Minimum function v. Darwinism.

The Designed Body, Continued: Coherence Wins, Gradualism Fails -
Steve Laufmann

In a post yesterday, I explored seven insights from Dr. Howard Glicksman’s 81-part series, The Designed Body. Glicksman takes us on a remarkable exploration of the ways that the human body works to stay alive in a world that’s essentially trying to kill it. To survive, the human body must control 40 chemical and physiological factors. Failure with any one of these results in death.

Coherence, Interdependencies, and Fine-Tuning

Though Glicksman uses medical rather than engineering terminology, the human body is an engineering marvel — an amalgam of interlocking chemical and engineering solutions, sort of like chainmail armor — with dozens of diverse, interdependent control systems driving hundreds of functional subsystems, composed of tens of thousands of specialized parts, and comprised of ~37 trillion individual cells. Each cell is itself an engineering marvel, comprised of thousands of interdependent parts, precisely arranged and coordinating their actions. To make this work, the human body generates around 200 specialized cell types and well over ten thousand specialized proteins. All this “unfolds” from a single cell at fertilization, in a precisely choreographed process.

This is not gratuitous complexity — the complexity is real and necessary for survival:

Finely tuned control systems to manage each of the 40 chemical and physiological factors.
Functional coherence across multiple levels of systems and subsystems.
Process coherence across systems, and throughout an individual’s lifecycle.
Interdependencies among systems and processes.
Failure prevention systems to detect and defend against threats, correct errors, and keep everything working.
Coherence is a distinctive property in which each piece-part is necessary for function, but none by itself is sufficient. Only when all the parts operate as a coherent whole does the body survive. Coherence is difficult to achieve and maintain under any circumstances. But survival of the human body takes functional coherence at a scope and scale that we can scarcely fathom — so far beyond our experience as human engineers that we have no comparable systems to compare it to.

At the same time, coherence makes change more difficult. In a coherent system, a major change in one component (or subsystem) usually requires corresponding changes in other components (or subsystems). The more interdependencies, the more work is required to change a component, yet retain overall function of the whole. As any systems architect can attest, once a complex, coherent, interdependent system is built, it takes no small effort to adapt it in significant ways (e.g., to meet new functional requirements).

Are other organisms similarly fine-tuned?

Is similar coherence present in other body plans? Given that survival depends on controlling so many factors, it seems likely that every body plan must have its own version of coherence. Though the types of control systems and their tuning parameters may vary, we’d expect all such controls to be similarly fine-tuned.

Asked the other way, are there any body plans, currently active or anywhere in the fossil record, that do not exhibit finely tuned coherence? I’ve not heard much discussion of this subject, suggesting that either the question is not being asked, or the answers are not defensible.

How to generate a fully functioning, coherent system

Coherent interdependent systems, like the human body, are tough to “bootstrap.” This occurs in two different processes that must overcome the same basic problems:

Phylogenesis (How does a functioning body plan come into existence?)

If all 40 factors must be controlled at all times, else the organism dies, how can a complex control system like any of those presented by Glicksman come into existence? How do you control a chemical or physiological factor while the body waits for evolution to generate a complete control system capable of controlling that factor?

For example, how do you supply oxygen to every cell in a large, complex body without every part of each required body subsystem (e.g., for oxygen exchange, carbon dioxide removal, circulation, iron harvesting, hemoglobin manufacture, and many more). Sure, we might theorize a simpler system to perform these functions, but it’s hard to imagine a partial system that still gets the job done.

Regardless of how simple the simplest possible version of a control system might be, it still requires all the basic functionality of a control system, and these are, by definition, irreducibly complex. In the human body, and most (all?) other complex body plans, the control systems are also interdependent, so having just one of them, or even all but one, isn’t enough.

How many generations are required for random causes to generate the dozens or thousands of parts needed for even one control system, with the correct control logic and just the right fine-tuning? No one knows, but it’s a lot — certainly more than could fit into the age of the universe.

How many generations are available in the absence of all the needed control systems? Exactly zero, since no individuals will survive long enough to reproduce, and any gradual steps toward a functional whole disappear from the population.

Ontogenesis (How does an individual of the body plan come into existence?)

Humans have an elegant solution to the body plan assembly problem — one we’re quite familiar with.

At the moment of fertilization, the human body consists of a single cell. As it grows into thousands and then to hundreds of millions of cells, it must bootstrap the control systems for all 40 survival factors. Each of the systems and subsystems (and their component parts, and the specialized cell types, etc.) must be generated, assembled, and activated, in the right places, in the right order, at the right times. It takes about 9 months for that single cell (aka, zygote) to grow into a coherent, independent whole (aka, tax deduction).

As it’s developing its internal controls, this new life is extremely vulnerable to the forces of nature, so must rely on outside help to survive. With humans this occurs in the mother’s womb. In this extraordinary process, the mother and unborn child coordinate their activities, such that the mother’s systems “cover for” the growing child’s inability to control all the necessary survival factors.

Only when all of its internal control systems are assembled and functioning can the child survive on its own. At the right time, through coordinated signaling (!), birthing occurs and the child’s body switches over to its internal systems to perform their survival chores (e.g., respiration).

It’s important to note that this process involves two different individuals, using completely different yet perfectly integrated mechanisms. Not only does this illustrate the survival challenges facing a complex body while it’s generating its systems, it also highlights the extraordinary engineering required to overcome those challenges — precise, interdependent, finely-tuned, coordinated functional and process coherence, in this case between two different individuals at two very different points in their life cycles.

Just because this is common does not mean it’s ordinary. Aside from the wonder of what’s happening in the process, it’s uncommonly nifty engineering.

Gradualism Fails

How could any gradual process generate coherent, finely tuned systems, when a failure in any part of those systems prevents an individual organism from surviving? This is problematic no matter how much time is available.

As an example, suppose I want to build a car that’s capable of getting me from point A to point B. It minimally takes several dozen parts to make a drivable car. I’m allowed to add only two or three parts at a time (gradual changes), but at each step, I can only keep what I’ve got if it meets the minimum functional requirement of getting me from here to there (survival requires a minimally functioning whole).

Based on these rules (which parallel the survival constraints of living systems), it doesn’t matter how I begin, where I begin, or in what order I add parts — if I start with a tire and add only a couple of parts, I will never get to minimal functionality, even if they’re the right parts and I add them in the right places!

When gradualism faces a complex assembly task, it inevitably fails unless (a) only a couple of parts are required, or (b) there are a number of intermediate stages, each of which is capable of minimal function, and each of which can be reached from a previous viable stage by only a couple of changes. Complex control systems fail on both counts, and thus present an insurmountable hurdle to gradualism.

And this is true regardless of whether the process is directed or undirected!

Knowing what, where, and how to bolt the parts together doesn’t get the whole built (when it must be done in discrete, gradual steps). Bolting random stuff together in random configurations is astoundingly unlikely to produce any useful function, much less ones that will enable survival at each discreet step. Random, undirected changes simply make the impossible even less possible.

This is the basic flaw in the various genetic algorithms that purport to show how life can build itself randomly — minimal functionality is needed in every area at each step along the way, or the whole endeavor crashes.

The Burden of Proof Grows

Coherent interdependence is an intriguing property — extremely difficult to achieve, and equally difficult to change. When coherent interdependence is essential to survival, as it seems to be for all living organisms, the systems view tells us to expect new body plans to appear suddenly, in a functionally complete form, and change rarely, generally in functionally minor ways.

The fossil record aligns almost perfectly with this view. Nearly all body plans appear suddenly, with essentially no precursors, and are followed by long periods of stasis (invariance) — in many cases hundreds of millions of years — during which only minor variations occur.

This greatly increases the burden of proof for anyone espousing gradual causation, like neo-Darwinism. It’s incumbent upon gradualist proposals to address two key requirements:

Hypothesize (and eventually find in the fossil record) a viable organism at each and every discrete step from a single-celled critter to a complex body plan like a human being (i.e., the theory must propose an adaptive continuum). Viability must account for all 40 of Glicksman’s survival factors at each step.
Explain how any proposed causal mechanism(s) are sufficient to produce all the necessary changes for that discreet step within a single generation. Random causes, for example, cannot explain more than a couple of coherent changes at any given step, much less at every step.
Efforts to date along these lines have been woefully lacking. Admittedly, this is an enormously hard problem, so perhaps we’re being too hard on the Darwinists. But science offers limited compassion for failed theories, especially when the supporting arguments consist mainly of vague story-telling about happy accidents in large quantities, using cool-sounding made-up words like de novo origination (new stuff that pops into existence out of nothing).

Any gradualist theory that fails to address these most fundamental issues with more than an appeal to authority (we’re smarter than you), or an appeal to faith (trust us, we’ll find the answer), should be viewed with skepticism at best.

Think Different

Of course, doctors like Glicksman, who face the real-world implications of body subsystems that have stopped working, and engineers, who need to build systems that work in the real world, already know these things.

Coherent, finely tuned, interdependent, systems of systems are essential to life. They’re needed at the outset, and at each step along the way. Even single-celled organisms cannot live without coherent, finely tuned internal subsystems.

Coherence is thus a prerequisite for life — not the outcome of life, as Darwin supposed. This simple fact is profoundly problematic for material causation. Gradual changes simply cannot produce such systems. Neither can random causes. For Darwinists, the burden of proof grows, while the explanatory power of neo-Darwinism fizzles. Maybe it’s time to rethink everything.

In the human body, Glicksman exposes a world of coherent complexity that we rarely think about, yet which demands a rational conversation. The questions raised are intriguing. Regardless of personal worldviews, any proposal that aligns with the preponderance of the data deserves less knee-jerk derision and more thoughtful consideration, both in the scientific community and in the public square.

Glicksman’s series, The Designed Body, is worth a read. Think, understand, and be amazed. And also, maybe, be thankful to the designing engineer — the architect of life — who made the human body, and you, possible.


- See more at: http://www.evolutionnews.org/2017/03/designed-body-coherence-wins-gradualism-fails/#sthash.dYZcIjAM.dpuf

The best heritage you can leave your kids.

A Ph.D in commonsense from real life U.

The maths of fakery

Precisely accurate?

The case for design remains undeniable.

The Envelope, Please? Doug Axe and Undeniable Are World Magazine 2016 Science Book of the Year! - 
David Klinghoffer

Update: I see that Doug Axe’s book is in its rightful place at the top of Amazon’s bestseller list under Organic Evolution. In fact, of the top ten books on that list, four are by authors affiliated with Discovery Institute’s Center for Science & Culture — Axe, Meyer, Behe, and Johnson. Nice

Unlike the Oscars, World Magazine and its editor Marvin Olasky don’t employ the accounting firm of PricewaterhouseCoopers  to tell them who won Book of the Year. So we trust there’s been no mix-up with the envelopes. In the category of “Science, math, and worldview,” the Book of the Year for 2016 is Undeniable: How Biology Confirms Our Intuition That Life Is Designed.  by Douglas Axe!

Congratulations to Dr. Axe of Biologic Institute — and to our biologist colleague Michael Denton too, who not only figures prominently in Axe’s book, but also tops World‘s shortlist in the same category with his book from Discovery Institute Press, Evolution: Still a Theory in Crisis. Dr. Denton is followed on the Short List by Tom Wolfe’s The Kingdom of Speech, which tweaks Darwin on the mystery of human language and its evolution.

Mr. Olasky is one journalist who has carefully studied the debate about biological origins. His write-up accompanying the announcement is characteristically well informed. It all starts with Denton:

In 1985 biologist Michael Denton noted — in Evolution: A Theory in Crisis — that Darwinism was cruising for a bruising. Now he’s back with Evolution: Still a Theory in Crisis, which shows — with three decades of new research — that Darwin’s theory needs hip replacements, for “there is now a growing chorus of dissent within mainstream evolutionary biology.”

He’s right. Darwin himself wrote, “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous successive slight modifications, my theory would absolutely break down.” It has broken down, as advances in paleontology, genomics, and developmental biology show.

For example, mainstream researchers Douglas Erwin and Eric Davidson have noted that “classic evolutionary theory, based on selection of small incremental changes,” is clearly inadequate. Günter Wagner in Homology, Genes, and Evolutionary Innovation writes, “Adaptive modifications often involve only the modification of existing cis-regulatory elements,” but truly new developments “require large-scale reorganizations of the gene regulatory network.”

Moving on to Doug Axe and his achievement:

Axe’s subtitle offers a shocking suggestion: How Biology Confirms Our Intuition That Life Is Designed. Axe has an elite science education and record of journal publication, but he commits treason to the scientism guild when he writes that “people who will never earn PhDs [can] become full participants in the scientific debates that matter to them.” Undeniable is our science book of the year because it’s a largely nontechnical argument showing the incredible improbability that life has evolved as Darwin theorized. Axe offers example after example to show that “functional coherence makes accidental invention fantastically improbable and therefore physically impossible. Invention can’t happen by accident.” He shows how “the claim that evolution did invent proteins, cell types, organs, and life forms is scientifically legitimate only if we know evolution can invent these things.” He then shows how we have learned that evolution can’t.

On Denton:

When Denton in 1985 wrote Evolution: A Theory in Crisis, he was a lonely PhD holder in biochemistry crying out in the wilderness. Now, just about everyone who doesn’t have a monetary or professional stake in defending Darwinism is seeing the theory’s ability to explain small changes but its incompetence in explaining macroevolution — and the adaptive transitional forms Darwin predicted we’d find are still absent without leave. Denton shows how advances in our knowledge of genetics, paleontology, and developmental biology have threatened the faith that macromutations by chance put together complex structures like a diaphragm, a bat’s wing, a branched bipinnate feather, etc.

The point about “monetary or professional stakes” is spot on. Social prestige, self-esteem, vanity — these figure into it as well, as Tom Wolfe repeatedly underlines in his excellent book.

Undeniably, Darwin’s theory is guarded at the highest level by scientists whose careers and the income and esteem that go with them are inextricably tied up with the defense of orthodox evolutionary theory. Scientists like Doug Axe and Michael Denton are a threat to all that, which is why they earn such venom from the establishment — and admiration from open-minded thinkers like Olasky and his colleagues at World.

History re:The ides of march.

Human history undersea.

Time to call it a day re:A United States of Europe?

Next to the witness stand for design;whales

More "Design of Life" Evidence: Whales

Evolution News & Views November 4, 2015 7:32 AM

Living Waters: Intelligent Design in the Oceans of the Earth shares amazing information about humpback whales: their enigmatic songs, their multiple adaptations for aquatic life that defy the evolutionary mechanism, and the "miraculous web" of blood vessels that refrigerates the male reproductive organs to safe levels for sperm production. All of it defies explanations based on natural selection. But that's just the beginning when it comes to the largest animals that have ever lived -- larger even than the largest dinosaurs (see Brian Switek's discussion onSlate). Want to see humpback songs as sheet music? The Smithsonianhas printouts and recordings.

More About the Male Refrigeration System

The system actually works better when the whale swims hard. How can that be, when the testes are located right between the abdominal swimming muscles? It's like trying to keep a refrigerator cold between two furnaces.

It works because the blood pumps harder during exercise, allowing more heat to escape into the water through the dorsal fin and tail. The higher volume of cool venous blood then enters the "miraculous web" (Latin rete mirabile, read more here) between the abdominal muscles, where the heat from the arteries is transferred to the cooler veins before entering the testes. It's a marvelous solution: a "counter-current heat exchanger" (CCHE) mechanism.

As Richard Sternberg and Paul Nelson explain in the film, without both internal testes and the refrigeration mechanism existing simultaneously, natural selection would halt, and whales would have gone extinct. Females, too, have a CCHE to protect the young during pregnancy. Similar CCHE systems are found in other marine mammals such as manatees and seals, providing more unlikely examples of "convergent evolution."

Conserving Energy

Blue whales are the largest whales, making them the largest animals on earth. How do they sustain their massive weight? An article from NOAA Fisheries says that they target the highest-quality prey in order to maximize energy gain.

These huge animals can span a basketball court and weigh as much as 25 large elephants combined, the article says. But they feed on tiny fish called krill that are less than an inch long. When prey is scarce, blue whales conserve oxygen for deep dives. When the fish are plentiful, they ram through the schools at high speed, a strategy called lunge-feeding. They have their ROI (return on investment) all figured out. By watching tagged blue whales off the California coast, Elliott Hazen and a NOAA research team were able to figure out their optimization strategy.

"The magic number for krill seems to be about 100 to 200 individuals in a cubic meter of water," Hazen said. "If it's below that range, blue whales use a strategy to conserve oxygen and feed less frequently. If it's above that, they'll feed at very high rates and invest more effort."

Long-Distance Travelers

Whales have an incredible capacity for long-distance migration. A pygmy blue whale set a new record. Science reports that a female named Isabela that had been photographed at the Galapagos Islands was seen eight years later off the coast of Chile, having traveled 5,200 kilometers, "the longest recorded latitudinal migration made by any Southern Hemisphere blue whale on record." Most likely this is an annual trip the whales make, over 3,200 miles one-way.

Humpback whales are long-distance migrators too. The Australians have "a cause for celebration" now that conservation efforts have led to a remarkable rebound in their numbers down under, Science Daily said.

Captain Dave Anderson, featured in the Illustra film, often sees humpbacks off Dana Point, California, that have traveled south from Alaska, where they had delighted viewers on cruise ships. PhysOrgreports the first sighting of a humpback near Hawaii on September 29, over a month earlier than normal. About 10,000 humpbacks winter in the oceans around Hawaii, usually November through May. That's where Anderson got that beautiful drone shot of a humpback with her calf.

Lucky Shot

You may recall the dramatic slow-motion scene in Living Waters of a humpback breaching the surface, rising high above the water and landing on its back with a mighty splash. Lad Allen and Jerry Harned got lucky on that shot. They were filming off the coast of Monterey with their Red Epic high-speed camera, looking for whales. But where are you going to point the camera, when they could be anywhere around the 360-degree horizon?arned pointed it out over the featureless water, turned on the pre-roll (a kind of camera memory) hopefully. As if on cue, the whale shot up right in the center of the field. Jerry hurriedly switched on the record button and got the whole sequence in high-definition slow motion -- a shot that still gives him chills when he thinks about it. As Paul Nelson said, "the language fails" when you see such wonders.

The Planet Needs Whales

Whales play a vital role in the global nutrient cycle. The Proceedings of the National Academy of Sciences published a special issue in October about large mammals. One of the papers discussed "Global nutrient transport in a world of giants," describing the oversized role that whales play in spreading nitrogen around for other ecological communities:

Despite their vastly decreased numbers, the important role of whales in distributing nutrients is just now coming to light.Whales transport nutrients laterally, in moving between feeding and breeding areas, and vertically, by transporting nutrients from nutrient-rich deep waters to surface waters via fecal plumes and urine. Studies in the Gulf of Maine show that cetaceans and other marine mammals deliver large amounts of N to the photic zone by feeding at or below the thermocline and then excreting urea and metabolic fecal N near the surface. [Emphasis added.]

The scientists estimate that whales transport almost four times as much nitrogen as terrestrial animals do. They also transport phosphorus and iron.

"Because of their enormous size and high mobility (and despite having many fewer species), great whales might have once transported nutrients away from concentration gradients more efficiently than terrestrial mammals," the writers say. These nutrients are also "assimilated more rapidly, and contribute to system productivity more directly than on land."

One of the diagrams in the paper, reproduced by Science Daily, shows the dependency of land animals on this nutrient cycle. Seabirds and "anadromous fish" like salmon carry these nutrients up rivers, where land animals like bears feed on the fish, profiting from the nutrients that whales had brought up from the deep ocean.

The authors even think that whales play a role in carbon dioxide levels that can affect the planet's climate. They estimate that whale populations have been reduced by 90 percent from levels before the Moby Dick whaling days -- raising alarms about ecological damage to planetary ecosystems. This interconnectedness of life raises fresh impetus to preserve these magnificent creatures.

A paper in Nature Communications reports something interesting about whale guts. Baleen whales have microbiomes with similarities to land animals, including humans. This is likely because, although they feed exclusively on marine animals, they have to digest chitin -- a polysaccharide from arthropod exoskeletons that is somewhat similar to the cellulose in plants that cows eat.

Like land herbivores, whales also have a foregut that helps pre-digest the polysaccharides. Since there are similarities and differences in the gut microbiomes, though, it's not clear they successfully tied the findings to the old tale of whale evolution from a four-footed land animal.

"Mammals host gut microbiomes of immense physiological consequence, but the determinants of diversity in these communities remain poorly understood," the paper begins sheepishly. "Diet appearsto be the dominant factor, but host phylogeny also seems to be an important, if unpredictable, correlate."

Sternberg explains in the film how the whale-evolution Captain Dave Anderson has taken an active role in rescuing whales. A thousand whales and dolphins a day, he says, die from being trapped in fishing nets. His Dolphin Safari website tells the story of Lily the gray whale, whose rescue made TV news and inspired an award-winning book Anderson wrote to raise awareness of the plight of marine mammals caught in nets.

Recently, he has been developing a low-cost floating beacon that whale watchers can fasten to nets that whales are dragging along with them. This allows rescuers to find the whale again and cut it free, using a special pole with V-shaped knife that allows the rescuer to cut off the net off without harming the animal.

Sadly, whales and dolphins are also threatened by a growing problem: plastic trash. PhysOrg show a picture of a dead sperm whale on a beach on Taiwan that was found to have plastic bags and fishing nets in its stomach. This may be one cause of the mysterious beachings of whales you hear about from time to time.

Anderson tells about how mylar balloons, let loose by thoughtless partygoers, often wind up in the ocean. Deflated and floating on the surface, they are mistaken for jellyfish, part of the whale's diet, and can lead to death when ingested. We all need to realize that trash washed down our storm drains can threaten the most magnificent animals on earth.

But let's end on a happy note. The drones that gave the Illustra team such spectacular aerial photographs of whales and dolphins are proving useful for science. NOAA Fisheries reports that hubcap-sized hexacopter drones are now being used to study gray whales from above. Like humpbacks, gray whales have made a remarkable comeback since 1994 when restrictions on whaling were imposed. With these new aerial monitoring tools, scientists hope to spread this success story to other species that are still endangered.

"Hopefully in the not-too-distant future," a NOAA marine biologist says, "there will be many healthy populations of large whales to study." With that, the beauty of their intelligent design will also be preserved for posterity.sequence is more "artistic license" than demonstrable fact.Captain Dave Anderson has taken an active role in rescuing whales. A thousand whales and dolphins a day, he says, die from being trapped in fishing nets. His Dolphin Safari website tells the story of Lily the gray whale, whose rescue made TV news and inspired an award-winning book Anderson wrote to raise awareness of the plight of marine mammals caught in nets.

Recently, he has been developing a low-cost floating beacon that whale watchers can fasten to nets that whales are dragging along with them. This allows rescuers to find the whale again and cut it free, using a special pole with V-shaped knife that allows the rescuer to cut off the net off without harming the animal.

Sadly, whales and dolphins are also threatened by a growing problem: plastic trash. PhysOrg show a picture of a dead sperm whale on a beach on Taiwan that was found to have plastic bags and fishing nets in its stomach. This may be one cause of the mysterious beachings of whales you hear about from time to time.

Anderson tells about how mylar balloons, let loose by thoughtless partygoers, often wind up in the ocean. Deflated and floating on the surface, they are mistaken for jellyfish, part of the whale's diet, and can lead to death when ingested. We all need to realize that trash washed down our storm drains can threaten the most magnificent animals on earth.

But let's end on a happy note. The drones that gave the Illustra team such spectacular aerial photographs of whales and dolphins are proving useful for science. NOAA Fisheries reports that hubcap-sized hexacopter drones are now being used to study gray whales from above. Like humpbacks, gray whales have made a remarkable comeback since 1994 when restrictions on whaling were imposed. With these new aerial monitoring tools, scientists hope to spread this success story to other species that are still endangered.

"Hopefully in the not-too-distant future," a NOAA marine biologist says, "there will be many healthy populations of large whales to study." With that, the beauty of their intelligent design will also be preserved for posterity.

Is democracy past its prime?:Pros and cons.

The revolution rolls on

Michael Behe's Challenge -- Past, Present, and Future
Evolution News & Views

Twenty years after Darwin's Black Box, the irreducibly complex outboard motors showcased by Michael Behe still confound Darwinism. That's one theme of our upcoming documentary Revolutionary:  Revolutionary: Michael Behe & The Mystery of Molecular Machines, which heads to Texas next month for previews. Behe's challenge is the past, the present, and the future.

Look at this quote from a paper in the  Proceedings of the National Academy of Sciences:

The bacterial flagellar system has been an object of intense study for many years. It has helped to elucidate issues of assembly, motility, and chemotaxis at a molecular level in a relatively simple system, typically containing ∼40 different proteins. It has also been the icon for creationists in the United States who deny evolution. [Emphasis added.]
Ah, the bacterial flagellar system. The paper by scientists from Germany, the Netherlands, Israel, and the U.S. (University of Virginia) purports to show how a simpler flagellum in a species of archaea provides evidence for evolution of the more complex flagellum in bacteria. It's satisfying to reflect that the authors remain irritated by the "creationist" icon. They can't let it rest.

As expected, they refuse to cite Behe directly (or any other ID source), so their only references supporting the "creationist" charge are to 6-to-12-year-old writings by Kenneth Miller, Barbara Forrest, and E.H. Egelmann. Have it your way. What matters is the substance of Behe's argument and evidence, which attracted the attention of researchers in four nations.

Meanwhile, farther east -- particularly in Japan -- scientists don't seem quite so motivated to defend Darwin. Two new papers dealing with molecular motors show their openness to design thinking.

Cilium Mimicry

The first deals with designing a mimic of cilia, another one of Behe's examples of irreducibly complex (IC) systems. Five biomedical engineers from Tokyo, writing in Science Advances, succeeded in making "Artificial cilia as autonomous nanoactuators." They call this "Design of a gradient self-oscillating polymer brush with controlled unidirectional motion."

Here, we have prepared a polymer brush surface similar to a living cilium, exhibiting self-oscillating and unidirectional wave motion of the grafted polymer at the nanometer scale.... This study provides a new concept to design autonomous polymer brush surfaces effective in the nanometer scale as bioinspired dynamic soft materials.
They pay tribute to the design in cilia and other cellular machines that inspired their own work:

Spatiotemporally well-ordered mechanical actuation of biomacromolecules in the nanometer-order scale driven by chemical reactions, such as enzymatic reactions, plays an important role in living organisms. For example, motor proteins bind to a polarized cytoskeletal filaments and use the energy derived from repeated cycles of adenosine 5′-triphosphate hydrolysis to move steadily along them. In addition, many motor proteins carry membrane-enclosed organelles to their appropriate locations in the cell. Cytoskeletal motor proteins move unidirectionally along an oriented polymer track. In this process, they use chemical energy to propel themselves along a linear path, and the direction of sliding is dependent on the structural polarity of the track. Recently, the construction and design of these biomolecular motor systems with well-controlled unidirectional motion have become an area of great focus in advanced sciences.
The word "design" appears ten times in the paper. References to evolution are completely absent.

Another team worked on imitating the cilia in hair cells of the inner ear. Publishing in Nature's journal Scientific Reports, they proudly announce, "Here we present a novel, completely biomimetic flow sensor which attempts to replicate the intricate morphological organization and function of the hair bundles of the hair cells" found in zebrafish. Neither of the cheap imitations, however, contain anything like intraflagellar transport in biological cilia (see our report). As for the origin of these intricate structures, the team treated evolution as magic: "Nature's evolutionary path led to sensors of high functionality and robustness, in terms of material properties, anatomical architecture and energy expenditure." That's all the press Darwin got. They used the word design, though, 15 times.

Flagellum Focus

Back in the 1990s, Behe relied on relatively crude electron micrographs of flagella. Imagine twenty years ago if he had been able to see in detail one protein in the stator of the flagellum. That's what Japanese scientists from Nagoya University revealed with advanced imaging techniques. So has the case for design grown stronger or weaker since Darwin's Black Box was published? A paper in Nature's open-access journal Scientific Reports reveals the answer. You can see their composite image of the stator protein MotA here:



It looks more like a well-designed outboard motor than ever!

Many bacterial species use spiral propellers (flagella) attached to motors to move through a liquid environment. An interaction between the rotor and stator components of the motor generates the rotational force required for movement. The stator converts electrochemical energy into mechanical force after undergoing a structural change caused by a movement of charged particles (ions) through an internal channel. Previous studies investigated the stator and its interaction with the rotor by constructing mutant proteins and analyzing their functions. However, little was known about stator structure.
A team of Japanese researchers led by Homma's laboratory of Nagoya University have now purified the stator protein MotA from a bacterium found in hot springs (Aquifex aeolicus) and analyzed its three-dimensional structure using electron microscopy mainly in cooperation with Namba's laboratory of Osaka University.

The stator protein MotA shows an elegantly crafted channel for ions. These are arranged in groups of four at the base of the stator on the cytoplasmic side. Two slender molecules of MotB extend into the periplasm. Identifying the structure is an important step on the way to figuring out how the flagellum works.

The stator is one of the most important parts for the proper functioning of the bacterial flagellar motor, and is believed to work as an energy-converting unit that transduces electrochemical potential gradient across the cytoplasmic membrane into mechanical force. The interaction surfaces of the stator and the rotor have been well studied by mutational analyses. However, the mechanism governing energy conversion remains unknown because of the lack of structural information on the stator.
How is chemical energy converted into rotational energy (torque)? "It is believed that the ion influx through the channel induces a conformational change in the stator, allowing its interaction with the rotor to generate torque," they say.

A little reflection suggests that the components must be well matched. Imagine for a moment a flow of ping-pong balls trying to turn a large metal turbine. It wouldn't work. Somehow, in ways still to be determined two decades after Behe's book was published, tiny hydrogen ions or sodium ions are able to make particular parts of the stator undergo conformational changes that can get the rotor to turn. How that works is bound to be interesting. We know from the discussion in Unlocking the Mystery of Life that not only must the parts be well matched, they must be assembled in the right order, in the right amounts, at the right place and time -- all directed by instructions in the genetic code.

While these Japanese researchers do not mention Behe or his conclusions, their work underscores the case for irreducible complex molecular machines as prima facie evidence for intelligent design. Nowhere do they credit evolution for the motors of the cell:

Various motor proteins are essential for different biological activities such as cell locomotion, cell morphogenesis, metabolism, and material transport. Motor proteins convert various types of energy, such as ATP hydrolysis or electrochemical potential, into mechanical force for directional motion. Motor proteins are divided into two types: linear motors, such as myosin-actin and kinesin/dynein microtubule motors; and rotary motors, such as ATP synthase and bacterial flagellar motor.
Behe's intuitive first impression of the flagellum, "That's an outboard motor!" has stood the test of time. That's what the Japanese teams still call the cilium and the flagellum in 2016.

Scratching the Itch

Now back to the PNAS paper. Did the Western nations solve Michael Behe's challenge? If so, they have a strange way of claiming success:

The proteins that form the bacterial flagellar system have no known homologs in eukaryotic cells. The eukaryotic flagellar [sic], based on a microtubule-containing axoneme, is vastly more complicated. In fact, the current estimate for the number of different proteins in the axoneme is ∼425. In contrast, the archaeal flagellar system appears simpler than the bacterial one and can contain as few as 13 different proteins. As with the eukaryotic flagellar system, the archaeal one does not have homology with the bacterial one and must have arisen by means of convergent evolution.
Ah yes, convergent evolution again. But think about what they say here. The "vastly more complicated" eukaryotic flagellum has no known commonalities with the bacterial flagellum, and the bacterial flagellum has no homolog in the archaeal flagellum: "In archaeal flagellins, however, no homology has yet been found outside of the N-terminal domain with any bacterial or eukaryotic proteins." Do they show any common ancestry between these motors? None. Are we to believe, then, that blind processes happened upon three naturalistic miracles independently?

Notice that the archaeal flagellar system that "appears simpler" contains as few as 13 different proteins. How many different parts were required for the mousetrap? Behe's pithy illustration of an IC system had only five parts. How much more is an IC system with 13 parts, or with 40 parts, each unrelated to machines with similar functions in other types of cells?

If the best that evolutionists can come up with in response to Behe is "convergent evolution," then his 1996 statement can be seen as prescient: "An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution" (p. 39). Only he could reword it now with much more confidence: Irreducibly complex biological systems continue to pose a powerful challenge to Darwinian evolution and are best explained by intelligent design.

Will the real macroevolution please stand up

“Macroevolution” and Its Discontents
Evolution News

The term “macroevolution” has problems. Why? Among other things, because it’s a term that means different things to different people. Case in point: an email correspondent points out a random usage on a BioLogos Forum thread, “Is evolution continuing? Is God still creating?” It’s a comment from a Forum participant, Socratic.Fanatic, about rabbits:

Northern and southern populations of a common species of North American rabbit is quickly becoming TWO distinct species and populations which can no longer cross-reproduce. It is a great example of macroevolution directly observable right in front of our eyes.

Without wishing to jump down Fanatic’s throat, we took a moment to Google that one and could not find anything that resembles it — nothing about speciation in a North American rabbits. It’s possible we didn’t look hard enough. In any case, the phrase “quickly becoming” suggests the populations have achieved reproductive isolation, which implies they aren’t truly distinct species.

We asked for a reference, and no doubt Fanatic will supply one in good time. It’s possible that he’s thinking of two squirrel populations on opposite sides of the Grand Canyon, which are almost identical.

In any event, let’s review two different classes of definitions of “macroevolution” found in a couple of college biology textbooks that we just grabbed off the shelf. They give two different definitions of the word.

(1) One, represented by Douglas Futuyma textbook Evolutionary Biology (1998),defines “macroevolution” in terms of the taxonomic hierarchy: “the origin and diversification of higher taxa.”

And what are “higher taxa”? Higher taxa are generally considered any taxa above “species.” That would include genera and above. That point will become important in just a moment.

(2) Others, represented by Campbell’s Biology (1999), define “macroevolution” in terms of the origin of biological novelty: “Evolutionary change on a grand scale, encompassing the origin of novel designs, evolutionary trends, adaptive radiation, and mass extinction.”

Regarding Definition (1), Michael Behe takes a similar approach in The Edge of Evolution  where he says evolution at the species level is feasible.

He allows that evolution at the genera, family, or order level could be possible. But as he argues in the book, evolution at the class level or above is “beyond the edge of evolution.” So if macroevolution includes evolution at the genera, family, or order level, Behe concludes that what some consider “macroevolution” might be possible.

As for Definition (2), the theory of intelligent design has no problems with macroevolution when defined as “mass extinction.” However, many ID proponents are skeptical that material mechanisms can produce novel traits. So here it might be fair to say ID poses its biggest challenge to “macroevolution.”

But the formation of a new species isn’t necessarily a big deal for ID. In fact, pending clarification on the rabbit issue, we’re skeptical that this rabbit example entails the evolution of any kind of biological novelty. At best it’s probably just two species that are partially reproductively separated.

In short, what’s at stake are somewhat semantic questions about how we define “macroevolution.” The key point is that we know there are limits to what Darwinian evolution can accomplish. We see these limits in experiments on features that require multiple mutations before giving any advantage. Darwinian evolution gets stuck.

For example, Douglas Axe has found that in prokaryotes the limit is more than six mutations to get an advantage. Behe suggests that in multicellular organisms, any feature that requires more than two mutations to give an advantage is beyond the limit of what unguided evolution can do.

Anything below these limits is microevolution. Anything above it cannot happen by Darwinian mechanisms, mathematically speaking. Perhaps one could say that is “macroevolution.”


- See more at: http://evolutionnews.org/2017/03/macroevolution-and-its-complaints/#sthash.tofHv6XE.dpuf

For a change,something we can all agree on.

The science of intelligent design typically focuses on details, “steel-hard facts,” as as Douglas Axe puts it.Sometimes, if carried to an extreme, that can be a fault. Now and again, therefore, it’s good to take a step back and ponder the biggest picture of life and its wonder, beauty, and charm.

In this from BBC One, David Attenborough offers the voiceover — a reading of the lyrics of Louis Armstrong’s “What a Wonderful World.” Perfect. All this from dumb natural forces and blind shuffling? Also nice to report that we came across on this over at Why Evolution Is True,where there would more typically be cause for clash than concord. Cheers, Dr. Coyne!

A discovery is turning OOL Science's circus into a full fledged carnival

Life in the Fast Lane — Microfossils, 3.77 Billion Years Old, Pose Challenge to Materialist Presuppositions - 
Evolution News

A paper in Nature reports the discovery of fossil microbes possibly older, even much older, than any found previously. The lead author is biogeochemist Matthew Dodd, a PhD student at University College London. If the paper is right, these Canadian fossils could be 3.77 billion years old, or even as old as — hold onto your hat, in case you’re wearing one — 4.28 billion years.

From the Abstract:

Although it is not known when or where life on Earth began, some of the earliest habitable environments may have been submarine-hydrothermal vents. Here we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,280 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Quebec, Canada. These structures occur as micrometre-scale haematite tubes and filaments with morphologies and mineral assemblages similar to those of filamentous microorganisms from modern hydrothermal vent precipitates and analogous microfossils in younger rocks. The Nuvvuagittuq rocks contain isotopically light carbon in carbonate and carbonaceous material, which occurs as graphitic inclusions in diagenetic carbonate rosettes, apatite blades intergrown among carbonate rosettes and magnetite–haematite granules, and is associated with carbonate in direct contact with the putative microfossils.

This new paper is interesting to compare with a paper from last year, Nutman et al.,“Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures,”  -   also in Nature, which found microbial structures that are a bit younger.

But the “microbial structures” from Nutman et al. 2016 are different from these new “microfossils” presented by Dodd et al. 2017. In Nutman et al., they only found stromatolite-type structures rather than actual microfossils. Some stromatolite experts were a bit skeptical that what they found were really stromatolites.

But the new paper by Dodd and his colleagues, “Evidence for early life in Earth’s oldest hydrothermal vent precipitates,”  seems to offer potential bacteria-like microfossils. They are tiny black carbonaceous spheres and “hematite tubes” which the authors think are biogenically created. We’ve seen more convincing ancient microfossils, but these aren’t bad.

According to Dodd et al., these new finds would be the oldest known microfossils, if that is in fact what they are. Very interesting. If so, that just keeps pushing unquestionable evidence of life’s existence on Earth further and further back, which leaves less and less time for the origin of life to have occurred by unguided chemical evolution after Earth became habitable.

If they are in fact 4.28 billion years old, then that would mean there was life very, very early in Earth’s history — as Cyril Ponnamperuma said, it’s like “instant life.”

In zeroing in on this point, theWashington Post  quotes Dodd:

If their results are confirmed, they will boost a belief that organisms arose very early in the history of Earth — and may find it just as easy to evolve on worlds beyond our own.

“The process to kick-start life may not need a significant length of time or special chemistry, but could actually be a relatively simple process to get started,” said Matthew Dodd, , a biogeochemist at University College London and the lead author of the paper. “It has big implications for whether life is abundant or not in the universe.”

A “relatively simple process”? He’s right about the discovery having “big implications,” but maybe not in the way he intends.

It seems there are three observations to make: 1) The more we know, the more it seems that life arose rapidly on the early Earth, even more quickly that we previously realized. 2) How even the simplest life could arise, given materialist presuppositions, remains a profound mystery. This is the subject of Stephen Meyer’s book Signature in the Cell. 3) If life arises so easily, as Coyne’s friend Dr. Dodd suggests, then it’s strange we’ve seen no signs of it, at least not in an intelligent form, across the cosmos.

Taken together, these call into question materialist presuppositions, in the light of which 1, 2, and 3 present a tangle of contradictions. On the other hand, as a source of purposeful agency able to bring life into existence 1) quickly, 2) despite obstacles in the path of purely material processes, 3) uniquely, as it appears for now, on one planet, intelligent design fits the bill.


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