Tuesday, 9 May 2017
Another day another zombie apocalypse.
Reviewing Zombie Science, Sean McDowell Asks the Toughest Question About Evolutionary Icons
David Klinghoffer | @d_klinghoffer
The science establishment that silences evolution skeptics in academia might have a shred of a plausible case to make in its defense…if the science itself were on their side. But of course it’s not, as Jonathan Wells explains in his new book
Zombie Science: More Icons of Evolution.
Sean McDowell reviews the book at The Stream, and he hits the main points admirably. Such as: If the icons were simply mistakes, innocent blunders, the equivalent of typos, why do the science textbooks retain them year after year? That is really the toughest question, that folks like Jerry Coyne won’t touch.
If these icons were innocent mistakes, then biologists would have eagerly corrected them, right? Since they persist, says Wells, there must be something else besides the evidence that keeps them “alive.”
Publishers could possibly be forgiven if this was the only mistake.
For instance, Darwin considered embryological development the best evidence for his theory. He cited drawings from the German Biologist Ernst Haeckel, which allegedly reveal how the development of various vertebrate animals mirrors the larger evolutionary story of common descent. Yet it has been known since at least 1997 that the Haeckel’s drawings were cherry-picked, inaccurate and fake. In fact, Wells concludes, “The real issue is that Haeckel’s drawings omitted half of the evidence — the half that doesn’t fit Darwin’s claim that embryos are most similar in their early stages” (58).
Nonetheless, Haeckel’s drawings continue to appear in textbooks published after 2000, such as Donald Prothero’s 2013 textbook Bringing Fossils to Life. And the 2016 textbook Biology, by Mader and Windelspecht, uses re-drawn versions of Haeckel’s embryos that make the same (mistaken) point.
Publishers could possibly be forgiven if this was the only mistake. But as Wells indicates, similar misrepresentations continue for other “icons” including the Miller-Urey experiment, Archaeopteryx, peppered moths, Darwin’s finches and more. Like zombies, these “evidences” simply won’t die.
No, there’s more going on than mere publishing blunders. Darwin advocates are trying to persuade their audience, including impressionable young people, and the evidence is shaped as needed to suit the purpose.
But the bottom is really out of the boat. McDowell notes, for one thing, the challenge of epigenetics:
One of the most interesting sections of the book was the discussion of epigenetics. Broadly speaking, epigenetics refers to the various factors involved in development, including genetics.
In the 20th century, the dominant view of biology was that evolution proceeded genetically from DNA to RNA to proteins to us. As a result, evolution could advance through genetic mutations that accumulate over time.
But according to Dr. Wells, there are significant carriers of information beyond DNA sequences. Biological membranes are one example. In other words, the claim that the genome carries all the information necessary to build an organism is false. As a result, mutations or changes in DNA alone are not enough to build new function and form.
Given the premise of neo-Darwinism, that evolution builds novelties precisely by mutation and selection, that would seem to seal the case. Wouldn’t it be interesting to see a scientist who’s a Darwin apologist honestly confront the argument in Dr. Wells’s book? That would be just fabulous. Don’t hold your breath.
David Klinghoffer | @d_klinghoffer
The science establishment that silences evolution skeptics in academia might have a shred of a plausible case to make in its defense…if the science itself were on their side. But of course it’s not, as Jonathan Wells explains in his new book
Zombie Science: More Icons of Evolution.
Sean McDowell reviews the book at The Stream, and he hits the main points admirably. Such as: If the icons were simply mistakes, innocent blunders, the equivalent of typos, why do the science textbooks retain them year after year? That is really the toughest question, that folks like Jerry Coyne won’t touch.
If these icons were innocent mistakes, then biologists would have eagerly corrected them, right? Since they persist, says Wells, there must be something else besides the evidence that keeps them “alive.”
Publishers could possibly be forgiven if this was the only mistake.
For instance, Darwin considered embryological development the best evidence for his theory. He cited drawings from the German Biologist Ernst Haeckel, which allegedly reveal how the development of various vertebrate animals mirrors the larger evolutionary story of common descent. Yet it has been known since at least 1997 that the Haeckel’s drawings were cherry-picked, inaccurate and fake. In fact, Wells concludes, “The real issue is that Haeckel’s drawings omitted half of the evidence — the half that doesn’t fit Darwin’s claim that embryos are most similar in their early stages” (58).
Nonetheless, Haeckel’s drawings continue to appear in textbooks published after 2000, such as Donald Prothero’s 2013 textbook Bringing Fossils to Life. And the 2016 textbook Biology, by Mader and Windelspecht, uses re-drawn versions of Haeckel’s embryos that make the same (mistaken) point.
Publishers could possibly be forgiven if this was the only mistake. But as Wells indicates, similar misrepresentations continue for other “icons” including the Miller-Urey experiment, Archaeopteryx, peppered moths, Darwin’s finches and more. Like zombies, these “evidences” simply won’t die.
No, there’s more going on than mere publishing blunders. Darwin advocates are trying to persuade their audience, including impressionable young people, and the evidence is shaped as needed to suit the purpose.
But the bottom is really out of the boat. McDowell notes, for one thing, the challenge of epigenetics:
One of the most interesting sections of the book was the discussion of epigenetics. Broadly speaking, epigenetics refers to the various factors involved in development, including genetics.
In the 20th century, the dominant view of biology was that evolution proceeded genetically from DNA to RNA to proteins to us. As a result, evolution could advance through genetic mutations that accumulate over time.
But according to Dr. Wells, there are significant carriers of information beyond DNA sequences. Biological membranes are one example. In other words, the claim that the genome carries all the information necessary to build an organism is false. As a result, mutations or changes in DNA alone are not enough to build new function and form.
Given the premise of neo-Darwinism, that evolution builds novelties precisely by mutation and selection, that would seem to seal the case. Wouldn’t it be interesting to see a scientist who’s a Darwin apologist honestly confront the argument in Dr. Wells’s book? That would be just fabulous. Don’t hold your breath.
Biomimetics v. Darwin.
Leading Biomimetic Scientist: Don’t Let Materialism Trump Evidence
Jonathan Witt
Here’s another ID-goes-international story, hard on the heels of the Discovery Institute-Mackenzie launch in Brazil last week: A groundbreaking South Korean scientist, Dr. Seung-Yop Lee, has come out against the practice of ruling intelligent design hypotheses out of bounds before considering the evidence.
“As a biomimetic researcher, I wonder how the complex photonic nanostructures of insects first arose,” he writes. “Biological designs are sparking a gold rush of innovation for engineers and scientists, but by and large, only materialistic explanations for these biological structures are allowed in the biomimetic field.”
Lee is a professor in the Department of Mechanical and Biomedical Engineering at Sogang University in Seoul and a leading figure in the field of biomimetics.
Lee’s recent reading of Jonathan Wells’s new book, Zombie Science: More Icons of Evolution, precipitated the comments. “In his excellent new book, Zombie Science, Jonathan Wells urges another approach to scientific investigation,” Lee wrote. “Don’t let materialistic philosophy trump the evidence, Wells says. Instead, follow the evidence wherever it leads.”
An article in the journal Nature reports on one of Dr. Lee’s biomimetic innovations, “a film that changes color according to the ambient humidity.” According to the article, the invention was “inspired by the natural design of the Hercules beetle” and paves the way to the development of a sensor that “would not need electricity and could be used in small medical or agricultural devices.”
Professor Lee’s success at making design breakthroughs by looking for inspiration from engineering marvels in the biological realm appears to have left him impatient with dogmatic materialism in origins biology, and sympathetic to the argument Wells makes in his new book. “The title, Zombie Science, is quirky and colorful,” Lee said, “but Wells uses it to highlight a real problem: Vivid ‘proofs’ of evolution still lumber along even after contrary evidence has killed them off and mainstream biologists have renounced them.”
Zombie Science is a sequel to Dr. Wells’s 2001 book, Icons of Evolution. “Wells brings readers up to date on the original ten icons, and debunks six more,” Lee comments in his endorsement of the book. “Wells argues that these debunked icons persist in textbooks and elsewhere only because they support a dominant evolutionary paradigm and a materialistic dogma. Zombie Science is a timely call for reform.”
Evolution News has reported here, here, here, here, and here on just a few of the many veins being mined in the field of biomimetics. Find many more articles on the subject by plugging “biomimetics” into the website’s search field.
Jonathan Witt
Here’s another ID-goes-international story, hard on the heels of the Discovery Institute-Mackenzie launch in Brazil last week: A groundbreaking South Korean scientist, Dr. Seung-Yop Lee, has come out against the practice of ruling intelligent design hypotheses out of bounds before considering the evidence.
“As a biomimetic researcher, I wonder how the complex photonic nanostructures of insects first arose,” he writes. “Biological designs are sparking a gold rush of innovation for engineers and scientists, but by and large, only materialistic explanations for these biological structures are allowed in the biomimetic field.”
Lee is a professor in the Department of Mechanical and Biomedical Engineering at Sogang University in Seoul and a leading figure in the field of biomimetics.
Lee’s recent reading of Jonathan Wells’s new book, Zombie Science: More Icons of Evolution, precipitated the comments. “In his excellent new book, Zombie Science, Jonathan Wells urges another approach to scientific investigation,” Lee wrote. “Don’t let materialistic philosophy trump the evidence, Wells says. Instead, follow the evidence wherever it leads.”
An article in the journal Nature reports on one of Dr. Lee’s biomimetic innovations, “a film that changes color according to the ambient humidity.” According to the article, the invention was “inspired by the natural design of the Hercules beetle” and paves the way to the development of a sensor that “would not need electricity and could be used in small medical or agricultural devices.”
Professor Lee’s success at making design breakthroughs by looking for inspiration from engineering marvels in the biological realm appears to have left him impatient with dogmatic materialism in origins biology, and sympathetic to the argument Wells makes in his new book. “The title, Zombie Science, is quirky and colorful,” Lee said, “but Wells uses it to highlight a real problem: Vivid ‘proofs’ of evolution still lumber along even after contrary evidence has killed them off and mainstream biologists have renounced them.”
Zombie Science is a sequel to Dr. Wells’s 2001 book, Icons of Evolution. “Wells brings readers up to date on the original ten icons, and debunks six more,” Lee comments in his endorsement of the book. “Wells argues that these debunked icons persist in textbooks and elsewhere only because they support a dominant evolutionary paradigm and a materialistic dogma. Zombie Science is a timely call for reform.”
Evolution News has reported here, here, here, here, and here on just a few of the many veins being mined in the field of biomimetics. Find many more articles on the subject by plugging “biomimetics” into the website’s search field.
Yet more preDarwinian tech v. Darwin.
Molecular Machines Reach Perfection
Evolution News | @DiscoveryCSC
ATP synthase is in the news again, and it’s even better than before. Before hearing the news, it might be worthwhile to review our animation of this tiny rotary engine that powers all life, from bacteria to humans. You’re running on quadrillions of these little motors right now. The news is that they are perfect.
One doesn’t often see the word “perfect” in a science paper, but four Japanese researchers are unabashed, using the word 13 times in their paper in the Proceedings of the National Academy of Sciences, , including the title: “Perfect chemomechanical coupling of F0F1-ATP synthase.”
Peter D. Mitchell, a Nobel awardee in 1978, proposed that F0F1-ATP synthase converts energy between electrochemical potential of H+ across biological membrane…, which is established by respiratory chain complexes, and chemical potential of adenine nucleotide [ΔG(ATP)]. However, the efficiency of the energy conversion has been a matter of debate for over 50 years. In this study, with a highly reproducible analytical system using F0F1-ATP synthase from thermophilic Bacillus, apparently perfect energy conversion was observed. Mitchell’s prediction thus has quantitative evidence. [Emphasis added.]
You can’t get better than perfect. This means that every proton (H+) coming into the machine, driving its rotation, yields 100 percent conversion of its energy into production of ATP. Can you think of any man-made motor that even approaches this kind of efficiency? Hardly. At our macro level of engineering, artificial motors waste energy through heat, friction, and escape of fuel to the environment. The second law of thermodynamics forbids perfection. Somehow, at the scale of nanometers, ATP synthase engines get maximum bang for their proton buck — with no loss at all.
The debate about ATP synthase energy efficiency centered on the numerical mismatch between the two halves of the machine. The F0 part, where protons enter, has 10 units called c subunits arranged like orange peels that rotate around a central axis. The F1 part, by contrast, has 3 units in pairs, called β subunits, where ATP synthesis takes place (the two halves are linked by a central stalk called the γ-subunit that works like a camshaft). This 10/3 non-integer pairing between F0 and F1 was unexpected, leading biophysicists to assume there must be some slippage in the camshaft during every rotation. Slippage would waste some of the proton motive force (pmf), reducing the efficiency.
One way to find the answer is to compare the input to the output as accurately as possible. These scientists rigged a proteoliposome from a thermophilic (heat-loving) bacterium in a new way that allowed them to reliably measure the incoming pmf as well as the outgoing production of ATP.
In this report, we used this system to determine the actual H+/ATP ratio. The results show the perfect agreement of H+/ATP ratio to c/β, indicating tight coupling efficiency of proton translocation in Fo and ATP synthesis/hydrolysis in F1. In addition, kinetic and energetic equivalence of transmembrane difference of pH (ΔpH) and electric potential (Δψ) was supported with unprecedented certainty over a wide range of pmf values.
The team carefully eliminated all contamination, ran the tests for tens of hours, and reduced error to achieve unprecedented levels of accuracy. “A long-anticipated, but unproved, conception that F0F1 achieves a perfect coupling between transmembrane H+ translocation and ATP synthesis/hydrolysis has direct experimental evidence now,” they conclude.
How is this even possible? Isn’t there slippage? Isn’t there twisting force of torque as the camshaft presses against the β subunits in F1? And what about other versions of ATP synthase in other organisms that have 8, 12, or 14 c subunits in F0? They address these questions in the final paragraph of the Discussion:
In a thermodynamic view, the perfect coupling means perfect energy conversions between chemiosmotic (H+ translocation), mechanical (rotary motion), and chemical energy (ATP synthesis/hydrolysis). A near-perfect energy conversion from ATP hydrolysis to rotary motion of γ-subunit in F1 was recently demonstrated in a thermodynamically defined manner, and this study predicts that other conversions should also be highly efficient. In a mechanistic view, the perfect coupling means that there is no slippage within and between F0 motor and F1 motor. Atomic structures of F1 are convincing that rotary motion of the γ-subunit could not occur without conformation change of the catalytic subunits. Structural basis for rotation of F0 motor without slippage has been suggested recently by atomic structures of whole F0F1 revealed by cryoelectron microscopy. The connection of the two motors should also be strong enough to endure the twisting force of torque. Crystal structures of F1·c-ring complexes indicate that the connection appears to be held by a small number of interactions between the bottom portion of F1’s rotor and polar loops in the c ring. Interestingly, this connection must be versatile, because the chimera TF0F1 with replaced F0 from Propionegenium modestum that has 11 c subunits shows good coupled activity.
This is a remarkable thing. Perfect — yet versatile! You can substitute a different c-ring into F0 and still get “good coupled activity.” Try that with man-made engines!
Other Perfect Scores
Kinesin, the walking machine (see our animation), is another “perfect 10” performer. Like ATP synthase, it converts chemical energy into mechanical energy. It even has what scientists call a “power stroke” as it walks. Tomonami Sumi from Okayama University in Japan compared the machine’s walking efficiency to its ATP consumption. Publishing in Nature Scientific Reports, he found that “the ratio of the number of ATP hydrolysis to the number of steps advanced suggests a tight coupling between the two.” Tight coupling; we heard that in the previous story. Although he doesn’t use the word perfect, he speaks admiringly of the “extraordinary motor properties” of kinesin. It appears that the Japanese are less inhibited about using the d-word design. Sumi’s title is, “Design principles governing chemomechanical coupling of kinesin.”
Cohesin and condensing are proteins that help keep DNA organized. An interesting article written like a mystery story in Nature News shows how scientists are trying to figure out if they work like motors. Writer Elie Dolgin calls it “DNA’s secret weapon against knots and tangles.” Something is seen extruding loops in DNA, working to “keep local regions of DNA together, disentangling them from other parts of the genome and even giving shape and structure to the chromosomes.” But whatever it is, it has to be beyond belief if MIT biophysicist Leonid Mirny’s model is correct:
For one thing, the identity of the molecular machine that forms the loops remains a mystery. If the leading protein candidate acted like a motor, as Mirny proposes, it would guzzle energy faster than it has ever been seen to do. “As a physicist friend of mine tells me, ‘This is kind of the Higgs boson of your field’,” says Mirny; it explains one of the deepest mysteries of genome biology, but could take years to prove.
The race is on to discover what kind of motor is consuming ATP to push and pull DNA. Loop extrusion not only prevents knots and tangles, it regulates gene expression by keeping parts of genes in proximity. We expect this mystery will have a “perfect” ending.
Lastly, that familiar icon the bacterial flagellum shows a new trick up its sleeve. How does the driveshaft know when to stop growing? A paper in Science shows that the “most efficient machine in the universe,” as Howard Berg calls it, has a perfect solution: it grows till it touches the periplasm (outer membrane layer). As we marvel at the engineering, let’s give evolution the credit, shall we?
The bacterial flagellum exemplifies a system where even small deviations from the highly regulated flagellar assembly process can abolish motility and cause negative physiological outcomes. Consequently, bacteria have evolved elegant and robust regulatory mechanisms to ensure that flagellar morphogenesis follows a defined path, with each component self-assembling to predetermined dimensions. The flagellar rod acts as a driveshaft to transmit torque from the cytoplasmic rotor to the external filament. The rod self-assembles to a defined length of ~25 nanometers. Here, we provide evidence that rod length is limited by the width of the periplasmic space between the inner and outer membranes. The length of Braun’s lipoprotein determines periplasmic width by tethering the outer membrane to the peptidoglycan layer.
Science Daily adds, “To function properly and propel the bacterium, the flagellum requires all of its components to fit together to exacting measurements.” The growing “driveshaft” somehow feels the outer layer and knows to stop growing. “The rod needs to touch the inside of the outer membrane,” one of the authors says. “So, if the outer membrane is farther away, the rod has to grow there to meet it.” The versatile growth process yields a perfect fit.
If you can think of any machine in your experience that is perfect yet flexible, it probably did not come about through blind, aimless natural processes. Let’s stop allowing Darwinians to get away, unchallenged, with saying they “have evolved” to perfection.
Evolution News | @DiscoveryCSC
ATP synthase is in the news again, and it’s even better than before. Before hearing the news, it might be worthwhile to review our animation of this tiny rotary engine that powers all life, from bacteria to humans. You’re running on quadrillions of these little motors right now. The news is that they are perfect.
One doesn’t often see the word “perfect” in a science paper, but four Japanese researchers are unabashed, using the word 13 times in their paper in the Proceedings of the National Academy of Sciences, , including the title: “Perfect chemomechanical coupling of F0F1-ATP synthase.”
Peter D. Mitchell, a Nobel awardee in 1978, proposed that F0F1-ATP synthase converts energy between electrochemical potential of H+ across biological membrane…, which is established by respiratory chain complexes, and chemical potential of adenine nucleotide [ΔG(ATP)]. However, the efficiency of the energy conversion has been a matter of debate for over 50 years. In this study, with a highly reproducible analytical system using F0F1-ATP synthase from thermophilic Bacillus, apparently perfect energy conversion was observed. Mitchell’s prediction thus has quantitative evidence. [Emphasis added.]
You can’t get better than perfect. This means that every proton (H+) coming into the machine, driving its rotation, yields 100 percent conversion of its energy into production of ATP. Can you think of any man-made motor that even approaches this kind of efficiency? Hardly. At our macro level of engineering, artificial motors waste energy through heat, friction, and escape of fuel to the environment. The second law of thermodynamics forbids perfection. Somehow, at the scale of nanometers, ATP synthase engines get maximum bang for their proton buck — with no loss at all.
The debate about ATP synthase energy efficiency centered on the numerical mismatch between the two halves of the machine. The F0 part, where protons enter, has 10 units called c subunits arranged like orange peels that rotate around a central axis. The F1 part, by contrast, has 3 units in pairs, called β subunits, where ATP synthesis takes place (the two halves are linked by a central stalk called the γ-subunit that works like a camshaft). This 10/3 non-integer pairing between F0 and F1 was unexpected, leading biophysicists to assume there must be some slippage in the camshaft during every rotation. Slippage would waste some of the proton motive force (pmf), reducing the efficiency.
One way to find the answer is to compare the input to the output as accurately as possible. These scientists rigged a proteoliposome from a thermophilic (heat-loving) bacterium in a new way that allowed them to reliably measure the incoming pmf as well as the outgoing production of ATP.
In this report, we used this system to determine the actual H+/ATP ratio. The results show the perfect agreement of H+/ATP ratio to c/β, indicating tight coupling efficiency of proton translocation in Fo and ATP synthesis/hydrolysis in F1. In addition, kinetic and energetic equivalence of transmembrane difference of pH (ΔpH) and electric potential (Δψ) was supported with unprecedented certainty over a wide range of pmf values.
The team carefully eliminated all contamination, ran the tests for tens of hours, and reduced error to achieve unprecedented levels of accuracy. “A long-anticipated, but unproved, conception that F0F1 achieves a perfect coupling between transmembrane H+ translocation and ATP synthesis/hydrolysis has direct experimental evidence now,” they conclude.
How is this even possible? Isn’t there slippage? Isn’t there twisting force of torque as the camshaft presses against the β subunits in F1? And what about other versions of ATP synthase in other organisms that have 8, 12, or 14 c subunits in F0? They address these questions in the final paragraph of the Discussion:
In a thermodynamic view, the perfect coupling means perfect energy conversions between chemiosmotic (H+ translocation), mechanical (rotary motion), and chemical energy (ATP synthesis/hydrolysis). A near-perfect energy conversion from ATP hydrolysis to rotary motion of γ-subunit in F1 was recently demonstrated in a thermodynamically defined manner, and this study predicts that other conversions should also be highly efficient. In a mechanistic view, the perfect coupling means that there is no slippage within and between F0 motor and F1 motor. Atomic structures of F1 are convincing that rotary motion of the γ-subunit could not occur without conformation change of the catalytic subunits. Structural basis for rotation of F0 motor without slippage has been suggested recently by atomic structures of whole F0F1 revealed by cryoelectron microscopy. The connection of the two motors should also be strong enough to endure the twisting force of torque. Crystal structures of F1·c-ring complexes indicate that the connection appears to be held by a small number of interactions between the bottom portion of F1’s rotor and polar loops in the c ring. Interestingly, this connection must be versatile, because the chimera TF0F1 with replaced F0 from Propionegenium modestum that has 11 c subunits shows good coupled activity.
This is a remarkable thing. Perfect — yet versatile! You can substitute a different c-ring into F0 and still get “good coupled activity.” Try that with man-made engines!
Other Perfect Scores
Kinesin, the walking machine (see our animation), is another “perfect 10” performer. Like ATP synthase, it converts chemical energy into mechanical energy. It even has what scientists call a “power stroke” as it walks. Tomonami Sumi from Okayama University in Japan compared the machine’s walking efficiency to its ATP consumption. Publishing in Nature Scientific Reports, he found that “the ratio of the number of ATP hydrolysis to the number of steps advanced suggests a tight coupling between the two.” Tight coupling; we heard that in the previous story. Although he doesn’t use the word perfect, he speaks admiringly of the “extraordinary motor properties” of kinesin. It appears that the Japanese are less inhibited about using the d-word design. Sumi’s title is, “Design principles governing chemomechanical coupling of kinesin.”
Cohesin and condensing are proteins that help keep DNA organized. An interesting article written like a mystery story in Nature News shows how scientists are trying to figure out if they work like motors. Writer Elie Dolgin calls it “DNA’s secret weapon against knots and tangles.” Something is seen extruding loops in DNA, working to “keep local regions of DNA together, disentangling them from other parts of the genome and even giving shape and structure to the chromosomes.” But whatever it is, it has to be beyond belief if MIT biophysicist Leonid Mirny’s model is correct:
For one thing, the identity of the molecular machine that forms the loops remains a mystery. If the leading protein candidate acted like a motor, as Mirny proposes, it would guzzle energy faster than it has ever been seen to do. “As a physicist friend of mine tells me, ‘This is kind of the Higgs boson of your field’,” says Mirny; it explains one of the deepest mysteries of genome biology, but could take years to prove.
The race is on to discover what kind of motor is consuming ATP to push and pull DNA. Loop extrusion not only prevents knots and tangles, it regulates gene expression by keeping parts of genes in proximity. We expect this mystery will have a “perfect” ending.
Lastly, that familiar icon the bacterial flagellum shows a new trick up its sleeve. How does the driveshaft know when to stop growing? A paper in Science shows that the “most efficient machine in the universe,” as Howard Berg calls it, has a perfect solution: it grows till it touches the periplasm (outer membrane layer). As we marvel at the engineering, let’s give evolution the credit, shall we?
The bacterial flagellum exemplifies a system where even small deviations from the highly regulated flagellar assembly process can abolish motility and cause negative physiological outcomes. Consequently, bacteria have evolved elegant and robust regulatory mechanisms to ensure that flagellar morphogenesis follows a defined path, with each component self-assembling to predetermined dimensions. The flagellar rod acts as a driveshaft to transmit torque from the cytoplasmic rotor to the external filament. The rod self-assembles to a defined length of ~25 nanometers. Here, we provide evidence that rod length is limited by the width of the periplasmic space between the inner and outer membranes. The length of Braun’s lipoprotein determines periplasmic width by tethering the outer membrane to the peptidoglycan layer.
Science Daily adds, “To function properly and propel the bacterium, the flagellum requires all of its components to fit together to exacting measurements.” The growing “driveshaft” somehow feels the outer layer and knows to stop growing. “The rod needs to touch the inside of the outer membrane,” one of the authors says. “So, if the outer membrane is farther away, the rod has to grow there to meet it.” The versatile growth process yields a perfect fit.
If you can think of any machine in your experience that is perfect yet flexible, it probably did not come about through blind, aimless natural processes. Let’s stop allowing Darwinians to get away, unchallenged, with saying they “have evolved” to perfection.
Monday, 8 May 2017
An extrapolation revisited. III
The Nylonase Story: The Information Enigma
Ann Gauger
Editor’s note: Nylon is a modern synthetic product used in the manufacturing, most familiarly, of ladies’ stockings but also a range of other goods, from rope to parachutes to auto tires. Nylonase is a popular evolutionary icon, brandished by theistic evolutionist Dennis Venema among others. In a series of three posts, of which this is the third, Discovery Institute biologist Ann Gauger takes a closer look. Look here for the first and second posts.
Returning to the story of the nylonase gene and the problem of where new information comes from, I’d like to make the point that there is a reason that molecular geneticist and evolutionary biologist Susumu Ohno made his hypothesis about a frame-shift having produced nylonase. Ohno is famous for his hypothesis that gene duplication and recruitment are the chief means by which “new” proteins are made — he wrote a famous book about it.
But he also knew that copying and tinkering weren’t enough, that there had to be a way to generate genuine de novo information, brand new coding sequence for genuinely new proteins, in order to account for all the diversity of information that must have been necessary as life became more complex. New proteins had to come from somewhere.
Ohno had an idea. He thought coding sequences made up of oligomeric repeats might allow there to be several alternate ways to read the same sequence. For an explanation of alternate reading frames, see my earlier post, “The Nylonase Story: How Unusual Is That?”
As a potential example, Ohno proposed nylB, the gene for nylonase. This gene has certain characteristics that make it plausible that a frameshift could have occurred, characteristics I described in that second post in this series, such as nylB’s sequence being GC-rich and deficient in TAs. These two characteristics reduce the chances of having stop codons, in any frame.
Ohno thus proposed that nylonase arose after a frameshift mutation in a perhaps nonfunctional, prior-coding sequence, resulting in an entirely new coding sequence with nylonase activity. The only reason Ohno could make this proposal was because nylB, the gene that codes for nylonase, has at least two potential open reading frames in the forward direction — the hypothetical “original” one proposed by Ohno from before any hypothetical T insertion took place, and the actual one that codes for nylonase now.
Ohno published his paper in 1984. In 1992, Yomo et al . noticed that one frame in the antisense direction of nylonase has no stop codons either. It also lacks a start codon, though, so Yomo et al. called it a non-stop frame (NSF) instead of an open reading frame (ORF). The probability of finding a DNA sequence with an ORF on the sense strand and a full NSF on the antisense strand are small. But surprisingly, not only does nylB have an NSF on the antisense stand, nylB has another fully overlapping NSF in the forward direction. That’s two NSFs plus the actual ORF for nylonase (I’m not counting the hypothetical frame-shifted “original” ORF, since that frame actually has several intervening stops. (See “The Nylonase Story: When Facts and Imagination Collide.”) That means nylB has no stop codons in three out of six frames.
The chances of avoiding a stop codon in three out of six frames are very low. Our simulation (described in the previous post) showed that the probability is very small indeed. For an ORF 900 nucleotides long to have two NSFs at 70 percent GC is 9 out of 28,603 or .0003. (See there for details.) If these figures are recast to include the total number of random trials required to get an ORF of the proper length and GC content in the first place, and then with two NSFs, then the probability would be nine out of ten million trials, or 0.0000009. No organisms have ten million genes (we only have about twenty thousand), and Flavobacterium certainly doesn’t. But it’s not outside the realm of possibility that such sequences should exist by pure chance somewhere. After all, nylB does. But take the following into consideration.
In addition, beyond the first appearance of such a sequence, there would also need to be some way to prevent random mutation from introducing any stop codons over evolutionary time, in any of the three open frames. Purifying selection would normally be invoked in such a case. Organisms that develop harmful mutations in genes that encode functional gene products — things that are important for the organism’s survival — are less successful at reproducing, and so organisms carrying harmful mutations tend to disappear from the population (they are sickly or dead). However, purifying selection by definition has no effect on non-functional sequences. The fact that stops are prevented from accumulating in nylB NSFs implies that all three frames are functional. No function has been reported for the NSFs, however. They have no ATGs in the vicinity and so may be non-coding (though it must be acknowledged there are alternate start codons in the vicinity). In addition, it has been reported that the pOAD2 plasmid on which nylB is located is non-essential. It can be cleared from its host with no effect, except the loss of the ability to degrade nylon.
One possibility is that nylB has a secondary DNA or RNA-based function that requires its sequence to be nearly completely conserved. It would have to be a very specific sequence requirement to prevent the accumulation of stop codons in three frames, though. We get a hint that the cause is not sequence specificity, because the nylB and nylB′ genes of Flavobacterium differ by 47 amino acids, and the nylB gene of Pseudomonas has only about 35 percent identity according to reports, yet all three lack stops in the anti-sense frames in addition to their coding sequence (based on available sequence information).
Yomo et al., who first reported the anti-sense NSF in nylB, were amazed and puzzled by the existence of anti-sense NSFs in nylB genes of multiple species.
The probability of the presence of these NSFs on the antisense strand of a gene is very small (0.0001-0.0018) [we observed .0001]. In addition, another gene for nylon oligomer degradation [Pseudomonas nylB] was found to have a NSF on its antisense strand, and this gene is phylogenetically independent of the [Flavobacterium] nylB genes. Therefore, the presence of these NSFs is very rare and improbable. Even if the common ancestral gene of the nylB family was originally endowed with an NSF on its antisense strand, the probability of this original NSF persisting in one of its descendants of today is only 0.007. Unless an unknown force was maintaining the NSF, it would have quickly disappeared by random emergences of chain terminators. Therefore, the presence of such rare NSFs on all three antisense strands of the [three member] nylB gene family suggests that there is some special mechanism for protecting these NSFs from mutations that generate the stop codons. Such a mechanism may enable NSFs to evolve into new functional genes and hence seems to be a basic mechanism for the birth of new enzymes. [Emphasis added.]
Later on, they continue:
… the lifetime of a nonessential NSF is very short, and it is impossible for such a NSF to persist for a long period of evolution. Therefore, we strongly suggest that the existence of the NSFs on all the three antisense strands of the nylB gene family points to an unknown force that is preserving these nonessential NSFs; otherwise, they would have quickly disappeared by random emergences of chain terminators.
Ohno himself was aware of this work and in some sense supported it. He was the one who communicated it to the Proceedings of the National Academy of Sciences. What he made of it I don’t know.
The highlighted proposal in the above quotes is on the face of it antithetical to the materialist worldview. What kind of force can preserve apparently non-functional NSFs? Certainly a mechanism to preserve non-functional sequences so that they might some day evolve into functional genes is more suggestive of design than evolution. It would take a fair amount of foresight on the part of evolution, don’t you think, to develop a mechanism to prevent stop codons from interrupting non-functional NSFs, all for some possible future benefit?
All this speaks to the origin and preservation of potential information, information such as Ohno was looking for, but by a means different than he foresaw. We have returned full circle. Explaining nylonase does not require a frameshift, as I have shown in the first post — nonetheless nylonase’s gene is an unusual sequence. Getting overlapping code in three frames might happen in very rare circumstances, but keeping the NSFs open in the apparent absence of selection to maintain them would seem to be highly, highly unlikely. So we have extreme rarity piled upon rarity. Bear in mind also, that whatever the peculiar characteristics of the nylB gene sequence, it must also encode a functional, stably folded enzyme, which is another constraint.
Why am I going on and on about nylonase? It has to do with problem of the origin of novelty. Are frameshifts a possible source of new functional information? Might a sequence with alternate frames stay open by chance or be created by chance over evolutionary time? It’s a highly improbable event, but not impossible, I suppose. Might the alternate frames someday be material for frameshifted novel proteins, provided they stay open? They might theoretically be a reservoir for future proteins, but given what we know about the rarity of these kinds of sequences and the rarity of protein folds in sequence space, the possibility of generating an entire new protein fold from a frameshift is extremely, extremely, extremely low, and would depend on a highly unusual starting sequence tailored in advance for a particular functional specificity. In other words it would need to be designed.
In addition, even should such a sequence exist, it would not long persist in the face of neutral evolution. According to neo-Darwinism there is no magic molecular bouncer who throws out inactivating mutations before they can do their damage to a potential gene. Or to use another metaphor, evolution does not bank potentially useful sequences for future use. For it to do so would require foresight, an idea antithetical to evolutionary theory. Thus, any putative frame-shifted sequences that have been shown to have a functional role are better explained by design than by chance and necessity.
Should anyone disagree with my argument above, I’d like to point out that for a long time it was the standard belief among evolutionary biologists (and geneticists) that random sequence could not generate a functional protein. Frameshifted proteins are almost universally disrupted by stop codons (unless they happen to have an NSF or two like nylB). And even if they aren’t interrupted, the new sequence will be unlikely to fold into a stable protein, given the rarity of functional folds in sequence space (see the first post).
As an aside, as one of the curious facts of history, the disruptive properties of frameshift mutations were used to discover the triplet nature of the genetic code. Says Sir F.H.C. Crick in a lecture on the genetic code he gave in 1964:
This [the ability to combine mutations] has enabled us to tackle the question: is it really a group of three that makes up a codon? The basic idea is the following. We are able to pick up mutants which we believe (from the way they behave in various contexts) are not merely the change of one base into another, but are either the addition or a deletion of a base or bases. What happens when you have a genetic message and you put in an extra base? The reading starts from the beginning until it comes to that point and from there onward the whole of the message is read incorrectly, because it is being read out of phase. In fact we find that these [frameshift] mutants are completely inactive — this is one of our bits of evidence that they are what we say they are. You can pick up a number of such mutants and can put them together, by genetic methods, into the same gene. For example you can put together two of them. Such a gene would be read correctly until it reached the first addition, and then it would be out of phase. When the reading came to the second addition it would [be] read out of phase again, and so the whole of the rest of the message would be read incorrectly. Now it so happens that the left-hand end of this gene is not terribly important for its function. We can actually delete it and the gene will work after a fashion. In this region we have constructed, by genetic methods, a triple mutant, using three mutants all of the same type, and we have found that the gene will nevertheless function fairly normally.
This result is really very striking. Each of the three different faults, used singly, will knock out the gene. You can put them together in pairs in any combination you like, but then the gene is still quite inactive. Put all three in the same gene and the function comes back. We have been able to do this with a number of distinct combinations of three mutants (Crick et al., 1961).
Crick and others found that when three single base frameshift mutations of a particular gene, each completely disruptive on its own, were combined into the same gene, the three insertions together restored the frame enough for the protein to function again! Hence the code must be based on threes.
The sheer improbability of getting a functional enzyme from frameshifted random sequence has been the accepted view for a long time. It is only recently, in the era of big genomic data, that it has begun to be accepted that new proteins do occasionally arise by frame-shift mutation. The reason? It’s because we find examples in the genome that appear to be products of such events, based on sequence comparisons.
The proteins apparently affected by such frameshifts in the genome are often transcription factors or membrane proteins involved in gene regulation. The apparent frameshift often affects alternative splicing and changes the coding sequence over an exon or so; alternatively, the frameshift affects the end of the protein, resulting in truncation. The fact that such a mutation is located near the protein’s end reduces the amount of disruption to the protein. Many such mutations have been documented to cause disease, however. For a demonstration, just use Google Scholar to search for “frameshift.”
At this point, the chief question that should be in everyone’s mind is, “Can evolution by neo-Darwinian means produce new functional information from frame-shifted sequence? Or are other explanations more likely?”
It boils down to this. Do we say that frameshifted functional proteins are easy to generate, because after all, they exist? Or do we acknowledge that such proteins are not easy to generate and so may be evidence for design?
To reiterate, it used to be standard knowledge that frameshift mutations were always bad. Disruptive. So, for example:
More radical mutational events, such as insertions and deletions that change the reading frame — frameshift mutations — are generally considered to be detrimental (e.g. by causing nonfunctional transcripts and/or proteins, through premature stop codons) and of little evolutionary importance, because they seriously alter the sequence and structure of the protein.
But now it has become popular to offer frameshifts as a quick way to get novelty. I am pretty sure it all began with Ohno, who said:
It has recently occurred to me that the gene started from oligomeric repeats at its certain stage of degeneracy (base sequence diversification) [nylB] can specify a truly unique protein from its alternative open reading frame.
Now the meme has spread. From the Abstract of a paper documenting the “Frequent appearance of novel protein-coding sequences by frameshift translation,” we hear that “Major novelties can potentially be introduced by frameshift mutations and this idea can explain the creation of novel proteins.” And how do they defend the possibility of a functional frameshift? “Some cases of recent evolution of new genes via frameshift have been reported. For example, in bacteria the sudden birth of an enzyme that degrades manmade nylon oligomers was explained by a frameshift translation of a preexisting coding sequence.”
Sigh. The record needs to be corrected. (See my first post, “The Nylonase Story: Where Fact and Imagination Collide.”)
Let us close by considering the nature of the argument being made concerning proposed frameshifts. The fact concerning such proposed frameshifts is that there are sequence similarities between two stretches of DNA, where one part appears to be frameshifted with respect to the other.
Notice that the argument used to explain the appearance of novel genes by frameshift uses a form of inference known as abduction, where one reasons from present effects to past causes.
The surprising fact A is observed.
If B were true, then A would be a matter of course.
Hence, there is reason to suspect that B is true.1
In other words:
The surprising fact of novel genes apparently arising by frameshift is observed.
If it is easy to get new functions from random sequence, then it is a matter of course that frameshifts can produce functional proteins.
Hence it is easy to get new functional proteins from random sequences
Abductive arguments are very weak. The problem is that there can be multiple competing causes that explain the observed effects. The only way to strengthen the argument is to rule out all other competing causes. And design is a particularly strong competing hypothesis. We know design is a cause capable of producing the effect in question, namely the generation of new functional proteins by the addition of frame-shifted code. In fact, given what we know about the rarity of functional proteins in sequence space, as demonstrated experimentally here, here, and here, and theoretically here, design is a better explanation than the neo-Darwinian one.
Until someone demonstrates experimentally, in real time, that a frameshift mutation can generate a new functional protein (not just a loss of function) by undirected processes, the inference that it is easy to do so is unjustified. And nylonase is not that demonstration.2
References:
(1) Stephen C. Meyer, Of Clues and Causes: A Methodological Interpretation of Origin of Life Studies. PhD dissertation (Cambridge: Cambridge University, 1990).
Charles S. Peirce, “Abduction and Induction,” In The Philosophy of Peirce, edited by J. Buchler (London: Routledge, 1956), 150–154. Charles S. Peirce, Collected Papers, edited by Charles Hartshorne and P. Weiss. 6 vols. (Cambridge, MA: Harvard University Press, 1931–1935).
(2) In a future post, I will discuss experiments that attempt to demonstrate that random sequence can perform simple functions.
Ann Gauger
Editor’s note: Nylon is a modern synthetic product used in the manufacturing, most familiarly, of ladies’ stockings but also a range of other goods, from rope to parachutes to auto tires. Nylonase is a popular evolutionary icon, brandished by theistic evolutionist Dennis Venema among others. In a series of three posts, of which this is the third, Discovery Institute biologist Ann Gauger takes a closer look. Look here for the first and second posts.
Returning to the story of the nylonase gene and the problem of where new information comes from, I’d like to make the point that there is a reason that molecular geneticist and evolutionary biologist Susumu Ohno made his hypothesis about a frame-shift having produced nylonase. Ohno is famous for his hypothesis that gene duplication and recruitment are the chief means by which “new” proteins are made — he wrote a famous book about it.
But he also knew that copying and tinkering weren’t enough, that there had to be a way to generate genuine de novo information, brand new coding sequence for genuinely new proteins, in order to account for all the diversity of information that must have been necessary as life became more complex. New proteins had to come from somewhere.
Ohno had an idea. He thought coding sequences made up of oligomeric repeats might allow there to be several alternate ways to read the same sequence. For an explanation of alternate reading frames, see my earlier post, “The Nylonase Story: How Unusual Is That?”
As a potential example, Ohno proposed nylB, the gene for nylonase. This gene has certain characteristics that make it plausible that a frameshift could have occurred, characteristics I described in that second post in this series, such as nylB’s sequence being GC-rich and deficient in TAs. These two characteristics reduce the chances of having stop codons, in any frame.
Ohno thus proposed that nylonase arose after a frameshift mutation in a perhaps nonfunctional, prior-coding sequence, resulting in an entirely new coding sequence with nylonase activity. The only reason Ohno could make this proposal was because nylB, the gene that codes for nylonase, has at least two potential open reading frames in the forward direction — the hypothetical “original” one proposed by Ohno from before any hypothetical T insertion took place, and the actual one that codes for nylonase now.
Ohno published his paper in 1984. In 1992, Yomo et al . noticed that one frame in the antisense direction of nylonase has no stop codons either. It also lacks a start codon, though, so Yomo et al. called it a non-stop frame (NSF) instead of an open reading frame (ORF). The probability of finding a DNA sequence with an ORF on the sense strand and a full NSF on the antisense strand are small. But surprisingly, not only does nylB have an NSF on the antisense stand, nylB has another fully overlapping NSF in the forward direction. That’s two NSFs plus the actual ORF for nylonase (I’m not counting the hypothetical frame-shifted “original” ORF, since that frame actually has several intervening stops. (See “The Nylonase Story: When Facts and Imagination Collide.”) That means nylB has no stop codons in three out of six frames.
The chances of avoiding a stop codon in three out of six frames are very low. Our simulation (described in the previous post) showed that the probability is very small indeed. For an ORF 900 nucleotides long to have two NSFs at 70 percent GC is 9 out of 28,603 or .0003. (See there for details.) If these figures are recast to include the total number of random trials required to get an ORF of the proper length and GC content in the first place, and then with two NSFs, then the probability would be nine out of ten million trials, or 0.0000009. No organisms have ten million genes (we only have about twenty thousand), and Flavobacterium certainly doesn’t. But it’s not outside the realm of possibility that such sequences should exist by pure chance somewhere. After all, nylB does. But take the following into consideration.
In addition, beyond the first appearance of such a sequence, there would also need to be some way to prevent random mutation from introducing any stop codons over evolutionary time, in any of the three open frames. Purifying selection would normally be invoked in such a case. Organisms that develop harmful mutations in genes that encode functional gene products — things that are important for the organism’s survival — are less successful at reproducing, and so organisms carrying harmful mutations tend to disappear from the population (they are sickly or dead). However, purifying selection by definition has no effect on non-functional sequences. The fact that stops are prevented from accumulating in nylB NSFs implies that all three frames are functional. No function has been reported for the NSFs, however. They have no ATGs in the vicinity and so may be non-coding (though it must be acknowledged there are alternate start codons in the vicinity). In addition, it has been reported that the pOAD2 plasmid on which nylB is located is non-essential. It can be cleared from its host with no effect, except the loss of the ability to degrade nylon.
One possibility is that nylB has a secondary DNA or RNA-based function that requires its sequence to be nearly completely conserved. It would have to be a very specific sequence requirement to prevent the accumulation of stop codons in three frames, though. We get a hint that the cause is not sequence specificity, because the nylB and nylB′ genes of Flavobacterium differ by 47 amino acids, and the nylB gene of Pseudomonas has only about 35 percent identity according to reports, yet all three lack stops in the anti-sense frames in addition to their coding sequence (based on available sequence information).
Yomo et al., who first reported the anti-sense NSF in nylB, were amazed and puzzled by the existence of anti-sense NSFs in nylB genes of multiple species.
The probability of the presence of these NSFs on the antisense strand of a gene is very small (0.0001-0.0018) [we observed .0001]. In addition, another gene for nylon oligomer degradation [Pseudomonas nylB] was found to have a NSF on its antisense strand, and this gene is phylogenetically independent of the [Flavobacterium] nylB genes. Therefore, the presence of these NSFs is very rare and improbable. Even if the common ancestral gene of the nylB family was originally endowed with an NSF on its antisense strand, the probability of this original NSF persisting in one of its descendants of today is only 0.007. Unless an unknown force was maintaining the NSF, it would have quickly disappeared by random emergences of chain terminators. Therefore, the presence of such rare NSFs on all three antisense strands of the [three member] nylB gene family suggests that there is some special mechanism for protecting these NSFs from mutations that generate the stop codons. Such a mechanism may enable NSFs to evolve into new functional genes and hence seems to be a basic mechanism for the birth of new enzymes. [Emphasis added.]
Later on, they continue:
… the lifetime of a nonessential NSF is very short, and it is impossible for such a NSF to persist for a long period of evolution. Therefore, we strongly suggest that the existence of the NSFs on all the three antisense strands of the nylB gene family points to an unknown force that is preserving these nonessential NSFs; otherwise, they would have quickly disappeared by random emergences of chain terminators.
Ohno himself was aware of this work and in some sense supported it. He was the one who communicated it to the Proceedings of the National Academy of Sciences. What he made of it I don’t know.
The highlighted proposal in the above quotes is on the face of it antithetical to the materialist worldview. What kind of force can preserve apparently non-functional NSFs? Certainly a mechanism to preserve non-functional sequences so that they might some day evolve into functional genes is more suggestive of design than evolution. It would take a fair amount of foresight on the part of evolution, don’t you think, to develop a mechanism to prevent stop codons from interrupting non-functional NSFs, all for some possible future benefit?
All this speaks to the origin and preservation of potential information, information such as Ohno was looking for, but by a means different than he foresaw. We have returned full circle. Explaining nylonase does not require a frameshift, as I have shown in the first post — nonetheless nylonase’s gene is an unusual sequence. Getting overlapping code in three frames might happen in very rare circumstances, but keeping the NSFs open in the apparent absence of selection to maintain them would seem to be highly, highly unlikely. So we have extreme rarity piled upon rarity. Bear in mind also, that whatever the peculiar characteristics of the nylB gene sequence, it must also encode a functional, stably folded enzyme, which is another constraint.
Why am I going on and on about nylonase? It has to do with problem of the origin of novelty. Are frameshifts a possible source of new functional information? Might a sequence with alternate frames stay open by chance or be created by chance over evolutionary time? It’s a highly improbable event, but not impossible, I suppose. Might the alternate frames someday be material for frameshifted novel proteins, provided they stay open? They might theoretically be a reservoir for future proteins, but given what we know about the rarity of these kinds of sequences and the rarity of protein folds in sequence space, the possibility of generating an entire new protein fold from a frameshift is extremely, extremely, extremely low, and would depend on a highly unusual starting sequence tailored in advance for a particular functional specificity. In other words it would need to be designed.
In addition, even should such a sequence exist, it would not long persist in the face of neutral evolution. According to neo-Darwinism there is no magic molecular bouncer who throws out inactivating mutations before they can do their damage to a potential gene. Or to use another metaphor, evolution does not bank potentially useful sequences for future use. For it to do so would require foresight, an idea antithetical to evolutionary theory. Thus, any putative frame-shifted sequences that have been shown to have a functional role are better explained by design than by chance and necessity.
Should anyone disagree with my argument above, I’d like to point out that for a long time it was the standard belief among evolutionary biologists (and geneticists) that random sequence could not generate a functional protein. Frameshifted proteins are almost universally disrupted by stop codons (unless they happen to have an NSF or two like nylB). And even if they aren’t interrupted, the new sequence will be unlikely to fold into a stable protein, given the rarity of functional folds in sequence space (see the first post).
As an aside, as one of the curious facts of history, the disruptive properties of frameshift mutations were used to discover the triplet nature of the genetic code. Says Sir F.H.C. Crick in a lecture on the genetic code he gave in 1964:
This [the ability to combine mutations] has enabled us to tackle the question: is it really a group of three that makes up a codon? The basic idea is the following. We are able to pick up mutants which we believe (from the way they behave in various contexts) are not merely the change of one base into another, but are either the addition or a deletion of a base or bases. What happens when you have a genetic message and you put in an extra base? The reading starts from the beginning until it comes to that point and from there onward the whole of the message is read incorrectly, because it is being read out of phase. In fact we find that these [frameshift] mutants are completely inactive — this is one of our bits of evidence that they are what we say they are. You can pick up a number of such mutants and can put them together, by genetic methods, into the same gene. For example you can put together two of them. Such a gene would be read correctly until it reached the first addition, and then it would be out of phase. When the reading came to the second addition it would [be] read out of phase again, and so the whole of the rest of the message would be read incorrectly. Now it so happens that the left-hand end of this gene is not terribly important for its function. We can actually delete it and the gene will work after a fashion. In this region we have constructed, by genetic methods, a triple mutant, using three mutants all of the same type, and we have found that the gene will nevertheless function fairly normally.
This result is really very striking. Each of the three different faults, used singly, will knock out the gene. You can put them together in pairs in any combination you like, but then the gene is still quite inactive. Put all three in the same gene and the function comes back. We have been able to do this with a number of distinct combinations of three mutants (Crick et al., 1961).
Crick and others found that when three single base frameshift mutations of a particular gene, each completely disruptive on its own, were combined into the same gene, the three insertions together restored the frame enough for the protein to function again! Hence the code must be based on threes.
The sheer improbability of getting a functional enzyme from frameshifted random sequence has been the accepted view for a long time. It is only recently, in the era of big genomic data, that it has begun to be accepted that new proteins do occasionally arise by frame-shift mutation. The reason? It’s because we find examples in the genome that appear to be products of such events, based on sequence comparisons.
The proteins apparently affected by such frameshifts in the genome are often transcription factors or membrane proteins involved in gene regulation. The apparent frameshift often affects alternative splicing and changes the coding sequence over an exon or so; alternatively, the frameshift affects the end of the protein, resulting in truncation. The fact that such a mutation is located near the protein’s end reduces the amount of disruption to the protein. Many such mutations have been documented to cause disease, however. For a demonstration, just use Google Scholar to search for “frameshift.”
At this point, the chief question that should be in everyone’s mind is, “Can evolution by neo-Darwinian means produce new functional information from frame-shifted sequence? Or are other explanations more likely?”
It boils down to this. Do we say that frameshifted functional proteins are easy to generate, because after all, they exist? Or do we acknowledge that such proteins are not easy to generate and so may be evidence for design?
To reiterate, it used to be standard knowledge that frameshift mutations were always bad. Disruptive. So, for example:
More radical mutational events, such as insertions and deletions that change the reading frame — frameshift mutations — are generally considered to be detrimental (e.g. by causing nonfunctional transcripts and/or proteins, through premature stop codons) and of little evolutionary importance, because they seriously alter the sequence and structure of the protein.
But now it has become popular to offer frameshifts as a quick way to get novelty. I am pretty sure it all began with Ohno, who said:
It has recently occurred to me that the gene started from oligomeric repeats at its certain stage of degeneracy (base sequence diversification) [nylB] can specify a truly unique protein from its alternative open reading frame.
Now the meme has spread. From the Abstract of a paper documenting the “Frequent appearance of novel protein-coding sequences by frameshift translation,” we hear that “Major novelties can potentially be introduced by frameshift mutations and this idea can explain the creation of novel proteins.” And how do they defend the possibility of a functional frameshift? “Some cases of recent evolution of new genes via frameshift have been reported. For example, in bacteria the sudden birth of an enzyme that degrades manmade nylon oligomers was explained by a frameshift translation of a preexisting coding sequence.”
Sigh. The record needs to be corrected. (See my first post, “The Nylonase Story: Where Fact and Imagination Collide.”)
Let us close by considering the nature of the argument being made concerning proposed frameshifts. The fact concerning such proposed frameshifts is that there are sequence similarities between two stretches of DNA, where one part appears to be frameshifted with respect to the other.
Notice that the argument used to explain the appearance of novel genes by frameshift uses a form of inference known as abduction, where one reasons from present effects to past causes.
The surprising fact A is observed.
If B were true, then A would be a matter of course.
Hence, there is reason to suspect that B is true.1
In other words:
The surprising fact of novel genes apparently arising by frameshift is observed.
If it is easy to get new functions from random sequence, then it is a matter of course that frameshifts can produce functional proteins.
Hence it is easy to get new functional proteins from random sequences
Abductive arguments are very weak. The problem is that there can be multiple competing causes that explain the observed effects. The only way to strengthen the argument is to rule out all other competing causes. And design is a particularly strong competing hypothesis. We know design is a cause capable of producing the effect in question, namely the generation of new functional proteins by the addition of frame-shifted code. In fact, given what we know about the rarity of functional proteins in sequence space, as demonstrated experimentally here, here, and here, and theoretically here, design is a better explanation than the neo-Darwinian one.
Until someone demonstrates experimentally, in real time, that a frameshift mutation can generate a new functional protein (not just a loss of function) by undirected processes, the inference that it is easy to do so is unjustified. And nylonase is not that demonstration.2
References:
(1) Stephen C. Meyer, Of Clues and Causes: A Methodological Interpretation of Origin of Life Studies. PhD dissertation (Cambridge: Cambridge University, 1990).
Charles S. Peirce, “Abduction and Induction,” In The Philosophy of Peirce, edited by J. Buchler (London: Routledge, 1956), 150–154. Charles S. Peirce, Collected Papers, edited by Charles Hartshorne and P. Weiss. 6 vols. (Cambridge, MA: Harvard University Press, 1931–1935).
(2) In a future post, I will discuss experiments that attempt to demonstrate that random sequence can perform simple functions.
Sunday, 7 May 2017
The lessons of recent history wasted on Russia's leadership?
Jehovah's Witnesses Had Foes Before Putin
Russia is reverting to Soviet-era restrictions on religion. But this denomination has survived worse.
By Leonid Bershidsky
Russia is reverting to Soviet-era restrictions on religion. But this denomination has survived worse.
By Leonid Bershidsky
When the Russian Supreme Court banned Jehovah's Witnesses and ordered the confiscation of the denomination's property on Thursday, it wasn't the first time. The faithful were outlaws in the Soviet Union, too, until that country's final year. The stubborn group will fight on -- but the court has delivered another chilling reminder that President Vladimir Putin's Russia is even less free than the USSR was.
Jehovah's Witnesses are a U.S.-based global religious organization, and they often are targeted by authoritarian and belligerent governments because members don't believe in government authority. They don't vote, serve in the military, salute flags or hail leaders. When the Nazis came to power in Germany, the Witnesses wouldn't use the Nazi salute because, according to their beliefs, it amounted to idolatry. Hitler responded by sending more than 10,000 "Bible Students," as they called themselves then, to prisons and concentration camps, where their pacifism particularly inspired torturers.
In the Soviet Union directly after World War II, Witnesses were mostly concentrated in western Ukraine and Transcarpathia, and they had the bad luck to trade Nazi persecution for the equally harsh Stalinist kind. In two secret operations in the late 1940s and early 1950s, the Witnesses were removed to Siberian labor camps. There were only about 10,000 of them then. But adherents of the denomination didn't stop practicing and preaching in exile and in the camps, and when, after Stalin's death, the state stopped systematically imprisoning them and switched to a harassment tactic, the flock started growing.
By January 1991, when President Mikhail Gorbachev's government officially permitted the organization, there were about 45,000 followers in the Soviet Union. They formed one of the most stubborn and resourceful resistance groups that ever existed in the Communist country. Emily Baran wrote in a 2014 book about Soviet Jehovah's Witnesses:
They organized a highly complex underground organization, with its own finances, leadership structures, and internal reporting system that kept careful record of its members' archives. While intellectual dissidents exercised caution in sharing their views with others who could denounce them, Witnesses spoke about their beliefs to complete strangers in an effort to convert them.
The 1990s were a time of unprecedented freedom for the Witnesses in Russia. They converted about 100,000 new members, acquired influence and, in some cities, expensive real estate. But in the early 2000s, after Putin came to power, harassment began anew, with courts regularly banning the Witnesses' regional communities and literature. That became easier with the passage of "anti-extremist laws" that ban the preaching of one religion's advantage over others. Witness literature readily fit the description: They don't just consider themselves the one true faith, but also proudly preach it.
The Witnesses fought the verdicts, sometimes reaching the European Court for Human Rights and winning there. But during Putin's latest presidential term, Russian courts have been encouraged to disregard the ECHR's decisions. Even though the European court is likely to overturn Thursday's Supreme Court ruling once the Witnesses' attempts to appeal reach Strasbourg, the Russian government is likely to stay firm on the ban, initiated by the justice ministry. The next step may be the prosecution of individual Witnesses for continuing to worship and proselytize.
Jehovah's witnesses are in many ways extreme, even though their non-violent creed is hardly "extremist." That makes them a test case for religious freedom: The less liberal and tolerant a country is, the harsher it treats this particular denomination.
Western democracies have struggled to accept Jehovah's Witnesses. At different times, they have faced bans in France, Spain and Canada because of their attitudes to military service and flags. But in recent years, following some protracted legal battles, European countries have come to recognize their right to their beliefs. The European Union has denounced the Russian ban.At the other end of the spectrum, African dictatorial regimes have killed, tortured and driven out Witnesses. A number of Muslim nations have banned them, and so has China. Russia is now positioning itself at the restrictive end of the spectrum, and that augurs ill for other Protestant denominations and smaller religious groups. Like Western non-governmental organizations and members of the news media, which have been driven from Russia in the last four years, these groups represent a fifth column. Perhaps they don't defy the state as openly as Jehovah's Witnesses, but to Putin and his circle they still somehow appear disloyal because of their reluctance to join the big religions that maintain a relationship with the state and are controllable.
Russia has no more patience with openness and tolerance. Putin's regime doesn't care whether it passes any tests on that score. In a way, it's as defiant as the Witnesses, and so far, it's just as resilient. But the Jehovah's Witnesses have been resilient for longer.
Saturday, 6 May 2017
Rated green.
Witnesses Receive Highest Rating by GBI for Sustainable Design of New World Headquarters
NEW YORK—Upon completion of their new world headquarters in August 2016, Jehovah’s Witnesses received official recognition for the sustainable design of their new facility in Warwick, New York. The Green Building Initiative (GBI), an organization which offers environmental assessment and certification programs for commercial buildings, awarded the Witnesses the highest possible rating of Four Green Globes for all seven of their buildings that qualified for consideration.
Shaina Weinstein, senior director of engagement for GBI, states: “Out of 965 projects nationwide, only 64 buildings have received the highest rating of Four Green Globes. For Jehovah’s Witnesses to receive Four Green Globes for all seven of their buildings at Warwick is remarkable. This accomplishment represents a very high level of commitment to water, energy, and environmental efficiency.”The GBI, according to their official website, is “a nonprofit organization dedicated to accelerating the adoption of building practices that result in resource efficient, healthier and environmentally sustainable buildings.” The GBI provides ratings in sustainable design and operation for newly constructed buildings. As part of the rating process, a third-party expert in the field conducts an on-site assessment to verify GBI’s findings.
David Bean, sustainable design coordinator for the Witnesses’ facilities in the United States, comments: “We appreciate these awards, which testify to the dedication of all involved to construct a campus that exemplifies many sustainable design features—a campus that integrates gracefully and appropriately into Sterling Forest State Park.”The Witnesses’ strategy included preserving the trees on the property and incorporating felled trees into the construction project. “I appreciated the decision to mill the trees that were cut down to clear the site and reuse them in the new building designs,” says Jeffrey Hutchinson, former park manager for Sterling Forest. “The environmental aspects of what the Witnesses have done are excellent.” Shaina Weinstein also comments, “In our opinion, the Warwick project exemplifies what environmentally conscious design and construction are all about.”
Richard Devine, who was chairman of the Witnesses’ Warwick Construction Project Committee, explains: “For decades, our organization has maintained the aesthetics of our properties in Brooklyn. Now we look forward to maintaining our eco-friendly facility in Warwick and preserving the existing beauty of Sterling Forest.”
Media Contact:
David A. Semonian, Office of Public Information, 1-845-524-3000
5 Reasons that justify an impartial investigation of the bible.
1. Historical Soundness
It would be hard to trust a book that is found to contain inaccuracies. Imagine reading a modern history book that dated the second world war to the 1800’s or that called the president of the United States a king. Would such inaccuracies not raise questions in your mind about the overall reliability of the book?
NO ONE has ever successfully challenged the historical accuracy of the Bible. It refers to real people and real events.
People.
Bible critics questioned the existence of Pontius Pilate, the Roman governor of Judea who handed Jesus over to be impaled. (Matthew 27:1-26) Evidence that Pilate was once ruler of Judea is etched on a stone discovered at the Mediterranean seaport city of Caesarea in 1961.
Before 1993, there was no proof outside the Bible to support the historicity of David, the brave young shepherd who later became king of Israel. That year, however, archaeologists uncovered in northern Israel a basalt stone, dated to the ninth century B.C.E., that experts say bears the words “House of David” and “king of Israel.”
Events.
Until recently, many scholars doubted the accuracy of the Bible’s account of the nation of Edom battling with Israel in the time of David. (2 Samuel 8:13, 14) Edom, they argued, was a simple pastoral society at the time and did not become sufficiently organized or have the might to threaten Israel until much later. However, recent excavations indicate that “Edom was a complex society centuries earlier [than previously thought], as reflected in the Bible,” states an article in the journal Biblical Archaeology Review.
Proper titles.
There were many rulers on the world stage during the 16 centuries that the Bible was being written. When the Bible refers to a ruler, italways uses the proper title. For example, it correctly refers to Herod Antipas as “district ruler” and Gallio as “proconsul.” (Luke 3:1; Acts 18:12) Ezra 5:6 refers to Tattenai, the governor of the Persian province “beyond the River,” the Euphrates River. A coin produced in the fourth century B.C.E. contains a similar description, identifying the Persian governor Mazaeus as ruler of the province “Beyond the River.”
Accuracy in seemingly minor details is no small matter. If we can trust the Bible writers in even small details, should that not bolster our confidence in the other things they wrote?
2. Candor and Honesty
Honesty provides the foundation for trust. A man who has a reputation for honesty may win your trust, but if he lies to you even once, he may lose it.
THE Bible writers were honest men who wrote with openness of heart. Their candor gives their writing the clear ring of truth.
Mistakes and shortcomings.
The Bible writers openly admitted their own failures and weaknesses. Moses told of a mistake he made that cost him dearly. (Numbers 20:7-13) Asaph explained that for a time he found himself envying the prosperous life of the wicked. (Psalm 73:1-14) Jonah told of his disobedience and the bad attitude he initially had when God showed mercy to repentant sinners. (Jonah 1:1-3; 3:10; 4:1-3) Matthew freely related that he had abandoned Jesus on the night of Jesus’ arrest.—Matthew 26:56.
Bible writers, such as Jonah, recorded their own mistakes
The writers of the Hebrew Scriptures laid bare the repeated grumbling and rebellion of their own people. (2 Chronicles 36:15, 16) The writers spared no one, not even the rulers of their nation. (Ezekiel 34:1-10) With similar candor, the letters of the apostles reported the serious problems experienced by individual Christians, including responsible ones, as well as by some congregations in the first century C.E.—1 Corinthians 1:10-13; 2 Timothy 2:16-18; 4:10.
Unflattering truth.
The Bible writers did not try to gloss over what some might have viewed as embarrassing truth. The first-century Christians frankly acknowledged that they were not admired by the world around them but were looked upon as foolish and ignoble. (1 Corinthians 1:26-29) The writers noted that Jesus’ apostles were seen as “unlettered and ordinary.”—Acts 4:13.
The Gospel writers did not color the facts in order to cast Jesus in a more favorable light. Rather, they reported honestly that he was born under humble circumstances into a working-class family, that he did not study at the prestigious schools of his day, and that the majority of his listeners rejected his message.—Matthew 27:25; Luke 2:4-7; John 7:15.
Clearly, the Bible gives ample evidence that it is the product of honest writers. Does their honesty win your trust?
3. Internal Harmony
Imagine asking 40 men from varied backgrounds to write a book, each writing a section. The writers live in a number of lands and do not all know one another. Some do not know what the others have written. Would you expect a book thus produced to be harmonious?
THE Bible is such a book.
* Written under even more unusual conditions than those described above, its internal harmony is nothing less than profound.
Was Jesus’ garment purple or scarlet?
Unique circumstances.
The Bible was written over a span of some 1,600 years, from 1513 B.C.E. to about 98 C.E. Many of the approximately 40 writers thus lived centuries apart. Their occupations were varied. Some were fishermen, others were shepherds or kings, and one was a physician.
A harmonious message.
The Bible penmen developed one central theme: the vindication of God’s right to rule mankind and the fulfillment of his purpose by means of his heavenly Kingdom, a world government. That theme is introduced in Genesis, expanded on in the books that follow, and brought to a climax in Revelation.—See “What Is the Bible About?” on page 19.
Agreement on details.
The Bible writers agreed on even minute details, but often this harmony was clearly unintentional. Note an example. The Bible writer John tells us that when a large crowd came to hear Jesus, Jesus specifically asked Philip where to buy some loaves to feed the people. (John 6:1-5) In a parallel account, Luke says that this took place near the city of Bethsaida. Earlier in his book, John happened to have said that Philip was from Bethsaida. (Luke 9:10; John 1:44) So Jesus naturally addressed his question to one of the men who had lived nearby. The details agree—but with an obvious lack of intent to make them harmonious.
Reasonable differences.
There are some differences between certain accounts, but should we not expect this? Suppose a group of people witnessed a crime. If each one mentioned the same details using the same words, would you not suspect collusion? Reasonably, the testimony of each would vary somewhat according to his particular angle of view. So it was with the Bible writers.
Consider an example. Did Jesus wear a purple garment on the day of his death, as Mark and John report? (Mark 15:17; John 19:2) Or was itscarlet, as Matthew says? (Matthew 27:28) Really, both can be correct. Purple has components of red in it. Depending on the observer’s angle of view, light reflection and background could have subdued certain hues, giving different casts to the garment.
The harmony of the Bible writers, including their unintentional consistency, further stamps their writings as trustworthy.
4. Scientific Accuracy
Science has made great strides in modern times. As a result, old theories have given way to new ones. What was once accepted as fact may now be seen as myth. Science textbooks often need revision.
THE Bible is not a science textbook. Yet, when it comes to scientific matters, the Bible is noteworthy not only for what it says but also for what it does not say.
Free of unscientific views.
Many mistaken beliefs gained wide acceptance in ancient times. Views about the earth ranged from the idea that it was flat to the notion that tangible substances or objects held it aloft. Long before science learned about the spread and prevention of disease, physicians employed some practices that were ineffective at best, lethal at worst. But not once in its more than 1,100 chapters does the Bible endorseany unscientific views or harmful practices.
Far ahead of its time, the Bible correctly stated that the earth is circular and hangs “upon nothing”
Scientifically sound statements.
Some 3,500 years ago, the Bible stated that the earth is hanging “upon nothing.” (Job 26:7) In the eighth century B.C.E., Isaiah clearly referred to “the circle [or, sphere] of the earth.” (Isaiah 40:22) A spherical earth held in empty space without any visible or physical means of support—does not that description sound remarkably modern?
Written about 1500 B.C.E., the Mosaic Law (found in the first five books of the Bible) contained sound laws regarding quarantining of the sick, treatment of dead bodies, and disposal of waste.—Leviticus 13:1-5; Numbers 19:1-13; Deuteronomy 23:13, 14.
Partly as a result of turning powerful telescopes toward the heavens, scientists have concluded that the universe had a sudden “birth.” Not all scientists like the implications of this explanation. One professor noted: “A universe that began seems to demand a first cause; for who could imagine such an effect without a sufficient cause?” Yet, long before telescopes, the very first verse of the Bible plainly stated: “In the beginning God created the heavens and the earth.”—Genesis 1:1.
Even though it is an ancient book and touches on many subjects, the Bible contains no scientific inaccuracies. Does not such a book merit, at the very least, our consideration?
5. Fulfilled Prophecy
Imagine a weather forecaster who has a long record of being right—every time. If he predicted rain, would you carry an umbrella?
THE Bible is filled with predictions, or prophecies.
Distinguishing features.
Bible prophecies are often specific and have been fulfilled down to the smallest of details. They usually involve matters of great importance and predict the opposite of what those living at the time of the writing might have been expecting.
An outstanding example.
Strategically built astride the Euphrates River, ancient Babylon has been called “the political, religious, and cultural centre of the ancient Orient.” About 732 B.C.E., the prophet Isaiah penned an ominous prophecy—Babylon would fall. Isaiah provided specifics: A leader named “Cyrus” would be the conqueror, the protective waters of the Euphrates would “dry up,” and the city’s gates would “not be shut.” (Isaiah 44:27–45:3) Some 200 years later, on October 5, 539 B.C.E., the prophecy was fulfilled in all its details. Greek historian Herodotus (fifth century B.C.E.) confirmed the manner of Babylon’s fall.
The Bible accurately foretold that a leader named Cyrus would conquer mighty Babylon
A bold detail.
Isaiah made a further startling prediction regarding Babylon: “She will never be inhabited.” (Isaiah 13:19, 20) To predict permanent desolation for a sprawling city occupying a strategic location was bold indeed. You would normally expect that such a city would be rebuilt if ruined. Although Babylon lingered on for a while after its conquest, Isaiah’s words eventually came true. Today the site of ancient Babylon “is flat, hot, deserted and dusty,” reports Smithsonian magazine.
It is awesome to contemplate the magnitude of Isaiah’s prophecy. What he foretold would be the equivalent of predicting the exact manner in which a modern city, such as New York or London, would be destroyed 200 years from now and then emphatically stating that itwould never again be inhabited. Of course, most remarkable is the fact that Isaiah’s prophecy came true!
In this series of articles, we have considered some of the evidence that has convinced millions of people that the Bible is trustworthy. They therefore look to it as a reliable guide to direct their steps. Why not learn more about the Bible so that you can decide for yourself whether you too can trust it?
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