One upping God?

Think You Can Design a Better Fruit Fly?

Evolution News & Views March 8, 2016 3:40 AM

What happens when you tinker with the design specs of a live flyer? Four European scientists with specialties in biology and aerodynamics got together and ran some clever experiments with fruit flies to find out. The biologists found ways to change the shape of the flies' wings, and the flight engineers measured what happened in performance tests. Their findings, published in Nature Communications, yield some lessons about the capabilities of mutation and natural selection to make modifications on the fly, so to speak.

Aircraft designers have the luxury of changing just one thing at a time and measuring the impact on flight performance. Living things, however, are bundles of requirements that must be optimized together as they develop from the embryo. The authors recognize this difference:

Wing shape is governed by the expression of a number of genes, the modulation of which leads to phenotypic variation. The results of changing the balance of expression bears little relation to the independent parameters engineers vary when designing aircraft wings, yet these are the gene expression-driven shape warps upon which natural selection acts. [Emphasis added.]

How far could natural selection vary a gene for wing shape without introducing unacceptable costs on other parts of the system? To find out, the scientists used RNA interference (RNAi) to alter expression patterns in a gene called narrow for only the wing tissues, without affecting other body parts. They bred four lineages with altered wing shapes that were progressively narrower than the wild type. Then they put them through a series of flight tests, including escape from a predator, a dragonfly.

All of the morphs could fly -- some with even better performance on tight turns. That "improvement" (from a human perspective) came at a cost (from the fly perspective).

Our aerodynamic model shows that all of the wing morphs we have tested show a decrease in aerodynamic efficiency in comparison with the control. Thus, measurable differences in flight performance are likely to be the result of a balance between the aerodynamic and mechanical modifications due to the shape change and its energetic cost. In the two milder morphs, we suggest that the energetic cost is not high enough to negate the performance benefits whereas, in the most extreme morph, an intersection is crossed beyond which the necessary power is more challenging to achieve. Akey factor contributing to this shift from improved to inferior performance is likely to be the disruption we have introduced into the system by altering the wing planform without changing the complex musculoskeletal apparatus that drives it. In an engineering sense, the induced changes in wing shape force the flight motor to operate off-design.

Using intelligent design, aircraft engineers can correct for the cost of one alteration with a subsequent alteration. Lengthening a wing, for instance, might increase lift, but will require more engine power to compensate for the extra weight. Ann Gauger talked about this in a recent ID the Future podcast in response to charges that some designs in the human body are sub-optimal.

The next thing I would say is that good design doesn't necessarily mean optimal design for all things because design often means multiple constraints... you can't be perfectly designed for one feature because it often goes against what you need for a second feature. The example I give is from airplane technology. Airplanes have to have a lot of design features that match a lot of different constraints. They have to be light so they can fly but they have to be strong so that they can withstand the kinds of stresses they undergo. They have to be able to keep people warm and keep it from being too loud, but that all adds weight. They have to keep the atmosphere breathable, but that also adds weight. All of those things have conflicting needs....

In the case of the fruit fly, the interconnectedness of constraints is even more evident. The entire fly must develop from a zygote containing all the instructions for building the final product. That final product must not only be capable of powered flight, it has to get to the point of reproduction, or else any fitness gains will be lost. The authors realize this. As human engineers, we cannot presume to know what is most important to the fruit fly:

Insect flight performance is a direct consequence of the interaction of the wings with the air and is determined by acombination of kinematics and morphology. Routine behaviour can be dominant over escape responses as the predictor of survival in dragonfly-fruit fly interactions, with sharp turns highlighted as vital for evading capture. Selective pressures on fruit fly morphology may have been expected, therefore, to promote adaptations that enable a high degree of manoeuvrability. Our findings show that fruit flies do not develop wings that are best suited for agile flight even when driven by their existing flight motor. Moreover, flight performance envelopes could be widened by affecting the function of a single gene. That flies are suboptimal in this regard is not particularly surprising but symptomatic of at least one antagonistic developmental, physical or behavioural selection pressure: for example, sexual selection mediated by the effect of wing planform on auditory or visual cues.

The more agile flyer, in other words, might not be able to get a date with a female who thinks he buzzes too loud or looks weird. He would have to find a female who has mutated into a kind that likes those things about him. More seriously, the agile flyer might need more powerful flight muscles to handle the stresses of a tighter turning radius. If there is "at least one antagonistic developmental, physical or behavioural selection pressure" constraining maneuverability, there are more likely several -- perhaps many. Is it reasonable to expect blind mutations to occur simultaneously such that all the constraints are satisfied in a coordinated fashion in one individual?

Animal morphologies reflect the cumulative effect of non-adaptive variation and time-integrated selective pressuresincluding -- but not limited to -- those optimizing form for function. Insect wings are under selective pressures driving towards local multi-objective optima, embodying a design compromise between features that are aerodynamically relevant (contributing to flight performance) and features that may contribute to fitness but are independent of aerobatic capability.

It's not surprising that genetic manipulation can improve one trait at the expense of others:

We did not encounter a physical limit along the principal component axis that we were able to influence; all our genotypes were able to fly, albeit with reduced performance maxima at the extremes of our morphological manipulations.

This is exactly what breeders do with artificial selection. Our prize cattle are optimized for humans' desires, but would likely not do well in the wild. By practicing "influence" and "manipulation" of existing champion flyers, the scientists did not provide insight into the "evolution of performance specialities in animals" as they had hoped. Rather, they showed the power of the engineering mind to optimize multiple competing constraints in a coordinated fashion.

In her podcast, Dr. Gauger recounted the epic flight of the Rutan Voyager, the first airplane to fly around the world without stopping or refueling. To achieve that feat, designer Burt Rutan had to optimize lift and discard every unnecessary weight. It's interesting that Rutgers scientists just identified a world-traveling insect of that caliber: a small dragonfly they determined is the "world's longest-distance flyer." Gene comparisons show the same species is found as far Texas, Korea, South America, and Canada. Pantala dragonflies can fly across oceans from continent to continent, some of them flying nonstop over 4,400 miles, besting the Monarch butterflies shown in Metamorphosis.

Pantala leaves many of its fellow dragonflies even farther behind. The mysteries of evolution are such that whilePantala and its cousin the Green Darner (Anax junius) havedeveloped into world travelers, Ware says that by contrast, other members of the family "don't ever leave the pond on which they're born -- traveling barely 36 feet away their entire lives."

Could this be an example of "non-adaptive influences" that "may exhibit some features that are unrelated to fitness" the researchers spoke of? It doesn't appear necessary for any dragonfly to acquire international flight ranking when their pond-dwelling cousins are doing just fine. If world-traveling dragonflies are a mystery to evolution, then evolution is not doing a good explanatory job.

By contrast, we know the power of minds to create flying machines that range from puddle jumpers to global circumnavigators. And that's what we find in biological flyers (birds and insects), each species exhibiting not only perfect balance between multi-objective optima but the ability to faithfully transmit its design instructions across generations. That's positive evidence for designing intelligence.

A remedy for the doubt;Just add oxygen?

The Great Cambrian Whitewash
Evolution News & Views February 23, 2016 3:26 AM

Stephen Meyer's book Darwin's Doubt has been out for almost three years. Paleontologist Mark McMenamin called it a "game changer for the study of evolution..." It has over 700 reviews on Amazon (78 percent five-star, 6 percent four-star). When it came out in 2013, it ranked #7 for hardback nonfiction on the New York Times bestseller list. And last year, a follow-up book, Debating Darwin's Doubt, addressed all the known objections to the original work.

To read most of the scientific journals, though, you would think they know nothing about this. Nature, PNAS, Current Biology, you name it: they avert their eyes from Meyer's 500-page challenge whenever they discuss the Cambrian explosion. (The journal Science is the noble exception.) It is simply not possible that the authors of these papers, and the editors of these journals, are unaware of the controversy. Meyer has raised a significant challenge to the usual Darwinian explanation for the sudden appearance of complex animal life in the fossil record. It's time for the journals to face it and engage the scientific debate.

The leading science journal Nature, sad to say, whitewashed the controversy once again in a recent piece, "What sparked the Cambrian explosion?" Author Douglas Fox gives the usual positivist spin:

An evolutionary burst 540 million years ago filled the seas with an astonishing diversity of animals. The trigger behind that revolution is finally coming into focus. [Emphasis added.]

Such writing has all the comfort of Pravda telling the captives behind the Iron Curtain, deprived of alternative sources of information, that the famine will soon be over. Science should abjure a closed society. Besides, journals cannot afford the luxury of one-sided propaganda in this internet age. You can't wall off information for long. Search on "Cambrian explosion" and critiques pop up for the entire world to see. Not the least of those is Darwin's Doubt. Journals look foolish when they adopt the three-monkey posture, "Hear no controversy; see no controversy; speak no controversy." The smart strategy is to deal with it openly, so that consumers in the marketplace of ideas can decide who has the better product.

What is implied by Nature's line that the trigger for the Cambrian explosion is "finally coming into focus"? It can only mean one thing. It's been out of focus till now. When you consider that the problem of the Cambrian explosion troubled Charles Darwin, it's a sad commentary on the ability of scientists to admit being unable to focus on a solution for 157 years. That's enough time for 31 Five-Year Plans proverbially launched by the dear leader of evolution to find the fossils that would support his theory.

But Nature isn't really looking for support. As doctrinaire believers in Darwin's "mechanism" of natural selection, they don't need support. It's self-evident to them that an "evolutionary burst... filled the seas with an astonishing diversity of animals." Douglas Fox just wants to help by finding the "trigger."

And what is that trigger that is finally coming into focus? Oxygen.

Sperling has looked for insights into Ediacaran oceans by studying oxygen-depleted regions in modern seas around the globe. He suggests that biologists have conventionally taken the wrong approach to thinking about how oxygen shaped animal evolution. By pooling and analysing previously published data with some of his own, he found that tiny worms survive in areas of the sea floor where oxygen levels are incredibly low -- less than 0.5% of average global sea-surface concentrations. Food webs in these oxygen-poor environments are simple, and the animals feed directly on microbes. In places where sea-floor oxygen levels are a bit higher -- about 0.5-3% of concentrations at the sea surface -- animals are more abundant but their food webs remain limited: the animals still feed on microbes rather than on each other. But around somewhere between 3% and 10% oxygen levels, predators emerge and start to consume other animals.

The implications of this finding for evolution are profound, Sperling says.The modest oxygen rise that he thinks may have occurred just before the Cambrian would have been enough to trigger a big change. "If oxygen levels were 3% and they rose past that 10% threshold, that would have had a huge influence on early animal evolution," he says. "There's just so much in animal ecology, lifestyle and body size that seems to change so dramatically through those levels."

This excerpt illustrates why airing of the controversy is so drastically needed. Fox's prose hardly rises to the level of fairy tale. Would anyone outside the iron curtain of Darwinian explanations fall for a "just add oxygen" theory for the emergence of a trilobite or Anomalocaris?

Meyer would grant Fox and Nature all the oxygen they could ever want. He would let them inject copious quantities of oxygen bubbles into the Cambrian oceans right at the start of the explosion. No trilobites would emerge, he would argue, because the Cambrian explosion is not about gases, triggers, or influences. It's about information: the specifications to build animal body plans. That is the central challenge that the journals ignore.

Fox whitewashes the problem by repeating the party line no matter what. He offers pipe dreams that solutions will come someday, as long as everyone holds to the dogma.

Understanding how oxygen influenced the appearance of complex animals will require scientists to tease more-subtle clues out of the rocks. "We've been challenging people working on fossils to tie their fossils more closely to our oxygen proxies," says Lyons. It will mean deciphering what oxygen levels were in different ancient environments, and connecting those values with the kinds of traits exhibited by the animal fossils found in the same locations.

Communist ideologues were masters at interpreting every economic condition, including the failures in Russia and the riches in the West, in terms of class struggle and economic determinism. Yet now we look back at the fruits of that closed system.

Science should abhor iron curtains. Nature's willful neglect of the controversy surrounding the Cambrian explosion subverts the ideals of science. Besides that, it just looks bad. What are they hiding behind that wall? What do they have to lose by engaging scientific challenges? Only the story that oxygen causes trilobites. That's a tale worth losing. The time for détente, for glasnost, has arrived. Good things follow.

Cellular information processing v. Darwin.

Is Messenger RNA Regulation Controlled by an Irreducibly Complex Pathway?.
Jonathan M.

What we know about the complexity of the cellular information storage, processing and retrieval mechanisms continues to increase exponentially, and at an unprecedented rate. Almost on a daily basis, new papers are published revealing the ingenuity of the elaborate mechanisms by which the cell processes information -- processes and mechanisms that bespeak design and continue to elude explanation by Darwinian means. For how exactly could such a system - apparently, an irreducibly complex one - be accounted for in terms of traditional Darwinian selective pressure?

A new paper has just been published in Molecular Cell, in which the researchers, Karginov et al. reported their discovery that messenger RNA (mRNA) can be targeted for destruction by several different molecules.

According to the paper's summary,
The life span of a mammalian mRNA is determined, in part, by the binding of regulatory proteins and small RNA-guided complexes. The conserved endonuclease activity of Argonaute2 requires extensive complementarity between a small RNA and its target and is not used by animal microRNAs, which pair with their targets imperfectly. Here we investigate the endonucleolytic function of Ago2 and other nucleases by transcriptome-wide profiling of mRNA cleavage products retaining 5′ phosphate groups in mouse embryonic stem cells (mESCs). We detect a prominent signature of Ago2-dependent cleavage events and validate several such targets. Unexpectedly, a broader class of Ago2-independent cleavage sites is also observed, indicating participation of additional nucleases in site-specific mRNA cleavage. Within this class, we identify a cohort of Drosha-dependent mRNA cleavage events that functionally regulate mRNA levels in mESCs, including one in the Dgcr8 mRNA. Together, these results highlight the underappreciated role of endonucleolytic cleavage in controlling mRNA fates in mammals.
Translated into English, the paper makes the following points:

RNA interference (RNAi) refers to a cellular pathway that helps to regulate the activity of genes within the cell. Fundamental to the process of RNA interference are small interfering RNAs (siRNA) and microRNAs (MiRNA).
Small RNAs can prevent the translation of a target messenger RNA into protein, thereby reducing the activity of the RNAs to which it binds.
MicroRNAs also act as regulators, binding to their complementary sequences on a target messenger RNA to result in gene silencing. MiRNAs also serve as guides to a family of proteins called Artonautes. When a miRNA-Artonaute complex binds to its complementary mRNA target, it triggers its destruction.
The researchers surveyed a population of cleaved mRNAs in mammalian embryonic stem cells, discovering that mRNAs had been sliced or cleaved by the enzyme Ago2 and other enzymes.
It was previously thought that the destruction was due to the destabilization of mRNA by initiation of cellular pathways. In contrast, Karginov et al. have discovered a host of ways that mRNA may be destroyed by enzymatic cleavage.
So, how exactly can these things be explained by traditional Darwinian selective pressure?

Consider, for example, the enzyme Dicer, which is responsible for activating the RNAi pathway. The pathway is initiated when Dicer cleaves long double-stranded RNA (dsRNA) molecules into shorter fragments, consisting of roughly 20 nucleotides each. Each fragment possesses two strands, one of which (called the "guide strand") is subsequently incorporated into the "RISC complex" (RNA-induced silencing complex). Following base pairing between the guide strand and its complementary sequence, a cleavage is brought about by the enzyme Argonaute.

One has to wonder whether there is any significant biological system that, in fact, can be accounted for in a Darwinian step-wise fashion. The adequacy of Darwinian selection to account for the features of biodiversity is never demonstrated. Rather, it is merely assumed that Darwinism can account for these systems, in the almost complete absence of corroborative data.


It might be asked of the Darwinian advocates what kind of system, in principle, could not be explained in Darwinian fashion. In the absence of such testable statements, Darwinism cannot be regarded as good falsifiable science.

A design filter for E.T?

To Rule Out False Positives in the Search for ET, Astrophysicist Advocates a Design Filter.
Evolution News & Views

Paul Sutter, an astrophysicist at Ohio State, writes occasional articles for lay people. Recently he put out a challenge to his readers. He wants to keep them from falling for media hysteria about space aliens. His reasoning poses an indirect challenge to any kind of explanation positing a hidden designer.

In "Aliens are never the answer" on Live Science, he begins by talking about recent reports of unusually strong signals from a sun-like star. Here's another one: physicist Carole Mundell asks, "Are aliens trying to tell us something? Brightest burst of radio waves detected" (The Conversation). The particular incident doesn't matter, because "mysterious radio signals from outer space are almost always in the news," Sutter says. What he doesn't like is the rush to attribute mysterious signals to the work of aliens. He recounts other incidents over the decades. The point he wants to make is that science demands better explanations. An appeal to aliens is useless, because it can explain anything.

Here's the thing: The hypothesis that aliens are causing a mysterious radio signal is almost always useless, because intelligent creatures can create almost any signal they want. Hear a bleep-bleep-bloop? Maybe aliens did it. Whoops! I meant bloop-bloop-bleep. Well, aliens could have done that, too. There's no predictive power in the "aliens did it" hypothesis. We can't ever disprove it. [Emphasis added.]
Of course, proof that "aliens did it" is the holy grail for SETI, the search for extraterrestrial intelligence. Sutter mentions SETI a couple of times, but he doesn't make clear whether he feels their quest is justified. He's mainly concerned about the rush to judgment.

When a natural astrophysical explanation is weak or not very convincing, there's often a temptation to wonder if aliens are behind it. After all, we can't rule out aliens! Exactly. We can't ever rule out aliens, because intelligent actors are capable of pretty much anything. We can't rule them out, so it's a scientifically useless position.
He's right, to a certain extent. Intelligent actors are sly. They can throw paint on a canvas, drive over it, and call it art. They can hide messages in noise. They can cough a certain way to signal a friend that the prison guards are coming. We can't rule out intelligent actors. So is the appeal to intelligent design a scientifically useless position?

It's a very, very, very big leap to go from "We don't know what's causing this signal," to "Maybe aliens are causing this signal."
Sutter is onto something. He's basically arguing that we need a design filter. And ID theory provides one. ID advocates agree that you don't infer intelligence until there is sufficient reason to reject chance and natural law. When other astronomers jump to conclusions about space aliens, they haven't done their homework. Proper use of the design filter would prevent invalid design inferences. The best-trained SETI folks will certainly want to rule out natural causes before running to the press.

Sutter cannot, however, rule out all intelligent actors, otherwise he would have to beat his head against a brick wall. Brick walls don't arise by natural causes, once you rule out columnar basalt and other cases of natural self-organization. We know of a cause that can build brick walls firm and straight, with right-angle corners, as part of buildings reaching tens of meters high. The walls don't even have to be straight. Consider Stonehenge. If Sutter were to rule out all intelligent causes as useless, he would have to beat his head against that wall for a lifetime trying to explain it by natural causes. That would be the "scientifically useless position."

Intelligent actors are indeed "capable of pretty much anything." That's why we can be fooled by false negatives, claiming something isn't designed when it really is (as in the modern art case and the hidden message case). But ID theory can protect us against false positives (calling something designed when there is a natural explanation) by using the design filter properly. Once you set up the "rejection region" appropriately (see Dembski, No Free Lunch, Chapter 1), the Design-Specification Criterion becomes so robust, there comes a point when refusing to acknowledge design is absurd.


If Paul Sutter detected a series of bloops and bleeps from space tapping out the first 100 prime numbers in a row, he would likely concede the point.

Sea turtles V. Darwin.

Sea Turtles from Pre-Turtles? No Evidence of It
Evolution News & Views

We recently shared news about  humpback whales. Here are some new findings about another group of stars of Illustra's film  Living Waters: sea turtles. There are seven species of sea turtles in the world today, all beautifully designed and, sadly, all endangered. Consider first, appropriately, the enigma of origins.

Fossils

Do we see progression in the fossil record of sea turtles? No; according to the University of Alabama at Birmingham , the oldest ancestor of modern sea turtles was -- a sea turtle. Apparently they profited from global warming.

"Climatic warming during the mid-Cretaceous resulted in elevated sea levels and temperatures that, in turn, provided an abundance of new niches for marine turtles to invade," said Drew Gentry, a UAB biology doctoral student and the lead researcher on the project. "Represented today by only seven living species, sea turtles were once one of the most diverse lineages of marine reptiles. Before the cataclysm that claimed the dinosaurs, there may have been dozens of specialized species of sea turtle living in different oceanic habitats around the world."
This won't likely switch turtle conservationists in favor of anthropogenic climate change. It does seem a little bit dubious, though, to make evolutionary diversity a function of temperature.

"There is strong evidence which indicates freshwater turtles may have evolved to occupy marine environments at several points in the past," Gentry said. "But most of those lineages went extinct, making the exact origins of living or 'true' sea turtles somewhat of a mystery."
Evolutionists can always concoct a just-so story to explain any observation. Not wanting to leave a mystery unsolved, UAB's Gentry offers one:

"Data from C. acris tell us not only that marine turtles are capable of occupying specialized oceanic niches, but also that many of the sea turtles we know today may have gotten their evolutionary start as something similar to an oversized snapping turtle in what eventually became the southeastern United States."
 Phys.org tells about volunteers who found turtles on Cape Cod suffering from hypothermia and released them in warmer waters. That's 54 "cold-stunned turtles" rescued this year, and 600 last year. If sea turtles are "capable of occupying specialized oceanic niches," should humans be interfering with their evolution?

Turtles and tortoises occupy the wettest and driest habitats on earth, yet we humans feel a need to help them out.  Phys.org also tells about citizen scientists helping save Australian land turtles from extinction, despite the fact that "A single female freshwater turtle may live more than 100 years and produce more than 2000 eggs in her lifetime." Apparently they aren't evolving fast enough to outfox the red fox, introduced in the 1800s by humans. But evolution is clever. It evolved humans to do the job:

"Our computer models show that one harvest population may provide enough hatchling turtles to restore 25 other similar sized populations to pre-European turtle densities."
"Creating low cost 'turtle nurseries' throughout the country will provide a way to out-fox the fox without a single poison bait or bullet."

Presumably evolution is capable of creating beings that can use intelligent design to solve problems of their own making.

The Tragedy of the Commons

Human beings seem to be the only creatures on earth that willfully fall into the tragedy of the commons -- or that can use their minds to recognize the tragedy and try to avert it. Sea turtles would probably be thriving without bad human actors, who capture them for their eggs and meat and destroy their habitats. Consider the case in Indonesia. Still another article at  Phys.org  shows volunteers releasing sea turtle hatchlings onto a beach:

A group of turtles scurried down a beach and glided into the sea, enjoying their newfound freedom after being cared for at an Indonesian conservation centre.
The sea turtles were released by local tourists in Pariaman city, on western Sumatra island, in front of the Turtle Conservation Technical Operating Unit. [Emphasis added.]

It's a curious case of humans protecting non-humans from other humans.

Six of the world's seven turtle species can be found in Indonesia, an archipelago of more than 17,000 islands that is home to a dizzying array of exotic wildlife.
Almost all turtle species are endangered. Their eggs are considered a delicacy and they are also slaughtered for their meat, skin and shells.

We see here another indication of human uniqueness: moral responsibility for the living world. Without it, nobody could claim the slaughter of turtles is wrong. It would just be survival of the fittest, and the turtles would lose the race.

Hawksbills

On the other side of the globe, Belize has good news: the hawksbill sea turtle, classed as "critically endangered," is doing "swimmingly well" thanks to conservation efforts, reports Fox News. Once again, it was humans killing them off for their shells, meat, and eggs, but protection efforts at a reef offshore have borne fruit: "The Wildlife Conservation Society says that the sea turtle's rebound is an indication of the success of protection efforts in this large reef system." After snorkeling, catching, tagging, and releasing turtles for years, marine biologists estimate a thousand juveniles in the area, a model for other conservation programs.  Phys.org has a picture of one marine scientist handling a hawksbill, and another photo of a turtle being hoisted onboard a ship for tagging. Stephen Dunbar, who appears in Living Waters, has been involved for years in conservation efforts of hawksbill sea turtles in nearby Honduras.

Leatherbacks

Leatherback sea turtles are the largest reptiles alive today. Take it from the Cornell Chronicle:

Leatherbacks, the world's largest reptiles, do not have hard shells like other turtles. Instead, they have a softer, leather-like shell. The turtles can weigh up to 1,500 pounds and are eating machines, as one can nosh daily on hundreds of pounds of its favorite meal -- jellyfish. Leatherback sea turtles and jellyfish are found throughout the world's oceans, but the authors of this study think that these leatherbacks are likely enjoying a bountiful jellyfish supply in the Mozambique Channel.
They hint at a further evolutionary conundrum: why would long-distance migration evolve?

Endangered leatherback sea turtles are known for their open-ocean migratory nature and nomadic foraging habits -- traveling thousands of miles. But a Cornell naturalist and his colleagues have discovered an area along the Mozambique coast that the turtles have made their permanent home, according to a study published in Nature's  Scientific Reports.

All that magnetic-field navigation equipment for nothing? One would think neo-Darwinism, stingy as it is, would stop here where life is good. Instead, some of the turtles ventured out 10,000 km toward the south Atlantic Ocean or into the Indian Ocean. The research news says nothing about evolution.

Unhyping big science.

Let's Tell the Truth about Science Funding
Evolution News & Views

A false and sentimental glow surrounds science in the minds of many outside the science world. A reverent belief in the purity of scientists, so tender and mild (except for those intelligent-design scoundrels), is a badge of membership for the enlightened. The cult of science all but denies that professionals in the field are human beings, subject to the familiar corruptions that go with money, power, and prestige.

But then occasionally a scientist or other insider will come along and dash a pitcher of cold water on all that. letter to the editor in the Wall Street Journal by Professor Daniel Metz is thus refreshing. He replies to an  op-ed by MIT president L. Rafael Reif, who laments what Reif sees as the underfunding of basic science.

Interesting guy -- Metz retired as a professor of General Engineering at the University of Illinois at Urbana-Champaign and now races cars among other pursuits. Writes Dr. Metz:

Mr. Reif ignores some facts associated with government funding of research, much of which is funded at universities. Nearly all government-sponsored projects are funded in response to a request for proposals (RFPs). The directions of funded research are thus established not by scientists, but by bureaucrats in the funding agencies. The bureaucrats are graduates of an old-boy network that rewards alumni, contacts, trendism and longevity, with proposal quality coming dead last. It is positively guaranteed that any big, new, government research initiative will send money to Palo Alto, Berkeley, Austin, Ann Arbor, Madison, Champaign and Cambridge.

Government funding of university research has bastardized the definition of a "professor." New assistant professors are quick to realize that actually teaching classes has nothing whatsoever to do with their desire for long-term success and tenure, and in fact teaching is a disincentive. Only bringing in outside research money counts. Universities have become addicted to the mother's milk of government funding. Any major research university could reduce its budget by 50% or more simply by requiring the faculty to actually teach a few classes now and then.

Em. Prof. L. Daniel Metz
Champaign, Ill.

Indeed, the incestuous world of science grants is one of the best-kept secrets of the Federal Government. Billions of dollars are involved and Congressional oversight is unimpressive. Moreover, the system is so big that it effectively shapes research priorities of universities, rather than responding to them. The Federal Government controls and monopolizes science research, and the whole business is in the service of something quite other than the legendary disinterested search for truth.

Addicted and engorged, Big Science isn't what most of the public pictures it to be. Professors don't so much profess -- they suck money as through a straw, thanks to a system that epitomizes the kinds of corruption we associate with government. Now give them more funding? Come to think of it, Rafael Reif is not exactly disinterested on the subject.


Among all the reasons to doubt the authority of a scientific consensus on all matters, this would be one.

False flag?

Michael Zimmerman of Clergy Letter Project Joins Atheists in Making Hay from Dubious "Petition"
David Klinghoffer 

Writing for the Huffington Post, Michael Zimmerman of the Clergy Letter Project has clambered onboard with atheist bloggers Jerry Coyne, P.Z. Myers, and Dan Arel to make hay from a petition effort to ban teaching evolution in public schools. As noted here yesterday, that effort is a very likely phony, transparently so, a false flag operation carried out not by evolution critics but by Darwinists.

That appears to be why the petition's initiator, purportedly seeking signatures, sent it out to P.Z. Myers and other likeminded folks. When I checked last, the few signatures it had received were almost all joke names.

Zimmerman, unlike Coyne, Myers, or Arel, is cagey and seems to hedge on whether the petition is genuine. He writes, "Make no mistake about it. I fully understand that the petition to ban the teaching of evolution is an amateurish publicity stunt -- one without any chance of becoming law." His headline announces, "A Petition Asking Mike Pence to Ban Evolution in the Name of Religion? Utter Hogwash!" But undeterred, he uses it to plunge into a standard lecture about how his Clergy Letter proves that evolution poses no challenge to religious faith.

The simplest and politest response to such a claim is to say that it is utter nonsense. Indeed, the mere existence of The Clergy Letter Project, an organization I founded and currently lead, offers incontrovertible proof of the absurdity of this claim. The Clergy Letter Project consists of more than 14,000 members of the clergy from all corners of the United States representing a wide array of religions and denominations. Members are liberal and conservative, male and female, young and old, and represent every race and ethnicity imaginable. They have only one thing in common: they know that religion and science can be compatible and that the latter poses no threat to the former.

What's that he said about "hogwash"? What Zimmerman has done is launched his own dubious publicity stunt on the back of another dubious publicity stunt. If the petition itself is phony, what you properly do is either point that out, or ignore it.

Obviously, a "moratorium" on teaching evolution is a stupid and wrong thing to propose (it's the opposite of what we advise). Or rather, it would be stupid and wrong if it were offered in sincerity. But a phony proposal intended to generate scare headlines by opportunistic atheists and Darwin apologists, to dishonestly cast evolution skeptics in a false and negative light, doesn't rise to the level of being evaluated on its merits. Zimmerman may think the petition is "hogwash" but if so, it should provide no platform for publicizing his Clergy Letter.

That having been said, I can't let this drop without addressing Zimmerman's own misleading stab at propagandizing for his organization. Take a moment to analyze his statement that "religion and science can be compatible and that the latter poses no threat to the former." As Darwinists often do, he elides there the question of whether Darwinian theory, the scientific idea in question, is satisfactory as science. Or is Darwinism, like the "petition," doubtful too? Agreed, religion is compatible with good science. Absolutely. However, is my religion or yours compatible with bad science, failed science, outdated science, any or all ideas that present themselves in the guise of "science"? That's not a case I'd be eager to try to make.

Zimmerman's Clergy Letter is all vague generalities, useful in efforts to cast orthodox evolutionary theory as something it's not: a harmless fuzzball. Empirical study tells a different story. As John West shows from new polling data in our recent report "Darwin's Corrosive Idea," the creaky, outdated science of neo-Darwinism is indeed at odds with traditional faith, on which it has a corrosive, documented effect. On the other hand, objective evidence of design, in biology and cosmology, is both strong science and what faith traditions would expect.


Take a moment and download the report now. See for yourself.

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.

This chart shows relative brain size as cm3 per 50 kg of body weight. Adapted with modifications from Robert Jurmain, Lynn Kilgore, et al.,

 Introduction to Physical Anthropology

 , 2013-2014 ed. (Wadsworth, Cengage Learning, 2014), p. 357, and "Homo habilis," 

 Encyclopedia Britannica

, 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.