Friday, 24 March 2023

the science concludes that that JEHOVAH may know a thing or two about engineering after all.

Peer-Reviewed Paper Answers Claims of “Bad Design” of the Human Foot/Ankle

In a peer-reviewed paper published in BIO-Complexity, Bristol University engineering professor Stuart Burgess explains “Why the Ankle-Foot Complex Is a Masterpiece of Engineering and a Rebuttal of ‘Bad Design’ Arguments.” Brian Miller has

previously Covered Professor Burgess’s arguments in a lecture, but those are framed as a response to arguments from ID-critics such as Jeremy DeSilva and Nathan Lents. Those critics claim that the human foot-ankle complex is sub-optimal because it reflects an unguided process where evolution attempted to convert a skeletal structure adapted for quadrupedal

locomotion to bipedalism. Burgess argues in response that the ankle-foot complex “show a very high degree of complexity and fine-tuning” and “masterful engineering.” Moreover, “Engineering insight reveals a close relationship between form and function in the ankle, a relationship seen in its multiple bones and the layout of those bones” and the “five midfoot bones are needed to form the optimal kinematic and structural interface between the hindfoot and forefoot.”

Burgess observes that many who have studied the foot without a preconceived bias have recognized its “excellent design.” He quotes Leonardo da Vinci who called the human foot “a masterpiece of engineering and a work of art,” and more modern researchers who observe the “nearly effortless human gait” or who note that various foot structures “work in perfect synchronisation” because it is “superbly constructed for ambulation.”

A Contrast with “Bad Design

In contrast, “bad design” proponents believe that most of the seven anklebones are pointless, poorly coordinated, and fundamentally a bad design because a “fused structure” would work better than “a joint with so many separate parts.” Burgess answers arguments that the ankle-foot performs poorly for bipedalism because it was originally evolved for quadrupedal locomotion by observing that such arguments “are based on circular reasoning and assumptions about what evolution could or could not do in the past.” He believes that “A better scientific approach to assessing the quality of design is to study the actual biomechanics and functions of the foot.”

Burgess observes that “The requirements for agile bipedal movement are extremely demanding.” After all, the foot must be “a compact multifunctioning precision device” which has to fulfill multiple requirements which are sometimes contradictory:

Act as a strong and stiff lever to propel the body forwards in walking and running. Joint movement is plantarflexion.

2. Act as a flexible platform to absorb shocks and adapt to uneven ground. Joint movements include dorsi-flexion, pronation, and supination.

3. Provide 3-point contact with the ground to allow standing on one or two legs and to enable controlled push-off from the ball of the feet. The control must involve fine adjustment of direction as well as power.

Difficult and Contradictory Demands

Yet Burgess further notes that “The requirements of a stiff lever and flexible platform are difficult to achieve because they are contradictory. To achieve these two requirements the foot must have stiffness and flexibility in just the right places. In addition, the foot must have the ability to adjust stiffness through precise control of muscles.” The foot is able to accomplish this because it “has three interconnecting flexible arches that perform multiple functions in particular three-point contact with the ground, stiff lever for take-off and flexibility for shock absorption.” Burgess notes how well-designed these arches are:

There are several features that maintain the integrity of the arches: (i) foot arches segmented like a Roman arch, which induces compressive forces, particularly the bone that forms the keystone to the arch; (ii) short ligaments that tie adjacent bones together; (iii) longer ligaments (like the spring ligament) that tie the arch across multiple bones; (iv) muscle-tendon groups that act like a sling, pulling the arches upwards; and (v) muscles that stiffen the arch.

He further notes that the bones of the midfoot allow it to perform five main sub-functions, including providing a “flexible transverse arch,” “Load bearing structure during pronation,” “Kinematic interfaces for pronation-supination,” “Structural interface for longitudinal loads,” and “Stiffening of the medial arch.”

Burgess also finds that “Another specialised design feature in the ankle-foot complex is the elastic hinge joints,” as some 17 of such joints allow “significant flexibility” in the foot and also aid in shock absorption. In fact, Burgess reports that these elastic hinge joints have at least five sub-functions, including “(i) flexibility; (ii) load-bearing; (iii) energy storage; (iv) failsafe design; and (v) ultra-low friction.”

Bad-design proponents have asked why there are paired bones at the bottom of the leg above the ankle instead of a single bone. Burgess notes there are good reasons for this as fibula is “well known to provide stability to the ankle joint” via “a type of linkage system with multiple bars.” He cites two specific advantages to having a fibula bone:

One advantage of the fibula is that it increases the moment arm (mechanical advantage) of muscles acting on the ankle-foot complex. A second advantage is that the fibula increases the attachment area for muscles and therefore allows more muscle to act on the joint.

Answering Bad Design

After providing this review of the engineering functions of the ankle-foot complex, Burgess is able to address claims that many foot and angle bones are functionless. In reality, “this paper has shown that all the bones of the ankle-foot complex have very important roles in the specialized design features. In particular, the five bones of the midfoot have multiple functions.” He also definitively shows that the fibula bone is necessary because it “provides essential stability to the ankle joint during pronation by forming a multi-bar linkage mechanism.” Burgess shows that a fused ankle structure would not function better because “It is well known in the medical field that ankle fusions lead to a degradation of ankle performance” and relative movement of ankle bones affords various functions, including shock absorption.

A major anti-design argument is that ankles are prone to sprains or other injuries, but Burgess notes that this confuses misuse with bad design:

The importance of this differentiation can be illustrated by analogy with a modern car. Most modern cars are well designed and very reliable when in good condition and used properly. However, despite the high quality of design, a modern car will fail if overloaded or neglected, or if it is simply very old. Therefore, when considering malfunctions in joints it is important to check why there was a malfunction. If the ankle-foot complex malfunctions due to overload, neglect, or health issues, this does not mean the design can be judged as bad.

Burgess ends with four conclusions:

There are four highly specialised design features in the ankle-foot complex

2. The ankle-foot complex is superior to human-engineered joints

3. Lents’s bad design arguments are contrary to scientific evidence

4. Engineering insight explains form and function

This last point is crucial because it shows that the very design and structure of the ankle-foot complex must exist to for it to perform its functions. According to Burgess, the system exhibits “very sophisticated engineering design.”

Pre-human powered flight v. Darwin.

Fossil Friday: The Abrupt Origin of Winged Insects

Gunter Bechly

This Fossil Friday features Lithomantis varius, a large fossil insect from the Carboniferous (Namurian) brickwork quarry of Hagen-Vorhalle in Germany, which is one of the most ancient fossil localities for winged insects and dates to about 318 million years ago. Lithomantis belongs to the winged insect order Paleodictyoptera, which only existed in the Palaeozoic era.

Insect wings are extremely complex structures that are highly adapted to their function Delitzschalan as flight organs. They have a fan-like plicated structure to give the wing surface stability; additionally they are enforced by a complex wing venation; the wing is also supplied with sensory hairs; and the wing base has a highly complex arrangement of articulatory plates to allow for sophisticated movement, enabled by an associated muscular and neural system.

According to Darwinism, the evolution of such a system would certainly have required a plethora of intermediate stages that brought this wonderful locomotory apparatus into being by an accumulation of many small changes over a long period of time. Since paleontologists have discovered thousands of fossil insects from the Paleozoic, we have certainly also found at least some of these transitional forms in the evolution of insect wings!? At least one? Nope, not a single one.

The oldest fossil winged insects belong the orders Palaeodictoptera (e.g., Delitzschala) and to the giant dragonfly order Meganisoptera, thus they were already equipped with the complete wing apparatus. There is not a single transitional form, so that the leading textbook on insect evolution, by Grimaldi & Engel (2005: 160), admitted: “An insect equivalent of an Archaeopteryx remains elusive but certainly existed.” Apparently, the engineering marvel of insect wings came into being abruptly rather than gradually, which is inexplicable with unguided evolution but quite expected with intelligent design.

Common sense has fallen?

Common sense re:Common ancestry?

Peer-Reviewed Paper Shows Vertebrate Embryonic Variation Contradicts Common Ancestry

Casey Luskin

Evolutionary biologists often argue that vertebrate embryos develop in highly similar manners, reflecting their common ancestry. But a peer-reviewed paper in BIO-Complexity, by David Swift (author of Evolution Under the Microscope), provides an insightful review on the subject. The Article is titled, “The Diverse Early Embryonic Development of Vertebrates and Implications Regarding Their Ancestry.” Swift shows that, despite common claims, vertebrates do not develop similarly, according to the predictions of evolution.

He opens by framing his thesis:

It is well known that the embryonic development of vertebrates from different classes (e.g., fish, reptiles, mammals) pass through a “phylotypic stage” when they look similar, and this apparent homology is widely seen as evidence of their common ancestry. However, despite their morphological similarities, and contrary to evolutionary expectations, the phylotypic stages of different vertebrate classes arise in radically diverse ways. This diversity clearly counters the superficial appearance of homology of the phylotypic stage, and the plain inference is that vertebrates have not evolved from a common vertebrate ancestor. The diversity extends through all stages of early development — including cleavage and formation of the blastula, gastrulation, neurulation, and formation of the gut and extraembryonic membranes.

Now intelligent design does not require common ancestry to be false, but even a guided form of common ancestry might lead to different predictions from strictly unguided descent with modification. Thus, Darwin and subsequent evolutionists such as Ernst Haeckel found embryology to be a crucial line of evidence supporting Darwin’s thesis. According to Swift, common ancestry predicts that vertebrate development should exhibit striking homologies. But more than that, “If common ancestry is the explanation for homologies, not only should homologous organs be derived from equivalent embryonic tissues (the cardinal criterion for homology) but they should also develop by comparable processes.”

Very Different Pathways

The crux of Swift’s thesis is that although vertebrate embryos do pass through a similar “phylotypic stage,” the pathways of development are very different:

[D]espite their morphological similarities and contrary to evolutionary expectations, the striking fact is that the “phylotypic stages” of different groups of vertebrates arise in remarkably diverse ways, even with key tissues such as the germ layers (see below) deriving from completely different early embryonic sources. These observations clearly refute the presumed evolutionary homology of the vertebrate phylotypic stage, and hence undermine the inference of common ancestry based on that supposed homology.

He reprints the “hourglass model” of vertebrate development and points out that this is merely an “observation” about development — not an explanation of how it arose:

From: Irie N, Satoh N, Kuratani S (2018) The phylum Vertebrata: A case for zoological recognition. Zoological Lett. 4(32):1–20. doi:10.1186/s40851-018-0114-y, under Creative Commons License

One of the key stages of development that leads to this similar “phylotypic stage” is gastrulation, which Swift notes is crucial because it establishes the basic body plan and “leads to the establishment of the germ layers — ectoderm, mesoderm and endoderm — from which all of the body’s tissues are derived.”

Differences in Vertebrate Development

Swift cites various specific differences in vertebrate development to make his case, especially in gastrulation. He predicts that “from an evolutionary perspective we would surely expect gastrulation to be ‘conserved’” but finds that “for almost all of the major classes of vertebrates” there are key differences in gastrulation, including “the mechanism of gastrulation is significantly different from any of the others,” and “the source tissues of the germ layers are different.”

After reviewing mechanisms of gastrulation in various vertebrate classes, Swift notes that “the wide variety of structures of the blastulas of different classes of vertebrate challenges the view that the resultant embryonic tissues can be considered equivalent or homologous.” Specifically, in different types of vertebrates different parts of the blastula ultimately become the embryo itself. He describes these differences as follows:

Chondrichthyans (lancelets): “It is a one-cell thick epithelial layer, forming the upper surface of the blastula.”

Teleosts (bony fish, e.g., zebrafish): “It is a multiple-cell layer, beneath the overlying enveloping layer.”

Amphibians: “It is the whole of the blastula, comprising the multilayered dome of the upper hemisphere and the mass of cells in the lower hemisphere.”

Reptiles and birds: “It is the upper surface of the blastula, comprising a single-cell thick epithelial layer, overlying the hypoblast.”

Placental mammals (e.g., primates): “It is part of the inner cell mass, within the outer trophoblast.”

He cites further differences between which cells become the endoderm and which become the mesoderm, noting:

in amniotes (reptiles, birds, mammals) cells that are internalized arise from a central area of the epiblast, i.e., the presumptive endoderm and mesoderm are surrounded by presumptive ectoderm; whereas

in anamniotes (chondrichthyans, teleosts, amphibians) the cells that internalize are from the edge of the epiblast, i.e., the presumptive endoderm and mesoderm surround the presumptive ectoderm.

Swift summarizes major differences in the mechanisms of gastrulation as follows:

Chondrichthyans: by cells rolling over a posterior overhang of the epiblast.

Teleosts: by involution around the edges of the epiblast as it spreads around the yolk.

Amphibians: by involution through an annular blastopore.

Reptiles: by involution through a canal-like blastopore.

Birds: by cells ingressing through a primitive streak, formation of the primitive streak being accompanied by growth of an underlying endoblast.

Placental mammals: by cells ingressing through a primitive streak.

Three Substantial Distinctions”

Swift thus finds that these diverse modes of development cannot be considered homologous:

In the light of these three substantial distinctions — the different overall structure of the blastulas, the different parts of the blastula that become the embryo, and the different relative positions of the presumptive ectoderm and mesoderm/endoderm in amniotes and anamniotes — there is no doubt that the tissues that become the embryo are not equivalent, and hence are far from being homologous across the various vertebrate classes.

According to Swift, these fundamental differences in early vertebrate mechanisms of development during gastrulation suggest that vertebrates do not share a common ancestry:

The straightforward conclusion to draw from this radical diversity of their early embryonic development is that it shows the vertebrates have not evolved from a common vertebrate ancestor. This conclusion can be avoided only if there are credible explanations for how such diversity of early development might have arisen from the development prevailing in a common ancestor (whether or not similar to present-day cephalochordates) in an evolutionary way, via changes that (i) had a realistic probability of occurring, (ii) maintained viability, and (iii) offered, in most cases, significant advantage that could be favored by natural selection.

Meeting these evolutionary requirements poses a great challenge, however. Swift quotes a prominent developmental biologist, Rudolf Raff, who wrote: “One might reasonably expect mechanisms of early development to be especially resistant to modification because all subsequent development derives from early processes.” Swift calls this a “commonsense conclusion” because the complexity of vertebrate development demands that many coordinated modifications would be required to fundamentally change how development proceeds. He thus finds that “because of the interdependence of the mechanisms that are involved, constructive changes to embryonic development must entail coordinated production of and/or changes to several genes, e.g., for transcription factors and the DNA sequences on which they act, which is prohibitively improbable.”

This leads to a “waiting time” problem where multiple coordinated change would be required to transition from one developmental regime to another, posing “a formidable challenge to supposed evolutionary scenarios” as generating these changes would be “generally far in excess of the time available.”

Thursday, 23 March 2023

An outbreak of journalism?

Darwinism's ministry of truth in action?

I Got Canceled by the National Science Teaching Association

Herman B Bouma

Cancel culture reigns supreme in mainstream science, as I can tell you from personal experience. A recent instance involves the National Science Teaching Association (NSTA) and its cancellation of my poster presentation, which had been scheduled for the NSTA annual conference going on right now in Atlanta, March 22-25.

In September 2022 I submitted a proposal to speak at the conference. My topic was “The Top 10 Scientific Arguments Against Darwin’s Theory — According to Darwin Himself.” Darwin took great care to reply thoughtfully to the scientific arguments against his theory and, by the time of the sixth edition of The Origin of Species in 1872, approximately one-third of his book consisted of his responses to 37 scientific arguments against his theory (all of which still have merit today). Based on Darwin’s discussion in The Origin of Species, I determined what Darwin likely would have considered to be the top ten scientific arguments against his theory. (For interested readers, see here for Dr. Casey Luskin’s own detailed take on the same Subject.)

On December 29, 2022, I received an email from the NSTA conference team inviting me instead to submit a proposal for a poster presentation. The email stated that my topic was “evaluated as one that is significant and of interest to your colleagues.” On January 9, 2023, I submitted a proposal for the poster presentation, which was then approved and, beginning in January, was listed in the online conference agenda. The listing presented the main takeaway of the poster presentation as follows: “Darwin acknowledged that there were ‘a crowd of difficulties’ with his theory and stated, ‘Some of them are so serious that to this day I can hardly reflect on them without being in some degree staggered; but, to the best of my judgment, [they] are not, I think, fatal to the theory.’”

Working on My Poster

In February I worked on my poster presentation and also prepared a handout for it. On February 22 I went to a local print shop and had 50 copies made of the handout. In the evening of the same day I attended “Atlanta 2023 — Poster Session Support Web Seminar,” a webinar sponsored by NSTA to help those preparing poster presentations.

However, on February 24 I received an email from Tricia Shelton, NSTA’s Chief Learning Officer, stating that “it has come to our attention that your session may be promoting creationism. … The purpose of this email is to inquire about your poster presentation to find out if it is focused on creationism or on modern evolutionary science ideas articulated in our national standards.” I responded on February 25, “My poster presentation is not focused at all on creationism. It is focused only on Darwin’s ideas and what he considered to be valid scientific arguments against his theory.”

Resolved by Modern Science?

I then received an email from her on February 28 in which she asked if I was seeking to challenge modern evolutionary theory by using intelligent design. She also said my poster would need to explain how each of the top ten scientific arguments against Darwin’s theory has been resolved by “modern scientific evidence.”

I replied that my poster presentation did not challenge evolution by using intelligent design. Rather, it only set forth what Darwin himself thought were the top ten scientific arguments against his theory, specifically, against his proposed mechanism for evolution, i.e., the application of natural selection to randomly produced variations. Thus, it sought to promote an objective evaluation of Darwin’s proposed mechanism.

I also stated that the scientific debate continues with respect to this mechanism and that I did not believe the top ten scientific arguments have been resolved using modern scientific evidence. I stated that if I was mistaken, I would appreciate her help and asked her to let me know what modern scientific evidence has resolved each of the ten arguments.

A Final Email

I received a third and final email from Ms. Shelton on March 7. In this email, instead of pointing out any modern scientific evidence resolving the ten arguments, she stated that my poster presentation focused only on Darwin’s words and did not “reference Framework-aligned teaching approaches.” However, the guidelines for poster presentations do not require that a poster presentation “reference Framework-aligned teaching approaches.” It seemed she was just looking for an excuse to cancel my poster presentation. She said my poster presentation could not be accepted “in its current state” and canceled it without giving me any opportunity to bring it into compliance.

It is bizarre that Ms. Shelton canceled my poster presentation when, as indicated earlier, the NSTA conference team found my topic to be “significant and of interest to your colleagues.” In her zeal to protect the established narrative about evolution, Ms. Shelton was determined to shut down any debate about Darwin’s theory, even if it was debate fostered by Darwin himself.

The “Censorship Industrial Complex”

At a Congressional hearing earlier this month, held by the House Select Subcommittee on the Weaponization of the Federal Government, one of the witnesses, Michael Shellenberger, warned the lawmakers of “the growth and power of a censorship industrial complex run by America’s scientific and technological elite,” a complex that has eroded Americans’ freedom of speech. This censorship industrial complex has been at work for quite some time now in attempting to shut down any debate about Darwin’s theory.

Most people believe that when it comes to disagreements on policy and scientific theory, the best approach is to promote debate rather than censorship. Open and honest debate has always been the American way. However, in the case of Darwin’s theory, debate is rejected in favor of censorship. This is contrary to the hope of Charles Darwin himself, who wrote, “I look with confidence to the future, — to young and rising naturalists, who will be able to view both sides of the question with impartiality.” Those “young and rising naturalists” are out there, and I’ve learned much from them. But the National Science Teaching Association, for one, has no interest in doing so.

Headlong into that long sleep?

Euthanasia’s Cultural Collateral Damage: Less Respect for Human Life

Wesley J Smith

Euthanasia causes egregious cultural damage beyond the direct consequences of allowing the killing — or facilitating the suicides — of sick and disabled people. Eventually, the lives of the elderly, disabled, mentally ill, and seriously ill come to be seen as less valuable than the “healthy” and able-bodied — to the point that their homicides are often winked at by society. We saw this phenomenon during Jack Kevorkian’s mass assisted suicides in the ’90s, supported by much of the media and accompanied by the unwillingness of several juries to convict for nearly a decade.

A recent homicide case in Canada further illustrates the point. As regular readers of my work are well aware, Canada has fallen off the euthanasia moral cliff by allowing broad categories of people to be killed by doctors as a means of ending “suffering.” But that denigrating attitude toward people with serious health conditions is catching on, and now, a man, Francois Belzile, who killed his disabled wife has only had his wrist lightly slapped by a judge for the crime.

No Question About the Impact

From the Edmonton Journal story:

A retired accountant who killed his severely disabled wife will be allowed to serve his sentence on house arrest rather than in prison, with a judge ruling the accused’s “caregiver burnout” lessens his moral responsibility for the crime.

Belzile pleaded guilty last month to manslaughter for injecting Christiane Belzile — a 69-year-old, non-verbal stroke survivor for whom Francois Belzile had been sole caregiver for seven years — with a lethal dose of insulin after she was injured in a fall in 2018. Belzile then tried to end his own life.

Despite Francois’s refusal of state assistance — and a threat before the crime to end both their lives if they ceased to be able to live “independently” — he was deemed unable to form intent to murder and allowed to plead guilty to manslaughter. Good grief.

There is no question that euthanasia advocacy and legalization impacted the case:

[Defense attorney] Hurley added that Belzile saw his actions as “the compassionate shortening of the final step.” Hurley also noted societal attitudes toward assisted death are rapidly changing, noting, “The world has changed since Latimer, at least in Canada.”

(Canadian Robert Latimer murdered his daughter Traci, who was disabled by cerebral palsy, back in the ’90s. He served about ten years — but only because it was mandatory — and had the support of a majority of Canadian people according to polls.)

Out of His Misery

So, in essence, Francios put Christiane out of his misery and out of pride — i.e., his preferring death over dependency — and the judge winked at the crime by imposing such a light sentence for an egregious act.

What a frightening illustration of the lowered respect for “compromised” human life that euthanasia consciousness breeds. People with disabling conditions and those who love them should be terrified.

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

David Coppedge

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?

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