The ID Update

by Denyse O'Leary
ARN correspondent

Every year, for some years now, the folk at Access Research Network have rank ordered the Top Ten intelligent design stories of the year. Due to volume, this last year, they were broken out into science news, media news, and 2009 resources. The Top Ten science news picks are here.

But why should ARN do it all? We're not wizards; we just put our heads together once a year.

For a free copy of Stephen Meyer's Signature in the Cell (Harper One, 2009), the top rated 2009 ID resource, courtesy the Discovery Institute, explain:

1. How would you have rated the stories differently?

Or

2. Are there stories that should have been on the list that are not?

In under 400 words. You can link at the comments box, so no need to reproduce swatches of copy if you don't want to use up your word count.

Here are the contest rules.

Go here to enter. If you are new to Uncommon Descent, you must register, a minor process.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

Review Of Probability's Nature And Nature's Probability - Lite, by Donald Johnson
ISBN: 978-0-9823554-4-2

By Robert Deyes
ARN Correspondent

PART I
If Intelligent Design is to be escorted out of science debating halls because of its compatibility with a belief in a deity, undirected naturalism should likewise be excluded on the premise that it lines up with an atheistic world view. Such is the opening message of the `Lite' version of a book whose title Probability's Nature And Nature's Probability is so captivatingly simple that one cannot help but take at least a cursory look through its pages. And the author Donald Johnson has an impressive list of scientific accolades to his credit brought about by a passion for (and not a disdain of) science- a PhD in chemistry from Michigan State University, ten years as a senior research scientist in the medical and scientific instrumentation field, a twenty year college-teaching career and a second PhD in Computer Science.

Johnson's personal reflections reveal a lot about how he came to espouse the views of the Intelligent Design movement. Over the course of his career, Johnson grew increasingly skeptical over natural causation as applies to the origin of life. Science as we know it, he notes, should make testable predictions. While speculation does have a place in science, it needs to be presented as such and not dressed up and served up as a `platter of facts' for consumption by a public unaccustomed to the nuances of scientific argumentation. Johnson brings to the fore the blatant misrepresentations of what is truly `probable', `plausible' and `feasible' in the context of origins of life research as he takes the reader on a whirlwind tour of mathematical notation and probabilistic reasoning.

Theories that are at loggerheads with the singular origin of our universe can in most cases be soundly discredited on the grounds that they lack empirical evidence and testability. The oscillating (Big Bang/Big Crunch) model in particular is easily pushed aside given a notable absence of data in support of a universe that will reach the critical density needed to cause its collapse. For an infinite-existence model we are confronted with the question of how a system that has reached maximum entropy over infinite time could ever give rise to a non-maximum entropy cosmos. In the words of Johnson "an infinitely old universe would be energy dead with no capacity for work, since one result of the second law of thermodynamics is that perpetual motion machines are impossible (zero probability)". Other attempts to eschew the extraordinary fine tuning of our universe, such as we see in the manifold iterations of String theory, posit the existence of multiple universes. The metaphysicality of such alternatives however, given that we cannot possibly hope to see beyond the horizon of our own cosmic abode, renders them unqualifiable as real science.

What are we to make of the abundance of life on our planet? As Johnson so clearly conveys, an acceptable definition of life naturally entails a consideration of observable phenomena such as metabolism, growth and reproduction. At the heart of life lies a myriad of proteins that perform critical functions all of which depend on the tight specification of highly-restricted amino acid sequences. Proteins in the ribosome are themselves translated by the very machinery of which they form a part. The DNA that supplies the instructions for their manufacture is a digital code of the highest order with alternative splicing and sequence overlap of the estimated 20-25,000 genes that exist in humans producing somewhere in the order of 100-200,000 distinct proteins.

Even one of the smallest organisms, Mycoplasma genitalium, sports 482 genes although estimates suggest that as few as 151 genes might be all that is needed to make the simplest life form. How might chemical evolution have taken the first baby steps on the road to what one might tentatively call a primitive cell? The reality as Johnson so emphatically hammers home is that science remains clueless over this singularly important question. Since proteins and nucleic acids have long been known to act as an integrated co-operative whole, models that assume a gradual evolutionary process are today considered woefully inadequate for explaining the origins of life. Truth be told, there exists a pervasive 'science as we don't know it' element in everything from RNA world hypotheses to panspermia and the host of proposed undirected natural processes that invoke the role of minerals in early biocatalysis.

With matter and information representing two distinct "domains of existence", biologists are at a loss to explain the origin of the digital code contained in genetic material. DNA carries a large degree of so-called traditional information which provides meaning for subsequent interpretation by the translation machinery. Trevors and Abel wrote how the codons of DNA represent "functional meaning only when the individual amino acids they prescribe are linked together in a certain order using a different language". This has to be one of the outstanding revelations of the bioinformatics revolution. In fact, using his exhaustive knowledge of information science, Johnson demonstrates the extraordinary parallels between a computer program's algorithmic language and the genetic information system contained within every living cell.

What is most impressive about Johnson's text is the breadth and diversity of scientific sources that he draws from. Even those who are heavily committed to undirected naturalism display an apparently unavoidable tendency to use a language that connotes design. So it is that while Darwin's heavyweights seem intent on embracing chance and natural selection as the only drivers of biological change, they are also perhaps unwittingly navigating towards intelligent design through their own corridors of reason.

Further Reading
Trevors, J.T.; Abel, D.L. Chance and necessity do not explain the origin of life. Cell Biol. Internat. 2004, 28, 729-739.

Anyone attempting to swat a fly will become aware of its remarkable aerodynamic capabilities. Its speed of response and ability to change direction abruptly far exceed our own powers as pursuers. The flight of insects has received considerable attention from researchers and some recent work was stimulated by the recognition of a gap in knowledge. The scientists realized that the previously-studied flight control system involving vision cannot be the explanation for how flies maintain stability in the face of unpredictable short disturbances.

"Corrective behavior often takes advantage of vision. For fruit flies, however, reaction time to visual stimuli is at least 10 wingbeats, so these insects must employ faster sensory circuits to recover from short time-scale disturbances and instabilities."

To study how fruit flies recover from in-flight disturbances, researchers glued magnetic pins to the insects' backs and zapped them with a magnetic field. This fly has a 1.5 mm pin on its back and is held in place by the tip of a sewing needle. (Credit: Wang, Cohen and Guckenheimer labs, Source here)

The experimental work required the research team to abandon ideas of tethering insects or imposing other restrictions on flight behavior. They needed to observe insects in free-flight.

"To probe this fast control strategy, we devised an experimental method that imposes impulsive mechanical disturbances to flying insects while allowing us to measure relevant aspects of flight behavior. We first glue tiny ferromagnetic pins to fruit flies and image their free flight using three orthogonally oriented high-speed video cameras. When a fly enters the filming volume, an optical trigger detects the insect, initiates recording, and activates a pair of Helmholtz coils that produce a magnetic field. The field and pin are both oriented horizontally, so the resulting torque on the pin reorients the yaw, or heading angle, of the insect. We then use a new motion tracking technique to extract the three-dimensional body and wing motions."

What they observed is that prior to the perturbation (which lasted 5ms, or about one wingbeat period), the wings beat symmetrically. After the magnetic torque was applied, 3 wingbeats were needed for the control system to respond, and then "asymmetries in the wing motions appear for about five wingbeats, indicating the insect is actively generating corrective torque". For small perturbations, the insects correct "nearly perfectly", whereas larger perturbations - although corrected to some extent - lead to permanent changes in heading.

"The accuracy of the recovery indicates that a refined control strategy underlies the response of fruit flies to in-flight perturbations. To reveal this strategy, we construct a physics-based model of the observed behavioral response."

Body motions are detected by the halteres: "small vibrating organs [. . .] that act as gyroscopic sensors. Anatomical, mechanical, and behavioral evidence indicates that the halteres serve as detectors of body angular velocity that quickly trigger muscle action." With this model, the halteres have a nonlinear response consistent with vibratory gyroscopes, so sensor saturation explains "why fruit flies are unable to accurately recover from strong perturbations". The control system design principles are as follows:

"These findings suggest that these insects drive their corrective response using an autostabilizing feedback loop in which the sensed angular velocity serves as the input to the flight controller. [. . .] [T]he velocity is sensed by the halteres, processed by a neural controller, and transmitted by the flight motor into specific wing motions that generate aerodynamic torque."

Halteres are remarkable organs and unique to the Diptera. The research raises questions about other autostabilization techniques found in the natural world and how such systems can be incorporated into flying robots.

"Flight control principles uncovered in this model organism may also apply more broadly, and this work provides a template for future studies aimed at determining if other animals employ flight autostabilization. The control strategies across different animals are likely to share common features, because the physics of body rotation is similar across many animals during flapping-wing flight. Additionally, animals that lack halteres may use functionally equivalent mechanosensory structures such as antennae. Finally, the control architecture of the fruit fly offers a blueprint for stabilization of highly maneuverable flapping-wing flying machines."

These design principles were incorporated by intelligent agents into aeroplanes very early in their history (further information is here). It is now apparent that flying insects got there first! In evolutionary terms, we have here a good example of convergence. Since these control systems represent complex specified information (with the greater complexity found in the insect control system), intelligent agency should be invoked in both cases.

"For fixed-wing machines, the need to overcome instabilities spurred the invention of autostabilizing systems by 1912, only 9 years after the Wright brothers first manually controlled airplane flight. The development of such automatic steering systems also led to the first formal description of proportional-integral-derivative control schemes and advanced gyroscopic sensor technology. The fruit fly's autostabilization response is well-modeled by a simple PD scheme that receives input from gyroscopic halteres, and, like airplanes, uses fine adjustment of wing orientation to generate corrective torques. Roughly 350 million years after insects took flight, man converged to this solution for the problem of flight control and joined animals in the skies."

Discovering the flight autostabilizer of fruit flies by inducing aerial stumbles
Leif Ristroph, Attila J. Bergou, Gunnar Ristroph, Katherine Coumes, Gordon J. Berman, John Guckenheimer, Z. Jane Wang and Itai Cohen.
Proceedings of the National Academy of Sciences, 2010, 107:4820-4824 | doi:10.1073/pnas.1000615107

Abstract: Just as the Wright brothers implemented controls to achieve stable airplane flight, flying insects have evolved behavioral strategies that ensure recovery from flight disturbances. Pioneering studies performed on tethered and dissected insects demonstrate that the sensory, neurological, and musculoskeletal systems play important roles in flight control. Such studies, however, cannot produce an integrative model of insect flight stability because they do not incorporate the interaction of these systems with free-flight aerodynamics. We directly investigate control and stability through the application of torque impulses to freely flying fruit flies (Drosophila melanogaster) and measurement of their behavioral response. High-speed video and a new motion tracking method capture the aerial "stumble", and we discover that flies respond to gentle disturbances by accurately returning to their original orientation. These insects take advantage of a stabilizing aerodynamic influence and active torque generation to recover their heading to within 2 deg in less than 60 ms. To explain this recovery behavior, we form a feedback control model that includes the fly's ability to sense body rotations, process this information, and actuate the wing motions that generate corrective aerodynamic torque. Thus, like early man-made aircraft and modern fighter jets, the fruit fly employs an automatic stabilization scheme that reacts to short time-scale disturbances.

by Denyse O'Leary
ARN correspondent

Here's an interesting article in New Scientist by Bob Holmes on a new approach to how animals become separate species ("Accidental origins: Where species come from", March 10, 2010):

Everywhere you look in nature, you can see evidence of natural selection at work in the adaptation of species to their environment. Surprisingly though, natural selection may have little role to play in one of the key steps of evolution - the origin of new species. Instead it would appear that speciation is merely an accident of fate.

So, at least, says Mark Pagel, an evolutionary biologist at the University of Reading, UK. If his controversial claim proves correct, then the broad canvas of life - the profusion of beetles and rodents, the dearth of primates, and so on - may have less to do with the guiding hand of natural selection and more to do with evolutionary accident-proneness.

[ ... ]

"When it works, it works remarkably well," he says. "But it only works in about 6 per cent of cases. It doesn't seem to be a general way that groups of species fill out their niches."

Then Darwin's theory just barely makes it to statistical significance, conventionally given as 4 per cent.

The otherwise most informative article is marred by the constant need to claim that Darwin was not wrong - but obviously, if Pagels is right, Darwin was indeed wrong, and so are all the people fronting his cause. Natural selection acting on random mutation was, precisely, Darwin's proposed mechanism.

No one supposes that natural selection doesn’t occur. But is it the main driver of new species, as Darwin thought, and Pagels doubts?

Pagels dances very nervously indeed around that point (presumably from fear of joining the Expelled, given that his genome research has failed to back Darwin up.

So, for a free copy of Expelled, which details what happened to a variety of people who questioned establishment Darwinism, based on its failures of evidence, and provide the best answer to this question: What do you think of Pagels’s evidence? Is it critical? Is he just blowing smoke? Will he be forced to recant?

Here's where you enter, which you do by posting a comment, 400 words or less. If you are new to Uncommon Descent, you will need to sign up.

Here are the contest rules, not many or difficult. The main thing is 400 words or less. Winners receive a certificate verifying their win as well as the prize. Winners must provide me with a valid postal address, though it need not be theirs. A winner's name is never added to a mailing list. There is no mailing list. Have fun!

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

The mollusc, known as the scaly-foot gastropod, has been known for about a decade. It was discovered living in the deep sea near the Kairei Indian hydrothermal vent field on the Central Indian Ridge. The natural environment for the animal is harsh. There are extremes of temperatures, high pressures and high acidity levels that can easily damage shells of calcium carbonate. Brachyuran crabs live in the vicinity and these "are known to compress gastropod mollusc shells between their chela" with loads of up to 60N.

"To understand how the valiant gastropod holds up to these trials, Christine Ortiz of MIT and her colleagues used nanoscale experiments and computer simulations to dig in to the shell's structure. Many other species' shells exhibit what Ortiz calls "mechanical property amplification," in which the whole material is hundreds of times stronger than the sum of its parts."

The scaly-foot gastropod uses a unique trilayered shell to protect itself from hazards. (Image credit: Anders Waren, Swedish Museum of Natural History. Source here)

Most exoskeletal structures are technically known as multilayered composites. The parameters are the layer thicknesses, the nano- and microstructure of each layer, the number of layers, the sequence of layers, etc. Each species appears to have its own resultant profile.

"Design, inspired by nature, of engineering materials with robust and multifunctional mechanical properties [i.e., those which sustain a variety of loading conditions] is a topic of major technological interest in a variety of civilian and defense applications. Here, we identify the design principles of the shell of a gastropod mollusc from a deep-sea hydrothermal vent [order Neomphalina, family Peltospiridae, species Crysomallon squamiferum]. This system has a trilayered structure unlike any other known mollusc or any other known natural armor, with a relatively thick compliant organic layer embedded between two stiffer mineralized layers, an outer iron sulfide-based layer and an inner calcified shell."

The outer layer is about 30 micrometres thick and is mineralised: it contains iron sulphide particles (greigite, Fe2S4). This gastropod is the only metazoan known to employ iron sulphide as a skeletal material. The middle layer is about 150 micrometres thick and is thought to be the periostracum (the template for shell mineralization, providing protection against corrosive and dissolutive marine environments, and also chemical protection from boring organisms). The inner layer is composed of aragonite that is itself layered:

"[It] possesses a gradient layer [. . .] with a typical crossed lamellar layer (CLL) microstructure (approximately 50 [micro]m thick), followed by a relatively thick layer also with a CLL microstructure (approximately 200 [micro]m thick, followed by a thin prismatic layer (PL) on the inner surface of the shell (approximately 1.5 [micro]m thick)."

This structure has been studied empirically and modelled. Simulations were performed to understand how the shell responds to impacts and applied loads. There are too many details to document here.

"It is interesting to see how C. squamiferum has created these additional different protection mechanism compared to other gastropod molluscs by using materials plentiful and specific to the deep-sea hydrothermal vent environment, i.e., vent fluids rich in dissolved sulfides and metals.
The design principles of the trilayered shell of C. squamiferum exhibit many aspects that are different from the highly calcified shells of typical gastropod molluscs or any other natural armor. Each material layer serves distinct and multifunctional roles leading to many advantages."

Design principles have emerged from this research. The authors have found new design features leading to enhanced functional performance. "Each material layer serves distinct and multifunctional roles leading to many advantages". They point out that design principles are extremely important because there are so many variables: "The design space for synthetic multilayered structural composites for protective applications is enormous". The great merit of biological systems is that they provide a chart to steer through this space. However, the authors attribute design in biological systems to an "evolutionary process".

"Biological systems, such as the one described here, greatly reduce the engineering design space since efficient threat-protection design concepts have emerged through the lengthy evolutionary process that fulfill the necessary functions and constraints."

The problem with this evolutionary framework is that it has no empirical validity. We have no warrant for explaining design principles via evolutionary processes. The authors explain that they do not know whether the observed design "represents an advanced functional adaptation as an antipredatory response or an exaptation (i.e., a trait that evolved to serve one function, but subsequently and simultaneously may serve other functions)". This comment is, unfortunately, entirely typical of the culture prevailing in science produced by philosophical materialism. Evolutionists have supreme confidence in their theoretical framework, but do not seem to see the need to constrain theory by reference to empirical data. Observed adaptations do not demonstrate the emergence of design concepts. The only sources of design concepts that we know of are intelligent agents. Replacing the culture of materialism by one that integrates information inputs with physics and chemistry is long overdue.

With this alternative culture, paragraphs like the following take on a new richness of meaning:

"In particular, the efficient natural armor structural system described here sustains both mechanical loading, as well as thermal fluctuations with inherent mechanisms to prevent catastrophic failure. The multimaterial, trilayer design and advantageous curved geometry enables structural stiffening, reduction of radial displacements, penetration resistance, and stability during thermal impulses even with the presence of large mismatches between constituent materials. Trilayered sandwich composite designs have had limited use in military applications, and the concepts reported here could lead to bioinspired improvements and broader applicability and improved performance for human, vehicle, and structural armor."

Protection mechanisms of the iron-plated armor of a deep-sea hydrothermal vent gastropod
Haimin Yao, Ming Dao, Timothy Imholt, Jamie Huang, Kevin Wheeler, Alejandro Bonilla, Subra Suresh, and Christine Ortiz
Proceedings of the National Academy of Sciences, January 19, 2010, vol. 107, no. 3, 987-992 | doi:10.1073/pnas.0912988107

Abstract: Biological exoskeletons, in particular those with unusually robust and multifunctional properties, hold enormous potential for the development of improved load-bearing and protective engineering materials. Here, we report new materials and mechanical design principles of the iron-plated multilayered structure of the natural armor of Crysomallon squamiferum, a recently discovered gastropod mollusc from the Kairei Indian hydrothermal vent field, which is unlike any other known natural or synthetic engineered armor. We have determined through nanoscale experiments and computational simulations of a predatory attack that the specific combination of different materials, microstructures, interfacial geometries, gradation, and layering are advantageous for penetration resistance, energy dissipation, mitigation of fracture and crack arrest, reduction of back deflections, and resistance to bending and tensile loads. The structure-property-performance relationships described are expected to be of technological interest for a variety of civilian and defense applications.

See also:

Grossman, L. Snail In Shining Armor, Science News, February 13th, 2010; Vol.177 #4 (p. 13)

Stephen Meyer responds to Francisco J. Ayala's review of his book Signiture in the Cell.

More...

A great example of ID...and far less complex than the working inside a human cell, as shown in THIS ANIMATION.

and in Unlocking the Mystery of Life

Here is the Rube Goldberg machine...

In the EnterpriseBlog, Jay Richards comments on the story in the New York Times about the linking of climate change and evolution.

Richards opines...there are budding initiatives in state legislatures and boards of education to encourage or require balance in classroom discussions of global warming. The point of the piece, though, is to connect the teaching of evolution to the climate change debate:

Critics of the teaching of evolution in the nation's classrooms are gaining ground in some states by linking the issue to global warming, arguing that dissenting views on both scientific subjects should be taught in public schools.

Now when I read anything on the environment in the New York Times, I try to keep a couple of deconstructionist qualifiers running in the back of my head: "This is what the New York Times wants me to believe about the issue" and "What are they trying to accomplish with this piece?" I know it's cynical, but when it comes to environmental stories, I just don't trust New York Times reporters to keep it straight.

Some things they want to accomplish with this piece:

More...

A fossil that was celebrated last year as a possible "missing link" between humans and early primates is actually a forebearer of modern-day lemurs and lorises, according to two papers by scientists at The University of Texas at Austin, Duke University and the University of Chicago.

In an article now available online in the Journal of Human Evolution, four scientists present evidence that the 47-million-year-old Darwinius masillae is not a haplorhine primate like humans, apes and monkeys, as the 2009 research claimed.

They also note that the article on Darwinius published last year in the journal PLoS ONE ignores two decades of published research showing that similar fossils are actually strepsirrhines, the primate group that includes lemurs and lorises.

More...

Well known theologist, R.C. Sproul, interviewed Stephen Meyer, author of Signature in the Cell: DNA and the Evidence for Intelligent Design, on philosophy, evolution, education, Intelligent Design, and more.

The GospelCoalition has the link. Scroll down to Justin Taylor's March 5 post.

Click HERE.