Yet more on mindless intelligence.

More on "Intelligent Design Without a Designer"
Brendan Dixon April 3, 2016 3:22 AM

A reader, Eric, writes to ask about my post "Nature 'Learns' to Create Complexity? Think Again":

Like Brendan, I work on developing computer models and software for scientific applications. His comments about models vs. reality were, of course, spot on. It did occur to me that there is one possible partial response to a point that was made. Brendan writes:

Worse, whatever is "learned" by that organism must be passed along to the children. So, unless the paper's authors subscribe to some form of Lamarckism, which is exceedingly unlikely, without a clear inheritance path all the training value is lost.

A neo-Darwinist could respond with the same kind of switch that the synthesis used to rescue the original version of Darwinism. Darwinism originally did have a Lamarckian flavor to it (which is why it opposed and resisted Mendelian genetics). With the neo-Darwinian synthesis, they dropped the Lamarkian aspects, embraced genetics, and proposed that the gains were built in through genetic variations.

In a similar way, someone now could say that the "learning" isn't Lamarkian. Rather, it is the genetic variations to GRNs that succeed in being passed on (in contrast to those that were weeded out). The correspondence with environmental conditions comes in the form of the natural selection filtering that comes after the fact of the genetic change.

Yet, if that is how it should be understood, the issues raised in the preceding paragraph about training "over time and space" are still relevant. The genetic "learning" would not be limited to the life of any single individual, but it still would be constrained to accumulating within a line of ancestry.

That would make the "learning" generational in nature. Instead of a single copy of a network collecting "millions of data sets," one would have to look along an organism's ancestral line to observe the inherited network receiveing a multitude of tweaks down through the successful generations.

At first glimpse, it might seem that this way of viewing it could succeed at making it work for the neo-Darwinist. However, it does come back to the details, such as the limited amount of successful tweaking that can take place in any single generation and the limited number of generations down to the present organism.

Quite simply, there does still seem to be a serious problem about accumulating the extent of learning that would be needed.

The other main thought I had was this. You cannot have a second time without having a first time. You cannot learn to use building blocks more effectively apart from first having building blocks that can be used somewhat effectively.

In my software, I know the value of modularization and being able to recombine components, but that doesn't happen by accident. I wouldn't be able to reuse composable parts if I did not first have such parts that allowed from recombination. Flexibility comes by design, and before one could have a flexible, adjustable, "educated" GRN, one would need first to have a GRN that from the start flexibly allows for "learning." Otherwise, one could not get off the ground.

Even granting for the sake of argument that GRNs can learn across generations, how do we expect that a learning GRN can first come to exist?

Darwinists are forever pushing their present problems aside by building on the idea that whatever they need already existed earlier (without explanation), whether it is functional information or GRNs that can learn.

By the way, if you haven't seen the movie Next, staring Nicholas Cage, I would suggest giving it a look. (It's available for streaming on Netflix.)

It's not a "great" movie in any sense, but it does do a very clever job at cinematically portraying what is essentially a visual allegory to the evolutionary perspective of a finding a winning path that has been filtered from among many other failed attempts. As with evolutionary thought, the attempts are temporally concurrent.

People who have seen this will more easily and more intuitively feel that such a strategy could work (so long as one does not delve into the messy details).

I appreciate Eric's thoughts. I suppose the answer depends on how the paper's authors envision the GRN learning. If it is no different than modification + selection that preserves those GRNs producing "better" phenotypes, then Eric's point is sound. And he is correct in that case to point out that an entire ancestral chain matters. If the GRN learns dynamically (which I don't believe was clear in the original paper), then inheritance remains a significant problem.

However, if Eric's perspective is correct and a GRN "learns" through descent with modification, the analogy with Neural Networks breaks down. Neural Networks succeed by changing the entire network in response to massive data sets (along with some notion of correctness). For example, imagine two critters: The GRN in one "learns" to adapt part of the network while the other adapts the other part. They cannot share that information (unless you can specify a mechanism by which they can mate and successfully blend what both "learned"). And adaptation in one is made without respect for the adaptation in the other. NNs succeed because the entire network adapts as a unit; that is, each node learns how to respond to inputs based on how the entire network has faired. You cannot teach one node at a time or even part of the network at a time -- the entire network responds. Training a NN one node at a time will, by definition, fail.

And, as Eric agrees, the quantity of data to succeed is massive. AlphaGo contained "millions" of connections across 12 (or 13?) layers (networks) in two different NNs. AlphaGo was originally fed roughly 30 million moves from 160,000 games, yet that was far from sufficient. It required more training by playing itself (I failed to find the number of moves evaluated during this phase, but I suspect it completed many more than 160,000 games). And then, to allow the search tree to run deep, they distributed its execution across over 2,000 CPUs (some of which were the specialized, high-performance CPUs used in video games). Even then, a small number of "hand crafted" rules lurked within (see here).

Comparing GRNs to NNs remains uninteresting given what we've learned about training NNs. If anything, what we've learned says that GRNs could not have been self-taught since they just don't have access to the necessary data or a means by which to ensure the entire GRN benefits from the training.

The quantity of data needed to train an NN is proportional (though not linearly) to the number of connections within the network. The more connections a network contains, the more training data necessary.

I do not know how many nodes or connections a GRN contains, but, in a way, it is immaterial: If the number of connections is small, the network cannot "recognize" anything significant. If it is large, then the data requirements will rapidly exceed that available. A small, trainable network will be uninteresting and a large, interesting network will be untrainable. (I like that statement. I believe it captures the challenge succinctly with a bit of rhythm.)


If someone were to respond by saying, "Ah, but we have thousands of GRNs," then they have a large network (where each node is itself a GRN, something akin to a deep learning problem) that will require massive quantities of data.

Patron saint of the master race?

Why Darwinism Can Never Separate Itself from Racism

 David Klinghoffer | @d_klinghoffer

 

It’s great to have insightful colleagues. Denyse O’Leary, with Discovery Institute’s Bradley Center for Natural and Artificial Intelligence, has been writing about evolution for years as well. Having read my post “The Return of John Derbyshire,” she points out something I hadn’t quite grasped. Now a lightbulb goes off. 

Inherent, Unavoidable

The thread of racism in Darwinian thinking isn’t a chance thing, a mere byproduct of Charles Darwin’s personal views as a “man of his time.” You think if Darwinism had emerged not in the dark age of the 19th century but in our own woke era, it would be different? No, it wouldn’t. The racism is inherent, unavoidable:

That’s just the difference between Darwinism and any type of creationism OR non-Darwinian approaches to evolution. In a Darwinian scheme, someone must be the official subhuman.
I have been trying to get that across for years. It’s why Darwinism can never get away from racism. Racism is implicit in the Darwinian belief system about how things happen.  Even if one’s creationism amounts to no more than the idea that humans have an immortal soul, it makes all humans equal for all practical purposes. Take that away and believe instead that humans are animals that slowly evolved from less-than-human creatures and a variety of things happen, none of them conducive to non-racism.

True, O’Leary has been saying this for a long while. As she wrote over at Uncommon Descent last year:

The problem is not merely that Darwin, a man of his age, was a racist. The problem is that his bias resulted in his and others distorting the fossil record to suit a racist worldview.

Those issues with the fossil record are the theme of most of paleontologist Günter Bechly’s recent writing at Evolution News. She goes on:

To “get past” the fact that Darwin was a racist, we must be willing to undo science that begins by assuming that non-European features are sub-human. But the “hierarchy of man” is rooted in the fundamental assumptions of the “Descent of Man,” the idea that Darwin popularized. Rooting it out would call so many things into question as to produce a crisis. What will we be left with?
Indeed. But then an even bigger problem looms: In any Darwinian scheme, someone must be the subhuman. If not the current lot (formerly, the “savages,” currently the Neanderthals and/or Homo erectus), who will it be?
If they aren’t found, the Darwinist is looking down the maw of some sort of creationism. It need not be theistic creationism. But it does mean that a momentous event happened with explicable swiftness, like the Big Bang or the origin of language, findings naturalists do not like precisely because of their creationist implications.
Surely these are the true reasons Darwinists simply can’t confront the race issue and get past it, and so they resort to long-winded special pleading.

A Minimal Concept

The word “creationism” is used unfairly as a cudgel against proponents of intelligent design. But fine, let’s entertain it for a moment, if only to designate a minimal concept like the philosophical one that says humans, while sharing biological common descent with other creatures, are uniquely endowed with souls bearing some sort of exceptional quality, however you characterize that. It could be a divine image, but need not be. The consistent materialist must deny all this.

The idea of racial equality, perfectly natural to a design perspective, can be achieved by the Darwinist only by continually and ruthlessly suppressing a built-in tendency. It requires bad faith: fooling himself about his own way of thinking. Like an irremediable birth defect, it’s never going to go away.

“Tell It on the Mountain”

Or it’s like driving a car with misaligned wheels that always pulls you in one direction and cannot ever drive straight without your exerting continuous effort toward correction. If you don’t fight it all the time, you’ll go off the road and crash into a nasty, muddy ditch, as folks like John Derbyshire have done. John and other “Race Realists” humiliate their fellow evolutionists by dancing in the muck.

The alternative is to get those wheels nicely aligned. Of course it’s possible to find people who believe in creation and who are also racists. You can find bad apples in any community of thinkers. But the key point is that the two ideas are permanently at odds with each other. Whereas Darwinism and racism are a match made in… Well, they’re conjoined twins, let’s put it that way.

“Klinghoffer,” Denyse advises, “tell Derbyshire he needs a louder mike. He should go tell it on the mountain. Worldwide.” Okay, done.

 

Insect navigator vs. Darwin.

Monarch Butterfly's Sun Compass Investigated in Flight Simulator
Evolution News & Views

The amazing story of how Monarch butterflies navigate from Canada to Mexico is beautifully recounted in Metamorphosis, the Beauty and Design of Butterflies. "Here's a butterfly species that does something truly spectacular," Thomas Emmel says in the film. Flying over two thousand miles without an experienced leader who has made the trip before, millions of these artistically-colored flyers arrive on schedule in the same trees their grandparents or great-grandparents had wintered in the previous year.

Somehow, with a brain the size of a pinhead and a body weighing less than an ounce, the butterfly contains hardware and software for long-range precision navigation, efficient energy utilization and genetic alterations that enable the "Methuselah generation" to survive ten times as long as their parents. Emmel comments that this phenomenon will likely occupy biologists' attention for centuries to come. Researchers at the University of Washington announced this month that they have "cracked the secrets" of one small aspect of this wonder: the monarch's internal time-compensated sun compass.

We saw from the film that the angle of the sun and its traverse through the daylight hours plays a role in the choice of flight direction. Using sunlight to navigate requires processing dynamic inputs:

"Their compass integrates two pieces of information -- the time of day and the sun's position on the horizon -- to find the southerly direction," said Eli Shlizerman, a University of Washington assistant professor. [Emphasis added.]
But how is this information processed in the butterfly's tiny brain? The compass needs to be integrated with the clock.

Monarchs use their large, complex eyes to monitor the sun's position in the sky. But the sun's position is not sufficient to determine direction. Each butterfly must also combine that information with the time of day to know where to go. Fortunately, like most animals including humans, monarchs possess an internal clock based on the rhythmic expression of key genes. This clock maintains a daily pattern of physiology and behavior. In the monarch butterfly, the clock is centered in the antennae, and its information travels via neurons to the brain.
We saw electron micrographs of the antennae in the film. Covered with scales and tiny hairs, these organs are the sites for odor detection, enabling the monarchs to find mates and the females to find their host plants from miles away. Now we learn they are clocks, too:

In their model, two neural mechanisms -- one inhibitory and one excitatory -- controlled signals from clock genes in the antennae. Their model had a similar system in place to discern the sun's position based on signals from the eyes. The balance between these control mechanisms would help the monarch brain decipher which direction was southwest.
Using models and live butterflies in a flight simulator, the researchers determined how they get back on track if blown off course. There's a "separation point" that determines whether the individual will turn left or right. That point changes throughout the day. The insect's onboard computer won't let it cross the separation point, even if it requires a longer path to get back on course. The scientists also shed light on how the butterflies readjust their compasses for the return trip.

Their model also suggests a simple explanation why monarch butterflies are able to reverse course in the spring and head northeast back to the United States and Canada. The four neural mechanisms that transmit information about the clock and the sun's position would simply need to reverse direction.
"And when that happens, their compass points northeast instead of southwest," said Shlizerman. "It's a simple, robust system to explain how these butterflies -- generation after generation -- make this remarkable migration."

Simple, simply -- while appreciating the insights our neighbors at UW have gained, such talk is premature. There's a lot more going on. For one thing, not all individual butterflies head southwest and return northeast. The flight paths from Canada begin on different bearings and converge into a narrow flight path in southern Texas. Also, as Metamorphosis shows, a few individuals take a direct route across the Gulf of Mexico. Then, they all switch direction at a certain point, heading west through a pass toward the Trans-Volcanic Range. Then, within those mountains, they converge on specific trees in 12 known overwintering spots.

Time of day and sun position are necessary, but not sufficient, to explain these precise behaviors. If the researchers feel they have "cracked the secret" of maintaining a particular bearing, they have left all these other secrets unexplained. Their model only shows the bare outlines of a sophisticated, integrated system. The paper in Cell Reports says:

A long-standing, fundamental question about monarch migration has been how the circadian clock interacts with the changing position of the sun to form a time-compensated sun compass that directs flight. Here, we propose a neuronal model for both encoding of the sun's azimuthal position, and molecular timekeeping signals, and how they can be compared to form a time-compensated sun compass. Our results propose a simple neural mechanism capable of producing a robust time-compensated sun compass navigation system through which monarch butterflies could maintain a constant heading during their migratory flight.
But as we just said, the butterflies don't keep a constant heading. They make turns. And what tells individuals in Minnesota to head south and individuals in Pennsylvania to head southwest? Do their offspring for the three generations on the return trip keep the target information embedded in their memories? A compass is no good without a map. Both are no good without a brain to read them. Furthermore, as we reported about Bogong moths, some lepidopterans can reach their long-range destinations in the dark!

The researchers identified four genes that keep time by oscillating their expression levels. They identified how the compound eye determines azimuth and bearing even when the sun's position is changing throughout the day. A butterfly, however, needs much more. It needs controls for altitude, pitch, and yaw. It needs a map of where it has to go. And it needs to monitor resources to ensure it has the energy to get there.

Nevertheless, we're glad for any and all research that sheds light on the details of monarch butterfly navigation, especially when it can lead to intelligently designed applications that benefit everyone:

The model that we have built closes the loop between the time and azimuth stimuli and orientation control. As such, it provides an important framework for future studies of the monarch sun compass. Our framework can be used to design electrophysiological and flight recordings experiments to compare responses in monarchs' neurons and model units and to determine the detailed architecture of neural circuits that implement the integration mechanism postulated by our model. It also provides a simple mechanism for navigation that can be used in devices that do not have the benefit of a global positioning system.

A complex, functional system that, when partially understood, can be "used to design" something else must have been designed itself.

How OOL science can earn some respectability.

Announcing New Sewell Prize in Biological Origins Studies!
David Klinghoffer | @d_klinghoffer

Over at Uncommon Descent, mathematician Granville Sewell announces a new prize he will be administering. It sets a fascinating challenge but offers an enviable reward:

I plan to award a prize to anyone who can invent a non-trivial 3D machine which can replicate itself. The machine must be able to make copies of itself without human intervention, except possibly to supply the raw materials. Basically a 3D printer which can print a copy of itself which retains the ability to print a copy of itself, which… A page which can be photocopied does not count, because it is the photocopier which actually makes the copy, unless the photocopy machine also makes a copy of itself; a computer program which duplicates itself does not count unless the computer it runs on makes a copy of itself also.

The reward isn’t cash but something even better: 

The prize: the right to speculate about how life originated. Leave your artificial species alone and see how many generations it lasts before going extinct. If it makes accurate copies of itself for 100+ generations, then you also get to speculate about how genetic duplication errors might accumulate into major evolutionary advances.

Now go to it, you proponents of unguided abiogenesis and evolution through all sorts of brute unintelligent, and only unintelligent, natural forces. The first ever Sewell Prize in Biological Origins Studies awaits!

Blinded by fuzzy math?

Behe on Darwinism’s “Socially Inherited Dependence on Classical Yet Irrelevant Math”
David Klinghoffer | @d_klinghoffer

“Natural selection, irreducible complexity, and random mutation all reinforce each other to make Darwinian evolution very limited,” explains biochemist Michael Behe on a new ID the Future episode. That means Behe must tackle a tough question: if the limits of Darwinian evolution are so clear, as he shows in his new book Darwin Devolves, why do gifted scientists like Richard Lenski and Joseph Thornton persist in hanging on to the failed theory, against the evidence of their own experiments? 

Talking with host Andrew McDiarmid, Behe traces the errant thinking to an outdated mathematical picture taken from Ronald Fisher (1890-1962) and his 1930 book, The Genetical Theory of Natural Selection. This highly influential work was written before scientists knew what genes actually are. It’s not surprising that Fisher missed the role of broken genes in containing the creative potential of unguided evolution.

Through “a socially inherited dependence on classical yet irrelevant math,” present-day researchers are saddled with Fisher’s own “hopeful ignorance.” Download the podcast or listen to it here.

A fatwa from one of Darwinism's ayatollah's

Do Evolutionary Principles Derive from Observation, or Are They Imposed on It?
Evolution News & Views February 25, 2016 11:25 AM

Geneticist Dan Graur of the University of Houston is implacably opposed to intelligent design -- and brutally honest about his opposition, which makes for bracing clarity in what he writes. Recently he tweeted the following 12 principles of evolution, which he drafted.

You have to love Graur's principles, because they capture orthodox neo-Darwinism in its purest form:

All of Evolutionary Biology in 12 Paragraphs, 237 Words, and 1,318 Characters

Evolutionary biology is ruled by handful of logical principles, each of which has repeatedly withstood rigorous empirical and observational testing.

The rules of evolutionary biology apply to all levels of resolution, be it DNA or morphology.

New methods merely allow more rapid collection or better analysis of data; they do not affect the evolutionary principles.

The only mandatory attribute of the evolutionary processes is a change in allele frequencies.

All novelty in evolution starts as a single mutation arising in a single individual at a single time point.

Mutations create equivalence more often than improvement, and functionlessness more often than functionality.

The fate of mutations that do not affect fitness is determined by random genetic drift; that of mutations that do affect fitness by the combination of selection and random genetic drift.

Evolution occurs at the population level; individuals do not evolve. An individual can only make an evolutionary contribution by producing offspring or dying childless.

The efficacy of selection depends on the effective population size, an historical construct that is different from the census population size, which is a snapshot of the present.

Evolution cannot create something out of nothing; there is no true novelty in evolution.

Evolution does not give rise to "intelligently designed" perfection. From an engineering point of view, most products of evolution work in a manner that is suboptimal.

Homo sapiens does not occupy a privileged position in the grand evolutionary scheme.

It's fun to play around with these. Take principle 10 seriously, for instance, and taxonomically restricted genes (so-called "orphans") represent a significant puzzle to neo-Darwinian evolution. The deepest question, of course, is this: Do these principles -- in particular, numbers 4 through 12 -- derive from observations, or are they imposed on observations?

Historical parallel:

And we recall that Galileo never made use of Kepler's ellipsi, but remained to the end a true follower of Copernicus who had said "the mind shudders" at the supposition of noncircular, nonuniform celestial motion.

(Gerald Holton, Thematic Origins of Scientific Thought, Harvard University Press, p. 64)

Indeed, one could take this catechism to London in November, to the Royal Society meeting on alternatives to neo-Darwinism, as a template for where heresy may be expected to arise.

The end of innocence?

"People Are Starting to See Scientists the Way They Really Are"

David Klinghoffer 

The public used to see politicians in far more exalted terms than they do now. The same fate befell the clergy. Now it's scientists.

Dr. Ivan Oransky, MD, of Retraction Watch gets a delicious write-up from Forbes:

Among the American public, trust in professional scientists and scientific journals is declining. Yet an overwhelming majority still believes that science "remains a source for good in the world." Could the public be on to something? Medical-doctor-turned-journalist Ivan Oransky thinks so. And it's a growing problem.

As editor and publisher of Retraction Watch, a closely followed industry blog that tracks peer-reviewed journal articles withdrawn from publication, Oransky is raising awareness of the impact that competition for grants and career advancement is having on the quality of the science being produced. Far from being above the fray and immune to corrupting influences, "Scientists are just as human as anyone else," says Oransky. And increasingly, "People are starting to see scientists the way they really are."

This is especially relevant to our concerns here:

Another major problem is that many study results cannot be reliable reproduced. Oransky cites a famous paper by Dr. John Iaonnidis, "Why most published research findings are false," that shows the inherent biases and the flawed statistical analyses built into most "hypothesis driven" research, resulting in publications that largely represent "accurate measures of the prevailing bias."

Scientific pronouncements as an "accurate measure of the prevailing bias" -- those are words to commit to memory. When we say things like that, they say we're "anti-science." No, just pro-realism about scientists.

Also quoted, Dr. Thomas Stossel of Harvard Medical School:

"I realized how fundamentally honest business people are compared to my academic colleagues, who'd run their grandmothers over for recognition."

As for non-scientists who have not yet been disabused of their childlike faith, one can only say: Growing up is hard to do.

On the echo chamber called settled science.

How Consensus Can Blind Science
Evolution News & Views 

The ruins of Mayan civilization impress anyone who visits. For Harvard astronomer Avi Loeb, they spoke to him about the philosophy of science then and now. Recounting his experience for  Nature, he describes the questions that came to his mind:

This summer, I visited the Mayan city of Chichén Itzá in the Yucatán Peninsula, Mexico. It has an ancient observatory where priest-astronomers made detailed astronomical observations around AD 600-1200. The ruins -- stepped pyramids, temples, columned arcades and other stone structures -- reveal that astronomy was at the heart of this sophisticated society.
The Mayans accurately tracked changes in the positions and relative brightness of the Sun, Moon, planets and stars. They documented their astronomical data in folding books called codices, with many more quantitative details than other civilizations at the time. The priest-astronomers used observations and advanced mathematical calculations to predict eclipses, and devised a 365-day solar calendar that was off by just one month every 100 years.

So why, I wondered, didn't the Mayans go further and infer aspects of our modern understanding of astronomy? They determined the orbital periods of Venus, Mars and Mercury around the Sun, but Earth was at the centre of their Universe.

Dr. Loeb knows he is a leading figure in today's consensus views in astronomy and cosmology. But unlike some others in his profession, he did not merely dismiss the Mayan achievements as works of a backward people lost in religious superstition. Turning his contemplations inward, he asked, "Have we learned our lesson, or is today's science similarly trapped by cultural and societal forces?"

Loeb pondered how the Mayans' detailed calculations were used to support a civilization that engaged in human sacrifice and planned warfare by the stars. "I came to appreciate how limiting prevailing world views can be," he says. In their day, Mayan astronomers were held in high social esteem. So are today's astronomers. Loeb thought about how "Cosmologists today collect vast amounts of exquisite data in surveys of large parts of the sky, costing billions of dollars." But Good data are not enough, he realized.

What might have helped the Mayans break out of the box of their prevailing world view? He hit upon a solution that should be of great interest to the intelligent design community.

The consequences of a closed scientific culture are wasted resources and misguided 'progress' -- witness the dead end that was Soviet evolutionary biology. To truly move forward, free thought must be encouraged outside the mainstream. Multiple interpretations of existing data and alternative motivations for collecting new data must be supported.
We hasten to clarify that so far as we know, Dr. Loeb is not an advocate of intelligent design, even though he has proposed a design inference for SETI . His advice, though, harks back to Darwin's own admonition: "A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question." The question in Darwin's day was design v. naturalism, as it is today. When it comes to origins, there aren't any other options. Either the universe is designed, or it is not. Would it not be limiting to the prevailing world view to assert that naturalism is the only side of the question?

Loeb gives a brief catalog of massive projects being funded by NASA and ESA. But then he gives a Kuhnian view of these efforts. Today's astronomers and cosmologists work within a paradigm as members of a guild who cannot see outside their project. Anomalies do not alarm them, as they should. Instead, they focus their attention of puzzle-solving to establish the paradigm -- not to overthrow it.

Such projects have a narrow aim -- pinning down the parameters of one theoretical model. The model comprises an expanding Universe composed of dark matter, dark energy and normal matter (from which stars, planets and people are made), with initial conditions dictated by an early phase of rapid expansion called cosmic inflation. The data are reduced to a few numbers. Surprises in the rest are tossed away.
I noticed this bias recently while assessing a PhD thesis. The student was asked to test whether a data set from a large cosmological survey was in line with the standard cosmological model. But when a discrepancy was found, the student's goal shifted to explaining why the data set was incomplete. In such a culture, the current model can never be ruled out, even though everyone knows that its major constituents (dark matter, dark energy and inflation) are not understood at a fundamental level.

He's absolutely right; in recent news reports, dark matter remains as mysterious as ever. Astronomers have leapfrogged from WIMPs to MACHOs to axions, finding no evidence for any of them, despite expensive searches with super-sensitive detectors. Perhaps a candidate particle will turn up some day, but without empirical evidence, have physicists improved on Mayan divination? Dark energy is even more mysterious. Nobody has any idea what that is. And there's more darkness:

How each culture views the Universe is guided by its beliefs in, for example, mathematical beauty or the structure of reality. If these ideas are deeply rooted, people tend to interpret all data as supportive of them -- adding parameters or performing mathematical gymnastics to force the fit. Recall how the belief that the Sun moves around Earth led to the mathematically beautiful (and incorrect) theory of epicycles advocated by the ancient Greek philosopher Ptolemy.
Similarly, modern cosmology is augmented by unsubstantiated, mathematically sophisticated ideas -- of the multiverse, anthropic reasoning and string theory. The multiverse idea postulates the existence of numerous other regions of space-time, to which we have no access and in which the cosmological parameters have different values.

We can become "blinded by beauty" that keeps us attracted to our own beliefs. Loeb mentions some paradoxes in cosmology that hint the consensus is on the wrong track. Modern cosmology is not knowledge, he says; it is organized ignorance! Only openness to other approaches can help reveal the extent of it.

Cultivating other approaches avoids stalling progress by investing only in chasing what might turn out to be 'epicycles'. After all, the standard model of cosmology is merely a precise account of our ignorance: we do not understand the nature of inflation, dark matter or dark energy. The model has difficulties accounting for the luminous gas and stars that we can see in galaxies, while leaving invisible what we can easily calculate (dark matter and dark energy). This state of affairs is clearly unsatisfactory.
The only way to work out whether we are on the wrong path is to encourage competing interpretations of the known data.

ID proponents might take advantage of Loeb's appeal in a way Paul Nelson relates in the new film Origin:

Often, when I'm reading the origin-of-life literature, considering some proposal for the formation, let's say, of RNA or proteins -- and even the author admits it's chemically implausible -- and I ask myself, How did he get himself into this jam?...
And at that impasse I want to say to the author, Look you know it's implausible, I know it's implausible, the reason that you ended up here standing at the edge of this cliff staring at implausibility is because way back down the road you decided that only a materialist explanation would work.

Dr. Timothy Standish adds:

How many different explanations that fail within the materialistic box do we have to have before we decide, maybe we need to move outside of that box. Maybe we need another kind of explanation.
When it comes to cosmology, Dr. Loeb is painfully aware of implausibilities in the naturalistic box: dark matter, dark energy, inflation, the multiverse, and the Anthropic Principle. But he is not just standing at the cliff, staring at implausibility; he is welcoming new thinking outside the box. It's an opportunity for a meaningful discussion of alternatives. And it was published in Nature, the world's leading science journal.

A healthy dialogue between different points of view should be fostered through multidisciplinary conferences that discuss conceptual issues, not just experimental results and phenomenology. A diversity of views fosters healthy progress and prevents stagnation. In September, I had the privilege of founding an interdisciplinary centre, the Black Hole Initiative at Harvard University in Cambridge, Massachusetts, which brings together astronomers, physicists, mathematicians and philosophers. Our experience is that a mix of scholars with different vocabularies and comfort zones can cultivate innovation and research outside the box. Already the centre has prompted exciting insights on the reality of naked singularities in space-time, the prospects for imaging black-hole silhouettes and the information paradox.
The "information paradox" refers to the conservation of information in the case of black holes. Think about what ID has to offer the admittedly stagnant field of consensus cosmology:

Theory of information: its source and conservation

A cause to explain the fine-tuning of the universe (e.g., see New Scientist) without the "cop-out" of the Anthropic Principle (New Scientist)

Mathematics, as seen in Origin's probability calculations for the origin of life, the Universal Probability Bound, and the "No Free Lunch" theorems

Philosophy of science unlimited by naturalism

A different vocabulary and comfort zone

Research outside the box

Loeb concludes, "Such simple, off-the-shelf remedies [i.e., multidisciplinary conferences] could help us to avoid the scientific fate of the otherwise admirable Mayan civilization." Would he extend his hand far enough to consider design? Perhaps not. But while the rise and fall of Mayan civilization is on his mind, leading him to ponder modern cosmology's potential for worldview blindness, the time seems right to engage the discussion.

Toward a theory of devolution VI

Testing Behe’s Principle that Darwin Devolves
Evolution News | @DiscoveryCSC

As Michael Behe has explained in these pages and in ID the Future podcasts, natural selection can appear to produce benefits to an organism, but at a cost. Most often, organisms carry on by breaking existing genes and proteins. This is the overriding message of his new book, Darwin Devolves. The tendency for existing complex functions to degrade in order to allow an organism to survive swamps any beneficial mutations that might arise de novo. 

Occasionally, excited headline writers proclaim that scientists are watching evolution happen in real time. Let’s scrutinize some of these claims to see what really happened. Did a new, innovative function arise by a beneficial mutation? Or did something break that provided a benefit in special circumstances?

News from the University of Wisconsin-Madison announces, “Radiation-resistant E. coli evolved in the lab give view into DNA repair.” Accompanied by a photo of undergrads (above, with postdoc Steven Bruckbauer) who “are watching evolution happen in real time,” the story appears ready to challenge Behe’s principle.

In a recent study published online in the Journal of Bacteriology, biochemistry professor Michael Cox and his team describe blasting E. coli bacteria with ionizing radiation once a week, causing the bacteria to become radiation resistant. In doing so, they have uncovered genetic mutations and mechanisms underlying this resistance.

Needless to say, high-energy ionizing radiation is not life’s friend. It’s a serious hazard for living things, including astronauts in the space station. If a microbe found a way to resist it, that’s something! First, though, the article calls this another case of “directed evolution” (aka intelligent design), not Darwinian evolution.

Their experiment in “directed” evolution is simple. Lead author and postdoctoral researcher Steven Bruckbauer split a population of E. coli into four groups. Once a week, he and a team of undergraduate researchers use equipment in the Department of Medical Physics to hit each population with ionizing radiation until 99 percent of the cells are dead. They then grow the survivors — the one percent that best resisted the radiation — in culture. Most of the new bacteria that grow from these carry beneficial mutations for radiation resistance.

Maybe it bears looking closer at what actually happened in this case. Lo and behold, the genes for resistance were already present in all the bacteria. 

While the overall mechanisms, such as enhanced DNA repair, are the same as in naturally resistant bacteria, many of the mutations that caused those changes have never been seen before. Bruckbauer adds that beyond DNA repair and changes to RNA polymerase, there are entirely new ways of being resistant that could arise.

Actual new functions were found! — but only in the imagination:

“These mechanisms for conferring resistance are just the ones we’ve seen,” he says. “It’s exciting to think about the novel possibilities we haven’t identified or that haven’t even evolved yet. There are some other mechanisms seen in nature that we expect to pop up eventually but then new ones might start evolving.”

The team celebrated after 125 rounds of zapping the bacteria, but then admitted that they only uncovered a previously existing “latent ability to become highly radiation resistant with modifications to a few existing DNA repair proteins.” It means that a stressful environment brought out something that was already present. Most likely, the “modifications to a few existing DNA repair proteins” broke regulatory controls on the repair system so that it became unleashed under this specific barrage of radiation. In any case, the bacteria survived, but nothing new evolved.

Gut Feelings

The human gut microbiome is a good place to test for innovative functions undergoing selection. Mutations happen so frequently, the microbiome could be evolving within our lifetimes. Isabel Gordo in PLOS Biology analyzes theoretical and experimental work on what kind of evolution is going on in those dark passageways. No surprise; it’s Darwinism by devolution:

The observed patterns of between-host polymorphism reject the predictions of a simple neutral model of molecular evolution for several human gut bacteria. Synonymous site polymorphism (i.e., that does not lead to changes in the protein sequence) exhibits a variance clearly inconsistent with a model, in which neutral mutations arise in each host and a single lineage transmits between hosts. However, the pattern of polymorphism at synonymous and nonsynonymous sites is consistent with the slightly deleterious theory of molecular evolution, in which widespread purifying selection may keep a microbial ecosystem functional, at long time scales, for all hosts. Much of the variation observed can be explained by postulating the recurrence of a high fraction (90%) of mutations whose effects decrease fitness by a very modest amount (approximately 0.01%) but still strong enough to be purified in the long run.

Staying Afloat

A study reported by Stanford University says that “Species evolve ways to backup life’s machinery.” Essentially, “A new analysis of biological data reveals that every species from bacteria to primates has developed ways to bypass breakdowns in the networks of proteins vital to sustaining life.” As Behe would put it, are organisms removing car doors to improve gas mileage? Are they tossing cargo overboard to keep from sinking?

The scientists studied 1,840 species — from bacteria to primates — to understand how evolution built life forms that could survive in the face of natural adversities. What they discovered was profound yet intuitive: Every species has evolved backup plans that allow its protein machinery to find bypasses and workarounds when nature tries to gum up the works. No previous study has ever surveyed such a broad swath of species to find a survival strategy common to all life: Develop a versatile and robust molecular machinery.

The “interactome” of life — the set of gene regulatory networks and protein interactions — must survive perturbations to keep organisms alive. Mutations do not construct new complex machines. This study says that they “gum up the works.” Unless species “from bacteria to primates” had pre-existing strategies to backup and survive degradation by mutations, life would quickly devolve to extinction.

Short Stories

Briefly, here are some other tests of Darwinism’s ability to innovate:

• A paper in PNAS by Milner et al. shows that fungi can gain new functions! Yes, but the method is by horizontal gene transfer (HGT) — i.e., by borrowing existing genes. Scientists found that fungi can gain transporter-encoded genes by HGT, giving them a “distinct competitive advantage in a given environment,” they say. “This has wide implications for understanding how acquisition of single genes by HGT can drastically influence the environments fungi can colonize.” How many other claimed instances of gain-of-function mutations are really cases of HGT?
• Darwin is devolving in beehives. Here is the honeybee version of the children’s story, “The Town Mouse and the Country Mouse.” Phys.org says that the “waggle dance” method of communication is disappearing in urban settings. “One possible reason may be human-induced habitat change,” which led to the loss of this complex, informative behavior.
• Another Phys.org article says that antibiotic resistance genes “spread faster than so far thought.” The reason? It’s not the emergence of novel genes by mutation. Instead, “resistance genes hop around the genome.” Methods of gene sharing include viruses, phages, and transposons. An international team was surprised to find that “mobile genetic elements induce a fast distribution of resistance genes among genomes of different organisms.” One said, “The finding that resistance is also extensively transferred between bacteria without the involvement of plasmids is really quite surprising.”
• Scientists found a plant genome with “among the most GC-biased genomes observed to date.” The parasitic plant uses only six amino acids, and is 95 percent composed of AT base pairs. “Darwin help us!” exclaims the exasperated author David Roy Smith in Current Biology. Apparently these two parasitic plants have forsaken richer genomes because they are able to get by with less.
• Let’s all evolve like the birds evolve. How do birds adapt their songs? With “preexisting genetic variation.” Lai et al., writing in PNAS, seemed to want to hear their favorite Darwin tune, but found that parrotbills in Taiwan select “standing genetic variation” instead of de novo mutations. They found that “the evolutionary potential of a population depends significantly on its preexistinggenetic diversity.” Selection of existing genetic variation is likely to swamp new beneficial mutations, because “a high level of standing variation may allow a faster response to environmental changes than waiting for appropriate mutations to arise.” Understandably so.
• Are humans evolving new beneficial mutations? Analysis of the human genome at the University of Barcelona identified 2,859 genes that apparently have been under selective pressure. Further reading shows that some of these result from “hybridisation of the human species with the Neanderthals and other hominid species,” which implies sharing of existing genetic information. Other genetic changes aiding survival in certain environments, such as for lactose tolerance or ability to endure high altitudes (hypoxia), may result from relaxation or breaking of controls of existing genes. Overall, the research is revealing “how the introgression of archaic genomes have modelled our current genomes.”

These examples show that all life, from cells to primates, do survive the onslaught of nature’s attempts to “gum up the works” with mutations. They do this, though, not by innovation of complex new functions by chance. Instead, they go to desperate extremes to stay alive in spite of mutations. They can exchange pre-existing genetic information from other sources. They can rely on built-in mechanisms to fix and work around the mutations. In short, Behe is right: Darwin devolves, yet life goes on.

Darwin just keeps on Devolving?

Behe on Joseph Thornton’s Work: “A Big Monkey Wrench that Even I Did Not Expect”
David Klinghoffer | @d_klinghoffer

In  Darwin Devolves,  Michael Behe demonstrates the limitations of unguided evolution from the work of “dyed in the wool” Darwinists themselves. We’ve focused so far on National Academy of Sciences member Richard Lenski at Michigan State, with whom Behe has had an extensive back-and-forth.

Lenski has conducted the famed Long Term Evolution Experiment on which Behe draws extensively. But another outstanding researcher, Joseph Thornton at the University of Chicago, also comes in for praise and examination in the book. Professor Behe talks with host Andrew McDiarmid about Thornton’s work, which throws “a big monkey wrench [in the strained argument for Darwinism] that even I did not expect.”

Download the podcast or listen to it here.

It was interesting to see fellow University of Chicago biologist Jerry Coyne casually shoehorn Thornton into a Washington Post review of Darwin Devolves as a supposed defeater for irreducible complexity.  As Behe noted here,  “I spent half of Chapter 8 on Thornton’s work, discussing why it shows deep and unexpected problems for Darwinian evolution. Coyne not only doesn’t summarize my argument, he doesn’t even tell readers I make one.” That is typical.

Physics vs. Darwin

Physicist David Snoke on Denton's Evolution: Still a Theory in Crisis
David Klinghoffer February 23, 2016 12:50 PM

I highly recommend reading a review, by University of Pittsburgh physicist David Snoke, of Michael Denton's Evolution: Still a Theory in Crisis. It's fascinating and wonderfully lucid. While expressing some disagreement, he concludes that the book deserves to sit on the same shelf with Stephen Jay Gould's work -- a high compliment whatever your position on evolutionary questions.

I think that Dr. Snoke's comments as a physicist are particularly helpful and illuminating. He draws a comparison to the "topological argument" well known in his profession:

We are all so programmed by the current evolutionary debate to see Darwinian evolution as the only viable materialist theory that it is hard to understand at first what Denton is proposing, if not intervention from a spirit world, and it is hard to grasp that there were evolutionists who preceded Darwin, with strong arguments against Darwin's ideas. To understand Denton's view (and Owen's) it is crucial to realize that it is first and foremost an empirical theory. Science has a long tradition of empirical theories which simply state the facts in unifying language without proposing any mechanism at all to explain them. Thus, for example, Newton famously proposed that gravity force could act at a distance, without proposing any explanation why. We are all so used to Newton's laws now that we forget how empirically driven it was. The same empirical approach was used to build the Periodic Table of chemistry, long before quantum mechanics explained why it has the form it does. In the same way, Denton, following Owen, draws us to look at a glaring and obvious fact of nature: that living organisms do not exist in a continuum of small differences with gradual transitions between them; rather, they exist in highly distinct types and forms, with specific identities and unique features for each type. Thus, for example, mammals all have four limbs, five digits per limb, two eyes, mammary glands in pairs, etc. These patterns persist over hundreds of millions of years despite all manner of selective pressure in different directions.

Darwinian evolutionists are familiar with these properties, of course, and have a standard explanation that they are leftover vestiges from archetypal ancestors. Against this, Denton has two main arguments. First, the record strongly supports the view that new Forms appear suddenly, without precursors. This is known as "saltation" -- the sudden appearance of a fully formed new structure. In all of the cases we know, the "transitional forms" between one type of organism and another do not consist of creatures with half-novelties, but rather, creatures with whole and complete novelties. Their transitional nature is identified because they have a subset of a larger set of several wholly novel features belonging to later descendants. But in each step that we see along the way, that which is new is whole and complete. The problem this creates for Darwinian evolution is similar to what is called a "topological argument" in physics. There are some things that can be continuously transformed into other things, while some things cannot. In the canonical example, a coffee cup can be transformed continuously into a doughnut, but not into a saucer. In the same way, all feathers are tubular, which requires a follicle with circular form, while reptile scales are flat sheets. Topologically, a flat sheet cannot be continuously transformed into a tube. (It was fascinating to me to hear that the dinosaurs-acquiring-feathers story actually creates new problems for Darwinism.) There are also more generalized topological arguments. Some molecular cycles in the cell are circular -- the so-called "chicken-and-egg problems" in which element A is required to create element B, and B is required to create C, but C is required to create A. These loops therefore have the same toplogical problem of lack of continuous generation from a prior process.

The transitional forms which indicate common descent also therefore create huge problems for gradual change via Darwinian selection as a mechanism. The most plain reading of the data is "descent with saltation." This occurs at every level. New organs occur suddenly, new processes occur suddenly (such as human language), and new genes occur: in every form of life there are whole genes (known as ORFans) that appear to be utterly unique to that form, with no homolog in any other type of creature. In some cases, even when genes from an ancestor are used, they are pressed into service to perform utterly new functions via the sudden appearance of a completely new set of switches and timers.

Snoke wrote his review for the Christian Scientific Society, so not surprisingly he asks about the relevance for Christians of Denton's "heavily empirical and materialist book." The "materialist" descriptor may be a little confusing, since Denton's view also "sounds a lot like neo-Platonism." Anyway, Snoke says this about anatomical features that seem to serve no purpose:

The idea of robust Forms is worth examining for the Christian. As Denton notes, much Christian thinking has been as utilitarian as Darwinist thinking. We tend to assume that everything in living systems must have a useful function. Perhaps some things, especially overall architectures, have their particular form not for function but for beauty or diversity. This leads to, for example, a helpful way of looking at the problem of male nipples. If we ask "What are male nipples for?" we are assuming a fully utilitarian view of living forms, and can get into knots trying to decide what they are good for, or if God has made a mistake. If we adopt a view of Forms, we can say that male nipples exist because the proper form for human bodies is to have nipples there.

Also, regarding the implications of Denton's thinking that run contrary to Darwinian racism:

The idea of Forms also makes a difference when think about race and racism. Darwinism has always had an ugly flirtation and sometimes open marriage with racism. If all of life is a continuum of gradual changes, then it makes sense that various subgroups of humans would be at different stages in evolutionary development, some closer to apes and others closer to the next upward step. Darwin argued in The Descent of Man that "lower" versions of humans such as Hottentots were proof of his theory of evolution. But Denton makes the case that, like other creatures, humans have had a stable single Form since they first existed, with all the basic gifts of language and culture in all geographical locations from the very beginning.

Snoke observes the irony that current evolutionary thinking is so hidebound -- "calcified," is how he puts it -- that it took Discovery Institute, leading advocate of intelligent design (not a materialist theory), to give a forum to Dr. Denton, whom Snoke sees as a sort of latter-day Gould. I think Denton's structuralism is in fact best understood as a form of ID. But the point is well taken. In today's orthodox evolutionary circles, protected from criticism behind walls of academic prestige, the spirit of intellectual exploration and discovery is largely extinguished.


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