On the making of a bomb-thrower

Three Flagellum Updates Amplify Behe’s Challenge to Darwinism from Irreducible Complexity
Evolution News | @DiscoveryCSC

Depictions of the bacterial flagellum in 1996, the year Darwin’s Black Box was published, and in 2002, when Unlocking the Mystery of Life brought it to the screen in animation, look crude by comparison to the latest ones that show all the parts in near-nanometer resolution.* But they were sharp enough to motivate Michael Behe’s “Revolutionary” argument for intelligent design from irreducible complexity. Three new papers do nothing to undermine that design inference, despite some of the researchers’ appeals to evolution. Instead, the papers add new details about the precision working of these machines, unknown 15 years ago, that accentuate the argument for design.

Stators and Speed

The first paper, in the Proceedings of the National Academy of Sciences (PNAS), was edited by Howard Berg. He’s the Harvard expert on flagella who was mentioned briefly in Unlocking as having called the flagellum the “most efficient machine in the universe.” In this paper, researchers from Oxford, Japan, and China wanted to know if the rotation speed was affected by the number of stator units. Previous work had suggested that flagella could rotate at full speed independently of stator subunit count. Through a series of precise measurements on flagella from different bacterial species mutated to vary the number, here’s what they found:

The bacterial flagellar motor is a rotary molecular motor responsible for swimming, swarming, and chemotaxis in many species of bacteria. It generates torque by interactions between a rotor 50 nm in diameter and multiple stator units. We overturn the prevailing understanding of how stator units interact with each other by showing that motor speed is dependent on the number of stator units even at high speed near zero torque.

The relationship held for both the sodium-ion type (Na+) and hydrogen-ion type (H+) motors. The team could not explain the discrepancy with previous findings, but offered an evolutionary hypothesis for the difference between clockwise (CW) and counterclockwise (CCW) measurements:

We speculate that the CCW torque–speed relationship may indicate selection pressure for high power output, as it combines high torque and high speed at viscous drag coefficients similar to those experienced in the bundle of a swimming E. coli cell. By contrast, the linear relationship seen in CW rotation is easier to achieve in mechanistic models and may represent a lack of selection pressure given that CW rotation is not typically used to propel swimming.

This evolutionary “speculation” about “selection pressure” could easily be recast as a functional design requirement. In a stick-shift car, for instance, you may have several forward gears but only one reverse gear. Other than this one paragraph, the authors said nothing about evolution. They did, however, suggest an intriguing possibility that slower flagella might result from mutations or other degrading processes:

If a fully functional unit rotates at 240–300 Hz, lower speed levels might represent partially functional units. Speculations as to the possible nature of these include units attached to the peptidoglycan at suboptimal orientations or distances from the rotor and half-functional units with one channel blocked, misfolded, or otherwise misassembled.

Shape-Switching Mechanism in the Propeller

As mentioned in Unlocking, bacteria can reverse the direction of rotation rapidly. The propeller itself, though, must also quickly adjust its protein subunits to “supercoil” in the opposite direction. Here’s news: the supercoiling is required for function. That fact inspired some machine language, found in this paper in  Nature Communications

The bacterial flagellar filament has been intensively studied for many years. It has served as an enlightening system for understanding how a protein polymer composed of a single protein, flagellin (except for the cap protein at the end that acts as an assembling chaperone) switches among different states to supercoil. This supercoiling allows the rotating filament to behave as an Archimedean screw and produce thrust. The filament can adopt different conformational states due to mechanical forces, such as when the motor switches the sense of rotation, allowing the bacteria to swim forward, backward, in a screw-like fashion and to tumble.

As Behe had pointed out, mutations to essential parts of an irreducibly complex system can lead to loss of function:

With the motor linked to sensory receptors, the bacteria are capable of moving towards nutrients and away from dangerous environments, resulting in a significant survival advantage. On the other hand, mutations within the flagellin protein that fail to form supercoiled filaments generate no thrust when such straight filaments are rotated, leading to non-motile bacteria.

Here we find another critical detail that wasn’t known before: a straight filament won’t work. It has to supercoil, so it can function like an Archimedean screw (the kind that Archimedes invented to draw water up out of a ditch). Beautiful depictions of the filament proteins arranged in geometrical works of art can be seen in Figure 1 of this open-access paper. The proteins must be packed just right so that they will not only supercoil, but quickly change between left and right orientations in a process called “polymorphic switching.” Notice how finely tuned this architecture is. If it’s not tightly balanced, it won’t work!

From the analysis of seven straight mutants in B. subtilis and two straight mutants in P. aeruginosa, we confirmed the bi-state mechanism of polymorphic switching: that only two types of subunit-subunit interactions (L-type and R- type) exist. This suggests that the wild type flagellar filaments with swimming motility must adopt an intricate “balance” in the flagellin sequence, so that the sequence does not generate a strong preference for either the L- or R- type conformation. Such a balance is required for the sharp transition of flagellar filaments switching between different waveforms during bacterial swimming and tumbling. The fact that straight phenotypes can be readily found due to single point mutations indicates that this balance is exquisitely sensitive to small changes, such as a single mutation, and can be easily tipped towards a dominant conformation, either all L or all R, which eliminates motility.

Amazing. Yet they attribute this all to evolution. They speak of how the sequence of flagellin proteins has been “tuned” by evolution. Incredibly, at the end of the paper, they appeal to convergence to claim that blind chance hit the jackpot on fine tuning three different times in all three kingdoms of life!

The bacterial flagellar filament is an exquisitely tuned system that represents evolutionary development over hundreds of millions of years. In contrast to the simplicity of the bacterial flagellum [sic], the eukaryotic flagellum, which has no homology to the bacterial one, is based upon microtubules and dynein rather than a homolog of flagellin and is currently estimated to contain more than 400 different proteins. The archaeal flagellum, which has no homology to either the bacterial or eukaryotic ones, has only recently been solved at near-atomic resolution showing how the core of these archaeal filaments is formed by a domain that is homologous to the N-terminal domain of bacterial Type IV pilin. Convergent evolution has thus yielded three very different flagellar filaments that all allow cells to swim, although by entirely different mechanisms. We are now entering a new era where the structure of such filaments can be solved at a near-atomic level of resolution using cryo-EM. We expect that the present study and future ones will yield new insights into how flagella-based swimming motility has independently arisen at least three different times in evolution using very different components, and how these convergent adaptations use very different mechanisms to achieve a similar function.

What can one say? Perhaps the best response is the title of a book by Frank Turek: “I don’t have enough faith to be an atheist.”

High-Powered Sheathed Flagella

Did you know that some bacteria have sheaths over their propeller filaments? Apparently this helps them generate higher torque and speed, and demonstrates that flagella come, like automobiles, in a variety of forms. Maybe these are the SUV’s of the bacterial world, because they can really move!Another paper in PNAS investigates bacteria in the Vibrio genus with sheathed flagella, which have not been studied as much as the unsheathed forms like in E. coli. Let’s listen to their praise of these molecular motors in their introduction:

A sophisticated chemotactic signaling system allows the bacterium to sense chemical stimuli and effectively swim toward favorable environments by a biased random walk, a combination of “runs” and “tumbles”.

The flagellum is a large macromolecular assembly composed of a long filament, a hook, and a motor. The flagellar motor is a remarkable nanomachine embedded in the bacterial cell envelope. More than 20 different proteins are required for the assembly of the motor, which can be divided into several morphological domains. The MS ring is embedded in the cytoplasmic membrane. The C ring, known as the switch complex, and the export apparatus are located in the cytoplasmic side of the MS ring. The rod connects the MS ring and the hook and is commonly divided into the distal rod and the proximal rod. The L and P rings on the rod function as bushings at the outer membrane and at the peptidoglycan layer, respectively. The stator is the torque generator embedded in the cytoplasmic membrane…. Powered by the proton motive force, the stator generates the torque required to rotate the motor, the hook, and the filament. The stator shares several common features despite the difference in ions and proteins involved. Typically, multiple stator units work together, although a single stator is enough to generate rotational torque. Stepwise photo-bleaching of a functioning motor region revealed that the stator is highly dynamic and can associate into or dissociate from the rotor rapidly. Recent reports revealed that the stator–rotor association is dependent on conducting ions and torque load.

The authors found new parts in the sheathed flagella motor, which might not be surprising given the higher performance demands. They found a T-ring, with 13-fold symmetry, which seems to increase torque; an H-ring, which is apparently essential during motor assembly; and an O-ring, which seems to help build the sheath. These new parts are all intricately tied into the motor, just as you would expect hub lockers, the transfer case and redesigned differentials to be built to coordinate with all the other parts in a 4-wheel-drive vehicle. The diagrams of these new parts are really stunning. They look like they were made in a machine shop.

The researchers found that the sheath flexes over the filament with a sliding action. Maybe that provides flexibility like good shocks on a Jeep. The new parts of this motor add more levels of irreducible complexity to the flagellum, resulting in a high performance engine!

In comparison with the well-studied unsheathed flagellar motor in E. coli (Fig. 1 F and I), these Vibrio-specific components not only reflect the complexity of Vibrio sheathed flagellum (Fig. 5C) but also provide a solid foundation for establishing the characteristic high velocity and robustness of Vibrio motility….

These overall properties of the distal rod are consistent with its main function as a drive shaft and may allow the outer membrane-bound complex to move flexibly with the membranous sheath during flagellar rotation. Alternatively, the distance variations may reflect structures that are fixed for each motor, but differ in length among different motors.

This paper has nothing to say about evolution. We already know that the peer-reviewed journals have Behe and intelligent design on their minds — they just won’t address us by name. Fine. But really, how much more machine-shop lingo can Darwin stand?

*Many of the stunning new images of flagella have been made possible by cryo-electron microscopy, for which three inventors received the Nobel Prize in Chemistry this month. Their contributions converged in 2013 with the best images ever of the three-dimensional structure of biomolecules. “Biochemistry is now facing an explosive development and is all set for an exciting future,” the Nobel Committee said. We can look forward to sharper images of molecular machines that showcase the argument for design.

Free-falling into the abyss?

A Rock Star of the Euthanasia Movement
Wesley J. Smith

Philip Nitschke is the Jack Kevorkian of Australia — without the late Kevorkian’s courage, as he avoids being at the assisted suicides he helps facilitate, to avoid legal entanglements.

Still, he has had his troubles. Back in 2001, I was instrumental in alerting the Australian government that he was importing “Exit Bags,” plastic bags with Velcro ties that were to be put over one’s head after swallowing barbiturates. Those were soon banned and Nitschke become semi-persona non grata in his own country.


That effort was aided mightily by Kathryn Lopez, who interviewed Nitschke and got him to admit he wanted assisted suicides to be available to “troubled teens.”  From her interview:

I do not believe that telling people they have a right to life while denying them the means, manner, or information necessary for them to give this life away has any ethical consistency. So all people qualify, not just those with the training, knowledge, or resources to find out how to “give away” their life.

And someone needs to provide this knowledge, training, or recourse necessary to anyone who wants it, including the depressed, the elderly bereaved, [and] the troubled teen.


If we are to remain consistent and we believe that the individual has the right to dispose of their life, we should not erect artificial barriers in the way of sub-groups who don’t meet our criteria.

I used that interview to great effect to the point that he was pressured by other advocates to deny he ever said it. But I had the proof!

Still, Nitschke remains a rock star of the euthanasia movement and travels the world teaching people how to off themselves.

As Australian states are again debating legalizing assisted suicide — the biggest threat currently is in Victoria — Nitschke remains true to the principles and values of the euthanasia movement — without sugar-coating the poison (a candor he shares with Kevorkian) as so many of his colleagues do.

The euthanasia movement has two fundamental principles. The second is an absolutist belief in personal autonomy. The first, which can override the second in certain circumstances to permit non-voluntary euthanasia, is that killing/suicide is a proper answer to human suffering.

That is why limiting encouraged suicide to those with a terminal illness is nonsensical. That restriction is just the proverbial camel nose under the tent.

Nitschke recently told Aussie media that suicide pills should be made available to anyone over seventy who wants to die. He actually believes that should be anyone who wants to die, even “troubled teens”; see Lopez’s interview above.  From the Sky News Australia story::

‘Rational people make decisions, and of course suicide is not a crime,’ he told Sky News on Monday.

‘The only assistance people want is access to the best drugs. You don’t have to actually assist you simply have to remove the restrictions on the best drugs.

‘What’s being proposed here is that elderly people have a right to get the best drugs.’

Mr Nitschke says people over the age of 70 should be able to have legal access to 10mg of Nembutal to use ‘if they wish’.

It’s funny how the media keep forgetting that Nitschke has been saying such things for decades. But I am glad they rediscover him periodically and report what he says.

Nitschke represents the true face of the euthanasia movement, one mostly kept hidden as a political tactic by assisted suicide promoters behind euphemisms of “compassion” and “choice” and toothless “guidelines to protect against abuse.”

On racism in the name of 'settled science'

Human Zoos — An Untold Story, Until Now
David Klinghoffer | @d_klinghoffer





We’ve already noted the November 11 public premiere of Human Zoos, a new documentary from Discovery Institute, by director and writer John West. You can see it in Portland, Oregon, at the  Oregon Documentary Film Festival. Tickets are on sale now.

A remarkable thing about the film is how thoroughly unfamiliar this history will be to most Americans. Did I say “most”? I mean, surely, almost all.


Dr. West was interviewed by the festival   and he tells how he learned of the subject matter himself:

Several years ago, I read a book about an African named Ota Benga who was put on public display in the Monkey House of the Bronx Zoo in the early 1900s. I later learned that there was a widespread practice in both the United States and Europe of putting indigenous peoples on public display, and that in many cases this practice was carried out and promoted not by hucksters but by leading members of America’s scientific community. I am fascinated by the use and abuse of scientific ideas in public policy, and I was interested not only in telling the story of what happened but also probing why so many members of the scientific community supported the practice. As I began to work on the story, I found that it had connections with the American eugenics movement, which was an effort to breed better humans by controlling the direction of human evolution, and so the documentary also delves into that story. There are also connections between what happened in the past and today’s white supremacists. One of the points I hoped to make in this film is that we don’t get beyond the past by forgetting it. We need to face it in order to make sure the same mistakes don’t happen again.

West is a political scientist with a journalism background. The visual style of filmmaking was largely new to him. He offered advice to aspiring documentarians:

Especially if you are working on a limited budget (as I was), the more you can plan out in advance, the better. Also, learning to think visually is important when writing a script. My background is as a former college professor and as someone with training in journalism. So I have more experience with the written word than with visuals. When I started learning how to make documentaries, I had to stretch myself to write for a medium where what you show visually (and how you show it) is just as important (sometimes more important) than the words you use. I also learned that you need to be as concise as possible. Wordiness doesn’t work well in the visual medium.

He also discussed the response from (limited) audiences so far:

The reactions at the private screenings have been positive, but somber. I think some people were shocked at what they learned. After the violence in Charlottesville, VA this past summer, I added a new ending to the film because I found a pretty explicit connection between the issues I was covering with some things being debated right now. Only one audience has seen the new ending, and I think it made some of the viewers uncomfortable to see how the scientific racism of the past was rearing its ugly head in a new way today.

“Shocked” is right, because the story told here is truly shocking. Human Zoos will be released to the general public in 2018. But you can already see the trailer, above.

Your friendly neighborhood spider v. Darwin.

Don’t Be Frightened! It’s Just a Spider — An Exemplar of Intelligent Design
David Klinghoffer | @d_klinghoffer

Spiders are part of the iconography of Halloween. Don’t be frightened, though. Sure, a Facebook friend advises today that for black widow spiders common in Central Oregon, a squirt of brake cleaner works great, followed, just to be safe, by application of yesterday’s newspaper. Thanks, fine, but for the rest of spiderkind, how about leaving them alone and, instead, appreciating the valuable services they perform? Gobbling mosquitoes, for one thing.

And that’s not all. Take a moment to appreciate the awesome natural design of their webs. A new video from Discovery Institute explains why biomimetic researchers would love to be able to duplicate the strength and flexibility of dragline silk.

There’s much more to admire in these tiny predators than there is to be scared of. Spiders are among the natural wonders described in Billions of Missing Links: A Rational Look at the Mysteries Evolution Can’t Explain, by Discovery Institute Fellow Geoffrey Simmons, MD. Get a copy now!

A clash of Titans. LXII

 

Security trumps privacy?:Pros and cons.

The late Michael Crichton Vs. settled science

Is There a "Consensus" in Science? Remembering the Late Michael Crichton
Casey Luskin 


Anyone who was awed when they watched Jurassic Park and saw realistic-looking dinosaurs walking around on the big screen for the first time should take a moment to remember Michael Crichton. Crichton, a famous science-fiction author, wrote the books that became the Jurassic Park movie series, as well as many other popular novels. He also had an appreciation for the importance of dissenting views within the scientific community and was a keen observer of how some in the scientific community use rhetoric to quash minority scientific viewpoints. Crichton passed away earlier this month after losing a battle with cancer, so in remembrance of Michael Crichton, I'd like to re-post this quote from a speech he gave that was recently reprinted in the Wall Street Journal:

"I want to pause here and talk about this notion of consensus, and the rise of what has been called consensus science. I regard consensus science as an extremely pernicious development that ought to be stopped cold in its tracks. Historically, the claim of consensus has been the first refuge of scoundrels; it is a way to avoid debate by claiming that the matter is already settled. Whenever you hear the consensus of scientists agrees on something or other, reach for your wallet, because you're being had.
"Let's be clear: The work of science has nothing whatever to do with consensus. Consensus is the business of politics. Science, on the contrary, requires only one investigator who happens to be right, which means that he or she has results that are verifiable by reference to the real world. In science consensus is irrelevant. What is relevant is reproducible results. The greatest scientists in history are great precisely because they broke with the consensus.

"There is no such thing as consensus science. If it's consensus, it isn't science. If it's science, it isn't consensus. Period. . . .

"I would remind you to notice where the claim of consensus is invoked. Consensus is invoked only in situations where the science is not solid enough. Nobody says the consensus of scientists agrees that E=mc2. Nobody says the consensus is that the sun is 93 million miles away. It would never occur to anyone to speak that way. ."

(Michael Crichton, "'Aliens Cause Global Warming'," reprinted in Wall Street Journal, November 7, 2008.)

Rest in peace, Michael Crichton.

On attempts to reanimate the RNA world scenario.

An Extraterrestrial Spin on the RNA World
Stephen C. Meyer

As  Evolution News has previously noted, a recent article in the Proceedings of the National Academy of Sciences  presents an extraterrestrial spin on the standard RNA World origin-of-life proposal. The authors argue that RNA molecules appeared in warm little ponds (WLPs) more than 4.17 billion years ago, transported by “meteorites and interplanetary dust particles…to warm little ponds whose wet–dry cycles promoted rapid polymerization.”

The Abstract states:

Before the origin of simple cellular life, the building blocks of RNA (nucleotides) had to form and polymerize in favorable environments on early Earth. At this time, meteorites and interplanetary dust particles delivered organics such as nucleobases (the characteristic molecules of nucleotides) to warm little ponds whose wet–dry cycles promoted rapid polymerization. We build a comprehensive numerical model for the evolution of nucleobases in warm little ponds leading to the emergence of the first nucleotides and RNA. We couple Earth’s early evolution with complex prebiotic chemistry in these environments. We find that RNA polymers must have emerged very quickly after the deposition of meteorites (less than a few years). Their constituent nucleobases were primarily meteoritic in origin and not from interplanetary dust particles. Ponds appeared as continents rose out of the early global ocean, but this increasing availability of “targets” for meteorites was offset by declining meteorite bombardment rates. Moreover, the rapid losses of nucleobases to pond seepage during wet periods, and to UV photodissociation during dry periods, mean that the synthesis of nucleotides and their polymerization into RNA occurred in just one to a few wet–dry cycles. Under these conditions, RNA polymers likely appeared before 4.17 billion years ago.

RNA World advocates envision a process of pre-biotic natural selection beginning once a primitive RNA replicator — an RNA molecule capable of copying itself — arose on the early Earth. RNA World scenarios also favor the idea that the chemical evolution started with RNA molecules because RNA is capable of storing genetic information (like DNA) and catalyzing some important biochemical reactions (like proteins). The new PNAS model advocates this same basic approach but envisions the RNA molecules forming much earlier than other RNA World models do, in warm little ponds during the period of heavy meteorite bombardment ove 4 billion years ago.

Unfortunately, the PNAS model lacks credibility for most of the same reasons that other RNA World models do. In Signature in the Cell, I describe those several problems in detail. One that leaps to mind is the problem of the instability of RNA molecules and their constituent subunits (especially their nucleobases and sugars) — a fact the authors effectively acknowledge by insisting that these chemical subunits of RNA “must have” polymerized extremely rapidly to avoid dissolution. However, the new model seems even less plausible than other RNA models as an origin-of-life scenario because the frequent impact of meteorites in such an early epoch would have sterilized the surface of the Earth and vaporized the oceans.

Even if whole RNA molecules could polymerize under these conditions, the PNAS model does nothing to explain how the precise sequencing of bases — the genetic information — in the RNA molecule could have arisen. Yet, as I show in Signature in the Cell, we now know that precise RNA nucleotide base sequencing would be a precondition of any self-replicating RNA molecule. I note there that ribozyme engineering experiments have succeeded in producing an RNA molecule capable of copying a small portion of itself but only after the intelligent chemist or the “ribozyme engineer” arranges the RNA bases in very specific sequences — i.e., only after chemists provide the information necessary to achieve even that limited replicase function. Thus, RNA self-replication doesn’t explain the origin of the information necessary to getting natural selection going (let alone life). Instead, RNA self-replication depends upon preexisting unexplained sources of information.

In any case, the PNAS model fails to provide a plausible solution to an even more basic problem: the origin of the constituent subunits of the RNA molecules and the synthesis of the whole RNA molecules under realistic pre-biotic conditions.

The authors acknowledge that the nucleobases (adenine, cytosine, guanine, uracil, and thymine) essential to RNA and DNA could not have been easily produced on the early Earth. Therefore, they speculate that these organic molecules must have originated in outer space and then were transported to Earth via dust particles and meteorites. They explain that, “as to the sources of nucleobases, early Earth’s atmosphere was likely dominated by CO2, N2, SO2, and H2O. In such a weakly reducing atmosphere, Miller–Urey-type reactions are not very efficient at producing organics. One solution is that the nucleobases were delivered by interplanetary dust particles (IDPs) and meteorites.” They further speculate that small amounts of nucleobases (.25 to 515 parts per billion) from these meteorites would have dissolved into the warm little ponds. At the same time, ribose purportedly formed through the formose reaction and quickly combined with the nucleobases and phosphorous to form nucleotides. They then envision nucleotides combining into RNA chains through cycles of the ponds evaporating and then refilling with water. Their rationale: building blocks can only be produced in water, but the nucleotides can only form into long chains through cycles of dehydration. They acknowledge that the entire process had to take place within a few years — a geological instant — otherwise everything would have been eliminated by such forces as UV radiation, hydrolysis, and seepage.

In  Signature in the Cell, I describe several factors that argue strongly against the formation of RNA in any realistic pre-biotic environment given the entire history of the Earth, let alone a few years.

First, nucleobases would have been highly unstable in the Earth’s early environment (even if trace amounts of these RNA subunits were transported from space on meteorites). As I note:

[T]he bases of RNA are unstable at temperatures required by currently popular high-temperature origin-of-life scenarios. The bases are subject to a chemical process known as “deamination,” in which they lose their essential amine groups (NH2). At 100 degrees C, adenine and guanine have chemical half-lives of only about one year; uracil has a half-life of twelve years; and cytosine a half-life of just nineteen days. (p. 302)

Second, the formation of ribose would have been next to impossible, particularly in the presence of the nucleobases:

The presence of the nitrogen-rich chemicals necessary for the production of nucleotide bases prevents the production of ribose sugars. Yet both ribose and the nucleotide bases are needed to build RNA. As Dean Kenyon explains, “The chemical conditions proposed for the prebiotic synthesis of purines and pyrimidines [the bases] are sharply incompatible with those proposed for the synthesis of ribose.” Or as Shapiro concludes: “The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.” (p. 303)

Third, interfering cross reactions would have inhibited the synthesis of RNA molecules and further chemical evolution in a life-friendly direction:

[B]oth the constituent building blocks of RNA and whole RNA molecules would have reacted readily with the other chemicals present in the prebiotic ocean or environment. These “interfering cross-reactions” would have inhibited the assembly of RNA from its constituent monomers and inhibited any movement from RNA molecules toward more complex biochemistry, since the products of these reactions typically produce biologically inert (or irrelevant) substances. (p. 303)

To assess the plausibility of the RNA World scenario, I invite you to  read an excerpt here from Chapter 14 of Signature in the Cell. This excerpt addresses five critical problems facing the RNA World hypothesis, including the implausibility of forming the chemical subunits of RNA and getting them to link together on the early Earth whether in warm little ponds or elsewhere. The excerpt addresses even more significant weaknesses of the — oddly — still popular RNA World. After you read them, you might want to go back and reread the Abstract of the PNAS article. Does the scenario it outlines still seem at all plausible?

How Settled science's gatekeepers are putting the squeeze on free enquiry

Science Philosopher: Science World Beset by “Filters,” “Conformity,” “Hidebound” Thinking
David Klinghoffer | @d_klinghoffer

How often have we heard the stale line about how science adores fresh thinking that topples past idols? Oh sure, we’re told, if there were anything of substance to the theory of intelligent design, some young maverick scientist would just love to make his mark by being the guy who knocked over Darwinism in favor of ID.


This familiar appeal to the myth of professional scientists as free thinkers receives a blow from philosopher of science Adrian Currie, writing for  writing for Aeon. Currie is not someone we’d heard of before, not an ID proponent. He’s not trying to insert himself in the Darwin debate. But man, his frank depiction sure rings a bell:

Nowadays scientists tend to shun the ‘maverick’ label. If you’ve hung out in a lab lately, you’ll notice that scientific researchers are often terrible gossips. Being labelled a ‘maverick’, a ‘crank’ or a ‘little bit crazy’ can be career-killing. The result is what the philosopher Huw Price at the University of Cambridge calls ‘reputation traps’: if an area of study gets a bad smell, a waft of the illegitimate, serious scientists won’t go anywhere near it.

Mavericks such as Newton, Buffon and Darwin operated in a very different time to our own. Theirs was the age of the ‘gentleman scholar’, in which research was pursued by a moneyed class with time to kill. Today, though, modern science encourages conformity. For a start, you need to get a degree to become a scientist of some stripe. You also need to publish, get peer-reviewed, obtain money from a funder, and find a job. These things all mould the young scientist: you aren’t just taught proper pipette technique, but also take on a kind of disciplinary worldview. The process of acculturation is part of what the philosopher and historian Thomas Kuhn called a ‘paradigm’, a set of values, practices and basic concepts that scientists hold in common.

On top of this standardisation, careers in science are now extremely hard to come by. There’s a scarcity of jobs compared with the number of applicants, and very few high-ranking and ‘big impact’ journals. This means that the research decisions that scientists make, particularly early on, are high-risk wagers about what will be fruitful and lead to a decent career. The road to academic stardom (and, for that matter, academic mediocrity) is littered with brilliant, passionate people who simply made bad bets. In such an environment, researchers are bound to be conservative — with the stakes set so high, taking a punt on something outlandish, and that you know is likely to hurt your career, is not a winning move.

Of course, all these filters help to ensure that the science we read about is well-supported and reliable, compared with Darwin’s day. There’s much good in sharing a paradigm; it makes communication easier and helps knowledge accumulate from a common base. But professional training also involves learning how to convince colleagues in your field that your work is legitimate, that it meets their ideas of what the good questions are and what good answers look like. This makes science more productive, but less creative. Enquiries can become hidebound and unadventurous. As a result, truly revolutionary research — the domain of the maverick — is increasingly hard to pursue.

Maybe he didn’t know anyone was listening, or at least anyone who would think to consider this candid admission in the context of the evolution controversy.

And remember, all his talk about “reputation traps,” “filters,” a sensitivity to “career killing” “bad smells,” a system set up to “encourage conformity,” ensuring “conservative,” “hidebound and unadventurous” thinking — all this is true when the maverick science that might be investigated or championed has no philosophical implications to it.

In the case of ID, the implications for your picture of reality are, naturally, enormous. So the institutional conservatism of science is really going to kick in and resist new thinking. As we know it does.

Reconciling the genealogies of Jesus Christ:The Watchtower Society's commentary.

GENEALOGY OF JESUS CHRIST

In the first chapter of Matthew we find the genealogy of Jesus running from Abraham forward. At Luke chapter 3 is a genealogy back to “Adam, son of God.” Jesus’ genealogy is the only one given in the Christian Greek Scriptures. Part of his genealogy appears at 1 Chronicles chapters 1 to 3, running from Adam through Solomon and Zerubbabel. The books of Genesis and Ruth combined give the line from Adam to David.

The latter three lists (Genesis/Ruth, 1 Chronicles, and Luke) agree fully from Adam to Arpachshad, with minor differences as to certain names, such as Kenan, which is “Cainan” at Luke 3:37. The Chronicles and Genesis/Ruth lists agree down to David, while another “Cainan” is found in Luke’s account between Arpachshad and Shelah.—Lu 3:35, 36.

From Solomon to Zerubbabel, the Chronicles record and Matthew agree in the main, Matthew omitting some names. These differences and differences in Luke’s account from David to Jesus will be discussed later.

Under GENEALOGY, we have shown that besides many private family records, the Jews kept public records of genealogies and that the chroniclers, such as Ezra, had access to these when compiling their lists; also, that the public registers existed in the first century evidently up until 70 C.E. The matter of the descent of the Messiah from Abraham, and through David, was of prime importance to them. So we can be confident that both Matthew and Luke consulted these genealogical tables.

Reliability of the Gospel Genealogies. The question arises: Why does Matthew leave out some names that are contained in the listings of the other chroniclers? First of all, to prove one’s genealogy it was not necessary to name every link in the line of descent. For example, Ezra, in proving his priestly lineage, at Ezra 7:1-5, omitted several names contained in the listing of the priestly line at 1 Chronicles 6:1-15. Obviously it was not essential to name all these ancestors to satisfy the Jews as to his priestly lineage. Similarly with Matthew: He doubtless used the public register and copied from it, if not every name, the ones necessary to prove the descent of Jesus from Abraham and David. He also had access to the Hebrew Scriptures, which he could consult alongside the official public records.—Compare Ru 4:12, 18-22 and Mt 1:3-6.

The lists made by both Matthew and Luke were comprised of names publicly recognized by the Jews of that time as authentic. The scribes and Pharisees as well as the Sadducees were bitter enemies of Christianity, and they would have used any possible argument to discredit Jesus, but it is noteworthy that they never challenged these genealogies. If either Matthew’s or Luke’s genealogy of Jesus had been in error, what an opportunity it would have been for these opponents to prove it then and there! For until 70 C.E. they evidently had ready access to the public genealogical registers and the Scriptures.

The same is true regarding the first-century pagan enemies of Christianity, many of whom were, like those Jews, learned men who would readily have pointed to any evidence that these lists of Matthew and Luke were unauthentic and contradictory. But there is no record that the early pagan enemies attacked Christians on this point.

Also, both Matthew and Luke achieved their objective, and that was all they needed to do. To prove that Jesus was descended from Abraham and David, it was not necessary to make a new genealogy. All they had to do was copy from the public tables that the nation fully accepted regarding the lineage of David and of the priesthood and all other matters requiring proof of one’s descent. (See Lu 1:5; 2:3-5; Ro 11:1.) Even if there was an omission in these tables, it did not detract from what these Gospel writers intended and indeed accomplished, namely, presenting legally and publicly recognized proof of the genealogy of Jesus the Messiah.

Problems in Matthew’s Genealogy of Jesus. Matthew divides the genealogy from Abraham to Jesus into three sections of 14 generations each. (Mt 1:17) This division may have been made as a memory aid. However, in counting the names we find that they total 41, rather than 42. One suggestion as to how they may be counted is as follows: By taking Abraham to David, 14 names, then using David as the starting name for the second 14, with Josiah as the last; finally, by heading the third series of 14 names with Jeconiah (Jehoiachin) and ending with Jesus. Notice that Matthew repeats the name David as the last of the first 14 names and as the first of the next 14. Then he repeats the expression “the deportation to Babylon,” which he links with Josiah and his sons.—Mt 1:17.

As stated earlier, Matthew may have copied his list exactly from the public register that he used, or he may have purposely left out some links with a view to aiding memory. However, a suggestion as to the omission here of three kings of David’s line between Jehoram and Uzziah (Azariah) is that Jehoram married wicked Athaliah of the house of Ahab, the daughter of Jezebel, thereby bringing this God-condemned strain into the line of the kings of Judah. (1Ki 21:20-26; 2Ki 8:25-27) Naming Jehoram as first in the wicked alliance, Matthew omits the names of the next three kings to the fourth generation, Ahaziah, Jehoash, and Amaziah, the fruits of the alliance.—Compare Mt 1:8 with 1Ch 3:10-12.

Matthew indicates that Zerubbabel is the son of Shealtiel (Mt 1:12), and this coincides with other references. (Ezr 3:2; Ne 12:1; Hag 1:14; Lu 3:27) However, at 1 Chronicles 3:19 Zerubbabel is referred to as the son of Pedaiah. Evidently Zerubbabel was the natural son of Pedaiah and the legal son of Shealtiel by reason of brother-in-law marriage; or possibly, after Zerubbabel’s father Pedaiah died, Zerubbabel was brought up by Shealtiel as his son and therefore became legally recognized as the son of Shealtiel.

A Problem in Luke’s Genealogy of Jesus. Available manuscript copies of Luke list a second “Cainan,” between Arpachshad (Arphaxad) and Shelah. (Lu 3:35, 36; compare Ge 10:24; 11:12; 1Ch 1:18, 24.) Most scholars take this to be a copyist’s error. In the Hebrew Scriptures, “Cainan” is not found in this relative position in the genealogical listings in the Hebrew or the Samaritan texts, nor is it in any of the Targums or versions except the Greek Septuagint. And it does not seem that it was even in the earlier copies of the Septuagint, because Josephus, who usually follows the Septuagint, lists Seles (Shelah) next as the son of Arphaxades (Arpachshad). (Jewish Antiquities, I, 146 [vi, 4]) Early writers Irenaeus, Africanus, Eusebius, and Jerome rejected the second “Cainan” in copies of Luke’s account as an interpolation.—See CAINAN No. 2.

Why do the genealogies of Jesus Christ as given by Matthew and by Luke differ?

The difference in nearly all the names in Luke’s genealogy of Jesus as compared with Matthew’s is quickly resolved in the fact that Luke traced the line through David’s son Nathan, instead of Solomon as did Matthew. (Lu 3:31; Mt 1:6, 7) Luke evidently follows the ancestry of Mary, thus showing Jesus’ natural descent from David, while Matthew shows Jesus’ legal right to the throne of David by descent from Solomon through Joseph, who was legally Jesus’ father. Both Matthew and Luke signify that Joseph was not Jesus’ actual father but only his adoptive father, giving him legal right. Matthew departs from the style used throughout his genealogy when he comes to Jesus, saying: “Jacob became father to Joseph the husband of Mary, of whom Jesus was born, who is called Christ.” (Mt 1:16) Notice that he does not say ‘Joseph became father to Jesus’ but that he was “the husband of Mary, of whom Jesus was born.” Luke is even more pointed when, after showing earlier that Jesus was actually the Son of God by Mary (Lu 1:32-35), he says: “Jesus . . . being the son, as the opinion was, of Joseph, son of Heli.”—Lu 3:23.

Since Jesus was not the natural son of Joseph but was the Son of God, Luke’s genealogy of Jesus would prove that he was, by human birth, a son of David through his natural mother Mary. Regarding the genealogies of Jesus given by Matthew and by Luke, Frederic Louis Godet wrote: “This study of the text in detail leads us in this way to admit—1. That the genealogical register of Luke is that of Heli, the grandfather of Jesus; 2. That, this affiliation of Jesus by Heli being expressly opposed to His affiliation by Joseph, the document which he has preserved for us can be nothing else in his view than the genealogy of Jesus through Mary. But why does not Luke name Mary, and why pass immediately from Jesus to His grandfather? Ancient sentiment did not comport with the mention of the mother as the genealogical link. Among the Greeks a man was the son of his father, not of his mother; and among the Jews the adage was: ‘Genus matris non vocatur genus [“The descendant of the mother is not called (her) descendant”]’ (‘Baba bathra,’ 110, a).”—Commentary on Luke, 1981, p. 129.

Actually each genealogy (Matthew’s table and Luke’s) shows descent from David, through Solomon and through Nathan. (Mt 1:6; Lu 3:31) In examining the lists of Matthew and Luke, we find that after diverging at Solomon and Nathan, they come together again in two persons, Shealtiel and Zerubbabel. This can be explained in the following way: Shealtiel was the son of Jeconiah; perhaps by marriage to the daughter of Neri he became Neri’s son-in-law, thus being called the “son of Neri.” It is possible as well that Neri had no sons, so that Shealtiel was counted as his “son” for that reason also. Zerubbabel, who was likely the actual son of Pedaiah, was legally reckoned as the son of Shealtiel, as stated earlier.—Compare Mt 1:12; Lu 3:27; 1Ch 3:17-19.

Then the accounts indicate that Zerubbabel had two sons, Rhesa and Abiud, the lines diverging again at this point. (These could have been, not actual sons, but descendants, or one, at least, could have been a son-in-law. Compare 1Ch 3:19.) (Lu 3:27; Mt 1:13) Both Matthew’s and Luke’s genealogies of Jesus vary here from that found in 1 Chronicles chapter 3. This may be because a number of names were purposely left out by Matthew and possibly also by Luke. But the fact should be kept in mind that such differences in the genealogical lists of Matthew and Luke are very likely those already present in the genealogical registers then in use and fully accepted by the Jews and were not changes made by Matthew and Luke.

We may conclude, therefore, that the two lists of Matthew and Luke fuse together the two truths, namely, (1) that Jesus was actually the Son of God and the natural heir to the Kingdom by miraculous birth through the virgin girl Mary, of David’s line, and (2) that Jesus was also the legal heir in the male line of descent from David and Solomon through his adoptive father Joseph. (Lu 1:32, 35; Ro 1:1-4) If there was any accusation made by hostile Jews that Jesus’ birth was illegitimate, the fact that Joseph, aware of the circumstances, married Mary and gave her the protection of his good name and royal lineage refutes such slander.

[Chart on page 913, 914]

BIBLE LISTS OF JESUS’ GENEALOGY

Genesis 1 Chronicles Matthew Luke

and Ruth Chaps 1, 2, 3 Chap 1 Chap 3

Adam Adam Adam

Seth Seth Seth

Enosh Enosh Enosh

Kenan Kenan Cainan

Mahalalel Mahalalel Mahalaleel

Jared Jared Jared

Enoch Enoch Enoch

Methuselah Methuselah Methuselah

Lamech Lamech Lamech

Noah Noah Noah

Shem Shem Shem

Arpachshad Arpachshad Arpachshad

Cainan

Shelah Shelah Shelah

Eber Eber Eber

Peleg Peleg Peleg

Reu Reu Reu

Serug Serug Serug

Nahor Nahor Nahor

Terah Terah Terah

Abram Abraham Abraham Abraham

(Abraham)

Isaac Isaac Isaac Isaac

Jacob (Israel) Jacob Jacob Jacob

Judah (and Judah Judah Judah

Tamar) (and Tamar)

Perez Perez Perez Perez

Hezron Hezron Hezron Hezron

Ram Ram Ram Arni (Ram?)

Amminadab Amminadab Amminadab Amminadab

Nahshon Nahshon Nahshon Nahshon

Salmon Salmon (Salma, Salmon (and Salmon

1Ch 2:11) Rahab)

Boaz (and Boaz Boaz (and Boaz

Ruth) Ruth)

Obed Obed Obed Obed

Jesse Jesse Jesse Jesse

David David David (and David

Bath-sheba)

Solomon Solomon Nathan ⁠1

Rehoboam Rehoboam Mattatha

Abijah Abijah Menna

Asa Asa Melea

Jehoshaphat Jehoshaphat Eliakim

Jehoram Jehoram Jonam

Ahaziah Joseph

Jehoash

Judas

Symeon

Amaziah Levi

Azariah (Uzziah) Uzziah Matthat

(Azariah)

Jotham Jotham Jorim

Ahaz Ahaz Eliezer

Hezekiah Hezekiah Jesus

Manasseh Manasseh Er

Amon Amon Elmadam

Josiah Josiah Cosam

Jehoiakim Addi

Melchi

Jeconiah Jeconiah Neri

(Jehoiachin)

Shealtiel Shealtiel Shealtiel ⁠3

(Pedaiah) ⁠2

Zerubbabel ⁠4 Zerubbabel Zerubbabel

Rhesa

Abiud Joanan

Joda

Eliakim Josech

Semein

Azor Mattathias

Maath

Zadok Naggai

Esli

Achim Nahum

Amos

Eliud Mattathias

Joseph

Eleazar Jannai

Melchi

Matthan Levi

Matthat

Jacob Heli (father

of Mary)

Joseph Joseph (Heli’s

son-in-law)

Jesus Jesus

(foster son) (Mary’s son)

1 At Nathan, Luke begins reckoning the genealogy through Jesus’ maternal line, while Matthew continues with the paternal line.

2 Zerubbabel evidently was the natural son of Pedaiah and the legal son of Shealtiel by brother-in-law marriage; or he was brought up by Shealtiel after his father Pedaiah’s death and became legally recognized as the son of Shealtiel.—1Ch 3:17-19; Ezr 3:2; Lu 3:27.

3 Shealtiel the son of Jeconiah possibly was the son-in-law of Neri.—1Ch 3:17; Lu 3:27.

4 The lines meet in Shealtiel and Zerubbabel, afterward diverging. This divergence could have been through two different descendants of Zerubbabel, or Rhesa or Abiud could have been a son-in-law.