Neodarwinism's star witness defects.

Genetics and Epigenetics — New Problems for Darwinism
Evolution News | @DiscoveryCSC

New findings in genetics and epigenetics are creating new problems for evolution. The simplistic version of neo-Darwinism expects all variation come from genetic mutations, which nature selects for fitness. Non-coding DNA was relegated to the junk pile — trash left over from natural selection, which favors DNA that codes for proteins. In a notion called subfunctionalization, copies of genes might be free to mutate and become new proteins, or decay into “pseudogenes,” one type of junk DNA. As usual, simplistic theories are often wrong. 

How Many Genes?

The Human Genome Project ended with a surprisingly low number of genes. But what if they missed some ? Researchers at Yale have been finding genes that were misidentified as non-protein coding due to the methods previous researchers used to annotate them. One of the newly identified genes, they say, plays a key role in the immune system. Are there others? 

The findings suggest many more protein-coding genes and functions may be discovered. “A large portion of important protein-coding genes have been missed by virtue of their annotation,” said first author Ruaidhri Jackson. Without vetting and identifying these genes, “we can’t fully understand the protein-coding genome or adequately screen genes for health and disease purposes.” 

The first sentence of their paper in Nature says, “The annotation of the mammalian protein-coding genome is incomplete.” They have identified a “large number of RNAs that were previously annotated as ‘non-protein coding,’” some of which are “potentially important transcripts” able to make protein. Restrictive methods in the past “may obscure the essential role of a multitude of previously undiscovered protein-coding genes.”

Epigenetics in Archaea

Does epigenetic inheritance and regulation work only in eukaryotes? No. Scientists at the University of Nebraska-Lincoln discovered that members of the “simple” kingdom of Archaea also have it. They watched microbes inherit extreme acid resistance in Yellowstone hot springs not through genetics, but through epigenetics.

    “The surprise is that it’s in these relatively primitive organisms, which we know to be ancient,” said Blum, Charles Bessey Professor of Biological Sciences at Nebraska. “We’ve been thinking about this as something (evolutionarily) new. But epigenetics is not a newcomer to the planet.”

The discovery “raises questions … about how both eukaryotes and archaea came to adopt epigenetics as a method of inheritance.” Now they have to confront whether an even earlier common ancestor had it, or whether it evolved twice. “It’s a really interesting concept from an evolutionary perspective,” said a doctoral student involved in the research. Critics of neo-Darwinism might describe those alternatives differently from just “interesting.” Ridiculous, perhaps, or falsifying.

Epigenetics in Plants

Briefly, a paper in  PNAS finds that “Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation.” Why do clones, with identical genomes, differ? The answer is epigenetics. 

   We found that phenotypic novelty in clonal progeny was linked to epigenetic imprints that reflect the organ used for regeneration. Some of these organ-specific imprints can be maintained during the cloning process and subsequent rounds of meiosis. Our findings are fundamental for understanding the significance of epigenetic variability arising from asexual reproduction and have significant implications for future biotechnological applications.

    

Non-Genetic Order

Here’s a cellular phenomenon that really is interesting, because it reveals a newly discovered structural order in the cell membrane. This structural order surely is inherited somehow, but may have little to do with genes. Biochemists had thought for a century that the inner space in the membrane is fluid and disordered, but techniques to probe that space have been difficult because the detergents used disrupt the membrane. Now, researchers at Virginia Commonwealth University, in conjunction with Nobel laureate Joachim Frank, used a new method without detergents. They were surprised — no, startled — to find an orderly hexagonal 3-D structure between the molecules in the lipid bilayer. Is there a reason for this orderly structure?

     Where earlier models had shown a fluid, almost structureless lipid layer — one often-cited research paper compared it to different weights of olive oil poured together — the VCU-led team was startled to find a distinct hexagonal structure inside the membrane. This led the researchers to propose that the lipid layer might act as both sensor and energy transducer within a membrane-protein transporter.

“The most surprising outcome is the high order with which lipid molecules are arranged, and the idea they might even cooperate in the functional cycle of the export channel,” said Joachim Frank, Ph.D., of Columbia University, a 2017 Nobel laureate in chemistry and co-author of the paper. “It is counterintuitive since we have learned that lipids are fluid and disordered in the membrane.”

    Their paper in PNAS says nothing about genetics, so maybe this comes about through physical interactions of the lipids and the protein channels. Whatever causes this orderly arrangement, it appears to interact with transmembrane channels, adapting to the conformational changes of the proteins, particularly a transporter called AcrB. Without the hexagonal mesh around the channel, and just a disordered fluid, the channels action might be less efficient, like a boxer without a sparring partner beating the air. Not only that, the hexagonal mesh also transmits the channel’s activity down the membrane to its neighbors. Fascinating!

       Through defined protein contacts, the lipid bilayer senses the conformational changes that occur in each TM [transmembrane] domain and then transduces effects of these changes through the lipid bilayer to neighboring protomers in a viscous interplay between cavity lipids and the AcrB trimer.

                 

Another Blow to the Central Dogma

Mauro Modesti gives his perspective on a new finding in Science, “A pinch of RNA spices up DNA repair.” The Central Dogma of genetics that views DNA as the master molecule controlling everything downstream, with no feedback, has been suffering since it was first taught the 1960s. In the same issue of Science, a paper reveals that RNA plays an essential role in DNA repair. What does this mean? Modesti explains,

                   Pryor et al. report the surprising discovery that ribonucleotides are frequently incorporated at broken DNA ends, which enhances repair. This important finding overturns the central dogma of molecular biology by demonstrating that transient incorporation of ribonucleotides in DNA has a biological function.

Genetic Determinism Lives On

The idea that humans are pawns of their genes has a long history, mostly negative. Genetic determinism undermines free will and character, giving people something physical to blame for their problems. Materialists continue the bad habit, though, as shown in this paper in Nature Scientific Reports, “A genetic perspective on the relationship between eudaimonic –and hedonic well-being.” The news from the University of Amsterdam puts it bluntly: “Discovery of first genetic variants associated with meaning in life.” But can something as psychological or even spiritual be reduced to genes? 

They checked DNA samples of 220,000 individuals, and had them answer a questionnaire. The genetic variants, they say, “are mainly expressed in the central nervous system, showing the involvement of different brain areas.” 

“These results show that genetic differences between people not only play a role in differences in happiness, but also in differences for in meaning in life. By a meaning in life, we mean the search for meaning or purpose of life.”

Did these researchers ever learn that correlation is not causation? Did they inspect their own genes? Did they answer a questionnaire, saying that they felt eudaimonia when proposing genetic determinism? Did their genes determine their own philosophy of mind? If so, then how can anyone believe them? What are universities teaching scientists these days?

Simplistic notions of neo-Darwinism seemed more plausible before new techniques uncovered the evidence of splendid design going on in cells. If the trend continues, 2019 will be a great year for intelligent design.

Sacred cows?

In Europe, Animal Rights Are Steamrolling Religious Freedom
Wesley J. Smith

As Western society secularizes, religious liberty is in danger of becoming passé. Increasingly, jurisdictions are enacting laws in furtherance of legitimate social considerations that, concomitantly, shrivel the freedom of religious believers to live according to their personal faith precepts.

Western Europe is leading the way. Belgium now requires all food animals be stunned before slaughter, which prevents their meat from being declared kosher or halal — hence edible — in accordance with the religious requirements of Judaism and Islam.

A Terrible Bind

Of course, such animal welfare laws are absolutely appropriate. But, until recently, comity was also preserved by allowing limited religious exemptions. Those accommodations are now systematically being removed. From the New York Times story:

Most countries and the European Union allow religious exceptions to the stunning requirement, though in some places — like the Netherlands, where a new law took effect last year, and Germany — the exceptions are very narrow. Belgium is joining Sweden, Norway, Iceland, Denmark and Slovenia among the nations that do not provide for any exceptions.

That puts observant Jews and Muslims in a terrible bind. They can have food shipped from elsewhere, which is more expensive. But what if other countries also ban such practices, or their home countries forbid the import of kosher or halal meat? Believers would be forced to choose between eating meat and violating their religious beliefs.

Some secularists would be just fine with that since these laws don’t infringe their own freedoms, while those who are anti-religious would delight in forcing such hard choices upon believers.

“The Law Is Above Religion”

Some non-religionists even presume to tell the faithful what their rules do and don’t require:

   Ann De Greef, director of Global Action in the Interest of Animals, a Belgian animal rights group, insisted that stunning does not conflict with kosher and halal doctrine, and “they could still consider it ritual slaughtering,” but the religious authorities refuse to accept that.

“They want to keep living in the Middle Ages and continue to slaughter without stunning — as the technique didn’t yet exist back then — without having to answer to the law,” she said. “Well, I’m sorry, in Belgium the law is above religion and that will stay like that.”

That kind of religious intolerance is only going to present in brighter hues going forward. There is great pressure, for example, to ban infant circumcision, a sacred and absolute requirement of Jews, also practiced as a religious duty by many Muslims. Efforts are also afoot to force doctors to participate in abortion and/or euthanasia — even when a doctor considers such acts to be a grievous sin materially impacting their own eternal destinies. I am sure readers can think of many other examples.

Freedom cannot be a one-way street. Steamrolling traditional believers’ faith values is a recipe for tearing society apart.

American healthcare on its deathbed?:Pros and cons.

How fish school humans on design.

Fish Teach Humans about Design
Evolution News & Views April 1, 2016 3:48 AM

Why do fish bob their heads back and forth as they swim? Is that wasted movement? Is it an inescapable consequence of undulatory motions during swimming? That's what many scientists used to think. What a team found out reminds us never to assume nature's methods are wasteful.

A new paper in Nature Communications summarizes the find: "Fish optimize sensing and respiration during undulatory swimming." That word optimize has design written all over it, especially when the fish optimizes three things at once:

Previous work in fishes considers undulation as a means of propulsion without addressing how it may affect other functions such as sensing and respiration. Here we show that undulation can optimize propulsion, flow sensing and respiration concurrently without any apparent tradeoffs when head movements are coupled correctly with the movements of the body. This finding challenges a long-held assumption that head movements are simply an unintended consequence of undulation, existing only because of the recoil of an oscillating tail. We use a combination of theoretical, biological and physical experiments to reveal the hydrodynamic mechanisms underlying this concerted optimization. [Emphasis added.]
Using a "bio-inspired physical model" with flow sensors, the team from Harvard and the University of Florida found that head bobbing actually improves swimming efficiency. Then they studied how the fish's lateral line sense improves with the resulting water flow. One might think that the extra motion of the head would confuse the lateral line sense, but the opposite is true.

We discovered that the motions associated with undulation can automatically enhance lateral line sensing on the head by minimizing self-generated stimuli. Fish move their heads in a way that minimizes pressure up to 50%, establishing a twofold greater sensitivity to an external stimulus than would otherwise be possible (Fig. 3a). At swimming speeds up to 2 L s−1, we found a heightened sensitivity around the anterior region of the head, which is where the majority of the encounters related to feeding and locomotion are initiated. We propose that during swimming, fish may not have to rely as extensively on the efferent system to distinguish between external and self-generated stimuli if they rotate their head in an appropriate phase with respect to side-to-side motion.
Simultaneously, this head motion increases the flow across the gills, enhancing respiration. This is the first time the coupling of motion with respiration has been demonstrated in fish like it has been with birds, horses and humans. Scientists used to view undulation and respiration as independent processes. No longer:

Here, we discover that fishes swimming with body undulations also show respiratory-locomotor coupling. Our pressure model reveals that undulation-generated pressures around the mouth and opercula oscillate dramatically. We found that fishes exploit these pressures by timing their respiratory movements accordingly, which likely minimizes the energetic cost of pumping the dense medium of water. High-speed, high-resolution video reveals that respiratory movements are tightly synchronized with head movements (Fig. 3b). When the pressure difference between the outside and inside of the mouth reaches 0.2 mm Hg, fishes open their mouth to allow water to flow in passively. Perhaps not coincidentally, this exact pressure difference is generated by the active buccal expansion of stationary fish. In this way, we hypothesize that swimming fishes exploit self-generated pressures to circumvent the work of buccal pumping.
This is really neat. The undulatory motion of swimming with the fins moves the head back and forth in phase such that the work of breathing is reduced, and the sensitivity of the lateral line is optimized. It's a three-for-one gain with no tradeoff in cost.

Life requires the successful, simultaneous execution of basic physiological functions. The coordination of these functions usually relies on distinct neural networks that run in parallel. Over the past several decades, a number of studies have demonstrated that the passive mechanical properties of the body can simplify individual functions, releasing them from the need for precise neural control. Here, we show that during aquatic axial undulation, head movements can allow seemingly disparate but fundamental functions to be coordinated simultaneously without tradeoffs.
Isn't evolution smart to pull this off? Actually, the authors didn't have much to say about evolution. Their only mention of evolution seems to falsify its expectations:

Given that the respiratory system is located in the head and the locomotory system is associated with the trunk, it is not unreasonable to assume that respiration and swimming would be decoupled. The contemporary view point is that the origin of the lung enabled respiratory-locomotor coupling to evolve in terrestrial animals.
Here, we discover that fishes swimming with body undulations also show respiratory-locomotor coupling....

But why would evolution optimize two or three things at once? Selection for traits can only act on immediate benefit from a random mutation. Like they say, "it is not unreasonable to assume" that selection for benefit in one trait would be independent of selection for other traits. The "contemporary view" may be that the lung "enabled" coupling, but if that were a useful idea, they would have said more about it. They didn't. We know from experience, however, that when engineers succeed in optimizing multiple things at once without tradeoffs, they win prizes and promotions for intelligent work.

More evidence that this work supports intelligent design is seen in their desire to imitate it. "The power of this simple control architecture is that it can be universally applied to any size and species of undulating fish, as well as to autonomous, underwater vehicles," they note. Yet the salmon seen bobbing their heads in Living Waters beat engineers to it. Engineers can just imitate what they see and win a design prize.

Non-Clogging Filters

Another case of intelligent design was announced in a second paper in Nature Communications. Biologists from the College of William and Mary liked this design so much, they immediately thought of how to apply it. Notice that the design is found in birds and mammals as well as fish.

Suspension-feeding fishes such as goldfish and whale sharks retain prey without clogging their oral filters, whereas clogging is a major expense in industrial crossflow filtration of beer, dairy foods and biotechnology products. Fishes' abilities to retain particles that are smaller than the pore size of the gill-raker filter, including extraction of particles despite large holes in the filter, also remain unexplained. Here we show that unexplored combinations of engineering structures (backward-facing steps forming d-type ribs on the porous surface of a cone) cause fluid dynamic phenomena distinct from current biological and industrial filter operations. This vortical cross-step filtration model prevents clogging and explains the transport of tiny concentrated particles to the oesophagus using a hydrodynamic tongue. Mass transfer caused by vortices along d-type ribs in crossflow is applicable to filter-feeding duck beak lamellae and whale baleen plates, as well as the fluid mechanics of ventilation at fish gill filaments.
A hydrodynamic tongue -- what a concept! Fish "engineer" previously unknown flow patterns to transport the particles they need into their esophagus. Those humpback whales seen in Living Waters use this technique as they gulp krill with their huge mouths, and the small tropical fish do it with their gills. The ducks in Flight: The Genius of Birds do it with their beaks. Who taught a fish, a duck, and a whale about fluid dynamics? It must have been natural selection. Tell us, please, how that came about:

In addition to the ecological and evolutionary relevance, these problems are of substantial interest to industrial filtration engineers who seek to reduce the major operating expenses associated with clogging.
One reads with bated breath for an evolutionary explanation that never comes.

As more than 30,000 fish species possess branchial arches that may form d-type ribs, potential vortex formation in the slots between branchial arches has substantial implications for the fluid dynamics of fish feeding and ventilation throughout ontogeny and evolution. Vortical cross-step filtration could be applicable to feeding in a diversity of fish species. In addition, many filtration structures involved in vertebrate suspension feeding are composed of d-type ribs in crossflow, including fish gill rakers, tadpole gill filters, bird beak lamellae and whale baleen plates, suggesting that principles of vortical cross-step filtration could have widespread application.
And that's it. That's all they have to say about evolution. This beautifully designed trait, so envied by engineers, is found in all these unrelated animals. How? Because "principles of vertical cross-step filtration" work, and are found all over the animal kingdom, they must have evolved. Does that make any sense?

It should be clear to anyone that intelligent design did the heavy lifting in both papers. Evolution played no role in the experimental setup, the explanation, or the application in either case. As usual, evolution only tags along in the role of post-hoc narrative gloss.

The 'talking ape' vs. Darwin

Language as an Evolutionary Conundrum
David Klinghoffer February 26, 2016 6:10 AM

In Chapter 10 of his new book Evolution: Still a Theory in Crisis, Michael Denton argues for the proposition that language and the higher intellectual faculties -- the gifts that uniquely make us human -- arose by saltation. In other words, they are gifts -- sudden ones. Denton's view, as he makes clear, has precedents reaching from Alfred Russel Wallace to linguist Noam Chomsky.

In a nice coincidence, Chomsky and MIT colleague Robert C. Berwick are just out with a book of their own, from MIT Press, provocatively titled Why Only Us: Language and Evolution. To be sure, Chomsky and Berwick are not advocates of Denton's structuralist take on the theory of intelligent design. Still, their own argument for language by saltation is not hard to reconcile with Denton's view.

The recognition that language poses a problem for Darwinian gradualism is presumably what makes linguist Vyvyan Evans uneasy about the book, which Dr. Evans reviews in New Scientist:

Their argument goes like this. As our capability for grammar is genetically programmed, and as no other species has language, it stands to reason that language emerged fairly suddenly, in one fell swoop, because of a random mutation. This is what the authors refer to as the "gambler's-eye view" in contrast to a "gene's-eye view" of evolution. The sudden appearance of language occurred perhaps no more than 80,000 years ago, just before modern humans engaged in an out-of-Africa dispersion.

A sudden "random mutation"...

But to be convinced by this, the reader has to swallow a number of sub-arguments that are debatable at best. For one thing, the authors presume the Chomskyan model of human language -- that the rudiments of human grammar (or syntax) are unlearnable without an innate knowledge of grammar. Its position seems less reasonable today that it once did.

Remember, as surly geneticist Dan Grauer formulates the 12th and final of his principles of new-Darwinism (Evolution News pointed this out yesterday), "Homo sapiens does not occupy a privileged position in the grand evolutionary scheme." A sudden gift, mutation, call it what you will, endowing our ancient ancestors alone with language is thus, on principle, to be disallowed. Language must be shared with other, non-human creatures. And so it is, Evans assures readers.

[R]esearch in primatology and animal behaviour suggests that some of the precursors for language do exist in other species, ranging from European starlings to chimpanzees -- with the latter using a sophisticated gestural form of communication in the wild. In fact, gesture may well have been the medium that incubated language until ancestral humans evolved the full-blown capacity for it.

Yet no one would confuse the most eloquent chimp "gestures" with modern sign language. That leaves in place the question of where language, whether communicating through hand or mouth, came from.

The "scientific consensus" cannot accept saltations of such a staggering kind:

Ultimately, Why Only Us is something of a curiosity. It takes a reverse engineering perspective on the question of how language evolved. It asks, what would language evolution amount to if the Chomskyan proposition of universal grammar were correct? The answer is language as a mutation that produces a phenotype well outside the range of variation previously existing in the population -- a macromutation. This flies in the face of the scientific consensus. Indeed, the book attempts to make a virtue of disagreeing with almost everyone on how language evolved.

Evans makes an interesting point. If the sudden mutation occurred in one person, it would provide no benefit since there would be no one to talk to. Did the "random mutation," the gift, then occur in a pair of individuals, living in the same time and place? Don't even think of going there. All parties to the argument are agreed on that. Evans:

The reader is asked to swallow the following unlikely implication of their logic: language didn't evolve for communication, but rather for internal thought. If language did evolve as a chance mutation, without precedent, then it first emerged in one individual. And what is the value of language as a communicative tool when there is no one else to talk to? Hence, the evolutionary advantage of language, once it emerged, must have been for something else: assisting thought.

For the spectator, it's not without pleasure to see evolutionists going at each other this way. Evans accuses Chomsky and Berwick of "reverse engineering" -- but more orthodox Darwinian "perspectives" do the very same thing. They assume the negation of the human exceptionalist view and impose that principle, as Evolution News suggested, on whatever is observed.

Every take on the origin of language that leaves the creative work entirely to one or more "random mutations" is doomed. We will be excerpting Denton's Chapter 10 in good time. Stay tuned.

Editor's note: Get your copy of Evolution: Still a Theory in Crisis now. For a limited time, you'll enjoy a 30 percent discount at CreateSpace by using the discount code QBDHMYJH.

Free dessert as well?

Get Out of Jail Free: Playing Games in an RNA World
Evolution News & Views September 23, 2013 5:20 AM

Four Darwinian mathematicians and biologists from New York University (one from Puerto Rico) think that RNA molecules played games to invent life. Even if the RNA could spontaneously form, why would mindless molecules scheme to create a universal, nearly optimal genetic code via a pointless game?

Jee, Sundstrom, Massey and Mishra, writing in the Royal Society Interface, ask, "What can information-asymmetric games tell us about the context of Crick's 'frozen accident'?" Francis Crick viewed the origin of the genetic code as an accident that caught on and became universal. But how did gene sequences become associated with polypeptide sequences having function? They know that the genetic code, as is, is pretty darn good:

The genetic code, the mapping of nucleic acid codons to amino acids via a set of tRNA and aminoacylation machinery, is near-universal and near-immutable. In addition, the code is also near-optimal in terms of error minimization, i.e. tRNAs recognizing similar codons may be mistaken for each other during translation, yet these mistakes often have no negative impact on translation because similar codons map to identical amino acids or ones with similar physiochemical properties. Biochemists have long wondered: If immutability and universality were early properties (i.e. the genetic code was a "frozen accident"), then how could natural selection encourage error-minimization? If selection for an error minimizing genetic code predated immutability and universality, then why is the standard code less than optimal? (Emphasis added.)

Although "numerous models have been proposed" to explain this "apparent paradox," they each have problems, such as "premature freezing" of the code, or in the case of neutral evolution, inability to explain the code's universality. So these guys enter the fray.

Like Crick, they know that hitting upon a functional enzyme by chance in the space of random polypeptides is improbable to the extreme:

Because of the relative length and complexity of modern enzymes, it may be possible that the earliest peptides were not enzymes in the traditional sense. To "accidentally" stumble upon genes encoding such enzymes at the same time an error minimizing code occurred by chance, as suggested by Crick, has vanishingly small probability.

Their job, therefore, is to find pointless polypeptides associating with pointless polynucleotides in some sort of "signaling game" that makes them both "help" each other over time until universality, immutability and optimality reach an equilibrium that just happens to be near maximum. Their very helpful tool in this endeavor is game theory:

As suggested by Maynard-Smith, games in a biological setting, unlike traditional ones in game theory, might not require "rational agents." A population of animals of the same species, for instance, may over the course of evolution behave according to game-theoretic principles even though none of those animals is a "rational agent," in a traditional sense. A species may "learn" over evolutionary time to select certain behaviors through random mutations, genetic drift, and selection, and ultimately reach a Nash equilibrium, in this case defined as an evolutionarily stable state in which each agent does not deviate strategies so long as all other agents in the system also do not deviate from their adopted strategies. "Utility" in the game-theoretic sense physically manifests as reproductive fitness.

They put "utility" in quotes, because it takes a rational agent to determine what is useful. What they are looking for is an equilibrium between mindless players aiming nowhere. Life and optimal coding become incidental byproducts of the equilibrium. Is there any other chemical reaction in nature that arrives at such coding specificity without trying? One might get an oscillation between states, but not a code that specifies a function.

Overall this paper presents a framework for studying signaling game dynamics in instances where both message length and distortion are factors in the utility of both senders and receivers. Although we have applied the framework here primarily to the evolution of the genetic code, similar analyses might be applied to the evolution of many other seemingly fixed processes, where the evolutionary clock appears to have frozen a biological process prematurely to an arbitrary conventional structure.

Well, best of luck. We find them personifying the molecules. The molecules adopt "strategies." They "learn" over evolutionary time. They send "information" or receive it, as they "signal" each other with "messages." Does this make any sense? Take out the words implying personality, goal and purpose, and the idea seems silly, much more so than for antelope strategizing to outwit a lion. These are just dumb molecules!

It's not necessary to delve into the equations of their "game," because math cannot rescue a bad premise. What we find them doing is weaving a fantastic tale in their own imaginations, starting with already-existing complex molecules in a mythical RNA world (which has its own problems).

It is usually hypothesized that the genetic code formed in the context of an RNA world, gradually exposed to an emerging amino acid world. We envision a scenario with two agents: proto-mRNA (strings of codons with information) and sets of proto-tRNA (RNAs with distinct anticodons, each able to bind a particular amino acid). In a given generation proto-mRNA and a particular set of proto-tRNA interact. The pair replicates via RNA replicase ribozymes. However, they may also chemically aid their own replication through the accurate production of proteins (possible identities of these proteins are stipulated in Discussion).

These gamers assume the existence of (1) RNA ribozymes capable of replication, (2) information, (3) transfer RNA with distinct anticodons, (4) accurate production of proteins. Who, we might ask, "usually hypothesized" such things? They should be dismissed from the science lab on account of "envisioning scenarios" instead of doing real chemistry.

Many other problems are completely ignored or glossed over in their visionary scenario, such as the problem of getting one-handed amino acids and sugars by chance. They also assume that natural selection would operate at the scale of molecules in an RNA world before life -- a fallacy, because natural selection requires not just replication, but accurate replication, accurate enough to avoid error catastrophe.

The news release from New York University, as expected, sanctifies this proposal as the inspired work of genius professors. It also won the uncritical acclaim of Science Daily and other news outlets: "Researchers have created a model that may explain the complexities of the origins of life." Be sure to thank the NSF for funding this paper in a down economy.

Well, It Could Happen

Throughout this weird paper, the authors display reckless imagination with frequent assertions that various miracles of chance "could" or "may" or "might" happen. (If a pig had wings, we all know, it "could" fly, provided it also had flight muscles, feathers, avian lungs, and all -- watch Flight.) Added to the heavy spicing of "possibility" words, they frequently endowed the molecules with goal-directed behavior, personifying them as willing game players. Here is but one egregious example from the abstract:

Such a framework suggests that cellularity may have emerged to encourage coordination between RNA species and sheds light on other aspects of RNA world biochemistry yet to be fully understood.

So, out of nowhere, "cellularity emerges" to "encourage coordination." Are you seeing any light that has been shed yet? Later, the personification, assumed goal-seeking, and speculation gets even worse:

The model presented here demonstrates that the modern genetic code evolved most likely by a combination of previously hypothesized forces, involving neutral and selective evolution. Whereas a natural predisposition toward an error-minimizing code is not a necessary condition for an optimized genetic code, neutral evolution may have been an important force in establishing universality. At the same time, selective pressure can provide a powerful impetus for a genetic code to move toward error-minimization and, somewhat surprisingly, also enforce its immutability so as to maintain compatibility with the genome.

Who does the enforcing? Who does the establishing? Who does the maintaining? Who follows an impetus to move toward error minimization? What is an error, anyway, to a mindless molecule? This is crazy, but not crazy enough for the Royal Society to publish it.

They get away with this because it fits the requirement of naturalism: "No intelligence allowed." Within that constraint, they follow Finagle's 6th Rule: "Do not believe in miracles. Rely on them."

Good-bye, RNA World

The authors feel somewhat justified in "envisioning" their make-believe "scenario" on the grounds that "Evidence for such a world [RNA world]... is growing." Too bad this paper came out about the same time that Steven Benner, a veteran origin-of-life researcher, poured cold water on the idea at the Goldschmidt Conference in Florence in August. Here's what he said happens to ribose (an essential sugar for RNA) and other biomolecules when exposed to the watery conditions assumed on the early earth, according to an NBC News article:

The early environment on Earth, however, was challenging to the rise of life as we know it, at least in Benner's view. One of the biggest challenges has to do with the process by which organic molecules gave rise to life's chemical building blocks: RNA, DNA and proteins.

If left to themselves, adding energy to organic molecules just tends to turn them into tar or an oily substance. That's what Benner calls the "tar paradox": How could organic materials ever give rise to biopolymers like DNA?

Science Magazine describes the depressing picture:

However and wherever life began, one thing is sure: Its first organic building blocks, called hydrocarbons, had a number of hurdles to clear before evolving into living cells. Fed with heat or light and left to themselves, hydrocarbons tend to turn into useless tarlike substances. And even when complex molecules like RNA (most biologists' best guess for the first genetic molecule) arise, water quickly breaks them down again.

The RNA-world scenario is so hopeless, in fact, that Benner took the extreme step of claiming that life must have formed on Mars (on dry ground under special conditions), and then got transported to earth via meteors. While some reporters leaped onto the sci-fi suggestion that "We may all be Martians!" (e.g., Space.com), thinking people will surely catch the cry of desperation in such a proposal.

Conclusions

So, even if one were willing to grant the time of day to Jee et al.'s "game theory" notion, Darwinians can't even get the starting materials to play with. It would be more realistic for them to start with balls of tar, and racemic biological gunk broken down by water.

Any way you slice it, the "game theory" approach of these imagineers is an exercise in futility. And that's before even thinking rationally about the problem of the origin of genetic information, discussed in depth in Stephen Meyer's Signature in the Cell.

What a crazy world Darwinism and methodological naturalism (MN) has bequeathed us. The way out is to relax the arbitrary MN rule, to think outside the naturalistic box, and once again, to follow the evidence where it leads. Optimized codes do not "arise" from "frozen accidents." From our universal experience, they are products of intelligent design. That's no game. That's no "scenario." It's reality.