Is mind or matter the nearer/better bridge re:those gaps?

Materialism of the Gaps
Michael Egnor

I must say that I've never understood the rhetorical force of the 'God of the Gaps' argument. The God of the Gaps sneer is invoked to imply the inexorability of materialism as a complete explanation in natural science. Any critique of materialist dogma in science from a design or immaterial perspective is derided as a 'God of the Gaps' argument. But the real issue is the gaps, which are plentiful and very wide.

Dr. Novella is fond of the God of the Gaps sneer, in the form of "Dualism of the Gaps." I have not met a materialist as supremely confident of the complete explanatory power of materialism as he is. It's ironic, as Dr. Novella claims the appellation "skeptic," yet he shows no skepticism for his own materialist dogma. Profound skepticism for the views of opponents, combined with complacent credulity for one's own views, is the stuff of ideological advocacy, not skepticism.

Dr. Novella responded recently to my post in which I clarified my views on the mind-brain problem. He accuses me of using a 'Dualism of the Gaps' argument. I've merely pointed out that the salient characteristics of the mind, such as intentionality, qualia, free will, incorrigibility, restricted access, continuity of self through time, and unity of consciousness (the 'binding problem') seem to be impossible to explain materialistically. Materialistic explanations for subjective mental states are not impossible merely because we lack experiments or evidence. Materialistic explanations for the mind are impossible within the framework of materialism itself, because mental properties are not physical properties. Nothing about matter as understood in our current scientific paradigm invokes subjective mental experience. The essential qualities on the mind are immaterial. Invocation of immaterial causation that incorporates subjectivity seems necessary for a satisfactory explanation of the mind.

Dr. Novella argues:

My "dualism of the gaps" point, however, is that lack of complete knowledge does not justify inserting a magical answer. Our lack of complete knowledge about life does not justify inventing a vital life force to explain it, our incomplete knowledge of evolution does not justify inventing an intelligent designer who miracled life into existence, and our current state of neuroscience does not require inserting a non-corporeal mind separate from the brain.. Further - you cannot logically justify a positive claim based upon a lack of information. Where is the evidence for a vital force, or an intelligent designer, or the ghost in the machine? There isn't any, such claims are based entirely on perceived gaps in knowledge.
But we don't 'lack knowledge' about the mind. We have a rich knowledge of the mind. Much of philosophy, art, literature, psychology, politics, and history are essentially knowledge of the human mind. It's fair to say that most of what mankind knows is knowledge about the mind. By any measure, we probably know much more about the mind than we do about the natural world.

And we certainly don't 'lack knowledge' about the brain. We have made astonishing strides over the past century in understanding neuroscience, from the molecular level to the functioning of the nervous system as a whole. We can image the brain functionally in real time with considerable precision. We can record brain waves with relative ease from the whole brain, and we can do surgery that enables us to record electrical activity in regions of the brain a few cubic millimeters in volume. We know an enormous amount about the brain.

Yet we know nothing -- nothing -- about how subjective experience could arise from matter alone. We certainly know a lot about correlations. But about causation -- how matter even could cause subjective mental states -- we know nothing. We don't even have a scientific paradigm by which we could even imagine what such an answer could be like. Subjective mental states share no properties whatsoever with matter. The 'explanatory gap' -- our inability to explain the subjective in terms of the objective -- is as wide as ever. It's infinitely wide. We don't even know where to begin to answer the question 'how does subjectivity arise in association with matter' from a materialistic standpoint.

Dr. Novella is wrong to attribute the inference to dualism to an argument from ignorance. The exact opposite is true. The reason that immaterial causation is invoked to explain the mind is because we know so much about the mind and about the brain, and it's evident to most people (that is, people who aren't dogmatic materialists) that the mind isn't material. It isn't an argument from ignorance. It's an argument from deep knowledge -- deep knowledge of the mind and of the brain. The invocation of immaterial causation for aspects of mental states is the result of our deep knowledge of the difference between mind and matter.

Perhaps it was more understandable several centuries ago for the philosophically naive to hold to a confident assurance that science would ultimately explain the mind purely in terms of the material brain. Neuroscience has rendered that view no longer tenable. The explanatory gap is real, and our evolving knowledge of neuroscience only makes the futility of materialist attempts to close the explanatory gap even more clear. This is not, pace Dr. Novella, infering a positive conclusion from negative evidence. This is coming to accept the obvious; neuroscience has failed to show how subjective experience arises from objective matter. In this, materialist neuorscientists are a bit late. Philosophers have pointed out the fundamentally different ontologies of mind and matter for several millenia, and it's time for materialistic neuroscientists to admit the obvious. The inference to immaterial causation is an honest effort to address the questions inherent to the mind-brain problem.The inference to materialism is an effort to evade the questions; materialism is an effort to explain the gap away.

And Dr. Novella's reference to "magic" is ironic. It is materialism that invokes "magic" in the mind-brain problem. Materialists insist that meaning and subjective experience arise spontaneously from amalgams of carbohydrates, lipids, and proteins, although a rigorous scientific description of brain physiology can be done without any reference to subjective experience. There's no 'science' there; the inference to subjective experience is epiphenomenal on materialistic science, which inherently lacks reference to subjective states. By denying the real problems raised by the subjective nature of mental states, materialism invokes magical explanations for the mind. The materialist argument is essentially this: 'materialism is the complete explanation for the mind, and if you ask questions, you're a neuroscience denialist'.

Dr. Novella asserts:

...it is clearly established, in my opinion, that the brain causes mind. The gap in our knowledge is in how the brain causes mind. I am open to any hypothesis that is scientifically testable and is compatible with existing established scientific knowledge...To put it another way - Egnor would have you believe that any scientific hypothesis is the same as a "god of the gaps" argument, but they are not. A hypothesis is testable. A"god of the gaps" argument simply inserts a final and untestable answer into a current gap in our scientific knowledge.
Dr. Novella insists that the only question that remains is how the brain causes the mind. And he implicitly restricts the explanations to his dogmatic philosophical materialism, which he confuses with the scientific method, which is the method by which natural effects are studied. Yet natural effects in science need not have natural causes; Big Bang theory, which posits the creation of all matter and time ex-nihilo, explains material effects (matter, time, and natural laws) using an immaterial cause (creation ex-nihilo). 

There is no philosophical, logical, or empirical basis to insist that materialism, or any monistic understanding of nature, is the necessary explanatory framework in natural science. Science is the inference to best explanation for the natural world, and, in keeping with contemporary evidence and scientific gestalt, materialism is no longer in ascendency in the scientific world. Its scientific heyday was in the 18thand 19th centuries, in which Laplace famously bragged that given all of the current physical information about the world he could know the future with certainty. In the 19th century, Darwin proposed to explain all of the complexity of life as a product of material chance and necessity. Yet the 20th century has not been kind to materialist complacency. Quantum mechanics, in many of its interpretations, invokes an observer in order to collapse a waveform. Relativistic cosmology invokes creation ex-nihilo and multiverses. The origin of life problem is essentially intractable, an inference that is supported, rather than weakened, by the panoply of wild guesses as to how it could have happened. Random genetic variation and 'survival of survivors' is grossly inadequate to explain the genetic code and intracellular molecular nanotechnology. The inference that brain matter entirely explains the immaterial aspects of mental states isn't even logically coherent, let alone scientifically verified. The 20th century, materialist denial notwithstanding, has been a catastrophe for strict materialism.

It's mere dogma on Dr. Novella's part-- and historically ignorant dogma, at that-- to assert that materialism explains everything, and to insist that we just wait patiently for the next materialistic revelation.

Materialism explains what it can. As a method -- the invocation of material and efficient causatio n-- it has been quite successful, particularly in classical physics and chemistry as they were developed in the 18th and 19th century. But the 20th century has been very hard on materialism -- creation of the universe ex-nihilo, the observer effect in quantum mechanics, the origin of life, the origin of biological information, the cause of the immaterial mind -- all seem to belie materialist reduction.

There's much that materialism can't explain. Some philosophers and scientists believe that the problem may lie with the artificial restrictions that dogmatic materialism imposes on natural science. Perhaps the natural phenomena on which materialism flounders, such as the Big Bang, the origin of life, the overwhelming evidence for intricate intelligent design in molecular biology, and the immaterial aspects of mental states, are better understood using all four Aristotelian causes -- formal and final causes, as well as material and efficient causes. Perhaps design and teleology play a role in natural science.

To the dogmatic materialist, teleology in nature is a very dangerous inference, because it's incompatible with atheism, which is the materialists' religion. Acceptance of the obvious evidence for design and teleology in nature would force materialists to rethink their worldview, which never comes easy, especially for fundamentalists.


The evidence that some aspects of the mind are immaterial is overwhelming. It's notable that many of the leading neuroscientists -- Sherrington, Penfield, Eccles, Libet -- were dualists. Dualism of some sort is the most reasonable scientific framework to apply to the mind-brain problem, because, unlike dogmatic materialism, it just follows the evidence. 

Materialism's new gods are experts with dice.

Cosmic Coincidences? Materialism Faces a Choice Between Unsavory Options
Evolution News & Views

It's convenient for ID advocates when materialists point out their own predicament so we don't have to do it for them. Such is the case in a recent series for New Scientist about fine-tuning.

One of the articles  begins with an image of a pencil balanced on its point. Stuart Clark says:

Next time you fancy doing something really frustrating, try balancing a pencil on its sharpened tip. Your efforts will succeed for a second at most. Yet the universe has been succeeding at a similar gravitational trick for the last 13.8 billion years. [Emphasis added.]
Clark is describing cosmology's "flatness problem," the ultra-precise balance between expansion and collapse, which one cosmologist likened to balancing a pencil on its point for billions of years. "The universe is as flat as a pancake," his title says. "Coincidence?"

That headline forms a template for five articles in the series, "Our implausible universe: the universe's five most startling coincidences."

"Cosmic dark matter and energy balance -- for now. Coincidence?"

"The universe lines up along the 'axis of evil'. Coincidence?"

"The universe is as flat as a pancake. Coincidence?"

"Space is all the same temperature. Coincidence?"

"The Higgs boson makes the universe stable -- just. Coincidence?"

Each article describes its particular coincidence, suggests models that might explain it, admits that such models don't exist, and leaves the mystery unresolved. Here's a sample about temperature (i.e., the horizon problem). The leading natural explanation is "totally bonkers":

Cosmologists try to explain this uniformity using the hypothesis known as inflation. It replaces the simple idea of a big bang with one in which there was also a moment of exponential expansion. This sudden, faster-than-light increase in the size of the universe allows it to have started off smaller than an atom, when it would have had plenty of time to equalise its temperature.
"On the face of it, inflation is a totally bonkers idea -- it replaces a coincidence with a completely nonsensical vision of what the early universe was like," says Andrew Pontzen at University College London.

After that chastisement, Stuart Clark leaves inflation as the best explanation because nobody has a better idea. It's a bit like Harold S. Bernhardt's quip about the leading origin-of-life theory as shown in Illustra's film Origin: "The RNA world hypothesis: the worst theory for the early evolution of life (except for all the others)."

Accompanying each article, a graphical image of an egg balanced in a loop of string conveys the challenge facing materialists, who by definition are obligated to explain things using only matter and energy.

The more we look at the universe, the stranger it appears. From the geometry of space-time to the masses of the elementary particles, its properties are finely tuned to allow life to exist. More bizarrely, though, it seems to be teetering on the brink of not existing at all. Here we look at five of its seemingly most implausible traits -- and ask what might lie behind them.
Appealing to coincidence is scientifically unsatisfying, so a follow-up article examines the alternatives. The buildup is electric. Like an energetic ringmaster, Gilead Amit introduces the big show. Ladies and Gentlemen! "One idea explains all the weird coincidences in the universe.." Drum roll... five hoops are lit on fire. The door opens. What animal can jump through all five hoops in a single bound? The ringmaster has not only one beast to try it. He has two!

"Don't believe in coincidences but stuck for an explanation? Time to call up the ...." Here come the two contestants. To groans from the audience, he sends in the clowns.

The first clown gets escorted out of the ring by the ringmaster himself. Shoo!

Physicists dislike coincidences such as those set out on these pages, suspecting them of covering up some new principle they don't yet grasp. But when they run out of theories, there's a one-size-fits-all explanation that can answer everything without really answering much at all: the universe is as it is because we're here to see it.
This piece of circular logic is the anthropic principle. A universe inhospitable to life would have no human beings around to observe it, so the one we see must, by definition, possess features essential to accommodating intelligent life. But that doesn't tell us whether a slightly different universe might still host life, why our particular universe exists and not some other, or why we see finely balanced features with no bearing on the emergence of life.

The second clown makes its entrance.

And yet there is an idea that sweeps all these objections away: all conceivable universes exist side by side in a patchwork multiverse. We merely inhabit one out of the infinite selection.
Michael Behe escorts this clown out of the ring. In The Edge of Evolution  (pp. 221-227), he shows why this explanation is the stranger of the two. "The Twilight Zone was never so bizarre" as the multiverse, he says (p. 225), because in a multiverse, everything can happen - and does happen. Brains pop into existence out of the void. "All false thoughts, no matter how detailed, no matter how vivid, will occur without end" (Ibid.). Multiverse theory becomes indistinguishable from brain-in-a-vat theory or solipsism.

Behe proceeds to show that multiverse scenarios are self-refuting and vacuous. "If they were true, you would have no reason to trust your reasoning" (p. 227). And when you think about them a little more, both the anthropic principle and the multiverse reduce to coincidences themselves. It's a coincidence that the universe is at it is so that we are here to see it. It's a coincidence that we won the cosmic lottery. Both ideas appeal to nothing beyond coincidence. So materialists have three choices to explain the fine-tuning of the cosmos: (1) coincidence, (2), coincidence, and (3) coincidence. New Scientist ends the series by admitting as much:

But some still see the multiverse as an abdication of scientific responsibility: a fancier way of simply saying "coincidences happen". And, if true, it means some astronomers out there are forced to justify a universe even more replete with coincidences than ours, while others could be bored stiff in a completely random cosmos.
There is a way out of the coincidence trap. It's no coincidence that Behe argues for another option. His alternative takes explanation out of the circus and back to the academy. Instead of abdicating scientific responsibility, it responsibly assigns known causes that are necessary and sufficient to explain the effects. Instead of shooting itself in the foot, it justifies reason. And it's not bizarre; it's intuitively obvious.

Instead, I conclude that another possibility is more likely: The elegant, coherent, functional systems on which life depends are the result of deliberate intelligent design (p. 166).

Only intellectual bias would forbid using this option in scientific explanation.

Healing in the scriptures:The Watchtower Society's commentary.

HEALING

The restoring of health to the sick; the making sound, or whole, that which is broken or injured; the curing of various diseases and defects; the returning of a person to the general state of well-being. The Hebrew verb ra·phaʼʹ and the Greek verb i·aʹo·mai are the principal words in the Bible that describe such healing in both a literal and a figurative sense. The Greek verb the·ra·peuʹo is rendered ‘cure.’ (Mt 4:23, 24) Sometimes the healing was a gradual matter; at other times it was instantaneous.

Among the blessings Jehovah bestowed on all mankind is the regenerative power of their physical organisms, the ability of the body to heal itself when wounded or diseased. A physician may recommend certain measures to speed recovery, but in reality it is the God-given recuperative powers within the body that accomplish the healing. Hence, the psalmist David acknowledged that though he was born imperfect, his Creator was able to sustain him during illness and heal all his maladies. (Ps 51:5; 41:1-3; 103:2-4) Jehovah restored the bodily health of afflicted Job (Job 42:10) and God also provided physical healing for his people Israel.—Ex 15:26.

Of Jehovah it is written that he both wounds and heals, and he does this literally and figuratively. Hence, with him there is a time to wound and a time to heal. (De 32:39; compare Ec 3:1, 3.) Unfaithful Jehoram, king of Judah, for example, was punished by Jehovah with a physical disorder of the intestines for which there was no healing. (2Ch 21:16, 18, 19) Moses recognized that it was Jehovah who had stricken Miriam with leprosy; hence, he pleaded with the only One who could cure her, saying: “O God, please! Heal her, please!” (Nu 12:10, 13) In the matter of childbearing, Jehovah healed King Abimelech, his wife, and his slave girls after the crisis had passed involving Sarah and the seed of promise.—Ge 20:17, 18.

In the Bible, spiritual rather than physical breakdown, and spiritual healing in turn, are subjects of particular significance. Attention is called to the responsibility of natural Israel’s leaders in these matters. “From the prophet even to the priest, each one [was] acting falsely” in Jeremiah’s day, they at the same time making a pretense of healing the breakdown of God’s people, claiming that all was well. (Jer 6:13, 14; 8:11) In this they were very much like Job’s comforters, “physicians of no value.”—Job 13:4.

In a few instances inanimate objects were healed, in the sense of being made whole again, like the torn-down altar Elijah mended. (1Ki 18:30) Also, the prophet Elisha healed the waters near Jericho so that they no longer caused miscarriages. (2Ki 2:19-22) Jeremiah, however, shattered the potter’s flask so completely that it was beyond repair, that is, beyond healing, and thus furnished a fine illustration. “In the same way,” Jehovah declared, “I shall break this people and this city as someone breaks the vessel of the potter so that it is no more able to be repaired [a form of ra·phaʼʹ; literally, healed].”—Jer 19:11; compare 2Ch 36:15-17.

Jesus and His Fellow Healers. Jesus Christ recognized that “teaching . . . and preaching the good news of the kingdom” was of first importance in his ministry and that “curing every sort of disease and every sort of infirmity among the people” was secondary. That is why he felt pity for the crowds primarily “because they were skinned and thrown about like sheep without a shepherd.”—Mt 4:23; 9:35, 36; Lu 9:11.

This Great Teacher also showed compassion on the multitudes that followed him because they hoped that he would heal their physical ailments. (Mt 12:15; 14:14; 19:2; Lu 5:15) His miraculous healing work served as a visible sign to his generation and gave added evidence of his Messiahship, as prophesied. (Mt 8:16, 17) It also foreshadowed the healing blessings that will be extended to mankind under God’s Kingdom rule. (Re 21:3, 4) In a very real sense Jesus healed and restored the health of many persons—the lame, the maimed, the blind, the dumb (Mt 15:30, 31), the epileptic, the paralytic (Mt 4:24), a woman suffering from a hemorrhage (Mr 5:25-29), one with a withered hand (Mr 3:3-5), a man with dropsy (Lu 14:2-4), and on many occasions those who were demon possessed were released from their Satanic enslavement and bondage.—Mt 12:22; 15:22-28; 17:15, 18; Mr 1:34; Lu 6:18; 8:26-36; 9:38-42; Ac 10:37, 38.

Jesus’ manner of curing people took various forms at different times. “Get up, pick up your cot and walk,” is all that Jesus said on one occasion, and a sick man near the pool of Bethzatha was cured. (Joh 5:2-9) In another instance, Jesus just spoke the word and the ailing one, though a distance away, was healed. (Mt 8:5-13) At other times he personally laid his hand on the sick one (Mt 8:14, 15) or touched a wound and healed it. (Lu 22:50, 51) Several diseased persons simply touched Jesus or even the fringe of his garment and were healed. (Mt 14:36; Mr 6:56; Lu 6:19; 8:43-47) And it made no difference that the persons had been afflicted with the disease for many years.—Mt 9:20-22; Lu 13:11-13; Joh 5:5-9.

Some persons opposed Jesus, not appreciating the wonderful healing work he was doing. The religious leaders were greatly angered when Jesus healed persons on the Sabbath. (Mt 12:9-14; Lu 14:1-6; Joh 5:10-16) On one such occasion Jesus silenced opponents by saying: “Hypocrites, does not each one of you on the sabbath untie his bull or his ass from the stall and lead it away to give it drink? Was it not due, then, for this woman who is a daughter of Abraham, and whom Satan held bound, look! eighteen years, to be loosed from this bond on the sabbath day?”—Lu 13:10-17.

It was not the application of Jesus’ own power, knowledge, or wisdom that healed the sick. Neither was hypnotherapy, psychotherapy, or any similar method used. Rather, it was the spirit and power of Jehovah that effected such healing. (Lu 5:17; 9:43) Not all, however, were grateful enough to give God the glory for these cures. (Lu 17:12-18) Today, not everyone recognizes the everlasting healing benefits made available through the ransom sacrifice of Christ.—1Pe 2:24.

Jesus delegated this divine power of healing to others who were closely associated with him in his ministry. When the 12 apostles were sent out, and later the 70 disciples, they were empowered to cure the sick. (Mt 10:5, 8; Lu 10:1, 8, 9) After Pentecost of 33 C.E., certain ones, including Peter, John, Philip, and Paul, were given this divine power to heal completely. (Ac 3:1-16; 4:14; 5:15, 16; 8:6, 7; 9:32-34; 28:8, 9) After Christianity became firmly rooted, and with the passing of the apostles off the scene, such “gifts of healings” also passed away.—1Co 12:8, 9, 28, 30; 13:8, 13.

It was important that the one performing the cure have full faith and confidence in Jehovah and acknowledge, as Jesus did, that the curing was accomplished by God’s power. (Mt 17:14-20; Joh 5:19) It was not necessary, however, for the afflicted ones to have faith before being cured. (Joh 5:5-9, 13) Many, though, did have strong faith.—Mt 8:5-13; 15:28; Mr 5:34; Lu 7:1-10; 17:19; Ac 14:8-10; see FAITH.

Miraculous healing was to be a “sign” of divine backing. (Ac 4:22, 29, 30) Those who refused to recognize and acknowledge this sign were spiritually blind and deaf. (Isa 6:10; Joh 12:37-41) For the reason, then, that divine healings were to serve as a sign to unbelievers, they were not ordinarily performed in behalf of those who were already spirit-begotten Christians. So when Timothy had stomach trouble, instead of performing a miraculous cure, Paul recommended that he take a little wine for his ailment.—1Ti 5:23.

Spiritual Healing. On the other hand, true spiritual healing comes from Jehovah to repentant ones. It means a return to his favor and the enjoyment of his blessings once again. (Isa 19:22; 57:17-19; Jer 33:6) Such healing has the effect of strengthening the weak hands and wobbly knees, opening blind eyes, restoring hearing to the deaf, healing the lame, and giving speech to the dumb, in a spiritual way. (Isa 35:3-6) But those incorrigible in their apostasy never experience a healing, or restoration to good health and prosperity spiritually. (2Ch 36:15-17; Isa 6:10; Jer 30:12, 13; Ac 28:24-28) Similarly, there was to be no healing for Egypt, her Pharaoh, and for the “king of Assyria.”—Jer 46:11; Eze 30:21; Na 3:18, 19.


The Scriptures prescribe the remedy for persons who are spiritually sick.—Heb 12:12, 13; Jas 5:14-16; Re 3:18.

The origin of our universe remains as mysterious as ever.

What came before the big bang?
By Douglas Heaven

PAUSE. Rewind. Suddenly the outward rush of 200 billion galaxies slips into reverse. Instead of expanding at pace, the universe is now imploding like a deflating balloon: faster and faster, smaller and smaller, everything hurtling together until the entire cosmos is squeezed into an inconceivably hot, dense pinprick. Then pshhht! The screen goes dead.

According to the big bang theory – our best explanation for why space is expanding – everything exploded from nothing about 13.8 billion years ago. Cosmologists have been able to wind things back to within a tiny fraction of a second of this moment. But now they’re stuck.

The trouble is, our understanding of space-time, and gravity in particular, is built from Einstein’s equations of general relativity, whereas the extreme conditions of the very early universe can only be described by quantum mechanics. No one knows how to reconcile the two to take us further back. “The rules we have simply don’t work in that regime,” says Carlo Contaldi at Imperial College London. “Nothing makes sense any more.”

That’s a problem for our origin story. Did time begin with the big bang? Or was there an epoch before it?

Some insist that if we rewind the universe far enough, time just stops.But Lee Smolin of the Perimeter Institute for Theoretical Physics in Waterloo, Canada, is having none of it.


“It’s a cute idea but there’s not much evidence for it,” he says. In fact, Smolin wants to see the idea that the universe has a starting point dropped entirely. We can only hope to explain why our universe is the way it is, he says, if there was something before the big bang. It’s about cause and effect; to arrive at satisfying explanations ...

Time to unhype A.I?:Pros and cons.

A clash of Titans XXXVII

File under "Well said" XLII

He is richest who is content with the least, for content is the wealth of nature. Socrates

On the "my I.D is better than yours" argument against I.D.

Alien Physics: Scientist Offers Novel Escape Hatch from Intelligent Design

David Klinghoffer

As I've said before, intelligent design can take or leave extraterrestrial life. It doesn't affect the cogency of ID arguments one way or the other. Materialism, on the other hand, must have ETs and the more intelligent and advanced, the better. After all, human life can't be special, therefore something like us must be replicated across the cosmos.

The problem is that the universe offers no hint of objective evidence for ETs. So the race is on to find plausible rationales for why the heck not. Enter Columbia University astrophysicist Caleb Scharf with a novel idea: We can't see advanced otherworldly life because it's so advanced it has encoded itself in the structure of the universe itself ("Is Physical Law an Alien Intelligence?").

Actually it's literally a novel idea since, as he points out at the end of an article for Nautilus, Carl Sagan came up with it in his science fiction classic Contact back in 1985.

[I]f the cosmos holds other life, and if some of that life has evolved beyond our own waypoints of complexity and technology, we should be considering some very extreme possibilities. Today's futurists and believers in a machine "singularity" predict that life and its technological baggage might end up so beyond our ken that we wouldn't even realize we were staring at it. That's quite a claim, yet it would neatly explain why we have yet to see advanced intelligence in the cosmos around us, despite the sheer number of planets it could have arisen on -- the so-called Fermi Paradox.

For example, if machines continue to grow exponentially in speed and sophistication, they will one day be able to decode the staggering complexity of the living world, from its atoms and molecules all the way up to entire planetary biomes. Presumably life doesn't have to be made of atoms and molecules, but could be assembled from any set of building blocks with the requisite complexity. If so, a civilization could then transcribe itself and its entire physical realm into new forms. Indeed, perhaps our universe is one of the new forms into which some other civilization transcribed its world.

These possibilities might seem wholly untestable, because part of the conceit is that sufficiently advanced life will not just be unrecognizable as such, but will blend completely into the fabric of what we've thought of as nature. But viewed through the warped bottom of a beer glass, we can pick out a few cosmic phenomena that -- at crazy as it sounds -- might fit the requirements.

What's that about a beer glass?

Actually, this is clever as a thought experiment. As an illustration of how his alien physics idea might be true, he suggests that mysterious dark matter, thought to constitute 27 percent of the mass and energy of the universe we see, might not be the formless, structure-less stuff we imagine. Perhaps it's more like cloud storage for alien civilizations that have uploaded themselves.

Coming on top of biologist Andy Gardner's proof against ID that I mentioned this morning -- from the fact that gazelles don't leap into the mouths of waiting cheetahs, as a perhaps "slightly facetious" Dr. Gardner would design things if he were in charge -- this is a good day for some rather underwhelming attempts to escape from scientific indications of ID.

So Scharf's escape hatch is to posit alien design in the cosmos in the form of physics and its laws. At first glance this doesn't sound radically at variance with Discovery Institute biologist Michael Denton's argument (see the Privileged Species website) that chemistry and physics, with their extraordinarily detailed fitness for life, give evidence of design.

One difference is that a suggestion like Scharf's is intended, perhaps not consciously, to evade the possibility that a designer is outside nature, something that the game of science as currently played arbitrarily excludes. Denton more reasonably leaves the question open. The other difference is that Denton's evidence is massive, while Scharf's is hard to distinguish from sci-fi.

On the "If I were God" argument against I.D

Biologist's New Argument Against Intelligent Design: Under ID, Gazelle Should Run Toward Cheetah

David Klinghoffer

It will be a treat to have the recording of last week's Royal Society conference, "New Trends in Evolutionary Biology,," to confirm the exact wording of a few choice quotes from the event. We've already pointed out this slide from Andy Gardner   of the University of St. Andrews. It says that Darwinism's "process" is "natural selection," its "purpose" being to "maximize fitness." ID's "process," on the other hand, is "God did it" while its purpose is "???"

What a way to turn a serious argument into a ludicrous cartoon. Completing the picture, Evolution News contributor Jonathan M., who was in the audience, notes on Facebook today that Dr. Gardner added a further observation. We alluded to this briefly before, but it deserves special highlighting. Jonathan writes, "And of course, if God made the gazelle, he would have made it run towards the cheetah. He really said this."

We've now had two reports of this. I double-checked to make sure there was no misunderstanding on my part or humorous intent on Jonathan's.

I am not joking. He said that, if the gazelle was designed, then its "purpose" is to provide food for the cheetah; and so we should expect it to be designed to run towards the cheetah rather than away. I think he was being slightly facetious but he really did say that.
"Slightly facetious" or not, folks, what we have here is a biologist speaking on "Anthropomorphism in evolutionary biology" before the world's most august scientific body and telling those assembled that, if ID is true, the direction of the gazelle's fleet running is in the wrong direction. It ought to jump straight into the cheetah's mouth.


Can you make this stuff up? Maybe you could. For myself, I don't have the imagination for it.

It's irreducible complexity all the way down.

What It Takes to Build a Hook for the Flagellum
Evolution News & Views

You've just been hired as a software engineer. Your first project is to write code that will operate robotic machines. The robots need to build a high-speed universal joint and fasten it to a shaft that will rotate at high speed. The code needs to select materials that can tolerate the high stresses they will face, and arrange them into flexible, mutually-reinforcing configurations that will provide high performance and fault tolerance over many cycles of switching between prograde and anterograde rotations. Oh, and it needs to be hollow so that other materials can pass through during operation. Good luck.

Would everyone agree a new hire facing this challenge had better have high intelligence, combined with a great deal of experience with materials and Einsteinian knowledge of physics? What if you were told the company is considering farming out the task to a brainless entity with no sensors that can only rely on sheer dumb luck?

New light has been shed on just one part of the molecular machine that started Michael Behe on his revolutionary role as a champion of intelligent design: the bacterial flagellum. We often hear the parts of this iconic molecular machine rattled off in a list: rotor, stator, hook, propeller etc. The elegant animations in our new documentary Revolutionary certainly make the point, but not shown are some additional levels of complexity beneath the exterior that put extra oomph into the case for ID. A new paper opens Darwin's black box further.

In Nature Communications, five researchers from the Okinawa Institute of Science and Technology in Japans describe the "complete structure of the bacterial flagellar hook" in Campylobacter jejuni, a bacterium with a single flagellum at one end of its spiral-shaped rod-like cell (some varieties have two flagella, one at each pole). C. jejuni colonizes the digestive tracts of cattle and many birds without apparent harm, but we humans don't want it in our guts, because it is a major cause of food poisoning. Proper cooking of poultry and meat usually prevents disease. But we digress; such matters are beyond the domain of intelligent design theory. The focus is on whether the flagellar hook is designed or not.

Before looking at C. jejuni's flagellum, let's compare the outboard motor styles of different bacteria. The authors write:

Flagella are found in both gram-positive and gram-negative bacteria. Although flagellar hooks appear identical at first sight, the diversity of flagellar hook proteins suggests that the hooks have diverged to specifically fit the motility requirements of each bacterium. The cells of the food-borne pathogen, Campylobacter jejuni (C. jejuni) are spiral-shaped and are able to move using unipolar or bipolar flagella, in comparison with rod-shaped S[almonella] enterica cells, which move using many peritrichous flagella over the cell surface. Uniquely, the C. jejuni flagellar hook is also used to export virulence factors during colonization of the avian or human host. Intriguingly, the C. jejuni hook protein, FlgEcj, has one of the longest amino acid sequences compared with other bacterial FlgE proteins. Compared with FlgE from S. enterica, FlgEcj is about twice as large. We solved the structure of the hook of a fliK null mutant strain derived from C. jejuni strain 81116 (NCTC 11828) by electron cryo-microscopy, using single-particle averaging methods with image segment classification followed by systematic symmetry exploration. [Emphasis added.]
As stated, there appear to be "motility requirements" behind the different motor styles, even though the authors do not question whether they evolved:

Flagella, although macroscopically similar, have evolved features that will make them specially adapted to particular tasks. The intestinal jejunum is a viscous environment where C. jejuni is adapted for swimming. The results shown here tend to support the idea that additional strengthening of the hook in C. jejuni is necessary to enable motility in this viscous environment.
So they are really talking about adaptation, not evolution. Nowhere do they describe how this extra-strong flagellum originated or how it evolved from another species. One story they tell is beside the point:

Amino acid sequence variability in the central parts of FlgE proteins of C. jejuni strains was proposed to occur because of selection pressure during host invasion to generate variations in surface-exposed antigenic determinants. The variable regions do indeed correspond to the surface-exposed region of C. jejuni hook domains D3 and D4. The variability is tolerated because these regions are not essential for intra-molecular contacts that organize the hook.
That appears to be a case of degeneration, not innovation. It's a type of variation not related to function.

What they really know is that this flagellar hook meets the design requirements for its particular environment. The point of their paper is that the hook region of this species' outboard motor, "reveals extensive set of stabilizing interactions."

That's where things get interesting, because a hook is really a universal joint. A universal joint has to be able to transmit rotary power from a shaft through a range of angles. The laws of physics come into play here: torque, angular momentum, and material strain. An outboard motor with a universal joint will have to meet design requirements to handle extra strain, especially when the viscosity of its medium increases. Think of the stresses on a universal joint operating in oil instead of water, for instance. Now rev up the RPMs, and you can see what the software engineer is up against!

Bacterial flagella have long been studied, but many aspects of their structure and function are still eluding us. The structure of the hook can be described as a tubular helical structure. The hook functions like a universal joint. It transmits the torque, produced by the motor located in the cell membrane, to the filament that acts like a propeller. The assembly of about a 100 copies of a single protein, FlgE, makes the bacterial flagellar hook. An exported molecular ruler protein, FliK, controls the hook length. Cells bearing mutations in the fliK gene produce abnormally long 'polyhook' structures. The bacterial flagellar motor rotates at frequencies that vary between 100 Hz and 2,000 Hz depending on bacterial species. The hook undergoes multiple conformational changes while rotating around its axis. During these conformational changes, the interactions between the FlgE molecules must secure the stability while enabling the dynamic nature of the hook.
Get that calculator out. 100 Hz is 6,000 RPM; 2,000 Hz is, let's see, yikes! 120,000 revolutions per minute! Our software engineer is getting really worried. His application only has one shaft, but the universal joint has to handle extreme torque in viscous fluid. The strain on the material is going to be enormous! How can he make it strong enough without compromising its flexibility?

Extra domains in FlgE, found only in Campylobacter and in related bacteria, bring more stability and robustness to the hook. Functional experiments suggest that Campylobacter requires an unusually strong hook to swim without its flagella being torn off.
If the engineer is smart, he will just mimic the elegant solution of the bacterium C. jejuni. Take a look at Figure 2 in the open-access paper. It's beautiful. Multiple strands of the FlgE protein (remember, it's twice as long as its counterparts in other species) intertwine in five layers. Each layer contains complex interactions with the other layers, providing the strength needed for the application, "while still allowing it to curve." Even more amazing, "the interactions between the molecules that make the hook are transient interactions where interacting amino acid residues will constantly change partners during the rotation of the hook."

A committed Darwinist might still be able to weave a just-so story about how this hook evolved. Once upon a time, Campylobacter having a simpler hook with fewer strands of FlgE invaded a new environment that was more viscous. By accident, a mutant with duplicate layers of FlgE succeeded in swimming without its flagella being torn off, so its descendents survived. By another accident, the ones with longer FlgE proteins also survived, perhaps by duplication. Somehow, blindly, complex transient interactions arose... etc. Sound convincing?

Evolutionists might argue that the hook only employs FlgE proteins, so it is not irreducibly complex. Nothing about Behe's irreducible complexity principle, however, requires multiple types of materials. It's their arrangement for function that matters. All the parts for a mousetrap, for instance, could be made of iron. In the case of the flagellar hook, the arrangement of the proteins in multiple layers with multiple transient interactions is the key to its operation. Remove these layers and interactions, and the flagellum would be torn off when the bacterium tried to swim.

We haven't even addressed the issue of how this hook is assembled in the cell. To be heritable, mutations would have had to occur in the DNA. Those mistakes would have to evade the proofreading mechanisms of the cell during transcription and translation. But even if the mutant proteins arrived at the construction site (at the right time and in the right quantities, don't forget), how would other molecular machines know what to do with them? Unless they got assembled correctly so that the transient interactions would take place properly during operation, they would provide no benefit; there would be no "selection pressure" to maintain them. The evolutionary story seems even more implausible at the level of coding and construction.


So there you have it: even the hook of the famous flagellum is irreducibly complex. It is amazingly well designed for its task within a task, that of being an essential part of a multi-part molecular machine. As Jonathan Wells says, "What we have here is irreducible complexity all the way down."

Doing well by doing good.

Witnesses Win Major Awards for Green Building Design and Construction

NEW YORK—Jehovah’s Witnesses, well-known for their global Bible education work, are receiving recognition for excellence in environmentally sustainable building design and construction.



The Green Building Initiative (GBI) awarded certifications for two new buildings at the Witnesses’ United States branch facilities in Wallkill, New York: the Watchtower Farms F Residence, completed in late 2012, and the Watchtower Wallkill Office Building, completed in 2014. Both of the buildings received the highest award of Four Green Globes.


Watchtower Wallkill Office Building


Shaina Sullivan, Marketing Director for GBI, notes: “Worldwide, less than 4 percent of all buildings assessed under the program have achieved this top certification of Four Green Globes.” Ms. Sullivan added that the Watchtower Wallkill Office Building “is the first nonresidential project in New York State to earn this rating.” Jenna Middaugh, Project Manager for GBI, commented: “Of the 23 buildings [in the United States] that have been certified with Four Green
 Globes since 2006, the Watchtower Wallkill Office Building achieved the highest point score with 94 percent.”


Watchtower Farms F Residence

GBI administers Green Globes as a commercial rating system and certification program that utilizes a third-party on-site assessment of sustainable design and construction. Achieving a Green Globes rating requires environmentally sensitive site design that focuses on water management, minimization of energy consumption and greenhouse gas emissions, minimizing the impact on natural resources by selection of appropriate materials, and creating a healthful indoor environment.


Photovoltaic panels provide at least 10 percent of the electrical energy needs for the Watchtower Wallkill Office Building, a feature of the building’s award-winning sustainable design.

David Bean, sustainable design coordinator for the Witnesses’ facilities in the United States, says: “The achievement of these awards attests to the high standard of design and construction work that we set for all of our projects. We are also pursuing Green Globes certification in the design and construction of our new world headquarters in Warwick, New York.”


Installation of a green roof, one of the sustainable features of the Witnesses’ new world headquarters in Warwick, New York.

Zeny St. Jean, who coordinates global building projects for Jehovah’s Witnesses from their world headquarters, states: “While our primary focus is the advancement of Bible education, we appreciate these awards as professional recognition of the environmentally conscientious building design and construction that we strive to implement at our facilities around the world.”

Media Contact(s):


International: J. R. Brown, Office of Public Information, tel. +1 718 560 5000

Phone call for Dr.Moreau!

"The Link," or Science Fiction Double Feature: Dr. X Builds a Creature...
Richard Sternberg 

(Cue music.) Or, rather, a lemur. Almost every TV channel it seems ran a commercial announcing a documentary about the fossil find of the century, The Link, which will be encored on the History Channel tonight. "Ida," as the female holotype of Darwinius masillae has been playfully dubbed, is the prehistoric prosimian that is the focus of attention. The story of her discovery is the stuff of every good science-fiction B-movie from the 1950s : A "secret study" conducted by an "international team of scientists," has led to earth-shattering results that can only now be revealed to the world. Think Creature from the Black Lagoon (because of the fossil find) meets When Worlds Collide (because of the impact that will be felt on your everyday life) and you'll be close to the stated importance of the program. All that's missing are some Tesla coils, a hidden lair in a dead volcano, the fallout from an atomic explosion, and a UFO landing on the National Mall. Presumably such extra features, along with more specifics about the significance of her all too brief life -- "a child when she died, but she'll change history forever" -- can be gathered from the just-released book, The Link.

It's just a jump to the left...

Of the cladogram, I mean. There is one clade of primates called the Strepsirrhini ("wet noses") that includes the lemurs, the dwarf and mouse-lemurs, the Aye-aye, the lorisids, and the galagos. Ida falls within this suborder according to one hypothesis.

With your hands on your hips...

You will kindly note the other clade of primates termed the Haplorrhini, the sister group of the strepsirrhines. This taxon of the "dry noses" contains the apes, monkeys, and tarsiers. An alternative phylogenetic hypothesis would place Darwinius at the base of this assemblage.

All the brouhaha thus boils down to whether Ida had a wet nose or a dry nose that -- given her status as a transitional form -- was occasionally runny. The theme of The Link is that the latter is a sure bet. For myself, regarding these two alternative evolutionary scenarios, I say...Let's do the Time Warp again...

Anyhow, there I sat yesterday evening, with voyeuristic intention no less, my gin and tonic prepared and my lit cigarette firmly affixed in its black holder, shivering with antici......pation. For, indeed, I wanted to go up to the lab in order to see what's on that slab. But it wasn't the rain that was to blame for my later symptoms of underwhelment. No. It was that after all the commercial hoopla, I expected to hear a speech close to that given by the indefatigable Dr. Furter (Tim Curry) just prior to the dramatic vivification of his creature. That is, my expectation was to see and listen to a pronouncement much like this:

Tonight my conventional unconventionalists, you are to witness a new breakthrough in phylogenetic research and career paradise...is to be mine!

It was strange the way it happened. Suddenly you get a break...All the pieces seem to fit into place. What a sucker you've been...what a fool. The answer was there all the time [on the fossil market, that is]. It took a small accident to find it...an accident! And that's how I discovered the secret, that elusive ingredient, that spark...that is The Link. Yes. I have that knowledge. I hold the secret...to evolution itself!

My interest of course did not concern who actually said it. Or that he would be wearing a tee shirt and jeans as opposed to a green surgical smock over a corset and fishnets (and adorned with oversized pearls). Not at all. What I instead wanted to view was a program where the could-be's and perhapses, the equivocations and qualifications, the oh so many "well, on the one hand...but, then again, on the other" semantic hedges, that are de rigueur in documentaries about evolution, had been dropped with an unabashed flair.

Is it not The Link? Does it not change everything? I asked.

Obviously, as no doubt anyone of you could have told me, my expectations were misplaced. Part of me also desired to see an animation of Ida throw a bone into the air and then have the scene immediately segue to that of a futuristic Pan Am spacejet on its way to an orbiting station called "Darwin 9000," set to the opening strains of Johann Strauss II's "On the Beautiful Blue Danube." I was mentally blending genres in my hopes, true, but in my defense the commercial had promised so very much.

Alas, the disappointment that soon arose in me after the documentary stemmed from the vagueness of it all...that The Link is actually a kind of, sort of, nth cousin mth removed of the side lineage that some hypothesize possibly gave rise to the distant ancestors of what quite conceivably became the hominid branch of the Darwinian tree. And to think that I could have been watching reruns of Mystery Science Theatre 3000 or the cult classic, The Phantom of the Paradise.

To be certain, the authors of the PLoS One paper were appropriately circumspect in their paper, so one should not misconstrue my peeve as really being about the finer details of basal primate taxonomy. As far as I'm concerned, Ida may well be the transitional taxon linking the Strepsirrhini and Haplorrhini. Fine. Who is going to get strung out -- to again borrow a phrase from the illustrious Dr. Furter -- if the Notharctidae and Cercamoniinae are rendered by implication paraphyletic, wastebasket taxonomic groupings? Who? Nor is there a limit to such theoretical gratuity...should someone even want to posit that each and every genus in the Cercamoniinae, from Anchomomys to Darwinius to Pronycticebus, is in its own right a missing link -- the same way, you know, that everyone's special -- no complaint will be uttered from this quarter. Not so much as a peep.

Irksome, though, was the way in which an old story was sold as something profoundly novel. While watching it, I could almost hear the creator of this work of science fiction (defined by that definitive fount of knowledge Wikipedia as "science-based depictions of phenomena that aren't necessarily accepted by mainstream science," emphases mine) singing as the fossil was presented: In just seven days...I can make you a humaaaannnnnn. (My sincerest apologies to Richard O'Brien of the Rocky Horror Picture ShowR for the way I have twisted his lines and songs from the film.) But the issue is that a familiar feeling emerged while watching the piece, the one we have all had in the theater. It arises the moment you realize that you know the plot, the narrative. The only difference is that the characters and the actors playing them have changed, along with the music and the CGI effects. Eight years ago it was the Urwhale. Last year it was the Ursalamander. Last night it was the Urmonkey. Still, the same story...

That said, I would not have been so underwhelmed had someone just blurted out in the first few minutes -- like the inimitable Charles Gray does at the end of Rocky Horror -- the central theme of the documentary, that "crawling...on the planet's face...some insects called the human race. Lost in time...lost in space...and meaning."


R(Rated R) -- For mature audiences only.

On the grandfather of I.D.

Michael Behe on the Legacy of Denton's Evolution: A Theory in Crisis
David Klinghoffer









Ever wonder what major and highly original scientific advocates of intelligent design think of each other's work? In a brief video conversation, Michael Behe comments on the impact and significance of Michael Denton's books Evolution: A Theory in Crisis  and Evolution: Still a Theory in Crisis , culminating in the typological understanding of life's structures and the fundamental challenge to Darwinian theory that poses.


Dr. Behe's case for ID, first advanced in Darwin's Black Box twenty years ago, is the subject of the new hour-long documentary  Revolutionary: Michael Behe and the Mystery of Molecular Machines, written and directed by John West. Get your copy of Revolutionary, on DVD or Blu-ray, today.

Rich gene,poor gene?

Prince or Pauper? Researchers Find Functional Pseudogene in Fruit Fly
Evolution News & Views 

Suppose we introduced you to a friend and said he works as a pseudoscientist. You would be immediately suspicious of his white lab coat and apparent command of scientific language in subsequent conversation. After all, he just pretends to be a scientist. He's fake. He's false. He is bogus, sham, phony, mock, ersatz, quasi-, spurious, deceptive, misleading, assumed, contrived, affected, insincere, and all the other negative synonyms we associate with the prefix pseudo.

But then suppose we corrected the description and said that, actually, he is a "pseudo-pseudoscientist." The double negative suddenly opens the possibility that he really is a scientist. He's faking his fakery, contriving his contrivance, mocking insincerity for some reason. Maybe he's a psychologist studying the effects of perceived pretentiousness, using you as his lab rat. Maybe he's a real MD playing a doctor on a fictional TV show, leading us to believe he is "just an actor." Think of the guards in Mark Twain's The Prince and the Pauper who quickly escort the shabbily dressed prince off the palace grounds without noticing the royal seal in his pocket. Have scientists too quickly dismissed pseudogenes as broken genes, worthless transcripts of DNA without function? Could at least some of them be "pseudo-pseudogenes"?

A surprising paper in Nature actually uses that term: "Olfactory receptor pseudo-pseudogenes." Researchers in Switzerland found a case in a species of fruit fly that defies the pseudogene paradigm. Pseudogenes are often suspected of being broken genes when a premature termination codon (PTC) is found in the DNA sequence. Obviously, such a gene could not be translated into a functional protein, right? Translation would stop before the messenger RNA is complete. Often, that is the case. What good is that?

These scientists found something interesting about an olfactory receptor gene in Drosophila sechellia, "an insect endemic to the Seychelles that feeds almost exclusively on the ripe fruit of Morinda citrifolia." They looked at its Ir75a locus, a gene that encodes an olfactory receptor for acetic acid in its more famous cousin D. melanogaster, Finding a PTC in this species' Ir75a gene, they initially thought it was a broken gene -- a pseudogene. The abstract begins with the usual evolutionary rhetoric about pseudogenes:

Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes. Although certain pseudogene-derived RNAs have regulatory roles, and some pseudogene fragments are translated, no clear functions for pseudogene-derived proteins are known. Olfactory receptor families contain many pseudogenes, which reflect low selection pressures on loci no longer relevant to the fitness of a species. [Emphasis added.]
That's their setup for the surprise announcement. This pseudogene might just be a "pseudo-pseudogene"! It might be a prince masquerading as a pauper.

What started them on their paradigm-breaking find was noticing that this apparent pseudogene is fixed in the population, suggesting it has a function. Taking a closer look, they found that the translation machinery is able to "read through" the premature stop codon, the PTC. How? They're not sure, but they found something else interesting: the read-though operation works efficiently only in neurons, not other types of cells. That opens up a whole new way of looking at pseudogenes: some of them might be tissue-specific regulators.

It is not yet clear how the D. sechellia Ir75a PTC is read through. It cannot be because of insertion of the alternative amino acid selenocysteine (which is incorporated at UGA18). Moreover, no suppressor tRNAs are known in D. melanogaster and ribosomal frame-shifting is also unlikely because there is no change in the reading frame after the PTC. We suggest that read-through is due to PTC recognition by a near-cognate tRNA that allows insertion of an amino acid instead of translation termination. Although the trans-acting factors regulating read-through are unclear, the neuronal specificity of this process is reminiscent of RNA editing and micro-exon splicing, in which key responsible regulatory proteins are neuronally enriched. We therefore speculate that tissue-specific expression differences in tRNA populations underlie neuron-specific read-through.
We might be tempted to dismiss this as a rare case of evolutionary tinkering. The gene broke, but natural selection found a way to tinker with it and get it to work. Perhaps. But further experimentation with D. melanogaster suggests that "pseudogenization" has a logical function: it works to tune odor sensitivity. The part of the gene downstream from the PTC apparently affects the type of receptor produced. What's more, this kind of regulation might not be rare.

Read-through is detected only in neurons and is independent of the type of termination codon, but depends on the sequence downstream of the PTC. Furthermore, although the intact Drosophila melanogaster Ir75a orthologue detects acetic acid -- a chemical cue important for locating fermenting food found only at trace levels in Morinda fruit -- D. sechellia Ir75a has evolved distinct odour-tuning properties through amino-acid changes in its ligand-binding domain. We identify functional PTC-containing loci within different olfactory receptor repertoires and species, suggesting that such 'pseudo-pseudogenes' could represent a widespread phenomenon.
Experiments showed that the Ir75a 'pseudo-pseudogene' actually yields a functional odor receptor, but not for acetic acid as in D. melanogaster. Instead, it makes a receptor tuned for similar acidic odorants unique to food sources available on the Seychelles. The tissue-specific read-through capabilities of this gene provide the fly with a way to detect food sources it needs in its environment.

Perhaps nothing beyond chance mutation or neutral drift is needed to explain this. On the other hand, the research team may have stumbled onto an important function for pseudogenes.

Our efforts to understand the molecular basis of the loss of olfactory sensitivity to acetic acid in D. sechellia led us to discover a notable and, to our knowledge, unprecedented evolutionary trajectory of a presumed pseudogene. Efficient read-through of a PTC in D. sechellia Ir75a permits production of a full-length receptor protein, in which reduction in acetic acid sensitivity and gain of responses to other acids is due to lineage-specific amino acid substitutions in the LBD pocket. The PTC does not noticeably influence the activity of D. sechellia Ir75a, suggesting that it is selectively neutral from an evolutionary standpoint. We propose that it became fixed through genetic drift, given D. sechellia's persistent low effective population size.
They can call it an "evolutionary trajectory" if they wish. Another way of looking at this is a design feature. The premature stop codon, or PTC, may be more elegant than a stop sign. It may be a switch, telling the translation machinery to pay attention to the downstream code if -- and only if -- translation is taking place inside neuronal cell. In non-neuronal cells, the PTC might indeed say "stop," delivering the transcript to the trash. In neurons, though, environmental cues may trigger pre-existing routines to fine-tune the sensitivity to odorants available in food sources.

A design perspective could accelerate discoveries along this line. We've seen the tendency to dismiss things as evolutionary castoffs when their functions were not understood, only to find higher levels of organization at work. Introns are spliced out of messenger RNAs; they must be junk. Methyl groups interfere with translation; they must be mistakes. Retrotransposons must be parasites. Pseudogenes must be broken genes. Maybe not. If scientists had expected design, maybe they would have hit upon today's paradigms about epigenetics, alternative splicing and gene regulation sooner.


Intelligent design theory doesn't require everything to be designed. It does, however, prevent a "premature stop" to dismissing things as not designed.