Is the most prized of Darwinism's crown jewels actually costume jewelry?

Early Whale Echolocation Was Fully Formed
Evolution News & Views

Evolutionists are determined to keep the narrative of whale evolution, one of their "Great Transformation" stories, despite the evidence. It's too good to give up. Picture the egg on the faces of PBS producers if, after 15 years of promoting their TV series Evolution (and they're still promoting it on their website with teachers' guides and student guides), they had to backtrack and tell teachers that those animations of land creatures evolving into whales owed more to fancy than fact. Imagine the blush on former Nature editor Henry Gee's face if he had to confess that one of his "Evolution Gems" was junk jewelry.

Case in point: a paper in Current Biology says a fossil dolphin was a product of evolution, even as the authors admit it had modern-looking echolocation. More on that in a bit. Suffice to say the evidence debunking whale evolution has been out there a long time. Our free online book, Getting the Facts Straight: A Viewer's Guide to PBS's Evolution, shows by logic and evidence that the story can't float. Jonathan Wells found back in 2007 that schools were still using the flawed TV series; but here we are, almost a decade later, and it's still a flagship product on the PBS website Evolution. Nature still promotes its "15 Evolutionary Gems" including the whale narrative. They observe memorably:

This study demonstrates the existence of potential transition forms in the fossil record. Many other examples could have been highlighted, and there is every reason to think that many others await discovery, especially in groups that are well represented in the fossil record.
Wishful thinking should not take the place of observational evidence. Yet Henry Gee and his co-authors exhibited Ambulocetus and Pakicetus as fossils that could fill in the narrative, even though they had four legs (Pakicetus was no more aquatic than a tapir, its discoverer admitted, and terrestrial Ambulocetus had large feet, nothing like flippers). The only "transitional" characteristic alleged from these fossils is their inner ear anatomy. Casey Luskin also wrote here in 2010 about the other fossil mentioned, Indohyus, a small mammal like a mouse-deer that is even less whale-like than the other two. From this raccoon-sized four-legged land animal the great sperm whale sprang -- if you have sufficient evolutionary imagination.

With those reminders as a backdrop, let's see what Morgan Churchill and four others found to support "The Origin of High-Frequency Hearing in Whales." Here's their list of highlights from analysis of a fossil they named Echovenator ("echo hunter"), found in South Carolina (across the globe from Pakistan, home of the other purported whale ancestors):

An ancient toothed whale is described, which possesses a well-preserved inner ear

Features associated with ultrasonic hearing are preserved in the ear of this whale

Ultrasonic hearing evolved with echolocation in the first toothed whales

Hearing at higher frequencies began in the ancestors of toothed whales

In other words, an extinct dolphin with complete echolocation and high-frequency hearing, just like in modern dolphins. If the Darwinians cannot build up a transitional form from the starting line, it doesn't look like they're doing well showing whale evolution from the finish line. This fossil is already across.

But here comes the spin:

When viewed in a phylogenetic context (Figure 3), this indicates that Eocene cetaceans could hear higher frequencies than their terrestrial ancestors. This suggests that adaptations for hearing higher frequencies preceded the evolution of Odontoceti [toothed whales] and that this capability was further developed and then co-opted for echolocation by early members of this clade.
Figure 3 is a phylogenetic tree, topped by drawings of inner ear structures. The more detailed drawings in the Supplement appear to show complex inner ears with all the parts. Without Darwin-colored glasses on, it's hard to see what the authors claim to see.

Other than Echovenator belonging to a class of extinct Odontocetes, it doesn't seem that different from living dolphins. The artwork at Phys.org shows actively echolocating dolphins. What, exactly, makes this animal part of the "Great Transformations" narrative? Phys.org teases with verbiage about this "ancient relative of the modern dolphin". We are told, "A newly-named fossil whale species had superior high-frequency hearing ability, helped in part by the unique shape of inner ear features that have given scientists new clues about the evolution of this specialized sense."

Maybe Figure 4 will help display the promised clues. This shows animals with ultrasonic hearing, and other animals with infrasonic hearing. All the toothed whales (including Echovenator) are within the ultrasonic group. Baleen whales and hippos are in the infrasonic group. Principal-component analysis shows "no overlap" between the groups. But wait! We need a transition. We see two data points between, both called "Archaeocetes" (ancient whales), which we are told represent "the paraphyletic stem group that gave rise to all extant cetaceans." But the very next sentence admits, "The hearing abilities of archaeocetes have been difficult to infer, with some studies supporting high-frequency hearing and others supporting low-frequency hearing."

Here's where a "phylogenetic context" maintains the narrative. There are hundreds of fossils of archaeocetes, such as Basilosaurus, but these were large extinct whales that probably lived full-time in the ocean and were incapable of terrestrial locomotion. Since evolution theorists teach that archaeocetes lie somewhere between hippos and toothed whales, they must have been on the way to developing high-frequency hearing -- even though their hearing abilities have been "difficult to infer." Got it? So we'll place them in a transitional position in the diagram in Figure 4, and we'll put Echovenator near the inside lower edge of the ultrasonic group to make it look like it co-opted high-frequency hearing for echolocation.

We learn more clues from the Phys.org article. First, the fossil was found back in 2001, but its ear structures were just analyzed now after the NSF provided $220,000 in funds "to conduct the first wide-ranging study of cetacean skull development in nearly a century."

Another thing we find is that the ability to hear high-frequency sounds will require rewriting the textbooks. "The research pushes the origin of high frequency hearing in whales farther back in time -- about 10-million years than previous studies have indicated." That gives evolutionists even less time to find the lucky mutations for this complex trait.

Another difficulty for the narrative becomes evident when we learn that "the specializations associated with high frequency hearing evolved about 27 million years ago -- about the same time as echolocation, although a few features evolved even earlier." This could be called "pressing your luck" when one must rely on chance to supply mutations as the raw material for selection. Now they have to account for two unlikely wins at the same time.

A review of the evidence from Illustra's film Living Waters is helpful here. As Richard Sternberg explains there, the probability of getting two coordinated mutations for a trait exceeds by an order of magnitude the time available for the transformation from a land animal to a whale, according to best estimates from the fossil record for the transformation. And as Sternberg says with dramatic irony, "In my estimation, it would take a lot more than two mutations." The transformation from a land dweller to an obligate ocean swimmer, where "you have to do everything there, including reproduction," is enormous. The film lists some of the complex systems that would require dramatic overhauls.

That's the negative evidence. The positive evidence is apparent from the animated sequence about echolocation, with all its coordinated parts. Paul Nelson identifies four prerequisites: the ability to produce the sounds, the ability to receive them, the ability to interpret them, and the ability to act on the information. If any one of those traits were missing, echolocation would not work. Think of just a few of the parts involved: phonic lips, sealed chambers, expanding storage sacs, a melon with the right audio characteristics and muscles to focus the sounds, a jaw with teeth and specialized tissues to amplify the echoes, a specialized cochlea that can hear high frequencies, and a brain that knows how to process all that information. How many coordinated mutations would that take? It's far, far beyond the reach of chance.

Evolutionists should stop insisting on the arbitrary rule that excludes intelligent causes from science. That rule (methodological naturalism) distorts reality, requiring dot-to-dot pictures of widely separated data points to maintain a predetermined conclusion. Science progresses by following the evidence where it leads, employing causes that are known to be necessary and sufficient to explain the phenomenon under investigation.

Darwinism's non-functional crystal ball

Failed Predictions Weekend: Cornelius Hunter on Darwinian Evolution
Evolution News | @DiscoveryCSC

Enjoy your weekend with a classic episode of ID the Future. Dr. Cornelius Hunter, a contributor to Evolution News, talks about his website  Darwin’s Predictions, which critically examines 22 fundamental predictions of evolutionary theory.

In this first podcast of the series, Dr. Hunter discusses why he was inspired to pursue this work. Download the podcast or listen to it here.

The Darwin of the gaps?

Inexplicable Species and the Theory of Evolution
Geoffrey Simmons

Editor’s note: We were delighted recently to introduce a new series, “Modernizing Darwin,” cross-posted at Shabbat.com, by Geoffrey Simmons, MD. The first post is here. Dr. Simmons is the author of What Darwin Didn’t Know and Billions of Missing Links. He is a Fellow with Discovery Institute’s Center for Science & Culture.

Man has been searching for fossils, or stumbling upon them, for millennia. The ancient Greeks and Romans saw the fossilized bones of giant creatures as proof that horrible monsters once walked the land or swam in the seas. Darwin utilized fossils to bolster his theory of evolution. He spent an enormous amount of time hunting down fossils and is rightfully known for a number of interesting finds, including the giant ground sloth Mylodon darwinii.

A Striking Absence of Transitions

Many modern authorities continue to use fossils as proof of evolution, chronologically lining up those which appear similar, yet the gaps have only grown more glaring with time. We now delve into the cellular level comparing chemical processes, electrical charges, and genetic differences. It seems to be a secret, but researchers know that it would take millions of internal changes for dinosaurs to evolve into birds, flat plants into trees, fish into amphibians. Note there are no half-fish/half-salamanders or one-third monkey/two-thirds humans, ever.

Upon close inspection, the absence of transitions (smaller steps) is striking. We should be up to our collective elbows with transitional species that once came about by trial and error, and failed to survive. Not so. Even for whales, the largest animal alive. We’ve been told repeatedly that transitional forms will eventually be found, but that hasn’t happened and the problems are steadily increasing in our awareness. Saying that two fossils with similar appearances, yet found thousands of miles apart, are related, begs the question.

Some whales can grow up to 100 feet long and weigh 200 tons. The rib cage of a blue whale is large enough to accommodate a minivan or small truck. Their hearts are the size of a Volkswagen Beetle. Every aspect is so massive. A few fossilized bones from their putative predecessors have been found. But the story is still mysterious, because of the changes required.

Darwin wrote that whales came about as a result of bears going to sea. He had to retract that statement after the first edition of On the Origin of Species was published. Some modern paleontologists say the whale’s ancestor must be the hippopotamus. Maybe because they are mammals and linger in the water most of their lives? But, otherwise they are strikingly (impossibly) different. Other coastal animals, that are now extinct, are also cited, but none of them could survive a day or two at sea. Of interest, the whale’s tail moves up and down, not sideways like fish. And, whales never had scales.

No one knows how blow holes came about, certainly not by small successive steps, or how the internal lungs became connected up to these holes in a way that prevents drowning. Or, how a massive communication center, found in their heads, came about. Or, how the ability to depressurize body segments during deep dives evolved. Calves are born tail first (they cannot go head first in case the process is too slow) and these newborns must rise to the surface immediately for air or else they will drown. The ability to swim must be present from the beginning. Trial and error would never have worked.

Not the Only Misfit

Whales are not the only misfit to smooth transitions, just the largest. The number of exceptions may actually be equal to the number of species on this planet. Standouts are kangaroos, woodpeckers, platypuses, giraffes, butterflies, octopuses, skunks, bombardier beetles, the red tide, dolphins, fireflies, tardigrades, sloths, and all micro-organisms. Maybe viruses, too. 

Something besides unguided evolution is going on. In actuality, all living organisms are likely exceptions. Just breeding a horse into a faster horse doesn’t eventually change it into something fast like a cheetah. It’s simply a faster horse. The same goes for pet dogs to guard dogs. It’s true, natural selection does happen in a variety of situations, but it doesn’t change a species into another.

An incomprehensibly intelligent engineer and designer must be responsible.

And still yet more civil war? II

I.D is already mainstream?

Research Showcases Intelligent Design Principles
Evolution News

One of our responses to critics of ID is that scientists use it every day. If intelligent design were not scientific, we would have to throw out forensics, archaeology, cryptology, informatics, optimization theory, engineering and SETI Here are some instances of ID in action that recently showed up in the journals. The principles for inferring design are similar. If some of these examples seem weak for inferring design, it makes our favorite cases stronger when we argue for design in the genetic code, molecular machines or the fine-tuning of the universe.

The Jungle Book

What is etched in the landscape of Amazonia? Something strange and unexpected has come to light. For decades, the rainforests of Brazil exemplified wild, untamed nature. Its few human inhabitants, portrayed romantically as noble savages, carried on their simple lives in harmony with nature as a rebuke to us European-American polluters and ravagers of the planet. This was Darwin’s world, a land of competition and cooperation producing ecological systems by unguided natural law (especially the “law” of natural selection).

Under the forest canopy, though, bizarre structures have now betrayed different forces also at work: intelligent forces. Natural laws don’t usually create concentric circles and squares. Since 1980, earthworks called geoglyphs [“earth messages”] have come to light over a vast area between Amazon’s river systems. A new picture of this region reveals evidence of purpose, intent, and plan: i.e., intelligent design. A dramatic paper by researchers from the University of São Paulo and the University of Exeter, published last month in the Proceedings of the National Academy of Sciences,overthrows the paradigm of untamed wilderness.

Over 450 pre-Columbian (pre-AD 1492) geometric ditched enclosures (“geoglyphs”) occupy ∼13,000 km2 of Acre state, Brazil, representing a key discovery of Amazonian archaeology. These huge earthworks were concealed for centuries under terra firme (upland interfluvial) rainforest, directly challenging the “pristine” status of this ecosystem and its perceived vulnerability to human impacts.…

The notion of Amazonia as a pristine wilderness has now been overturned by increasing evidence for large, diverse, and socially complex pre-Columbian societies in many regions of the basin. The discovery of numerous, vast terra preta (anthropogenic dark earth) sites bordering the floodplains of major rivers, and extensive earthwork complexes in the seasonally flooded savannas of the Llanos de Mojos (northeast Bolivia), Marajó Island (northeast Brazil), and coastal French Guiana, are seen to represent examples of major human impacts carried out in these environments. [Emphasis added.]

— carried out, that is, by intelligent design. This vast region has been “extensively transformed by humans over the course of millennia,” they say In news from the University of Exeter, lead author Jennifer Watling expresses how dramatic this change of thinking is:

Dr Watling said: “The fact that these sites lay hidden for centuries beneath mature rainforest really challenges the idea that Amazonian forests are ‘pristine ecosystems’.

“We immediately wanted to know whether the region was already forested when the geoglyphs were built, and to what extent people impacted the landscape to build these earthworks.”

The team used multiple methods to infer design — important for making a robust design inference. Most obvious are the geoglyphs themselves. Additional inferences about their functions can be adduced by close examination of the structural details:

With ditches up to 11 m wide, 4 m deep, and 100–300 m in diameter, and with some sites having up to six enclosures, the geoglyphs of western Amazonia rival the most impressive examples of pre-Columbian monumental architecture anywhere in the Americas. Excavations of the geoglyphs have shown that they were built and used sporadically as ceremonial and public gathering sites between 2000 and 650 calibrated years before present (BP), but that some may have been constructed as early as 3500–3000 BP. Evidence for their ceremonial function is based on an almost complete absence of cultural material found within the enclosed areas, which suggests they were kept ritually “clean,” alongside their highly formalized architectural forms (mainly circles and squares) — features that distinguish the geoglyphs from similar ditched enclosures in northeast Bolivia.

Is it necessary to know who the designers were? Does ID require knowing their motives?

Surprisingly, little is known about who the geoglyph builders were and how and where they lived, as contemporary settlement sites have not yet been found in the region. It is thought that the geoglyph builders were a complex network of local, relatively autonomous groups connected by a shared and highly developed ideological system. Although some have proposed a connection between the geoglyphs and Arawak-speaking societies, the ceramics uncovered from these sites defy a close connection with Saladoid–Barrancoid styles normally associated with this language family, and instead present a complex mixture of distinct local traditions. Furthermore, it is likely that the geoglyphs were used and reused by different culture groups throughout their life spans.

Here’s where it gets even more interesting. Additional clues reveal that the ecology was intentionally modified by these unknown people. By studying charcoal, plant fossils and carbon isotopes, and by following patterns between geoglyph sites, the researchers inferred that the inhabitants transformed the rainforest to enhance the production of fruits, nuts and other plants they found useful. The team was also able to infer which species were modified and which were ‘natural’ for the climate, and even to determine how the people used fire for controlled land clearing. Not only that, they inferred that “the geoglyphs were used on a sporadic basis rather than continually inhabited.”

Rather than being built within largely “untouched” bamboo forest, our phytolith data suggest that the geoglyphs were constructed within anthropogenic forests that had already been fundamentally altered by human activities over thousands of years.

How can they be sure? “No natural explanation exists” for the patterns they found. Bamboo, they figure, is in its natural abundance, but fruit and nut trees show patterns of “agroforestry,” as if the inhabitants intentionally created “a kind of ’prehistoric supermarket’ of useful forest products.” The team even went so far as to estimate when the geoglyph sites were abandoned, and to tell whether the ecosystem had recovered or not since they left. From the phytolith data (silica deposits from plant remains) alone, they conclude that “legacies of pre-Columbian agroforestry still exist today within Acre’s remaining forests.” That’s a lot of design inference from silent remains!

Similar conclusions were reached by Levis et al. in Science Magazine. From plant patterns alone in the Amazon Basin, a large team of archaeologists concluded that “The marks of prehistoric human societies on tropical forests can still be detected today.” Erin Ross at Nature News concurs, “Amazon rainforest was shaped by an ancient hunger for fruits and nuts.” Scientists can tell that the rainforest is not in a natural state. Rather, “The trees that live in these populated areas may be relics of a vibrant past.”

Lest one argue that these marks of design are no different in kind than bird nests, termite mounds, beaver dams or any other animal structure that modifies the ecology, just turn the argument back on the researchers. Would it make any sense to state that a scientific paper in a journal is the work of unguided natural causes? Of course not. We all recognize the marks of intelligence. Humans are exceptional in that regard, forming unnatural structures for creative purposes that go beyond mere survival and reproduction. Whether beavers and birds obtained their abilities from a programming intelligence is a good question, but humans are under no obligation to build geoglyphs or automobiles, or to think up “ideological systems” that leave their marks centuries later. If humans are just animals, why did they shape the whole forest? Why not develop an appetite for bamboo, like pandas?

Mineral Clues to Design

Let’s expand the above reasoning to a case that is global in scale. Geologists and anthropologists are currently debating whether to name our time the “Anthropocene Epoch.” We’ve heard about the Eocene, Paleocene and other “natural” epochs, but the Anthropocene idea would be characterized by something unnatural. Defined in New Scientist as “a new geological time interval distinguished by the impact of human activities,” the Anthropocene differs from all previous epochs. Watch reporter Chelsea Whyte apply ID reasoning:

Think of large gem collections in museums. Those mineral samples wouldn’t occur naturally in close proximity, but they are likely to get be buried together and cemented in the record as neighbors.

Picture also places like Arlington National Cemetery in Virginia. That ordered array of headstones isn’t likely to occur naturally, without human influence. The mineral record will reveal not only our technological processes, but also our culture.

What gets really interesting is how at least one ardent evolutionist uses the same reasoning to infer human intelligent causes from the mere existence of certain rare minerals:

The evidence of humans changing the planet is solid as rock. A new catalogue of minerals counts 208 that result solely or primarily from human activity, says Robert Hazen of the Carnegie Institution for Science in the US, who led the study.

Most minerals can be accounted for naturally, he says, but one can tell something unnatural has happened from observational evidence. Hazen has identified 208 minerals — about 4 percent of the 5200 some minerals catalogued — that are unusual. They had to be man-made. And that’s not the only evidence for human design.

It’s not just that these new minerals exist, but how they are distributed and how they will persist. Our activity has led to large scale movement of rocks, sediments, and minerals, thanks to mining, transport and infrastructure, as well as global redistribution of highly valued natural minerals such as diamonds and gold. And there are substances in things like cement and bricks that are rare in nature but are now widespread across the globe.

“These are mineral-like and they will form a marker layer for all geologic time,” Hazen says.

Unwarranted Design Inference

In contrast to these examples of legitimate design inference, let’s look at one that’s a bit on the loony side. The UK’s tabloid The Express posted a video clip by some unknown conspiracy theorist pointing to a “bizarre” object under the Pacific Ocean. He points to a straight pathway 41 miles long that he alleges was left by a circular object 2.5 miles in diameter that appears next to it. He claims it “looks man-made rather than natural” — maybe even made by space aliens!

It’s reminiscent of the Face-on-Mars craze that dominated late-night talk shows before spacecraft got a closer look. This just goes to show that design inferences require a minimum level of rigor. It doesn’t appear that these wishful thinkers ruled out chance or natural law as causes. If the object had flashing lights and carved out “Hello, world!” in English, we might be impressed.

Actually, the evidence for design in DNA and cosmic fine-tuning is far stronger than the evidence presented in the two prior citations about geoglyphs and Anthropocene minerals. They illustrate that common-sense reasoning about intelligent causes is alive and well in the sciences, published readily in leading journals — except when the implications might favor a certain world view.

The tree v. the graph.

Of Species and Software: What Is a Dependency Graph?
Cornelius Hunter

A recent paper in the journal BIO-Complexity, authored by Winston Ewert, uses a dependency graph approach to model the relationships between the species. This idea is inspired by computer science which makes great use of dependency graphs for packaging of software and optimization of software architecture.

Complicated software applications typically use a wealth of lower level software routines. These routines have been developed, tested, and stored in modules for use by higher level applications. When this happens the application inherits the lower-level software and has a dependency on those modules.

A Design Diagram

Such applications are written in human-readable languages such as Java. They then need to be translated into machine language. The compiler tool performs the translation, and the build tool assembles the result, along with the lower level routines, into an executable program. These tools use dependency graphs to model the software, essentially building a design diagram, or blueprint which shows the dependencies, specifying the different software modules that will be needed, and how they are connected together.

Dependency graphs also help with software design. Because they provide a blueprint of the software architecture, they are helpful in designing decoupled architectures and promoting software reuse.

Dependency graphs are also used by so-called “DevOps” teams to assist at deployment time in sequencing and installing the correct modules for enterprise applications.

A Failed Model

What Ewert has developed is a model to explain the pattern of similarities in different organisms that mimics how computer applications inherit software from a diverse range of lower-level modules. Species seem likewise to use lower-level modules that perform a diverse range of biological applications. Ewert specifically studied how genomes incorporate various gene families which group into a wide range of genetic modules and how genetic modules feed into a diverse range of genomes.

Superficially, from a distance, the pattern of module use may appear similar to the traditional evolutionary tree. But that model has failed repeatedly as scientists have studied the characters of species more closely. Ewert’s initial research suggests that dependency graphs, on the other hand, could provide a far superior model of the relationships between the species, and their genetic information flow.

And still yet more primeval tech v. Darwin.

Inside the Machine Room of the Nucleus
Evolution News | @DiscoveryCSC

We’re living in exciting times. It was only a little over 65 years ago that we began to realize that life is information-based, with coded genetic information embedded in alphabet-like molecules. In the years that followed, biochemists also began to discover that the chemical reactions carried on by life were unlike the valence-based reactions we learned about in chemistry class, but were machine-like, with moving parts that function mechanically like rotors and engines. More recently, these machines have been found to interact in large networks of integrated systems, like factories. Is it any wonder that intelligent design rose as a movement in the late 20th century?

The wonders continue at a rapid pace into the 21st century. With increasing resolution thanks to techniques like cryo-electron microscopy, biochemists are focusing on the molecular machines at nearly nanometer scale and determining their modes of action. Let’s look at news about a few of the major players inside the nucleus of cells.

The Majestic Spliceosome

Researchers at the International School of Advanced Studies (SISSA) in Italy use a rare word in a scientific paper: “majestic.” It’s an appropriate adjective for what they saw by examining, for the first time, the spliceosome at near-atomic detail. Their paper in PNAS begins:

The spliceosome (SPL) is a majestic macromolecular machinery composed of five small nuclear RNAs and hundreds of proteins. SPL removes noncoding introns from precursor messenger RNAs (pre-mRNAs) and ligates coding exons, giving rise to functional mRNAs. Building on the first SPL structure solved at near–atomic-level resolution, here we elucidate the functional dynamics of the intron lariat spliceosome (ILS) complex through multi-microsecond-long molecular-dynamics simulations of ∼1,000,000 atoms models. The ILS essential dynamics unveils (i) the leading role of the Spp42 protein, which heads the gene maturation by tuning the motions of distinct SPL components, and (ii) the critical participation of the Cwf19 protein in displacing the intron lariat/U2 branch helix. These findings provide unprecedented details on the SPL functional dynamics, thus contributing to move a step forward toward a thorough understanding of eukaryotic pre-mRNA splicing.

One paper could never do justice to all that the spliceosome does, but in their examination of a couple of protein parts, they could not help but stand in awe at the majesty of this huge molecular machine. They didn’t have much to say about evolution, except pointing out that one “intricate RNA-based active site has been extraordinarily conserved across evolution from bacteria to humans.” News from SISSA via  Phys.org recaps the awe by showing the precision the team found in this machine’s operation:

To have a molecule able to transport information usefully, precisely and effectively, the introns must be eliminated by the spliceosome to transform it into mature mRNA.” It is an extremely precise snip-and-stitch process, explains the researcher, because any tiny error can alter the information with serious effects on cell activity and the health of the entire organism.

Topoisomerase the Great

“Supercoil me!” begins the headline of another article from SISSA about “the art of knotted DNA maintenance”(see Science Daily).Is it any surprise that long strands of DNA have knotty problems? Like those old phone cords that would knot up with coils upon coils, DNA can develop messy knots. Specialized enzymes must untangle them; otherwise, important genes might become inaccessible. Like Alexander the Great cutting the Gordian knot, they say, the topoisomerase family of nuclear machines is up to the challenge. They get some help, though, by a physical property of DNA that works to the advantage of the cutting machines: “Supercoiling can keep DNA knots locked in place for long enough that they can be untied by specialised enzymes,” the new study shows.

“We know that living cells routinely deal with DNA knots, and we also know that these forms of entanglement are usually detrimental to biological functionality; for instance they can prevent the genetic information from being read and translated into protein products. Specific enzymes of the topoisomerase family are responsible for disentangling DNA. Their modus operandi recalls the efficient, if not drastic, way in which Alexander the Great untied the proverbial Gordian knot with a cut of his sword. Similarly, these enzymes untie DNA filaments by a sophisticated cutting and sealing action.” 

The machines have another problem not faced by Alexander: DNA strands are constantly wiggling. Using computer simulations, the team found that free knots would slide relatively fast along the filaments. This should make it more difficult for the topoisomerases to get to them and repair them. The team then noticed that accidental knots are often associated with supercoiled regions, which are more stable. This led to an “Aha!” moment:

Our study suggests that DNA supercoiling can favour the action of topoisomerases by keeping knots in a stable configuration for a time span that is much longer than other molecular rearrangements. In this way, the enzymes could have sufficient time to recognise the target sites and, in turn, their cut-and-paste action would be simpler, more reliable and efficient. 

Their hypothesis will require further testing, but suggests an additional purpose for supercoiling inside the nucleus. It was already known that supercoiling is involved in “exposing or hiding genetic information” for transcription, but now another possibility presents itself: supercoils hold an accidental knot in place long enough for Topoisomerase the Great to arrive with his sword.

“We studied the DNA filament and noted that without supercoils, the knotted region would move relatively fast along the filament. Likewise, supercoiled regions can rapidly change in knot-free DNA. However, when knots and supercoiling are simultaneously present, then the crucial contact points in DNA knots become locked in place, persistently. And this unexpected effect is particularly interesting because it could be key to a specific and unexpected biological functionality.” 

It will be interesting to find out if other machines notice the knots and induce supercoiling at those locations. Sounds like a good plan at least.

Scalpel in a Sheath

For our last example of nuclear machines today, consider 53BP1. This enzyme has a critical job: repairing double-stranded breaks, when both strands of DNA are broken. It’s a catastrophic condition leading to cell death. Fortunately, cells come equipped with machinery that can stitch them back together. One of them is 53BP1. But just as you don’t want open knives floating around, you only want this machine activated when it is needed. Fortunately again, this machine comes with a sheath named TIFF. News from the Mayo Clinic explains (you can ignore the evolutionary claim in the first sentence):

Damage to DNA is a daily occurrence but one that human cells have evolved to manage. Now, in a new paper published in Nature Structural & Molecular Biology, Mayo researchers have determined how one DNA repair protein gets to the site of DNA damage….

While the human genome is constantly damaged, cells have proteins that detect and repair the damage. One of those proteins is called 53BP1. It is involved in the repair of DNA when both strands break.

Dr. Georges Mer and team found that TIFF normally binds to 53BP1, rendering it harmless like a sword in its sheath. 

The authors report that when DNA damage occurs, RNA molecules produced at that time can bind to TIRR, displacing it from 53BP1 and allowing 53BP1 to swing into action.

Presumably the binding is reversible after the repairs are made, and the Swiss army knife goes back into the pocket till next time. Pretty cool, heh? Read more about the machine in Nature Reviews Molecular Cell Biology (2014).These are brief looks at the amazing machines and processes that keep us going without our conscious awareness. When you ponder the fact that until our day nobody knew about these wonders, our reasons for feeling like a Privileged Species in the 21st century take on historic significance.

Time to decanonise Darwin?

For This Physicist, “Overthrowing” Darwinism Is on the Table
David Klinghoffer | @d_klinghoffer

than Siegel is a physicist who writes a pretty consistently interesting regular blog for Forbes. Yesterday he offered thoughts on “How To Overthrow A Scientific Theory In Three Easy Steps.” He concedes, “Even our best theories of today may be superseded with tomorrow’s science.”


And no one, except perhaps some ultra-Darwinists, would disagree. He notes that theories have limits:

Any theory, no matter how successful, has a finite range of validity. Stay within that range and your theory works very well to describe reality; go outside of it, and its predictions no longer match observations or experiments. This is true for any theory you pick. Newtonian mechanics breaks down at small (quantum) scales and high (relativistic) speeds; Einstein’s General Relativity breaks down at a singularity; Darwin’s evolution breaks down at the origin of life.

That last point is the theme of Stephen Meyer’s first book, Signature in the Cell.  Siegel’s three steps are actually four:

Step 0: recognizing successes and failures of the leading theory.
Step 1: reproducing all the successes of the leading theory.
Step 2: succeeding where the prior theory did not.

Step 3: you must make new, testable predictions that differ from the original theory’s.

Whether proponents of intelligent design have succeeded in any of those is a question you could debate. But it’s beyond doubt that they are trying, in a rigorous manner, to advance through each of those steps. It is striking that Darwin defenders typically refuse to acknowledge that or to address the science of ID. They are mostly content with name-calling.

The Hunt Is On

The ID research community isn’t alone, of course, as as Sarah Chaffee mentioned here. The hunt is on for a successor to Darwinism:

Scientific controversy over evolution exists, quite apart from proponents of intelligent design. Think of the researchers associated with the Third Way of Evolution and the 2016 Royal Society Conference and its subsequently published journal Problems with conventional scientific explanations for the origin of life and of biological diversity are widely acknowledged — and scientists around the world tackle these issues.

This means, in any event, that ID is a rival theory, a scientific theory, doing the normal work that scientific ideas must do to supplant a currently dominant idea. That’s not to say that ID will succeed. But to brand it is as a “religious” rather than “scientific” idea is plainly false.

The Right Stuff

Siegel addresses what it would take to succeed:

Want to go beyond Darwin’s evolution? You still need to explain the emergence of biological diversity, the response to selection pressures, and how inheritance works, among others.

That, again, is something that no ID advocate would disagree with. “[E]xplain[ing] the emergence of biological diversity,” the theme of Meyer’s second book, Darwin’s Doubt , is precisely where the ID argument tackles Darwinism most forcefully. It’s a way of thinking that led Alfred Russel Wallace to his break with Charles Darwin, as Michael Flannery tells in  his new book.


Don’t get me wrong. I don’t see any indication that Ethan Siegel has a drop of sympathy for design theory. But recognizing how and where the “overthrow” of Darwinian evolution could happen, if it were to happen, is a step in the right direction. It puts our question on the table.

Yet more on JEHOVAH'S folly v. man's genius.

Oral Cavity’s Supposedly “Lousy” Design Is a Key to Human Speech
Evolution News | @DiscoveryCSC

It’s a staple for Darwinists who compile lists of human anatomical features supposedly demonstrating “unintelligent” or “botched” design. We’re constantly told that the design of the human larynx, trachea, and oral cavity is poor because it allows for choking on food.

The point is made by the snarky Centre for Unintelligent Design, which lists “The ease with which we can choke” as an example of “unintelligent design,” and by Wikipedia. On the “Argument for poor design“ page they include this under “Fatal flaws” in human anatomy:

The existence of the pharynx, a passage used for both ingestion and respiration ,with the consequent drastic increase in the risk of choking. 

In a conversation with Edge on “Unintelligent Design,” anthropologist Scott Atran complains, “Humans are more liable than other animals to choke, as they attempt to simultaneously coordinate eating, breathing and speaking.” RationalWiki adds, “Drinking and laughing at the same time — makes the drink come out of the person’s nose. Or potentially choke the victim of such a lousy design.” And so on.

The design does come with an increased chance of choking, but it’s also something that allows us to speak as we do. An interesting new article at The Scientist goes into some detail. From “Why Human Speech Is Special,” by Philip Lieberman:

  

In On the Origin of Species, Darwin noted “the strange fact that every particle of food and drink which we swallow has to pass over the orifice of the trachea, with some risk of falling into the lungs.” Because of this odd anatomy, which differs from that of all other mammals, choking on food remains the  fourth leading cause of accidental death in the United States. This species-specific problem is a consequence of the mutations that crafted the human face, pharynx, and tongue so as to make it easier to speak and to correctly interpret the acoustic speech signals that we hear.

At birth, the human tongue is flat in the mouth, as is the case for other mammals. The larynx, which rests atop the trachea, is anchored to the root of the tongue. As infants suckle, they raise the larynx to form a sealed passage from the nose to the lungs, allowing them to breathe while liquid flows around the larynx. Most mammalian species retain this morphology throughout life, which explains why cats or dogs can lap up water while breathing. In humans, however, a developmental process that spans the first 8 to 10 years of life forms the adult version of the SVT [supra-laryngeal vocal tract]. First, the skull is reshaped, shortening the relative length of the oral cavity. The tongue begins to descend down into the pharynx, while the neck increases in length and becomes rounded in the back. Following these changes, half the tongue is positioned horizontally in the oral cavity (and thus called the SVTh), while the other half (SVTv) is positioned vertically in the pharynx. The two halves meet at an approximate right angle at the back of the throat. The tongue’s extrinsic muscles, anchored in various bones of the head, can move the tongue to create an abrupt 10-fold change in the SVT’s cross-sectional area….

As it turns out, the configuration of the adult human tongue’s oral and pharyngeal proportions and shape allow mature human vocal tracts to produce the vowels [i], [u], and [a] (as in the word ma). These quantal vowels produce frequency peaks analogous to saturated colors, are more distinct than other vowels, and are resistant to small errors in tongue placement. Thus, while not required for language, these vowel sounds buffer speech against misinterpretation. This may explain why all human languages use these vowels.
  
o Darwin and his latter-day followers may complain about the design of the oral cavity but they’d have a harder time doing so (and being understood) if it weren’t for this instance of “poor design.” Note that “all human languages use these vowels,” an indication that this is no negligible feature for clear communication. And speech, of course, is arguably the keystone of humanity’s exceptional status in the world of life.

None of which, of course, is to make light of the peril of choking. But to put things in perspective, according to the National Safety Council, “5,051 people…died from choking in 2015,” which works out to 0.0018 percent of all deaths in the United States, and of those “2,848 were older than 74.” (See  here and here.) There is no doubt some relationship to the prevalence of age-related conditions like Alzheimer’s disease. As an article for The Conversation points out, “The result is that millions of brain disease patients are at risk for inhaling food and saliva into the lungs, leading to death by pneumonia or even choking.”


That having been said, the design of the human oral cavity looks more like a trade-off than a botch. As Evolution News has put it, “Trade-offs are compromises made to optimize the highest design goal.” They are not errors but necessary features of design in a material world.

God continues to make fools of the 'wise'.

^{Ecclesiastes8:17ESV"}then I saw all the work of God, that man cannot find out the work that is done under the sun. However much man may toil in seeking, he will not find it out. Even though a wise man claims to know, he cannot find it out."

Why Does Biology Still Have the Ability to Surprise Us?

Ann Gauger

About forty years ago, a biochemistry professor told my class that now that the genetic code had been worked out and the lac operon discovered, the only thing left for us students was to work out the details. Boy, was he wrong!

If there's one thing I've learned over the last forty years, it is that every ten years or so the biological apple cart is upset, and a long-established "fact," an assumption based on incomplete knowledge, is proven to be wrong.

I am sure you can find textbooks that still include some of these old "facts." Below is a partial list of those assumptions that have had to be revised, and some that are still under discussion.

1. Old fact: DNA is stable and genes don't hop around.

New discovery: Mobile genetic elements can hop from place to place in the DNA, duplicating themselves and changing gene expression. Sometimes they carry surrounding genes with them.

2. New "old" fact: Mobile genetic elements are selfish DNA that replicate themselves without benefit to the organism, thus cluttering the genome with garbage.

New discovery: Mobile genetic elements appear to be involved in the regulation of many important genes, and their distribution in the genome is nonrandom.

3. Old fact: A gene is an uninterrupted stretch of DNA that encodes a single protein. Genes are arranged like beads on a string.

New discovery: Genes in eukaryotes are interrupted, sometimes multiple times, by non-coding sequences called introns. The introns get spliced out of the messenger RNA before the message is translated. Because of splicing, one gene can produce many different but related proteins.

New discovery: Genes can overlap one another on the same stretch of DNA, on the same strand or on opposite strands. Thus one piece of DNA can produce multiple different proteins.

Take home message: 1 stretch of DNA ≠ 1 gene ≠ 1 protein

4. Old fact: There are only 3 forms of RNA: messenger RNA, transfer RNA, and ribosomal RNA.

New discovery: New classes of short and long RNA transcripts serve to regulate gene expression.

5. Old fact: Pseudogenes are useless broken remnants of former genes.

New discovery: Not all pseudogenes are useless. Pseudogenes can be transcribed, and their products can be used to regulate the expression of their full-length sister genes. Related to #4.

6. Old fact: The genome is full of junk, the remnants of wasteful evolutionary processes and selfish DNA (see #1, #2 and #5 above).

New discovery: "Junk" DNA isn't junk after all. It has many important regulatory functions in the cell.

Revolutionary discoveries like these often happen when someone tries something new, stumbles across some contrary evidence, and begins to question the validity of an established "fact." The results have been astonishing -- and have even won the Nobel Prize. Because of these discoveries we have gained a new and better, though still imperfect understanding of biology.

Why should we still have the "facts" wrong? After all, we've been studying biology for sixty years after the discovery of DNA's structure, and 50 years after the code was worked out.

Perhaps a better question would be, "Why does biology have the ability to surprise us?" It's because life is much more sophisticated than anything we can imagine. We look at biology from our very limited perspective, and at almost every turn we are puzzled or amazed. You can even read it in the understated, carefully couched language of published articles, where words like "surprising" or "unexpected" appear often.

Remember that biochemistry professor who claimed that all the important work in biology was done? He also said we'd never find gears or wheels in biology. Poor guy!

You'd think that scientists would be more cautious about our pronouncements if we can be so wrong. But we are only human, like everyone else, and our accepted "facts" are often deeply entrenched in our thinking. In truth, though, only one rock solid "fact" exists -- that some time in the not too distant future a strongly held "fact" will be proven mistaken.

Like Darwinian evolution, perhaps?