Yet more on life's anti-Darwinian bias.

Octopus Genome Defies Evolutionary Expectations

Evolution News & Views August 21, 2015 3:20 AM

Cephalopods, from the Latin for "head-foot," are among the strangest creatures in the ocean. Though classified in phylum Mollusca, they seem vastly different from snails or clams. Colorful octopus and cuttlefish swim by in the introduction to Living Waters: Intelligent Design in the Oceans of the Earth, but it would require whole separate films to do them justice -- for they are among the smartest and most functionally diverse animals on the planet: flexible, adaptable, and well-equipped for rapid motion, effective hunting, and quick camouflage.

Their numbers include the giant squid, cuttlefish, and the beautifully coiled shelled nautilus. Now that the first octopus genome has been sequenced, scientists are beginning to learn about the complex genetic information behind their capabilities.

Nature published the first genome of a cephalopod, the California two-spot octopus, Octopus bimaculoides. It was a massive undertaking. The octopus genome is comparable to the human genome in size and complexity. In fact, it has "a greater number of protein-coding genes -- some 33,000, compared with fewer than 25,000 in Homo sapiens," says Alison Abbott in the same issue of Nature.

This excess results mostly from the expansion of a few specific gene families, Ragsdale says. One of the most remarkable gene groups is the protocadherins, which regulate the development of neurons and the short-range interactions between them. The octopus has 168 of these genes -- more than twice as many as mammals. This resonates with the creature's unusually large brain and the organ's even-stranger anatomy. Of the octopus'shalf a billion neurons -- six times the number in a mouse -- two-thirds spill out from its head through its arms, without the involvement of long-range fibres such as those in vertebrate spinal cords. The independent computing power of the arms, which can execute cognitive tasks even when dismembered, have made octopuses an object of study for neurobiologists such as Hochner and for roboticists who are collaborating on the development of soft, flexible robots.

A gene family that is involved in development, the zinc-finger transcription factors, is also highly expanded in octopuses. At around 1,800 genes, it is the second-largest gene family to be discovered in an animal, after the elephant's 2,000 olfactory-receptor genes. [Emphasis added.]

Is this an example of the power of Darwinian evolution to progressively expand existing traits? Don't ask the geneticists; they're too busy trying to figure out where all the unique genes came from.

The analysis also turned up hundreds of other genes that are specific to the octopus and highly expressed in particular tissues. The suckers, for example, express a curious set of genes that are similar to those that encode receptors for the neurotransmitter acetylcholine. The genes seem to enable the octopus'sremarkable ability to taste with its suckers.

Scientists identified six genes for proteins called reflectins, which are expressed in an octopus's skin. These alter the way light reflects from the octopus, giving the appearance of a different colour -- one of several ways that an octopus can disguise itself, along with changing its texture, pattern or brightness.

Another discovery hinted at the basis of an octopus'sintelligence. The genome contains systems that can allow tissues to rapidly modify proteins to change their function. Electrophysiologists had predicted that this could explain how octopuses adapt their neural-network properties to enable such extraordinary learning and memory capabilities.

How could so many unique genes arise by blind neo-Darwinian processes? It's unsatisfying to hear scientists assume they "developed" somehow.

The octopus's position in the Mollusca phylum illustrates evolution at its most spectacular, Hochner says. "Very simple molluscs like the clam -- they just sit in the mud, filtering food. And then we have the magnificent octopus, which left its shell and developed the most-elaborate behaviours in water."

The paper is no help. It just speaks of "cephalopod morphologicalinnovations, including their large and complex nervous systems." And then, the authors find they cannot appeal to a favorite explanatory tool, gene duplication:

Based primarily on chromosome number, several researchersproposed that whole-genome duplications were important in theevolution of the cephalopod body plan, paralleling the role ascribed to the independent whole-genome duplication events that occurred early in vertebrate evolution. Although this is an attractive framework for both gene family expansion and increased regulatory complexity across multiple genes, we found no evidence for it. The gene family expansions present in octopus are predominantly organized in clusters along the genome, rather than distributed in doubly conserved synteny as expected for a paleopolyploid.... Although genes that regulate development are often retained in multiple copies after paleopolyploidy in other lineages, they are not generally expanded in octopus relative to limpet, oyster and other invertebrate bilaterians.

With whole-genome duplication out, what's left? Essentially, magic:

Mechanisms other than whole-genome duplications can drive genomic novelty, including expansion of existing gene families,evolution of novel genes, modification of gene regulatory networks, and reorganization of the genome through transposon activity. Within the O. bimaculoides genome, we found evidence for all of these mechanisms, including expansions in several gene families, a suite of octopus- and cephalopod-specific genes, and extensive genome shuffling.

"Evolution of novel genes" --? Isn't that the question at hand? Where do novel genes come from? They found "a suite of octopus- and cephalopod-specific genes" that seem to have appeared out of nowhere. As for mechanisms that "can drive genomic novelty," their list does little more than assume that making more of existing things and shuffling them around will create novel things that do something useful. Try that with a copy machine, a book, and scissors. "Modification of gene regulatory networks" is no help, either. Stephen Meyer documented in Darwin's Doubt how modifications to GRNs are almost always lethal, and never innovative.

Running out of options, the authors turn to a perennial cop-out: convergence.

A search of available transcriptome data from the longfin inshoresquid Doryteuthis (formerly, Loligo) pealei also demonstrated an expanded number of protocadherin genes... Surprisingly, our phylogenetic analyses suggest that the squid and octopus protocadherin arrays arose independently. Unlinked octopus protocadherins appear to have expanded ~135 Mya, after octopuses diverged from squid. In contrast, clustered octopus protocadherins are much more similar in sequence, either due to more recent duplications or gene conversion as found in clustered protocadherins in zebrafish and mammals....

Finally, the independent expansions and nervous system enrichment of protocadherins in coleoid cephalopods and vertebrates offers a striking example of convergent evolution between these clades at the molecular level.

Maybe octopus evolved from fish into mammals. We jest, of course, but the genomic data are not proving helpful to Darwin. After comparing the genome to other creatures near and far, finding more examples of unique genes and convergences, the authors close by trying to put the octopus in context with the family tree of lophotrochozoans ("crest-wheel" animals, a controversial supergroup of phyla that includes animals as diverse as worms, clams, and brachiopods). Watch again for the magical appearance of innovations:

Using a relaxed molecular clock, we estimate that the octopus and squid lineages diverged ~270 Mya, emphasizing the deep evolutionary history of coleoid cephalopods... Our analyses found hundreds of coleoid- and octopus-specific genes, many of which were expressed in tissues containing novel structures, including the chromatophore-laden skin, the suckers and the nervous system.... Taken together, these novel genes, the expansion of C2H2 ZNFs, genome rearrangements, and extensive transposable element activity yield a new landscape for both trans- and cis-regulatory elements in the octopus genome, resulting in changes in an otherwise 'typical' lophotrochozoan gene complement thatcontributed to the evolution of cephalopod neural complexity and morphological innovations.

Maybe this is why Alison Abbott jokes about the octopus having the genome of an alien. "With its eight prehensile arms lined with suckers, camera-like eyes, elaborate repertoire of camouflage tricks and spooky intelligence, the octopus is like no other creature on Earth."

Over at Science, Dennis Normile has nothing new to offer. The octopus genome "surprises and teases," he says. He quotes a team member from the University of Chicago who speaks for the team: "We were really pretty surprised by a bunch of things we found." Another researcher offers this unhelpful comment on the implications for evolution: "there is more than one way to grow a genome."

The popular media took all these surprises in stride, never doubting Darwin, but having little to say about him, either. Most pointed out that the genome-duplication trick doesn't work for the octopus. Discussion of evolution is remarkably scarce in the articles. One exception is Science Daily. Its write-up not only credits blind nature for all the octopus's innovations, but launches into a victory speech for cosmic Darwinism:

As humans, we like to think we are unique in evolutionary terms, but the octopus could reveal that this is not the case. One reason the octopus fascinates scientists is that its brain became organized to be able to carry out such incredible, complex taskswithout adopting the principles of the vertebrate brain. Further examination will tell if the building blocks of its nervous system are as radically different from those of vertebrate landlubbers like us, as the octopus's abilities suggest.

This is not as unlikely as it sounds. Even if the octopus evolvedin a completely different ecosystem, evolution can have only so many solutions to a given problem. If similarities are in fact found, this would significantly alter our perspective on the emergence of life elsewhere in the universe.

David Klinghoffer has pointed out how off-putting triumphalism like this can be. Can't reporters just be honest about the problems with traditional evolutionary explanations? In Living Waters, Discovery Institute's Richard Sternberg and Paul Nelson discuss how improbable it is to get two coordinated mutations for a new function. For the case of whale evolution, the time required for just two mutations for some adaptation vastly exceeds the time available for the transition. A similar problem is evident with octopus evolution from a "simple" mollusk.

Science can observe and enjoy wonders of nature without a Darwinian narrative gloss. Though Live Science's coverage of the Nature paper was heavy on the gloss, a different Live Science article described another species, the large Pacific striped octopus (LPSO), with whimsical delight and very little talk about evolution. This species (despite its name, able to compact itself the size of a tennis ball), tricks its prey the way a human jokester taps on a friend's opposite shoulder, making him turn the wrong way.

"One of the things that impresses me most about this species is 

its great diversity of predatory behavior," Caldwell told Live Science. Not only does this striped octopus trick unsuspecting shrimp, but it also eats snails by first boring small holes into their shells with the end of its arm and then injecting its prey with a deadly, digestive fluid, he said. And despite their diminutive size, LPSOs are strong enough to break apart a clam shell and spritely enough to pounce on a quick-footed crab.

But the extraordinary eating habits of this critter don't end there. Once an LPSO catches its supper, it isn't above sharing the meal with others, said Caldwell, who notes that the animal's ability to peacefully share food with other octopuses is both unusual andvery exciting to biologists.

Scientific investigation can still be "very exciting" without the Darwinian angle. There are many more species of cephalopods worth investigating. Some live deep at hydrothermal vents. Some live in shallow tide pools. They come in all sizes. The mimic octopus amazes scientists. There is much to occupy biologists' time learning about these wonderful animals, without having to fit them into an evolutionary tree.

"There are over 300 known species of octopus, and more are described every year. But the fact is that while we think we knowa lot about octopus behavior and physiology, everything we knowcomes from a handful of species," Caldwell said. "So when I tell you the LPSO is an unusual species with very unique behavior, I really don't know that."

Meanwhile, several of the articles mention that engineers are studying octopuses in search of ideas for soft robots, distributed networks, and propulsion techniques. "Humans invented flying machines by mimicking birds," Science Daily says. "We can look forward to octopuses inspiring robots that give us easy access to the ocean floor."

It's unlikely to be productive trying to trace an assumed evolutionary ancestry that requires heavy doses of "innovation" or "convergence" to accept. Why not tackle the questions amenable to observation and understanding? Biomimetics is showing the usefulness of a design approach. Let's follow that evidence where it leads.

On Dawkins' 'own goal'

Richard Dawkins Opens Mouth; Inserts Foot

Jonathan M. June 21, 2010 9:51 AM

In 2003, the BBC launched a documentary series known as Atheism: A Rough History of Disbelief, presented by the atheist Jonathan Miller. The interviews that were conducted, being too lengthy for inclusion in the 2003 series, were later archived in a 2004 documentary series, entitled The Atheism Tapes, a supplementary series of six programs, consisting of the uncut interviews with a single contributing atheist.

One such film featured Jonathan Miller interviewing our old friend, Richard Dawkins

Three minutes into the embedded interview, in speaking of the purported instances of irreducible complexity in nature, Richard Dawkins succeeds in decimating any pretense to neo-Darwinism's status as a falsifiable proposition. He states, "There cannot have been intermediate stages that were not beneficial. There's no room in natural selection for the sort of foresight argument...It doesn't happen like that. There's got to be a series of advantages all the way...If you can't think of one, then that's your problem, not natural selection's problem."

Is Richard Dawkins suggesting that the purported explanatory adequacy of neo-Darwinism is not a testable proposition? If there are no biochemical systems which cannot, in principle, be accounted for by natural selection, then how is one to evaluate Darwinism's explanatory adequacies? At what point is one justified in saying, "Natural selection is an inadequate explanation and we must hence search for an alternative explanation"?

One might have thought that Richard Dawkins would have stopped digging at this point. But Dawkins had not finished: "Well, I suppose that it is a sort of matter of faith on my part since the theory is so coherent and so powerful."

What is so coherent and so powerful? If defined simply as common ancestry, critics of Darwinism may be inclined to agree. If he means the efficacy of the mechanism, then that is what he is intent on demonstrating. Thus, simple appeals to 'matters of faith' is not what one might regard as a sound argument.

Exjunk:A prequel.

"Junk" RNA Found to Encode Peptides That Regulate Fruit Fly Development

Jonathan M. July 27, 2010 9:21 AM |

Advocates of intelligent design have long been skeptical of the claim that the majority of our genome is nonfunctional gibberish, a mere relic of our evolutionary past. Many of the key arguments for common ancestry are based around the supposition that certain loci of our genome are functionless. But the gaps in our knowledge of the genome (in which such supposition resides) are continually shrinking.

A recent paper published in Science by Kondo et al. reported on the discovery that some of the supposed "non-coding" regions of the RNA transcript actually actively encode for short peptides that regulate genes involved inDrosophila development.

According to the Abstract,

A substantial proportion of eukaryotic transcripts are considered to be noncoding RNAs because they contain only short open reading frames (sORFs). Recent findings suggest, however, that some sORFs encode small bioactive peptides. Here, we show that peptides of 11 to 32 amino acids encoded by the polished rice (pri) sORF gene control epidermal differentiation in Drosophila by modifying the transcription factor Shavenbaby (Svb). Pri peptides trigger the amino-terminal truncation of the Svb protein, which converts Svb from a repressor to an activator. Our results demonstrate that during Drosophila embryogenesis, Pri sORF peptides provide a strict temporal control to the transcriptional program of epidermal morphogenesis.

The paper states that,

We and others recently identified an evolutionarily conserved sORF gene, referred to as polished rice ( pri) or tarsal-less (tal) in Drosophila, and mille-pattes (mlpt) in Tribolium (9-11). primRNA is a polycistronic transcript that encodes four similar peptides, 1 to 32 amino acids in length, that play a redundant role in Drosophila embryogenesis (9, 10). Embryos that lack pri display prominent defects, including the absence of trichomes and aberrant tracheal architecture (9, 10). Reduced pri activity in imaginal development results in abnormal leg morphogenesis (10, 12). Similarly, mlpt knockdown in Tribolium leads to appendage defects and the transformation of segmental identity (11).

The gene containing the Short Open Reading Frame (sORF) is a polycistronic transcript (meaning it carries the information of several genes, which are translated into multiple proteins) from a gene called polished rice, so named because the flies that have a mutation in the gene lack characteristic hairs in the fly embryo which resemble grains of rice. The researchers found that this RNA transcript encodes for four short peptides, ranging from 1 to 32 amino acids long.

The researchers report their finding "that the polished rice peptides trigger the truncation of a protein called Shavenbaby, which regulates the development of the hairs."

A related report by Nature News makes the following comment:

Short peptides could be lurking virtually anywhere in the genome, says Desplan. Sequence analysis suggests that DNA regions capable of encoding tiny peptides exist in front of many protein-coding genes, but few researchers believe that these regions are doing anything useful, he adds.

The article further comments,

Meanwhile, Gerstein notes that the polished rice peptides could also have implications for how we view pseudogenes, which have long been thought to be defunct relics of protein-coding genes. Pseudogenes often contain many signals that would stop protein synthesis and, as a result, could only encode short amino-acid chains. "Maybe this would provide a new way for pseudogenes to have some sort of function," he says.

The researchers conclude, 

Besides the mechanisms of epidermal differentiation, our studies suggest broader functions for Pri peptides. Although pri is also required for tracheal morphogenesis (9), we observed normaltrachea in svb mutant embryos (fig. S9), indicating that Pri peptides probably regulate additional developmental factors. Recent large-scale analyses indicate that thousands of unexplored transcripts are also probably encoding polypeptides of less than 100 amino acids in mice and humans (1, 21, 7). Future functional analyses should elucidate how small peptides encoded by transcripts improperly termed ncRNAs contribute to various biological processes including development and differentiation. [Emphasis mine]

Indomitable Design.

A Salmon Called Indomitable

Evolution News & Views August 19, 2015 3:57 AM

They called him Indomitable. This Coho salmon's migratory adventure seems almost impossible to believe, but it's not just an old fish tale -- it's true. Illustra producer Lad Allen and editor Jerry Harned documented the story back in the VHS days of 1992. When planning the new documentaryLiving Waters: Intelligent Design in the Oceans of the Earth a couple of years ago, Lad was hoping to retell it in high-definition, but the constraints of time often call for painful decisions that leave good material on the cutting room floor. We can at least share this and other stories in words.

At the Prairie Creek Fish Hatchery on the northern California coast, workers were surprised on the morning of December 2, 1964, to find a large male Coho salmon swimming among juveniles in a concrete rearing pond. It had the distinctive mark on its fin of fish raised in this particular pond. The puzzle was how it got there. The only route was a vertical pipe that drained the pond's overflow out into Lost Man Creek behind the hatchery, which joined Prairie Creek and then Redwood Creek before flowing into the ocean. Scientists retraced this fish's route to figure out what it would have had to do to make it into the pond.

As Living Waters shows, a juvenile salmon imprints on the distinctive odor of its birthplace before it heads downstream. Water from a salmon's natal stream produces a powerful neurological response when dripped into its nasal cavity, but other samples do not -- even those from nearby streams. Indomitable's rearing pond had a unique chemical "bouquet" this fish had locked into its brain. The fish and its peers had been taken a couple of years earlier from the rearing pond and released into the ocean, but that scent would not be forgotten.

After two years, driven by the instinct to spawn, Indomitable made its way back from the deep ocean to the mouth of Redwood Creek where it had been released. The odor from home would have been very faint as it adapted its biology from salt water to fresh water for a few days. Swimming upstream three miles, the salmon faced a decision at the junction of Redwood and Prairie Creeks. The growing scent of home made it choose to continue north. Another 1.5 miles ahead, the shortest route would have been to turn onto Lost Man Creek that goes under the highway 100 yards to the east -- but that route had been blocked by floods from a winter storm.

Up Prairie Creek, however, water from the rearing pond trickled out of a culvert passing under Highway 101. Heavy rains that year increased the trickle to a small channel nine inches deep. Indomitable swam up that channel, fighting vegetation along the way. Then it entered a storm sewer, requiring a jump into a 12-inch pipe under the hatchery's parking lot. It seemed like a hopeless dead end, but the fish continued on, only to find another obstacle. The only path forward, following the scent, was a concrete flume that seemed like a dead end. The fish hunted till it found a 4-inch drain pipe. Squirming through the pipe, the fish hit the worst obstacle of all.

The pipe now made a 90-degree bend upward. The fish was now three feet below its home, but would have to jump and wriggle straight up to make it. Then, to make matters worse, its path was blocked by an 8-pound frame screen covering the top of the pipe. The screen weighed five times more than the fish itself. Somehow, Indomitable must have rammed the screen over and over with its head, jumping upward in that narrow vertical pipe, until it dislodged the screen, allowing it to wriggle out into the pond. That's where workers found him that December morning, swimming alongside the hatchlings.

"And now," as Paul Harvey would say, "the rest of the story." Amazed as they were by this salmon's persistence, the workers had another surprise coming. As they were trying to reconstruct Indomitable's route back to the hatchery, they decided to lift some of the boards covering the drainage flume. What they found stirred their imaginations with awe and wonder. Another 72 Coho salmon, each with the distinctive fin clip of the rearing pond, were trapped in the channel, having made it all the way back save for that final narrow pipe with its vertical leap.

When Lad Allen returned to the site and talked to the staff years later, he was shown a jar where Indomitable had been preserved in memory of its Olympic feat. The fish hatchery is now gone, but we thought Indomitable's story makes a great follow-up anecdote to illustrate the olfactory genius designed into the Pacific salmon: its ability to detect extremely dilute odor molecules, its incredible memory, and its instinct that can drive it home despite seemingly insurmountable obstacles.

National Geographic posted a "Friday Fact" that claims that "a salmon's sense of smell is thousands of times better than a dog's." One part per billion is equivalent to one tablespoon of salt dissolved in a volume equal to 18 Olympic-size swimming pools. As Timothy Standish says in Living Waters, the fish can probably detect odors at that level, and perhaps parts per trillion (equivalent to a fingernail's width compared to the diameter of the earth). These specifications far exceed the requirements of mere survival. Intelligent design can build such systems; tinkerers and blind watchmakers cannot.

If you missed our Pacific Northwest premiere, don't despair; Living Waters is now available on DVD and will soon be out on Blu-ray. Consider setting up your own premiere for your neighborhood or organization.

On Darwinism's unicorn.

Evolution's Grand Challenge

Steve Laufmann July 10, 2015 4:44 AM

Editor's note: We are delighted to welcome Steve Laufmann as a new contributor. Mr. Laufmann is a consultant in the growing field of Enterprise Architecture, dealing with the design of very large, very complex, composite information systems that are orchestrated to perform specified tasks in demanding environments.

In a recent ENV article, mathematician Granville Sewell asked an intriguing question:

In the current debate between Darwinism and intelligent design, the strongest argument made by Darwinists is this: In every other field of science, naturalism has been spectacularly successful, so why should evolutionary biology be different? Even most scientists who doubt the Darwinist explanation for evolution are confident that science will eventually come up with a more plausible explanation. That's the way science works. If one theory fails, we look for another one; why should evolution be so different? [Emphasis added.]

Dr. Sewell's post mainly explored entropy and theory-based reasoning. From my own perspective as an architect of large information systems, I would like to suggest a different (but complementary) answer.

Enter Information, Stage Right

Evolutionary biology was very much like other sciences up until the 1950s, when the information-bearing capabilities of DNA and RNA were discovered inside living cells.

These discoveries fundamentally changed biology. And as the information payload is increasingly unraveled, we're seeing ever more complex and interdependent assembly instructions, activation circuits, programming sequences, and message payloads. This information is decoded and operated on by molecular machines of similar complexity, and the whole (information + machines) is self-generating, self-sustaining, and self-replicating.

The information has some intriguing properties:

• It must perform an astounding number of complex functions in order to create, sustain, and replicate life. Each function requires multiple distinct programs or sequences for the various phases of its lifecycle: assembly, operation, complex orchestration with other functions, error detection and correction, replication, and so on. These are functionally distinct types of activities, so it's almost certain that they are encoded separately, perhaps with completely different coding structures and mechanisms.
• It has no value without a complex collection of molecular machines, yet it must also include the instructions for generating those same machines. The result is an immensely complex choreography of separate but interrelated information and molecular machines. Neither can function without the other -- a ginormous chicken-and-egg problem.
• It exhibits the design properties of the best human-engineered software systems, yet its capabilities extend well beyond any current human-engineered systems. For example, no human-engineered system is capable of self-replicating both the software that operates on the machinery and the machinery that decodes the software.

Further, based on the observed functionality in living organisms, there are many undiscovered types of information that must be present in a living cell, but which haven't been decoded or understood yet.

Kinesin offers a fascinating example of undiscovered information in action. What programs and machinery are required to assemble the structure and function of kinesin? What information is needed for kinesin to achieve its "runtime" functions? How does kinesin know where to go to pick up a load, what load to pick up, what path to take, and where to drop its load? How does it know what to do next? All this functionality takes information, which must be encoded somewhere.

Indeed, the level of complexity is monotonically increasing, with no end in sight.

With no possibility that new discoveries will ever decrease the observed complexity, it may not be long before we see a seismic shift in the research paradigm -- from the study of biological systems that happen to contain information, to the study of information systems that happen to be encoded in biology.

Causal Requirements and Causal Forces

Aside from the obvious (and intriguing) challenge of understanding the enormous complexity of life's information payload, evolution purports to explain its origins.

The origin of life is perhaps the most obvious example of information's formidable hurdle to evolutionary explanations. First life requires all of the following:

• Sufficient complex programs and sequencing to support first life's complete lifecycle (i.e., the directions have to be complete and correct).
• Sufficient machinery to interpret the programs and to operate life (i.e., the directions must have proper effect).
• Sufficient programs and machinery to replicate both the programs and the machinery (i.e., the directions must be passed to the next generation).

And all this must be present at the same time, in the same place, in at least one instant in history, at which point the whole must somehow be animated to create life. And all this must occur, by definition, before an organism can reproduce. Without reproduction, there is no possibility to accumulate function, from simple to complex, as required by evolution. Hence, the programs must have contained all the complexity required for first life at inception.

By definition, then, the minimal programs and machinery required for first life must have predated any creative capabilities (real or imagined) of Darwinian processes.

Further, since the information necessary for first life must have been assembled prior to the animation of first life, the minimal information payload must have predated first life. And it must therefore have derived from a source beyond biology as we know it.

This poses a causal quandary for evolutionary biology. For there are only two known classes of causal forces, and these have dramatically different qualities.

First, there are physical laws, which include mathematics, physics, and chemistry. These are repeatable (i.e., the same inputs always produce the same results) and purposeless (i.e., the same inputs produce the same results, no matter who gets hurt). Their repeatability makes science effective. But physical laws are not capable of acting with intent, which limits their creative capabilities.

Operating within the physical laws are random events that can change the information payload of life in various ways. But these are constrained by the same physical laws, so are similarly incapable of acting with intent. Random events cannot create complex information, except in two circumstances: (a) there is some predefined notion of a desirable outcome, and (b) any "positive gains" toward that outcome are protected from random degradation through some external mechanism. Both of these special circumstances require intention, which the physical laws cannot offer.

Second, there are intelligent causes, which are purposeful and therefore not generally repeatable. The creation of complex programming requires non-repeatability. While intelligent causes are capable of generating the right kind of information, it's difficult to pin down when and how their actions occurred, or what their intent might have been. All sciences that deal with intelligent causes (e.g., archaeology) are made more difficult by non-repeatability.

An Impending Worldview Crisis

The search for a purposeful cause that predates biology as we know it inevitably drives the conversation to metaphysics. And this places evolution (and biology) at the center of a conflict between worldviews.

For materialists, the first class of causal force is insufficient and the second is unacceptable. Materialist biologists are thus pressed to find a third class of causal force -- one that works without purpose (required to adhere to materialist philosophy), yet produces purposeful outcomes (required to adhere to the observed world). As yet no reasonable candidate forces have been proposed.

So materialists face growing dissonance between their philosophical commitment and biology's complex programming. As the quality and quantity of the discovered interdependent programs and processing machinery increases, the plausibility of material causation gets weaker. So the materialist position is weak, and going in the wrong direction (from their perspective).

On the other hand, for anyone not fully committed to materialist philosophy the options are much more interesting. For those willing to consider the second class of causal force, things begin to fall into place and the dissonance dissipates.

For theists, the second class of causal force is not only acceptable, but expected. Further, theists are unsurprised to learn that the causal forces in class #1 are finely tuned to enable life, and they have no problem with the notion that random events are more likely to destroy information than create it (e.g., there are far more possible non-functioning programs than functioning programs).

Ongoing discoveries about the nature of the information at the core of life present a growing hurdle for the materialist worldview, but are increasingly friendly to any worldview that's open to a pre-biological intelligencewith some means to assemble the programs and machinery minimally required for first life.

And this sets up a worldview collision.

Evolution's Grand Challenge

Molecular biology is characterized by growing questions and shrinking answers.

It's like the guy who, after untying his boat, finds himself with one foot on the dock and one foot in the boat. As the gap grows, it becomes increasingly hard to ignore. And uncomfortable. And temporary.

And this is evolution's grand challenge: The complex programs and amazing molecular machines at the heart of life simply cannot be explained by any current or proposed theory of evolution, nor by any other completely material cause. Apologists for materialism cannot hide this fact much longer. Neither the volume of their arguments nor any level of vitriol can change the fact that the data is skewing against them.

Rarely has any field of science had to deal with questions so difficult, or that cut so deeply into the worldviews, minds, and hearts, of thoughtful men and women.

Evolution sits at the center of a front-and-center debate -- with too much to explain, in too little time, with insufficient causal power, and with so many watching and so much at stake.

That, I would say, is what makes evolution different.

A line in the sand XXI

To chance and necessity be the glory?II

File under 'Well said' IV

"The only wealth which you will keep forever is the wealth you have given away."
Marcus Aurelius Meditations. 167 AD 

More on Atheists' mysticism.

Quashing Materialist Appeals to Magic (Again)

Ironically enough, materialists are a mystical lot. They say they reject irrational and superstitious beliefs, but when one pushes them past their ability to explain life, the universe and everything in materialist terms, they are very quick to resort to obscurantist pseudo-explanations. And “it emerged” is their favorite dodge.

As we have explained many times before, “it emerged” is the explanatory equivalent of “it’s magic.” But like bugs scattering when the lights are turned on, we have to stomp on this one again and again. Like today for instance. In my Why there is no Meaning if Materialism is True post I argued that on materialist premises – that nothing exists but space, time, particles and energy – there can be no meaning.

Popperian says I can do better. There is “emergence” after all.  And I poked a little fun at Pop:

as Popperian argues on these pages ad nauseam, it’s all emergent. You see, if you stack up the burned out star stuff this way, nothing. But if you stack it up ever so slightly differently, poof!! out of a cloud of smoke emerges rabbits, doves, silly string, consciousness, and morality.

Yes, that is the level to which we have descended — the invocation magic.

And then REC gave us this gem:

Barry, @29, seems close to denying that different arrangements of matter will have different properties. If ID wants to fight with chemistry, that is a development I look forward to.

Sigh.

REC, as we have explained over and over and over, we do not reject emergence as an explanation as such. See here where we said this in so many words.  No, we reject “it emerged” when materialist like you and Popperian use it as a pseudo-explanation to obscure the fact that you haven’t the faintest idea how consciousness arises from the physical properties of the brain.

Your fellow atheist Thomas Nagel also rejects your antics:

Merely to identify a cause is not to provide a significant explanation without some understanding of why the cause produces the effect.

To qualify as a genuine explanation of the mental, an emergent account must be in some way systematic. It cannot just say that each mental event or state supervenes on the complex physical state of the organism in which it occurs. That would the kind of brute fact that does not constitute an explanation but rather calls for an explanation.

If emergence is the whole truth, it implies that mental states are present in the organism as a whole, or its central nervous system, without any grounding in the elements that constitute the organism, expect for the physical character of those elements that permits them to be arranged in the complex form that, according to the higher-level theory, connects the physical with the mental. That such a purely physical elements, when combined in a certain way, should necessarily produce a state of the whole that is not constituted of of the properties and relations of the physical parts still seems like magic even if the higher-order psychophysical dependencies are quite systematic.

Emphasis added.

And if you don’t believe Nagel, maybe you’ll believe Elizabeth Liddle:

[“Emergent” is] simply a word to denote the idea that when a whole has properties of a whole that are not possessed by the parts, those properties “emerge” from interactions between the parts (and of course between the whole and its environment). It is not itself an explanation – to be an explanation you would have to provide a putative mechanism by which those properties were generated. . . .

‘It’s emergent’ would be on an intellectual par with saying ‘It’s magic!’

REC, you most certainly cannot provide a putative mechanism by which immaterial consciousness arises from the material properties of the brain. I know this, because if you could I feel sure I would have seen you on the news accepting your Nobel prize.


Since you cannot provide such a putative mechanism, your own buddy Elizabeth Liddle would say you have done the equivalent of invoking magic. And I bet you think ID proponents are credulous.

More reasons to just say no to atheists' magic.

Professor Paul Davies is no friend of Intelligent Design. Nevertheless, he puts forward a formidable argument against its best scientific alternative, the multiverse, in an interview with Robert Lawrence Kuhn, creator and host of “Closer To Truth,” and author of a recent article titled, Is our universe a fake? (Space.com, July 31, 2015). Kuhn summarizes Davies’ argument as follows:

“If you take seriously the theory of all possible universes, including all possible variations,” Davies said, “at least some of them must have intelligent civilizations with enough computing power to simulate entire fake worlds. Simulated universes are much cheaper to make than the real thing, and so the number of fake universes would proliferate and vastly outnumber the real ones. And assuming we’re just typical observers, then we’re overwhelmingly likely to find ourselves in a fake universe, not a real one.”

So far it’s the normal argument.

Then Davies makes his move. He claims that because the theoretical existence of multiple universes is based on the laws of physics in our universe, if this universe is simulated, then its laws of physics are also simulated, which would mean that this universe’s physics is a fake. Therefore, Davies reasoned, “We cannot use the argument that the physics in our universe leads to multiple universes, because it also leads to a fake universe with fake physics.” That undermines the whole argument that fundamental physics generates multiple universes, because the reasoning collapses in circularity.

Davies concluded, “While multiple universes seem almost inevitable given our understanding of the Big Bang, using them to explain all existence is a dangerous, slippery slope, leading to apparently absurd conclusions.”

Davies’ reductio ad absurdum is a devastating one: the multiverse undercuts the basis of physics itself. And Davies is not alone. Physicist Paul Steinhardt, who helped create the theory of inflation but later came to reject it, declared last September: “Our universe has a simple, natural structure. The multiverse idea is baroque, unnatural, untestable and, in the end, dangerous to science and society.” Steinhardt believes that the multiverse hypothesis leads science away from its task of providing a unique explanation for the properties of nature. Instead, it simply deems them to be random – which, for Steinhardt, feels like giving up on the scientific enterprise. It’s a scientific cop-out. In an interview with John Horgan for Scientific American (Physicist Slams Cosmic Theory He Helped Conceive, December 1, 2014), Steinhardt made no secret of his disdain for both inflation theory and the multiverse (emphases mine – VJT):

Horgan: You were one of the originators of inflation theory. When and why did you start having doubts about it?

Steinhardt: From the very beginning, even as I was writing my first paper on inflation in 1982, I was concerned that the inflationary picture only works if you finely tune the constants that control the inflationary period. Andy Albrecht and I (and, independently, Andrei Linde) had just discovered the way of having an extended period of inflation end in a graceful exit to a universe filled with hot matter and radiation, the paradigm for all inflationary models since. But the exit came at a cost — fine-tuning. The whole point of inflation was to get rid of fine-tuning – to explain features of the original big bang model that must be fine-tuned to match observations. The fact that we had to introduce one fine-tuning to remove another was worrisome. This problem has never been resolved.

But my concerns really grew when I discovered that, due to quantum fluctuation effects, inflation is generically eternal and (as others soon emphasized) this would lead to a multiverse…

To me, the accidental universe idea is scientifically meaningless because it explains nothing and predicts nothing. Also, it misses the most salient fact we have learned about large-scale structure of the universe: its extraordinary simplicity when averaged over large scales…

Scientific ideas should be simple, explanatory, predictive. The inflationary multiverse as currently understood appears to have none of those properties.

These concerns and more, and the fact that we have made no progress in 30 years in addressing them, are what have made me skeptical about the inflationary picture.

    
 ven MIT Professor Alan Guth, a strong supporter of the theory of inflation (which he helped originate) and the multiverse, has acknowledged that it has some philosophically bizarre implications. As he put it in an interview with Natalie Wolchover and Peter Byrne (In a Multiverse, What Are the Odds?, November 3, 2014):

“In a single universe, cows born with two heads are rarer than cows born with one head,” he said. But in an infinitely branching multiverse, “there are an infinite number of one-headed cows and an infinite number of two-headed cows. What happens to the ratio?”

Why I think a transcendent Creator would make computer simulations of consciousness impossible

An interesting question for Intelligent Design proponents to ponder at this point is: supposing that the universe was designed by a Being Who wished to make His existence scientifically knowable to any intelligent life-forms living within the cosmos, and suppose that this Being was not only intelligent but also transcendent, how would He design the universe in such a way as to prevent human beings (and any other intelligent life-forms that might exist in outer space) from drawing the wrong inference about the nature of the Designer, and conceiving of Him as merely super-human (like the Greek and Roman gods of antiquity), rather than transcendent?

In his article, Robert Lawrence Kuhn finds that the argument that our universe might be a simulation rests upon five critical premises: “(i) Other intelligent civilizations exist; (ii) their technologies grow exponentially; (iii) they do not all go extinct; (iv) there is no universal ban or barrier for running simulations; and (v) consciousness can be simulated.” Kuhn goes on to say that the notion that our own universe is a simulation is not incompatible with theism, but he adds that it would be a weak form of theism, as the super-intelligent designer(s) of our universe “wouldn’t need unlimited or infinite minds.” Kuhn wonders how scientists, philosophers and theologians would distinguish between “the traditional creator God and hyper-advanced creator-simulators.”

Here is a prediction I would make. If the transcendent God of traditional theism exists, and wishes to make Himself known to His creatures, then the last thing He’d want to do is give the intelligent life-forms within this universe the power to create other universes. For if these intelligent life-forms discovered that they had this power, then they would also realize that it was highly likely that they, in turn, were created by intelligent life-forms in another universe. This disturbing realization would make it much harder for them to infer the existence of a transcendent God. So my prediction would be that to prevent this from happening, a Transcendent Creator would make it impossible for intelligent life-forms to simulate human consciousness on a computer – and probably animal consciousness, as well. This is just what we find, as I reported in my article, Could the Internet ever be conscious? Definitely not before 2115, even if you’re a materialist. In that article, I calculated that the human brain is 31 orders of magnitude more complex than the entire Internet. And to those who would appeal to Moore’s law as a way for scientists of the future to catch up, I have some bad news: Moore himself declared in 2005 that his law would reach a “fundamental limit” in 10 or 20 years – i.e. by 2025 at the latest – and according to Intel’s former chief architect, Robert Colwell, Moore’s law will be dead by 2022, largely for economic reasons. Darwinist philosopher Daniel Dennett is also skeptical of the Internet ever becoming conscious. In a recent article by Slate journalist Dan Falk (September 20, 2012), he remarked:

“The connections in brains aren’t random; they are deeply organized to serve specific purposes,” Dennett says. “And human brains share further architectural features that distinguish them from, say, chimp brains, in spite of many deep similarities. What are the odds that a network, designed by processes serving entirely different purposes, would share enough of the architectural features to serve as any sort of conscious mind?” (Emphasis mine – VJT.)

Dennett also pointed out that while the Internet had a very high level of connectivity, the difference in architecture “makes it unlikely in the extreme that it would have any sort of consciousness.”

The massive number of assumptions upon which the multiverse hypothesis is built

In addition to the reductio ad absurdum advanced above, Professor Paul Davies has other objections to the multiverse. In an interview last year on Closer to Truth titled, Are There Multiple Universes? (August 23, 2014), Professor Davies explained why he finds the multiverse hypothesis intellectually unsatisfying (emphasis mine – VJT):

[0:40]
It’s not an unreasonable speculation. However, it falls far short of being a complete theory of existence, which it’s often presented as. That is, if there’s a multiverse, we can forget about all the mysteries of the universe because it’s all explained: everything’s out there somewhere. End of story. Well, it’s simply not true, because to get a multiverse, you need a universe-generating mechanism – something has got to make all those Big Bangs go “Bang!” – so you’re going to need some laws of physics to do that. All of the theories of the multiverse assume quantum mechanics, quantum physics, to give the element of spontaneity to make the bangs happen. They assume pre-existing space and time, they assume the normal notion of causality – a whole host of things. You write down a list, there’s about ten different basic assumptions they have to make to get the theory to work. And you can say, well, “Where did they all come from? What about these meta-laws that generate universes and impose effective local by-laws, as Martin Rees would call it, upon these universes? What is this distribution mechanism? How does that work? Where do those rules come from? So all you’ve done is shift the problem of existence up from the level of universe to the level of multiverse. But you haven’t explained it.

Davies’ philosophical misgivings about the multiverse – and Intelligent Design

Continuing in a philosophical vein, Davies explains why he rejects both the multiverse andIntelligent Design (emphases mine – VJT):

[3:00]
I suppose for me, the main problem is that what we’re trying to do is explain why the universe is as it is by appealing to something outside of it – in this case, an infinite number of universes outside of it – that, to me, is no better than traditional religion, that appeals to an unseen, unexplained God that is outside of the universe.

[5:01]
I would like to try to find an explanation for the universe from entirely within it, without appealing to anything external. And as a matter of fact I believe that if somebody did a proper mathematical analysis, they would find that the complexity of the explanation of the multiverse – an infinite number of universes we don’t see – is the same as the explanation of traditional theology: an infinitely complex God outside the universe that we don’t see. They’re really the same thing, in different language, and so my point of view now is: a plague on both your houses. We need to try to find the explanation for the universe from within it, from what we see, and not multiply these unseen entities.

Religious believers will point out, correctly, that the God of classical theism is not complex at all, but utterly simple. However, one needs to distinguish between God’s necessary Being and God’s contingent operations: the former is dogmatically defined to be simple, whereas the latter is not. Even supposing God’s operations to be complex, however, it does not follow that they are infinitely complex. The question that mathematicians should be asking, in my opinion, is: how much information would you need to put into the universe, if you were going to fine-tune not only its laws but also its initial conditions, in such a way that it would be guaranteed to ultimately generate living cells and later on, complex life-forms, some of which would possess consciousness?

More problems with the multiverse

Finally, I should point out that the multiverse is plagued by no less than five severe problems, which I briefly enumerated in a recent post. The first two have already been discussed above; the last three are equally devastating (emphases mine – VJT):

The multiverse hypothesis faces five formidable problems: first, it merely shifts the fine-tuning problem up one level, as a multiverse capable of generating even one life-supporting universe would still need to be fine-tuned; second, the multiverse hypothesis itself implies that a sizable proportion of universes (including perhaps our own) were intelligently designed; third, the multiverse hypothesis predicts that most of the intelligent life-forms that exist should be “Boltzmann brains” that momentarily fluctuate into and out of existence; fourth, the multiverse hypothesis predicts that a universe containing intelligent life should be much smaller than the one we live in; and fifth, the multiverse hypothesis cannot account for the fact that the laws of physics are not only life-permitting, but also mathematically elegant – a fact acknowledged even by physicists with no religious beliefs.

Further discussion of these problems can be found here. The elegance of the laws of Nature has been remarked on by many scientists, including Paul Davies, who wrote in his best-selling book, Superforce: The Search for a Grand Unified Theory of Nature (New York, NY: Simon and Schuster):

A common reaction among physicists to remarkable discoveries of the sort discussed above is a mixture of delight at the subtlety and elegance of nature, and of stupefaction: ‘I would never have thought of doing it that way.’ If nature is so ‘clever’ that it can exploit mechanisms that amaze us with their ingenuity, is that not persuasive evidence for the existence of intelligent design behind the physical universe? (1984, pp. 235-36. Emphasis mine – VJT.)

That was what Davies wrote in 1984. In recent years, sadly, he has changed his mind – not for scientific but for philosophical reasons. In a 2007 article for the Taking Science on Faith

, Davies stated why he now prefers an explanation of the universe’s laws from within the cosmos, even as he candidly acknowledged that no such theory presently exists (emphases mine – VJT):

It seems to me there is no hope of ever explaining why the physical universe is as it is so long as we are fixated on immutable laws or meta-laws that exist reasonlessly or are imposed by divine providence. The alternative is to regard the laws of physics and the universe they govern as part and parcel of a unitary system, and to be incorporated together within a common explanatory scheme.

In other words, the laws should have an explanation from within the universe and not involve appealing to an external agency. The specifics of that explanation are a matter for future research. But until science comes up with a testable theory of the laws of the universe, its claim to be free of faith is manifestly bogus.

The way forward for ID?

For my part, I do think Davies is right about one thing. It is not enough to argue that the laws of the universe must have been designed by some Intelligence. For a hypothesis to be scientifically fruitful, it needs to make predictions. What the Intelligent Design movement needs is physicists who are not afraid to “get inside the mind of God,” and freely speculate about why the universe has the laws, fundamental principles and underlying mathematical structures that it does. Why was the universe designed this way, and not some other way? To say that it was designed to support intelligent life is all well and good, but we need to go further, and explain why alternative life-permitting designs for the cosmos would have been less suitable than the one that we find ourselves in. I have previously suggested that Intelligent Design could be rendered more fruitful if it incorporated the assumption that one of the Designer’s aims was to make His existence known to His intelligent creatures, and I also suggested above that the Designer wants to make His transcendence known to us. Finally, I would suggest that the cosmos is asbeautiful in its underlying principles as it possibly can be, while at the same time remaining mathematically comprehensible to the human mind. Taken together, these three assumptions might narrow the range of life-permitting possible universes to the point where we can eventually conclude, on purely scientific grounds, that this universe is the best possible design that a Transcendent Creator could have selected, had He wished to make His existence known to human beings. That, I think, would be a fruitful line of inquiry.

What do readers think?