Dual coding genes in the dock for design

Dual-Coding Genes "Nearly Impossible by Chance" -- How Would Francisco Ayala Respond.
Casey Luskin

We mortals are easily impressed by palindromes -- words or phrases that have the same spelling forwards and backwards. But try writing a sentence which has two different meanings: One meaning is gained when you start with one letter of the first word, and then an entirely different meaning is understood when you start reading with the second letter of the first word. Such a sentence would be most impressive, but what if such "sentences" existed in our DNA?

Leading evolutionary biologist Francisco Ayala recently wrote in Proceedings for the National Academy of Sciences (PNAS) that "Chance is an integral part of the evolutionary process." Ayala then explained why he thinks Darwinian evolution is right and ID is wrong: "Biological evolution differs from a painting or an artifact in that it is not the outcome of preconceived design. The design of organisms is not intelligent but imperfect and, at times, outright dysfunctional." ("Darwin's greatest discovery: Design without designer," PNAS, 104:8567--8573 (May 15, 2007), emphasis added.) This questionable standard and conclusion is Ayala's punchline against ID.

What, then, does Ayala think of organisms whose design is intelligent and highly functional? A recent article in Public Library of Science discussed how dual-coding genes -- genes which overlap and code for multiple proteins when read through different reading frames -- are "hallmarks of fascinating biology" and "nearly impossible by chance" to the extent that evolutionary biologists have held "skepticism surrounding" their very existence. Now it seems they do exist, and they don't quite match Ayala's vision of biology, where "[c]hance is an integral part" of the "design of organisms is "dysfunctional" and "not intelligent." As the article, "A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes," states:

Coding of multiple proteins by overlapping reading frames is not a feature one would associate with eukaryotic genes. Indeed, codependency between codons of overlapping protein-coding regions imposes a unique set of evolutionary constraints, making it a costly arrangement. Yet in cases of tightly coexpressed interacting proteins, dual coding may be advantageous. Here we show that although dual coding is nearly impossible by chance, a number of human transcripts contain overlapping coding regions. Using newly developed statistical techniques, we identified 40 candidate genes with evolutionarily conserved overlapping coding regions. Because our approach is conservative, we expect mammals to possess more dual-coding genes. Our results emphasize that the skepticism surrounding eukaryotic dual coding is unwarranted: rather than being artifacts, overlapping reading frames are often hallmarks of fascinating biology.
(Wen-Yu Chung, Samir Wadhawan, Radek Szklarczyk, Sergei Kosakovsky Pond, Anton Nekrutenko, "A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes," PLOS Computational Biology, Vol. 3(5) (May, 2007), emphasis added.)


Does this sound like a "dysfunctional" process that is "not intelligent" in its design?

Predarwinian tech for design.

Rotary Engine Technology in Living Cells
Evolution News & Views

Gone are the days when evolutionists asserted that life would never produce wheels or gears. It was impossible, they thought, for structures like that to arrive by natural selection, because too many coordinated mutations would be required. A wheel without an axle would provide no fitness advantage. One gear could achieve nothing without a matching gear. That was before we learned about the planthopper with its gear-driven jumping feet and the exquisite rotary engines of cells: the bacterial flagellum and the ATP synthase motor, on which all life depends.


Since ATP synthase earned its discoverers a Nobel Prize in 1997, it has remained an object of fascination. New imaging techniques have been steadily improving the focus on these miniature rotary motors that measure a mere 20 x 10 nanometers (billionths of a meter) yet spin at up to 42,000 rpm (see here), generating 3 ATP per revolution. As some years have passed since we discussed these motors in detail, readers may wish to pause to refresh their memories with our video about these amazing machines before learning about some new discoveries:





The Glue-bricator

Even at their tiny scale, molecular motors have to deal with laws of physics that might limit their efficiency. These laws include friction and thermodynamics. A new essential fatty acid, named cardiolipin, has been identified in the membrane right where protons enter to drive rotation in the Fo ring. Cambridge scientists describe it in the Proceedings of the National Academy of Sciences as a molecule that "binds selectively but transiently to conserved lysine residues in the rotor," appearing to function both as a stabilizer (glue) and a lubricant.

It interacts specifically, transiently, and repeatedly with the rotor of the machine, possibly lubricating its rotation or participating directly in the generation of rotation from the transmembrane proton motive force. [Emphasis added.]
The interactions are "highly specific" in location and timing, the authors say:

These highly specific but brief interactions with the rotating c-ring are consistent with functional roles for cardiolipin in stabilizing and lubricating the rotor, and, by interacting with the enzyme at the inlet and exit of the transmembrane proton channel, in participation in proton translocation through the membrane domain of the enzyme.
In a review article in PNAS, two researchers from Max Planck Institute find this remarkable about the already "remarkable proteins that regenerate the molecular fuel for cellular processes in all domains of life." The Cambridge team "found a remarkable interaction pattern" in the glue-lubricator molecule cardiolipin (CL).

The results of Duncan et al. have major implications for our understanding of Fo action. Efficient c-ring rotation demands minimal friction with the surrounding membrane. Tightly bound CL, with the long residence times reported for cytochrome c oxidase and cytochrome bc1, could be unfavorable. Such tight interactions should interfere particularly with the functionally required rotation of the c-ring past the a-subunit. A tightly bound lipid would lock the rotor in a manner similar to some inhibitors. However, selective binding of CL to the c-ring appears to be required for the function and assembly of ATP synthase. The results of Duncan et al. help resolve this paradox: CL binds selectively but, at the same time, intermittently. In complexes III and IV, CL appears to act as a bridging glue; by contrast, it acts here as a lubricant.
This interaction clearly requires careful fine-tuning. Too much glue function would make the motor seize up. Too much lubricant would impair the ability of proton motive force to drive the rotor. High-resolution images of this interaction are eagerly awaited, they say; "Looking forward, we can expect further exciting developments in the CL story." And that story goes beyond just this molecular machine. The Cambridge scientists "point the way for both experimentation and computation to explore one of the most fundamental questions of molecular membrane biology: protein-lipid interactions in ATP synthase and beyond."

Freeze Frame

Freezing the little motors for cryo-electron microscopy has revealed details previously unnoticed. Two Canadian researchers review what is known about ATP synthase and its cousins, the vacuolar ATPases (V-ATPase) we wrote about last year. Now that cryo-EM has reached 6.9 angstrom resolution, the authors, writing in Science Advances, remind us that mutations to V-ATPase can lead to serious disorders, including kidney malfunction, brittle bones, cancer, and even deafness. No wonder the genetic sequences that build these machines are "highly conserved" down to specific amino acids. Here are some tidbits from the review:

More than a third of an organism's genome is devoted to the construction of membrane-embedded proteins.

Some F-type ATP synthases can work in reverse, pumping protons instead of using them to make ATP. Some can also pump sodium ions.

In eukaryotes, vacuolar ATPases can adjust the pH (acidity) inside of organelles. In archaea and some bacteria, they can adjust the pH outside the cell.

Since 10 protons in the Fo domain lead to 3 ATP in the F1 domain, scientists think that intrinsic flexibility of most F-type ATP synthases appears necessary for efficient function.

The most difficult parts to image are two half-channels embedded in the membrane that deliver protons to the rotating c-ring. Specifically placed arginine and glutamate residues appear to be thermodynamically essential for transferring the protons into the c-ring carousel and making it turn.

In some eukaryotes, vacuolar ATPases can dissociate their two primary components, essentially deactivating some of them to regulate their activity.

Within yeast cells, different isoforms of the ATPases can be found. One particular 62-residue loop shows the least sequence conservation. "Although a lack of conservation often indicates a lack of functional importance, evolutionary covariance analysis shows that this sequence varies between different sequences for the a-subunit in a remarkably coordinated way," the authors say. "Consequently, the proximity of this loop to the cytoplasmic half-channel, its net charge, and its isoform-dependent sequence suggest a functional role that differs in different subcellular compartments."

"V-ATPases have many interacting partners in cells, a testament to their importance in cell physiology."

When J.B.S. Haldane argued in a 1949 debate that natural selection would not be expected to produce wheels or magnets, he basically proposed a test: finding such structures would falsify Darwinian evolution. But holding evolutionists to their rules is like trying to win at Calvinball; they can change the rules of the game as they play. In 2003, molecular biologist Robin Holliday pulled a fast one. Knowing about ATP synthase and the bacterial flagellum by that time, he imagined that wheels should be ubiquitous, not limited to a few forms. Wikipedia says that he argued that "the absence of biological wheels argues against creationist or intelligent design accounts of the diversity of life, because an intelligent creator -- free of the limitations imposed by evolution -- would be expected to deploy wheels wherever they would be of use." Uncommon Descent responded:

Wheels need roads. Roads require a lot of exhausting, expensive maintenance and must be defended/policed. The off-road vehicle is a late invention because in former times, its function was performed by life forms who didn't need roads, like horses and camels.
Which the designer of nature did invent.


Holliday used a religious argument. He (and Wikipedia) should stick to science. In our uniform experience, machines and rotary engines are products of intelligent causes. So when we find rotary engines in living things, the inference to the best explanation is that intelligence had a role in their origin. That inference is strengthened by their abrupt appearance, ubiquity, conservation, efficiency, irreducible complexity in both structure and interactions, and indispensable functionality. It also helps to see that they are manufactured from coded instructions. Let the evidence drive the conclusions.

Is drone warfare turning the U.S into 'the empire'?:pros and cons.

Climate change a crisis?:Pros and cons

O.O.L requires technology say those who should know.

Scientists Say Intelligent Designer Needed for Origin of Life Chemistry
Casey Luskin 

In a recent ENV post, Stephen Meyer critiqued a May 2009 Nature paper co-authored by John D. Sutherland titled, "Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions." The paper claimed to have produced RNA nucleobases under prebiotic conditions, but Meyer observed that it utterly failed to address the most crucial question in the origin of life (OOL): the origin of information, a topic Meyer addresses extensively in his new book Signature in the Cell.

Other scientists agree with Meyer. Organic chemist Dr. Charles Garner recently noted in private correspondence that "while this work helps one imagine how RNA might form, it does nothing to address the information content of RNA. So, yes, there was a lot of guidance by an intelligent chemist."

Sutherland's research produced only 2 of the 4 RNA nucleobases, and Dr. Garner also explained why, as is often the case, the basic chemistry itself also required the hand of an intelligent chemist:

As far as being relevant to OOL, the chemistry has all of the usual problems. The starting materials are "plausibly" obtainable by abiotic means, but need to be kept isolated from one another until the right step, as Sutherland admits. One of the starting materials is a single mirror image for which there is no plausible way to get it that way abiotically. Then Sutherland ran these reactions as any organic chemist would, with pure materials under carefully controlled conditions. In general, he purified the desired products after each step, and adjusted the conditions (pH, temperature, etc.) to maximum advantage along the way. Not at all what one would expect from a lagoon of organic soup. He recognized that making of a lot of biologically problematic side products was inevitable, but found that UV light applied at the right time and for the right duration could destroy much (?) of the junk without too much damage to the desired material. Meaning, of course, that without great care little of the desired chemistry would plausibly occur. But it is more than enough for true believers in OOL to rejoice over, and, predictably, to way overstate in the press.
Another anonymous pro-ID Ph.D. chemist privately wrote me similar criticisms of Sutherland's paper:

They used pH manipulation, phosphate buffers and irradiation all at the correct times and amounts to achieve their goal, which was to produce "activated pyrimidine ribonucleotides." Indeed, they could have shortened their title by chopping off the last four words and sent the paper to the Journal of Organic Synthesis and had a good chance of getting it accepted as a novel synthetic route with full credit to themselves for their clever manipulations. Certainly the fingerprints of several intelligent chemists are all over this pathway if not their rather ham fisted signatures.
Other control they exercised includes careful selection of the precursors, control of competing reactions by pH selection and the phenomenal phosphate concentration they used. Life in the modern ocean is phosphate limited as phosphate is generally about 0.5 micro-molar at the sea surface and only 2-4 micro-molar at depth. But what is a six order of magnitude enrichment among friends if it helps the cause!? Now they could argue that one gets that kind of enrichment in a tide pool but even that is a stretch.

Incidentally, now comes the hard parts: first, selectively hydrolyzing the cyclic 2', 3' phosphates to 3'- only, then getting them to polymerize ONLY at the 5' position. And second, once you have a supply of various RNA molecules, spontaneously developing the required biochemical structure to convert the coded sequences into proteins. Of course, we have to hope that we get lucky and we guess the correct code on the first try. And all of this has to happen in the same tide-pool otherwise, well, you get the picture. It's a bit of a stretch.

It is no wonder that whenever I see the word "plausible" in the title of an article, that I am reminded of the quote attributed to P.T. Barnum, "there is a sucker born every minute."

"Plausible" is in the Eye of the Beholder
There are thus many instances in this research where the conditions they used were anything but, as the paper's title claims, "prebiotically plausible conditions." One such instance may have been the careful addition of the 'just right' quantity of UV light, where even the original Nature paper admits: "Although the issue of temporally separated supplies of glycolaldehyde and glyceraldehyde remains a problem, a number of situations could have arisen that would result in the conditions of heating and progressive dehydration followed by cooling, rehydration and ultraviolet irradiation."

It's no groundbreaking news story that there are potential sources of heat on the early earth. These "number of situations" referred to typically include proposals of heating and drying in intertidal pools or volcanic ridges where repeated cycles of heating and drying can take place. But mundane sources of heat are only a small part of the problem, which largely comes down to the fact that the proper amount of heat has to be carefully applied so as to not wipeout the desired molecular products. It's quite easy to over-cook (or under-cook) the organic molecules, which tend to break down rapidly (i.e. cook) in the presence of heat. This would have to be a fine balancing act that would also require just the right input of organic material, heat, and UV light, so as to avoid destroying the molecules. In other words, it's a finely tuned system, the kind in which a successful scenario is very difficult to imagine without the input of intelligence. And of course, intelligently directed chemistry is exactly what provided the glycolaldehyde and glyceraldehydes in this recent research.

The Nature paper claims that the starting molecules are all "plausible prebiotic feedstock molecules," but as Garner suggests, that claim turns on what we mean by "plausible." In this case, the mechanisms of producing glycolaldehyde and glyceraldehyde are about as "plausible" as saying that if you have a pile of flour, baking powder, salt, butter, and eggs, you can produce a cake, given "the conditions of heating." Any baker knows that the ingredients must be applied in the right quantities and the right order, and that "the conditions of heating" have to be applied at just the right level or you produce nothing worth eating. In the world of creating even the mere precursor molecules to ribonucleotides, it's not just heating that's necessary but also the proper amount and sequence of "the conditions of heating and progressive dehydration followed by cooling, rehydration and ultraviolet irradiation."

As a third chemist put it to me, "The work was very carefully done. The problem is that it was very carefully done." No kidding.

Of course, even some origin of life theorists recognize that this research is not relevant to plausible conditions on the early earth. A news article on the website of the Royal Chemistry Society stated:

However, Robert Shapiro, professor emeritus of chemistry at New York University disagrees. 'Although as an exercise in chemistry this represents some very elegant work, this has nothing to do with the origin of life on Earth whatsoever,' he says. According to Shapiro, it is hard to imagine RNA forming in a prebiotic world along the lines of Sutherland's synthesis.
'The chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely,' argues Shapiro. Instead, he advocates the metabolism-first argument: that early self-sustaining autocatalytic chemosynthetic systems associated with amino acids predated RNA.

(Robert Shapiro quoted in James Urquhart, Insight into RNA origins, Royal Society of Chemistry (May 13, 2009).)

Of course Shapiro's preferred "metabolism-first argument" has its own problems, but that's a discussion for another day. Perhaps the most generous among the critical comments came from Albert Eschenmoser:
'Of course, it is referring to an event of the past and therefore conclusions will never achieve a level of certainty as in other scientific fields,' says renowned synthetic organic chemist Albert Eschenmoser. 'But Sutherland's work is a fundamental study referring to the problem of the origin of life. It is an exemplary piece of how to do synthetic organic chemistry research under very serious constraints of prebiotic chemistry,' Eschenmoser adds.
(Albert Eschenmoser quoted in James Urquhart, Insight into RNA origins, Royal Society of Chemistry (May 13, 2009).)


Eschenmoser's words are worth remembering next time someone objects to intelligent design on the grounds that it isn't scientific because it pertains to events that took place in the deep past.

A brother in Christ and a fellow servant of Jehovah.

How do Jehovah's Witnesses view Charles T. Russell?

As Jehovah’s Witnesses today review the work that he did, the things he taught, his reason for teaching them, and the outcome, they have no doubt that Charles Taze Russell was, indeed, used by God in a special way and at a significant time.

This view is not based solely on the firm stand that Brother Russell took with regard to the ransom. It also takes into account the fact that he fearlessly rejected creeds that contained some of the foundation beliefs of Christendom, because these clashed with the inspired Scriptures. These beliefs included the doctrine of the Trinity (which had its roots in ancient Babylon and was not adopted by so-called Christians until long after Bible writing was completed) as well as the teaching that human souls are inherently immortal (which had been adopted by men who were overawed by the philosophy of Plato and which left them open to such ideas as the eternal torment of souls in hellfire). Many of Christendom’s scholars, too, know that these doctrines are not taught in the Bible, but that is not generally what their preachers say from the pulpits. In contrast, Brother Russell undertook an intensive campaign to share what the Bible actually does say with everyone who was willing to hear.

Noteworthy too is what Brother Russell did with other highly significant truths that he learned from God’s Word. He discerned that Christ would return as a glorious spirit person, invisible to human eyes. As early as 1876, he recognized that the year 1914 would mark the end of the Gentile Times. (Luke 21:24, KJ) Other Bible scholars had likewise perceived some of these things and had advocated them. But Brother Russell used all his resources to give them international publicity on a scale then unequaled by any other individual or group.

He urged others to check his writings carefully against God’s inspired Word so that they would be satisfied that what they were learning was in full harmony with it. To one who wrote a letter of inquiry, Brother Russell replied: “If it was proper for the early Christians to prove what they received from the apostles, who were and who claimed to be inspired, how much more important it is that you fully satisfy yourself that these teachings keep closely within their outline instructions and those of our Lord;—since their author claims no inspiration, but merely the guidance of the Lord, as one used of him in feeding his flock.”

Brother Russell claimed no supernatural power, no divine revelations. He did not claim credit for what he taught. He was an outstanding student of the Bible. But he explained that his remarkable understanding of the Scriptures was due to ‘the simple fact that God’s due time had come.’ He said: “If I did not speak, and no other agent could be found, the very stones would cry out.” He referred to himself as being simply like an index finger, pointing to what is stated in God’s Word.

Charles Taze Russell wanted no glory from humans. To readjust the thinking of any who were inclined to give excessive honor to him, Brother Russell wrote, in 1896: “As we have been to some extent, by the grace of God, used in the ministry of the gospel, it may not be out of place to say here what we have frequently said in private, and previously in these columns,—namely, that while we appreciate the love, sympathy, confidence and fellowship of fellow-servants and of the entire household of faith, we want no homage, no reverence, for ourselves or our writings; nor do we wish to be called Reverend or Rabbi. Nor do we wish that any should be called by our name.”

As his death neared, he did not take the view that there was nothing more to be learned, that there was no more work to be done. He had often spoken of preparing a seventh volume of Studies in the Scriptures. When asked about it before he died, he said to Menta Sturgeon, his traveling companion: “Some one else can write that.” In his will he expressed the desire that The Watch Tower continue to be published under the direction of a committee of men fully devoted to the Lord. He stated that those who would thus serve were to be men “thoroughly loyal to the doctrines of the Scriptures—especially so to the doctrine of the Ransom—that there is no acceptance with God and no salvation to eternal life except through faith in Christ and obedience to His Word and its spirit.”

Brother Russell realized that there was much work yet to be done in preaching the good news. At a question-and-answer session in Vancouver, B.C., Canada, in 1915, he was asked when Christ’s spirit-anointed followers then living could expect to receive their heavenly reward. He replied: “I do not know, but there is a great work to be done. And it will take thousands of brethren and millions in money to do it. Where these will come from I don’t know—the Lord knows his own business.” Then, in 1916, a short while before he began the speaking tour on which he died, he called A. H. Macmillan, an administrative assistant, to his office. On that occasion he said: “I am not able to carry on the work any longer, and yet there is a great work to be done.” For three hours he described to Brother Macmillan the extensive preaching work that he saw ahead, on the basis of the Scriptures. To Brother Macmillan’s objections, he replied: “This is not man’s work.”


- Jehovah’s Witnesses—Proclaimers of God’s Kingdom, 1993 WTB&TS

How's that manifest destiny thing working for you?Pros and cons.

Pakistan playing Janus with the war on terror?Pros and cons.

A clash of titans XXVI

Meals on wheels?

One man's terrorist...?Pros and cons.

A crisis of leadership among the Palestinian elite? Pros and cons.

Time for the west to mediate from the middle re: the Israeli/palestinian conflict?Pros and cons.

A clash of titans XXV

David Berlinski on becoming David Berlinski.

How David Berlinski Came to Doubt Darwin
David Berlinski 

ENV: When did you start thinking, as a critic, about Darwinian evolution? Did anythingIt was the fall of 1965. My graduate school roommate Daniel Messenger and I were ambling along Nassau Street in Princeton. We were munching the kind of wonderful Winesap apples that seem to have disappeared as a variety. I wonder why that is? Daniel's girlfriend, Sandra Petersen, was there too. Daniel was a fine philosopher and Sandra was doing a degree in classical philosophy. We walked over to Darwin's theory of evolution, living at the time in one of Princeton's back alleys.

A back alley was the right place to look for Darwin. No one in the philosophy department at Princeton had ever introduced his name into a seminar, or thought to argue that his theory was relevant to our concerns.

At Columbia College I had been given a ten minute introduction to the theory of evolution in a class otherwise devoted to comparative anatomy. The impression conveyed was that Darwin's theory was far less interesting than the details embedded in the anatomy of the Dogfish.

-- Now if you will turn to your specimens, Gentlemen...

If I had had those ten minutes to count on, Daniel had more. At Brown, he had once read Darwin's On the Origin of Species. This made him a considerable expert in my eyes. He knew what it was all about. I asked the obvious question: So is that it? 

Apparently it was.

Daniel shrugged his rounded shoulders. Someone, he said, had figured it all out.

As she always did, Sandra kept her counsel. She was fond of Daniel; she thought me an idiot.

A year later, I found myself promoted from east coast snow to west coast sunshine. And promoted to more, far more. I was an assistant professor at Stanford: That was more. And I had been given access to the splendor of northern California: That was far more. What is that wonderful line by Robert Lowell? All of life's grandeur is something with a girl in summer.

One night I was having dinner with my great friend, Daniel Gallin. At the time, he lived in San Francisco, his Delmar Street apartment high above the city. We could see the fog roll in, Nassau Street Daniel emerging briefly to offer Delmar Street Daniel the same reprise of Darwin's theory that he had once offered me. Delmar Street Daniel was doing a PhD at Berkeley with Dana Scott; he was an excellent mathematician, and an even better logician. He reserved his approval for mathematical model theory, and his admiration for Alfred Tarski.

"Can you imagine?" he would ask on reading something absurd. 

And Darwin?

Can you imagine!

*******************************************

At some time in the early 1970s, I came across the papers that Murray Eden and M.P. Schutzenberger had delivered to the 1966 Wistar Symposium, Mathematical Objections to Neo-Darwinism. I read them closely; I was impressed; and I discussed them at Columbia with Josh Kornberg, a molecular biologist, and George Pieczenik, a biochemist. Pieczenik had just finished his PhD, writing a thesis on the grammatical constraints embedded in the nucleic acids. Sympathetic to Murray's position, he had discovered two facts: The first, that the nucleic acids contain internal terminator codons and the second, that they often express very long palindromes. Josh Kornberg, on the other hand, had no intellectual capital to invest in either Murray or Marco. Not a dime, he said.

Who cares, he added?

For a while, I thought I might find a way to represent an evolutionary process in automata-theoretic terms. And for obvious reasons. The construction of a complex system demands some scheme of anticipation and deferral -- anticipation to determine where things are going, deferral to keep intermediates in reserve for later use. Finite state automata will not do; push-down storage automata are needed.

Sidney Morgenbesser accepted my paper for the Journal of Philosophy without asking for revisions. That my paper had very little to do with philosophy, he regarded as nothing more than an inconvenience. "Stick the word 'philosophy' in the title somewhere," he said. So I called my paper, "Philosophical Aspects of Molecular Biological Systems." Everyone was well satisfied, the philosophers because I was writing about biology, and the biologists because I was writing about philosophy.

It was my introduction to irrelevance, the writer's natural state.

Somewhat later, Noam Chomsky gave me a letter of introduction that allowed me to meet Marco Schutzenberger in Paris.

I've written about Chomsky and Marco in Black Mischief: Language, Life, Logic & Luck.

But this is the way it was. Darwin and I go back. He has long since moved from that scruffy back alley to something grand -- near Lake Cuomo, I believe. Still, it is lucky that we met. I might have encountered Marx instead of Darwin on Nassau Street, another one of the back-alley boys, the fall of the Berlin Wall leaving me, like Roger Kimball, dancing with ghosts. in your biography incline you to freethinking in that area?

On human cloning:looks like the fun is just getting started.

Dolly Clones Pave the Way for Human Cloning
Wesley J. Smith 

Apparently clones of the same dead sheep from which Dolly was manufactured are in good health and aging normally. From the Live Science story:

Four cloned sheep that are genetically identical to Dolly, the first cloned mammal, are still healthy even in old age, a new study found. The four sheep, which were derived from the same batch of cells as Dolly and could be considered her clone "sisters," have just reached their 9th birthday, which is equivalent to age 70 in human years, researchers who have been studying the sheep said.

A detailed study of these four sheep and nine other cloned sheep that are not related to "the Dollies" found that the animals were healthy. All of the sheep were free from many diseases commonly found in older sheep, such as diabetes and high blood pressure, the study showed.

What does this mean for the future of human cloning?

The technique, known as somatic cell nuclear transfer (SCNT) can be refined so as to permit normal mammals made in such a manner.
Human SCNT has already been done, creating embryos that were developed to the blastocyst stage (the time when stem cells can be derived).
SCNT is cloning. The result is an embryo. The question after that is how will that embryo be used.
Some human cloning apologists say that "therapeutic cloning" is different from "reproductive cloning." That's false. Those terms merely reflect different uses of the cloned embryo, the former being destroyed for research, the latter implanted in a uterus and -- as with Dolly -- brought to birth.
Bioethicists and Big Biotech support have said that human reproductive cloning should be banned until it is "safe."
Animal cloning moves that process forward as does therapeutic human cloning, since the point is to perfect the still faulty techniques needed to do in humans what is currently done in sheep.
The goals of human cloning include, but are not limited to research, learning how to genetically engineer, fetal farming, and reproductive outcomes.
Banning "reproductive cloning" is not banning cloning, but a use of a cloned embryo, in other words, a phony ban intended to fool people.
The time to outlaw human cloning is now -- meaning all human SCNT, regardless of the use to which the embryo will be put. If we wait until the sector perfects its techniques, it will be too late.

Will we? Not a chance. The media are asleep and/or active boosters of Big Biotech and Congress is safely in their campaign donation-paid special interest pockets.


There will be consequences.

On S.E.T.I or still waiting by the phone.

After Fifty Years of Searching for ETs, Materialists Won't Take No for an Answer
Evolution News & Views

Ideas have consequences. If your idea is that life on Earth is nothing special, it follows that life should be plentiful in the cosmos. If you believe life and intelligence are accidental byproducts of matter and energy, you would probably want to communicate with others like us -- that is, unless (like Stephen Hawking) you think aliens might be as dangerous as we are to each other. Optimists in the SETI community outnumber pessimists. So they search.

And search. Half a century later, no signal has been detected. Astrobiologists (those who look for any kind of life beyond Earth, intelligent or not) can't even find microbes within our own solar system.

People are certainly free to pursue their own dreams. SETI only gets controversial when taxpayers have to pay for it. Search enthusiasts are chagrined that astrobiology gets NASA money, but they do not. Ever since Congress laughed it out of chambers with jokes about little green men, SETI advocates have had to raise their own money. With help from billionaires like Paul Allen and Yuri Milner, the search has continued. But even with technological innovations allowing the monitoring of a million channels simultaneously (far beyond Frank Drake's single-channel search of two stars in 1960), no signal of intelligent origin has yet turned up.

The true believers have one point in their favor; the search space is too vast to expect success in just 56 years, given our current search technology. But other possibilities exist. Life is rare; we are alone; or, perhaps, alien life is so different from what we know, we have no idea how to find it. From another direction, molecular biologists have continued to uncover unexpected complexity in even the simplest life, leading some to conclude life is rare.

These and other ideas are discussed in a paper by Nathalie A. Cabrol in the journal Astrobiology. A senior research scientist for the SETI Institute, Cabrol feels it's time for a major new interdisciplinary effort to look for intelligent aliens (see also Elizabeth Howell's write-up at Space.com, with video clip, "Are We Alone in the Universe?"). To succeed, Cabrol argues, we will need to expand our search to "life as we do not know it."

The evolutionary pathways that lead to complex life on Earth strongly suggest that advanced life as we know it may be rare in the Universe and unlikely to be in a state of advancement that is temporally synchronous with us. However, that does not mean that other types of advanced intelligences are as rare. Limiting our search to something we know and can de facto comprehend is, probabilistically, a constraining proposition, one that leaves no room for an epistemological and scientific foundation to explore alternate hypotheses. To find ET, we must expand our minds beyond a deeply rooted Earth-centric perspective and reevaluate concepts that are taken for granted. [Emphasis added; italics in the original.]
One way we can expand our minds is to play Mr. Spock and do a kind of "mind meld" with the aliens, using imagination. Here, Cabrol runs the risk of eliciting more Congressional guffaws:

Rather than constraining the search, SETI efforts must involve the most expansive exploration tool kit possible. If we unbind our minds, it should not matter whether ET looks or thinks like us, has a logic that makes any sense to us, or uses familiar technology for interstellar communication. ET is likely to be very different from us and completely alien to our evolutionary processes and thought processes, which may be deeply connected (see Section 5.2.3). Ultimately, to find aliens, we must become the aliens and understand the many ways they could manifest themselves in their environment and communicate their presence.
Such an intellectual framework not only moves the Drake equation forward toward the existence of drastically different probabilistic civilizations, it also brings us to consider alternate evolutionary pathways, including life as we do not know it and do not yet understand. Further, such a framework allows us to look at evolutionary pathways in our own biosphere and question the emergence of complex, intelligent life with a different set of eyes. For that to happen, we must conceptualize something we do not know, which can be approached in a number of different ways. One is by trying to access unknown concepts and archetypes that are literally alien to us (i.e., not part of our own evolutionary heritage) through imagination and discourse. This is what science fiction attempts to do in its depictions of alien worlds and civilizations. Not surprisingly, this process results in more or less elaborate versions of ourselves, since these representations are generated by neural systems wired to our own planetary environment. To conceptualize a different type of life, we have to step out of our brains. [Italics in the original.]

For those of us preferring to keep inside our brains, we see that ET can become an obsession to believers, like Richard Dreyfuss in Close Encounters, who would not take no for an answer. The silence does not mean aliens are not out there. They are just so alien we can't use the scientific method; we have to imagine them. We have to become them. Whether Cabrol's appeal will rouse support remains to be seen.

Cabrol is not alone. Fact-challenged as it is, SETI is a running theme in the popular science media. And there's a lot of money being thrown at it.

Ian O'Neill from Discovery News reports on a "targeted SETI" approach, using the Allen Telescope Array to listen for signals from candidate planets discovered by the Kepler Spacecraft. (Space.com)

China has just completed the world's largest radio telescope, in hopes of "finding new worlds and alien life." Though built for traditional science, "it can also eavesdrop on distant worlds to search for intelligent life," says Elias Brinks at The Conversation.

English scientists are practicing searches for exotic life deep in a salt mine, hoping to transfer what they learn to searches for life underground on Mars. (New Scientist)

New Scientist reports that several scientists are upset that NASA is not doing enough to search for alien life. They want more attention on the search in the Mars rover programs and the James Webb Space Telescope goals. Why? "As well as many other scientists who support the search for life elsewhere, it tops the lists of the most exciting questions driving science today for people outside the field," Shannon Hall writes.

At Live Science, Mindy Weisberger explores the fascination with "little green men" by examining the historical roots of the familiar icon that has persisted for decades.

Last month, a Cornell student, Evan Solomonides, presented "A Probabilistic Analysis of the Fermi Paradox," excusing the silence on the "Mediocrity Principle" wrongly attributed to Copernicus (see The Privileged Planet for refutation). Solomonides was inspired by Carl Sagan's view that humans are nothing special in the vastness of space. With that as his guide, he calculated (with no data on aliens) that it will be 1,500 years before aliens contact us. (Cornell Chronicle)

To appreciate how scientifically groundless these speculations are, imagine for a moment that a cult of religious fanatics controlled the reins of science. Convinced that ghosts are real, they search diligently for decades, creating more and more elaborate devices to find them. They refuse to take non-detection as an answer. Speculation joins imagination to explain why they are not found. Some of the true believers propose becoming ghosts to understand them. Others propose that ghosts are so clever, they are purposely concealing themselves. Another group speculates that they are so weird, we cannot even begin to imagine what they are like. Go ahead; use all the SETI speculations for this scenario. Even if these searches understood quantum physics and relativity and used sophisticated engineering, would that rationalize the ideology?

In the history of science, some searches for "occult phenomena" (referring not to spiritual entities, but to suspected-but-as-yet-unobserved realities) have borne fruit; recent examples include the Higgs Boson and gravitational waves. Other searches have not (caloric, phlogiston, alchemy). The search for dark matter is currently in crisis, failing the most sensitive search to date (Space.com). At some point, a quest must acquire data to justify its claim to be scientific.

Despite continued failures, SETI is unlikely to cave anytime soon. Its motivations are too deeply grounded in evolutionary ideology. The believers think it too incredible to imagine humans as unique or exceptional in such a vast universe. To be sure, this "gut feeling" extends outside evolutionary circles. But where is the evidence? While the complexity of life and the uniqueness of Earth have become more apparent, the aliens have remained silent.

Here are two points to note about this undying fascination with aliens in the SETI community and in the science media. One is its dependency on the materialist, Darwinian worldview. Cabrol's paper contains over a hundrew references to evolution in the text and references.


The second is the inherent inconsistency of this perspective. The SETI community is almost entirely composed of people who attack ID as unscientific. Yet over and over we see them using a framework of intelligent design, though not by that name, in their searches! SETI rests on the premise that intentional, purposeful signals can be distinguished from natural processes. They speak effusively about communication channels, signals, and intentions of beings that they don't even know exist. Remember this next time someone levels the charge against ID that it points to a designer outside of science.

Why appeals to common design re:homology are not a cop out.

Why Similarities Do Not Prove the Absence of Design
Granville Sewell 

The idea that the "survival of the fittest" could produce all the magnificent species on Earth, and human brains and human consciousness, is so unreasonable -- how did such an idea ever become so widely accepted in the scientific world? There are two reasons.

First, science has been so successful explaining other phenomena in Nature that -- understandably -- today's scientist has come to expect that nothing can escape the explanatory power of his science. And Darwinism, as far-fetched as it is, is the best "scientific" theory he can come up with for evolution. As microbiologist René Dubos puts it in The Torch of Life, "[Darwinism's] real strength is that however implausible it may appear to its opponents, they do not have a more plausible one to offer in its place." But we have already seen why evolution is a very different and much more difficult problem than others solved by science, and why it requires a very different type of explanation.

Second, for most modern minds, the similarities between species not only prove common descent, they prove that evolution was the result of entirely natural causes, even in the absence of any evidence that natural selection can explain the major steps of evolution. The argument is basically, "This doesn't look like the way God would have created things," an argument used frequently by Darwin in the Origin of Species. But if the history of life does not give the appearance of creation by magic wand, it does look very much like the way we humans create things, through testing and improvements.

In fact, the fossil record does not even support the idea that new organs and new systems of organs arose gradually. Instead, new orders, classes, and phyla consistently appear suddenly. For example, Harvard paleontologist George Gaylord Simpson writes:

It is a feature of the known fossil record that most taxa appear abruptly. They are not, as a rule, led up to by a sequence of almost imperceptibly changing forerunners such as Darwin believed should be usual in evolution.... This phenomenon becomes more universal and more intense as the hierarchy of categories is ascended. Gaps among known species are sporadic and often small. Gaps among known orders, classes and phyla are systematic and almost always large. These peculiarities of the record pose one of the most important theoretical problems in the whole history of life: Is the sudden appearance of higher categories a phenomenon of evolution or of the record only, due to sampling bias and other inadequacies?
Actually, if we did see the gradual development of new orders, classes and phyla, that would be as difficult to explain using natural selection as their sudden appearance. How could natural selection guide the development of the new organs and entire new systems of interdependent organs which gave rise to new orders, classes, and phyla, through their initial useless stages, during which they provide no selective advantage? French biologist Jean Rostand, in A Biologist's View, wrote:

It does not seem strictly impossible that mutations should have introduced into the animal kingdom the differences which exist between one species and the next... [H]ence it is very tempting to lay also at their door the differences between classes, families and orders, and, in short, the whole of evolution. But it is obvious that such an extrapolation involves the gratuitous attribution to the mutations of the past of a magnitude and power of innovation much greater than is shown by those of today.
Rostand says, nevertheless, "However obscure the causes of evolution appear to me to be, I do not doubt for a moment that they are entirely natural."

We see this same pattern, of large gaps where major new features appear, in the history of human technology. (And in software development, as discussed in my Mathematical Intelligencer article "A Mathematician's View of Evolution.") For example, if some future paleontologist were to unearth two species of Volkswagens, he might find it plausible that one evolved gradually from the other. He might find the lack of gradual transitions between automobile families more problematic, for example, in the transition from mechanical to hydraulic brake systems, or from manual to automatic transmissions, or from steam engines to internal combustion engines. But if he thought about what gradual transitions would look like, he would understand why they didn't exist: There is no way to transition gradually from a steam engine to an internal combustion engine, for example, without the development of new, but not yet useful, features. He would be even more puzzled by the huge differences between the bicycle and motor vehicle phyla, or between the boat and airplane phyla. But heaven help us when he uncovers motorcycles and hovercraft, the discovery of these "missing links" would be hailed in all our newspapers as final proof that all forms of transportation arose gradually from a common ancestor, without design.

The similarities between the history of life and the history of technology go even deeper. Although the similarities between species in the same branch of the evolutionary "tree" may suggest common descent, similarities (even genetic similarities) also frequently arise independently in distant branches, where they cannot be explained by common descent. For example, in their Nature Encyclopedia of Life Sciences article on carnivorous plants, Wolf-Ekkehard Lönnig and Heinz-Albert Becker note that

...carnivory in plants must have arisen several times independently of each other... the pitchers might have arisen seven times separately, adhesive traps at least four times, snap traps two times and suction traps possibly also two times.... The independent origin of complex synorganized structures, which are often anatomically and physiologically very similar to each other, appears to be intrinsically unlikely to many authors so that they have tried to avoid the hypothesis of convergence as far as possible.
"Convergence" suggests common design rather than common descent: the probability of similar designs arising independently through random processes is very small, but a designer could, of course, take a good design and apply it several times in different places, to unrelated species. Convergence is a phenomenon often seen in the development of human technology. For example, Ford automobiles and Boeing jets may simultaneously evolve similar new GPS systems.

So if the history of life looks like the way humans, the only other known intelligent beings in the universe, design things -- through careful planning, testing, and improvements -- why is that an argument against design? Somehow we got the idea that nature's designer shouldn't need to get involved in the details, and so should be able to create anything from scratch, using a magic wand. But no matter how intelligent a designer is, he still has to get involved in the details -- that's what design is!

Some people counter by saying that of course cars cannot evolve like animals, because they cannot reproduce, so there are no "variations" for natural selection to work with. But the main point here is not about natural selection -- it is only that similarities between "species" (of cars or animals) do not prove the absence of design.


However, even though it is irrelevant to my main point here, let's look at the argument that evolution is easier to explain if there is reproduction. Is that really so? If cars were able to reproduce themselves almost perfectly (the copies even retaining the ability to reproduce themselves!), with occasional minor errors, would that make the evolution of cars easier to explain without design, than if individual cars experienced slight changes or improvements directly, though rust or crashes or other natural causes? We are so used to seeing animals make nearly perfect copies of themselves that we dismiss this as just another "natural" process; but if we saw cars giving birth to cars, maybe we would realize that this would actually make automobile evolution even more amazing and more difficult to explain without design.

Darwinism Vs. the real world XXX

The Neuromuscular System: Your Body's Balancing Act
Howard Glicksman 

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News is delighted to offer this series, "The Designed Body." For the complete series, see here. Dr. Glicksman practices palliative medicine for a hospice organization.

The nerves and muscles of our body allow us not only to breathe, but also to move around and manipulate things. But how do they do it? In my last I article showed that nerve cells (neurons) and muscle cells (myocytes) are excitable. This means that when adequately stimulated, they depolarize. By letting large amounts of Na+ ions enter, they cause the plasma membrane to go from being negatively charged to positively charged. Depolarization triggers large amounts of Ca++ ions to enter the cell, causing the neuron to release its neurotransmitter and the myocyte to contract.

The nervous system is set up like a military operation. Reconnaissance from sensory neurons within the peripheral nerves is sent to and organized by the spinal cord and transmitted to the brain. The brain, acting as headquarters, analyzes the sensory information, makes decisions, and sends out orders. The orders travel to and are organized by the spinal cord and sent through the motor neurons within the peripheral nerves. The messages tell the muscles to contract, which results in controlled and purposeful movement. The success of a military operation is dependent on having good information about the enemy and one's own troops. Let's look at some of the ways the body acquires the information it needs about its external and internal environment so it can know what to do and act accordingly.

Everyone knows that an odometer measures distance and a speedometer measures velocity. Each device is essentially a sensory transducer with a mechanism in place that enables it to sense a physical phenomenon and convert it into useful information. We have seen that the body has a whole host of sensory transducers, which provide the information necessary to maintain its internal environment. They are divided into three different categories: chemoreceptors, which respond to chemicals, like oxygen, glucose and calcium; mechanoreceptors, which respond to motion and stretch, like the baroreceptors in the walls of the arteries leading to the brain that monitor blood pressure; and physical sensors, which respond to natural phenomena, like the thermoreceptors in the hypothalamus that detect core temperature.

The skin not only protects the body from infection and injury. It also provides sensory information about its immediate surroundings. The skin has different sensory receptors that can detect light touch, pressure, motion, vibration, and temperature. It has pain receptors that react to chemicals related to nearby cell injury. They also react to too much pressure or motion and extreme temperatures. Adequate stimulation of any one of these sensory receptors causes the associated neuron to depolarize and release its neurotransmitter. The neurotransmitter then depolarizes a nearby connecting neuron in a cascade that transmits the message all the way to the brain, usually in the sensory region of the cerebral cortex.

In addition to the skin, which provides sensory information about the body's external environment, there are pain and mechanoreceptors in and around the joints, ligaments, and deep soft tissues. These, in addition to chemoreceptors within the major organs, provide sensory information about the body's internal environment. Although we are aware of many of the sensations caused by our external and internal environment, one set, the proprioceptors, acts unconsciously and without them life would be impossible.

Proprioception involves joint position awareness and kinesthesia, or the awareness of joint and limb movement through muscular effort. The proprioceptors tell the central nervous system about muscle length, joint position, and limb movement. If the body had no way of knowing what its muscles and joints were doing and where its bones were located in space, then how could it control its position and movements? In addition to the mechanoreceptors in and around the joints, the two main proprioceptors are the muscle spindles and the Golgi tendon organs, which provide sensory information on joint position and muscle movement.

The Golgi tendon organ joins the muscle to the tendon as it is attached on one end to the muscle fibers and on the other end to the tendon. Because it is directly connected, in series, to the muscle and the tendon, the Golgi tendon organ is sensitive to the degree of tension applied by muscle contraction.

An increase in tension causes the Golgi tendon organs to increase their impulses to the spinal cord, causing an immediate reflex inhibition of muscle contraction and a reduction in tension. This explains one of the important functions of the Golgi tendon organs: preventing muscle injury and tendon rupture by causing automatic muscle relaxation in the presence of dangerously high levels of tension.

Conversely, a decrease in tension causes the Golgi tendon organs to decrease their impulses to the spinal cord, which results in an immediate reflex reduction in inhibition causing an increase in muscle contraction. This explains another important function of the Golgi tendon organs, which is to help the body maintain its posture while performing goal directed activities.

Muscle fatigue, with its resulting diminished contraction, can lead to inadvertent falling or unexpected changes in position. But the information sent by the Golgi tendon organs to the spinal cord reflexively makes the flagging muscles contract more to allow the body to maintain its posture. Clearly, without the Golgi tendon organs to tell the central nervous system what's going on at the level of where the muscle attaches to the tendon, our ability to move around would be impossible.

Muscle spindles are sensory organs consisting of modified muscle fibers positioned in between and parallel to the skeletal muscle fibers, allowing them to compare their respective lengths. Since each skeletal muscle is usually attached to two different bones across a joint, its length also determines the angle of the joint and its position.

For example, when the elbow is fully extended to zero degrees, the biceps are at their greatest length and the triceps are at their shortest. In contrast, when the elbow is fully flexed at about 160 degrees, the biceps are at their shortest length and the triceps are at their greatest. When the angle of the elbow is in between, at 80 degrees, so too are the lengths of the biceps and the triceps. This demonstrates one of the functions of the muscle spindles, which is to provide the central nervous system with information about the length of each skeletal muscle and the angle and position of its associated joint.

If the skeletal muscle fibers are longer than the muscle spindles (an indication of being stretched) the muscle spindles react by sending more impulses to the spinal cord, reflexively causing muscle contraction. Conversely, if the skeletal muscle fibers are shorter than the muscle spindles (an indication of muscle contraction) the muscle spindles react by sending less impulses to the spinal cord which reflexively results in muscle relaxation. This demonstrates another important function of the muscle spindles. Like the Golgi tendon organs, they help the body maintain its posture and position in space while performing purposeful movements.

In a static situation, such as carrying a load in front of the body, it is easy to understand how the muscle spindles maintain position through changes in muscle function. In this setting, the elbows must be maintained at about ninety degrees by the combined actions of the biceps and triceps. During this activity, stretching (lengthening) of the biceps, due to muscle fatigue, will at the same time cause a shortening (contraction) of the triceps. If this is not corrected quickly the angle of the elbow will decrease and allow gravity to take more effect which may cause the load to be dropped.

To prevent this from happening, the muscle spindles in the biceps detect the lengthening and send more messages to the spinal cord, reflexively causing an increase in the contraction of the biceps. This maintains the angle of the elbow at ninety degrees so as to not drop the load. At the same time, the muscle spindles in the triceps detect the shortening of its muscle fibers and send out fewer messages to the spinal cord, reflexively resulting in relaxation of the triceps so that the ninety-degree elbow angle is maintained.

Clinical experience with diabetics and others who suffer from sensory nerve malfunction indicates that without any one of the above-mentioned sensory devices, it would have been impossible for our earliest ancestors to survive. Evolutionary biologists must explain how each of them came about and their presence in the precise locations where they are needed in addition to how intermediate life forms could have survived throughout this developmental process.


Next time we will look at the special sense of vision and see what it requires.

Yellow journalism will be the death of Britain?:Pros and cons.

Demythifying peer review II

The Hoax on Us
Drivel, Fraud & Gibberish in Scientific Papers
by Denyse O'Leary

An entertaining but revealing development in science culture in recent years has been the intentionally nonsensical academic paper. Earlier this year, political scientist Peter Dreier admitted at Prospect that his abstract for a panel of six years ago, "On the Absence of Absences," was "academic drivel":

I tried, as best I could within the limits of my own vocabulary, to write something that had many big words but which made no sense whatsoever. I not only wanted to see if I could fool the panel organizers and get my paper accepted. . . .1

Well, not only was it accepted, but he was also invited to join fellow academics in Tokyo at the annual international conference of the Society for Social Studies of Science.


Sokal & His Imitators

The hoax journal paper genre was started, as Dreier explains, by New York University physicist Alan Sokal in 1996. Sokal aimed to skewer the postmodern dogma that facts, even in mathematics and physics, are merely a social construct. He submitted an article to Social Text, a postmodern cultural studies journal, that, "shorn of its intentionally outrageous jargon, essentially made the claim that gravity was in the mind of the beholder." The paper, "Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity," was published in the Spring/Summer 1996 issue of the journal. Writes Dreier:

As soon as it was published, Sokal fessed up in another journal (Lingua Franca, May 1996), revealing that his article was a sham, describing it as "a pastiche of Left-wing cant, fawning references, grandiose quotations, and outright nonsense . . . structured around the silliest quotations [by postmodernist academics] he could find about mathematics and physics."2

Sokal has had many imitators since, a disquieting number of whom have been successful. One entertaining 2015 hoax purportedly showed that boo-boo kisses from mommy did not help heal children's scrapes and recommended "a moratorium on the practice." Other entries don't sound quite so cute, however.

For example, in 2005, MIT researchers developed software they called SCIgen, which "randomly combines strings of words to produce fake computer-science papers." Their aim was to demonstrate that "conferences would accept meaningless papers."3 That was no idle concern. In 2014, computer scientist Cyril Labbé catalogued 120 computer-generated "gibberish" papers that had been published as conference proceedings in the five years between 2008 and 2013 alone. Sixteen papers had appeared in publications of the well-regarded science publisher Springer, and more than 100 were published by the Institute of Electrical and Electronic Engineers. All the papers had to be removed from the relevant databases.

Once discovered, hoax papers can sometimes be retracted with little fuss, but other times the matter doesn't end well. In a very recent case, the authors of a hoax paper about death-camp guard dogs had intended to satirize postmodern attempts to "interpret historical events through the perspective of affected animals." Unfortunately, the authors failed to let the journal or their readers in on the joke. The paper was retracted with some pointed criticism.4

Along with hoax papers, there has been an increase in fraudulent journal papers as well,5 but here we should recognize a distinction: frauds are not the same thing as hoaxes. Piltdown Man and the feathered dinosaur ("Piltdown Chicken"), to cite two concrete examples, were frauds. The fraudster needs the world to believe—and go on believing—the fraud. The hoaxer, by contrast, delights in the moment he can reveal the truth, for that is the point of the exercise.

Left-Wing Bias Paints the Target

Both fraudulent and hoax papers riff off the needless complexity of today's academic prose. Granted, lay readers are often going to be baffled by forbidding but essential technical terms in a research paper. But papers that baffle everyone—even those in the field—while sounding profound are a different matter. Such papers can be seen as resulting from the postmodern invasion of the sciences by nihilist philosophies. Indeed, wags now offer tongue-in-cheek directions for perpetrating a science hoax, and explain how to construct a gibberish paper that gets accepted by journals.5 Perhaps many journals find it easier just to accept a few such papers than to confront the troubling reality they represent: that words don't need to mean anything to be accepted in their discipline.

Social science is especially hard-hit these days; one psychologist described it as "riddled with flaky research and questionable theories."6 There is a surprisingly broad consensus about the cause—that is, everyone from Michael Shermer to Uncommon Descent agrees on it—namely, that the field's overwhelmingly progressive-left bias makes it an easy mark for both hoaxes and frauds.7

It also makes it an easy target for a third category of problem paper that is neither a hoax nor a fraud exactly: the nonsense paper that may well be believed by its authors. Examples of these include the widely cited "positivity ratio" in psychology, which was assessed as "entirely unfounded" in 2013,8 and the recent, apparently serious attempt to "feminize" melting glaciers.9

This sort of thing should come as no surprise. Monochromatic bias exposes a community to greater risk because few of its members even notice a hoax, fraud, or nonsense thesis that passes their bias filter. Usually, the person to whom it doesn't sound right has different commitments and life experiences, and he or she is the one motivated to investigate.

Ironically, many defenders of the status quo in recent years have claimed to be "scared to death of the anti-science lobby."10 Their worries are misplaced. It's actually science that is coming to get them. Soon. •

Notes
1. Peter Dreier, "Academic Drivel Report," Prospect (Feb. 22, 2016): http://bit.ly/1QeFT8Q.
2. Ibid.
3. Nature News (Feb. 24, 2014): nature.com/news/publishers-withdraw-more-than-120-gibberish-papers-1.14763.
3. "Death camp dog satire retracted when German journal wasn't in on joke," Retraction Watch (Mar. 1, 2016): http://bit.ly/1Tt5vEU.
4. Ibid.
5. Adam Ruben, "Forging a Head," Science (Apr. 22, 2011): http://bit.ly/21ZSNCF; Rob Sheldon, "How, exactly, to construct a gibberish paper that gets accepted by journals," Uncommon Descent (Mar. 6, 2014): http://bit.ly/1XcVycU.
6. Claire Lehmann, "How a rebellious scientist uncovered the surprising truth about stereotypes," Quillette (Dec. 4, 2015): http://bit.ly/1SExNbD.
7. Michael Shermer, "Is Social Science Politically Biased? Political bias troubles the academy," Scientific American (Mar. 1, 2016): scientificamerican.com/article/is-social-science-politically-biased.
8. The Scientist (Aug. 7, 2013): the-scientist.com/?articles.view/articleNo/36910/title/-Positivity-Ratio--Debunked.
9. "As glaciers melt, more voices in research are needed," Around the O (Feb. 25, 2016): http://bit.ly/1QW7efz.
10. Robin McKie, "Attacks paid for by big business are 'driving science into a dark era,'" The Guardian (Feb. 19, 2012): http://bit.ly/1nwMgfE.