biology for Me, and How I Got Past It

Evolution news

On a new episode of ID the Future, Tom Gilson, a writer and editor for The Stream, shares his experiences in high school biology. Important mysteries (i.e., major problems) with evolutionary theory were hurried past and papered over, yet his biology teacher could take an entire class period to tell Charles Darwin’s life story, and then repeat the same class, virtually verbatim, five more times that same semester. Hear how the class put Tom Gilson off of biology, but how he now finds the subject fascinating, thanks to the work of intelligent design researchers and the larger community of life scientists. Download the podcast or listen to it Here.

Gilson’s commentary is taken from, and builds on, a recent essay of his, available at Evolution News.

Operating in the shadows.

ID is perfectly natural?

Let’s Help Harvard Understand Intelligent Design

Jonathan McLatchie

Last week, my wife and I spent an afternoon at the Harvard Museum of Natural History, in Cambridge, MA, near where we live. We both were generally impressed by the exhibitions, particularly the dinosaur section, and would recommend the museum to anyone visiting Boston. I was, however, quite disappointed to see this notice at the entrance to the display on evolution:

It was disappointing to see the inaccurate representation of intelligent design (ID), along with the poor scientific epistemology.

A “Super-Natural Explanation”?

First, proponents of ID have long stressed that ID, in its purest sense, does not necessarily postulate a supernatural cause but is consistent with a natural or supernatural intelligence. Furthermore, I would contend that the natural / supernatural distinction is problematic. What precisely is meant when a phenomenon is described as supernatural, and by what set of criteria is it distinguished from the natural? Often, the word “supernatural” is used to describe the capacity to perform miracles, defined as violations of natural law. I would, however, offer a more nuanced definition of a miracle, which is that a miracle describes an interruption in the way nature normally behaves when left to itself. A miracle does not violate natural law, because natural law only describes what happens when nature is left to itself – not what happens when there is an intervention by an external agent. I am not by any means the first to define a miracle in these terms. Indeed, the atheist philosopher John Mackie in his classic book, The Miracle of Theism, defines a miracle along similar lines.1 As agents ourselves, we have the capability of interrupting the normal course of nature, determined by natural law. When I consciously choose to catch a ball with my hands, I am interrupting the trajectory it would have otherwise taken if left to itself. Agency itself is not governed by natural law, nor can it be reduced to material constituents. Human free will — my belief in which I take to be strongly justified by direct acquaintance — is, in my view, utterly incompatible with a materialistic reductionist perspective on the mind. Since, in my judgment, the strong burden of proof required to demonstrate that the strong appearance of free agency is merely illusory has not been met, this provides a strong prima facie justification for believing the mind to not be reducible to material components. Few would want to use the term “supernatural” to describe the human mind. A more helpful distinction, then, is between material and non-material causes. But non-material causes — assuming my judgment about the non-reducibility of agency to be correct — are already demonstrably a part of the natural world, since all of us have minds. Thus, the fact that ID postulates a non-material entity cannot be used to exclude ID from the natural sciences. Moreover, if our epistemology arbitrarily excludes one possible answer to an inquiry a priori, there is a real danger of being led to an incorrect conclusion about the natural world.

“Observation”

Second, the invocation of an unobservable entity should not be a demarcating factor that renders ID unscientific, for that would exclude other scientific disciplines, such as particle and nuclear physics, as well. Unobservable entities can often be detected by their effects, even without direct observation. For example, black holes are not directly observable since they do not emit electromagnetic radiation that can be detected with telescopes. Their existence and presence, however, is inferred by the effects that they exert on nearby matter, since gas flowing around a black hole increases in temperature and emits radiation that can be detected (their gravitational effects on surrounding objects, such as nearby stars, and the bending of light passing by a black hole, can also reveal the presence of a black hole).

“Testing”

Third, ID is testable in the same way that other hypotheses purporting to explain events in the distant past (including evolution by natural selection) are tested — by the historical abductive method of inference to the best explanation.2 Given that functionally specific information content is, in every other realm of experience, habitually associated with conscious activity and no other category of explanation has been demonstrated to be causally sufficient to account for its origin, ID is the most causally adequate explanation of the relevant data.

“Predictions”

Fourth, a scientific theory can be well justified even if it does not make strong predictions; it just needs to render the evidence significantly more probable than it would have otherwise been. For example, the hypothesis that you were in the vicinity of a nuclear plant does not strongly predict that you will have radioactive poisoning (few such workers suffer this). But if you did have radioactive poisoning, it would be significant evidence that you were in the vicinity of a nuclear plant since that data is more expected (or, less surprising) given the truth of the hypothesis than given its falsehood. Thus, even if ID only weakly predicts the observed data, it can still be strongly justified if the data is extremely unlikely if ID is false. ID, I would argue, also has a reasonably high intrinsic plausibility (what probability theorists call prior probability) given the independent evidence of there being a mind behind the universe who has an interest in creating complex life (that is, the evidence of cosmic fine tuning3 and prior environmental fitness4). It shouldn’t be too surprising, then, if the data also indicate that life was purposely brought about.

An “Inherent Conflict”?

Fifth, ID is not postulated because there is a perceived incompatibility between evolution and religion, but rather because we understand it to be the best interpretation of the scientific evidence. That being said, the “many scientists and religious leaders” who “do not perceive an inherent conflict between religion and the scientific theory of evolution” are correct that God and naturalistic evolution are logically compatible. However, naturalistic evolution, if true, would constitute significant evidence against theism and by extension religion. Why? First, if the conclusion that teleology best explains biological phenomena is evidence for theism, it necessarily follows that the falsehood of this conclusion would be evidence against theism. Second, atheism, and in particular naturalism (which, I would contend, is the most consistent version of atheism), strongly predicts that there be a naturalistic evolutionary account of life’s origins and development on earth. However, this is significantly less well predicted by theism. Therefore, though not by itself sufficient grounds on which to reject theism, unguided evolution — being more surprising given theism than given atheism — would, if true, constitute significant evidence against theism.It is unfortunate that the administrators of the Harvard Museum of Natural History seem to have failed to do their due diligence to understand the claims of ID, and how its advocates propose to test it, before dismissing it as being outside of the scope of science.

On the roots of the interslavic conflict?

The new Roman empire.

Tuesday, 21 March 2023

Privacy is dead and soon to be buried?

Yet more on how we know that the technology is real.

Engineering Language Enters Biology — The Case of the Endosome

David Coppedge

Design advocates can welcome research that mentions engineering and ignores Darwinism. Biological research papers have for some time now used the word “orchestrated” to describe complex processes in the cell. Another word, though similar, conveys more clarity about the design implications: “engineered.” That word appeared recently in the journal Science under the title, “The Endosome as Engineer.” It was written by Maria Clara Zanellati and Sarah Cohen, cell biologists at the University of North Carolina.

The take-home lesson could be stated: If parts of a cell can re-engineer other parts for function, without which action the cell would die, and if the process involves signal communication between multiple other parts, what does that imply about the origin of the system? Can undirected mindless processes create engineers? Or does an automated engineering system presuppose a designer with foresight and a mind that understands how to make things work?

Zanellati and Cohen begin,

There has been increasing interest in organelle communication at membrane contact sites — where two organelles are anchored in close apposition by “tether” proteins. These contact sites allow the exchange of materials and information between cellular compartments. Intriguingly, organelles can also influence one another’s abundance and morphology. Most studies have focused on the role of the endoplasmic reticulum (ER) in shaping other organelles. However, on page 1188 of this issue, Jang et al. show that the endosome can reengineer ER shape in response to changing nutrient levels, which in turn affects the morphology and function of additional organelles.

The paper by Jang et al., Written by 11 scientists primarily from the Leibniz Institute in Berlin, investigated complex responses to nutrient starvation in muscle cells. The names of molecular players in this multi-part automatic response may be unfamiliar except for three key players explained below, but the upshot of the process is described as follows:

A cell can sense when it is getting starved for nutrients. When this happens, the powerhouses of the cell (the mitochondria) should not be allowed to carry on as if everything is fine, lest the cell go into self-destruction mode (autophagy). Distinct proteins fly into action, rewiring connections and preserving the powerhouses until conditions improve. One way they do this is by changing the shape of the ER from a tubular form to a sheet form.

Key Players in the Response

Here are the key players in this engineered response:

Mitochondria: The cell’s powerhouses, essential eukaryotic organelles where energy is produced via ATP synthase rotary engines. In “fed” conditions, mitochondria routinely undergo fusion and fission dynamically. The tubular ER membrane promotes genesis of lipid droplets that serve as a backup energy source for the mitochondria. In starvation conditions, “mitochondria fuse into tubular networks. This protects mitochondria from degradation by mitophagy and enables a metabolic shift to fatty acid oxidation.”

Endoplasmic Reticulum (ER): The cell’s central manufacturing and distribution center for proteins and lipids. As “the largest source of membrane in the cell and a major site of protein and lipid synthesis, the ER can act as a central node to convey environmental cues and exert effects on the growth and division of other organelles.” In starvation conditions, the ER changes shape. “The resulting loss of peripheral ER tubules induces mitochondrial network formation and the delivery of fatty acids to mitochondria to sustain cellular energy supply.”

Endosome: a package of nutrients sent from outside the cell to the ER. Endosomes in muscle cells contain a nutrient sensor. This sensor recruits “tether” proteins that bind the endosome along the microtubules in the ER, promoting fission of the mitochondria and lipid droplet formation (learn about droplets and other membraneless organelles Here and Here).

Shape-Shifting Automatic Response

If the nutrient sensor detects starvation, it recruits proteins that disassemble the sensors within the endosomes. This breaks the “tethers” to the transport proteins. The ER tubules change shape into sheets encompassing the mitochondria, stopping their fission delivering fatty acids to them.

The authors note that a failure in this system leads to a muscular disease that can be fatal. This indicates irreducible complexity, because a failure in any of the proteins and organelles involved leads to cell death, muscle failure, and potentially death to the organism.

From Engineered Instance to Engineered Cell

This shape-shifting strategy of organelles, mediated by sensor proteins, may be one example of a whole category of cellular systems now being discovered. The key finding in this research on the starvation response in the ER is that one organelle can change the shape of another organelle, altering its activity. As shown in the passage quoted above, Zanellati and Cohen expect other cases will be found now that organelles are often observed to be in contact or tethered to one another via threadlike proteins that exchange materials and information.

Membrane contact sites mediate the exchange of lipids, ions, and proteins between organelles. The first hint that organelles can influence one another’s morphology came from movies showing ER tubules wrapped around mitochondria at sites where the mitochondria divided. Mitochondria undergo constant fusion and fission. Fission can be associated with mitochondrial biogenesis needed for cell proliferation, or it can be a mechanism to degrade damaged pieces of mitochondria. Although cytoplasmic proteins were known to affect mitochondrial fission, it was surprising to discover that the ER regulates this process.

Engineered morphological modification and communication between organelles could be a ubiquitous feature within cells. They conclude,

In addition to modulating mitochondrial fission, ER tubules regulate endosome fission. Thus, endosomal effects on ER morphology could feed back onto the morphology of endosomes themselves. The ER is a central hub of organelle communication. However, endosomal signaling lipids have been identified as an important mechanism for engineering ER shape, which relays nutrient information to distant mitochondria and lipid droplets.

Engineering Doesn’t Just Happen

Inanimate objects do not reengineer one another for function. Engineering, as one of the principal examples of mental activity in our culture, must be learned and taught by those who understand it. The regress of causality for engineering does not terminate downward to blind, unguided nature. In every case we know, it regresses upward to genius. Scientists doing pure research discovered the principles by which things work through laborious experimentation (exemplified by Faraday), and through mental prowess encapsulating them into theories (exemplified by the work of Maxwell), which were turned into practical applications (exemplified by Lord Kelvin, Marconi, and many others). From the giants of engineering, textbooks were written and taught to millions of students who continue to apply the design principles to projects that enrich our lives. The “phylogeny” of the tree of engineering traces back to a root of mind.

What, then, shall we think of microscopic systems in living cells that utilize engineering principles with finesse, which often keep an organism like Your Designed Body running for a century or more? Is it any surprise that none of the authors of the research described here made any reference to Darwin, evolution, ancestry, beneficial mutations, or natural selection? As Neil Thomas Wrote recently,

Natural selection reveals itself as not just a metaphor but a mixed one: Nature being dumb but nevertheless capable of discrimination. It is a poetic concept rather than a scientific one, appealing more to emotional and aesthetic sensibilities than to reason.

Some engineers may enjoy poetry as an avocation, but when at work must subjugate their aesthetic sensibilities to reasoning about realities. They must learn to apply scientific principles discovered by theoreticians and experimentalists to practical situations involving interacting parts. Life can serve as an example and a motivation, but in both life and engineering, function doesn’t emerge without intelligence.

The vice of Baal?

Monday, 20 March 2023

Dr. Doolittle's dream courtesy of AI?

The dominos are tumbling?

The honeybee learned to code?

The Role of Learning in the Honey Bee Waggle Dance

Eric Cassell

The honey bee “waggle dance” is well known as the method that the bees use to communicate to other members of a hive information about the location of food sources as well as potential nest locations. The information includes direction, distance, and food quality. Ethologists James and Carol Gould call the waggle dance, “the second most information-rich exchange in the animal world,” meaning second only to human language.1

A new study in Science Magazine has determined that in addition to the basic behavior being innate (programmed), there is also a learning element.2 As described in my book Animal Algorithms, “The duration of the dance conveys the distance of the source, where one waggle run (in the figure eight) signifies a standard distance, which varies between five and fifty yards, depending upon the species.”3 Studies have found that the determination of distance is based on optic flow, the progression of objects across the animal’s visual scene.4While the distance calibration varies with species, it does remain remarkably constant.

Interpreting the Distance

However, it is still unclear how bees that interpret the distance associated with the dance translate that to the behavior controlling travel distance. This new study concludes that the distance calibration, as well as the directional component, requires fine-tuning through learning. Both learning mechanisms occur when young bees observe older experienced bees (termed social learning) as they forage and perform the waggle dances. Experiments demonstrated that the accuracy of both direction and distance improved over time through this social learning method.

A Unique Feature

Social learning is common among many animal species. A good example occurs in songbirds, where young birds learn from adults to perform species-specific songs. In that case the basic melodies of the songs are innate, but performance improves as the birds hear adults. Bees have also been shown to be capable of learning other types of complex behaviors. One study demonstrated that they could learn by observing a demonstration of how to move balls in order to obtain a reward. One thing that was unique about this was that the behavior is not one bees naturally perform. The authors of the study concluded, “That bees solved this novel, complex goal-directed problem — and solved it via observation and using a better strategy than originally demonstrated — shows an unprecedented degree of behavioral flexibility in an insect.”5 Very impressive for animals that have brains containing only about one million neurons.

It must be noted that learning is also largely a programmed behavior, governed by a type of algorithm, particularly for animals with limited cognitive ability. The general mechanism for learning is based on the concept of feedback, where a desired output is compared to a current value, which is then adjusted based on the difference. In the case of the honey bee waggle dance young bees must observe an experienced bee’s flight and dance, encode this information in the brain, compare it to innate programming, and finally compute and adjust the calibration as necessary. Again, this is an algorithmic process, all of which is the product of design.

AI as a tool/weapon.

The mammalian jaw takes a bite out of Darwinism?

Evolutionists have a simple proposal for the evolution of the mammalian jaw.

Cornelius G Hunter

Somehow random mutations creating an incredibly complicated set of bones, muscles, teeth, and behaviors, with “extremely precise” functions, all of which “likely” arose independently rather through common descent, just doesn’t sound right. So as usual evolutionists view the problem teleologically. According to the latest Study of the mammalian jaw, it seems that “mammal teeth, jaw bones and muscles evolved to produce side-to-side motions of the jaw, or yaw, that allowed our earliest ancestors to grind food with their molars and eat a more diversified diet.”

To produce?

As usual, the infinitive form tells all. Aristotelianism was not rejected, it was incorporated.

But how could such interdependent complexity evolve in the first place? The jaw, dental, and ear characters comprise so many highly complex, moving parts that need each other to work. And furthermore, they appear in different lineages. The answer is simple: simultaneous, concurrent, convergent evolution.

Based on results of the morphometrics and functional analyses, I develop a novel hypothesis for the simultaneous origin of unique jaw, dental, and ear characters in cladotherians. […] Here, I examine concurrent evolutionary changes to functional anatomies of jaws, molars, and ears in early cladotherian mammals […] The jaws, molars and ears of australosphenidans (which include monotremes) are morphologically similar to those of therians, suggesting convergent evolution of similar functional traits in this group.

All of this, the study concludes, “may have been an especially significant event in mammalian evolution.” Indeed. But for a paper entitled, “The evolutionary origin of jaw yaw in mammals,” there is remarkably little explanation of just how this design evolved.

The bottom line is the evidence does not fit the theory. If the answer is simultaneous, concurrent, convergent evolution, then let’s just admit the obvious.

And even smaller world?

Et tu science?

Sunday, 19 March 2023

Game over for human exceptionalism?

Pushing Insect Welfare

Wesley J Smith

A few years ago, some wag created a Parody website called the Society for the Prevention of Cruelty to Insects. But here’s the thing: If a satirist can think it, some professor or media handwringer will actually propose or support it.

And So It Has Come to Pass

Matt Reynolds, the climate, food, and biodiversity reporter for Wired, urges us to worry that we are hurting insects. From “Insect Farming Is Booming: But Is It Cruel?“:

It’s a weird twist in our already strange relationship with bugs. We squash them, spray them, eat them, and crush them to make pretty dyes. But we also fret about plummeting wild insect populations and rely on them to pollinate the crops we eat. And with the industrialization of insect farming, bugs are being offered up as a solution to the human-caused climate crisis.

But before we go down that route, we need to ask some really basic questions about insects. Can they feel? And if so, what should we do about it?

Of course, we know that insects are not inanimate. A fly senses when you try to swat it. It is wrong to pull wings from a butterfly, regardless of what it feels, because it is gratuitously cruel with no human benefit. But do we really want to tie ourselves up in knots over whether — and how much — different insect species may experience discomfort when we make beneficial use of them?

I don’t. We have far more urgent issues with which to contend.

But Matt Reynolds Does

It’s about compassion, don’t you know:

For [Professor Lars] Chittka, the fact that scientists have found multiple indicators of sentience in certain insects is reason enough to argue that these animals can have unpleasant experiences. Chittka puts flies and bees in this category, but it’s not at all clear whether findings can be extrapolated to other species. The most commonly farmed insects include crickets, beetles, and flies, and we know a lot less about their lives than those of bees or ants, which are pretty well-studied in insect terms. Even fewer studies have been done on insects when they’re still larvae. This adds another problem because mealworms and black soldier fly larvae are usually killed before they are adults. Are insect larvae less capable of feeling pain than adults? We really don’t know.

Honestly, I don’t care whether larvae feel pain or the extent of a bee’s sensory experiences. What matters is the benefits our various uses of insects provide: the necessity of killing them in mass quantities to prevent human disease, protect animals, and preserve food.

But since we are now farming bugs, advocates are pushing for “insect welfare” standards:

If we’re going to farm animals that are candidates for sentience, then there should be welfare standards, says [philosophy processor Jonathan] Birch. Right now there are no widely recognized welfare guidelines for farmed insects, and few laws that specifically require insect farmers to meet certain welfare standards. . . .

“If there are welfare concerns, you’ve got to intervene at the planning stages, when those facilities are being designed and constructed,” says Bob Fischer, a professor at Texas State University who works on insect welfare. There are many factors that farm designers need to take into account, including temperature, moisture levels, lighting, how crowded the insects are, and what they eat. For insect farmers, these are all engineering problems — they want to make sure as many bugs survive as possible and that the farms are cheap to run — but they’re also intricately tied to animal welfare. . . .

In the EU, most animals must be stunned unconscious before they’re killed, but no such regulations exist for insects. Bugs can be microwaved, steamed, boiled, roasted, frozen, or minced to death. Better Origin’s larvae are fed alive to farmed chickens. We have no idea which method of slaughter is least painful for insects, beyond a general sense that a quick death is better than a protracted one.

Oh well. Whatever gets the job done.

I am tempted to say that the anti-suffering crowd has gone beyond reductio ad absurdum. But these days, there is no such thing as going too far. After all, six rivers now have enforceable rights. And rivers can’t feel a damn thing.

A clash of ultra-titans.

Charles Darwin champion abolitionist? III

Darwin and Agassiz: An Imaginary Picture

Robert Schedinger.

In a series of posts, I have been commenting on a book by Adrian Desmond and James Moore, Darwin’s Sacred Cause: Race, Slavery, and the Quest for Human Origins. This is Part III of the series. Look here for Part I and Part II.

Given the close relationship Louis Agassiz shared with pro-slavery factions in the South, Desmond and Moore focus much on Darwin’s relationship with Agassiz. Surely Darwin, if he was motivated as much by abolitionist impulses as Desmond and Moore believe he was, would greatly disapprove of Agassiz. Here I will consider several places where Desmond and Moore create an imaginary picture of this relationship.

Simply an Observation

To start, Desmond and Moore quote a complaint they say Darwin made to Lyell about Agassiz:

Agassiz’s Lectures in the U. S.’ uphold ‘the doctrine of several species, — much, I daresay, to the comfort of the slave-holding Southerns’ (242).

An endnote refers to three letters from volume 4 of the correspondence, the first being a September 4, 1850, letter to his cousin Fox where Darwin writes:

I wonder whether the queries addressed to about (sic) the specific distinctions of the races of man are a reflection from Agassiz’s Lectures in the U. S. in which he has been maintaining the doctrine of several species, — much I daresay, to the comfort of the slave-holding Southerns.

The “complaint” Desmond and Moore say Darwin made to Lyell about Agassiz is really just an off-hand comment he made to Fox. And there is no sense that Darwin is complaining in this letter to Fox. He is simply making an observation.

But things get worse. Desmond and Moore continue:

From the slave port of Charleston, Agassiz also collected barnacles for Darwin. Along with them also went his latest book, Lake Superior (‘is not that an immense Honour!’, Darwin asked Lyell with a hint of sarcasm).

On June 8, 1850, Darwin did write in a P. S. to Lyell, “Agassiz has sent me his Lake Superior Book, — is not that an immense Honour!” But there is no hint of sarcasm here. This is confirmed by Darwin’s June 15 letter to Agassiz:

I have seldom been more deeply gratified, than by receiving your most kind present of “Lake Superior”: I had heard of it, and had much wished to read it, but I confess that it was the very great honour of having in my possession a work with your autograph, as a presentation copy, that has given me such lively & sincere pleasure.

A Scathing Attitude?

Next, Desmond and Moore claim to document a scathing attitude they say Darwin harbored toward Agassiz by citing from a March 26, 1854, letter Darwin wrote to Joseph Dalton Hooker. Desmond and Moore quote Darwin to the effect:

How very singular it is’, he blurted out to Hooker, ‘that so eminently clever a man’ (referring to Agassiz) should write such ‘stuff & bosh as he does’ (246).

Note how Desmond and Moore chop up the directly quoted material into three parts. What did they leave out? Here is the full quote as it appears in the letter to Hooker:

How very singular it is that so eminently clever a man, with such immense knowledge on many branches of Natural History, should write such wonderful stuff & bosh as he does.

Desmond and Moore conveniently leave out Darwin’s affirmation of Agassiz’s immense knowledge of natural history and the adjective wonderful before stuff. They also fail to provide the full context of the quote, for Darwin continues:

I seldom see a Zoological paper from N. America, without observing the impress of Agassiz’s doctrine’s — another proof, by the way, of how great a man he is.

Clearly, Darwin thought Agassiz’s work on the separate creation of the human races was “bosh” because it challenged his view of common descent. But he nevertheless had great respect for Agassiz’s contributions to geology and the study of glaciers. There is no hint of the sarcasm and disdain for Agassiz that Desmond and Moore try to conjure up from the primary sources.

No Evidence of Anger

As one final example, Desmond and Moore are drawn to Darwin’s reaction to a comment made by S. P. Woodward, a professor at the Royal Agricultural College, about Agassiz. Woodward had written to Darwin on July 15, 1856, with information requested by Darwin about geographical variation in shells. After a long list of technical taxonomic details, Woodward dropped into the end of the letter the following:

I presume you are acquainted with Dr. Pickering’s “Races of Man” — & with that chapter in which, when discussing the probable scene of the Creation of man, he speaks more respectfully of the Orang & Gorilla than Agassiz does of “our black brethren.” It is fortunate for those of us who respect our ancestors & repudiate even the contamination of Negro blood — that Agassiz remains, to do battle with the transmutationists.

Desmond and Moore quote the last sentence of this passage, leading them to comment, “This was intolerable to Darwin. He replied by return, saying he would not be begging ‘any further favours’” (273).

Desmond and Moore give the impression that Darwin cut off his correspondence with Woodward over the latter’s seeming approval of Agassiz’s racism. Yet Darwin’s July 18 return letter to Woodward tells a different story. Desmond and Moore fail to note that Darwin begins the letter to Woodward with:

Very many thanks for your kindness in writing to me at such length, and I am glad to say for your sake that I do not see that I shall have to beg any further favours.

Darwin then goes on to discuss some of the taxonomic details Woodward had sent him. Darwin’s not needing to “beg any further favours” from Woodward was simply because Woodward had provided him with the scientific information he requested. There is no evidence that Darwin was cutting Woodward off in anger over Woodward’s approval of Agassiz’s racism. Darwin always subordinated his disagreements over slavery to his scientific interests. Once again, Desmond and Moore have imputed to Darwin attitudes not to be found in the primary sources they cite.

And yet there is more.

A walk through the mind of a titan?

Saturday, 18 March 2023

Uncle Sam is broke?

The Mongolian empire: a brief history.

Sentinels asleep at their post?

Another clash of titans

A clash of titans(again)

Friday, 17 March 2023

Yet another question mark in the fossil chronicles.

Fossil Friday: The Abrupt Origin of Ichthyosaurs

Gunter Bechly

This Fossil Friday features Stenopterygius quadricissus from the Lower Jurassic Posidonia shale of Holzmaden in southern Germany, which is about 190 million years old. As a child I went collecting fossils from this fossil locality, which was close to my childhood home, and with a bit of luck you could not only find ammonites but even vertebrae of such ichthyosaurs. Apart from dinosaurs and pterosaurs, the ichthyosaurs are one of the iconic groups of Mesozoic reptiles. Even though they look like a hybrid between a dolphin and a shark, they were marine reptiles that are believed to have descended from monitor-lizard-like terrestrial ancestors.

Darwinism would predict a long and gradual transition between these very different body plans, but actually ichthyosaurs appeared very abruptly about 4 million years after the great end-Permian mass extinction event about 252 million years ago, which annihilated about 81 percent of marine and 70 percent of terrestrial biodiversity. There is general consensus that ichthyosaurs did not yet exist before this cataclysm, and the oldest fossils indeed only appeared in the Lower Triassic of China about 248 million years ago. Jiang et al. (2016) concluded that “ichthyosauriforms evolved rapidly within the first one million years of their evolution.” Well, that was the state of knowledge until a few days ago, when a brand new study (Kear et al. 2023) changed the picture and made the origin of ichthyosaurs even much more abrupt. A team of scientists from Norway and Sweden described ichthyosaur remains from the Arctic island of Spitsbergen, which are about 250 million years old but already show clear evidence for a fully marine way of life.

Revealing Admissions

The press release by Uppsala University (2023) makes some very revealing admissions about this unexpected discovery:

As the story goes, land-based reptiles with walking legs invaded shallow coastal environments to take advantage [of] marine predator niches that were left vacant by this cataclysmic event. Over time, these early amphibious reptiles became more efficient at swimming and eventually modified their limbs into flippers, developed a fish-like body shape, and started giving birth to live young; thus, severing their final tie with the land by not needing to come ashore to lay eggs.

The new fossils discovered on Spitsbergen are now revising this long accepted theory. …

Unexpectedly, these vertebrae occurred within rocks that were supposedly too old for ichthyosaurs. Also, rather than representing the textbook example of an amphibious ichthyosaur ancestor, the vertebrae are identical to those of geologically much younger larger-bodied ichthyosaurs, and even preserve internal bone microstructure showing adaptive hallmarks of fast growth, elevated metabolism and a fully oceanic lifestyle.

This means nothing less than that the transition from a land-living reptile to a fish-like marine reptile was completed in less than 2 million years, which corresponds to about half the average longevity of a larger vertebrate animal species. This is incredibly short in geological and biological terms and does not allow for the required genetic changes to have originated by an unguided process. This waiting time problem of neo-Darwinism is proven by population genetic calculations, which is the subject on an ongoing research project by Discovery Institute scientists.

Even the time span of 4 million years that was implied by the previously known fossil record of Early Triassic ichthyosaurs is shockingly short, so much so that a friend and colleague of mine, who is a renowned expert on ichthyosaurs and neither a theist nor an advocate of intelligent design, confidentially told me that he came to doubt the neo-Darwinian explanation for this very reason. He said: “That this transition happened by a Darwinian mechanism in such a short time is simply IMPOSSIBLE!” With this window of time now cut in half, the transition becomes even more incredible.

A Temporal Paradox

But there is another problem: The new discovery makes fully marine ichthyosaurs older than their alleged amphibious relatives such as Cartorhynchus (Motani et al. 2015, Jiang et al. 2016) and likely older than their unknown terrestrial relatives. This creates a temporal paradox of assumed descendants appearing before their assumed stem group. Thus, ichthyosaurs joined the numerous other examples of such paradoxes, such as early tetrapods or early birds. Not exactly a success story for Darwinism.

With increasing knowledge of the fossil record, the mainstream narrative is rendered more and more untenable and inconsistent with the empirical evidence. It’s time to move on and consider more adequate explanations like intelligent design theory.

Now the ICC pokes the bear?

Zombie apocalypse now?

Gulf war II revisited.

It's causal circularity all the way down?

Here’s That Paper on MicroRNAs in Brown Algae

Cornelius G Hunter

MicroRNAs are small RNA gene products, typically consisting of 20-24 nucleotides, which help to regulate protein synthesis, for example by pausing or halting the ribosome translation process. Like the small drill bit which is inserted into the much larger drill tool, the small microRNAs are attached to a much larger molecular machine that performs the regulation. The microRNA role is to help the molecular machine recognize the correct RNA target. In other words, instead of the cell having to construct a large quantity of different molecular machines to perform the regulatory role on a large quantity of RNA targets, the cell can construct a more generic type of molecular machine, and then simply attach the instructions—the microRNA—as needed. This design approach requires the existence of these two entities: the big molecular machine and its little instruction set. Remove either entity, and this particular regulatory process isn’t going to happen. That does not fit the evolutionary narrative. According to evolution you need a slow, gradual buildup of designs, not all-or-none scenarios. But not surprisingly biology is chocked full of the latter, and so with evolution we must say that the different parts just happened to arise, perhaps serving some other roles, and then just luckily they worked fantastically together to achieve a new function. MicroRNAs are yet another finding that must be force-fit into evolutionary theory. But this irreducible complexity is only the beginning of the problem. With microRNAs, it only gets worse.

A completely different problem that microRNAs pose for evolutionary “theory” is that microRNAs do not fit the common descent pattern. As a recent Paper admitted:

There is no evidence of conservation of miRNAs between the phylogenetic groups, indicating that miRNA systems evolved independently in each lineage

Evolved independently?

In other words, microRNAs do not fit the evolution model. The evidence contradicts the theory. Of course one can always make up an explanation. In this case, we say that the microRNAs “evolved independently.”

There you go, problem solved.

But let’s be honest—this is not indicated by the evidence. When the paper states that there is no evidence of conservation of miRNAs between the phylogenetic groups, thus “indicating” that miRNA systems evolved independently, it is simply misrepresenting the science.

There is precisely zero scientific evidence that microRNAs “evolved independently.”

Zero.

That is not my opinion. That is not conjecture. That is scientific fact.

Evolutionists talk a lot about scientific “fact.” They insist evolution is a scientific “fact.” But let’s just be honest. What is a scientific fact here is not evolution, but rather the exact opposite. The “fact” is the microRNAs show “no evidence of conservation.”

That fact does not “indicate” evolution, it contradicts evolution.

Let’s just be honest. For once.

The paper finds yet another example of this failure in the microRNAs in brown algae. The study investigated the microRNAs in the species, Saccharina japonica, and compared them to previously investigated microRNAs, including those in a different brown algae species. Their findings were, as usual, “surprising.” The microRNAs in the two brown algae species were different.

Completely different.

There was not a single pair of microRNAs, between the two species, that showed any sign of statistically significant sequence similarity.

Interestingly, the microRNAs in the two species did generally share some structural and genomic features. So the evolutionists had to conclude that the microRNAs in the two species evolved from a common ancestor, but then their respective sequences evolved like crazy, leaving zero trace of sequence similarity.

This. Makes. No. Sense.

Here how the paper spun the results:

Surprisingly, none of the S. japonica miRNAs share significant sequence similarity with the Ectocarpus sp. miRNAs. However, the miRNA repertoires of the two species share a number of structural and genomic features indicating that they were generated by similar evolutionary processes and therefore probably evolved within the context of a common, ancestral miRNA system. This lack of sequence similarity suggests that miRNAs evolve rapidly in the brown algae (the two species are separated by ∼95 Myr of evolution). The sets of predicted targets of miRNAs in the two species were also very different suggesting that the divergence of the miRNAs may have had significant consequences for miRNA function.

“Probably evolved within the context of a common, ancestral miRNA system”? So what does “within the context” mean?

The answer is this is a meaningless cover phrase that masks the fact that the evidence contradicts the theory. It is evo-speak for “We don’t know what we’re talking about.” A more polite description is “hand-waving.”

A less polite, and more accurate description won’t be repeated here.

I will now consider the elephant in the room: Why is evolution being used to interpret the results in the first place? The theory is superfluous. It is redundant. It is vacuous. It is non-parsimonious. It is meaningless.

The theory does nothing to help us understand, interpret, elucidate, guide, or formulate meaningful predictions. Its only justification is itself.

We use the theory of evolution to interpret the results because the theory is true. And how do we know it is true? Because it is true?

The theory is self-referential. It is circular. It is famous for being famous.

It is a hold-over from the Epicureans of antiquity, the schoolmen of the Middle Ages, the rationalists of the seventeenth century, and the Darwinists today, and it has made a mockery of science.

Actual intelligence is non-computable?

On the impassible border between artificial intelligence and actual intelligence.

The Origin of Life v. Darwinism's Simple beginning.

Yet more on molecular biology and the edge of Darwinism

Our AI overlords to the rescue?

Prisoner of conscience?

Thursday, 16 March 2023

Another look at the thumb print of JEHOVAH.

Cosmic Fine-Tuning: A Look at the Implications

Evolution News

On a new episode of ID the Future host and geologist Casey Luskin continues his conversation with astrobiologist Guillermo Gonzalez about the many ways Earth’s place in the cosmos is fine-tuned for life. In this second half of their conversation, Gonzalez zooms out to discuss the galactic habitable zone and the cosmic habitable age. Luskin says that the combination of exquisite cosmic and local fine-tuning strongly suggests intelligent design, but he asks Gonzalez whether he thinks these telltale clues favor theism over deism? That is, does any of the evidence suggest a cosmic designer who is more than just the clockmaker God of the deists who, in the words of Stephen Dedalus, “remains within or behind or beyond or above his handiwork, invisible, refined out of existence, indifferent, paring his fingernails”? Gonzalez answers in the affirmative, but the reasons he offers for this conclusion may surprise you. Download the podcast or Listen to it here.

Charles Darwin :champion of abolitionism?

“Sacred Cause”? Reconsidering Charles Darwin as Abolitionist

Robert Schedinger

In 2009, noted Darwinian biographers Adrian Desmond and James Moore published Darwin’s Sacred Cause: Race, Slavery, and the Quest for Human Origins. They argued the radical new thesis that Darwin’s species work was primarily motivated by an abolitionist desire to combat racist polygenist views of human origins and instead draw all humans together under the umbrella of common descent. This book has been both widely praised and widely criticized.

But agree with the thesis or not, many view the book as a premier example of historiographical research. The book contains 820 endnotes citing hundreds of primary sources, not the least of which are many hundreds of references to Darwin’s voluminous correspondence. One can always disagree with Desmond and Moore’s interpretation of the evidence, but one would be hard pressed to criticize them for not doing their homework.

Or So I Thought

I have been reading the Darwinian correspondence myself for several years and have never seen anything in Darwin’s letters that would seem to support Desmond and Moore’s thesis about the motivating factor for Darwin’s species work. However, given how deeply their book is rooted in primary source documentation, surely I must have missed something in my own reading. Curious to figure out what, I decided to undertake a careful re-reading of Darwin’s Sacred Cause, paying special attention to places where Desmond and Moore register Darwin’s views on slavery and race. I then checked the references they cite to document this new portrait of Darwin.

Shockingly, it turns out that these highly esteemed scholars play fast and loose with their sources and with basic tenets of historiographical research.

Therefore, I offer a series of posts here designed to lay out the evidence in detail. It is not merely that Desmond and Moore are selective in the sources they cite, filtering out only those which support their thesis. Many historians are selective. What I found in their historiography rises, instead, to a different level.

A Sweeping Statement

For example, let’s consider Desmond and Moore’s sweeping statement regarding the impact on Darwin of his encounters with indigenous peoples during the Beagle voyage:

Interestingly it was in Tierra del Fuego, perplexed and troubled by an alien race, that Darwin decided to spend his life studying natural science (97).

It sounds like Darwin’s scientific work was primarily motivated by anthropological concerns. Let’s check the sources. An endnote points us to Darwin’s autobiography (p. 26) and volume 1 of his correspondence (pp. 305, and 311-12. Desmond and Moore cite the correspondence by volume and page number, never by date and addressee of the letter).

In his autobiography, Darwin does indeed write:

I remember when in Good Success Bay, in Tierra del Fuego, thinking, (and I believe that I wrote home to the effect) that I could not employ my life better than in adding a little to natural science.

Darwin does say he contemplated a career in science while in Tierra del Fuego, but he gives no indication that it was due to being “perplexed and troubled by an alien race,” as Desmond and Moore indicate.

Volume 1 of the correspondence, page 305, reflects a March 1833 letter of Darwin to his sister Caroline written during the Beagle voyage. He makes several references to his growing love for geology, and his ability to withstand the difficulties of the voyage because of his increasing pleasure from natural history, but nothing about alien races. Pages 311-12 reflect a May 1833 letter to another sister, Catherine, in which Darwin says, referring to the numerous invertebrate animals in the intertropical ocean, “If it was not for these & still more for geology — I would in short time make a bolt across the Atlantic to good old Shropshire.”

These references clearly demonstrate that Darwin’s interest in a career in science was stoked by his natural history pursuits during the voyage. The idea that he was motivated by being “perplexed and troubled by an alien race” has no support in the sources that Desmond and Moore cite, a point that undercuts their entire thesis that combatting slavery was his sacred cause.

An Emigration Daydream

As another brief example, consider their story about how Darwin bought his children a copy of Mary Howitt’s book Our Cousins in Ohio, which painted a portrait of “an English family living as neighbors to liberated blacks, their children playing in the lush countryside only miles from the Slave States’ border” (238). Desmond and Moore claim that in response to this book, Darwin also harbored an emigration daydream in which he

plumped for the ‘middle States’ as ‘what I fancy most’ — New York, Pennsylvania, maybe even Ohio; free soil situated between New England’s snobbery and Lyell’s beloved south.

An accompanying endnote refers to volume 4 of the correspondence (p. 362). There we find Darwin writing to his cousin William Darwin Fox in October 1850. In noting that his eighth child was on the way, Darwin made the offhand comment:

I often speculate how wise it would be to start off to Australia, or what I fancy most the middle States of N. America.

He then quickly changes the subject to a question Fox asked about his pear tree.

No Connection at All

Darwin’s brief speculation about possibly moving to America is not connected at all to the difference between slave or free states and he makes no mention of Howitt’s book. But more problematic is Desmond and Moore’s gloss, “New York, Pennsylvania, maybe even Ohio; free soil situated between New England’s snobbery and Lyell’s beloved south.” Darwin neither said nor implied this. Desmond and Moore, with brief phrases actually quoted from the letter, give the impression that they are paraphrasing Darwin’s words. In reality, Darwin was simply concerned about finding economic opportunities for his many children and thought Australia or America might provide them.

These are just two of many examples of Desmond and Moore creating a portrait of Darwin as abolitionist that is poorly supported by their intimidating apparatus of primary source citations which are mostly irrelevant to their argument. Readers have a right to trust that the sources cited support the claims made in the text. But most readers will not check obscure references buried in over 800 endnotes at the back of the book. They haven’t met me!

In future posts, we will see many more illustrations of Desmond and Moore’s historiographical methodology, and how that bears on Darwin’s “sacred cause.”

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