But, But, But … We’re 98% Similar to the Chimp!

Not.

Transposable elements just don’t make sense. These so-called “jumping genes” are segments of junk DNA that insert themselves at random in our genomes. That is the evolutionary interpretation of these genetic units, but how and why do they move about, and why don’t they wreak havoc on the genome? The answers to these questions, which have been emerging in recent years, is that transposable elements are exquisite, finely-tuned, highly-functional molecular machines that contradict evolutionary expectations. Evolutionists have a long, failed history of presumed disutility—after all, the world arose by chance, surely it doesn’t work very well—and transposable elements are just one more example of this failed prediction. But the junk-to-hero story is only one of three ways that transposable elements utterly demolish evolutionary theory. The other two prongs in this Darwin-destroying triad are serendipity and pattern.

By serendipity, I am referring to the rather awkward findings, which are undeniable at this point, that if evolution is true, then it must have come about by highly complex, non adaptive, mechanisms. From diploid genetics to horizontal gene transfer, alternate gene splicing, genetic regulation, epigenetics, mechanisms that cause adaptive mutations, and transposable elements, evolution must have bumbled along by luckily constructing fantastically complex mechanisms. Those mechanisms would provide no immediate adaptive value, yet somehow would persist and become vital agents in evolutionary history. Simply put, evolution must have created evolution in a most unlikely (astronomically unlikely) set of circumstances. That’s serendipity, not science, and transposable elements heaps more fuel onto the fire.

By pattern, I am referring to another set of awkward findings, again undeniable, that the pattern of structures observed across the species consistently contradicts evolution’s predictions. One of those contradictions are the enormous differences found in otherwise allied species.

All three of these contradictions—disutility, serendipity, and pattern—are on display this week in new, systematic study of transposable elements out of Didier Trono’s lab in Switzerland. The study details the interactions between transposable elements and a class of proteins. The findings indicate the complexity and interdependency of these molecular mechanisms. As the press release admits:

Long considered as junk DNA, transposable elements are now recognized as influencing the expression of genes. … the extent of this regulation and how it is harnessed were so far unknown. EPFL scientists have now taken the first extensive look at a family of ~350 human proteins, showing that they establish a complex interplay with transposable elements … KZFPs can convert transposable elements in exquisitely fine-tuned regulatory platforms that influence the expression of genes, which likely takes place at all stages of development and in all human tissues. … It is a highly combinatorial and versatile system … As a field, epigenetics has come into prominence in recent years, revealing a previously unimagined complexity and elegance in genetics.

Not exactly junk DNA. And of course all of this would require large amounts of serendipity. For evolutionists are now forced to say that transposable elements would have to have played a, err, key role in evolution itself. Evolution would have had to have constructed this highly specific, detailed, system including hundreds of proteins and genetic elements, with hundreds of specific interactions, providing no immediate benefit. As Trono explains:

The vast majority of KZFPs binds to specific motifs in transposable elements. For each KZFP we were able to assign one subset of transposable elements, and also found that one transposable element can often interact with several KZFPs.

Finally, all of this contradicts the expected common descent pattern. This failure has become so common we now have non evolutionary terminology, such as “species-specific” and “lineage-specific.” The paper uses the term “species-restricted”:

KZFPs partner with transposable elements to build a largely species-restricted layer of epigenetic regulation

Species-restricted? In other words, the designs we are discovering in biology are unique to particular species. This is precisely the opposite of what evolution expects. Note also the teleological language (which as usual is evident in the infinitive form): The proteins “partner” with the transposable elements “to build” a largely “species-restricted” layer of epigenetic regulation. This is a classic example of evolution’s absurd creation story language.

The contradictory pattern was, of course, unsuspected. As Trono explains:

KZFPs contribute to make human biology unique. Together with their genomic targets, they likely influence every single event in human physiology and pathology, and do so by being largely species-specific -- the general system exists in many vertebrates, but most of its components are different in each case. … This paper lifts the lid off something that had been largely unsuspected: the tremendous species-specific dimension of human gene regulation.

Yes, it was largely unsuspected. For what these findings reveal is a tremendous species-specific dimension of human gene regulation. In other words, we would need proteins and genetic elements to evolve, via independent and yet interdependent, random mutations, to construct an entirely new set of genetic regulation instructions. This is astronomically unlikely, no matter how many millions of years are available. From a scientific perspective, these findings demolish evolution.

Religion drives science, and it matters.

About Those Placental Regulatory Genes

Evolution Recruits and Deploys Genes

Last time we noted the teleological ideas and language used to describe the hypothetical evolution of several genes that are expressed for a mere few hours, in the early development stages of many placental mammals. And by early we mean when we consist of only 8-16 cells. The teleology is not a mere slip-up. As we have documented many times, it is a common thread running throughout the genre of evolutionary literature. It is needed to make sense of the data, because evolution doesn’t.

That teleological language appeared in an article about the research. Not too surprisingly, teleological language also appears in the research journal paper as well. To wit:

A small number of lineage-specific tandem gene duplications have occurred, and these raise questions concerning how evolutionarily young homeobox genes are recruited to new regulatory roles. For example, divergent tandem duplicates of the Hox3 gene have been recruited for extra-embryonic membrane specification and patterning in dipteran and lepidopteran insects, a large expansion of the Rhox homeobox gene family is deployed in reproductive tissues of mouse, and duplicates of TALE class genes are expressed in early development of molluscs.

Two of the evolutionists’ favorite words are “recruited” and “deployed.” They sound so active. What better way to obviate the rather awkward problem that, if evolution is true, all biological variation must be random with respect to fitness (a claim which, by the way, has been falsified so many times we stopped counting). Evolutionists nonetheless continue to spread this fake news.

And no teleological idea would be complete with the mandatory infinitive form (“for … specification and patterning”). Religion drives science and it matters.

Metaphysics From John Ray to Nima Arkani-Hamed

An Ad Hoc, Capricious Creation

When John Ray refused to conform to the 1662 Act of Uniformity—aimed mainly at the Puritans—and so was forced to leave his position at Cambridge University, he roamed Europe for three years doing what he loved: observing nature. Ray and his companions were in for a surprise: unfathomable diversity. They found thousands of different kinds of insects, animals and plants. Every place had a different flora and fauna, and with different interactions. Life did not seem to follow the kind of compact formulas Isaac Newton was discovering for the new physics. With the overthrow of Aristotelianism, physics was becoming more parsimonious in line with Occam’s Razor. But biology was headed in the opposite direction. Were all these organic life forms and their detailed life histories really necessary? Ralph Cudworth had warned that the immense details of the world, while refuting Descartes’ rejection of final causes, were surely beneath the sovereign Creator’s dignity, and Ray’s three-year tour upped the ante. The Infra Dignitatem argument for a less hands-on creation story was born. There must have been something between the majestic Creator and this ad hoc, capricious, gritty creation. Like the Gnostics, the Aristotle of England, who would also become the father of natural theology, called for a separation between the Creator and the world.

The ancient Greeks described the cosmos as a set of concentric spheres that rotated and rubbed against each other producing harmonious tones. We have always wanted a simple, beautiful world. Certainly that is what God would have wanted too. But nature has not lived up to our expectations.

In fact ever since Newton, physics has been backsliding and becoming increasingly complex. All this was well explained in a Quanta magazine article from last week about leading physicist Nima Arkani-Hamed:

in recent years one question about the universe has come to preoccupy him, along with the field as a whole. Particle physicists seek to know whether the properties of the universe are inevitable, predictable, “natural,” as they say, locking together into a sensible pattern, or whether the universe is extremely unnatural, a peculiar permutation among countless other, more mundane possibilities, observed for no other reason than that its special conditions allow life to arise. A natural universe is, in principle, a knowable one. But if the universe is unnatural and fine-tuned for life, the lucky outcome of a cosmic roulette wheel, then it stands to reason that a vast and diverse “multiverse” of universes must exist beyond our reach — the lifeless products of less serendipitous spins. This multiverse renders our universe impossible to fully understand on its own terms. As things stand, the known elementary particles, codified in a 40-year-old set of equations called the “Standard Model,” lack a sensible pattern and seem astonishingly fine-tuned for life. Arkani-Hamed and other particle physicists, guided by their belief in naturalness, have spent decades devising clever ways to fit the Standard Model into a larger, natural pattern. But time and again, ever-more-powerful particle colliders have failed to turn up proof of their proposals in the form of new particles and phenomena, increasingly pointing toward the bleak and radical prospect that naturalness is dead.

Like Ray’s seventeenth century findings about biology, today’s physicists are finding what seems to be a capricious creation. There is no natural explanation as the world seems to consist of a long list of ad hoc, randomly selected designs. One thing they know for sure: no creator would have done this. It must have arisen by chance.

Religion drives science, and it matters.

Berkeley’s “Understanding Evolution” Website Explains Natural Selection

Secrets Of The Trade

With a small army of evolutionists working on it, and several National Science Foundation grants funding it, the University of California at Berkeley’s “Understanding Evolution” website has a surprising number of errors. One of the more egregious ones is on a page that is intended to clarify the concept of natural selection. It is entitled “Misconceptions about natural selection,” but it begins with what is perhaps the worst of all: “natural selection can produce amazing adaptations.”

While it is true that the species display a wide assortment of amazing adaptations, they have nothing to do with natural selection. Remember the chameleon that changes color? A recent study discovered the incredible mechanism responsible behind it:

Many chameleons, and panther chameleons in particular, have the remarkable ability to exhibit complex and rapid colour changes during social interactions such as male contests or courtship. It is generally interpreted that these changes are due to dispersion/aggregation of pigment-containing organelles within dermal chromatophores. Here, combining microscopy, photometric videography and photonic band-gap modelling, we show that chameleons shift colour through active tuning of a lattice of guanine nanocrystals within a superficial thick layer of dermal iridophores.

Wow—active tuning of a lattice of guanine nanocrystals. Biology students will recognize guanine as one of the four main bases used to form the chemical letters in our DNA. The chameleon forms crystals of guanine to control the reflected light. In an outer layer of skin, the chameleon has guanine nanocrystals in a triangular shape in special light-reflecting cells called chromatophores. Then, in a deeper layer the chromatophores contain brick-shaped guanine nanocrystals. The active control occurs in the outer skin layer. Using some sort of cell signaling, such as hormones, the triangular guanine nanocrystals are excited, altering the crystal spacing and with it the wavelength of the reflected light and so changing color.

It is a fantastic mechanism and, needless to say, natural selection plays no role in it.

What about the origin of this mechanism? Did it evolve via random mutations and natural selection? According to the paper it did. In fact the authors write that they have demonstrated such an incredible feat:

Combining histology, electron microscopy and photometric videography techniques with numerical band-gap modelling, here we show that chameleons have evolved two superimposed populations of iridophores [chromatophores] with different morphologies and functions

Is that true? Does the paper “show that” this incredible active color control mechanism evolved?

No.

In fact this claim is utterly false. The paper shows nothing of the sort. In fact the authors admit they cannot even settle on an “evolutionary scenario.”

They also admit that the mechanism is an evolutionary novelty:

This combination of two functionally different layers of iridophores [chromatophores] constitutes an evolutionary novelty that allows some species of chameleons to combine efficient camouflage and dramatic display, while potentially moderating the thermal consequences of intense solar radiations.

But it gets worse.

Not only do the authors lack a convincing evolutionary scenario for what must be an evolutionary novelty, but they fail to present an explanation for how this fantastic active color control mechanism evolved.

I’m not saying their explanation is weak. I’m not saying it lacks credibility. I’m not saying it is yet another “just-so” story. I’m not saying it is improbable. I’m not saying any of those things for the simple reason that there is no explanation given. Nothing. Nada. What the research does show is some of the details of how this fantastic mechanism works.

Believe it or not, for evolutionists, elucidating structure, mechanism and function equates with demonstrating that it evolved.

Newcomers to evolutionary literature might be nonplussed. How can a research paper unequivocally state that it “shows” X, and then do nothing of the sort? Nothing at all.

In fact this rather strange literary device runs throughout the evolutionary genre. Researchers make utterly unfounded claims of discovering, demonstrating, confirming and proving evolutionary events, and then journalists follow along with popular articles rehearsing the refrain. Evolution is demonstrated yet again.

And not just evolution.

Evolutionists also say that examples such as this are demonstrations of natural selection—demonstrations of natural selection producing amazing adaptations.

This brings us back to the UC Berkeley “Understanding Evolution” website. It abuses science in its utterly unfounded claim that “natural selection can produce amazing adaptations.”

In fact natural selection, even at its best, does not “produce” anything. Natural selection does not and cannot influence the construction of any adaptations, amazing or not. If a mutation occurs which improves differential reproduction, then it propagates into future generations. Natural selection is simply the name given to that process. It selects for survival that which already exists. Natural selection has no role in the mutation event. It does not induce mutations, helpful or otherwise, to occur. According to evolutionary theory every single mutation, leading to every single species, is a random event with respect to need.

This Piece by Lawrence Krauss is a Damning Indictment

Follow the Evidence

When Eric Metaxas wrote a Christmas Day piece in the Wall Street Journal about how science is lending support to modern-day arguments for design in the universe, he drew fire from all quarters. Apparently Metaxas arguments were full of fallacies. Of particular interest was a criticism by leading physicist, Lawrence Krauss. Surely a top scientist would leave no doubt about Metaxas’ flubs.

Krauss’ first point was that Metaxas is a “religious writer with an agenda,” and so his arguments cannot be trusted. But religious people in general, and Christians in particular, are all over the map when it comes to design. Indeed, many of Metaxas’ critics are Christian theologians.

Clearly Metaxas, qua “religious writer” or Christian, is not bound to an agenda regarding design. Why then does Krauss sense an agenda at work? Perhaps because, in fact, it is Krauss who is the one with the agenda. You see Krauss is an atheist, and when it comes to design, atheists are most definitely not all over the map. If you are an atheist, then you can’t accommodate arguments that the science strongly points to a designer. In fact, elsewhere, when not claiming others have an agenda, Krauss has advocated the abolishment of religion:

Religion will go away in a generation, or at least largely go away - and that's what I think we have an obligation to do.

And Krauss says Metaxas is the one with the agenda?

Unfortunately Krauss’ criticism goes downhill from there. Krauss explains that “The piece was rife with inappropriate scientific misrepresentations.”

Misrepresentations?

Metaxas makes two basic arguments. First, evolution’s just-add-water view of life had led astronomers to expect that the universe is teeming with life. ETs should be common and if we point our radios to the stars we should eventually pick up some interesting signals. But no such signals have been found. It is a clear example of yet another falsified evolutionary expectation. In fact Metaxas cites some astronomers who have argued the probabilities for ET life is far lower than previously expected.

Second, Metaxas points out that the universe is fine-tuned for life. And while this is a more subtle point, no one questions that this is an interesting and powerful set of evidences that must be reckoned with. That is, except Krauss.

Metaxas is pointing to fundamental findings. While there is much more to say about them, there is no misrepresentation as Krauss charges.

In fact, again, it is Krauss who is the one who is guilty of his charges. Krauss makes the common evolutionary appeal to future findings. “We currently DO NOT know,” the publicly-funded professor begins, “the factors that allow the evolution of life in the Universe.” [emphasis in original]

I’ve seen this response many times. Evolutionists argue the science proves their theory, and when they are presented with the actual evidence they then make the argument from ignorance. So what if the evidence is against them, future science might switch things around.

Absolutely. That certainly is true. Who knows what science may discover in the future.

But that is irrelevant.

No one is talking about unknown findings at some unknown time in the future made by some unknown scientist. Metaxas is talking about the here and now. He made no sweeping metaphysical claims, as evolutionists do. He was merely discussing today’s science.

It gets worse.

Krauss next resorts to a silly straw man version of Metaxas’ simple point:

The mistake made by the author is akin to saying that if one looks at all the factors in my life that led directly to my sitting at my computer to write this, one would obtain a probability so small as to conclude that it is impossible that anyone else could ever sit down to compose a letter to the WSJ.

At this point Krauss wasn’t even wrong. Did he write this while standing in line to board his next flight?

Krauss continues with more misrepresentations of both science and Metaxas’ points. It is true that science isn’t going to prove anything for Krauss and the evolutionists. One can always interpret the evidence to support the chance-creationism hypothesis. Just look at how Krauss ends his rebuttal:

The appearance of design of life on Earth is also overwhelming, but we now understand, thanks to Charles Darwin that the appearance of design is not the same as design, it is in fact a remnant of the remarkable efficiency of natural selection.

The remarkable efficiency of natural selection?

Krauss is apparently unaware of the most basic biological research in the past half century. Yes, Charles Darwin hoped for such remarkable efficiency. And yes he presented many thought experiments for why he believed it to be true. But that was nineteenth century naturalism. There was no scientific evidence for it then, and we now understand much more about the many problems with that view.

Krauss’ criticism of Metaxas reveals the pathetic state of evolutionary thinking. Religion drives science, and it matters.

Here’s That Protein-Protein Interaction Problem

Evolutionists Don’t Know What They’re Doing

In Chapter 7 of The Edge of Evolution, Michael Behe explained why protein-protein interactions are a problem for evolution. Here is a summary of the problem. First, protein-protein interactions are important. Proteins often work in teams where half a dozen or more proteins may be interacting with each other to form a molecular machine. Protein-protein interaction is ubiquitous throughout life—so ubiquitous that we now have a name for the collective set of such interactions: the interactome. You can’t do much without protein-protein interactions. It is not as though protein-protein interactions are a convenient extra that makes cells a bit more efficient or bequeaths a few nice-to-have functions. Protein-protein interactions are fundamental to life, and are fundamental at all levels. Evolution must have been creating protein-protein interactions throughout evolutionary history as new species and capabilities arose.

And yet it is difficult to get two proteins to interact in a meaningful way. Such interactions must not be too strong or too weak. Imagine that you had two proteins that you needed to bind meaningfully to each other. If you randomly selected the amino acids at the binding patch on the surface of one of the two proteins, then meaningful binding would be unlikely. In fact, you would have to repeat the experiment millions of times before you could expect to get a good result.

But evolution does not have such resources. It cannot conduct millions of evolutionary experiments in order to luckily find amino acid sequences on protein surfaces that are required for important biological functions. And even if it could, that would only be the first step, because molecular machines are often comprised of multiple proteins, interacting with each other at multiple sites. So evolution would have to luckily find several sequences, in multiple proteins, and get them to arise in similar time frames, so the molecular machine would function.

But that is not all, for molecular machines often work in conjunction with other molecular machines. Having a molecular machine without its neighbors would often not help much.

And yet even with all this there remain more problems. For instance, most proteins are not highly modifiable. You can’t just randomly go about swapping in different amino acids. Protein function typically degrades rapidly with amino acid substitutions. So it is challenging for very much interaction site experimentation to take place in the first place. And of course another problem is that it is astronomically difficult for evolution to evolve a single protein to begin with, let alone meaningful interaction sites.

Simply put, from a scientific perspective protein-protein interaction is another problem for evolution.

Mouse Retinal Assembly “Immensely Complex” and “Confounding”

Beyond Lineage-Specific Biology

The fundamental unit of life is the cell and there are many different types of cells. In humans, for example, there are skin cells, muscle cells, blood cells and so forth. In all there are hundreds of different kinds of cells that need to work together in various ways. Now a recent study has investigated the different cell types in the retina of mice. The research focused on the number of cells present in the retina. That may not sound very interesting, but the results were indeed eye-opening.

The researchers looked at 12 different types of cells in the retina, across 30 different strains of mice. Naturally they expected to find some fairly strong patterns. The population sizes for the different cell types should be similar. And if two different types of cell work together and perhaps are synaptically connected, then their cell counts should be correlated across the different strains. That is, if the count is a bit low for one of those cell types, then it should also be on the low side for the other type of cell.

But such patterns were not found. Instead the researchers were surprised to find all kinds of variability. The population sizes of the different cell types varied substantially with little correlation across the different strains.

The researchers also looked at which parts of the genome influence the population counts of the different cell types and concluded that multiple genes, acting differently in the different strains, are involved in specifying these population counts.

The study concluded that retinal assembly is far more flexible than thought. For instance, they concluded that the different retinal cells adjust their size and shape according to their local environment, including the density of the different types of cells around them.

What is emerging is a far more sophisticated retinal assembly process than was imagined. As one report summarized the study:

The circuitry of the central nervous system is immensely complex and, as a result, sometimes confounding. When scientists conduct research to unravel the inner workings at a cellular level, they are sometimes surprised by what they find.

Needless to say, this sort of variability between highly-related strains, and this level of sophistication and complexity, are inconsistent with evolutionary theory.

Minor Spliceosomes as Real Time Sensors In Gene Regulation

More Theoretical Complexity

New research out of the University of Pennsylvania reveals yet another fascinating aspect of gene expression regulation. In the higher species genes are not one continuous DNA segment. Instead there are intervening segments within genes known as introns (intervening regions). Many introns are quite long and some are short. After a gene is copied by the transcription machinery (known as RNA polymerase), resulting in an mRNA transcript, these major and minor introns are spliced out of the mRNA by the major and minor spliceosomes, respectively. The new research shows that the minor spliceosomes can be turned off, thus turning off the expression of that gene.

When introns were first discovered, evolutionist figured they were yet more junk DNA. After all, why should genes have intervening regions which are simply removed from the gene copy? But introns are found throughout the genome. If they were junk why would they be so prevalent? Furthermore, how is it that spliceosomes can edit introns so precisely? If there were no introns then there would be no need for spliceosomes and so they would never evolve. And even if they did evolve there would be nothing for them to do and so evolution would discard them. On the other hand, if introns evolved first, then there would be no spliceosome to remove them. The resulting proteins would not function and the organism would quickly die. Either way, it is yet another conundrum for evolutionists.

In fact spliceosomes are incredibly complicated and perform sophisticated functions. The new research has found another function, and it presents yet another problem for evolution. The research discovered that the abundance of one of the key parts of the minor spliceosome can vary dramatically. Its abundance is controlled by a special protein and its abundance, in turn, controls whether the minor spliceosome is turned on or off. And this, in turn, controls whether or not a large number of very important genes are expressed.

Thus one single action has severe consequences for the cell. It is not a design that is gradually implemented. So not only are separate and independent structures and mechanisms simultaneously required for successful splicing, and not only are those structures and mechanisms incredibly complex, but the design space is highly nonlinear and discontinuous. This is yet another conundrum for evolution, the theory that calls for slow gradual change. Here is how one report described the findings:

The investigators found that a scarce, small RNA, called U6atac, controls the expression of hundreds of genes that have critical functions in cell growth, cell-cycle control, and global control of physiology. … These genes encode proteins that play essential roles in cell physiology such as several transcription regulators, ion channels, signaling proteins, and DNA damage-repair proteins. Their levels in cells are regulated by the activity of the splicing machinery, which acts as a valve to control essential regulators of cell growth and response to external stimuli. Dreyfuss, who studies RNA-binding proteins and their role in such diseases as spinal muscular atrophy and other motor neuron degenerative diseases, describes the findings as “completely unanticipated.”

The theory of evolution attempts to explain how the species arose. With the inexorable march of science, that explanation is becoming increasingly complex.

Biomemetics This Time: Tunable Photonic Materials

Another Astonishing Design

We have discussed some amazing examples of how species control their color (here and here, for example) and how such technology in nature has inspired engineers creating advanced new technologies such as low-power video displays. Now new research is helping to explain how squids and octopuses change color and it is amazing.

We usually think of color as resulting from chemistry, such as in dyes. But different colors can also result from repeating, detailed submicron geometrical structures at the object’s surface. The new research reveals yet another, even more complex system for manipulating the frequency of light (i.e., the color) coming from squids and octopuses.

It begins with nerve signals which are sent to special cells containing special proteins. The signal causes the proteins to congregate and deep pleats to form in the cell membrane, altering the osmotic pressure and ultimately its refractive index.

Here is how one of the researchers described the process:

Initially, before the proteins are consolidated, the refractive index -- you can think of it as the density -- inside the lamellae and outside, which is really the outside water environment, is the same. There's no optical difference so there's no reflection. But when the proteins consolidate, this increases the refractive index so the contrast between the inside and outside suddenly increases, causing the stack of lamellae to become reflective, while at the same time they dehydrate and shrink, which causes color changes. The animal can control the extent to which this happens -- it can pick the color -- and it's also reversible. The precision of this tuning by regulating the nanoscale dimensions of the lamellae is amazing.

And here is a more technical description, from the journal paper:

Squids have used their tunable iridescence for camouflage and communication for millions of years; materials scientists have more recently looked to them for inspiration to develop new “biologically inspired” adaptive optics. Iridocyte cells produce iridescence through constructive interference of light with intracellular Bragg reflectors. The cell’s dynamic control over the apparent lattice constant and dielectric contrast of these multilayer stacks yields the corresponding optical control of brightness and color across the visible spectrum. Here, we resolve remaining uncertainties in iridocyte cell structure and determine how this unusual morphology enables the cell’s tunable reflectance. We show that the plasma membrane periodically invaginates deep into the iridocyte to form a potential Bragg reflector consisting of an array of narrow, parallel channels that segregate the resulting high refractive index, cytoplasmic protein-containing lamellae from the low-index channels that are continuous with the extracellular space. In response to control by a neurotransmitter, the iridocytes reversibly imbibe or expel water commensurate with changes in reflection intensity and wavelength. These results allow us to propose a comprehensive mechanism of adaptive iridescence in these cells from stimulation to color production. Applications of these findings may contribute to the development of unique classes of tunable photonic materials.

What we see here is a beautiful design consisting of a sequence of highly complex, intricate and finely-tuned mechanisms, molecules and structures allowing these organisms to precisely control their image. There is no scientific evidence that such optical technology arose from random mutations as evolutionists believe. Evolutionists like to call upon natural selection as a sort of natural designer, but that does not help for such intricate designs as these.

Photosynthesis Relies on Quantum Coherence

When Will They Cry Uncle?

It is no secret that nature’s process of photosynthesis—which harnesses the energy in sunlight—is astonishingly efficient. And researchers have known for years that quantum mechanisms play a role in the protein antenna farms deployed in these marvelous molecular machines. Now new research, based on a experimental technique that tracks these proteins at the femtosecond level (there are a million billion femtoseconds in a second), elucidates some of these quantum mechanisms and, as usual, the results are surprising.

Photosynthesis begins with special proteins that capture and transmit the energy from sunlight. The new research shows that these proteins use specific energy-transfer pathways that apparently are adaptive to the current conditions. These pathways are protein-specific and time-varying.

And part of the reason why these energy-transfer processes are so efficient is that they are coordinated. This quantum coherence is long-lived, persisting for hundreds of femtoseconds. As one of the researchers put it:

These results show that coherence, a genuine quantum effect of superposition of states, is responsible for maintaining high levels of transport efficiency in biological systems, even while they adapt their energy transport pathways due to environmental influences.

It would be an abuse of science to say the evolution of such systems is a fact, or likely. I don’t care if evolution is true or not, but from a strictly scientific perspective (which is not how the theory is motivated or evaluated), the idea is, to be frank, just silly.

These new results continue to make that clear.

Here is That New, Unique, Fluorescent Protein

More Lineage Specific Biology

Some proteins are fluorescent—shine a light on them and they glow. And as usual nature gives us all kinds of variations including different colors. These proteins are wonderful tools for molecular biologists who use them to tag and track molecular machines at work in the cell. Now another type of fluorescent protein has been discovered. Not only is it from a vertebrate (the Japanese eel), but its fluorescence mechanism is different (it uses bilirubin, the four-ring molecule that we shouldn’t have too much of). As one researcher put it, “It’s totally different. There’s not anything you can point to that’s the same.”

This new protein is another example of the incredible genius and creativity we find in biology, and it appears to be another example of the lineage-specific biology which runs counter to the expectations of common descent.

William Bialek: More Perfect Than We Imagined

Roll Over Voltaire

Three hundred years ago Gottfried Leibniz said we live in the best of all possible worlds but today Princeton’s world reknown theorist William Bialek explains that it is more perfect than we imagined. This video is long and it sometimes dwells on Bialek rather than the slide he is talking to, but those drawbacks are minor compared to what you will learn. If you want to hear an intelligent, thoughtful scientist scratch the surface of creation’s wonders and reflect on what it all means, then this video is for you.

Bialek, for instance, discusses compound eyes of insects such as the fly. These compound eyes have a large number of small lenses packed into an array. A large number of small lenses gives high resolution, just as does a digital camera with a large number of pixels.

But when the lens becomes too small its optics become distorted due to diffraction. So in determining the best lens size there is a tradeoff between resolution and diffraction. In the optimum solution the lens size is roughly proportional to the square root of the radius of the head. An indeed, Bialek shows an old paper surveying the compound eye designs in more than two dozen different insects. That paper shows that for the different size insects, the lens size is proportional, as predicted, to the square root of the head size.

This is one of Bialek’s half a dozen or so examples showing the optimization of biological designs and, as Bialek assures the audience, there are many, many more. Here is how one science writer explained it:

Yet for all these apparent flaws, the basic building blocks of human eyesight turn out to be practically perfect. Scientists have learned that the fundamental units of vision, the photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped.

“Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” …

Photoreceptors exemplify the principle of optimization, an idea, gaining ever wider traction among researchers, that certain key features of the natural world have been honed by evolution to the highest possible peaks of performance, the legal limits of what Newton, Maxwell, Pauli, Planck et Albert will allow. Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them the superb efficiency with which bacterial cells will close in on a food source; the precision response in a fruit fly embryo to contouring molecules that help distinguish tail from head; and the way a shark can find its prey by measuring micro-fluxes of electricity in the water a tremulous millionth of a volt strong — which, as Douglas Fields observed in Scientific American, is like detecting an electrical field generated by a standard AA battery “with one pole dipped in the Long Island Sound and the other pole in waters of Jacksonville, Fla.” In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants.

But there is much more to Bialek’s talk than examples of nature’s optimal designs. In a thoughtful segment Bialek discusses his philosophy of science. At the [16:30] mark he asks “That was fun, but what does it mean?” The answer, he begins, is that nature’s many examples of optimization help to highlight the difference between two ways of doing and thinking about science.

Bialek describes a cartoon in which a family is driving the car over a bridge with a posted weight limit. The son asks the father how they know what is the weight limit. The father responds that they wait until a sufficiently heavy truck destroys the bridge, they then weigh the remains of the truck, rebuild the bridge exactly as it was, and post the sign.

Bialek uses this funny cartoon as a metaphor for evolutionary theory’s reliance on contingency. This trial-and-error approach to understanding and invention is, Bialek explains, a very common view. The species are the way they are because that is the way they happened to evolve.

In fact, Bialek cogently points out, evolution’s promotion of contingency and trial-and-error is not so much out of scientific necessity. In the bridge example, we could actually model and compute the load limit, based on the design of the bridge and the types of materials used.

But given the “political context” in which many of these discussion occur, it is understandable why evolution is presented as a process of tinkering and not design. [19:30] In fact, the Yale biophysicist notes, these arguments are opposed to the idea of a “interventionist designer,” rather than the question of whether there are design principles in biology.

Bialek contrasts this approach with another view—the view that guides so many physicists—which he represents with Galileo’s famous quote that “The book of Nature is written in the language of mathematics.” Physics, Bialek points out, has been remarkably successful using this formula. It is, he notes, an “astonishing achievement” of the human mind over these four hundred past years. Bialek laments the evolutionary view that Galileo would never have said such a thing if he had known about biology.

Bialek’s point that evolution opposes the idea of a interventionist designer is crucial. For far from reflecting atheism, as so many have charged, and far from being a scientific finding as today’s positivist sentiment wants to believe, this foundation of evolutionary thought is religious.

That is not to say evolution is right or wrong, or true or false. It simply is religious. And until we understand the religion we are immersed in, we will not comprehend its influence on our thinking.

Without this religion, which is ubiquitous, evolution could certainly continue as a theory of mechanical origins. But evolutionary thought would be stripped of its core theoretic and its metaphysical certainty. The theory of evolution would then, rather than be mandated to be a fact, lie exposed to the light of science which shows it to be so improbable.

But it is precisely this distinction, this parsing of the religion from the science, that is so difficult to achieve. When I first began to study the evolutionary literature I was constantly fooled by its intertwining of metaphysics with the empirical science. The evolution literature is rife with religious claims in hiding.

But when properly distinguished and separated, one immediately can see that the conviction of evolution’s truth lies in the non scientific claims whereas the empirical evidence, alone, gives us no such confidence.

Religion drives science, and it matters.

Circular RNAs: A Hidden, Parallel Universe

When Are These Surprises Going to Stop?

Remember when microRNA burst onto the scene a few years back and revolutionized our knowledge of cellular regulatory processes? Evolutionists had to scramble because, after all, when you say your theory explains something and it turns out you don’t really understand that something, well it looks like you don’t know what you’re talking about. It wasn’t much of a scramble though, because evolutionists can pretty much say anything they want, at any time, about their theory. So when microRNA burst onto the scene, evolutionists said “oh, evolution did that.” Well now it is happening all over again, but this time with long RNA which often interacts with microRNA, and this week it was with long RNA that is circular.

Evolutionists once dismissed these long, circular RNA macromolecules—which can be thousands of nucleotides long—as rare genetic accidents or experimental artefacts. Now circular RNA appears to be, err, an abundant and crucial part of genetic regulation. There are thousands of them, probably fulfilling a multitude of functional roles in what one evolutionist admitted is “a hidden, parallel universe” in the molecular world.

And amazingly the genes encoding these RNA macromolecules often overlap with protein-coding genes. Recall that protein-coding genes, in addition to coding for an incredible protein machine, may also contain several more layers of information encoding signals for the transcript (mRNA) stability, mRNA editing, DNA copy error correction, the speed of translation, the protein’s three-dimensional protein structure, the stability of that structure, the multiple functions of the protein, interactions of the protein with other proteins, instructions for transport, avoiding an amyloid state, any other genes that overlap with the gene, and controlling tRNA selection which can help to respond to different environmental conditions.

That is a tall order and now we have yet another layer of information for which genes much encode: circular RNA macromolecules which just happen to interact with microRNA and which just happen to be expressed at the right time, because if they are expressed at the wrong time you don’t have a normal brain. And amazingly, in protein-coding genes, circular RNA macromolecules may be encoded both in the antisense strand and in the sense strand. In fact numerous circular RNAs form by head-to-tail splicing of exons.

Not surprisingly, beyond “oh, evolution did that,” evolutionists have no scientific explanation for how circular RNAs could have evolved. As one evolutionist admitted, “You just wonder when these surprises are going to stop.”

This Circadian Clock Protein is Finely-Tuned (and a Bunch of Other Things)

Making Evolution Even More Ridiculous

That new paper on the circadian clock protein is not only an example of how evolution lacks theoretical content and so anything can be explained (“Many genes exhibit little codon-usage bias, which is thought to reflect a lack of selection for messenger RNA translation. Alternatively, however, non-optimal codon usage may be of biological importance.”) or of fine-tuning in biology (“Living organisms’ inner clocks are like Swiss watches with precisely manufactured spring mechanisms”). Nor is the paper merely an example of yet another falsification of evolutionary predictions (“The team … was perplexed when it found a paradoxical result”) or even of bad writing (“And that’s essentially a discovery”).

In addition to all those usual contradictions, the paper is another good example of the many signals in protein sequences and how crucial and fine-tuned they are. Coding genes specify the amino acid sequence in the resulting protein that is synthesized when the gene is expressed. Only a relatively few of the possible DNA gene sequences could code for a typical native protein, and these magical sequences are statistically impossible for evolution to find by known mechanisms.

Background

But that is not all. Coding genes carry all kinds of signals, in addition to the information that specifies the amino acid sequence. For instance, the gene’s DNA sequence is also implicated in the control of transcription—the gene copying process. And the gene’s DNA sequence determines the important stability of the DNA copy—the so-called mRNA strand, and the mRNA interactions with proteins such as splicing machinery.

Of course the gene sequence also determines the protein’s three-dimensional protein structure, the stability of that structure, the function of the protein, interactions of the protein with other proteins, instructions for transport, and so forth.

But on top of that information, the gene also contains signals that help to control the speed at which the new protein is synthesized. These signals have been found to be quite sophisticated and the resulting speed changes can cause the protein to take on a different conformation and influence the protein’s function and regulation.

And it appears that the DNA sequence can make the expression level of the protein sensitive to different environmental conditions. For instance, perhaps some proteins should have lower priority than other proteins, in certain conditions. That could be coded for in their respective gene sequences.

Also it has been discovered that gene sequences are cleverly arranged to complement the cell’s error correction mechanisms and so minimize copying errors.

One interaction that must be avoided is the propensity of proteins to stick to each other and form fibrils in what is known as an amyloid. As one researcher explained, “The amyloid state is more like the default state of a protein, and in the absence of specific protective mechanisms, many of our proteins could fall into it.” So the DNA gene sequence must avoid this problem.

Also, some genes are overlapping with other genes. In other words, the stretch of DNA where a gene resides may be shared with another gene entirely. So the genetic information is now doubled. And even if this is not the case, researchers are increasingly finding that genes perform multiple tasks. In what is known as gene sharing, the protein product of a gene may carry out several separate and distinct functions. As one researcher concluded, “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.”

One more thing

So a gene does not merely code for a protein. As difficult as it is for evolution to find a protein-coding gene sequence, it would be far more difficult to find a real gene because they carry so many more signals.

That brings us to the new paper on the circadian clock protein. For in addition to it demonstrating how evolution lacks theoretical content, fine-tuning in biology, yet another falsification of evolutionary predictions, and even of bad writing, the paper also shows just how important and sensitive are these layers of information.

In this case, the research found that speed at which the mRNA strand is translated into the protein amino acid sequence is finely-tuned. The DNA sequence contains signals to slow this process, and that is crucial. For otherwise the protein takes on a different conformation, is not properly regulated, and the circadian rhythms are lost.

It is not as though we find gradual pathways leading to ever more useful and fit designs. Instead, function is lost, even when relatively minor DNA sequence changes occur. The idea that such incredible designs spontaneously arose via evolution’s random chance events (no, selection doesn’t help, each event must be random with respect to need, multitudes of such events are needed, and we don’t generally find gradual pathways) continues to grow ever more unlikely.

Religion drives science and it matters.

Evolutionist Professor Quotes Laplace

Getting Destroyed

The brilliant Isaac Newton could harmonize Aristotle’s super- and sub-lunar worlds, show that nature’s laws were universal and in the process explain how the solar system worked, but the Cambridge professor could not explain how the solar system arose or how it will end. Most troublesome was his finding that the planets circling about the Sun formed one giant accident waiting to happen. One day the planets were liable to careen about and the only solution seemed to be an occasional divine finger to adjust the errant machine. That sent Newton’s continental nemesis Gottfried Leibniz into his own instability, for the Lutheran co-founder of calculus could not envision God creating a less than optimal world. Certainly not a world so crude so as to be in need of occasional adjustment. Newton also said that his new physics was not capable of evolving the solar system in the first place. Like Adam’s naval, the planets had to get their start somehow other than their normal operation. Did God then also have to interfere with His creation to set the planets initially in their orbits and with the proper speeds?

Newton had left the world in a shambles and the cultural mandate was on. A respectable origins and end game were needed and a century later Pierre Laplace supplied both. His Nebular Hypothesis described a condensing cosmic cloud that evolved the solar system and the brilliant Frenchman solved Newton’s instability problem and showed the solar system to be stable after all. The planets would safely and steadily oscillate around their orbits until the end of time.

Theists could rest assured that God was, after all, the master designer, and skeptics such as Laplace could replace God with natural laws. When Napoleon wondered why the Creator was not mentioned Laplace could respond that he had no need of that hypothesis.

But while Laplace was one of the greatest mathematicians in the world, he wasn’t much of a metaphysician. Every freshman philosophy student knows that inserting natural laws doesn’t give one a theory of everything.

First there is that little problem that natural laws don’t actually explain what they’re supposed to explain (Laplace’s Nebular Hypothesis was bloated with unfounded speculation and the solar system stability problem ended up being far more complex than Laplace ever imagined. The problem is so difficult that we speak of probabilities of instability). In fact what we do know today is the incredible level of fine-tuning design built into the solar system. For instance the Earth-Moon system (EM) has profound and subtle effects on the solar system stability. As one paper from 1998 explained:

Evidence from self-consistent solar system n-body simulations is presented to argue that the Earth- Moon system (EM) plays an important dynamical role in the inner solar system, stabilizing the orbits of Venus and Mercury by suppressing a strong secular resonance of period 8.1 Myr near Venus’s heliocentric distance. The EM thus appears to play a kind of “gravitational keystone” role in the terrestrial precinct, for without it, the orbits of Venus and Mercury become immediately destabilized. … First, we find that EM is performing an essential dynamical role by suppressing or “damping out” a secular resonance driven by the giant planets near the Venusian heliocentric distance. The source of the resonance is a libration of the Jovian longitude of perihelion with the Venusian perihelion longitude.

This is just one example of the fine-tuning of the solar system’s design.

And second, even if there was a convincing naturalistic narrative, it wouldn’t mean one has “no need of God.” Rid yourself of God if you like, but don’t fool yourself that you have established some intellectual basis for your metaphysical priors.

This is an elementary mistake by those who desire materialism and reminds us of the cartoon showing two tiny insects on the back of a dog. As they walk through the forest of hairs the one insect says to the other, “Sometimes I wonder if there really is a dog.”

Unfortunately this reflects the level of thought not only with Laplace but in today’s atheism as well. In fact Laplace’s retort to Napoleon is one of their favorite slogans, as we were reminded this week when atheist-evolutionist Jerry Coyne wrote this gem in his naïve response to a challenger:

I have always argued that most scientists, including myself, take the absence of God as a provisional working hypothesis based on the history of science, for, like Laplace, we have never needed the assumption of God. I am, and have always been, willing to entertain evidence for the presence of a divine being. I just haven’t seen any.

There you have it. More cogent insights from the evolutionary camp. Their ignorance is exceeded only by volume level at which they proclaim it. As Paul warned Timothy, “For the time will come when they will not endure sound doctrine, but according to their own desires, because they have itching ears, they will heap up for themselves teachers; and they will turn their ears away from the truth, and be turned aside to fables.”

The Exosome: RNA Degradation and Evolution

Major Problems

When the cell makes a copy of a segment of DNA the result is called RNA. This long, thin molecule has many roles, including transmitting information, regulating the cell’s activities and helping molecular machines perform various tasks. But when its job is done, an RNA molecule must be broken apart. The job of destroying RNA is crucial for without it the cell’s RNA would rapidly build up and kill the cell. So cells are equipped with an intricate machine that chops up RNA molecules when they no longer are needed. This RNA degradation machine is called the exosome and it is comprised of ten finely-tuned proteins, nine of which form a cylinder through which the spent RNA is threaded. The tenth protein then chops up the RNA molecule. New research is now elucidating just how the exosome works, and the results pose yet more profound problems for evolution.

Different versions of the exosome are found across biology’s different types of life, but the exosome’s basic mechanisms for degrading RNA are conserved. For evolutionists this means that the exosome must have been present very early in evolutionary history, in the common ancestor of all life. This unlikely juxtaposition of high complexity in early life is a common theme in evolutionary thought. Repeatedly the patterns of life force evolutionists to suppose that evolution, somehow, struck upon profound designs early on.

Of course it makes sense that the exosome would be present from nearly the beginning, given its crucial role. But how could it have evolved? For instance, the mere presence of those different proteins is an immediate problem for evolution. After all, beyond speculation evolutionists cannot even explain how a single such protein could have evolved.

And even if those proteins could somehow have evolved, how would the cell know how to assemble them together to form the exosome?

And how would the exosome know where to position itself within the cell? And how would the cell know which RNA molecules to send its way?

But that’s not all. Not only does the exosome have incredible proteins, but it requires all of them in order to function. Remove any one of them and all you have is a useless hulk of molecules. As one researcher explained:

Cells lacking any of the ten proteins do not survive and this shows that not only the catalytic subunit but also the entire barrel is critical for the function of the exosome.

But how could evolution construct such a marvel which is useless until the final brick is in place? If the machine doesn’t work without all its parts, that means there is no gradual evolutionary path leading up to it.

To avoid this problem evolutionists must say that the different proteins each evolved for some other reasons. They did other jobs in the cell, and then once all were constructed, they happened to fit together to form the exosome.

But that story is unlikely for it would require a substantial dose of serendipity. Evolution would have gotten lucky yet once again.

The problem here is that once again evolutionists have set themselves against the science. Once again they put themselves in the position of having to demonstrate what clearly goes against the facts.

But it’s even worse yet. Not only do evolutionists go against the empirical grain, but they repeatedly insist that theirs is the only answer. Evolution, they cry, is the obvious and the only acceptable explanation. They contrive false histories of science, accuse others of abusing science, and blackball those who don’t go along.

As you can see this just doesn’t add up. I’m more than willing to consider evolution. But the science isn’t there while evolutionists misrepresent the facts, make undefendable truth claims, and mistreat people. This isn’t a pretty picture.

Evolution is Getting Slammed Again in This Transcription Factor Research

This is Getting Ridiculous

New research on how certain transcription factors work together is causing major problems for the theory of evolution. Transcription factors are proteins that attach to DNA and turn genes on or off. These regulatory proteins have recently been promoted to star status by evolutionists because their expectation that evolution proceeds by creating new proteins has fallen short. Instead of creating new proteins, our modern-day Epicureanism is now supposed to have reprogrammed how existing proteins are used in a mind boggling circuitry of molecular regulators, of which transcription factors play a major role. As one evolutionist explained:

Although the number of protein coding genes has remained fairly constant throughout metazoan evolution, the number of regulatory DNA elements has increased dramatically.

With this move evolutionary theory not only becomes far more complex, it also takes on yet more serendipity. For instance, can you imagine that evolution created all those proteins which just happened to have set the stage for the higher life forms?

Likewise those DNA regions, where transcription factors bind, had to have evolved while the transcription factors themselves had to have evolved. And these separate evolutionary pathways not only had to result in the right kind of binding at the right place in the billion-nucleotide long genome, but said binding had to sometimes produce something useful. Simply put, those DNA regions and the transcription factors have special properties that evolution must have somehow accidentally created. In fact, as one evolutionist explained, evolution must have created these DNA regions “which may allow evolutionary adaptation to novel conditions.” In other words, evolution created special DNA regions so that evolution could then occur.

And the new research makes all of this even more improbable, if that were so possible. The research elucidates how different transcription factors work together. Specifically, not only are DNA regions and transcription factors finely tuned to work together, but transcription factors are finely tuned to work together. In this case, when one transcription factor binds to a second transcription factor, that second transcription factor is then able to bind to DNA. This occurs via a rather dramatic structural change in the second transcription factor—a very difficult and unlikely stunt.

It is a great piece of research on a very interesting system, and the result is yet more absurdity for evolutionary theory. For evolution’s random mutations must have hit upon dozens of different mutations that just happened to result in this coordinated action between the two transcription factors and the right DNA region. It is astronomically unlikely.

Evolutionists once argued that deep time solved all their problems. Now they argue that on top of all those eons of time, there is a near infinity of universes in which evolutionary experiments are constantly on-going. Yes evolution is unlikely, but given all those universes, you’re bound to get lucky sometime.

And how many universes would that be? That’s easy: as many as are required. Infinity raises philosophical problems, but so what. With each new finding, evolutionists can simply ratchet up the universe count to whatever is needed.

Religion drives science, and it matters.

The Elaborate Nanoscale Machine Called Photosynthesis: No Vestige of a Beginning

Plants use carbon dioxide and produce oxygen while animals use oxygen and produce carbon dioxide. It’s one of nature’s many Huttonian cycles with “no vestige of a beginning—no prospect of an end.” But what James Hutton could not have dreamt of is the literally astonishing magnificence of the invisible machinery working behind the scenes to sustain the carbon cycle. What would the often misunderstood Scottish polymath say today in response to photosynthesis and the electron transport chain? What would the father of the Scottish Enlightenment conclude from “Nature’s most elaborate nanoscale biological machine” which “converts light energy at unrivaled efficiency of more than 95 percent compared to 10 to 15 percent in the current human-made solar technologies”?

Two centuries later Hutton’s deism is as strong as ever. But the limits of scientific knowledge Hutton warned have been dramatically pushed back. It is no longer “in vain to look” for now we do see. No longer is there no observable vestige of a beginning, rather we now observe there is no vestige of a beginning. To speak of the spontaneous evolution of the world is now at best a sign of scientific illiteracy. More often it is a religious mandate imposed on science for which there is no excuse.

And so now we have a choice. We can continue to with centuries-old religious dogma or we can follow the science.

Optical Metamaterials and the Hercules Beetle

You may recall that objects have particular colors because, at the molecular level, light rays at certain frequencies (corresponding to certain colors) are reflected while at other frequencies the light is absorbed. In other words, an object’s color has to do with its chemistry. But, as David Tyler points out here, coloration can also arise from repeating, detailed submicron geometrical structures at the object’s surface. These surface structures are finely tuned to interact with and control the incoming light, including controlling the frequencies, and hence color, of the reflected light. In these cases, the object’s color has to do with its repeating surface geometry, rather than its chemistry.

That’s interesting because not only can surface structures be designed and fabricated to have a certain color, the structure can also be designed to be sensitive to environmental factors, such as temperature and humidity. Therefore one can construct a panel whose color indicates an environmental reading. Scientists and engineers are busy researching and developing these and other applications for these so-called metamaterials.

But those scientists and engineers were not the first to create metamaterials. Once again, the biological world has “been there, done that,” and has many of its own such metamaterials. One study analyzed the hercules beetle which changes color in high humidity due to an incredibly complex three-dimensional carapace surface structure. As the study explains:

The elytra from dry specimens of the hercules beetle, Dynastes hercules appear khaki-green in a dry atmosphere and turn black passively under high humidity levels. New scanning electron images, spectrophotometric measurements and physical modelling are used to unveil the mechanism of this colouration switch. The visible dry-state greenish colouration originates from a widely open porous layer located 3 micro-meters below the cuticle surface. The structure of this layer is three-dimensional, with a network of filamentary strings, arranged in layers parallel to the cuticle surface and stiffening an array of strong cylindrical pillars oriented normal to the surface. Unexpectedly, diffraction plays a significant role in the broadband colouration of the cuticle in the dry state. The backscattering caused by this layer disappears when water infiltrates the structure and weakens the refractive index differences.

According to evolution all of biology arose via random causes such as mutations. No, natural selection didn’t help—it just killed off the bad designs. The hercules beetle and its fantastic optical metamaterial (and everything else in biology) must have arisen by a long, long series of random mutations, which just happened to lead up to marvelous designs.

Religion drives science, and it matters.

Of Gaps, Fine-Tuning and Newton’s Solar System

New research is providing a fascinating new perspective on fine-tuning and a three hundred year old debate. First for the context. When Isaac Newton figured out how the solar system worked he also detected a stability problem. Could the smooth-running machine go unstable, with planets smashing into each other? This is what the math indicated. But on the other hand, we’re still here. How could that be?

According to the Whig historians, Newton, a theist, solved the problem by invoking a divine finger. God must occasionally tweak the controls to keep things from getting out of control. It explained why the solar system hasn’t come to ruin, and it provided a role for divine providence which, otherwise, might not be needed for the cosmic machine that ran on its own.

About a century later, Whig history tells us, the French mathematician and scientist Pierre Laplace solved the stability problem when he figured out that Newton’s bothersome instabilities would iron themselves out over the long run. The solar system was inherently stable after all, with no need of divine adjustment, thank you.

Newton’s sin was to use god to plug a gap in our knowledge. What a terrible idea. First, using god to plug gaps is a science-stopper. Why investigate further if god fixes the tough problems? And second, it damages our faith when science eventually solves the problem and the divine role is further diminished. The key to avoiding this problem is to sequester religious thinking to its proper role. Science and religion must be separated lest both be damaged.

That’s the Whig history. Now for what actually happened. Instead of Newton being wrong and Laplace being right it was, as usual, the exact opposite. Newton was right and Laplace was wrong, though the problem is far more complex than either man understood.

And Newton was not the doctrinaire and Laplace was not the savior as the Whigs describe. Again, the truth would be closer to the exact opposite. Newton was more circumspect than is told, and Laplace didn’t actually solve the problem. True, he thought he had solved the problem, but his claim may indicate more about evolutionary thinking than anything to do with science.

And Newton’s allowing for divine creation and providence never shut down scientific inquiry. If that were the case he never would have written the greatest scientific treatise in history.

After Newton, the brightest minds were all over the problem of solar system stability (though it is a difficult problem and would take many years to even get the wrong answer). And no one’s faith was shattered when Laplace produced his incredibly complicated calculus solution because they were banking on some Newtonian interventionism.

But what did raise tempers was the very thought of God not only creating a system in need of repair, but then stooping so low as to adjust the controls of the errant machine. The early evolutionary thinker and Newton rival, Gottfried Leibniz found the idea more than disgraceful. The Lutheran intellectual accused Newton of disrespect for God in proposing the idea the God was not sufficiently skilled to create a self-sufficient clockwork universe.

The problem with Newton’s notion of divine providence was not that it is a science stopper (if anything such thinking spurs on scientific curiosity) or a faith killer when solutions are found. The problem is that it violates our deeply held gnosticism, which is at the foundation of evolutionary thought.

Darwin and later evolutionists have echoed Leibniz’ religious sentiment time and again. Everyone knew what the “right answer” was, and this was the cultural-religious context in which Laplace worked.

Indeed, Laplace’s “proof” for his Nebular Hypothesis of how the solar system evolved came right out of this context and was, not surprisingly, metaphysical to the core. You can read more about that here.

Today the question of the solar system’s stability remains a difficult problem. It does appear, however, that its stability is a consequence of some rather fine-tuning. Fascinating new research seems to add to this story. The new results indicate that the solar system could become unstable if diminutive Mercury, the inner most planet, enters into a dance with Jupiter, the fifth planet from the Sun and the largest of all. The resulting upheaval could leave several planets in rubble, including our own.

Using Newton’s model of gravity, the chances of such a catastrophe were estimated to be greater than 50/50 over the next 5 billion years. But interestingly, accounting for Albert Einstein’s minor adjustments (according to his theory of relativity), reduces the chances to just 1%.

Like so much of evolutionary theory, this is an intriguing story because not only is the science interesting, but it is part of a larger confluence involving history, philosophy and theology.