Darwinsplainin' ?

Where Design Explains, Darwinism Explains Away
Evolution News | @DiscoveryCSC

Look at the photos in an article on Live Science. They report: 

Hundreds of stone structures dating back thousands of years have been discovered in the Western Sahara, a territory in Africa little explored by archaeologists.

The structures seem to come in all sizes and shapes, and archaeologists aren’t sure what many of then were used for or when they were created.

Immediately you know these structures were designed. How should you know that? How did the scientists know that? The discoverers didn’t know who made them. They didn’t know why they made them. No obvious purpose for the structures came to their attention, yet they knew someone made them intentionally. 

A new book documenting hundreds of rock structures in the Western Sahara has been published: The Archaeology of Western Sahara: A Synthesis of Fieldwork, 2002 to 2009 (Oxbow Books, 2018). The article explains that the region has long been too dangerous for research because of a state of war between Morocco and the Sahrawi Arab Democratic Republic. Because of that, this region remains mysterious and largely unknown, and research has been “extremely limited.”

Like the archaeologists, people living in the area intuitively knew the structures were designed. (See additional photos in a slide show on Live Science.) Rocks on their own don’t arrange themselves like these ones are put together.

The stone structures are designed in a wide variety of ways. Some are shaped like crescents, others form circles, some are in straight lines, some in rectangular shapes that look like a platform; some structures consist of rocks that have been piled up into a heap. And some of the structures use a combination of these designs. For instance, one structure has a mix of straight lines, stone circles, a platform and rock piles that altogether form a complex about 2,066 feet (630 meters) long, the archaeologists noted in the book. 

We’ve seen other design inferences like this in Brazil, Jordan, Israel, and Arabia. After concluding that structures are designed, archaeologists often pursue additional questions. The makers must have had the ability to mobilize many people to do the work. Perhaps powerful rulers drove their subjects to make elaborate tombs or grave markers. In some cases, structures can be correlated with rock art. A design inference does not, therefore, stop the science. It stimulates additional questions for investigation. And it is falsifiable: something originally thought to be designed can turn out to be a natural phenomenon.

The Design Inference

Books by intelligent design leaders clarify the nature and extent of the design inference. Douglas Axe, in his book Undeniable, explains why our intuition that things are designed is corroborated by biochemistry. Stephen Meyer, in his books Signature in the Cell and Darwin’s Doubt, shows that intelligent design uses the same form of explanation Darwin and Lyell used to appeal to causes known from our uniform experience. William Dembski, in The Design Inference and No Free Lunch, provides mathematical rigor to the design inference. The point is that, while intuitive, the design inference can withstand all the rigor necessary for scientific reasoning. 

Darwinism Explains Away

While intelligent design explains the origins of things by reference to causes known to be in operation, Darwinism usually explains things away. All Darwinians accept the appearance of design, but they have limited themselves to undirected causes by embracing methodological naturalism (MN). They may as well limit themselves to wind and erosion to explain the structures in the Western Sahara — or Mount Rushmore, for that matter. Insistence on MN often leads to very counter-intuitive stories. For instance, when similarities appear in species that Darwinians insist are unrelated, they posit that the species evolved the similarities independently. 

Argument by Assertion

MN takes the rigor out of biological explanation. Since Darwinian scientists limit themselves to undirected causes, and MN disallows intelligent causes, there’s only one category of explanation in the toolkit. Darwinians, therefore, can feel satisfied with argument by assertion: whatever it is, it evolved. For example, in news from the Max Planck Institute for Chemical Ecology, the biologists say that “Desert ants have an amazing odor memory.” The article describes the odor memory in detail, but when it comes to explaining where it came from, here’s the answer: “Desert ants have evolved impressing abilities to survive in the salt pans of the Tunisian Sahara, which are pretty barren habitats.” End of story. The desert ants are far more complex than the Saharan archaeological finds, but that’s all you get: the ants’ impressive abilities “have evolved.” 

Argument by Extrapolation

Another method Darwinians use to explain away the appearance of design is argument by extrapolation. With this technique, they provide examples of biological change by “evolution” that would not worry an ardent young-earth creationist. Then, they extrapolate their claimed success to the whole natural world. It’s like saying, “Butterfly wings change color; therefore, humans evolved, unguided, from bacteria.” 

An example of this technique got lots of fanfare recently. Science Magazine took a case of coat color in mice and made a mountain out of a molehill. Harvard University, on Phys.org, trumpeted this as “Evolution, Illustrated,” calling it “one of the clearest pictures yet of evolution in vertebrates.” What evolved, actually? Very little. Under controlled conditions, some fur in one species of mice (Peromyscus maniculatus) changed shade from light to dark or vice versa, to fit in with the background:

What do you get when you put together several tons of steel plates, hundreds of mice, a few evolutionary and molecular biologists and a tiny Nebraska town near the South Dakota border?

Would you believe one of the most complete pictures ever of vertebrate evolution?

This demonstration of evolution took years in the field, we are told, which is to say years of intelligent design. All kinds of things went wrong during the experiment. As Ed Yong at  The Atlantic remarked, “Nature itself seemed eager to select against the team.” But in the end, they got the results they wanted: the mice that fit their background survived better against predators, and showed a change to one gene, named Agouti.  Yong turns this episode into a colorful story of success against great odds: determined evolutionists brave the cold and wind to (at long last) vindicate Darwin.

That’s another reason evolutionary explanations work: Darwinians are great storytellers.

But let’s take stock of this claimed success, “The Wild Experiment That Showed Evolution in Real Time.” The experiment began and ended with one species of mice. Nothing evolved. Many mammals already show variation in coat color. A litter of dogs can have multiple coat colors, depending on the parents. This is simple Mendelian inheritance. Is it any wonder that owls picked off the ones that were easier to see? 

As for the Agouti gene, variations exist in many genes. But proving that the variants in this gene causedthe owls to not prey on them? That’s a stretch. What they really say in the paper in Science is, “we find allele frequency changes at the Agouti locus consistent with selection [as opposed to neutral drift], and thus, patterns at the genetic level parallel the change observed at the phenotypic level.” And thus, humans evolved from bacteria. If this sounds like a new peppered mice story, it is: and about as rigorous and overblown, too. Why didn’t they consider epigenetic effects? Why could not the variations in Agouti represent pre-programmed variation for survival, like in the adaptive immune system, or in the quasispecies concept? Why must it be explained by natural selection?

The design inference is clear to all, even to Richard Dawkins, who said, “Biology is the study of complex things that appear to have been designed for a purpose.” Intelligent design explains design with references to causes now in operation that we know from our universal experience are necessary and sufficient. Doug Axe used his rigorous research into biochemistry to show “How biology confirms our intuition that life is designed.” Darwinians must explain away that intuition, using clever methods of assertion, extrapolation, and storytelling.

Afterword

The article in The Atlantic reveals that 160 years after The Origin, common people still maintain their design intuition. When the locals in the sand hills heard about what the researchers were up to, the researchers had to walk on eggs.

Roughly a third of Nebraskans believe that living things were created as they are now. Another third think that evolution occurs, but through God’s design. Given those beliefs, I asked Barrett whether he ever encountered resistance when talking to his new friends about his work. “In the early trips, when first meeting people, I would talk generally about genetics and natural selection. I wouldn’t use the E word,” he said. “It’s one of those trigger words where, in certain parts of the U.S., people just stop listening to you.”

A little storytelling helped put the locals at ease:

But he added that all of them comprehended the essence of evolution, even if they explicitly rejected it. “A lot of them are farmers, who have a very good understanding of inheritance, and genetics,” he said. “A lot of them hunt, so they’ve got the survival-of-the-fittest thing down. They understand variation, and they know that a slow deer is easier to shoot than a fast deer. Inheritance, variation, fitness … all the pieces are there.”

There you go: slow deer are easier to shoot than fast deer. Survival of the fittest is proved. And humans evolved, unguided, from bacteria.

On a fresh tilt at the origin of life windmill.

The origin of abiotic species: Seven epic fails

January 7, 2016 Posted by vjtorley under Intelligent Design
A team of researchers led by Professor Sijbren Otto of the University of Groningen, in the Netherlands, has announced that it has observed not only self-replication, but also mutants and even new “species,” in a bunch of molecules in the lab. Does this research show how life might have arisen spontaneously, or is it nothing more than a case of intelligent design by clever chemists?

In today’s post, I’m going to argue that the claims made by Professor Otto and his team are flawed, on no less than seven counts. But before I examine their press release and their paper in Nature Chemistry, I’d like to discuss a Science LinX video that was posted on Youtube last year (March 17, 2015), titled, “Chemical evolution: creating life?”, which explains the work being carried out Otto and his group:
The text of the video reads as follows (note: all bold emphases shown in this post are mine – VJT):

This is Sijbren Otto, a chemistry researcher from Groningen. A while ago, he and his research group discovered molecules that can reproduce. Start out with a handful, and after a while, you’ve got twice as many. A bit later, there are four times as many, and so on. There are even different kinds of reproducing molecules that compete for building blocks. “That looks exactly like animals competing for food,” Otto thought. Now, he wants to trick molecules into real evolution – you know, the Charles Darwin kind of evolution that all living organisms have been going through for some four billion years. Who knows? His research might one day result in some kind of chemical life form.

It all started with a pot of pretty simple molecules able to couple on two sides. Also, they have a little tail that exactly fits the tail of the other molecules. The idea was that this would help create some structure. And so it did. The molecules hook up and form rings, counting six, seven or eight molecules each. And as the tails fit onto each other, so do the rings. A six-ring fits a six-ring, a seven-ring fits a seven-ring, and so on. Stacks of rings become towers. Towers become long threads. If you stir the pot, the threads will break apart. But each piece will start to grow again – from both ends. Soon, Otto’s pots were teeming with small threads of molecules.

However, in real evolution, species also change when they reproduce every once in a while. A mutation causes a child to be slightly different from its parents. So, Otto’s students started working with several different tails that might sometimes not fit together so well. When the molecules stack, mistakes happen. These errors may cause the thread to grow faster, or to stop growing, or to grow into complicated shapes, or to do something else yet. In fact, Otto doesn’t know, because this is what his students are finding out now. In any case, Otto’s pots are brewing. The question is: when can it be considered life? Otto thinks there is a gray area between “really alive” and “really dead.” But when it waves at us and says, “Hello,” you can be pretty sure it’s alive.

Seven reasons why the new paper fails to shed light on the origin of life and of new species

1. The peptide structures were the product of intelligent design
The Methods section of the paper (by Sandownik, Mattia, Nowak and Otto) describes how the peptide library was prepared: “Peptide building blocks 1 and 2 were synthesized by Cambridge Peptides Ltd from 3,5-bis(tritylthio)benzoic acid, which was prepared via a previously reported procedure…”. Building blocks 1 and 2 consisted of “an aromatic core functionalized with two thiol groups and a peptide chain”. The paper’s authors produced a dynamic combinatorial library from “building blocks that can react with each other through reversible covalent chemistry combine and recombine to give rise to a diverse set of products”.

The paper also states:

“Each building block is equipped with two thiol groups which, when oxidized to disulfides, form macrocyclic species of different ring sizes. The peptide sequence is designed to have alternating hydrophilic and hydrophobic residues to promote self-assembly into parallel β-sheets.”

(The following very brief explanation is intended for the benefit of readers who don’t have a strong background in chemistry. 3,5-Bis(tritylthio)benzoic acid looks like this and has the chemical formula C45H34O2S2. The term “aromatic” may be used to refer informally to any chemicals derived from the hexagonal, ring-shaped hydrocarbon, benzene, although it can also broadly refer to any flat, cyclic molecule that’s highly stable: for instance, the double-ringed bases in RNA and DNA are also described as aromatic. A thiol group is simply an -SH group, where S represents a sulfur atom and H represents a hydrogen atom. A disulfide refers to a functional group with the general structure R–S–S–R: the two sulfur atoms in the middle are bonded to one another, and the two R’s are groups of atoms containing carbon and/or hydrogen. A peptide is a sequence of amino acid molecules which are bonded together in a short chain. Finally, a molecule which is attracted to water is called hydrophilic, while one which is not attracted to water is called hydrophobic.)

An anonymous biochemist whom I contacted has forwarded his comments to me. The following is a brief summary of his remarks:

This is a very well-designed and skillfully performed piece of chemical engineering (based on some very nicely done research), in which peptide building blocks (as distinct from pure natural peptides) were made by a chemist, not via a natural process. Hopwever, its significance in relation to the origin of biological replication is highly questionable.

Additionally:

The description of the study shows how strong the design component was in these experiments. The carefully ordered formation of covalent bonds was guided by the designed structure of the building blocks, and the alternating hydrophobicity and hydrophilicity was designed to promote the formation of higher order structures.

I have to ask: since when does evidence of Intelligent Design count as evidence for unguided evolution?
2. The reactions would never occur under realistic conditions – and if they did, they’d rapidly come to a halt
The biochemist whom I contacted didn’t think that the conditions in the experiment were very realistic, either. He also pointed out that the reactions described in the paper would soon grind to a halt, under natural conditions. The following two paragraphs are intended to convey the gist of his comments.

This experiment is far removed from OOL [origin of life] conditions, where the reactions and structures would occur at random, and where a very large number of “undesirable” reactions would inevitably occur, drastically reducing the chances of obtaining the “correct” reactions under the assumed OOL conditions.

Under natural OOL conditions, a large number of unwanted reactions could (and probably would) occur, in a solution containing a multitude of different chemical components. Instead of obtaining a functioning system with life-like properties, the end result would be chaotic and unpredictable. Additionally, under natural conditions, the chemical reactions could lead to a dead end, and they would probably not be very useful for generating a replication system from nucleic acids. If this kind of self-organization were common in nature, then we could end up with a very large number of competing systems, which would rapidly deplete the chemical raw materials being used to build nucleic acids. In practice, however, hydrolysis and decomposition, as well as the formation of large amounts of “unwanted” chemical products, would seem to be the dominant trends.

Despite these criticisms, the biochemist whom I contacted wished to compliment the authors of the paper, on the quality of their scientific work. He added that it would indeed be possible for intelligent chemists to build systems that were capable of undergoing intelligently guided molecular evolution, as Otto et al. have done, and he expressed his opinion that they had actually generated a very interesting “evolutionary molecular system.”
3. The structures observed could not possibly have been precursors to the first living organisms on Earth
Another reason why the new paper by Sandownik, Mattia, Nowak and Otto fails to shed light on the origin of life on Earth is that the structures which they created are totally unrelated to those found in living things today. Want proof? I would invite readers to have a look at the article, Diversification of self-replicating molecules in Nature Chemistry, and scroll down and click on Figure 1: Library synthesis and the mechanism of self-replication. Have a look at the ring-structures created by the team of researchers. You’ll notice the six-rings and seven-rings described in the Youtube video at the top of this post. That’s what Professor Otto’s team created.

And now have a look at the diagram below, which depicts three possible representations of the three-dimensional structure of the protein triose phosphate isomerase. Hideously complicated, isn’t it? That’s what life is like. I don’t see any nice little rings of six, seven or eight molecules each. Do you?
I have focused on proteins here, because they’re the next step up from polypeptides. A protein consists of one or more long chains of amino acid units (or residues, in chemical jargon). A protein contains at least one long polypeptide. Short polypeptides, containing less than 20-30 amino acid units (or residues), aren’t usually considered by biochemists to be proteins. Instead, they’re just called peptides, or oligopeptides.

Now my point is that if the peptide structures created by Professor Otto and his team don’t look anything like proteins (much less anyother biological molecule found in living things), then we can safely assume that their relevance to the origin of life on Earth is: nil, nada, nothing, zip, zilch. Zero.  
4. There are good reasons to believe that life didn’t begin with a self-replicating molecule
In any case, there are solid scientific reasons for rejecting the idea that life on Earth began with a self-replicating molecule – in which case, the claim by Professor Otto and his team to have created such a molecule is neither here nor there.

The late Professor Robert Shapiro (1935-2011) explained what’s wrong with the replicator-first theory in an interview with Vlad Tarko of Softpedia (Life Did Not Appear with A Self-Replicating Molecule, May 17, 2006):

A scientist proposes an alternative theory to the “replicator” theories of the origin of life – the idea that a self-replicating molecule, such as RNA, has spontaneously appeared and then spread and diversified.

Robert Shapiro from New York University calls such a possibility a “stupendously improbable accident”, although chemists managed to create “prebiotic” syntheses in the lab – syntheses of various building blocks of life such as amino acids. Shapiro says that the use of modern apparatuses and purified reagents is very unlikely to mimic the actual conditions on early Earth.

He says that one of the problems of replicator theories is that a high diversity of molecules of all sorts seems to hamper and endanger the replicator. The mere complexity of the assumed original replicator makes it to be unstable. He argues that what probably happened was the exact opposite – chemical variety was probably beneficial and increased the probability of life. The issue is how this chemical diversity eventually turned into self-replicating chemicals – i.e. life…

The appearance of a molecule that can self-replicate was not the first step, because this requires the combination of diverse chemicals in a long sequence of reactions in a specific order.

Of course, Professor Robert Shapiro’s “metabolism first” theory of the origin of life on Earth faces its own problems, as Leslie Orgel pointed out in an article titled, The Implausibility of Metabolic Cycles on the Prebiotic Earth (PLoS Biology 6(1): e18. doi:10.1371/journal.pbio.0060018 – see here for a non-technical overview by microbiologist Rich Deem). But the point I wish to make is that the “replicator-first” theory espoused by Professor Otto and his team is a very fragile one. It cannot work without just the right sequence of reactions occurring in just the right order, in just the right environment (to ensure that no decomposition occurred, along the way) – in other words, a miracle.
5. The new structures are not alive, in any meaningful sense of the term
Former “Science” editor-in-chief Daniel Koshland Jr. attempted to define “life” in a widely-cited article titled, “Seven pillars of life” (Science 22 March 2002: Vol. 295 no. 5563 pp. 2215-2216, DOI: 10.1126/science.1068489). Koshland listed what he saw as the seven defining features of life:

(1) a program, i.e. “an organized plan that describes both the ingredients themselves and the kinetics of the interactions among ingredients as the living system persists through time” (Koshland, 2002, p. 2215);

(2) improvisation, or a way of changing its master program (achieved on Earth through mutation);

(3) compartmentalization (a surface membrane or skin, and for large organisms, a subdivision into cells, in order to preserve the ingredients required for chemical reactions at their required concentrations);

(4) energy (which on Earth comes from the Sun or the Earth’s internal heat), to keep living systems metabolizing;

(5) regeneration (this includes reproduction), to compensate for the wear and tear on a living system;

(6) behavioral adaptability to environmental hazards; and

(7) seclusion, or some way of preventing one set of chemical reactions from interfering with another, in a cell.

When we look at the peptide structures created by Professor Otto and his team, what do we find? Which conditions are satisfied?

First, the structures lack a master program. Second, lacking a master program, they also lack the ability to modify their master program. Third, the structures possess no internal compartments whatsoever. While they have access to a source of energy (heat), they don’t metabolize, so Koshland’s fourth condition isn’t satisfied, either. (That’s why Professor Otto’s reference to “food” in the press release is misleading.) However, the fifth and sixth conditions are met, in some fashion: the structures can replicate, and they adapt to changes in the availability of different kinds of building blocks. Finally, the structures possess no mechanism for preventing one set of chemical reactions from interfering with another.

Overall Score: 2 out of 7. That’s a pretty long way from what I’d call “life.”

Of course, if you’re intellectually lazy, and you want to define the term “life” to mean anything that can replicate, then don’t let me stop you. But by the same token, many other things would also qualify as alive. As Dr. Steve Wolfram points out in his book, A New Kind of Science (Wolfram Research, 2002, p. 824, it has been known since the 1950s that abstract computational systems possess this capacity as well. Computer viruses would also qualify as alive, on the definition proposed, and there are mechanical devices (such as the “RepRap” machine shown below) that can make copies of themselves, too. How many readers would want to call these devices “alive”?
6. The term “mutant” is an inappropriate way of describing the variants that arose
In their press release, Professor Otto and his team use the term “mutant” to refer to a replicating molecule which is slightly different from the original version, because it tends to specialize in different building blocks, when assembling itself. However, as we have seen from Daniel Koshland’s article, “The Seven Pillars of Life“, which I cited above, the word “mutation” properly refers to an organism’s ability to change its master program. Since the structures described in the University of Groningen press release don’t possess anything analogous to a master program, or a genetic code, it follows that they can’t properly be said to mutate.
7. The processes observed in the lab shed no light on speciation, whatsoever
Finally, the processes described in the press release by Professor Otto and his team have absolutely nothing to do with speciation in living things. How can I be so sure of that? There are two things that give the game away.

The first is a very damaging admission in the last paragraph of the press release:

The next step is to introduce death. This can be done by feeding the system a constant flow of building blocks, while draining the contents of the reaction vessel. Replicators can only survive in this system when their growth rate exceeds the removal rate. ‘We could then seed such a system with one set of replicator mutants, and then change the environment, for example by adding another solvent. This would change the fitness of the various replicator mutants and shift the population of mutants towards those that are best at replicating in the new environment.’ The result would be a form of natural selection that Darwin would recognize. ‘We’re not the only ones to be really excited about these experiments – the evolutionary biologist I’ve consulted is too.’

Stop right there. The structures created by Professor Otto and his team don’t die. Consequently, they don’t undergo natural selection. The term, “survival of the fittest,” simply doesn’t apply to them, because they don’t even possess the property of “fitness.”

Without natural selection, speciation which results from a population becoming reproductively isolated from a founder population as it enters and colonizes a new niche, would never get off the ground. Such a model assumes that the new population becomes “fitter,” in relation to its new environment, over the course of time – which means that natural selection has to occur. But as we’ve seen, Professor Otto and his team haven’t achieved natural selection yet. Their excitement is, to say the very least, premature.

The other give-away is that the press release makes no mention whatsoever of a genetic code. And without a genetic code, there can be no genes – and hence, no genetic drift. That rules out other mechanisms of speciation, which rely on the occurrence of genetic drift in a population, in order to achieve reproductive isolation.

No natural selection, no genetic drift: no speciation. Of course, there are also species which are created through hybridization, but that presupposes the existence of genes and sexual reproduction – neither of which are found in the peptide structures created by Professor Otto and his team.

I conclude that the January 4 press release by the University of Groningen on the research conducted by Professor Otto and his team has very little relevance for the origin of life on Earth via an unguided process, much less the origin of living species.

Toward a theory of Devolution V

Darwin Devolves: Another Huge Advance Against Darwinism and for Intelligent Design
Tom Gilson

Michael Behe, professor of biochemistry at Lehigh University, has been keeping committed Darwinists awake nights for years. His 1996 book Darwin’s Black Box: The Biochemical Challenge to Evolution asked a long-ignored question: If Darwin’s theory explains everything so well, why hasn’t anyone shown how it works at the minutest level, biochemistry? If it doesn’t work there, it doesn’t work anywhere.

Now Behe has released a new book, based on new science, showing once again that it doesn’t work there. Darwin Devolves: The New Science About DNA That Challenges Evolution is going to cause a lot more sleepless nights.

     The new science he covers in this book shows that Darwin’s theory can explain some changes, but quickly breaks down. DNA sequencing has only been available in the past decade or two. Its findings show that when organisms change, they do it almost always by breaking genes, not by making new ones. So in general, the evidence shows that when species evolve, they’re really devolving. And that devolution prevents future evolution.

Evolution (Unguided) Breaks Things

Behe defines his terms carefully. Evolution, in particular, means many different things. On one level, it simply says things change over time. No controversy there. On another level, it’s a theory of common descent, saying that all organisms came by something like a branching tree from one common ancestor. But classic evolutionary theory also claims that this common descent, and all the adaptations of life, happened by an unguided process: natural selection sifting random variations. This, Behe says, flatly conflicts with the evidence.

Past critics of his work, including his 2008 work The Edge of Evolution: The Search for the Limits of Darwinism, have assailed it as “religiously motivated.” Behe certainly defends intelligent design, the theory that much if not all of nature is best explained as the product of a purposeful Mind. He didn’t go there, though, until he read an early work on evolution by Michael Denton. That led him to realize he’d never asked evolution the hard questions.

Now with new findings from genetics, the questions are harder than ever. Experiments show that even adaptive changes — changes that seem like improvements — almost always come by way of breaking genes. In a recent podcast, Behe likened it to a car for which gas mileage suddenly became its most important feature. (Full disclosure: I work with Discovery Institute in helping produce the ID the Future podcast.) The mileage problem is easy for a car, actually. Just remove some of its seats. In organisms this principle works, for example, when a gene that’s been holding back an existing capability gets damaged. That capability then shows up. It’s not a new capability, just newly expressed

Breaking Things Is Easier

It makes sense, really. It’s a whole lot easier to break a thing than it is to make one. Ask the poor nursery owner who thought I could help him one summer removing an old building and building a new one. I lasted there as long as the job was only about tearing things down.

Not only that, but once nature finds a way to improve a function by degrading a gene, nature is happy with that. It will spread that new answer throughout a population just as fast as Darwin ever supposed. That’s what natural selection does: It preserves helpful (adaptive) changes and spreads them around while letting less lucky populations die off. Once nature is happy with one quick answer produced by breaking things, though, it’s not going to hang around waiting for another, more elaborate answer produced by making things.

Misdirected and Unsupported Criticism

I’m oversimplifying, obviously, trying to summarize in a few words what Behe details over some 300 highly readable pages. I’m sure critics will find things not to like about my summary. And why not? Darwin’s Black Box was vilified, even by Behe’s colleagues at Lehigh. Yet as he has shown in an appendix to Darwin Devolves and elsewhere, no one has ever refuted its arguments. Not even close.

The most emphatic reactions come from critics who can’t stomach the idea that God had anything to do with life’s origin and development. Behe quotes philosopher John Searle as saying the whole idea of a greater mind behind nature “does not fit in and seems intellectually repulsive.” Which is a lot like saying, “I don’t like the taste of it, therefore it isn’t science.” (See the book’s website for discussion of criticisms and responses.)

This book is built on solid science. It’s going to be harder than ever for critics to spit it out just because they don’t like its taste. It will also be hard for critics to ignore the conclusion Behe reaches in his final chapter. Materialists, those who deny the larger reality of mind, typically end up denying even the human reality of mind. The world only makes sense if we see it as the product of a great, purposeful, highly intelligent designing Mind.

Atheism of the gaps?

Averick Takes on the “God of the Gaps” Objection
Evolution News | @DiscoveryCSC

On a new episode of ID the Future, Rabbi Moshe Averick, author of Nonsense of a High Order: The Confused World of Modern Atheism,responds to the objection that intelligent design is a feeble “God of the Gaps” approach, an argument from ignorance. Provocative and entertaining, Averick describes the attack as “less than feeble.” He says it isn’t because of what we don’t know, but because of what we do know.

Download the podcast or listen to it here.

He offers as an illustration the widespread skepticism in the physics community toward the possibility of anyone ever building a perpetual motion machine. Their skepticism is not driven by ignorance of how to build such a machine, Averick notes. It’s driven by their knowledge of the fundamental laws of physics.

Primate phylogeneticists out of their tree?

Primate Phylogenetics Researchers Swinging from Tree to Tree
Casey Luskin

A recent article on ScienceDaily, titled "A New Evolutionary History of Primates," claims that by combining genetic data from 54 genes (totalling 34,927 base pairs) from a variety of primates, researchers have created "[a] robust new phylogenetic tree" which "resolves many long-standing issues in primate taxonomy." That sounds great--until you read the fine print. The paper used dozens of genes or "large-scale sequencing" to create the phylogeny--a method which is designed to smooth over conflicts between trees based upon individual genes. This method fails to test whether individual genes paint a consistent picture of common descent. Moreover, even after using this method, not everything about the tree is neat and tidy. Even when using many genes to construct the tree, the paper reports there were a variety of potential sub-trees which conflicted with one another:

However, greater frequency of phylogenetic inconsistencies or unresolved nodes occur in these subset trees, compared with the entire concatenated data set.

(Perelman et al., "A Molecular Phylogeny of Living Primates," PLoS Genetics, Vol. 7(3):e1001342 (March, 2011) (internal figure citations removed).)

Indeed, such phylogenetic inconsistencies between different phylogenetic trees are not uncommon at all, particularly in important parts of the purported primate tree. While this paper used methods that smoothed over conflicts between trees, another recent paper found primate phylogenetic data that pointed in opposite directions. A recent article on ScienceDaily, titled "Genetic Archaeology Finds Parts of Human Genome More Closely Related to Orangutans Than Chimps," stated:

In a study published online in Genome Research, in coordination with the publication of the orangutan genome sequence, scientists have presented the surprising finding that although orangutans and humans are more distantly related, some regions of our genomes are more alike than those of our closest living relative, the chimpanzee.
Of course this finding is "surprising" because it contradicts the phylogeny preferred by most evolutionists. The ScienceDaily article noted: "[I]n about 0.5% of our genome, we are closer related to orangutans than we are to chimpanzees ... and in about 0.5%, chimpanzees are closer related to orangutans than us," and the paper cited concluded:

Our analyses find that for ~0.8% of our genome, humans are more closely related to orangutans than to chimpanzees.

(Asger Hobolth et al., "Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection," Genome Research, Vol. 21:349-356 (2011).)

Since humans are typically said to be most closely related to chimps, this data conflicts with the standard supposed tree. As discussed here, the basic problem is that one gene (or portion of the genome) gives you one version of the tree, while another gene (or portion of the genome) gives you a very different version of the tree. This leads to discrepancies between molecule-based trees, wherein DNA data fails to provide a consistent picture of common ancestry. (We've discussed a number of such examples lately, such as here, here, and here. Jonathan M. also cites some discordant data pertaining to human/chimp phylogenetics here.)

0.8% of our genome might not sound like a lot, but that equates to over 20 million base pairs. That's means that over 500 times more raw genetic information than was used in the PLoS Genetics paper (to purportedly create a "robust new phylogenetic tree") is supposedly pointing in the wrong phylogenetic direction. Perelman et al.'s paper in PLoS Genetics could only find a "robust new phylogenetic tree" after using methods that are designed to avoid this problem and ignore conflicts between trees. That might sound good, but their methods are wholly assuming, rather than testing, common descent.

That brings us to the final point of this discussion. In the end, molecular trees are based upon the sheer assumption that the degree of genetic similarity reflects the degree of evolutionary relatedness. One paper makes this assumption explicit:

molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the 'molecular assumption.' ... For historians and philosophers of science the questions that arise are how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central ...

(Jeffrey H. Schwartz, Bruno Maresca, "Do Molecular Clocks Run at All? A Critique of Molecular Systematics," Biological Theory, Vol. 1(4):357-371, (2006).)

Clearly this assumption fails when different genes paint contradictory pictures of evolutionary relationships. But are there other mechanisms that can explain DNA similarities besides inheritance from a common ancestor? As explained here, one equally good explanation for the reason that genetic similarity is continuously being found in places both predicted, and unpredicted, by common descent, could be common design.

The Watchtower Society's commentary on the coming day of Jehovah.

The Day of Jehovah—A Vital Theme:
“THE great day of Jehovah is near. It is near, and there is a hurrying of it very much.” (Zephaniah 1:14) God’s prophets time and again warned of the approaching day of Jehovah. Usually, they pointed out how its coming should affect people’s daily life, their morals, and their conduct. Urgency was always attached to their proclamations. If you had heard these messages with your own ears, how would you have reacted?

2 In reading the 12 prophets, you will find that they all, directly or indirectly, spoke of the day of Jehovah.* Thus, before considering in the following chapters the valuable information that these prophets delivered, think of the recurring theme: the day of Jehovah. Six of the prophets directly used that expression or similar terms. Joel graphically described “the great and fear-inspiring day of Jehovah.” (Joel 1:15; 2:1, 2, 30-32) Amos told the Israelites to get ready to meet their God, for the day of Jehovah would be one of darkness. (Amos 4:12; 5:18) Later, Zephaniah spoke the words quoted in paragraph 1. And near the time of the destruction of Jerusalem, Obadiah warned: “The day of Jehovah against all the nations is near.”—Obadiah 15.3 You will also see that two prophets who were sent to the Jews after their return from exile used similar expressions. Zechariah told of the day when all nations coming against Jerusalem would be annihilated. He described vividly what would take place on “one day that is known as belonging to Jehovah.” (Zechariah 12:9; 14:7, 12-15) And Malachi alerted God’s people to the coming of “the great and fear-inspiring day of Jehovah.”—Malachi 4:1-5.4 Though not using the expression “the day of Jehovah,” the others of the 12 alluded to that day. Hosea talked of Jehovah’s settling accounts with Israel and later with Judah. (Hosea 8:13, 14; 9:9; 12:2) These messages often related to what Jehovah did back in those days. For example, Jonah proclaimed God’s judgment on Nineveh, and Micah described what would happen when God acted against rebellious peoples. (Jonah 3:4; Micah 1:2-5) Nahum promised that Jehovah would take vengeance on His adversaries. (Nahum 1:2, 3) Habakkuk cried out for justice and described “the day of distress.” (Habakkuk 1:1-4, 7; 3:16) Some messages in these books definitely pointed to developments that would involve true Christians. For instance, Haggai, one of the postexilic prophets, foretold the rocking of the nations. (Haggai 2:6, 7) The apostle Paul quoted from the words of Haggai 2:6 to urge Christians to be in a fit condition when God removes the symbolic wicked heaven.—Hebrews 12:25-29; Revelation 21:1.
THE DAY OF JEHOVAH—WHAT IS IT?
5 You have good reason to wonder what the day of Jehovah will be like. You may ask, ‘Does the day of Jehovah have any bearing on how I live now and on my future?’ As the prophets indicated, the day of Jehovah is a period when Jehovah acts against his enemies to execute judgment, a day of battle. That fear-inspiring day will likely be a day of celestial phenomena. “Sun and moon themselves will certainly become dark, and the very stars will actually withdraw their brightness.” (Joel 2:2, 11, 30, 31; 3:15; Amos 5:18; 8:9) What will happen on the earth, where we live? Micah stated: “The mountains must melt under [Jehovah], and the low plains themselves will split apart, like wax because of the fire, like waters being poured down a steep place.” (Micah 1:4) This description may be figurative, but we can conclude from it that God’s acts will bring disastrous effects on the earth and its inhabitants. Not on all humans, though. The same prophets pointed to abundant blessings for those who “search for what is good” and thus keep living.—Amos 5:14; Joel 3:17, 18; Micah 4:3, 4.

6 Others of the 12 prophets painted more graphic pictures of the day of Jehovah. Habakkuk vividly portrayed how Jehovah will smash “the eternal mountains” and bring low “the indefinitely lasting hills,” fitting representations of human organizations, which might seem enduring. (Habakkuk 3:6-12) Yes, the day of Jehovah “is a day of fury, a day of distress and of anguish, a day of storm and of desolation, a day of darkness and of gloominess, a day of clouds and of thick gloom.”—Zephaniah 1:14-17.
7 Imagine what a scourge will come upon those fighting against God! “There will be a rotting away of one’s flesh, while one is standing upon one’s feet; and one’s very eyes will rot away in their sockets, and one’s very tongue will rot away in one’s mouth.” (Zechariah 14:12) Whether this vision will be fulfilled literally or not, you can tell that it portends tragedy for many. At the very least, the tongues of God’s enemies will rot in the sense that their defiant speech will be silenced. And any vision of taking unified action against God’s people will be blurred.
WHY A GOD OF LOVE ACTS
8 You may have heard people ask: ‘How can a loving God bring such a disaster upon his enemies? Does God have to wreak havoc on the earth? Did not Jesus urge continuing to love even enemies and thus proving to be sons of the Father in the heavens?’ (Matthew 5:44, 45) In response, you might direct attention to the very beginning of mankind’s troubles. God created the first human couple in his image and likeness—they were perfect. Yet, they introduced sin and death into the human family and thus into our life. They took sides with Satan the Devil on the issue of who has the supreme right to rule mankind. (Genesis 1:26; 3:1-19) Over the centuries, Satan has tried to prove that if humans are given an incentive to do otherwise, they will not serve Jehovah. You know that Satan has failed. Jesus Christ and many other servants of Jehovah have kept integrity to God and have shown that they serve him out of love. (Hebrews 12:1-3) Can you not think of many by name who are thus serving God loyally?

9 Moreover, you are involved in this issue that will end in Jehovah’s eliminating wickedness. For example, as you read these 12 books, you will note that some of the prophets drew attention to the luxurious lifestyle of people who were neglecting the worship of Jehovah. The prophets admonished God’s people to ‘set their heart upon their ways’ and to transform their lives. (Haggai 1:2-5; 2:15, 18; Amos 3:14, 15; 5:4-6) Yes, the prophets were showing the people how to live. Those who accepted that exhortation showed that Jehovah is their Sovereign, thereby proving Satan a liar. Jehovah will prove loyal to such ones when he annihilates his enemies.—2 Samuel 22:26.10 There is another reason for God to act. Turn your attention back to the eighth century B.C.E. when Micah prophesied in Judah. Speaking as if he were the nation, he likens the situation to a vineyard or an orchard after the harvest, with no leftover grapes or figs. That was how it was in Judaean society, where upright ones could hardly be found. Israelites were hunting their fellow citizens, lying in wait to shed blood. Their leaders and judges were out for selfish gain. (Micah 7:1-4) If you lived in that kind of situation, how would you feel? Likely, you would feel compassion for the innocent victims. Thus, how much more Jehovah feels for the oppressed! Today Jehovah scrutinizes mankind. What do you think he finds? Oppressors are viciously taking advantage of others and violently attacking their neighbors. As for loyal ones, they are relatively few compared with the world population. But we need not despair. Out of love for the victims, Jehovah will render justice.—Ezekiel 9:4-7.
  11 Clearly, Jehovah’s day means destruction for his enemies and deliverance for those who fear and serve him.* Micah foretold that nations would stream to the mountain of Jehovah’s house, resulting in worldwide peace and unity. (Micah 4:1-4) Back in that time, did the fact that the prophets were proclaiming the day of Jehovah make any difference in people’s lives? For some, it did. Recall that when Jonah proclaimed a judgment against Nineveh, the violent, wicked inhabitants of that city “began to put faith in God” and “turned back from their bad way.” As a result, Jehovah refrained from causing calamity then. (Jonah 3:5, 10) The message about the impending day of Jehovah’s judgment did affect the lives of the Ninevites!
 HOW DOES THAT DAY AFFECT YOU?
12 ‘But those prophets lived centuries ago,’ someone might object. ‘What do their messages about Jehovah’s day have to do with me?’ Granted, those prophets lived many years even before Jesus’ birth, yet we should consider how their words about Jehovah’s day are relevant in the 21st century. What practical benefits can we derive from what they said about Jehovah’s great day? There is a key to seeing the relevance and benefiting from their message. It is our recognizing that the prophets warned of Jehovah’s day against Israel, Judah, surrounding nations, and certain world powers of the day.* The point is that such prophecies were fulfilled! The Assyrians did invade Samaria, Judah was desolated in 607 B.C.E., and the surrounding hostile nations were soon devastated. Eventually, the Assyrian and Babylonian world powers fell, all in fulfillment of specific prophecies.
13 Now turn your thoughts to the day of Pentecost 33 C.E., long after many of those prophecies saw their first fulfillments. On that day, the apostle Peter applied Joel’s prophecy to the pouring out of God’s holy spirit. Then Peter quoted from the book of Joel: “The sun will be turned into darkness and the moon into blood before the great and illustrious day of Jehovah arrives.” (Acts 2:20) This shows that there would be still further fulfillments of the prophecies about the day of Jehovah. As for Joel’s prophecy, it had a second fulfillment in 70 C.E. when the Roman army destroyed Jerusalem, certainly a time of darkness and blood.
  14 However, Joel’s prophecy and other prophecies about the day of Jehovah are yet to have a final fulfillment, which applies to us living in the 21st century. How so? Peter admonished Christians to keep “close in mind the presence of the day of Jehovah.” The apostle went on to say: “There are new heavens and a new earth that we are awaiting according to his promise, and in these righteousness is to dwell.” (2 Peter 3:12, 13) No new heavens (a new theocratic government) with a new earth (a society of righteous people under that government) was established right after the destruction of Jerusalem in 70 C.E. So the prophetic words about the day of Jehovah must have another fulfillment. Yes, these prophecies concern us today, who are living in “critical times”!—2 Timothy 3:1.

15 The combined description of Jehovah’s day as presented in these 12 Bible books makes us think of Jesus Christ’s words: “There will be great tribulation such as has not occurred since the world’s beginning until now, no, nor will occur again.” He said that “immediately after” the beginning of that great tribulation, “the sun will be darkened, and the moon will not give its light, and the stars will fall from heaven, and the powers of the heavens will be shaken.” (Matthew 24:21, 29) This helps us to pinpoint the timing of the day of Jehovah. It is just ahead. The Scriptures indicate that the great tribulation will destroy “Babylon the Great,” the world empire of false religion. Then, as the climax of the great tribulation, Jehovah’s day will wipe God’s enemies off the face of the earth.—Revelation 17:5, 12-18; 19:11-21.16 Jehovah’s Witnesses have discerned the nature of fulfillments of prophecies about Jehovah’s day. Often and in various ways, apostate Jerusalem, renegade Samaria, the hostile Edomites, the violent Assyrians, and the Babylonians prefigured aspects of false religion. All such religion will be destroyed in the initial phase of the great tribulation. In the following “great and fear-inspiring day of Jehovah,” her political and commercial lovers will meet their end.—Joel 2:31.
 17 Because the judgment messages apply mainly to false religion, some Christians might feel that they will not be affected by the fulfillment of these prophecies. However, what Amos told the Israelites has practical value to all: “Woe to those who are craving the day of Jehovah!” Some Israelites in Amos’ day thought that Jehovah’s day would mean only blessings for them, believing that it would be the day when God acts for his people. They even craved that day! To self-conceited ones, though, the day of Jehovah would “be darkness, and no light,” Amos continued. Yes, those Israelites were on the receiving end of Jehovah’s wrath!—Amos 5:18.

18 Amos then described what would happen to those who were craving the day of Jehovah. Think of a man who flees from a lion and ends up meeting a bear. Running away from the bear, he takes refuge in a house. Panting for breath, he closes the door behind him and leans on the wall, only to be bitten by a snake. In a way, that is the destiny of the ones who are not really ready for the day of Jehovah.—Amos 5:19.
19 Do you see the practical value this account might have for you? Recall that Amos was directing his words to people who were in a dedicated relationship with God. Still, there were things about their actions and attitudes that needed adjustment. Is it not worthwhile to examine your life to see whether you are proving yourself ready for that vital day or whether some adjustments are in order? How can you prove that you really are ready? Obviously, it is not by building a shelter, storing basic food items, learning how to purify water, or stockpiling gold coins, as some survivalists have done. “Neither their silver nor their gold will be able to deliver them in the day of Jehovah’s fury,” says Zephaniah. So being ready would not depend on the storing up of material items. (Zephaniah 1:18; Proverbs 11:4; Ezekiel 7:19) Rather, we have to be alert spiritually and live day by day as ones who are ready. We need the right attitude—and actions to match. Micah said: “As for me, it is for Jehovah that I shall keep on the lookout. I will show a waiting attitude for the God of my salvation.”—Micah 7:7.
  20 If you have this waiting attitude, you will give evidence that you are ready, on the lookout for the day of Jehovah. You will not be concerned about the date on which that day may come or how long you have waited for it. All the prophecies regarding that day will be fulfilled in Jehovah’s due time and will not be delayed. Jehovah told Habakkuk: “The vision is yet for the appointed time, and it keeps panting on to the end, and it will not tell a lie. Even if it should delay [from a human standpoint], keep in expectation of it; for it will without fail come true. It will not be late [from Jehovah’s viewpoint].”—Habakkuk 2:3.
 21 In this book, you will learn how you can show a waiting attitude for the God of salvation. What benefits can you expect? Well, the focus will be on a part of the Bible that may be somewhat unfamiliar to you—the 12 so-called Minor Prophets. Hence, there will be stimulating insights. For example, in Section 2, you will consider how to “search for Jehovah” and keep living. (Amos 5:4, 6) Based on these 12 books, you might discern how to get to know Jehovah better and sharpen your view of serving him, even in expanded ways. With help from these prophets, you will doubtless deepen your understanding of his personality. In Section 3, you will see more clearly what Jehovah expects of you in your dealings with your family members and others. That can help you to be ready for his great day. Finally, in Section 4, you will look into the prophets’ advice on what your attitude should be as Jehovah’s day draws nearer, learning, too, how your Christian ministry may be impacted. No doubt, you will be thrilled as you consider the prophets’ message about what your future can be like.
22 Do you recall the urgent words of Zephaniah quoted at the outset of this chapter? (Zephaniah 1:14) His message affected the life of young King Josiah. When he was but 16 years of age, Josiah started to seek Jehovah. When he turned 20, he set out on a campaign against idol worship, in line with Zephaniah’s encouragement to the people of Judah and Jerusalem. (2 Chronicles 34:1-8; Zephaniah 1:3-6) Has the warning about the day of Jehovah touched your daily life as much as it did Josiah’s?