OOL's black box.

ID’s Top Six — The Origin of Information in DNA and the Origin of Life
Evolution News | @DiscoveryCSC

Editor’s note: In the past we’ve offered  top 10 problems with Darwinian evolution (see here for a fuller elaboration), and the top five problems with origin-of-life theories.But somehow we neglected to offer a parallel listing of the top evidence supporting intelligent design. Many different sources pointing to design in nature could be adduced, but we decided to distill it all down to six major lines of evidence. Sure, five or ten would have been more conventional, but when did ID advocates start playing to expectations?So here they are, their order simply reflecting that in which they must logically have occurred within our universe. Material is adapted from the textbook Discovering Intelligent Design, which is an excellent resource for introducing the evidence for ID, along with Stephen Meyer’s books  Signature in the Cell and Darwin’s Doubt.

The Origin of Information in DNA and the Origin of Life

The laws of the universe are necessary for life to exist. But they aren’t sufficient to explain how life arose. The origin of life requires a massive infusion of information, which can only be explained by intelligent design. Stephen Meyer’s book Signature in the Cell puts it best:

Hume’s objections to the classical design argument fail to refute the argument of this book for several reasons. First, we now know that organisms come from organisms, because organisms possess information-rich macromolecules and a complex information-rich system for processing and replicating the information stored in those molecules. Thus, [Hume’s] argument that uniform experience suggests that organisms necessarily arise from an infinite regress of primeval organisms (or an eternally self-existent one) fails. Repeated experience about the origin of information-rich systems suggests two possibilities, not one. Either information-rich systems arise from preexisting systems of information via a mechanism of replication, or information-rich systems arise from minds. We have repeated experiences of both. Even so, our experience also affirms — based on cases in which we know the cause of such systems — that systems capable of copying and processing other information ultimately arise from intelligent design. After all, the computer hardware that can copy and process information in software originated in the mind of an engineer.

Beyond that, advances in our understanding of planetary and cosmic evolution have ruled out the possibility that biological life has always existed, either on earth or in the cosmos. At some point in the remote past, the conditions on earth and in the larger cosmos were simply incompatible with life. The big-bang theory alone implies that the cosmos itself is finite. Thus, scientifically informed people generally don’t argue that biological life always existed or even that it always existed on earth. The question is whether life originated from a purely undirected material process or whether a mind also played a role. Between these two options uniform experience affirms only the latter as an adequate cause for information-rich systems capable of processing and copying information. Since we know that organisms capable of reproduction constitute information-rich systems, a Humean appeal to uniform experience  actually suggests intelligent design, not undirected processes, as the explanation for the origin of the first life.

Second, the contemporary case for intelligent design (such as the one made in this book) is not an analogical argument, even though many interesting similarities do exist between living organisms and human information technology. If, as Bill Gates says, “DNA is like a computer program,” it makes sense, on analogical grounds, to consider inferring that DNA also had an intelligent source. Nevertheless, although the digitally encoded information in DNA is similar to the information in a computer program, the case for design made here does not depend upon mere similarity. Here’s why.

Classical design arguments in biology typically seek to draw analogies between whole organisms and machines based on similar features present in both systems, reasoning from similar effects back to similar causes. These arguments are a bit like those sixth-grade math problems in which students are given a ratio of known quantities on one side of the equation and a ratio of an unknown to a known quantity on the other and then asked to “solve for x,” the unknown quantity. In analogical design arguments, two similar effects are compared. In one case, the cause of the effect is known. In the other case the cause is unknown, but is presumed to be knowable because of the alleged similarity between the two effects. The analogical reasoner “solves for x,” in this case, the unknown cause.

The status of such design arguments inevitably turns on the degree of similarity between the systems in question. If the two effects are very similar, then inferring a similar cause will seem more warranted than if the two effects are less similar. Since, however, even advocates of these classical design arguments admit there are dissimilarities as well as similarities between living things and human artifacts, the status of the analogical design argument has always been uncertain. Advocates argued that similarities between organisms and machines outweighed dissimilarities. Critics claimed the opposite.

But the DNA-to-design argument does not have an analogical form. Instead, it constitutes an inference to the best explanation. Such argument do not compare degrees of similarity between different effects, but instead compare the explanatory power of competing causes with respect to a single kind of effect.

As noted, biological information, such as we find in DNA and proteins, comprises two features: complexity and functional specificity. Computer codes and linguistic texts also manifest this pair of properties (“complexity” and “specificity”), what I have referred to throughout this book as specified information. Although a computer program may be similar to DNA in many respects and dissimilar in others, it exhibits a precise identity to DNA insofar as both contain specified complexity or specified information.

Accordingly, the design argument developed here does not rely on a comparison of similar effects, but upon the presence of a single kind of effect — specified information — and an assessment of the ability of competing causes to produce that effect. The argument does not depend upon the similarity of DNA to a computer program or human language, but upon the presence of an identical feature in both DNA and intelligently designed codes, languages, and artifacts. Because we know intelligent agents can (and do) produce complex and functionally specified sequences of symbols and arrangements of matter, intelligent agency qualifies as an adequate causal explanation for the origin of this effect. Since, in addition, materialistic theories have proven universally inadequate for explaining the origin of such information, intelligent design now stands as the only entity with the causal power known to produce this feature of living systems. Therefore, the presence of this feature in living systems points to intelligent design as the best explanation of it, whether such systems resemble human artifacts in other ways or not.

(Signature in the Cell pp. 384-386)

A primeval internet v. Darwin?

Internet of Cells: The Next Revolution?
Evolution News | @DiscoveryCSC

Cells are the fundamental units of biology. They have long seemed like individuals. Sure, they communicate, like humans, and they build structures together, sharing the work with division of labor. But like factory workers going home at the end of the day, cells can be treated as independent units with their own lives to live. To evolutionary biologists, cells divide alone and evolve independently. Isn’t that one of the basic premises of modern biological science?

Take heed: the next biological revolution is coming. Nature calls it “The Internet of Cells” and says that it has biologists buzzing.

The revolution began, Monya Baker writes, when biologists noticed that proteins engineered to appear in certain cells appeared to have “teleported” to a different group of cells entirely. Then came the discovery of molecular nanotubes that appear to transmit genetic information and even organelles between cells. Gradually, cells seemed to be losing their independence.

Yamashita’s tubes joined a growing catalogue of cryptic conduits between cells. Longer tubes, reported in mammalian cells, seem to transport not just molecular signals but much larger cargo, such as viral particles, prions or even mitochondria, the cell’s energy-generating structures. These observations suggest an unanticipated level of connectivity between cells, says Amin Rustom, a neurobiologist at the University of Heidelberg in Germany, who first spotted such tubes as a graduate student almost 20 years ago. If correct, he says, “it would change everything in medical applications and biology, because it would change how we see tissues”. 

A short video clip reveals what appear to be “interstate highways” reaching out and connecting between cells, passing material between them. The concept of intercellular trafficking through conduits is controversial, because no one knows exactly what is being transported and how often this occurs. The nanotubes, a mere 200 nm in diameter (wide enough to transport protein scraps), have been observed in the lab, but not as clearly in living organisms. They are hard to see. What are they doing?

Baker recounts lab findings in 2004 that showed “something even more radical: nanotubes in mammalian cells that seemed to move cargo such as organelles and vesicles back and forth.” Since then, more “membrane nanotubes” have been found.

Meanwhile, other labs have reported cell-connecting tubes in neurons, epithelial cells, mesenchymal stem cells, several sorts of immune cell and multiple cancers. Further types of tube have been spotted as well. In 2010, Gerdes and his team reported that some tubes end in gap junctions: gateways that bestow the neuron-like ability to send electrical signals and can also pass along peptides and RNA molecules.

The “internet of cells” might also explain how disease agents, such as viruses, spread among tissue cells, or how cancer cells hijack their neighbors. Not everyone is jumping aboard the new paradigm, because the implications are huge. Eliseo Eugenin at Rutgers Medical School

thinks that other researchers are sceptical of nanotubes because they are unable to reconcile themselves to the idea that cells are constantly exchanging materials, including genetic information. “Our definition of a cell is falling apart,” Eugenin says. “That is why people don’t believe in these tubes, because we have to change the definition of a cell.”

The race is on to convince skeptics with better imaging of functional transport within multicellular organisms. Baker doesn’t say much about evolution. She notes that one researcher speculated, “Membrane protrusions might have evolved first, and higher organisms could have started upgrading them to make neurons for more complicated functions.” Such personification language is not particularly helpful for materialists. Baker quickly pivots and says, “Most researchers who study these cellular pipelines care less about their evolutionary origin than about their role in human health and disease.” As such, the “internet of cells” looks like it will be a boon for design research, and a challenge to Darwinian evolution.

Sharing Genetic Information

A separate paper in PNAS discusses “Intercellular mRNA trafficking via membrane nanotube-like extensions in mammalian cells.” Notice how this team of Americans and Israelis describes the finding as a revolutionary development in biology:

mRNA molecules convey genetic information within cells, beginning from genes in the nucleus to ribosomes in the cell body, where they are translated into proteins. Here we show a mode of transferring genetic information from one cell to another. Contrary to previous publications suggesting that mRNAs transfer via extracellular vesicles, we provide visual and quantitative data showing that mRNAs transfer via membrane nanotubes and direct cell-to-cell contact. We predict that this process has a major role in regulating local cellular environments with respect to tissue development and maintenance and cellular responses to stress, interactions with parasites, tissue transplants, and the tumor microenvironment.

The team admits that “The biological importance of mRNA transfer between cells is still unknown,” but the concept of sharing of genetic information between cells appears to overturn long-held assumptions about the independence of cells.

As for what cells are sharing, many possibilities come to mind. For instance, “the transfer of mRNAs involved in cell differentiation during embryonic development might act as means to induce or repress neighboring cells.” Conceptualizing the rapid transfer of genetic information via “nanotubular highways” between cells opens up many new avenues for research. “Determining the scope of this process and deciphering the mechanism and physiological outcome of mRNA transfer will be the goal of future studies,” they conclude.

More Evidence

Hormones and signal molecules have long been known to travel between cells, but direct transport by contact is fairly new. Science Daily reported on work at Vanderbilt to learn how cells communicate during wound healing. The cell’s signals are “surprisingly complex”, the headline says. One hypothesis had been that cells send proteins to their neighbors that trigger them to boost their calcium levels.

The second hypothesis proposes that the trigger signal spreads from cell to cell through gap junctions, specialized intercellular connections that directly link two cells at points where they touch. These are microscopic gates that allow neighboring cells to exchange ions, molecules and electrical impulses quickly and directly.

“What is extremely exciting is that we found evidence that cells use both mechanisms,” said Shannon. “It turns out cells have a number of different ways to signal injury. This may allow them to differentiate between different kinds of wounds.”

Implications for Design Research

Darwinian theory presupposes some kind of “unit of selection” in biology. Evolutionists have long debated whether the unit of selection is a gene, a cell, an organism, or (less commonly proposed) a population of organisms. Neo-Darwinism has long focused on cells as units of selection, because that’s where genetic mutations take place that might be beneficial. Essential to the theory, though, is some degree of independence of the unit of selection, so that whatever beneficial variation appears can be victorious in the struggle for existence.

If organisms routinely share their information, however, all evolutionary bets are off. There won’t be competition if all the players share the benefit. We saw this conundrum when evidence grew for rampant horizontal gene transfer between microbes, and then between higher organisms. Some biologists considered the existence of a “quasi-species” in which a population could rapidly recover from individual stresses because of information sharing.

The “internet of cells” bears more similarity to “cloud computing” than to classical notions of Darwinian evolution. If functional information is routinely shared throughout the internet of cells, that looks a lot more like cooperation than competition. Prospects for research in this hot new paradigm appear wide open for non-Darwinian interpretations.

The Iconoclasm continues?

Upsetting Another Evolutionary Icon — Blindness in Cave Fish Is Due to Epigenetics
Cornelius Hunter

A recent paper out of Brant Weinstein’s and William Jeffery’s laboratories on eye development, or the lack thereof, in blind cave fish has important implications for evolutionary theory (the paper is discussed  here). The study finds that the loss of eyes in fish living in dark Mexican caves is not due to genetic mutations, as evolutionists have vigorously argued for many years, but due to genetic regulation. Specifically, methylation of key development genes represses their expression and with it eye development in this venerable icon of evolution. But the finding is causing yet more problems for evolutionary theory.

Darwin appealed to the blind cave fish in his one long argument for evolution. It is a curious argument in many ways, and the first sign of problems was in Darwin’s presentation where he flipped between two different explanations. At one point he explained the loss of vision in the cave fish as an example of evolutionary change not due to his key mechanism, natural selection. Instead, the Sage of Kent resorted to using the Lamarckian mechanism or law of “use and disuse.” Privately, Darwin despised and harshly criticized Lamarck, but when needed he occasionally employed his French forerunner’s ideas.Elsewhere Darwin hit upon a natural selection-based mechanism for the blind cave fish, explaining that elimination of the costly and unneeded vision system would surely raise the fitness of the hapless creatures.

This latter explanation would become a staple amongst latter-day evolutionary apologists, convinced that it mandates the fact of evolution. Anyone who has discussed or debated evolutionary theory with today’s Epicureans has likely encountered this curious argument that because blind cave fish lost their eyes, therefore the world must have arisen by itself.

Huh?

To understand the evolutionary logic, or lack thereof, one must understand the history of ideas, and in particular the idea of fixity, or immutability, of species. According to evolutionists, species are either absolutely fixed in their designs, or otherwise there are no limits to their evolutionary changes and the biological world, and everything else for that matter, spontaneously originated.

Any evidence, for any kind of change, no matter how minor, is immediately yet another proof text for evolution, with all that the word implies.

Of course, from a scientific perspective, the evidence provides precisely zero evidence for evolution. Evolution requires the spontaneous (i.e., by natural processes without external input) creation of an unending parade of profound designs. The cave fish evidence shows the removal, not creation, of such a design.

The celebration of such evidence and argument by Darwin and his disciples reveals more about evolutionists than evolution. That they would find this argument persuasive reveals their underlying metaphysics and the heavy lifting it performs.

We are reminded of all this with the news of Weinstein’s new study. But we also see something new: The insertion, yet again, of Lamarck into the story. The irony is that the epigenetics, now revealed as the cause of repressed eye development in the cave fish, hearkens back to Lamarck.

Darwin despised Lamarck and later evolutionists made him the third rail in biology. Likewise they have pushed back hard against the scientific findings of epigenetics and their implications.

The environment must not drive biological change.

False.

Well then, such biological change must not be transgenerational.

False.

Well, such inheritance must not be long lasting, or otherwise robust.

False again.

This last failure is revealed yet again in the new blind cave fish findings.

False predictions count. A theory that is repeatedly wrong, over and over, in its fundamental expectations, will eventually be seen for what it is.

The rise of epigenetics is yet another such major failure. Evolutionists pushed back against it because it makes no sense on the theory, and that means it cannot now be easily accommodated.

One problem is that epigenetics is complex. The levels of coordination and intricacy of mechanism are far beyond evolution’s meager resources.

Another problem is the implied serendipity. For instance, one epigenetic mechanism involves the molecular tags placed on the tails of the DNA packing proteins called histones. While barcoding often seems to be an apt metaphor for epigenetics, the tagging of histone tails can influence the histone three-dimensional structures. It is not merely an information-bearing barcode. Like the tiny rudder causing the huge ship to change course, the tiny molecular tag can cause the much larger packing proteins to undergo conformational change, resulting in important changes in gene accessibility and expression.

This is all possible because of the special, peculiar structure and properties of the histone protein and its interaction with DNA. With evolution we must believe this just happened to evolve for no reason, and thus fortuitously enabled the rise of epigenetics.

Another problem with epigenetics is that it is worthless, in evolutionary terms that is. The various mechanisms that sense environmental shifts and challenges, attach or remove one of the many different molecular tags to one of the many different DNA or histone locations, propagate these messages across generations, and so forth, do not produce the much needed fitness gain upon which natural selection operates.

The incredible epigenetics mechanisms are helpful only at some yet to be announced future epoch when the associated environmental challenge presents itself. In the meantime, selection is powerless and according to evolution the incredible system of epigenetics, that somehow just happened to arise from a long, long series of random mutations, would wither away with evolution none the wiser.

These are the general problems with epigenetics. In the case of the blind cave fish, however, there is a possible explanation. It is a longshot, but since this case specifically involves the loss of a stage of embryonic development, evolutionists can say that genetic mutations caused changes in the methylating proteins, causing them to be overactive.

This explanation relies on the preexistence of the various epigenetic mechanisms, so does not help to resolve the question of how they could have evolved. What the explanation does provide is a way for evolutionists to dodge the bullet presented by the specter of the cave fish intelligently responding to an environmental shift.

Such teleology in the natural world is not allowed. So the evolutionary prediction is that these proteins will be found to have particular random changes causing an increase in their methylation function, in particular at key locations in key genes (i.e., the genes associated with eye development).

That’s a long shot, and an incredible violation of Occam’s razor. My predictions are that (i) this evolutionary prediction will fail just as the hundreds that came before, and (ii) as with those earlier failures, this failure will do nothing to open the evolutionist’s eyes.

The God and Father of Jesus is the one God and Father Of Jehovah's people.

The wild east?

A clash of Titans.LXIII

The West in self-destruct mode?:Pros and cons.

The Original artist v. Darwin.

Design in Living Color
Evolution News | @DiscoveryCSC  

Our colorful world — what a joy it is! Who doesn’t love the beauty of butterflies, the colors of birds and tropical fish, or the colorful eyes of a loved one? Mechanistically speaking, though, color is ‘nothing but’ wavelengths of light reflecting off surfaces or emanating from energy sources within a particular range of frequencies we artificially designate as “visible light.” We respond physically to wavelengths only because our bodies come equipped with highly complex sensory systems. We respond emotionally to the qualia of color — the redness of red, the greenness of green, the beautiful spectrum in a rainbow — because of something deeper in our consciousness.

Blind nature is oblivious to qualia. It has no obligation to invent creatures able to manipulate color, or to perceive it. Least of all is nature obliged to produce artists that use color for purely aesthetic reasons unrelated to survival. Yet the living world is filled with colors in profusion, often with spectacular effect. This fact requires an explanation. One could think of reasons natural selection might favor an ecological system of uniform browns or blacks. Camouflage would be perfect in such a world! What does blind evolution care about color?

To outline evolutionary explanations for color, Science Magazine recently presented “The Biology of Color,” a review article by Innes C. Cuthill with 27 authors from the U.K. and U.S. The editors summarize the goal:

Animals live in a colorful world, but we rarely stop to think about how this color is produced and perceived, or how it evolved. Cuthill et al. review how color is used for social signals between individual animals and how it affects interactions with parasites, predators, and the physical environment. New approaches are elucidating aspects of animal coloration, from the requirements for complex cognition and perception mechanisms to the evolutionary dynamics surrounding its development and diversification. 

“Elucidating” means shedding light, which presupposes that science does not only observe light, but produces light in the realm of understanding: i.e., scientific explanation. Since we know from the “rules of science” these days that design explanations must be excluded, it’s fair to say this article summarizes the state of the art in evolutionary explanations for color. Contributors include a broad spectrum (so to speak) of scientific disciplines: “evolutionary biologists, behavioral ecologists, psychologists, optical physicists, visual physiologists, geneticists, and anthropologists” — all committed to evolutionary theory. For curious readers, these experts will map the route to proper Darwinian answers, shedding colorful light along the way:

The interdisciplinary field of animal coloration is growing rapidly, spanning questions about the diverse ways that animals use pigments and structures to generate color, the underlying genetics and epigenetics, the perception of color, how color information is integrated with information from other senses, and general principles underlying color’s evolution and function. People working in the field appreciate linkages between these parallel lines of enquiry, but outsiders need the easily navigable roadmap that we provide here.

Following their roadmap, we proceed down the yellow brick road to the wizard of ahh’s, hoping the promised understanding will be forthcoming. For openers, let’s check the flashlight they provide (the “elucidating” device).

In the past 20 years, the field of animal coloration research has been propelled forward by technological advances that include spectrophotometry, digital imaging, computational neuroscience, innovative laboratory and field studies, and large-scale comparative analyses, which are allowing new questions to be asked. For example, we can now pose questions about the evolution of camouflage based on what a prey’s main predator can see, and we can start to appreciate that gene changes underlying color production have occurred in parallel in unrelated species. Knowledge of the production, perception, and evolutionary function of coloration is poised to make contributions to areas as diverse as medicine, security, clothing, and the military, but we need to take stock before moving forward.

This is some high-tech flashlight! We need to learn how to use it, in other words. How do we use evolution to shed light? It is “daunting to the outsider,” they warn. They outline key questions needing elucidation:

How nanoscale structures are used to manipulate light

How dynamic changes in coloration occur on different time scales

The genetics of coloration (including key innovations and the extent of parallel changes in different lineages)

Alternative perceptions of color by different species (including wavelengths that we cannot see, such as ultraviolet)

How color, pattern, and motion interact

How color works together with other modalities, especially odor

Some of us will prefer carrying our trusty ID flashlights for illumination, but let’s give the Darwinians a chance to show off their brand. First, we listen to the commercial:

From an adaptive standpoint, color can serve several functions, and the resulting patterns frequently represent a trade-off among different evolutionary drivers, some of which are nonvisual (e.g., photoprotection). These trade-offs can vary between individuals within the same population, and color can be altered strategically on different time scales to serve different purposes. Lastly, interspecific differences in coloration, sometimes even observable in the fossil record, give insights into trait evolution. The biology of color is a field that typifies modern research: curiosity-led, technology-driven, multilevel, interdisciplinary, and integrative.

Before we rush to buy this amazing flashlight on Amazon, let’s see how well it works. We should be concerned about “evolutionary drivers”, since they are blind, and blindness entails color blindness. How can a blind process understand a trade-off? One thing we learn from the article is that questions about color evolution are producing a flurry of activity among evolutionists:

The study of animal coloration has a venerable history. During the 19th century, early evolutionary biologists set out to explain the diversity of colors that they observed as products of natural selection. The 20th century saw color phenotypes adopted as genetic markers contributing to our understanding of development, genetics, and evolutionary theory.

Before proceeding, we should ask why there is anything else to learn. Didn’t the 19th and 20th century evolutionists figure it out? Apparently not.

In the past two decades, the field has again witnessed explosive growth. Coloration provides exceptional access to phenotypic diversity because we can quantify how color is perceived by the visual systems of diverse species, and humans are visual animals. Contemporary technologies enable biologists to investigate nanoscale and cellular mechanisms producing color; the sensory, neural, and cognitive bases of color perception; and the adaptive implications of external appearances. Progress in each area is rapid, making animal coloration an exciting interdisciplinary field, but one with which it is difficult to keep pace.

Let’s catch our breath in this frenetic race down the yellow brick road, and assess what it is we are looking for. Explanation is not merely description. It’s good to know what gene turns on what color. It’s helpful to find out which colors a predator can perceive. We can even be pleased to learn that a bird of a certain color might have better camouflage. None of these details explain animal coloration. The job of the Darwinians is to tell us how a color-blind process (that doesn’t care whether a creature lives or dies) ended up with a Ladybird beetle’s brilliant reds or a ruby-throated hummingbird’s shimmering throat feathers. It’s not enough to say, “It exists, therefore it evolved.” Nor can they say, “It’s useful, therefore it is adaptive, and natural selection would favor it.” Do you see the circular reasoning inherent in such statements? We seek evidence that evolution did occur, not restatements of what evolutionists believe occurred.

Across animals, coloration serves as a dynamic form of information (Fig. 1). Colorful body parts are moved in behavior, and both pigments and structural colors change at various temporal resolutions. Cephalopods are perhaps the most well-known example, but mobilization of pigments and nanostructures to change coloration is taxonomically widespread. Considerable opportunities exist for dissecting color pigment movements and manipulating their hormonal or neural control. Dynamically changing structural coloration can also manipulate the polarization of light. There is high potential for discoveries regarding how animals perceive polarization and integrate it with color information.

What is “information” to a blind, unguided process? Information fits in well with design theory (e.g., Dembski’s book  Being as Communion), but we can’t let scientific materialists employ undefined terms nor import them from a worldview they don’t believe. Information doubles the challenge for evolution, because it requires a transmitter and a recipient that agree on the meaning of the communication.

So far, all we have seen are descriptions, not explanations. Body parts are moved. Animals perceive polarization of light. Animals integrate color information. Great, but how? Why?

We anticipate answers in the subsection, “Genetics of color and evolutionary change.” But careful reading reveals only tricks of the evolutionary trade: co-option, convergence, and similarity. Underneath these superficial narratives, evolutionists need to deal with the origin of complex genetic information, molecular machines, and developmental processes of exquisite order. They try:

For instance, a ketolase enzyme that evolved to modify carotenoid pigments in the retina of birds paved the way for the expression of red pigments in bills and plumage; similarly, the ALX3 transcription factor has come to regulate the expression of melanocyte differentiation in striped rodents.

Saying that something evolved does not mean it did. Can a bird reason, “Oh, now I have this ketolase enzyme. I think I’ll color my beak with it.”? Can a rodent think, “Now that I have ALX3, I can put racing stripes on my back and look really cool.”? Obviously not; the materialist cannot ascribe desires or powers to organisms nor to the molecules involved. We cannot stress enough that evolution is blind and color-blind! It is not personal. It is not a force. It could not care less what happens.

Genes underlying color variation offer insight into the predictability of evolution. Convergent phenotypes commonly arise in parallel; the accurate characterization of color phenotypes has revealed independent changes in similar genetic mechanisms, leading to phenotypic similarity between species.

Predictability is certainly a good quality to have in a theory, but did they predict any of this? No; it is all description after the fact, combined with circular reasoning: “It exists, therefore it evolved.” To have the same accidents occur in independent lineages should amount to falsification of the theory. It certainly does not qualify as an explanation.

Multidisciplinary research into the workings of coloration, from genotype to phenotype, and from development to adult, is certainly valuable. We might compare it to discovering an alien spacecraft and figuring out how it works. Such research cannot explain how it emerged by blind, unguided processes. So while we celebrate the progress in understanding coloration, we don’t see in this paper any explanation for it that does not presuppose the success of evolutionary theory.

Whenever they try to link accidents with functions, they run into problems and have to admit ignorance. For instance, Darwin’s sexual selection theory provides a shiny-object narrative at a superficial level, but not at the genetic level:

Genomic insights will prove valuable in investigations of mechanisms by which colorful traits honestly signal individual quality. It is widely accepted that a sexual ornament can reveal quality, because of the challenges associated with producing or bearing such traits, but we remain largely ignorant of the mechanisms that underlie gene-environment interactions causing condition-dependent signaling. Epigenetic studies at the genome scale may offer insight into this question.

Even worse is accounting for structural color. This kind of coloration, seen in birds and insects, relies on precise placement of geometrical molecules at the nanoscale rather than on pigments. How can evolution even approach such masterpieces of “apparent” design?

Knowledge of genetic mechanisms underlying the creation and transport of pigments, such as melanin and carotenoids, has advanced considerably in the past 15 years, but outstanding questions about structural coloration remain. Understanding the genetic control of size and shape dispersion is important because these properties ultimately control optical structures. An appreciation of the genetics of nanostructural color production could also be important for biotechnological applications — for example, the creation of sensors and reporting mechanisms.

The applications mentioned are matters of intelligent design by humans. How could natural selection invent genes that, by accident, are capable of placing molecules in precise positions at the nanoscale that enable them to refract certain wavelengths of light? Then, how does it position them in second-order artistic patterns like those on butterfly wings? Evolutionists admit they don’t know. They sure have their work cut out for them!

The challenge grows as they try to account for “Receptor processing and cognition” in the next section. It grows even more as they try to integrate colors with patterns and motion. We’ve given enough of a taste of their mode of explanation, we trust, to show that evolution is not an explanation; it is belief masquerading as explanation. Like Tom Bethell discussed in Darwin’s House of Cards, evolutionary explanation is a deduction from a pre-ordained worldview that asserts: It is, therefore it evolved. The public deserves better. The public would receive better were alternatives to neo-Darwinism permitted into the discussion. When you only allow one contender in the race, guess who is going to win?

Design detection is science except when it's not?

Mysterious Structures in Arabian Desert: All We Know Is that They Were Designed
Evolution News | @DiscoveryCSC

The news media were swept up in a mystery recently, when an Australian archaeologist told how he used Google Earth to discover mysterious rock structures in the Arabian desert. He and his team want to investigate and figure them out. “As of now, researchers have more questions than answers regarding what these structures were used for, who built them, how old are they, and their meaning,” says an article at Forbes. 

You can see a gallery of the so-called “gates” in  Live Science. You can even find them on Google Earth yourself, if you want to do a little armchair archaeology, by searching for “Harrat Khaybar” and scouting around, trying to match landforms to the photos. We’ve reported finds like this before (here and here). The article at  The Express UK says:

David Kennedy, a professor at the University of Western Australia, who helped to discover the gates through satellite imagery, said they “are stone-built, the walls roughly made and low.”

He adds that they “appear to be the oldest man-made structures in the landscape,” and that “no obvious explanation of their purpose can be discerned”.

Only one piece of evidence is helping to nail down the age of the structures. A few of the structures are partly covered by lava flows. That means that they had to be built before the most recent eruptions in this lava field, which could be as recent as 1,300 years ago, or up to 7,000 years ago. Kennedy wants to radiocarbon date the remains if he can launch an expedition. Knowing the date of the oldest structures can help identify what humans lived in that area at the time. Forbes says,

The team will soon publish their research in the journal Arabian Archaeology and Epigraphy. However, this is just the tip of the iceberg, as the saying goes. The next steps will be to lead an archaeological survey of the area, allowing the research team to collect samples and inspect the gates more closely. They will be able to carbon age date the lava fields and potentially the stone walls to determine the timing of construction. In addition, they may find more examples of what these strange people were like in this remote region of Saudi Arabia.

We can relate to Kennedy’s immediate sense that these structures were man-made, because we are human and know what humans do. And readers of Evolution News, as intelligent design advocates, could run our handy-dandy Design Filters and decide that these structures pass the test: they are not products of chance or natural law, and they contain specified information. But we would want to apply sufficient rigor, because a look at the surroundings with Google Earth shows some parallel lines that could be “natural.” Some of the perfect circles we see are clearly volcanic vents, also not candidates for design. Then there is the issue of distinguishing the ancient “mysterious” structures from a few modern roads and buildings out there.

Assuming our results concur with Kennedy’s, we can also relate to his enthusiasm to find an “explanation for their purpose”. But we know that intelligent design theory does not need to know the purpose of an artifact; it is sufficient to deduce that some purpose or intent was involved. Intelligent design stops when we try to figure out the who and the why. For instance, in cases where we have good reason to think a cosmic designer made something, we go too far in ID to specify it was God, or to presume to know what God’s purpose was. Those questions are better addressed by theologians after the design inference is made.

But we must also clear up another issue as well: what do we mean by purpose or intent? If not careful, we attribute intent to honeybees who build elaborate honeycombs for the purpose of laying their eggs. The living world is rich with complex patterns exhibiting function that result from animal behaviors: bird nests, termite mounds and ant hills, and this striking example produced by a puffer fish as part of its mating dance (see this  BBC video). Are we to locate the intention in the tiny brains of bees and ants?

We might argue that the Arabian ‘gates’ show design because they go beyond mere survival needs. But even then, we can’t easily dismiss animal behaviors with that argument, because some animals seem to make artworks of gratuitous beauty. The elegant glass houses of diatoms, for instance, don’t seem to require such elegant geometrical perfection to be functional. Nor do the  Golden Ratios of plants that we talked about recently seem necessary for survival.

Evolutionists, in their reductive mindset, are likely to lump human designs into the same basket as termite mounds. Building things is just something the human animal does. Rock structures in the desert are mere consequences of large human brains and evolved behaviors, they might say. In this view, intent and purpose get swallowed up by the all-encompassing blob of natural selection. How do we escape that line of argument? How do we defend true intention for intelligent design?

Nancy Pearcey, a Discovery Institute Fellow and a  contributor to these pages, has shown one sure-fire strategy. In her latest book Finding Truth, she argues that if Darwinians want to reduce human purposes to natural selection, then we need to show them that their explanation points both ways. What’s good for the goose is good for the gander: if natural selection produced humans who built the Arabian structures, then it also produced academic professors who write journal papers attributing everything to natural selection. Obviously, such an argument implodes in on itself. The only way to argue for evolution is to plagiarize theistic positions, which take truth and purpose seriously. Without believing in truth and intent, a Darwinian commits intellectual suicide.

Having established that truth and intention cannot be artifacts of chance and natural law, we can employ them to re-examine cases of animal designs. Instead of attributing intent to honeybees, plants, or birds, we can locate the intent in something higher. Our own programmed systems (robots, computer networks, and so on) were intended to function using parts that we arranged for that purpose; the parts would never do those things without our guidance. This distinguishes the ‘human animal’ from the rest of nature without diminishing our physical attributes and commonalities with primates. Bodies enable our human minds to choose to design things.

Since in our uniform experience every system exhibiting functional coherence (to use Doug Axe’s term in Undeniable) — wherein we witnessed the system coming into being — was the product of human intelligent design, we can use the principle of uniformity to infer that a mind was behind the functionally-coherent systems we did not witness coming into being (provided they pass the Design Filter). The designing mind, additionally, must have the ability to apprehend truth and intention as genuine qualities of personhood. (Without that, all explanation comes crashing down.) Any scientist proposing to offer a scientific explanation, therefore, must necessarily presuppose that truth and intention are fundamental properties of intelligent agents.

Looking back at those stone structures decaying in the desert over thousands of years, we can feel some kinship to the makers, even if we don’t know them. Like us, those human beings had minds. Like us, they had purposes. For whatever reason, their intelligent, designing minds set them to work building large rows of stones, some of them almost 1,700 feet long, for reasons we can only guess at. What’s not in doubt is that they had a plan.

Rehabilitating a fallen icon?

Peppered Moths, an Evolutionary Icon, Are Back

Jonathan Wells

Readers of Evolution News are probably familiar with -- perhaps even bored with -- the classic story of peppered moths. The story lay dormant for several years, but now it's in the news again.

In brief, the classic story is that peppered moths went from being mostly light-colored to being mostly dark-colored ("melanic") during the industrialization of 19th-century England. The shift was called "industrial melanism," and it was attributed to natural selection: Dark-colored moths were supposedly better camouflaged on pollution-darkened tree trunks and thus more likely to survive predatory birds. After air quality legislation was passed in the mid-20th century, light-colored moths became more common again, consistent with the story.

Darwin himself had no evidence for natural selection, but peppered moths were said to provide it. The story was called

 "Darwin's missing evidence,"

and it was used for years in biology textbooks to teach Darwinian evolution -- usually accompanied by photographs of light- and dark-colored moths resting on light- and dark-colored tree trunks.

The story had various problems, but the most serious emerged in the 1980s when biologists discovered that peppered moths don't normally rest on tree trunks. Instead, the vast majority of them probably rest high up in trees where they can't be seen. Almost all of the textbook photographs had been staged, many with dead moths pinned to tree trunks.

After the publication of  

Icons of Evolution 

in 2000, many textbooks stopped using the classic story. It enjoyed a brief resurgence in 2007, but then it mostly dropped from sight again.

Of course, even if the classic story were true, it would not demonstrate Darwinian evolution. Darwin didn't write a book titled How Existing Species Change Over Time. He wrote a book titledThe Origin of Species. His argument was that natural selection produces entirely new species, organs, and body plans. A temporary shift in the proportions of light- and dark-colored peppered moths is irrelevant to that argument.

Now peppered moths are back. Some 

scientists in England 

have identified a mutation that may explain why some peppered moths are dark-colored. The scientists found a transposable element, or "jumping gene," that is present in 105 of the 110 dark-colored moths they studied, but absent from 283 light-colored moths. Although it is not clear how the stretch of DNA where the transposable element was found affects wing color, the scientists concluded that this was "the mutation event giving rise to industrial melanism in Britain," and that their findings "fill a substantial knowledge gap in the iconic example of microevolutionary change."

(In the 1930s, evolutionary biologist Theodosius Dobzhansky distinguished between minor changes within existing species, which he called "microevolution," and the origin of new species, organs and body plans, which he called "macroevolution.")

This discovery was based on some impressive experimental work. Now it is accompanied by some impressive hype.

According to the journal 

Nature 

(in which the study was published), "there is perhaps no better example of natural selection in action than the case of the peppered moth." Unfortunately, some "technical criticisms" of the classic story "have leaked, out of context, into the propaganda of creationists. In response, some textbooks have -- heaven forbid -- evolved to not include the peppered moth story at all." But "there is enough in the pages that follow to update those textbooks."

The Science Daily 

news service quotes one of the scientists involved in the study to the effect that "this discovery fills a fundamental gap in the peppered moth story," which

Science Daily calls the "iconic textbook example of evolution by natural selection." Another scientist involved in the study says, "These findings provide an opportunity to further develop peppered moth industrial melanism as a tool for teaching evolutionary biology."

Repeating the discredited classic story, 

 BBC News 

reports that "peppered moths are nocturnal and spend their days dozing on tree trunks or walls," so the newly identified mutation "gave them a much better chance of hiding from hungry birds in the smoke-stained world of industrial England."

According to the 

Washington Post 

just as peppered moths "once helped illuminate the macro process of natural selection, the researchers hope their studies will illuminate how evolution happens at a microscopic level." But peppered moths never illuminated macroevolution. The Post continues by quoting one of the scientists involved in the study:

My hope is that by adding more scientific evidence, more modernscientific evidence, to this case study that eventually it will kind of make it easier for people to appreciate at different levels this isn't a made up story. There's more and more layers of evidence.

But how relevant is that evidence? These reports (and the scientists quoted in them) assume that the main problem with the classic story was that the genetic basis of melanism was unknown. But that was never the main problem. The fact that peppered moths don't normally rest on tree trunks makes it doubtful that industrial melanism was due to camouflage and bird predation, and the fact that a temporary shift occurred in the proportions of light- and dark-colored moths provides no evidence for Darwin's theory of the origin of species.

Maybe it's time for the peppered moth story to drop from sight once again.