To save the planet:Who you gonna call?

Darwinsplainin'? II

Insect Evolution: Another Illustration of How Darwinism “Explains Away”
David Klinghoffer | @d_klinghoffer

As Evolution News put it concisely the other day, “Where Design Explains, Darwinism Explains Away.” An illustration from paleontologist Günter Bechly: the evolution of insects, which he describes in a fascinating new ID the Future episode with host Andrew McDiarmid.

Download the podcast or listen to it here.

Dr. Bechly notes three contradictions at odds with Darwinian gradualism: Insects pop into existence at one blow, as do insect wings, as does the phenomenon of metamorphosis. None of these is led up to by the expected gradual evolutionary process. As with the Cambrian explosion, Darwinians have theories to explain away the problems.

Meanwhile the completeness of the fossil record grows more evident, and so the reliance on theories and excuses grows with it. But only a design inference explains such abrupt transitions. That’s how new ideas, in our own daily experience, get instantiated in physical reality — abruptly.

Iconoclast v. gatekeeper?

Bullet Points for Jerry Coyne
Michael Behe

As noted here earlier, University of Chicago evolutionary biologist Jerry Coyne reviewed Darwin Devolves for this past Sunday’s  Washington Post.  As you might expect, it’s written in the venerable style of Richard Dawkins’s review of The Edge of Evolution for the New York Times back in 2007: long on sneering, smearing, and assertion; short to nonexistent on telling readers what the book’s actual arguments are. Alas, Coyne’s piece has too little intellectual content to sustain any real engagement. So I’ll simply proceed from its beginning to its end, with lines from his review in bullet points and italics. My comments follow directly after each. 

“intelligent design” arose after opponents of evolution repeatedly failed on First Amendment grounds to get Bible-based creationism taught in the public schools. … : intelligent design, which scientists have dubbed “creationism in a cheap tuxedo.”

Good idea — let’s link the author to a scorned group right at the start and smear his motives.

Milk that Epithet

Behe does not rely on the Bible as a science textbook. Rather, he admits that evolution occurs by natural selection sifting new mutations and that all species are related via common ancestors.

But we’ll call him a “creationist” anyway, to milk that epithet for all it’s worth.

Scientists … pointed out numerous scenarios in which a system fitting Behe’s definition of “irreducible complexity” could evolve in a step-by-step manner (one is the hormone pathway studied by my Chicago colleague Joe Thornton).

I showed in the Appendix that no evidence beyond handwaving has been published since Darwin’s Black Box. Again, not even a mention by Coyne that I dispute his claim.

Jerry Coyne, Theologian

these systems … embody an absurd, Rube Goldberg-like complexity that makes no sense as the handiwork of an engineer but makes perfect sense as a product of a long and unguided historical process.

Wow, the great theologian Jerry Coyne has determined that God wouldn’t have done it that way — no need for actual evidence that Darwin’s mechanism can do the job. We all anxiously await the unveiling of Coyne’s superior designs for a clotting cascade and a flagellum.

Behe’s rationale for designed mutations is circular. He claims that biochemical pathways are designed rather than evolved because they’re based on the “purposeful arrangement of parts.” But which arrangements are those designed with a purpose? They’re simply the pathways that Behe sees as too complex to have evolved.

    So Coyne can’t think of a purpose for an eye? Or for the leg gears of the planthopper? Or for the supercharged flagellum of the magnetotatic bacterium MO-1? That’s funny — the authors of the science papers on those systems that I cite in the book seem to have had no trouble identifying their purpose.

Perhaps Behe’s most ludicrous claim is this: Evolution within the lowest levels of biological classification — genera and species — might be purely Darwinian, but the origin of higher level groups — families, orders and so on — requires designed mutations. Yet as every biologist knows, groupings above the level of species are purely subjective.

                 Can Coyne tell the difference between a plant and an animal? Between a bird and a fish? A cat and a dog? Sure, as I discuss in the book, a classification system is a human invention and so it inevitably has uncertainties, ambiguities, and mistakes. But implying that biological classification reflects nothing real is disingenuous at best.

                     Behe selectively gives a handful of examples in which mutations have produced broken genes that are nevertheless useful, but he simply ignores the large number of adaptive mutations that do not inactivate genes. These include duplications, in which a gene is accidentally copied twice, with the copies diverging in useful ways (this is how primates acquired our three-color vision, as well as different forms of hemoglobin).

                          

I wrote a section in Chapter 8 titled “Evolution by Gene Duplication Revisited” in which I explain why duplication and diversification by Darwinian processes may account for some things but not for others. I specifically explain why I changed my mind about sophisticated hemoglobin, which would require much more modification starting from a simple myoglobin-like gene than would mere duplication of opsin (color-vision) genes. Coyne doesn’t even let readers know I discuss it.

Separating What from How

Behe also argues that evolution is self-limiting because natural selection “adjust[s] a biological system to its current function” and thus “works to block the system from taking up a significantly different function.” But … Think of how feathers, which probably evolved to conserve body heat in dinosaurs, opened up the possibility of flight — leading to all the diverse birds on Earth.

              It never ceases to amaze me that Darwinists like Coyne are unable to separate the question of what happened from the question of how it happened. Okay, flightless dinosaurs had feathers and birds can now fly. So what exactly is the evidence that it happened by a Darwinian process? What is the evidence that a Darwinian process could even, say, differentiate owls and crows from a common ancestor? I argue at length in the book that unintelligent processes aren’t remotely up to those tasks. Without any substantive counter-argument, Coyne simply responds like a kid on a playground: “Yes they can too do that!”

A Terrible Thing to Waste

Like his creationist kin, Behe devotes his time not to giving evidence for intelligent design but to attacking evolutionary biology.

Gee, Coyne must have missed Chapter 10 in Darwin Devolves, “A Terrible Thing to Waste,” as well as Chapters 8 and 9 in Darwin’s Black Box (“Intelligent Design” and “Questions About Design”) and Chapter 11 in The Edge of Evolution (“All the World’s a Stage”). I explain at length in those chapters and elsewhere that the work of a mind — design — is evinced precisely by the purposeful arrangement of parts, such as is found in abundance in life. For pretty much the entirety of recorded history until Darwin almost everyone thought life was designed exactly for that reason — the arrangement of parts for a purpose — as I discuss in the Preface to the book. Contrary to Coyne, it is Darwin’s audacious assertion — that complex interactive functional structures could be produced by random variation and natural selection — that has gone unsupported by pertinent evidence. Coyne’s unwillingness or inability to grasp the argument for design does not mean the argument hasn’t been made.

Since humans are placed in the same family as other great apes (Hominidae), Behe’s theory predicts that we arose without a designer’s intervention. But here he backpedals, asserting that there are “excellent reasons to suspect those differences [between humans and other apes] are well beyond Darwinian processes.” Sadly, he doesn’t give these reasons, but I’d guess they stem from the Christian belief that Homo sapiens is a special creation of God.

Actually, they stem from our personal awareness that we can reason, speak, think abstractly, and so on — in other words, that we have minds — which arguably is the most profound attribute in the world. By the way, I also wrote in the book that there are good reasons to doubt that giraffes could arise from a shorter-necked relative like the okapi, even though they are in the same biological family. For some reason Coyne doesn’t ascribe my skepticism there to Christian belief.

A Horrible Threat

In 1998, the Discovery Institute drafted the “Wedge Document,” a secret plan (leaked in 1999) to spread Christianity in America by teaching intelligent design and fighting materialism. … Well, now it’s 20 years on, and despite the efforts of Behe and other neo-creationists, intelligent design has been discredited as science and outed as disguised religion.

Yes, the horrible threat of a group trying to persuade people of its ideas by writing books and articles has so far been countered by brave folks like Jerry Coyne, who use the kind of overwhelming evidence and impeccable logic showcased in his book review.

Coyne is quite the prominent evolutionary biologist, and has been antagonistic to intelligent design arguments for decades. If Darwin’s theory were actually the powerful idea it’s claimed to be, Coyne should have been able to counter design easily, simply by summarizing its arguments and showing how Darwin deals with them. Yet he can’t even bring himself to mention what those arguments are. Instead he tries to whip up hysteria against a book that argues for what most people already believe. That speaks volumes about the actual strength of Darwin’s theory.

The Future's so bright?

The future's So bright? II

File under "well said." LXI

“Science without religion is lame, religion without science is blind.” The lame and the blind excepted, who could object?” 
― David Berlinski, The Devil's Delusion: Atheism and its Scientific Pretensions.

In Russia:A ray of light re: religious liberty?

Court Overturns Sentence Against Brother Akopyan in Russia

On March 1, 2019, the Supreme Court of the Republic of Kabardino-Balkaria overturned a lower court’s conviction of Brother Arkadya Akopyan. He had been on trial for over a year, wrongfully accused of distributing “extremist” literature and ‘inciting religious hatred.’

Previously, a lower court sentenced 70-year-old Brother Akopyan to perform community service. This recent Supreme Court ruling dismissed the lower court’s sentence.

We thank Jehovah for this victory as we rejoice with Brother Akopyan. We continue to pray that our brothers will faithfully endure.—2 Thessalonians 1:4.

Chance:King of the new gods?

Crying “Chance, Chance” When There Is No Chance
Evolution News | @DiscoveryCSC

“Biology is the study of complex things that appear to have been designed for a purpose,” Richard Dawkins famously asserted. But if design is only apparent and not real, what else is there to create the appearance of design? Natural law might be the answer, but if nobody is guiding that, the results are still matters of chance. 

No Power of Agency

When it comes to biology, life as we know it involves more than just repetitive patterns wrought by natural law, beautiful as they might be. It involves operations based on coded instructions. During the origin of life, before there were coded instructions able to accurately replicate, sequences were purely matters of chance, even if molecules interacted by natural law. Nothing about natural law will sequentially organize building blocks with semantic information and syntax, and then translate that coded information into another code with the power to cause functional information. Natural law doesn’t care about trying to do that. It has no power of agency in the materialist conception.

 “Random mutation” might be the answer, but that is pure chance embedded in a fancy phrase. In short, they can only invoke chance for sequential information, and they can only invoke chance for random mutations. Chance plus chance equals chance. And yet life does appear designed for a purpose. Everyone acknowledges that. The only way out of this dilemma is to believe in fake chance: random processes mystically imbued with agency. Evolutionists imagine a personified chance wanting to evolve upward in complexity. Or they can invoke the post-hoc fallacy, saying, “We’re here, therefore we evolved.” This absolves them of having to explain how chance could create a coded information system. Any gambler watching  Illustra’s film clip from Origin on the improbability of a single protein self-organizing would agree, “Not a chance!” In Darwinland, the vast improbabilities are swept away by philosophical bias. They cry “Chance, chance,” but there is no chance. There is only fake chance, endowed with purpose and choice.

Demon Lingo

To see how this is done, consider a book review by Timo Hannay in Nature, where he comments on Paul Davies’s recent book, The Demon in the Machine: How Hidden Webs of Information Are Finally Solving the Mystery of Life (Allen Lane, 2019). Hannay’s review, titled “Maxwell’s Demon and the Hunt for Alien Life,” echoes the demon lingo. It sounds like agency, but we know neither writer is talking about real mind-directed design. How will they imbue chance with agency in this case?

Hannay is mostly kind to Davies, though we know that the book’s author often thinks outside the box. Hannay is glad that Davies is “certainly no believer in a vital force distinct from physics or chemistry” (emphasis added), but he worries that Davies tiptoes at the edges of real design, not just apparent design. 

Davies claims that life’s defining characteristics are better understood in terms of information. This is not as absurd as it may seem. Energy is abstract, yet we have little trouble accepting it as a causal factor. Indeed, energy and information are closely related through entropy.

    

Turning Chance into an Agent

Information “is not as absurd as it may seem,” he says. That’s an interesting way to put it, given that intelligent design theory relies substantially on the concept of information. ID proponents do not compare information to raw, unguided energy, though. Information is superior, because it can commandeer energy. It can take energy and force material to decrease entropy by organizing it in ways natural law alone would never do (i.e., natural law cannot arrange building blocks with sufficiently improbable complex specified information). But can unguided chance use energy to do it? Watch how both writers make chance into an agent:

Davies explains this connection by referring to Maxwell’s demon. Victorian physicist James Clerk Maxwell’s celebrated thought experiment features a hypothetical miniature beast perching at an aperture between two containers of gas, where it allows only certain molecules to pass, depending on their kinetic energy. The demon can thus create a temperature gradient between the containers: a reduction in overall entropy, apparently breaking the second law of thermodynamics. The resolution to this paradox seems to lie in the fact that the demon must gather information about the properties of each molecule, and for this it requires a recording device, such as a brain or a miniature notebook. When its storage space eventually runs out, the information must be deleted, a process that necessarily produces an increase in total entropy.

From this perspective, living systems can be seen as composed of countless such ‘demons’ (proteins and other cellular machinery) that maintain local order by pumping disorder (often in the form of heat) into their surroundings. Davies adroitly brings Schrödinger’s account up to date by way of Claude Shannon’s information theory, Turing machines (universal computers), von Neumann machines (self-replicating universal constructors), molecular biology, epigenetics, information-integration theories of consciousness and quantum biology (which concerns quantum effects in processes from photosynthesis to insect coloration and bird navigation).

Notice, though, how this account dodges the issue by appealing to virtual agents (Maxwell demons) as well as real agents, like Turing. To the materialist, all these agents emerge by a long series of chance events, direct things for a while, then delete themselves. How did that happen?

Cheating with Fake Chance

Sure, the Second Law is not violated, but Davies and Hannay have cheated with fake chance. They speak as if Maxwell’s demon emerges by chance, uses purposeful intelligence for a goal, then vanishes by chance. Now watch them dig a deeper hole:

What practical difference does it make to see life as informational? We don’t yet know, but can speculate. For one thing, if the essential characteristics of life are entropic, extraterrestrial searches based on chemistry could be misguided. It might be more useful to look for phenomena such as ‘anti-accretion’ — in which matter is regularly transferred from a planet’s surface into space. Earth has experienced this since the 1950s, when the one-way traffic in asteroids and meteorites plunging into the globe was finally counteracted by the launch of the first artificial satellites. Arguably, such situations are not merely consistent with the presence of life, but almost impossible to explain in any other way

Note the artfully deployed passive voice. One-way traffic “was finally counteracted by the launch of the first artificial satellites.” Who counteracted it? Did not intelligent engineers use design to launch satellites? It’s hard to exaggerate how ludicrous the thought could be that satellites are mirror images of the same chance processes that pockmarked the Earth with craters. This is fake chance, endowed with purposeful agency, but like Hannay said, to the materialist, “such situations are not merely consistent with the presence of life, but almost impossible to explain in any other way.”

Iconoclasm and Vitalism

Hannay takes issues with a few of Davies’ “iconoclastic” ideas in the book, but since Davies doesn’t cross the line into “vitalism” (a favorite epithet some Darwinians use to describe intelligent design), he ends with a compliment: “On the contrary, if only more of us were wrong in such thought-provoking ways, we might more readily uncover the truth.”

And so Hannay, with Nature’s pulpit, preaches about thoughts and truths. Those are ponderous demons to have to emerge from bouncing molecules, only to disappear after temporary violations of the Second Law. Presumably the truths that emerge on another planet would be quite different. Maybe, even, the truths that emerged here on the materialists’ unguided, naturalistic Earth are the real falsehoods. “Who” could ever judge the difference?

Argument by cliche?

Coyne: “The Tuxedo Is Fraying”!

David Klinghoffer | @d_klinghoffer

Over the weekend I took a look at the hysterical attempt, via the American Association for the Advancement of Science, to link Mike Behe and Darwin Devolves with a measles upsurge and catastrophic climate change. That’s one approach to dealing with a book you don’t like.

Now biologist Jerry Coyne weighs in at the Washington Post with his own review. It’s an improvement over the Science review, at least, as I count two whole paragraphs seeking to rebut the main thesis of the book that unguided Darwinian evolution is “self-limiting.”

I’ll let others respond on that. While Coyne has nothing to offer to compare with madly tarring Behe with global health threats as the AAAS does, he offers a gem in his own way. It’s not too often you see a denser collation of cliché taunts directed at intelligent design. It’s all here, from the “Wedge Document” to Behe as a “pious Catholic” to ID as “rejected…by judges” and “outed as disguised religion,” “derived from religion,” to “Who, exactly, is the designer?” to “neo-creationism,” “a mere re-labeling of creationism” (quoting Judge Jones), to “creationism in a cheap tuxedo.”

The potted false history is not left out, how ID “arose after opponents of evolution repeatedly failed on First Amendment grounds to get Bible-based creationism taught in the public schools,” nor the expected complaint about Behe’s choice of a publisher.

The Hoariest Cliché of All

The “tuxedo is fraying,” warns Professor Coyne, a delightful attempt to spruce up the hoariest cliché of all. I dare you to tell me what’s missing. Actually, there’s one ultra-hackneyed attack he leaves out. He forgets to demand, as if this settled the whole matter, “Who designed the designer?” Even Coyne nods.

Professor Coyne’s headline is perfectly juvenile: “Intelligent design gets even dumber.” Uh huh. Meanwhile, as I write, the current top story at his own website, Why Evolution Is True, informs the science community with the news that “Maru plays the drums,” referring to the Japanese cat and YouTube star who “has been on the Internet for eleven years.” Wow, eleven years. Has it really been that long? And the cat can play a drum with its tail!

Why does it matter? From my perspective as a science consumer, ID’s case could be wrong and it could be right. But credit it with this: the argument it presents, in the work of ID proponents like Behe, Meyer, Axe, Dembski, and others, is continually building. It’s dynamic, highly substantive, evolutionary you might say. It doesn’t depend on appeals to religion, but also not to emotion, to demonization, to cultural stereotypes, to clichés. ID has that over its opponents.

If the evidence of design is worth addressing at all, it’s worth addressing adequately on its own terms. And those terms are not static and stale, as the critiques from Darwinists overwhelmingly tend to be. Come on, guys. Let’s do better.

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.