Biological information v.Darwin

New Peer-Reviewed Paper Challenges Darwinian Evolution
Jonathan M.

Over recent months, papers challenging key elements of Darwinian theory -- the kind of papers which are supposed not to exist -- have increasingly been slipping through the net and finding their way into the peer-reviewed literature. One such paper, "Is gene duplication a viable explanation for the origination of biological information and complexity?," authored by Joseph Esfandier Hannon Bozorgmeh and published online last week in the journal, Complexity, challenges the standard gene duplication/divergence model regarding the origin of evolutionary novelty.

The abstract reports,
All life depends on the biological information encoded in DNA with which to synthesize and regulate various peptide sequences required by an organism's cells. Hence, an evolutionary model accounting for the diversity of life needs to demonstrate how novel exonic regions that code for distinctly different functions can emerge. Natural selection tends to conserve the basic functionality, sequence, and size of genes and, although beneficial and adaptive changes are possible, these serve only to improve or adjust the existing type. However, gene duplication allows for a respite in selection and so can provide a molecular substrate for the development of biochemical innovation. Reference is made here to several well-known examples of gene duplication, and the major means of resulting evolutionary divergence, to examine the plausibility of this assumption. The totality of the evidence reveals that, although duplication can and does facilitate important adaptations by tinkering with existing compounds, molecular evolution is nonetheless constrained in each and every case. Therefore, although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms.
The mechanism under discussion is the phenomenon of gene duplication, which occurs by means of unequal chromosomal crossovers, the retropositioning of spliced mRNA, and copying of an entire chromosome, or even an entire genome. The gene duplication paradigm, as far as the origin of evolutionary novelty is concerned, is as follows: When a gene becomes duplicated, one copy of the gene is retained for its phenotypic utility (e.g. encoding for a protein or functional RNA), while the other copy of the gene is free from selective constraint, and is thus able to mutate and 'explore' alternative combinatorial possibilities (promoted by near neutral drift), in the hope of stumbling upon something useful.

The review paper attempts to "determine the existence and extent of any novel information produced as a consequence of gene duplication." The author further remarks, 
"At stake is whether there is sufficient supporting evidence that the digitally communicated instructions encoded in DNA could have been constructed through known evolutionary processes, or whether the data suggests that an alternative explanation is required as in all codified nonbiological information. Therefore, this would serve as assessing the current arguments regarding the origins of biological and genomic complexity.
The author is careful to delineate what he is describing when he speaks of "information". Carefully contrasting the information present in biological systems with mere Shannon complexity, the author defines a gain in exonic information as "[t]he quantitative increase in operational capability and functional specificity with no resultant uncertainty of outcome." He then procedes to propose means of empirically verifying the role of natural selection in the creation of novel functionality.

Bozorgmehr winds up drawing similar conclusions to those drawn by Behe in his recent Quarterly Review of Biology paper: While many mutations can, at first glance, appear to have resulted in evolutionary novelty (such as in the case of antibiotic resistance), closer inspection reveals that the selected adaptations do not, in fact, result in novel genetic components. Bozorgmehr explains that "[i]n many instances...a loss of function and regulation in a harsh or unusual environment can have a beneficial outcome and thus be selected for -- bacteria tend to evolve resistance to antibiotics in such a way through mutations that would otherwise adversely affect membrane permeability," (see Delcour 2009). One example cited in the paper concerns the acquisition of organophosphorus insecticide resistance in blowflies, which is conferred by a single amino acid substitution in a carboxyl esterase. But this insecticide resistance -- though adaptively selected -- is not a case of neo-functionalization, but rather a loss in enzyme activity (Newcomb et al. 1997).


The paper goes on to examine eight case studies of adaptive evolution which have involved gene duplication, a few examples of which I will summarize in a second post.

Arguing with ghosts?

Revealing Michael Behe, Intelligent Design's "Revolutionary" Biologist

David Klinghoffer

Thanks to a cocktail of misguided public policies, Seattle's downtown core, where we work, is awash with the mentally ill homeless. A sadly familiar figure is the man or woman furiously shouting, cursing, and gesticulating at an unseen conversation partner. There are many such individuals roaming about, crossing paths with the tourists, businesspeople, high-end shoppers, and art museum and symphony patrons. They remind me of a strange feature of the evolution debate.Just as the mentally ill person's fury is directed at an unknown party, much of scientific and popular publishing about evolution is aimed at an unnamed opponent. As a random example, here's an article from Science Daily that crossed my desk this week, "A short jump from single-celled ancestors to animals," reporting a study in the journal Developmental Cell. Without going into detail on the merits of this effort to minimize a glaring difficulty with Darwinism, the article doesn't mention intelligent design. But it's surely directed at us. Major evolutionary transitions are an aspect of life's long history that Darwinian theory can't explain but design can.

Often, when evolutionists argue with an unseen ID proponent, when the context is the Cambrian explosion or life's mysterious origin, the object of their fury is Stephen Meyer. In other contexts, it might be Douglas Axe and Ann Gauger with their incisive questions on protein evolution. Mathematicians William Dembski and David Berlinski are invisible opponents, and so too is our daily reporting and analysis here at Evolution News.

Very often, though, when it comes to the concept of irreducible complexity -- typically unnamed -- the opponent they clearly have in mind is biochemist Michael Behe.

The highly effective new 60-minute documentary Revolutionary: Michael Behe and the Mystery of Molecular Machines, on sale now,makes the invisible visible. The film, written and directed by John West, is an introduction to Behe's thought timed to the 20th anniversary of his revolutionary book  Darwin's Black Box: The Biochemical Challenge to Evolution.I'm proud to have played a small part in bringing the book before the public. As the literary editor at National Review at the time, I commissioned the (laudatory) review from distinguished NYU chemist Robert Shapiro that is briefly shown in the film.

Among other things, Revolutionary is a vindication of Behe, showing how science has refuted objections by Brown University biologist Kenneth Miller and others to Behe's case for design, highlighting molecular machines like the bacterial flagellar motor. Those machines were of course unknown to Darwin, who would be flabbergasted by them. Their exquisite, irreducible complexity is still being investigated and revealed -- making the invisible visible in another sense. For more, see the film's trailer here. Of course Behe is not actually invisible on the stage of biology. His presence is strongly felt. As the film shows, he has changed the terms of evolutionary discussions, an honor that also belongs to another Discovery Institute biologist, Michael Denton, whose book  Evolution: A Theory in Crisis,we learn, inspired Behe's scientific journey.

Oh yes, evolutionists know who they're shouting at, and to prove it, the phrase "irreducible complexity" is sometime allowed to pass their otherwise carefully sealed lips. It's just that Darwin's defenders strain to avoid tainting themselves by directly confronting the mild-mannered professor at Lehigh University. Revolutionary undoes their discretion by introducing us to Behe (and other ID theorists) in a dramatic and personally and intellectually revealing way. It's a fine and accessible primer on ID that tells the story of what really is a scientific revolution.

We see Behe on the Lehigh campus, at home -- just a hundred miles from Dover, Pennsylvania, where he famously clashed with Professor Miller at the 2005 Kitzmiller trial, under the eyes of John E. Jones and his ghostwriters from the ACLU. (That is Judge John E. Jones who, the film amusingly reveals, hoped that Tom Hanks would play him in the movie version of the court battle.) Behe is shown with his family -- talking with his kids, and washing post-supper dishes. The humanizing effect is welcome.

As one paleontologist recounts here, after his own mind was opened to the cogency of design arguments, he met ID scientists and scholars and was surprised to find they bore little resemblance to what he expected based on media caricatures. The shy (as he describes himself), self-effacing, yet stubborn Dr. Behe may also come as a revelation to those who don't know him but assume he must be a cartoon "creationist."

Revolutionary is unlike other ID films I'm familiar with in the way it offers personal stories. One of the most startling concerns University of Idaho microbiologist Scott Minnich, who like Behe, testified at Dover and was censured for it by officials at his university. When contemplating the career perils of coming out for ID and publishing a journal article with Stephen Meyer on the bacterial flagellum, Dr. Minnich happened to be participating as a member of the Iraq Survey Group, assisting the U.S. government in a search for biological and chemical weapons hidden in the country.He was taking shelter, in fact, in Saddam Hussein's Perfume Palace, under approaching mortar fire, as a critical submission deadline loomed. Minnich recalls reflecting that "I may not be here tomorrow morning," as he finally hit the button on his computer to send the file. Now that's a kind of story from the scientific world that you don't hear every day.

Behe, Minnich, Meyer, et al. continue to take fire from opponents who, frankly, don't earn a lot of respect from me by failing to give credit to the authors of the theory they seek to surreptitiously assail. Revolutionary pays fitting tribute Professor Behe, who deserves to be called a hero.

Killer whales v. the walking dead.

A clash of Titans. LIV

And still yet more on the rise of the machines.

Atheistic science's love/hate relationship with the design inference.

Fairy Circles? The Design Inference at Work

Evolution News & Views

From time to time we point out illustrations of how scientists outside the ID movement use the design inference, demonstrating how natural and pervasive design reasoning is. Everyone, scientist or layman, uses such reasoning. It's both valid, when correctly applied, and inescapable.

In Undeniable , Douglas Axe talks about the "common science" that even children engage in, employing what he calls a "universal design intuition" with which we are all born. Axe is careful not to take this too far, but he argues that it's the default for human beings, even as materialists try to explain it away with question-begging Darwinian just-so stories.

In past articles, we've looked at scientists trying to understand the origin of rock piles under the Sea of Galilee or on a mountainside. We've talked about SETI. . And we puzzled over curious lines of rocks in the Jordanian desert. We too have been careful not to jump to conclusions, as two examples failed the design filter, and perfectly natural things like sandstone arches can be quite symmetrical and artistic, but still explainable by natural law and chance. The examples show that one can infer design without knowing anything about the designer.

Today's case study is a doozy. It's most likely a natural phenomenon, but to this day, scientists have been unable to explain it. Some are not ruling out intelligent design. Megan Gannon at Live Science introduces the phenomenon:

"Fairy circles" are regular, repeating patches of dirt in remote grasslands that, when viewed from above, look like whimsical rings that were scattered across a landscape. Despite their fanciful appearance, the patterns have been a source of serious scientific debate for the last four decades. While some have argued that the geometric patterns are the work of termites, others have postulated that the circles form naturally as vegetation self-organizes in competition for scarce water and other nutrients. [Emphasis added.]

Adding to the confusion is the fact that these orderly rings have been found in Namibia and in the Australian outback, but may or may not have the same cause. Here's a sampling of some recent literature on the subject. Notice the first article's premature celebration.

"Mystery of Desert 'Fairy Circles' Solved, Creators Found" (Live Science)

"Are Namibian 'Fairy Circles' the Consequence of Self-Organizing Spatial Vegetation Patterning?" (PLOS ONE)

"Mysterious 'Fairy Circles' Not Explained by Termites, Study Suggests" (Live Science)

"Gradual regime shifts in fairy circles" (PNAS)

"Experiments Testing the Causes of Namibian Fairy Circles" (PLOS ONE, 10/28/15)

"Discovery of fairy circles in Australia supports self-organization theory" (PNAS)

"Are 'Fairy Circles' Just the 'Ghosts' of Termite Nests?" (Live Science)

"Fairy circles or ghosts of termitaria? Pavement termites as alternative causes of circular patterns in vegetation of desert Australia" (PNAS)

It's hard not to chuckle at the talk of fairies in the august Proceedings of the National Academy of Sciences, knowing as we do that Richard Dawkins has often ridiculed the religious as believing in "fairies, goblins, hobgoblins, leprechauns" and other mythical creatures. But obviously it's just a figure of speech here.

Unlike the crop-circle craze, which many suspected from the beginning involved human design (later proved by eyewitnesses and the increasing elaboration of the patterns), this one is not so obvious. The default explanation has been to infer something natural. But what? Until a natural cause is demonstrated, scientists were not able to rule out an intelligent cause.

The last paper, from PNAS, appears to have nailed the solution, at least for the circles in Australia. They are the remains of active or abandoned nests from underground termites. It took years of careful observation to arrive at that conclusion, however, passing through theories of self-organization, tribal artwork or farming patterns, hydrocarbon seeps, or products of carnivorous ants.

It's still not clear that termites explain the Namibian circles. Even now, not everyone is convinced about the termite theory. The point is that the problem has occupied the attention of scientists from around the world, rightly so, who have published in leading journals. And so design science marches on. No apologies needed.

Epigenetics v. the walking dead.

Nematodes Push Epigenetics to the Limit, as Another “Zombie” Bites the Dust
David Klinghoffer | @d_klinghoffer

Evolution as “settled science” in the mind of the public and the media is based a range of persistent myths – documented by  Jonathan Wells  in his new book  Zombie Science: More Icons of Evolution, the sequel to Icons of Evolution. One myth, a shambling zombie if ever there were one, is what Dr. Wells calls in Chapter 4, “DNA – The Secret of Life.”

But isn’t DNA the one and only secret of life? Neo-Darwinism, a gene-obsessed doctrine, needs it to be. But increasing aware of epigenetic — that is, bypassing genetic – inheritance messes with the simple story that evolutionists have successfully sold up till now. New research with roundworms pushes the extent of epigenetic effects farther than they’ve ever been observed before – 14 generations.

By switching the worms back and forth between cooler and warmer environments, European scientists were able to induce an inherited change in gene expression producing a fluorescent glow. Nematodes, especially the species C. elegans, are a favorite with researchers because of their brief lives and the consequent rapid passing of generations. A phenomenon of comparable extent in humans would be much harder to document.

The work was reported in Science. They call it “environmental information” (“Transgenerational transmission of environmental information in Caenorhabditis elegans”):

Ancestral legacy effects

Environmental change can critically affect the lifestyle, reproductive success, and life span of adult animals and their for generations. Klosin et al. showed that in the nematode worm Caenorhabditis elegans, exposure to high temperatures led to expression of endogenously repressed copies of genes — sometimes called “junk” DNA. This effect persisted for >10 generations of worms. The changes in chromatin occurred in the early embryo before the onset of transcription and were inherited through eggs and sperm.

Note the reference to “Junk DNA,” another zombie of evolutionary science dealt with by Jonathan Wells another book, The Myth of Junk DNA.

From the story at  Science Alert, lucidly explained by Signe Dean:

To study how long the environment can leave a mark on genetic expression, a team led by scientists from the European Molecular Biology Organisation (EMBO) in Spain took genetically engineered nematode worms that carry a  transgene for a fluorescent protein. When activated, this gene made the worms glow under ultraviolet light.

Then, they switched things up for the nematodes by changing the temperature of their containers. When the team kept nematodes at 20° Celsius (68° F), they measured low activity of the transgene — which meant the worms hardly glowed at all.

But by moving the worms to a warmer climate of 25° C (77° F), they suddenly lit up like little wormy Christmas trees, which meant the fluorescence gene had become much more active.

Their tropical vacation didn’t last long, however. The worms were moved back to cooler temperatures to see what would happen to the activity of the fluorescence gene.

Surprisingly, they continued to glow brightly, suggesting they were retaining an ‘environmental memory’ of the warmer climate — and that the transgene was still highly active.

Furthermore, that memory was passed onto their offspring for seven brightly-glowing generations, none of whom had experienced the warmer temperatures. The baby worms inherited this  epigenetic change through both eggs and sperm.

The team pushed the results even further — when they kept five generations of nematodes at 25° C (77° F) and then banished their offspring to colder temperatures, the worms continued to have higher transgene activity for an unprecedented 14 generations.

What’s the purpose for the worms? One of researchers, lead author Adam Klosin, says it could be “a form of biological forward-planning.” That doesn’t sound very Darwinian.

Jonathan Wells concludes, “DNA does not contain the genetic program for an organism, and DNA is far from being the secret of life. Continued faith in it is rooted in materialism.” That is, a materialist understanding of evolution requires the dogma of DNA. But science, meanwhile, marches on and another zombie bites the dust.

Yet more on Darwinism's losing on every sale.

Macroevolution by Loss: Flightless Birds Grounded by “Relaxed Selection”
Evolution News | @DiscoveryCSC

Evolutionists wanting to make a big deal out of flightlessness in birds are like the merchant who lost money on every sale but tried to make it up in volume.

Watch any documentary about Darwin, and you’re certain to get scenes of animals on the Galápagos Islands. In the panorama of unique creatures, you’re likely to see the flightless cormorant with its pitifully shrunken wings. Darwin made up a story about how this might have been good for the birds, but surely they’d rather fly like all other cormorants. Now for the first time, researchers have now tried to determine what happened genetically…and here’s the reason: they’re sick with a genetic disease.

With the help of a Chilean local expert, eight American scientists looked into the genome of the flightless cormorant, Phalacrocorax harrisi, and compared it with its flying relatives. It’s surprising that since Darwin’s time nobody had a clue what caused the change in this icon of evolution. The Introduction to the paper in  Science Magazine states:

Changes in the size and proportion of limbs and other structures have played a key role in the evolution of species. One common class of limb modification is recurrent wing reduction and loss of flight in birds. Indeed, Darwin used the occurrence of flightless birds as an argument in favor of his theory of natural selection. Loss of flight has evolved repeatedly and is found among 26 families of birds in 17 different orders. Despite the frequency of these modifications, we have a limited understanding of their underpinnings at the genetic and molecular levels. [Emphasis added.]

Well, it’s about time to check Darwin on his speculative idea. Phys.org introduces the hero:

The flightless cormorant is one of a diverse array of animals that live on the Galapagos Islands, which piqued Charles Darwin’s scientific curiosity in the 1830s. He hypothesized that altered evolutionary pressures may have contributed to the loss of the ability to fly in birds like the Galapagos cormorant.

We see the Darwinian escape valve at work again. It’s crystalized in those two words, “may have.” Anything may have happened. Pigs may have flown millions of years ago, when nobody could observe them. As luck would have it, they didn’t leave any fossils. But altered evolutionary selection pressures “may have” contributed to pigs’ loss of ability to fly.

To Darwinians, “evolutionary pressure” can point in any direction: up, down, or sideways. But think again. Some forces, like gravity, point only down. Suppose we suggested that gravity can point in any direction: sometimes making pigs fly. That would be ridiculous. Darwin needs to prove that selection pressure can point up toward innovation and progress; he can’t merely assume it. But we’ll take him up on this example of negative selection. Sure, evolution can break things, and it did so in the case of flightless cormorants.

Phys.org explains what broke:

The team also found that the flightless cormorants have an abnormally high number of genetic mutations affecting cilia — small, hair-like structures that protrude from cells and regulate everything from normal development to reproduction.

Cilia play a critical role in bone growth. People born with skeletal ciliopathies have shorter limbs, narrowed chests and stunted rib cages — as do the Galapagos cormorants. The UCLA results suggest that CUX1 controls many aspects of cilia, some of which influence bone growth.

These birds are sick. They continue to breed because the genetic sickness has spread to the whole colony, and there’s nobody else to breed with. They have what’s called ciliopathy, or a genetic disease that hinders the healthy development of cilia. Cilia, remember, are examples of irreducible complexity that Michael Behe described in his book, Darwin’s Black Box. Almost all cells have these molecular machines; some are motile, like those that sweep dust out of the airways, but many are stationary, acting like antennae. A lack of healthy cilia, when not fatal, leads to numerous genetic diseases. One feels sorry for these poor birds, but good icons of evolution they are not.

Some evolutionists try to rescue Darwin in this case by suggesting that the genetic disease helps the birds in some way: “changes that lead to flightlessness may help birds survive because they enhance their ability to do something else, like swimming — so-called positive selection.” Nice try, but more likely, selection pressure for costly flight and wings was “relaxed” because of a lack of predators on the island. “When flying isn’t essential for survival, the mutations that hinder flight can gradually accumulate in the gene pool.” Lives there a Darwinist who would consider this a helpful argument for universal common descent by mutation and selection?

“Relaxed selection” is like relaxed maintenance on your car. Without upkeep, it will rust and parts will break. You still may be able to drive it a little, but relaxation is not going to build a better car, or build a car in the first place.

The researchers found a way to manipulate the genetic data to affirm that 3 out of 11 genes showed evidence of “positive selection toward flightlessness.” They do this not by measuring actual benefits to the bird, but just measuring the ratio of synonymous to non-synonymous mutations. “These results suggest that selection toward flightlessness may be partially responsible for the phenotype of P. harrisi.” The results “suggest” that it “may” be “partially” responsible. Let’s try that on our relaxed-maintenance automobile: “The results suggest that positive selection toward rust may have been responsible for the car’s inability to drive faster than 20 mph.” Hooray! Evolution confirmed!

In a last-ditch effort to rescue Darwin, the research team suggested that the birds are stuck in a Peter-Pan-like juvenile stage, a condition called “heterochrony” (“other-timing”). Scientific jargon loses some of its power to impress when you translate it out of Latin. They also dazzle with “paedomorphosis” — “baby shape” (pedo as in pediatrician, morph for shape or form). Translation: “other-timing” led to “baby-shape.” Question: What, exactly, does that explain, other than to conceal the observation in a language most people don’t understand? And what does it have to do with Darwinian evolution?

Although we have identified multiple variants that likely contribute to the flightless phenotype of P. harrisi, we cannot exclude the possibility that other genes and pathways may contribute to the phenotype, nor the contribution of noncoding regulatory variants. Further characterization of the individual and joint contributions of the variants found in this study will help us to reconstruct the chain of events leading to flightlessness and to genetically dissect macroevolutionary change. We hypothesize that mutations in cilia or functionally related genes could be responsible for limb and other skeletal heterochronic transformations in birds and diverse organisms, including humans.

All is not in vain. At least we now know a little bit about genetic variants in flightless cormorants compared to flying cormorants. That’s interesting. We’ve learned part of what broke to make the birds genetically sick and grounded. But if there was any macroevolution happening, it was downwards, from the skies to the dirt, from working cilia to broken cilia. If there was a transformation, it was from powered flight to pitiful flopping.

It’s a loss every way you look at it. But don’t worry; Darwin will make it up in volume!

Lunacy re:lunar origins.

How the Moon Formed: 5 Wild Lunar Theories
By Mike Wall

Capture

Some researchers suggest that the moon may have originally formed elsewhere — perhaps even around another planet, such as Venus — before being grabbed by Earth's gravitational pull. Other worlds have gained moons in this manner. For example, Phobos and Deimos, the two tiny satellites of Mars, are thought to be captured asteroids. 

The capture idea isn't really an origin theory, of course; it just concerns how the moon came to orbit Earth. And it has some major problems, the most serious of which is the geochemical similarity of the Earth and moon. The two bodies have nearly identical oxygen isotope ratios, suggesting that they formed from the same pool of raw material.

Fission

Another idea — apparently thought up by Charles Darwin's son George in the 19th century — posits that the material that formed the moon was ejected into space by a molten, fast-spinning Earth in the very early days of the solar system. 

Most scientists discount the fission hypothesis, saying that Earth could not have been spinning fast enough to expel a huge blob of rock. But one 2010 study suggested that a natural nuclear explosion, set up by the superconcentration of radioactive elements, may have provided the kick to dislodge a moon-size piece of the early Earth into orbit. 

Co-formation

It's also possible that the moon formed alongside Earth 4.5 billion years ago, coalescing from gas and dust in the same part of our solar system's protoplanetary disk. 

While this hypothesis can account for the isotopic similarities between the Earth and moon, it falls short in other ways. It cannot explain the high angular momentum of the Earth-moon system, for example, or why the moon has such a small iron core compared to that of our planet. 

Colliding planetesimals

Some scientists have suggested that the moon condensed from the debris produced when planetesimals — the building blocks that grew into Earth, Mars and other full-fledged planets — slammed into each other shortly after the solar system formed. 

Little evidence supports this theory, which also cannot explain the geochemical similarities between the Earth and its natural satellite. 

Giant impact

The leading theory of the moon's formation posits that it coalesced from material blasted into space when a planet-size body slammed into the newly formed Earth about 4.4 billion years ago.

One variant of this idea holds that the impactor, dubbed "Theia," was about the size of Mars. Another version, introduced in 2012, suggests that both the impactor and the target — the proto-Earth — were about 50 percent as massive as Earth is today.

While the giant-impact hypothesis continues to be tweaked and refined, it does the best job of explaining the moon's composition and orbit, most scientists say. For example, the theory predicts a small iron core for the moon, since it would have formed primarily from the mantles of the impactor and early Earth (both of which lacked iron, which had already been concentrated deep in the core).

The danger of scientism to pure science.

What Would Really Be “Catastrophic” for Science?
David Klinghoffer | @d_klinghoffer

Wailing about the threat to science from “deniers” and “anti-science” skeptics is an inescapable feature of public discussions at the moment. Recently, Discovery Institute’s Wesley J. Smith, Jay Richards, Stephen C. Meyer were at the  Heritage Foundation  to discuss actual threats to science. They nailed a couple of those that deserve a lot more attention than they receive.

It’s a new podcast episode of ID the Future.  Listen to it here, or download it here.

First, insofar as the general public perceives, rightly, that viewpoints on science are subject to distorting social, political, and financial pressures, that really is “catastrophic” (Jay Richards’s word). Why would anyone trust the institutions of science, knowing that researchers are not free to follow the truth wherever it leads? Certainly, in the context of the evolution debate, pressures to conform are intense, as we know.

Second, the Discovery team was joined by Marlo Lewis of the Competitive Enterprise Institute who also made a great point. Lewis highlights the problem of science’s dependence on government funding. In the conversation, there’s an interesting clash of opinions between Lewis and Wesley Smith on whether science realistically could be detached from the government. I think Wesely is right that it could not — not entirely.

Be that as it may, Lewis cites a telling passage from President Eisenhower’s 1961 Farewell Address. Beside the prophetic warning about the power of the “military-industrial complex,” Eisenhower was concerned about what you might call the scientific-governmental complex.

Of scientific research, he worried, “A steadily increasing share is conducted for, by, or at the direction of, the Federal government.”

The prospect of domination of the nation’s scholars by Federal employment, project allocations, and the power of money is ever present — and is gravely to be regarded.

Yet, in holding scientific research and discovery in respect, as we should, we must also be alert to the equal and opposite danger that public policy could itself become the captive of a scientific-technological elite.

That prospect, science as the fief of a privileged caste seeking to direct the lives and values of others, pursuing a less-than-transparent ideological agenda, would also call the integrity of the scientific enterprise into question. That too, in Jay’s expression, would be catastrophic.

Yet more iconoclasm.

A Darwinian contr.. sorry non-controversy over natural selection.

No Controversies About Darwinism? Try This One
Evolution News | @DiscoveryCSC

We are often told that the science on Darwinism is settled. Advocates of academic freedom urge that teachers be allowed to challenge students and encourage critical thinking skills by sharing scientific strengths and weaknesses of evolutionary theory — “teach the controvery,” in other words. Darwin defenders respond with expressions of disbelief. The theory has no weaknesses, they say, and no controversy exists.

There might be minor disputes at the fringes, but no scientist doubts the certainty of Darwinian evolution. We can see them now, nodding in agreement: “Evolution itself has long since passed out of the field of scientific controversy,” as William Patten of Dartmouth opined in 1930. “There is no other subject on which scientific opinion is so completely unanimous. It is the one great truth we most surely know.”

How about the controversy over the central tenet of Darwinian evolution?

Nothing could be more central to Darwinian evolution than natural selection. It was in the title of Darwin’s Origin. It is the major “mechanism” along with random mutation that comprises neo-Darwinian theory. Natural selection and Darwinian evolution are inseparable. But what does natural selection mean? What entity does natural selection act on? It’s a controversy that has raged since 1859.

One current battle, showing no sign of abating, is between the kin selectionists and the group selectionists (see Casey Luskin’s play-by-play call in 2011  here  and Denyse O’Leary’s post-skirmish analysis in 2015  here). Kin selectionists think that natural selection favors genes of related individuals. The idea, also called inclusive fitness, purports to explain self-sacrifice in animals and humans — why worker ants serve the queen without reproducing themselves, and why humans put themselves in danger for their families. Some of their genes, presumably, will be passed on through their kin. Kin selection theory was given a mathematical formulation by W. H. Hamilton in 1964, to the relief of many Darwinians eager to find an explanation for altruism. It was promoted by E.O. Wilson, father of sociobiology (which led to evolutionary psychology), Richard Dawkins, father of Selfish Gene theory, Jerry Coyne, and many other Darwinians.

But when E.O. Wilson jumped ship in 2004, expressing doubts about the empirical evidence for kin selection, his former friends turned on him. Wilson had joined forces with mathematicians who cast doubt on “Hamilton’s Rule” undergirding the theory. When Wilson, with Martin Nowak and Corina Tarnita criticized kin selection as empirically lacking in 2011 in Nature,, 150 other evolutionists banded together to defend it, attacking Wilson’s motivations and arguments. There’s been a standoff ever since.

Now, in the Proceedings of the National Academy of Sciences, Wilson, Nowak and two others have launched another attack, with a vengeance: kin selection is not just wrong, it’s not even scientific! Here’s the fightin’-words title of the new paper: “The general form of Hamilton’s rule makes no predictions and cannot be tested empirically.”

Hamilton’s rule is a well-known concept in evolutionary biology. It is usually perceived as a statement that makes predictions about natural selection in situations where interactions occur between genetic relatives. Here, we examine what has been called the “exact and general” formulation of Hamilton’s rule. We show that in this formulation, which is widely endorsed by proponents of inclusive fitness theory, Hamilton’s rule does not make any prediction and cannot be tested empirically. This formulation of Hamilton’s rule is not a consequence of natural selection and not even a statement specifically about biology. We give simple and transparent expressions for the quantities of benefit, cost, and relatedness that appear in Hamilton’s rule, which reveal that these quantities depend on the data that are to be predicted. [Emphasis added.]

Not even a statement about biology? Ouch! We can expect some fireworks over this paper. It gets worse:

Hamilton’s rule asserts that a trait is favored by natural selection if the benefit to others, B, multiplied by relatedness, R, exceeds the cost to self, C. Specifically, Hamilton’s rule states that the change in average trait value in a population is proportional to BR−C. This rule is commonly believed to be a natural law making important predictions in biology, and its influence has spread from evolutionary biology to other fields including the social sciences. Whereas many feel that Hamilton’s rule provides valuable intuition, there is disagreement even among experts as to how the quantities B, R, and C should be defined for a given system. Here, we investigate a widely endorsed formulation of Hamilton’s rule, which is said to be as general as natural selection itself. We show that, in this formulation, Hamilton’s rule does not make predictions and cannot be tested empirically. It turns out that the parameters B and C depend on the change in average trait value and therefore cannot predict that change. In this formulation, which has been called “exact and general” by its proponents, Hamilton’s rule can “predict” only the data that have already been given.

In short, Nowak, McAvoy, Allen, and Wilson are saying that proponents of kin selection are deluded. They think they have a natural law, when all they have is a tautology. It’s not just that evidence is lacking for their “intuition” about kin selection; the mathematical formulation it rests on is vacuous.

Is this just a minor dispute about particulars of Darwinism? Notice that the authors claim it is “commonly believed to be a natural law” about evolution, and “its influence has spread from evolutionary biology to other fields including the social sciences.” The whole apple barrel is rotten! Wilson’s friends have launched this salvo in an open-access paper, viewable by the public. Are school boards and teachers going to be allowed to quote this paper, seeing that it is by mainstream scientists for mainstream scientists? Can they teach this controversy that gets to the core of Darwinism?

Wilson’s colleagues note three “astonishing facts” about Hamilton’s Rule:

“First, HRG is logically incapable of making any prediction about any situation because the benefit, B, and the cost, C, cannot be known in advance. They depend on the data that are to be predicted.”

“The second astonishing fact of HRG [Hamilton’s Rule – general] is that the prediction, which exists only in retrospect, is not based on relatedness or any other aspect of population structure.”

“The third fact of HRG is that no conceivable experiment exists that could test (or invalidate) this rule.” I.e., it violates the falsifiability criterion.

From there, the mathematicians get to work, proving these assertions. In the ending discussion, they illustrate the problems with a joke:

The predictive power of HRG is equivalent to the following example: If you give me the shoe sizes and heights of a group of people, then I can predict the heights. My algorithm also works if you gave me the wrong shoe sizes.

They also say, “In short, there is a startling discrepancy between the common intuitive understanding of Hamilton’s rule and the derivation of this rule that has been described as exact and general.” Kin selection’s proponents have basically been trusting in fake science for over 50 years!

We can safely predict a powerful comeback by the proponents of inclusive fitness. Look for it in the pages of PNAS or elsewhere in the coming days and weeks. But it doesn’t matter, because they’re all wrong. Tom Bethell wrote in Darwin’s House of Cards that natural selection is unscientific no matter how it is formulated. After looking at the logic of it in Chapter 5, and the presumed evidence for it in Chapter 6, he concluded, “Natural selection functions in the realm of philosophy, not science.” For support, he quotes none other than staunch Darwinian Richard Lewontin of Harvard, who at least had the intellectual rigor to critically examine the meaning of natural selection:

For what good is a theory that is guaranteed by its internal logical structure to agree with all conceivable observations, irrespective of the real structure of the world? If scientists are going to use logically unbeatable theories about the world, they might as well give up natural science and take up religion. Yet is that not exactly the situation with Darwinism? (Lewontin, “Testing the Theory of Natural Selection,” Nature 236, no. 543 (1972): 181-182, cited by Bethell, p. 65).

We expect E.O. Wilson would be quick to defend natural selection. The dispute between the kin selectionists and group selectionists, he would probably respond, is about the target of selection, not the fact of selection. That would reduce the controversy to the deluded majority that believes kin selection is a law of nature or a valid target of natural selection. The problem runs deeper than that. How can any target of selection — from the gene to the group — be empirically or mathematically validated? Interestingly, Wilson does not attempt to offer a mathematical rule for his favorite alternative, group selection. We think that’s because his opponents could shoot his arrows back at him.

For an independent check, look at what Charles Lineweaver said about evolution in an interview in New Scientist back in November 2012. Asked about one proposed definition of life as “anything that undergoes Darwinian evolution,” he responded,

We pretend that makes sense, but if you look at it, it makes no sense at all. What is the unit of Darwinian evolution? Is it the gene? Is it the cell? Is it a multicellular organism? Is a city evolving? How about Gaia? Is that a life form?

To make matters worse (for the Darwinians), natural selection theory would still have deep problems even if all biologists could agree on the unit of selection. Bethell began his journey as a Darwin skeptic by pondering the circular reasoning inherent in selection theory. “Is there any way of deciding what is ‘fit’ other than seeing what survives?” he asks in the Introduction (p. 11). “If not, maybe Darwin was arguing in a self-confirming circle: the survival of the survivors.” Throughout his journey, as he documents in the book, he found leading Darwinists admitting to this core flaw in the logic of natural selection. In the end, he confirmed his hunch that “natural selection is not remotely law-like. All attempts to state it as a law collapse into the truism that I reviewed in earlier chapters” (p. 244).

Perhaps you’ve watched a magician tie a complex knot, rub it in his hands, and make the knot disappear before your eyes. The trick works because the ends never pass through any of the loops. Natural selection is like that; it can be complexified through jargon, mathematical tricks, and consensus. But when you tug on it, it unravels.

As the battle rages on between the kin selectionists and the group selectionists, or between the gene selectionists and the planet selectionists, keep in mind that the very idea of natural selection — the core principle of Darwinian evolution if there is one — is logically flawed. E.O. Wilson claims that kin selection is unscientific. His opponents will counter that group selection is unscientific. Perhaps it’s all unscientific. Its definitions are fuzzy, its units are unspecified, and it predicts opposite outcomes with equal ease. It cannot be falsified. Students, and thoughtful adults, deserve to know such things.

The Watchtower Society's commentary on the New Testament

CHRISTIAN GREEK SCRIPTURES

So designated to distinguish them from the pre-Christian Greek Septuagint translation of the Hebrew Scriptures. It is a common practice to call this latter portion of the Bible the New Testament.—See BIBLE.

There are 27 canonical books that make up the Christian Greek Scriptures. After the death of Jesus, these books were penned under inspiration by eight men: Matthew, Mark, Luke, John, Paul, James, Peter, and Jude. Not all these men followed Jesus during his ministry; in fact, as far as is known for a certainty, only the three apostles Matthew, John, and Peter did. Mark may have been the “certain young man” who followed Jesus at a distance after he was arrested. (Mr 14:51, 52) At Pentecost, James, Jude, and perhaps Mark were present along with them. (Ac 1:13-15; 2:1) Later the apostle Paul was converted. All these writers became closely associated with the governing body of the first-century congregation in Jerusalem.

In what language were these books originally written? With the exception of the book of Matthew, which was written originally in Hebrew and later translated into Greek, all the other 26 books were written in the common Greek, Koine, the international language of the day.—See MATTHEW, GOOD NEWS ACCORDING TO.

Nor was it a mere coincidence that these inspired Christian men, all of them natural-born Jews (Ro 3:1, 2), had their writings sent out in Greek. These were not private communications but were intended for wide circulation, to be read and studied by all the congregations. (Col 4:16; 1Th 5:27; 2Pe 3:15, 16) The writers were under divine command to spread this good news and teaching to the most distant part of the earth, to places where Hebrew and Latin were not read. (Mt 28:19; Ac 1:8) Even in territories closer to Palestine, there was an increasingly large number of non-Jews coming into the local congregations. Also, when quoting the Hebrew Scriptures, these writers frequently used the Greek Septuagint.

The books of the Christian Greek Scriptures, listed according to the approximate year (C.E.) written, are as follows: Matthew, 41; 1 and 2 Thessalonians, 50 and 51; Galatians, 50-52; 1 and 2 Corinthians, 55; Romans, 56; Luke, 56-58; Ephesians, Colossians, Philemon, Philippians, 60-61; Hebrews, Acts, 61; James, before 62; Mark, 60-65; 1 Timothy, Titus, 61-64; 1 Peter, 62-64; 2 Peter, 64; 2 Timothy, Jude, 65; Revelation, 96; John and 1, 2, 3 John, 98. This period of less than 60 years is quite a contrast with the nearly 11 centuries taken to complete the Hebrew Scriptures.

When it came time to combine these books of the Christian Greek Scriptures into a single volume, they were not assembled in the order in which they were written. Rather, they were put in a logical arrangement according to subject matter, which can be classified as (1) the five historical books of the Gospels and Acts, (2) the 21 letters, and (3) the Revelation.

The four Gospels (the word “Gospel” meaning “good news”), written by Matthew, Mark, Luke, and John, give us a fourfold historical account of the life and activity of Jesus, each account being an independent report. The first three of these are sometimes called synoptic (meaning “like view”) because they have a relatively similar approach to Jesus’ ministry in comparison with John’s Gospel, yet each reflects individualism on the part of the writer. John’s Gospel fills in certain details omitted by the other three. The Acts of Apostles then follows in logical sequence, carrying the history of the Christian congregation as established at Pentecost on down nearly 30 years after the death of Jesus.

The congregation’s inner workings, its problems, its public preaching, its other privileges, and its hopes are dealt with in the 21 letters that follow the historical section. Paul is named as the writer of 13 letters. The letter to the Hebrews is also generally ascribed to Paul. Following these writings is a group of letters, most of which were written to all the congregations in general, by James, Peter, John, and Jude. Lastly, as a delightful climax to the whole Bible, is the Revelation with its preview of profound events of the future.

To what extent did writers of the Christian Greek Scriptures quote from the Hebrew Scriptures?

The writers of the Christian Greek Scriptures quoted the Hebrew Scriptures hundreds of times. In the Christian Greek Scriptures, the New World Translation presents as direct quotations 320 passages from the Hebrew Scriptures. According to a listing published by Westcott and Hort, the combined total of quotations and references is some 890. (The New Testament in the Original Greek, Graz, 1974, Vol. I, pp. 581-595) Examples are drawn from the Hebrew Scriptures by all the inspired Christian writers. (1Co 10:11) These Christian writers undoubtedly employed the divine name Jehovah when they were quoting from the Hebrew Scriptures. These later writers acknowledge and include the Hebrew Scriptures as inspired of God and beneficial for completely equipping the man of God for every good work.—2Ti 3:16, 17; 2Pe 1:20, 21.

After the death of the apostles, uninspired writers quoted profusely from the Greek Scriptures, even as the inspired Christian Bible writers had quoted from what came before them.

There are available for comparative study more than 13,000 papyrus and vellum manuscripts containing the whole or a part of the Christian Greek Scriptures, dating from the 2nd to the 16th century. Of these, some 5,000 are in Greek, and the remainder in various other languages. More than 2,000 of the ancient copies contain the Gospels, and more than 700, the letters of Paul. While the original writings themselves are not currently extant, copies date back to the second century, which is very close to the time the originals were written. This vast number of manuscripts has enabled Greek scholars in the course of years to produce a highly refined Greek text of the Scriptures, confirming in many respects the dependability and integrity of our present-day translations of the Christian Greek Scriptures.—See MANUSCRIPTS OF THE BIBLE.

This vast mountain of manuscripts caused one scholar to remark: “The great bulk of the words of the New Testament stand out above all discriminative processes of criticism, because they are free from variation, and need only to be transcribed. . . . If comparative trivialities, such as changes of order, the insertion or omission of the article with proper names, and the like, are set aside, the words in our opinion still subject to doubt can hardly amount to more than a thousandth part of the whole New Testament.” (The New Testament in the Original Greek, Vol. I, p. 561) To this may be added the observation of Jack Finegan: “The close relationship in time between the oldest New Testament manuscripts and the original texts is also nothing less than amazing. . . . For our knowledge of the writings of most of the classical authors we are dependent upon manuscripts the oldest of which belong to a time between the ninth and eleventh centuries A.D. . . . Thus it is that the certainty with which the text of the New Testament is established exceeds that of any other ancient book. The words which the New Testament writers addressed to their world and time have crossed the further miles and centuries to us substantially unchanged in form and certainly undiminished in power.”—Light From the Ancient Past, 1959, pp. 449, 450.

As an integral part of the written Word of God, the Christian Greek Scriptures are of inestimable value. They contain four accounts of the ministry of God’s only-begotten Son, including his origin, his teaching, his example, his sacrificial death, and his resurrection. The historical record of the formation of the Christian congregation and the outpouring of the holy spirit, which enabled it to grow so successfully, as well as details concerning its problems and how they were resolved—all of this is so essential for the operation of the true Christian congregation today. The separate books that were independently written for particular persons or situations, or with a special view and purpose in mind, all merge to form a great unified complete entity with no details lacking. They complement and complete the Bible canon and are presently of universal importance, interest, and concern primarily to spiritual Israel, which is the congregation of God, but, additionally, to all persons who seek the approval of God.


For information on the contents of the 27 books, their writers, the time written, and proof of authenticity, see the individual books by name.

The Geneva study bible's commentary on Michael the great prince

Geneva Study Bible

Daniel 12

Verse 1
And at that ^a time shall Michael stand up, the great prince which standeth for the children of thy people: and there shall be a time of trouble, such as never was since there was a nation [even] to that same time: and at that time thy people shall be delivered, every one that shall be found written in the book.

(a) The angel here notes two things: first that the Church will be in great affliction and trouble at Christ's coming, and next that God will send his angel to deliver it, whom he here calls Michael, meaning Christ, who is proclaimed by the preaching of the Gospel

Hawker's Poor Man's Commentary

Daniel 12

 

Verse 1CONTENTS
The prophecy o f Daniel closeth in this Chapter, with some most gracious assurances of Israel's deliverance; from all her troubles. Daniel's mind is exercised with thoughts concerning the same. The Lord's gracious consolation to the Prophet.
Daniel 12:1
Here is a most lovely account of Jesus, and of his office-character, as Mediator. I do not hesitate to believe, that the Michael here spoken of is Christ. In confirmation, turn to those scriptures. Revelation 12:7-11. How Christ then stood up for all eternity: how in time, and how forever; all his offices typify. Proverbs 8:22-23; Psalms 40:6-8; Hebrews 7:24-25; 2 Thessalonians 1:10. In every point of view, it must be a time of trouble. When Christ comes to make up his jewels, he comes also to take vengeance of them that know not God, nor obey the gospel of Jesus. Malachi 4:1; 2 Peter 3:10-11. But what a sweet close is this verse, of the safety of Jesus own! Isaiah 4:3; Luke 10:20; Revelation 20:12-15.