Firing blanks?

Putting the RNA World Theory to the Test with "Pistol"
Evolution News & Views

Proponents of the RNA World theory for the origin of life need to produce the goods: RNA molecules that can store information and perform useful reactions and reproduce themselves and form spontaneously in a plausible prebiotic environment. A new candidate has emerged.

Behold Pistol: a "self-cleaving ribozyme," announced in the  Proceedings of the National Academy of Sciences. We know that the three authors from Yale -- Nguyen, Wang and Steitz -- think it is relevant to the origin of life, because they tell us so in the opening paragraph about the "Significance" of their paper.

Based on the "RNA world" theory, ribozymes likely carried out biochemical reactions long before organisms evolved to use protein enzymes as biocatalysts. The continued discovery of new structures for small self-cleaving ribozymes has shed light on conserved mechanisms in evolution, such as acid-base catalysis for self-cleavage reaction. Here, we present the crystal structure of a newly discovered class of self-cleaving ribozymes called Pistol and how it likely uses the phosphoester transfer mechanism for self-cleavage. The results presented here suggest that Pistol uses an evolutionarily conserved cleavage mechanism that is like other self-cleaving ribozymes, such as Twister, Hammerhead, Hairpin, and Hepatitis Delta Virus ribozymes. [Emphasis added.]
That's it? The ribozyme commits suicide? Like other ribozyme candidates? Next.

There's not much else to say. Still, let's read on and see if they can explain what on earth this Pistol has to redeem itself without shooting the RNA World in the foot. We searched for the phrases "RNA World" and "origin of life." The latter is not found. The former is only mentioned one more time in the Introduction:

The "RNA world" hypothesis speculates that RNA carried out the majority of biochemical reactions before the evolution of complex protein enzymes. Ribozymes are noncoding RNA that carry out catalytic activities. Unlike protein enzymes, only a handful of ribozymes have known biological functions. Their biological functions range from regulating gene expression (e.g., riboswitches) and performing peptidyl-transfer reactions (e.g., ribosome) to removing intron sequences in genes (e.g., self-splicing Group I intron ribozymes). The biological functions and mechanism of these ribozymes have been discovered through structural and biochemical studies.
So far, we learn that only a "handful" of ribozymes are known, they have some jobs to do in living cells, and the RNA World hypothesis "speculates." We would really like to see some testable science, not speculation.

Specifically, the RNA World hypothesis needs to satisfy four requirements:

A ribozyme must form spontaneously in plausible prebiotic conditions. No intelligent design allowed.

It must be able to replicate itself before the first cell appears, so that natural selection can kick in.

It must do something useful for a future living organism.

It must store the information on how to do that useful something. (Note: cutting yourself in half is a poor candidate for a useful function.)

A self-cleaving RNA like Pistol misses the boat on at least three of these requirements. In living cells, the Pistol class of ribozymes does have a function, participating in the destruction of other RNA molecules (while committing suicide in the process). The authors say:

Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation.
But having a function now in cells tells us nothing about any prebiotic ribozyme, because Pistol is synthesized from DNA. How could a naked RNA in a primordial soup emerge without any help from encoded information?

We learn from a paper in   Nature Chemical Biology that Pistol was discovered in 2015. It was a rare find.

Enzymes made of RNA catalyze reactions that are essential for protein synthesis and RNA processing. However, such natural ribozymes are exceedingly rare, as evidenced by the fact that the discovery rate for new classes has dropped to one per decade from about one per year during the 1980s. Indeed, only 11 distinct ribozyme classes have been experimentally validated to date. Recently, we recognized that self-cleaving ribozymes frequently associate with certain types of genes from bacteria. Herein we exploited this association to identify divergent architectures for two previously known ribozyme classes and to discover additional noncoding RNA motifs that are self-cleaving RNA candidates. We identified three new self-cleaving classes, which we named twister sister, pistol and hatchet, from this collection, suggesting that even more ribozymes remain hidden in modern cells.
We learn a little more about what Pistol does from a paper in the journal RNA (2015):

Self-cleaving ribozymes are widespread across all domains of life and their architectural diversity is unmatched by any other type of natural catalytic RNA. These ribozymes have the ability to cleave their ribose-phosphate backbone at specific sites via internal phosphoester transfer with rate constants that typically exceed 10 million fold over that of spontaneous RNA degradation. The nine known self-cleaving ribozyme classes are able to accomplish this function by using a variety of structures that form unique catalytic cores....
All of this is irrelevant to the origin of life. We've only been told that RNA ribozymes are exceedingly rare, and they are not nearly as versatile as protein enzymes. All the ribozymes described have been found in living cells, coded by DNA for specific functions. But in the primordial soup could it happen? In the Illustra film Origin, Ann Gauger explains how delicate RNA is in the lab. How much more unlikely would it form spontaneously in the "absolute mess" of the chemical soup, as Paul Nelson describes the primordial ocean? Tim Standish adds, "If you just look at an RNA molecule, it seems to fall to pieces" -- even faster in water!

In Susan Mazur's book The Origin of Life Circus, leading origin-of-life researchers describe the utter disaster of the RNA world scenario in one-on-one interviews she recorded in person.

Lawrence Krauss tells her (p. 35): "The question is, can RNA result naturally? That's been a big stumbling block."

David Deamer tells her (p. 43) that the RNA and DNA monomers don't link up naturally: "the laws of thermodynamics do not allow them to polymerize because there is a tremendous energy barrier to getting them to form bonds." That's especially true in water, he says, which breaks down (hydrolyzes) RNA.

Sara Walker tells Mazur that researchers need to move away from the RNA World, "because most of the origin-of-life community don't think that's the definitive answer." Walker herself says, "I don't see how an RNA world with only RNA can work" (p. 68).

Loren Williams tells her the original RNA World ("all RNA, all the time, and nothing else") is unreasonable and dead. RNA can't have done everything originally claimed. "Another problem is related to the origin of RNA itself. Where did RNA come from? Where did RNA precursors come from?" (p. 96).

Steven Benner tells Mazur (p. 81), "we don't know how useful function is distributed among sequence spaces. You have 4 raised to the power of 100 different sequences of RNA 100 nucleotides long. We don't know how productive function is distributed there compared to destructive function." Chances are destructive processes are increased as much as productive processes, he adds. On page 151-152, Benner lists four major "paradoxes" of the RNA world: the tar problem, the water problem, the entropy problem and the destruction problem.

RNA-world champion Nick Hud has abandoned the idea that RNA would form on its own. He's looking for candidates of not only proto-RNA, but "pre-proto-RNA" because, as Mazur reminds him, "RNA itself falls apart" (p.87).

Stuart Kauffman tells Mazur that they "tried for 40 years to get single-stranded RNA molecules to replicate, perhaps hundreds of chemists, and they all failed. It should work. But it hasn't. And after 40 years or 50 years, you think - maybe it's the wrong idea. People really tried hard" (p. 111).

Jack Szostak ups the time estimate to 60 years that researchers have worked on this problem of non-enzymatic replication. "The problem is RNA falls apart," he says (p. 218).

Norm Packard tells Mazur, "There are issues with the RNA world approach. The main one is how do you get RNA starting to get produced in the first place" (p. 297). He envisions an enzyme doing it. This speculation, of course, leads to an obvious problem: "But how do you get that enzyme?"

Pier Luigi Luisi is merciless in his attack, calling the RNA world a "baseless fantasy." Mazur puts his criticisms in bold print on pages 362-363, where he finds it "full of conceptual flaws," including its origin, the thermodynamics, the sequencing problem, the concentration problem, and more. The story of RNA turning into ribozymes he calls "chemical non-sense" (p. 363).

Luisi then makes a confession so bold, Mazur says, "It's remarkable to hear you say that."

The real problem is to make ordered sequences of amino acids, of or course ordered sequences of nucleic acids -- and on that the prebiotic RNA world is absolutely silent. But this view of the prebiotic RNA world is still the most popular. I think it is a case of social science psychology more than science itself.
We're reminded of Harold S. Bernhardt's description of the RNA world: "the worst theory of the early evolution of life (except for all the others)."

With these comments from leaders in the origin-of-life field in mind, we return to the Pistol paper. Don't you think it's a bit disingenuous of the authors to mention the RNA world? Given their findings only show programmed function within living organisms that build the ribozymes from the DNA code, what possible relevance does that have to a "baseless fantasy" with so many paradoxes and problems? Could they be engaging in "social science psychology more than RNA itself"?


You decide. We'll stick with the positive. We do know of a cause now in operation that can "make ordered sequences" of building blocks and get them to interact in functional ways. That cause (need one say?) is intelligence.

Engineering v.Darwin.

Doug Axe: Hidden Figures and the Engineering Challenge to Darwinism
David Klinghoffer


Ahead of tomorrow night's Academy Awards ceremonies, Doug Axe has an excellent post up at  The Stream on the film  Hidden Figures  and the engineering challenge to Darwinism. The film, with several nominations including Best Picture, is the story of African-American women who were math prodigies, or "computers," at NASA.

Hidden Figures -- the true story of three brilliant African-American women who proved themselves in a 1960s NASA culture dominated by white men -- is sure to inspire. The film is filled with emotive lessons, most powerfully a vindication of the hope that those who persevere honorably for a just cause will not be disappointed.
Another lesson, more pragmatic, occurred to me as the drama unfolded. Having migrated in my own career from the measurable-fact culture of engineering to the more descriptive culture of biology, I felt a tinge of nostalgia as I watched a roomful of nerds with their calculators and chalk boards working together to find the answer to a pressing question: How can we bring an orbiting astronaut back safely to Earth?

Notice the very pre-post-truth essence of that phrase find the answer. Engineers have always taken for granted that clearly posed questions have uniquely correct answers -- there to be found by anyone with the skill to find them, and unambiguously recognized as correct when found. The joy of Hidden Figures is that it sweeps away our prejudicial attitudes as to who might have these requisite skills.

Celebrating National Engineers Week here yesterday, Sarah Chaffee observed,"[E]ngineering and medicine differ from evolutionary biology in that they focus on how things work. Evolutionists can seem at times to disregard function, but doctors and engineers never can." Yes, there's a blurred, fudging quality to much of evolutionary thinking.

By contrast, Dr. Axe admires the steely, unforgiving nature of an engineer's calculations:

There's something comfortably reassuring about the existence of steel-hard facts -- assertions that either end all opposition by proving true or end all sympathy by proving false. Maybe there's even a hint of beauty here -- in the stark simplicity of people putting their heads and hands to a challenge in a way that either succeeds or doesn't, with no fuzziness in-between.
Of course, those who've turned fuzziness into a paid profession are apt to sense more threat here than beauty. A famous 1960s meeting demonstrated this, convened under the heading Mathematical Challenges to the neo-Darwinian Interpretation of Evolution. There, a group of slide-rule toting engineering types, unconcerned with matters of etiquette, tried to put the slippery blob of evolutionary theory through the grinder gears of hard reality. Among the Darwinists present was Harvard's Ernst Mayr, who (in protest) titled his talk: "Evolutionary challenges to the mathematical interpretation of evolution." Stick that in your gears, you nerdy engineers!

This is rather unforgiving of Dr. Axe:

Here's the steel-hard fact they most want to avoid:
The evolutionary explanation of life cannot stand up to NASA-style engineering scrutiny.

If you doubt this, please join me in testing it. Hand pick your Darwin sympathizers from the most esteemed places. It doesn't matter who they are, because all the pomp and prestige of the academic world is powerless to change hard facts. All claims of Darwin having discovered the only scientifically valid explanation of life get torn to tiny bits when you put them in the grinder.

The response to this challenge is sure to be either silence or protest. There won't be a nerdy evolutionary biologist who marches up to the chalkboard and does the math that saves the theory. The math has been done; the theory undone. Nor will there be a lab test that shows natural selection to be a worker of wonders. We've been there. Too many tests to count, and the blind watchmaker never showed up.

The protest will be familiar, organized around the usual defensive themes. Different sciences work differently! -- they'll say. It isn't reasonable to hold a historical science to engineering standards! -- they'll say. No practicing evolutionary biologist would accept your proposal as valid! -- they'll say.

Let them speak. Then remind them that the difference is simply one of seriousness. When we really need to know that something will work, tested-and-approved certainty has always been the standard. Evolutionists ignore that standard because they can. Storytelling works for them because they're all telling stories together. Their grand stories are all wrong, but as long as no one is dying in orbit, most people are content to let them carry on.

Merciless, but true. Evolutionary theory's authority rests on muzziness as to details, and on the public's being willing to overlook and forgive it, despite what Axe identifies in his book  Undeniable as our universal intuition of intelligent design in nature.


"Trust us," Darwinists in effect say. Trust our massive extrapolation to a grand theory from a spray of trivial observations (finch beaks, smaller voles, etc.). "Trust" is not a factor in engineering. Either you bring the astronaut safe and alive back to Earth, or you do not. There's no fudging that.

Trivial pursuit?

Smaller Voles: "Evolution in Action" Is Rare, Trivial
David Klinghoffer 

News from the  University of Zurich  is notable both for how underwhelming it is and for a "rare" admission. Researchers documented that as winter came earlier, snow voles got smaller. That seemed counterintuitive since, as the title of the publication in PLOS Biology asks rhetorically, "Bigger Is Fitter?"

Well, isn't it? Not so in this case, apparently. Why?

In principle, larger snow voles are fitter: They have better capabilities to survive and reproduce. Despite this positive correlation at the phenotypic level, however, a converse causal relationship was evident on the genotypic level. "The voles whose genetic make-up led to a lower body weight were the fittest, especially in years when the first winter snow fell earlier than usual," explains the biologist. This may be because lighter young are more likely to reach their final size before the weather deteriorates and winter comes.

Fine. Maybe so. But notice the welcome candor in announcing this result. Observing this cute mouse-like rodent getting a bit smaller seems to be pulled straight from the voluminous files of unimpressive evidence for Darwinian evolution's grand claims. Evolution is supposed to explain how fantastic novelties arise, not merely why a little animal gets a bit smaller (or bigger). Even such an instance, though, they say repeatedly, is "extremely rare."

Researchers from the University of Zurich have succeeded in documenting an extremely rare case of evolutionary adaptation "in action" among wild snow voles near Chur.

...

Although this process is well understood in breeding conditions and in the lab, it is still largely unclear how often and how rapidly it takes place under natural conditions. Examples of contemporary adaptive evolution remain extremely rare.

...

If the scientists had restricted their observations solely to phenotypic traits, such as body size and weight, this rare example of "evolution in action" in the wild would have remained hidden. [Emphasis added.]

And again, from the Abstract:

In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm.


So stasis is the "norm," and seeing "evolution in action" in the wild is "extremely rare." And where found, as it was here, one might add that it is pretty trivial. Perhaps they thought were weren't listening.

Third way=no way?

Munchausen Syndrome: Perry Marshall Debates Stephen Meyer on the "Third Way" of Evolution
Evolution News & Views 

Justin Brierly of the radio program Unbelievable? out of the U.K. is a gem of an interviewer, regularly bringing together advocates of competing views on biological origins for startlingly rich, serious, and civil discussion.

He's done that again now with  a program featuring our colleague Stephen Meyer and Perry Marshall, author of the book  Evolution 2.0. Meyer and Marshall were both present for November's  Royal Society meeting  and they debate whether the Third Way of Evolution folks, who organized the meeting, are hot on the trail of a replacement theory for failed neo-Darwinism.

Dr. Meyer, while respecting Third Way critiques of orthodox evolutionary thinking, argues that a more fundamental paradigm shift is called for by the scientific evidence -- namely an inference to intelligent design. Marshall promotes the Third Way view, and his slogan is "Darwinists underestimate nature, and Creationists underestimate God." (He puts ID "in that same camp," the "creationist" one, but we're not going to argue with him about that right now.) An electrical engineer with a background in marketing and sales, he explains his approach in terms of "market share."

I take the position I take, because if I take the old school Neo-Darwinist position I will lose market share every year as more and more things turn out to be orderly instead of random.
If I take the creationist or Intelligent Design/Discovery Institute position, I will lose ground every year as they explain more and more evolutionary steps with observable processes.

But if I take the Third Way view, my market share will grow and grow because the explanatory power of an integrationist, non-reductionist paradigm which also considers consciousness.

That may sound a bit crass. Meyer counters that science is about getting at the truth, not pursuing a "market."

I think a lot of what's driving Perry is what he was talking about with "market share." How do you position a more theistically oriented way of looking at the natural world to get people who are atheist or agnostic to take you seriously?
I think at the end of the day you have to set those things aside and say what is nature telling us, and then develop an understanding of both the origin and development of life that is consistent with the evidence.

The issue comes down to whether the information at the heart of biology can be accounted for without reference to a designing agent operating in the course of life's long history. As Marshal prefers to say, was this information required for biological innovation front-loaded in the first bacterial cells so that it comes from within the animal, not from a source without? Talking about the research of leading Third Way figure James Shapiro at the University of Chicago, Meyer identifies two key issues:

I also think Shapiro's work is extremely interesting, and it's certainly cutting some new ground in biology. What Shapiro is talking about -- and I discuss Shapiro's work and five of the other Third Way mechanisms that have been proposed, these non-neo-Darwinian mechanisms of evolutionary change -- in Darwin's Doubt in two of the key chapters of the book.
What I show there is invariably what is going on is these new mechanisms either presuppose unexplained sources of information, or they simply don't explain the origin of necessary information to get real anatomical novelty. In other words, there are limits on what these mechanisms can produce.

Take Shapiro's work. He's describing ways in which organisms respond in real time to environmental stresses. Then they produce a response in the way that either they express pre-existing genetic information, or the way they ramp up the mutation rate in very specific parts of the genome to explore possibilities that are already latent in the genetic information.

So what he's talking about is a kind of pre-programmed adaptive capacity which he says is under "algorithmic control."

That's all extremely cool. It is very elegant the way organisms can do that, but the question that Shapiro doesn't address is: where does the pre-programming come from? Where does that algorithm come from? There's a higher level of informational programming at work that's presupposed in this whole process that he doesn't attempt to explain.

My concern about using this as an explanation for the whole of what we see in biological evolution is two-fold. First, you can't really propose that all this information is already in all these different organisms, and every organism has its own preprogramming to respond in different ways according to its organismal needs.

I don't think it's plausible to say that all this information could have been front-loaded in the circular chromosome of the bacterial cell at the point of the origin of life. Clearly you're going to need additional information at discrete points along the biological timeline.

Just getting from prokaryotes to eukaryotes requires an extensive reworking of the whole system of storage of genetic information. But secondly, and I think this is really a key thing, this is one of the key problems, it is the problem of epigenetic information.

Not all the information to build a body plan is in DNA. DNA codes for building proteins, but proteins have to be organized into bio-synthetic pathways that would characterize different kinds of cells and cell types.

Different cell types have to be organized into different tissues. Different tissues have to reorganize into different organs.

And organs and tissues have to be organized into whole body plans. The information for doing that is not solely in the DNA. Higher levels of information stored elsewhere are required to organize all those different levels of the biological hierarchy.

Shapiro is focusing on Natural Genetic Engineering, and has said he might get novel proteins out of this, but he's not going to explain the origin of a body plan. And that's the really crucial question biologically. Where did that higher-level innovation come from?

Both the Third Way crowd and their advocate Mr. Marshall position themselves as offering an alternative to Darwinism and ID. Marshall thinks Darwinists and ID theorists alike are missing what he plainly can see -- that evolution is real and a beautiful thing because it comes from within the organism, within the universe, itself.

On his website, Marshall has  helpfully transcribed the whole program, adding annotations of his own. He writes:

It's the biggest untold story in the history of science and the Neo-Darwinists have completely missed it. The creationists and the Discovery Institute have completely missed it as well. You would never know from reading a Richard Dawkins book or a Stephen Meyer book that you can get a completely new species in two years, and maybe even two days, from symbiogenesis or hybridization. Or that you can witness a radical innovation from a single cell in just 12 hours.
Neo-Darwinism is about miracles of randomness which can never be quantified or demonstrated. It's the biggest mistake in the history of science. And despite Meyer's insistence to the contrary,   Intelligent Design is still God of the gaps. The two are symmetrical. Neither offers you a mechanism that qualifies as empirical science. Neither helps the scientist do his real job, which is to explain every evolutionary step in reproducible detail.

And neither is telling you the REAL story -- that organisms possess tools of Natural Genetic Engineering and freedom to evolve on their own. It's the purpose of my book Evolution 2.0 to tell that story.

He refers to symbiogenesis  and hybridization. But how much of those processes are an organism simply activating pre-programmed information? This is not macroevolution in action. Where does that pre-programmed information come from? It cannot be from the organism itself, as Marshall suggests.

Why? On the issue of pre-programming or front-loading information, our new colleague, the paleontologist and now Center for Science & Culture Senior Fellow  Günter Bechly, notes three problems. He writes:

One of the problems with Marshall's approach is that we have brains: according to Marshall the intelligent design in the genome is not to be explained with the infusion of information from outside the system, but with the organisms (including bacterial cells!) themselves being the intelligent agents of their own design. Given the lack of any physical basis for such intelligence on the level of simple organisms like bacteria, this intelligence must be based on an immaterial mind.
This is clearly documented by Marshall's explicit endorsement of Robert Lanza's "Biocentrism," which is one of the many popular varieties of "monistic idealism meets quantum mysticism." However, if even bacteria can achieve incredible intelligence and information processing abilities without a material brain, why is intelligent behavior in animals positively correlated with the complexity of their neural system? Why do we need brains at all?

A second problem is that it is not the organism that is said to evolve but populations, which would even imply a kind of hive mind to make sense of Marshall's approach.

Finally, there is the Munchausen problem that intelligent agents cannot be their own designers, because they have to come into existence before they can design anything.

In the end the crucial question is: What makes more sense when you already have come to the conclusion that biological design is caused by immaterial intelligent agency: that bacteria and worms are intelligent minds and brilliant genetic engineers, or that the intelligent designer is the omniscient and omnipotent immaterial mind (God), in which Marshall believes anyway for different reasons?


That Munchausen reference is to the satirical story of Baron Munchausen lifting and thus rescuing himself and his horse, stuck in a mire, by pulling upward on his own hair. That's not going to work. It's an apt image for what's wrong not only with Marshall's argument but with the Third Way approach in general.

Origin of life science's 5 main pressure points.

Top Five Problems with Current Origin-of-Life Theories
Casey Luskin 

Last summer I published a list of the "Top Ten Problems with Darwinian Evolution." Since that time, some readers have requested a list of major problems with theories seeking to explain the chemical origin of life. There are numerous problems, but here's my list of the top 5:

Problem 1: No Viable Mechanism to Generate a Primordial Soup.

According to conventional thinking among origin-of-life theorists, life arose via unguided chemical reactions on the early Earth some 3 to 4 billion years ago. Most theorists believe that there were many steps involved in the origin of life, but the very first step would have involved the production of a primordial soup -- a water-based sea of simple organic molecules -- out of which life arose. While the existence of this "soup" has been accepted as unquestioned fact for decades, this first step in most origin-of-life theories faces numerous scientific difficulties.

In 1953, a graduate student at the University of Chicago named Stanley Miller, along with his faculty advisor Harold Urey, performed experiments hoping to produce the building blocks of life under natural conditions on the early Earth.1 These "Miller-Urey experiments" intended to simulate lightning striking the gasses in the early Earth's atmosphere. After running the experiments and letting the chemical products sit for a period of time, Miller discovered that amino acids -- the building blocks of proteins -- had been produced.

For decades, these experiments have been hailed as a demonstration that the "building blocks" of life could have arisen under natural, realistic Earthlike conditions,2 corroborating the primordial soup hypothesis. However, it has also been known for decades that the Earth's early atmosphere was fundamentally different from the gasses used by Miller and Urey.

The atmosphere used in the Miller-Urey experiments was primarily composed of reducing gasses like methane, ammonia, and high levels of hydrogen. Geochemists now believe that the atmosphere of the early Earth did not contain appreciable amounts of these components. UC Santa Cruz origin-of-life theorist David Deamer explains in the journal Microbiology & Molecular Biology Reviews:

This optimistic picture began to change in the late 1970s, when it became increasingly clear that the early atmosphere was probably volcanic in origin and composition, composed largely of carbon dioxide and nitrogen rather than the mixture of reducing gases assumed by the Miller-Urey model. Carbon dioxide does not support the rich array of synthetic pathways leading to possible monomers...3
Likewise, an article in the journal Science stated: "Miller and Urey relied on a 'reducing' atmosphere, a condition in which molecules are fat with hydrogen atoms. As Miller showed later, he could not make organics in an 'oxidizing' atmosphere."4 The article put it bluntly: "the early atmosphere looked nothing like the Miller-Urey situation."5 Consistent with this, geological studies have not uncovered evidence that a primordial soup once existed.6
There are good reasons why the Earth's early atmosphere did not contain high concentrations of methane, ammonia, or other reducing gasses. The Earth's early atmosphere is thought to have been produced by outgassing from volcanoes, and the composition of those volcanic gasses is related to the chemical properties of the Earth's inner mantle. Geochemical studies have found that the chemical properties of the Earth's mantle would have been the same in the past as they are today.7 But today, volcanic gasses do not contain methane or ammonia, and are not reducing.

A paper in Earth and Planetary Science Letters found that the chemical properties of the Earth's interior have been essentially constant over Earth's history, leading to the conclusion that "Life may have found its origins in other environments or by other mechanisms."8 So strong is the evidence against pre-biotic synthesis of life's building blocks that in 1990 the Space Studies Board of the National Research Council recommended that origin-of-life investigators undertake a "reexamination of biological monomer synthesis under primitive Earthlike environments, as revealed in current models of the early Earth."9

Because of these difficulties, some leading theorists have abandoned the Miller-Urey experiment and the "primordial soup" theory. In 2010, University College London biochemist Nick Lane stated that the primordial soup theory "doesn't hold water" and is "past its expiration date."10 Instead, he proposes that life arose in undersea hydrothermal vents. But both the hydrothermal vent and primordial soup hypotheses face another major problem.

Problem 2: Forming Polymers Requires Dehydration Synthesis

Assume for a moment that there was some way to produce simple organic molecules on the early Earth. Perhaps they did form a "primordial soup," or perhaps these molecules arose near some hydrothermal vent. Either way, origin-of-life theorists must then explain how amino acids or other key organic molecules linked up to form long chains (polymers) like proteins (or RNA).

Chemically speaking, however, the last place you'd want to link amino acids into chains would be a vast water-based environment like the "primordial soup" or underwater near a hydrothermal vent. As the National Academy of Sciences acknowledges, "Two amino acids do not spontaneously join in water. Rather, the opposite reaction is thermodynamically favored."11 In other words, water breaks down protein chains into amino acids (or other constituents), making it very difficult to produce proteins (or other polymers) in the primordial soup.

Problem 3: RNA World Hypothesis Lacks Confirming Evidence

Let's assume, again, that a primordial sea filled with life's building blocks did exist on the early Earth, and somehow it formed proteins and other complex organic molecules. Origin-of-life theorists believe that the next step in the origin of life is that -- entirely by chance -- more and more complex molecules formed until some began to self-replicate. From there, they believe Darwinian natural selection took over, favoring those molecules which were better able to make copies. Eventually, they assume, it became inevitable that these molecules would evolve complex machinery -- like that used in today's genetic code -- to survive and reproduce.

Have modern theorists explained how this crucial bridge from inert nonliving chemicals to self-replicating molecular systems took place? Not at all. In fact, even Stanley Miller readily admitted the difficulty of explaining this in Discover Magazine:

Even Miller throws up his hands at certain aspects of it. The first step, making the monomers, that's easy. We understand it pretty well. But then you have to make the first self-replicating polymers. That's very easy, he says, the sarcasm fairly dripping. Just like it's easy to make money in the stock market -- all you have to do is buy low and sell high. He laughs. Nobody knows how it's done.12
The most prominent hypothesis for the origin of the first life is called the "RNA world." In living cells, genetic information is carried by DNA, and most cellular functions are performed by proteins. However, RNA is capable of both carrying genetic information and catalyzing some biochemical reactions. As a result, some theorists postulate the first life might have used RNA alone to fulfill all these functions.
But there are many problems with this hypothesis.

For one, the first RNA molecules would have to arise by unguided, non-biological chemical processes. But RNA is not known to assemble without the help of a skilled laboratory chemist intelligently guiding the process. New York University chemist Robert Shapiro critiqued the efforts of those who tried to make RNA in the lab, stating: "The flaw is in the logic -- that this experimental control by researchers in a modern laboratory could have been available on the early Earth."13

Second, while RNA has been shown to perform many roles in the cell, there is no evidence that it could perform all the necessary cellular functions currently carried out by proteins.14

Third, the RNA world hypothesis can't explain the origin of genetic information.

RNA world advocates suggest that if the first self-replicating life was based upon RNA, it would have required a molecule between 200 and 300 nucleotides in length.15 However, there are no known chemical or physical laws that dictate the order of those nucleotides.16 To explain the ordering of nucleotides in the first self-replicating RNA molecule, materialists must rely on sheer chance. But the odds of specifying, say, 250 nucleotides in an RNA molecule by chance is about 1 in 10150 -- below the "universal probability bound," a term characterizing events whose occurrence is at least remotely possible within the history of the universe.17 Shapiro puts the problem this way:

The sudden appearance of a large self-copying molecule such as RNA was exceedingly improbable. ... [The probability] is so vanishingly small that its happening even once anywhere in the visible universe would count as a piece of exceptional good luck.18
Fourth -- and most fundamentally -- the RNA world hypothesis can't explain the origin of the genetic code itself. In order to evolve into the DNA/protein-based life that exists today, the RNA world would need to evolve the ability to convert genetic information into proteins. However, this process of transcription and translation requires a large suite of proteins and molecular machines -- which themselves are encoded by genetic information.
All of this poses a chicken-and-egg problem, where essential enzymes and molecular machines are needed to perform the very task that constructs them.

Problem 4: Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code. 
To appreciate this problem, consider the origin of the first DVD and DVD player. DVDs are rich in information, but without the machinery of a DVD player to read the disk, process its information, and convert it into a picture and sound, the disk would be useless. But what if the instructions for building the first DVD player were only found encoded on a DVD? You could never play the DVD to learn how to build a DVD player. So how did the first disk and DVD player system arise? The answer is obvious: a goal-directed process -- intelligent design -- is required to produce both the player and the disk.

In living cells, information-carrying molecules (such as DNA or RNA) are like the DVD, and the cellular machinery that reads that information and converts it into proteins is like the DVD player. As in the DVD analogy, genetic information can never be converted into proteins without the proper machinery. Yet in cells, the machines required for processing the genetic information in RNA or DNA are encoded by those same genetic molecules -- they perform and direct the very task that builds them.

This system cannot exist unless both the genetic information and transcription/translation machinery are present at the same time, and unless both speak the same language. Not long after the workings of the genetic code were first uncovered, biologist Frank Salisbury explained the problem in a paper in American Biology Teacher:

It's nice to talk about replicating DNA molecules arising in a soupy sea, but in modern cells this replication requires the presence of suitable enzymes. ... [T]he link between DNA and the enzyme is a highly complex one, involving RNA and an enzyme for its synthesis on a DNA template; ribosomes; enzymes to activate the amino acids; and transfer-RNA molecules. ... How, in the absence of the final enzyme, could selection act upon DNA and all the mechanisms for replicating it? It's as though everything must happen at once: the entire system must come into being as one unit, or it is worthless. There may well be ways out of this dilemma, but I don't see them at the moment.19
The same problem confronts modern RNA world researchers, and it remains unsolved. As two theorists observed in a 2004 article in Cell Biology International:
The nucleotide sequence is also meaningless without a conceptual translative scheme and physical "hardware" capabilities. Ribosomes, tRNAs, aminoacyl tRNA synthetases, and amino acids are all hardware components of the Shannon message "receiver." But the instructions for this machinery is itself coded in DNA and executed by protein "workers" produced by that machinery. Without the machinery and protein workers, the message cannot be received and understood. And without genetic instruction, the machinery cannot be assembled.20
Problem 5: No Workable Model for the Origin of Life

Despite decades of work, origin-of-life theorists are at a loss to explain how this system arose. In 2007, Harvard chemist George Whitesides was given the Priestley Medal, the highest award of the American Chemical Society. During his acceptance speech, he offered this stark analysis, reprinted in the respected journal Chemical and Engineering News:

The Origin of Life. This problem is one of the big ones in science. It begins to place life, and us, in the universe. Most chemists believe, as do I, that life emerged spontaneously from mixtures of molecules in the prebiotic Earth. How? I have no idea.21
Many other authors have made similar comments. Massimo Pigliucci states: "[I]t has to be true that we really don't have a clue how life originated on Earth by natural means."22 Or as science writer Gregg Easterbrook wrote in Wired, "What creates life out of the inanimate compounds that make up living things? No one knows. How were the first organisms assembled? Nature hasn't given us the slightest hint. If anything, the mystery has deepened over time."23
Likewise, the aforementioned article in Cell Biology International concludes: "New approaches to investigating the origin of the genetic code are required. The constraints of historical science are such that the origin of life may never be understood."24 That is, they may never be understood unless scientists are willing to consider goal-directed scientific explanations like intelligent design.

References:

[1.] See Stanley L. Miller, "A Production of Amino Acids under Possible Primitive Earth Conditions," Science, 117: 528-529 (May 15, 1953).

[2.] See Jonathan Wells, Icons of Evolution: Why Much of What We Teach About Evolution Is Wrong, (Washington D.C.: Regnery, 2000); Casey Luskin, "Not Making the Grade: An Evaluation of 19 Recent Biology Textbooks and Their Use of Selected Icons of Evolution," Discovery Institute (September 26, 2011).

[3.] David W. Deamer, "The First Living Systems: a Bioenergetic Perspective," Microbiology & Molecular Biology Reviews, 61:239 (1997).

[4.] Jon Cohen, "Novel Center Seeks to Add Spark to Origins of Life," Science, 270: 1925-1926 (December 22, 1995).

[5.] Ibid.

[6.] Antonio C. Lasaga, H. D. Holland, and Michael J. Dwyer, "Primordial Oil Slick," Science, 174: 53-55 (October 1, 1971).

[7.] Kevin Zahnle, Laura Schaefer, and Bruce Fegley, "Earth's Earliest Atmospheres," Cold Spring Harbor Perspectives in Biology, 2(10): a004895 (October, 2010) ("Geochemical evidence in Earth's oldest igneous rocks indicates that the redox state of the Earth's mantle has not changed over the past 3.8 Gyr"); Dante Canil, "Vanadian in peridotites, mantle redox and tectonic environments: Archean to present," Earth and Planetary Science Letters, 195:75-90 (2002).

[8.] Dante Canil, "Vanadian in peridotites, mantle redox and tectonic environments: Archean to present," Earth and Planetary Science Letters, 195:75-90 (2002) (internal citations removed).

[9.] National Research Council Space Studies Board, The Search for Life's Origins (National Academy Press, 1990).

[10.] Deborah Kelley, "Is It Time To Throw Out 'Primordial Soup' Theory?," NPR (February 7, 2010).

[11.] Committee on the Limits of Organic Life in Planetary Systems, Committee on the Origins and Evolution of Life, National Research Council, The Limits of Organic Life in Planetary Systems, p. 60 (Washington D.C.: National Academy Press, 2007).

[12.] Stanley Miller quoted in Peter Radetsky, "How Did Life Start?" Discover Magazine (Nov., 1992).

[13.] Richard Van Noorden, "RNA world easier to make," Nature News (May 13, 2009).

[14.] See Stephen C. Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design, p. 304 (New York: HarperOne, 2009).

[15.] Jack W. Szostak, David P. Bartel, and P. Luigi Luisi, "Synthesizing Life," Nature, 409: 387-390 (January 18, 2001).

[16.] Michael Polanyi, "Life's Irreducible Structure," Science, 160 (3834): 1308-1312 (June 21, 1968).

[17.] See William A. Dembski, The Design Inference: Eliminating Chance through Small Probabilities (Cambridge University Press, 1998).

[18.] Robert Shapiro, "A Simpler Origin for Life," Scientific American, pp. 46-53 (June, 2007).

[19.] Frank B. Salisbury, "Doubts about the Modern Synthetic Theory of Evolution," American Biology Teacher, 33: 335-338 (September, 1971).

[20.] J.T. Trevors and D.L. Abel, "Chance and necessity do not explain the origin of life," Cell Biology International, 28: 729-739 (2004).

[21.] George M. Whitesides, "Revolutions In Chemistry: Priestley Medalist George M. Whitesides' Address," Chemical and Engineering News, 85: 12-17 (March 26, 2007).

[22.] Massimo Pigliucci, "Where Do We Come From? A Humbling Look at the Biology of Life's Origin," in Darwin Design and Public Education, eds. John Angus Campbell and Stephen C. Meyer (East Lansing, MI: Michigan State University Press, 2003), p. 196.

[23.] Gregg Easterbrook, "Where did life come from?," Wired, p. 108 (February, 2007).

[24.] J.T. Trevors and D.L. Abel, "Chance and necessity do not explain the origin of life," Cell Biology International, 28: 729-739 (2004).

Neo liberal v. libertarian.

The making of yet another anti-Darwinian bomb thrower.

Scientific Authority Becomes Scientific Authoritarianism: See Tom Bethell in Iconoclast Now
David Klinghoffer

Why the New World Translation?:The Watchtower Society's Commentary

Why Have We Produced the New World Translation?

For decades, Jehovah’s Witnesses used, printed, and distributed various versions of the Bible. But then we saw the need to produce a new translation that would better help people to learn the “accurate knowledge of truth,” which is God’s will for everyone. (1 Timothy 2:3, 4) Thus, in 1950 we began to release portions of our modern-language Bible, the New World Translation. This Bible has been faithfully and accurately translated into over 120 languages.

A Bible was needed that was easy to understand. Languages change over time, and many translations contain obscure or obsolete expressions that are difficult to understand. Also, ancient manuscripts that are more accurate and closer to the originals have been discovered, resulting in a better comprehension of Biblical Hebrew, Aramaic, and Greek.

A translation was needed that was loyal to God’s word. Rather than taking liberties with God’s inspired writings, Bible translators should be faithful to the original text. However, in most versions, the divine name, Jehovah, is not used in the Holy Scriptures.

A Bible was needed that gives credit to its Author. (2 Samuel 23:2) In the New World Translation, Jehovah’s name has been restored where it appears some 7,000 times in the oldest Bible manuscripts as illustrated in the example below. (Psalm 83:18) The result of years of diligent research, this Bible is a pleasure to read, as it clearly conveys God’s thinking. Whether you have the New World Translation in your language or not, we encourage you to get into a good routine of reading Jehovah’s Word every day.—Joshua 1:8; Psalm 1:2, 3.

Piercing the fog?

Disregarding Fake News from Darwin Promoters, South Dakota Scientist Applauds Academic Freedom Bill
Evolution News & Views

Pierre, SD -- This year, South Dakota has an opportunity to encourage more scientific inquiry in the classroom. The state's legislature is considering an academic freedom bill, SB 55, introduced by Senator Jeff Monroe. noted here last week, the bill seeks to thwart censorship, yet ironically is opposed by the National Coalition Against Censorship. The group has misrepresented its contents, comparing mainstream exploration of weaknesses in Darwinian theory with Holocaust denial.

The text of SB 55 says just this:

No teacher may be prohibited from helping students understand, analyze, critique, or review in an objective scientific manner the strengths and weaknesses of scientific information presented in courses being taught which are aligned with the content standards established pursuant to § 13-3-48.

A prominent South Dakota scientist we heard from gets it, applauding the bill as a means to foster critical thinking. "SB 55, under consideration by the South Dakota legislature, is a promising step forward for South Dakota science education," said William S. Harris, PhD. Dr. Harris is the President of OmegaQuant Analytics, LLC (Sioux Falls, SD), and an NIH-funded biomedical researcher with over 300 scientific publications.

Under this legislation, students would have the opportunity learn more about scientific topics, practice critical thinking, and engage with scientific questions facing researchers today. One of those questions pertains to the origin of biodiversity.

Harris commented:

Scientific controversy over the ability of Darwin's version of evolution (i.e., natural selection acting blindly on random mutations) to explain the expanse of life on this planet continues to grow with each new revelation of the exceeding complexity of even the "simplest" life forms, not to mention humans. In my view, it is very important for today's students to understand the evidence for and against important scientific theories like Darwinism and to honestly consider challenges even to such long-held dogmas.

"South Dakota students can only benefit from such an approach -- and hopefully, legislators will seize this occasion to promote scientific inquiry," added Harris. If the bill is enacted, South Dakota would join Louisiana, Tennessee, and at least five other states with science standards or laws recognizing the role of teaching scientific strengths and weaknesses in the classroom.


The law has been a target for activists and journalists spreading misinformation about what SB 55 would permit. We have addressed false claims from Americans United for Separation of Church and State and the Washington Post, which merit being described as fake news,   here and here .

Darwinism v. commonsense

A brief history of the Cuban missile crisis.

Negative to affirmative action on campus?

The fall of Rome II?

Through the looking glass?

South Dakota Science Education Controversy Gets Surreal as Anti-Censorship Group Demands Censorship

David Klinghoffer

We have patiently explained why the current academic freedom bill in South Dakota, SB 55, cannot possibly be construed in any reasonable manner as seeking to inject teaching intelligent design into public schools. As noted yesterday, that didn't stop a prominent lobbying group, Americans United for Separation of Church and State, from working the phrase, "intelligent design," six times into a statement directed against the bill.

One of those instances was in a photo caption of an instructor in front of his class, "Teachers should not be given leeway to introduce intelligent design in science classes."

But with evolution proponents, such distortions are absolutely routine. It's bizarre. It's farcical. But this tops it. In a surreal move, a group called the National Coalition Against Censorship has plunged into the South Dakota situation to demand continued restraints on teachers and their academic freedom -- in other words, censorship.

They complain that SB 55 would "remov[e] accountability in science education." "Accountability" there would seem to mean instructors being vulnerable to career retaliation for teaching critical thinking skills to science students. These "anti-censorship" proponents advocate retaining the option of punishing biology teachers for going off message on Darwinism.

They go on: "Essentially, [the bill] removes the restraints on teachers that prevents them from straying from professionally-developed science standards adopted by state educators." The National Coalition Against Censorship favors keeping "restraints" on teachers firmly in place.

The bill, they say, "may encourage teachers who object to the scientific consensus on evolution and climate change to bring their opinions into the classroom," instead of sticking slavishly to a uniform Darwin-only script. The teachers should stick to their script.

Then there's this. Look again at the  language of the bill. It's very brief:

No teacher may be prohibited from helping students understand, analyze, critique, or review in an objective scientific manner the strengths and weaknesses of scientific information presented in courses being taught which are aligned with the content standards established pursuant to § 13-3-48.

That is another way of saying no teacher may be censored for challenging students with balanced information from objective science sources. Notice that the language concludes by saying that the "strengths and weaknesses" approach may be extended only to "scientific information presented in courses being taught which are aligned with the content standards" already established.

Because intelligent design isn't part of those content standards, the law extends no protection for teaching about ID. Because the content standards are already defined, instruction that's not "aligned" with them, in other words that "stray[s] from professionally-developed science standards adopted by state educators," would also not be protected.

But interestingly, if you read the statement from the "anti-censorship" group, their quotation from the bill cuts off before getting to the part about how instruction must be "aligned with the content standards." The whole proposed law is just a sentence long, but they truncate it a little more than half way through, perhaps to keep the reader from realizing that their dire prediction of teachers "straying" is undercut by the clear language of SB 55 itself. The anti-censorship activists are engaging in censorship right there in the middle of their own statement.

They conclude by comparing exploring mainstream debate about evolutionary theory with, yes, denying the Holocaust. And that is where they transition from absurdity to obscenity.

Good gravy. These complaints, whether from Americans United or from the horrifically misnamed National Coalition Against Censorship, are totally detached from a straightforward reading of the law they wish to attack. They are mere scaremongering, and frankly, contemptible.

In this, though, they're not much worse than supposedly objective news outlets like the Washington Post or ProPublica. When it comes to defending evolutionary orthodoxy, journalism and propaganda merge seamlessly.