Search This Blog

Sunday 18 December 2016

A clash of Titans. XLI

History Judges Vladimir Lenin.

File under "Well said" XLIV

1Corinthians3:18NASB"Let no man deceive himself. If any man among you thinks that he is wise in this age, he must become foolish, so that he may become wise." The apostle Paul.

As tends to be the case:

Two Flagella Are Better than One
Evolution News & Views 

As imaging improves, so does knowledge of the workings of the bacterial flagellum. Two new papers point out new findings about these outboard motors that contribute to the argument that they are irreducibly complex and intelligently designed. As could be predicted, neither attempts any explanation of how they could have evolved.

Secondary Flagella


One  paper in PNAS by German scientists explores the advantage of having two flagella, one at the rear and another one or two on the sides. If you were a blind bacterium trying to find your way up a gradient, you would only have one trick in your steering kit: the "run-reverse-flick" move. Trouble is, when you operate that move, it often turns you 90 degrees. That's not helpful when you want to make progress up the gradient. The scientists found that having a secondary flagellum reduces that angle, even when it doesn't not provide extra power:

Flagella-mediated motility is an important or even crucial propagation factor for many bacteria. A number of polarly flagellated species possess a distinct secondary flagellar system, which, as current models suggest, allows more effective swimming under conditions of elevated viscosity or across surfaces. In this study, we demonstrate that such a secondary flagellar system may also exert beneficial effects in bacterial spreading by increasing the directional persistence through lowering the cellular turning angles. The strategy of increasing directional persistence to improve animal spreading efficiency has been proposed previously by theoretical modeling, and here we provide a specific example of how this strategy is used by bacteria. (Emphasis added.)
Corking the Torque

During assembly of a flagellum, the bacterium must avoid starting the engines before they are anchored in place. This is similar to fastening an outboard motor to a boat: turning the motor on could be dangerous.Another paper in PNAS  describes how a particular protein in the stator plugs its ion channel until the stator is properly positioned in the membrane. In essence, it waits for a signal that assembly is complete, then undergoes a conformational change that allows the ions that drive the motor to flow.
  Stator is the energy-converting membrane protein complex in the flagellar motor. Its ion-conducting activity is only activated when incorporated into the motor, but the mechanism for assembly-coupled activation remains a mystery. In this study, we solved the structure of a C-terminal fragment of the sodium-driven stator protein PomB (PomBC), the region responsible for anchoring the stator unit, at 2.0-� resolution. In vivo disulfide cross-linking studies of PomB double-Cys mutants and their motility assay suggested that the N-terminal region of PomBC changes its conformation, which is expected for MotB, the counterpart of PomB in the proton-driven Salmonella motor, in the final step of the stator assembly around the rotor.
It's remarkable that scientists can now look at parts of machines at two angstrom resolution -- two 10 billionths of a meter! The remarkable team at Nagoya University in Japan, who produced beautiful animations of flagella, has done it again, uncovering new aspects of these amazing molecular machines. The particular part of one protein essentially plugs up the ion channel, like a cork in a bottle:

Because the cross- linking did not affect stator assembly, we suspected that the cross-linking inhibits the ion conductivity of the stator channel. PomB/MotB has a periplasmic short segment called a "plug" just at the C terminal to their single transmembrane region...
The scientists mention in passing that the sodium-driven motors like in Vibrio routinely operate at over 100,000 RPM (1,700 Hz). Proton-driven flagella in E. coli and Salmonella are typically slower, about 300 Hz. The high-performance flagella have extra parts for their turbo-charged activity, just like one would expect to find in a Ferrari:

The basal body of the Vibrio motor has two unique ring structures, the T-ring and the H-ring. These extra rings are thought to reinforce the motor to resist the high-speed rotation. Recent structural study demonstrated that FlgT acts as an assembly base or scaffold for both the ring structures. The T-ring is made up of MotX and MotY, and is located beneath the P-ring, which is a part of a bushing structure for the rod, thereby believed not to rotate. The T-ring is an essential component to incorporate the stator into the motor. The periplasmic region of PomB is likely to bind to MotX, and MotX is connected to the basal body through the N-terminal domain of MotY. Thus, the stator of the sodium-driven motor is tightly fixed not only to the PG layer but also to the basal body through the interaction between PomB and the T-ring. Despite the rigid anchoring structure, the stator of the sodium-driven motor still shows a dynamic behavior dependent on the binding of sodium ion to PomB.
In this excerpt from their final discussion, notice how they describe the stepwise, coordinated assembly of parts before the ion-drive motor goes into action:

On the basis of this study and together with our previous results, we propose a model for activation mechanism of the Vibrio sodium-driven motor (Fig. S6). The stator diffusing in the cell membrane is in an inactive state. When the stator reaches around the rotor, PomA interacts with FliG. This interaction triggers opening of a"plug," allowing sodium ion to translocate into the channel of the stator. The sodium flow may induce the binding of PomB to the T-ring. This step probably includes a conformational change of the disordered N-terminal region of the PEM. After that, the N-terminal two-thirds of ?1 changes its conformation to an extended form to anchor to the PG layer [peptidoglycan layer, part of the external membrane].
This is just what Dr. Scott Minnich pointed out in  Unlocking the Mystery of Life 12 years ago. The assembly instructions, he said, are even more irreducibly complex than the motor itself. Parts are arriving on time and moving into place in a programmed sequence, with feedback to the nucleus affecting how many parts are to be manufactured. Dr. Jonathan Wells added, "What we see is irreducible complexity all the way down." Twelve years of closer looks at these astonishing machines have only amplified those conclusions.

Yet more iconoclasm

Now It's Whale Hips: Another Icon of Darwinian Evolution, Vestigial Structures, Takes a Hit
David Klinghoffer

In the case presented by advocates of Darwinian evolution, vestigial organs are a star in the firmament, frequently and gloatingly pointed to. Darwin himself cited them as such in The Origin of Species and The Descent of Man, referring to body parts like the human appendix that, he believed, no longer serve a function:

On the view of each organism with all its separate parts having been specially created, how utterly inexplicable is it that organs bearing the plain stamp of inutility... should so frequently occur.

Of course the appendix is a great example of an organ once thought to be without utility that now turns out to serve a vital role.


In the catalogue of purported vestigial parts, whale hips are "the marquee example,"  writes Stephanie Keep at the absurdly named "Science League of America" blog populated by our Darwin-lobbying friends at the National Center for Science Education. Unfortunately whale hips have now gone the way of appendix.  paper in the journal Evolution reports reports that rather than being a useless reminder of the evolutionary past, when whale ancestor Pakicetus strode the land on all fours, they in fact serve an unquestionably important The pelvic bone supports the muscles that guide the penis. In male whales and other cetaceans, performance and thus successful sexual competition hinge on the size of the hips. The paper explains:

Male genitalia evolve rapidly, probably as a result of sexual selection. Whether this pattern extends to the internal infrastructure that influences genital movements remains unknown. Cetaceans (whales and dolphins) offer a unique opportunity to test this hypothesis: since evolving from land-dwelling ancestors, they lost external hind limbs and evolved a highly reduced pelvis which seems to serve no other function except to anchor muscles that maneuver the penis. Here we create a novel morphometric pipeline to analyze the size and shape evolution of pelvic bones from 130 individuals (29 species) in the context of inferred mating system. We present two main findings: 1) males from species with relatively intense sexual selection (inferred by relative testes size) have evolved relatively large penises and pelvic bones compared to their body size, and 2) pelvic bone shape diverges more quickly in species pairs that have diverged in inferred mating system. Neither pattern was observed in the anterior-most pair of vertebral ribs, which served as a negative control. This study provides evidence that sexual selection can affect internal anatomy that controls male genitalia. These important functions may explain why cetacean pelvic bones have not been lost through evolutionary time.

Under selection pressure from reality, Darwinists have already had to back away from Darwin's own understanding of what it means for a structure to be vestigial. Rather than serving no purpose, writes Jerry Coyne in Why Evolution Is True, now being vestigial can mean serving a different purpose than in one's distant ancestors. He defines "vestigial trait" this way:

A trait that is the evolutionary remnant of a feature once useful in an ancestral species but that is no longer useful in the same way. Vestigial traits can be either nonfunctional (the wings of the kiwi) or co-opted for new uses (the wings of the ostrich).

Stephanie Keep agrees:[T]here's a problem when vestigial structures are defined as evolutionary remnants that have no function. As I discussed in a previous post , the correct way to describe a vestigial structure is to say that it no longer has its original function.
   She is excited about Carl Zimmer's post on the subject, which elaborates:
     While [whale hips] may not be essential for walking, they still matter a lot to whales. To see why, we have to go back to those hips of land mammals. They are important for walking on land, but they serve other purposes, too. Among other things, they anchor muscles that control the sex organs. If these muscles are anesthetized in men, for example, they have a hard time gaining an erection.

As whale hips stopped mattering to walking, they didn't stop mattering to having sex. In male whales, the pelvis controls the penis with an especially elaborate set of muscles. In some whale and dolphin species, these muscles make the penis downright prehensile.You see the problem. Whale hips are "vestigial" yet still extremely important. Comments our colleague Michael Behe, "So doesn't that make everything a vestigial structure from a Darwinian viewpoint? And if so, of what use is the word?" Or as Jonathan Wells wrote here back in 2009 in reviewing Coyne's book ("The Myth of Vestigial Organs and Bad Design: Why Darwinism Is False"):
  As [biologist Steven] Scadding had pointed out nearly thirty years ago, ... Darwin's argument rested on lack of function, not change of function. Furthermore, if vestigiality were redefined as Coyne proposes, it would include many features never before thought to be vestigial. For example, if the human arm evolved from the leg of a four-footed mammal (as Darwinists claim), then the human arm is vestigial. And if (as Coyne argues) the wings of flying birds evolved from feathered forelimbs of dinosaurs that used them for other purposes, then the wings of flying birds are vestigial. This is the opposite of what most people mean by "vestigial."

In this way, the concept of a vestigial trait is reduced to meaninglessness. In the most minimal definition, evolution denotes change over of time. No trait goes unchanged. Under the framework of Darwinian evolution, therefore, everything is vestigial. So nothing is.

This is not just our observation. The scientists who revealed the usefulness of whale hips are rethinking what it means to be vestigial. Or so it sounds from the remarks of biologist Matthew Dean at USC, a co-author of the paper in Evolution, commenting in  Science Daily:
   "Our research really changes the way we think about the evolution of whale pelvic bones in particular, but more generally about structures we call 'vestigial.' As a parallel, we are now learning that our appendix is actually quite important in several immune processes, not a functionally useless structure," Dean said.

Anyone who thinks whale hips are functionless, just like your appendix, should try telling that to a lonely gentleman whale. The career of this evolutionary icon isn't over yet, I'm sure, but its importance in the evolutionary pantheon is due for a serious downgrade.

On the Piltdown Hoax and human exceptionalism

What the Piltdown Hoax Tells Us, 104 Years Later

Michael Flannery 


A curious anniversary falls this weekend. On December 18, 1912, the infamous Piltdown hoax was unveiled to an astonished audience of the Geological Society of London by lawyer and amateur archeologist Charles Dawson (1864-1916) and Arthur Smith Woodward (1864-1944) of the British Museum. What they showed was nothing short of amazing: the apparent remains of a human-like skull attached to an ape-like jaw. Allegedly unearthed at the Piltdown gravel pit in East Sussex, England, it was hailed as the missing link -- a truly history-making discovery!

It would take nearly 41 years to expose the artifact as a fraud. On November 21, 1953, officials of the British Natural History Museum revealed the shocking truth: Piltdown man was a hoax, the combination of three species, a medieval human cranium, the jaw of a centuries-old young orangutan, and some fossilized chimpanzee teeth. Various culprits have been proposed, including famed Jesuit philosopher Teilhard de Chardin (1881-1955) and physician/novelist Sir Arthur Conan Doyle (1859-1930). But most recent investigation suggests that the imposture was likely perpetrated by Dawson alone in an effort to gain recognition and election as a Fellow into the Royal Society (see "Piltdown hoax solved," Forbes, August 10, 2016).

Writing for Harper's on the second anniversary of the Piltdown exposure, paleontologist Loren Eiseley (1907-1977), not one to look at an event or a phenomenon superficially, asked, "Was Charles Darwin Wrong About the Human Brain?" Eiseley noted that Alfred Russel Wallace (1823-1913), co-discoverer of the theory of natural selection, was unimpressed with the Piltdown "find" from the beginning. Writing to a friend in August 1913 (just three months before his death), Wallace exclaimed, "The Piltdown skull does not prove much, if anything!" Why, asked Eiseley, had Wallace, almost alone among the scientific community, so summarily dismissed this apparently stunning missing link? The answer was simple: "he did not believe in a skull which had a modern brain box attached to an apparently primitive face and given, in the original estimates, an antiquity of something over a million years." The archeological "discovery" would have confirmed Darwin's Descent of Man in dramatic fashion. Indeed Piltdown man was, from a Darwinian perspective, even something that would have been predicted.

But Wallace's "voice of lonely protest," observed Eiseley, underscored "the abyss which yawned between man and ape" that Darwinians at the time blissfully ignored. Having observed primitive cultures in South America and the Malay Archipelago for more than twelve years, Wallace concluded (quoting Eiseley) that humans' "mental powers were far in excess of what they really needed to carry on the simple food-gathering techniques by which they survived." Certainly no process of natural selection was adequate to produce such superior powers of art, reason, and morals. For Wallace, the human brain freed mankind from the tyranny of natural selection:

Here, then, we see the true grandeur and dignity of man. On this view of his special attributes, we may admit, that even those who claim for him a position as an order, or a sub-kingdom by himself, have some show of reason on their side. He is, indeed, a being apart, since he is not influenced by the great laws which irrestistibly modify all other organic beings (Contributions to the Theory of Natural Selection
, 1870).
How, then, do we account for this impressive array of human attributes? Wallace thought that mankind might well have emerged comparatively recently, and that the rapid evolution of the modern human brain would confirm that "distinct and higher agencies" have been responsible for these mental attributes and attainments.

Eiseley confessed, "Since the exposure of the Piltdown hoax all of the evidence at our command -- and it is considerable -- points to man, in his present form, as being one of the youngest and newest of all earth's swarming inhabitants. . . . Today, with the solution of the Piltdown enigma, we must settle the question of the time involved in favor of Wallace, not Darwin." Although Eiseley thought some other wholly naturalistic explanation might account for the late and virtually saltationist expansion of the human intellect, he confessed that "science . . . has yet to explain how we have come so far so fast, nor has it any completely satisfactory answer to the question asked by Wallace long ago."

Today we still wait for an explanation, and it must be admitted that various speculations along the lines of blind chance and necessity or natural selection remain as unsatisfactory as when Eiseley was writing more than sixty years ago. A century after Wallace's dismissal of Piltdown man, science still confirms Eiseley's assessment and Wallace's vindication. The chart below shows the timeline for ascending brain size/body weight estimates for Sahelanthropus, Australopithecus afarensis, early Homo, Homo habilis, Homo erectus, H. heidelbergensis, Neanderthals, and H. sapiens.

brain size chart_4.jpg

This chart shows relative brain size as cm3 per 50 kg of body weight. Adapted with modifications from Robert Jurmain, Lynn Kilgore, et al.,
 , 2013-2014 ed. (Wadsworth, Cengage Learning, 2014), p. 357, and "Homo habilis," 
, updated August 15, 2015.

Clearly brain size and capacity has not only increased, but increased at a very late and remarkably accelerated pace. Of course brain size is not the only measure of intellectual capacity, other factors may be involved. Some, for example, emphasize that Neanderthals, the closest historically to humans, possessed brains that were larger in absolute size to us. But as recent analysis has uncovered, the Neanderthal brain was quite different from its human counterpart. Being much more elongated than globular, the indications are that Neanderthals "reached large brain sizes along different evolutionary pathways." Their speculation that unique patterns of brain development in H. sapiens would have become "a target for positive selection" merely begs Wallace's original question (see Gunz et al., "Brain development after birth differs between Neanderthals and modern humans," Current Biology, Nov. 2010).

So the question remains: How did humans acquire such vast intellectual capacities so comparatively recently and so rapidly? Wallace called upon an "Overruling Intelligence" to explain human intelligence and many other features of complexity in biology and the cosmos. While Darwinians continue to search for some naturalistic cause, others, like British physician James Le Fanu, point out that the disappointments in high-tech solutions to the nature of the intellect and the human mind so touted by the human genome project and promised in the "Decade of the Brain" in the 1990s should force a reassessment of our species as truly unique (Why Us?: How Science Rediscovered the Mystery of Ourselves, 2009).

Eiseley's long forgotten but intriguing article is fortunately now available as "The Real Secret of Piltdown" in a new 2-volume set of his collected essays. As we reflect on the 104th anniversary of arguably science's greatest fraud, Eiseley's conclusion rings is as pertinent today as when it was first written:

The true secret of Piltdown, though thought by the public to be merely the revelation of an unscrupulous forgery, lies in the fact that it has forced science to reexamine carefully the history of the most remarkable creation in the world -- the human brain.
If the Cambrian period of 530 million years ago poses serious challenges to Darwin's insistence upon slow, incremental change in the amazingly rapid proliferation of animals over a mere 5 to 6 million-year timespan (see Darwin's Doubt), then how much more should the transformational changes in the human brain over the past 100 to 200,000 years cause as serious reevaluation of the nature of human beings and the means by which they came to be. If the Cambrian "explosion" is just too much change over too little time to be explained by Darwinian processes, the human brain is way too much change over way too little time. Perhaps Wallace's view of the Piltdown hoax still holds an important lesson for us today. Maybe the most dramatic "explosion" of all is the one that rests within our crania.