On recent attempts to explain(away) the Cambrian explosion.

This Just In — Latest Cambrian Explosion Excuses
Evolution News | @DiscoveryCSC

When evolutionists deny design, but admit that nature looks designed, they often wind up attributing the skills of a designer to inanimate matter. This is absurd, but what else is available in their explanatory toolkit?

Here’s an example. A headline by Amanda Doyle at NASA’s Astrobiology Magazine reads, “Microbes set the stage for the first animals.” How is this to be understood? Are animals waiting offstage for their debut? Are microbes arranging the props, clearing pathways, and turning on the lights? Surely she cannot mean that. So how can it be understood without personification? Assuming the prior existence of microbes, perhaps she means that their collective behavior resulted in changes in the balances of gases in the atmosphere, or the pH of seawater, or some other unplanned consequence. Does that help?

Doyle focuses on evidence dating from the Ediacaran Period, just prior to the Cambrian explosion. She weaves her plot around the story of a team from the University of Wisconsin-Madison working in Siberia. Photos show their tools beside unusual limestone rocks containing stromatolites and algal impressions. The photos don’t appear to show any Ediacaran creatures themselves. Indeed, those creatures play no role in her play, so they exit stage right: “The remains of these odd creatures, most of which have no evidence of a circulatory or digestive system, largely vanished from the rock record at the start of the Cambrian Period,” she admits [emphasis added], essentially agreeing with the scientists whom Stephen Meyer quotes in Chapter 4 of Darwin’s Doubt.

According to Doyle’s headline, microbes were recruited as the explanatory heroes in her play. Microbes altered the sediments, leaving records of levels of oxygen and sulfur at the time. The UW team found a stratum where “environmental conditions apparently changed,” going from euxinic (sulfidic) conditions that favored microbe growth to oxygenic conditions that would have favored animals.

The change from euxinic to non-euxinic conditions at the end of the Ediacaran Period allowed the Ediacaran animals to colonise the now more oxidized and habitable ocean, despite an overall oxygen level in the atmosphere and oceans that was far less than today’s.
We need go no further. This is a rehash of the Oxygen Theory we have dealt with over and over (for the latest, see here and here). It makes no sense; oxygen has no power to create animal body plans, nor can it “allow” the animals to create themselves. Mr. Oxygen can cry out, “Bring forth! I allow you to evolve!” all he wants on the stage, but nothing will happen. Can’t someone answer the real argument of Darwin’s Doubt, that the abrupt increase in functional information in the Cambrian animals requires a cause that is capable of producing it? The only such cause we know from uniform experience is intelligence. Oxygen has no such power.

We learn at the end of the article that “The research was supported by the Exobiology and Evolutionary Biology element of the NASA Astrobiology Program.” But Darwin’s Doubt came out four years ago, and Debating Darwin’s Doubt two years later. Is NASA really unaware of the challenge?

Let’s keep looking for an explanation that’s new and different. Here’s one: in Science Advances, the open-access journal of the AAAS, a team of six from four American universities spices up the story of the Cambrian.

Several positive carbon isotope excursions in Lower Paleozoic rocks, including the prominent Upper Cambrian Steptoean Positive Carbon Isotope Excursion (SPICE), are thought to reflect intermittent perturbations in the hydrosphere-biosphere system. Models explaining these secular changes are abundant, but the synchronicity and regional variation of the isotope signals are not well understood. Examination of cores across a paleodepth gradient in the Upper Cambrian central Missouri intrashelf basin (United States) reveals a time-transgressive, facies-dependent nature of the SPICE. Although the SPICE event may be a global signal, the manner in which it is recorded in rocks should and does vary as a function of facies and carbonate platform geometry. We call for a paradigm shift to better constrain facies, stratigraphic, and biostratigraphic architecture and to apply these observations to the variability in magnitude, stratigraphic extent, and timing of the SPICE signal, as well as other biogeochemical perturbations, to elucidate the complex processes driving the ocean-carbonate system.
Further reading doesn’t help. The authors know that “The Early Paleozoic era … encompasses an important time frame in metazoan evolution, including the Cambrian Explosion,” but their research only focuses on correlation, not causation. They mention the same “increase in atmospheric oxygen, possibly associated with an oceanic anoxic/euxinic event” that Amanda Doyle focused on.

Conceptual models have been constructed to explain the causes and effects of these sundry secular changes, including ocean anoxia/euxinia driving trilobite turnover, associated enhancement of organic carbon and pyrite burial forcing changes in atmospheric oxygen levels, and oxygenated coastal waters driving the diversification of plankton and perhaps the resulting Ordovician biodiversification.
The changes could well be consequences, not causes, of the Cambrian explosion. And whether the element is oxygen, sulfur, carbon, or anything else, it doesn’t matter. They’re inert. They’re dumb. None of them has creative powers to design new body plans, cell types, and organs, even if they were to “allow” such things to “emerge” onstage.

We’ll try one more. In Geology, the Ediacaran animal Cloudina is mentioned in a paper by seven researchers from Scotland, Russia, and Namibia. Do they describe a sufficient cause for the Cambrian animals?

The Ediacaran skeletal tubular putative metazoan Cloudina occurs globally in carbonate settings, which both provided lithified substrates and minimized the cost of skeletonization. Habitat and substrate preferences and the relationship of Cloudina to other metazoans have not been fully documented, so we know little as to its ecological demands or community dynamics. In situ Cloudina from the Nama Group, Namibia (ca. 550–541 Ma), formed mutually attached reefs composed of successive assemblages in shallow, high-energy environments, and also communities attached to either stromatolites in storm-influenced deep inner-ramp settings or thin microbial mats in lower-energy habitats. Each assemblage shows statistically distinct tube diameter cohorts, but in sum, Cloudina shows an exponential frequency distribution of diameter size.
Meyer doesn’t mention Cloudina, but it’s not much to look at. Visualize a stack of cups forming a tube. The Virtual Fossil Museum says, “The Cloudinids lived during the late Ediacaran, and became extinct at the base of the Cambrian.” Categorized with the “small shelly fossils” that preceded the explosion, they can’t have contributed to the Cambrian animal body plans, accordingly (see Chapters 13 and 14 in Debating Darwin’s Doubt). We read on, hoping.

In reefs, we document a periodicity of size variation, where mean, minimum, and maximum tube diameters vary together and show a systematic increase toward the top of each assemblage. We conclude that most Nama Group Cloudina represent one ecologically generalist taxon with highly variable size, that size was environmentally mediated, and that Cloudina could respond rapidly to periodic environmental changes. While Nama Group skeletal metazoans coexisted with soft-bodied biota, there was no apparent ecological interaction, as they were segregated into lithified carbonate and non-lithified clastic microbial mat communities, respectively. We infer that ecological flexibility allowed Cloudina to form varied communities that colonized diverse carbonate substrates under low levels of interspecific substrate competition. This is in notable contrast to the earliest Cambrian skeletal epibenthos that formed biodiverse reef communities with specialist niche occupancy.
So that’s it? Tube diameters increased or decreased according to environmental conditions? If they grew articulated legs, eyes and digestive systems, we might be impressed.


Ho-hum. Evolutionists are not responding to Meyer’s challenge. Looks like a forfeit.

And still yet more on reality's antiDarwinian Bias

Two Genetic Blows Against Darwinian Speciation
Evolution News | @DiscoveryCSC

Classical neo-Darwinism relies on genetic mutations (random mistakes) acted on by natural selection (an aimless effect dependent on what survives). From these two sources of unguided happenstance, all the adapted perfections in life are supposed to have emerged. But what if life is, instead, determined by active information content? An entirely different picture of “evolutionary” change becomes possible: one that involves information sharing. Two recent genomic studies provide additional validation for the new picture.

Insects: Rampant Horizontal Gene Transfer

Horizontal transfer (HT) of genetic information has been well known in microbes for some years now, but recently has been coming more visible in higher organisms. Transposable elements (TE) are, as the name implies, transposable or relocatable within a genome. But could they also play a role in genetic diversity between organisms? Apparently so. A new paper in PNAS announces “Massive horizontal transfer of transposable elements in insects.”

Eukaryotes normally receive their genetic material from their parents but may occasionally, like prokaryotes do, acquire DNA from unrelated organisms through horizontal transfer (HT). In animals and plants, HT mostly concerns transposable elements (TEs), probably because these pieces of DNA can move within genomes. Assessing the impact of HTs on eukaryote evolution and the factors shaping the dynamics of these HTs requires large-scale systematic studies. We have analyzed the genomes from 195 insect species and found that no fewer than 2,248 events of HT of TEs occurred during the last 10 My, particularly between insects that were closely related and geographically close. These results suggest that HT of TEs plays a major role in insect genome evolution.

This is very different from vertical inheritance. How could it happen? It’s like being told you could inadvertently get a piece of DNA from a chimpanzee at the zoo and pass it on to your kids. Impossible. That would scramble every animal’s identity, wouldn’t it? It might explain other people’s kids, but not yours!

The prevalence of HT in higher animals is only now coming to light through systematic studies. These authors examined genomes of “195 insect genomes, representing 123 genera and 13 of the 28 insect orders” to find the 2,248 events they report in the paper. Imagine what this must mean for evolutionary theories of common descent:

We show that DNA transposons transfer horizontally more often than retrotransposons, and unveil phylogenetic relatedness and geographical proximity as major factors facilitating HTT (horizontal transfer of transposons) in insects. Even though our study is restricted to a small fraction of insect biodiversity and to a recent evolutionary timeframe, the TEs we found to be horizontally transferred generated up to 24% (2.08% on average) of all nucleotides of insect genomes. Together, our results establish HTT as a major force shaping insect genome evolution.

The authors recognize that transposons can jump species barriers much easier than genes can. Even so, it’s astonishing to think that this much genetic information could pass readily between species, most likely via bacteria vectors.

In animals and plants, very few cases of such horizontal gene transfers (HGTs) have been reported so far. In fact, most of the genetic material that is horizontally transferred in animals and plants consists of transposable elements (TEs) which are pieces of DNA able to move from a chromosomal locus to another. The greater ability of TEs to move between organisms certainly relates to their intrinsic ability to transpose within genomes, which genes cannot do. HT of TEs (HTT) may allow these elements to enter naive genomes, which they invade by making copies of themselves, and then escape before they become fully silenced by anti-TE defenses.

Some interpretation is required in this kind of analysis. How does one tell HT from vertical inheritance in a stretch of DNA? The authors recognize the challenge, but give four reasons why their numbers are probably low estimates. They conclude, “HTT is not only widespread in insects, but the true number of HTT events is likely to be several orders of magnitude larger than the number we report.” And this is just for recently-diverged insects. Imagine how much transfer goes on worldwide over longer times! At the end of the article, they suggest that more of this is happening than we think, not only in insects, but in other higher eukaryotes:

Extrapolating our estimates over the ∼480 My of insect evolution and the whole insect biodiversity points toward millions of HTT events generating substantial fractions of insect genomes. These inferences, combined with the pronounced impact TEs have on genome structure and dynamics, establish HTT as a major factor driving insect molecular evolution. Our results call for further assessments of the influence of HTT on other taxonomic groups and of the ecological factors and relationships affecting HTT dynamics.

Bears that Care and Share

There’s another means of information sharing: hybridization. Last November we talked about how rampant hybridization is challenging evolutionary theory, weaving Darwin’s tree into a web. Another example just came to light. News from the Senckenberg Research Institute reports widespread gene flow across bears worldwide, leading to the speculation that all bears are interfertile and possibly members of a single species.

Senckenberg scientists have sequenced the entire genomes of four bear species, making it now possible to analyze the evolutionary history of all bears at the genome level. It shows that gene flow, or gene exchange, between species by extensive hybridization, is possible between most bear species – not only polar and brown bear. The DNA samples of different bear species came from different European zoos, underlining their importance not only for conservation, but also for research. The study published today in “Nature Scientific Reports” also questions the existing species concept in general, because other genome studies too have, frequently found gene flow among species.

How could this happen? Hybrids were supposed to be infertile, like the iconic mule. Many hybrids, though, can still bear young, passing on their shared information over generations. The scientists believe that the brown bear may be a “vector species” connecting all species of bears, whether in Asia, Alaska, America, or Europe — by acquiring genes from one region and passing them along between regions as they travel and breed.

As they indicate, this calls into question the very meaning of a species. Dr. Axel Janke wonders, “We have to ask ourselves: Does the species concept still hold true, given there is evidence of gene flow not only in bears, but also in other animals?” This comes close to home with increasing evidence that modern humans have Neanderthal genes. How, then, can we label them with another species label, Homo neanderthalensis? That’s very arbitrary.

Non-Darwinian Implications

In the light of these findings, it seems presumptuous of Darwin to write about “The Origin of Species” when we can’t even say what a species is. But neither would it be correct to think that all plants and animals have fluid boundaries, able to morph endlessly like shape-shifters into anything else. Clearly, you look different from a mushroom. How, then, are we to interpret the living world?

Try information. Notice that both these examples of information sharing are non-Darwinian. They don’t involve accidental mutations and blind natural selection. They are both methods whereby an organism’s genetic information can be given and received. We might consider the way people share good books with one another. That information might cause “change through time” in the way people behave based on what they come to know, but it would not be a blind, unguided process.

In the same way, a designer would give designed organisms the means to adjust to changing environments by the acquisition of pre-existing information, so that they remain what they are but don’t readily go extinct when entering a new habitat or climate regime. Programming for that kind of robustness would make a lot of sense.

On becoming a servant of JEHOVAH:The Watchtower Society's commentary.

How Do I Become One of Jehovah’s Witnesses?
The steps needed to become one of Jehovah’s Witnesses are described by Jesus and can be found at Matthew 28:19, 20. That passage outlines what a person needs to do to become a disciple of Christ, which involves speaking, or bearing witness, about Jehovah.

Step 1: Learn what the Bible teaches. Jesus instructed his followers to “make disciples . . . , teaching them.” (Matthew 28:19, 20) The word translated “disciple” literally means “a learner.” The Bible, especially the teachings of Jesus Christ found there, contains the information you need in order to have a happy and fulfilling life. (2 Timothy 3:16, 17) We are glad to help you learn what the Bible teaches by means of our free Bible study program.—Matthew 10:7, 8; 1 Thessalonians 2:13.

Step 2: Put what you learn into practice. Jesus said that those who learn must also “observe all the things [he] commanded.” (Matthew 28:20) This means that your study of the Bible must be more than an intellectual exercise—it may call on you to make significant changes in your thinking and behavior. (Acts 10:42; Ephesians 4:22-29; Hebrews 10:24, 25) Those who observe Jesus’ commands are then moved to make a personal decision to follow him by dedicating their lives to Jehovah God.—Matthew 16:24.

Step 3: Get baptized. (Matthew 28:19) In the Bible, baptism is compared to a burial. (Compare Romans 6:2-4.) It serves as a symbol of dying to a past course of life and beginning a new one. Your baptism, then, is a public acknowledgment that you have completed the first two steps described by Jesus and are asking God for a clean conscience.—Hebrews 9:14; 1 Peter 3:21.

How will I know if I’m ready for baptism?

Speak to the congregation elders. They will talk with you to ensure that you understand what is involved, are applying what you have learned, and have dedicated yourself to God of your own free will.—Acts 20:28; 1 Peter 5:1-3.

Do these steps apply to children of Witness parents?

Yes. We raise our children “in the discipline and admonition of Jehovah,” just as the Bible commands. (Ephesians 6:4) However, as they grow, they must make a personal decision to learn, accept, and apply what the Bible teaches before they can qualify for baptism. (Romans 12:2) Ultimately, each person must make his own choice concerning worship.—Romans 14:12; Galatians 6:5.

The skilled trades are not a consolation prize.

Reality is a computer program?

A clash of Titans. LII

The mathematics of escape.

Disinherited?

Science Magazine: Australopithecus sediba “Ousted from the Human Family”
Evolution News | @DiscoveryCSC

A few years ago we wrote about Australopithecus sediba, a hominid fossil that was discovered in South Africa in 2008. There was a lot of hype about this hominid when it was first published in 2010. Its discoverer, Lee Berger, called  sediba  “possibly the best candidate ancestor for our genus.”

The original hope for sediba is that it would help fill a “gap” in the fossil record that pertains to the precise time when evolutionary paleoanthropologists believe our genus Homo evolved from some australopithecine ancestor. ABC News  made this point  when sediba was first announced, calling the fossil a “game-changer”:

Scientists have long talked about a “missing link” between very old fossils, more than 3 million years old, and much newer ones that they believe are clearly ancestors of today’s human beings. There is a gap in the fossil record, so far unexplained. Does Australopithecus sediba help fill the gap? Not on its own, say most researchers, but it helps.
The media touted sediba as a spectacular confirmation of this prediction. The Washington Post ran the headline, “Scientists identify ancestor that bridges gap in human evolution, a potential ‘game-changer,’” while the Associated Press quoted paleoanthropologist Darryl J. DeRuiter, stating:

This is what evolutionary theory would predict, this mixture of Australopithecene and Homo … It’s strong confirmation of evolutionary theory.
Now, things have changed radically. As the journal Science reports, “A famous ‘ancestor’ may be ousted from the human family,” explaining that Australopithecus sediba is far removed from the human portion of the hominid tree:

Instead of belonging to the human lineage, the new species of Australopithecus sediba is more closely related to other hominins from South Africa that are on a side branch of the human family tree, according to a new analysis of the fossil presented here last week at the annual meeting of the American Association of Physical Anthropologists.
This isn’t exactly anything new. The article makes another point we’ve made here at Evolution News in the past, namely that “With its fossils dated to 1.98 million years ago, Au. sediba is too young to be directly ancestral to all members of the genus Homo.” However, this new study doesn’t argue against sediba as a human ancestor simply because the age of the species is wrong, but also on the basis of the fossil’s morphology:

In a talk here, though, paleoanthropologist Bill Kimbel of Arizona State University in Tempe analyzed the most complete skull of Au. sediba and systematically shot down the features claimed to link it to early Homo. Kimbel noted that the skull was that of a juvenile — a “7th grader” — whose face and skull were still developing. In his analysis, with paleoanthropologist Yoel Rak of Tel Aviv University in Israel, he concluded that the child already showed traits that linked it most closely to the South African australopithecine Au. africanus, a species that lived in South Africa 3 million to 2.3 million years ago. And had it survived to adulthood, its humanlike facial traits would have changed to become even more like those of Au. africanus.

For example, the breadth of the young Au. sediba’s cheekbones appears narrow, as in early Homo. But by studying other australopithecine, ape, and Homo fossils to see how features of the cheekbones change as individuals grow and chewing muscles develop, Kimbel and Rak could predict how the boy’s face and skull would have looked if he’d grown up to be an adult. The resemblance to Au. africanus is so striking, in fact, that Kimbel thinks Au. sediba is a closely related “sister species” of Au. africanus — and not a long-lost human relative. “We don’t believe … that Au. sediba has a unique relationship to the genus Homo,” says Kimbel.

Other researchers who have long been skeptical that Au. sediba was an ancestor of Homo found Kimbel’s talk persuasive: “Spot on,” says paleoanthropologist Bernard Wood of George Washington University in Washington, D.C. Paleoanthropologist Ian Tattersall of the American Museum of Natural History in New York agrees with Kimbel that Au. sediba is most closely related to Au. africanus and that neither species is ancestral to early Homo.
Those are some very big names who think that Au. sediba is merely an extinct side-branch of the hominid tree and not ancestral to Homo. So much for sediba being a human ancestor who is “what evolutionary theory would predict.”

But if not Au. sediba, from what did our genus Homo evolve? When Au. sediba was first reported, the science media admitted that we simply don’t know:

The oldest Homo specimens are scrappy and enigmatic, leaving researchers unsure about the evolutionary steps between the australopithecines and Homo. … “The transition to Homo continues to be almost totally confusing,” says paleoanthropologist Donald Johanson of ASU Tempe, who has seen the new fossils.

(Michael Balter, “Candidate Human Ancestor From South Africa Sparks Praise and Debate,” Science, Vol. 328:154-155 (April 9, 2010).)

With the fall of Australopithecus sediba, that confession of ignorance seems to be left firmly in place.

Need science be idolised to be of use.

Science as Cargo Cult – More Thoughts on the “March for Science”
David Klinghoffer | @d_klinghoffer

When even Slate  turns against a “progressive” event like this weekend’s March for Science, you know something’s wrong. Harvard Medical School instructor Jeremy Samuel Faust complains about the weird, mindless cult-like atmosphere infusing much of the adulation directed at “Science.”

Little of what I observed dissuades me from my baseline belief that, even among the sanctimonious elite who want to own science (and pwn anyone who questions it), most people have no idea how science actually works. The scientific method itself is already under constant attack from within the scientific community itself and is ceaselessly undermined by its so-called supporters, including during marches like those on Saturday. In the long run, such demonstrations will do little to resolve the myriad problems science faces and instead could continue to undermine our efforts to use science accurately and productively.

…Being “pro-science” has become a bizarre cultural phenomenon in which liberals (and other members of the cultural elite) engage in public displays of self-reckoned intelligence as a kind of performance art, while demonstrating zero evidence to justify it.
More:

[T]he march revealed the glaring dissonance of opposing that trough of ignorance by instead accepting a cringe-worthy hive-mind mentality that celebrates Science as a vague but wonderful entity, what Richard Feynman called “cargo cult science.” There was an uncomfortable dronelike fealty to the concept — an oxymoronic faith that information presented and packaged to us as Science need not be further scrutinized before being smugly celebrated en masse. That is not intellectually rigorous thought — instead, it’s another kind of religion, and it is perhaps as terrifying as the thing it is trying to fight.
This is…well, frankly it’s remarkably close to our own take on the event. Listen to Discovery Institute’s Stephen Meyer in an interview with  interview with Mike Opelka of The Blaze, explaining how the March for Science reflects a split in the way people think about what science means. There’s the conception we absorbed in school: science is a method of investigating the natural world by collecting facts and then posing and arguing over questions (“multiple competing hypotheses”) of how best to interpret those facts. When the debate stops, so does the science.

And then there’s the very different view that says science has closed all the books and figured out everything in need of being figured out. The debate is over, and properly so. Thus the public needs only to absorb a set of doctrines, while scientists themselves engage in a kind of apologetics campaign. The conclusions are preset and only need to be conveyed for the public’s benefit. In this perspective, that of many of the science marchers, science is rendered as a kind of religious faith.

That may explain why it treats rival religions the way it does. As our Senior Fellow Jay Richards explains in an  ID the Future podcast with Robert Crowther, advocates of materialist ideology habitually portray science as being in a state of perpetual warfare with Judeo-Christian faith.


In fact, the latter tradition was the “seedbed” of science, as Jay points out, not its persecutor. But the rival religion, Science as Cargo Cult, feels an imperative to compete with and blacken the reputation of its competitor. Hence the myth of unending warfare between the two.

Recognised as faithful stewards of our master's property.

Jehovah’s Witnesses Receive an Award for Protecting the Environment


The printing facilities operated by Jehovah’s Witnesses in Mexico received the Clean Enterprise certificate for the seventh year in a row.

On September 26, 2012, the government of Mexico awarded Jehovah’s Witnesses a special certificate of recognition “for [their] dedication to the care and protection of the environment.”

The Clean Enterprise program helps industries develop in ways that are safe for the environment. Jehovah’s Witnesses participate in it every year, though theirs is a not-for-profit organization. A spokesman for the Mexico printing facility said: “To receive the Clean Enterprise certificate, we have to give evidence that our procedures and emissions meet local environmental regulations in seven areas: air, water, urban waste, hazardous waste, safety, electrical energy, and environmental training. Industrial enterprises are not obligated to subscribe to this program. We participate voluntarily.”

Jehovah’s Witnesses around the world do all they can to avoid damaging earth’s precious environment.

Before getting the right answers.

Asking the Right Questions about the Evolutionary Origin of New Biological Information
Casey Luskin February 24, 2010 9:04 AM


As we've seen, it's easy to duplicate a gene, but the key missing ingredient in many neo-Darwinian explanations of the origin of new genetic information is how a gene duplicate then acquires some new optimized function. Evolutionists have not demonstrated, except in rare cases, that step-wise paths to new function for duplicate genes exist.

As we saw in an earlier post, Austin Hughes cautions against making "statistically based claim[s] of evidence for positive selection divorced from any biological mechanism."26 In other words, natural selection is invoked to explain the evolution of genes where we do not even know the functional effect of the mutations being asserted. In this regard, Hughes observes that even in one of the more sophisticated studies, "there was no direct evidence that natural selection was actually involved in fixing adaptive changes."27

Hughes also acknowledges a problem inherent in many appeals to natural selection, namely that required mutations may not give any selective advantage when they first arise. He thus writes regarding one study:

For example, a rhodopsin from the Japanese conger eel with λmax ≈ 480 nm achieved this sensitivity through the interaction of three different amino acid replacements (at sites 195, 195, and 292). There does not seem to be any way that natural selection could favor an amino acid replacement that would be of adaptive value only if two other replacements were to occur as well.28
In this case, there was no stepwise advantage gained with each successive mutation. Because no advantage could have been gained until all three mutations were present, Hughes finds it more "plausible" to believe that the first two mutations were "selectively neutral" and became fixed due to random, non-adaptive processes such as genetic drift. Once the third mutation arose it might have provided an advantage, but to paraphrase Scott Gilbert, at best this really only explains the survival of the fittest, not the arrival of the fittest.29

But Hughes' explanation has deep deficiencies: it requires that two mutations become fixed before any selective advantage for the third mutation is gained. This implies that there must be three specific mutations to gain any selective advantage. A key question is thus, Are multiple specific mutational changes likely to appear in the same individual through unguided chance mutations given known mutation rates and population sizes? Even Hughes, despite his exhortations to fellow evolutionary biologists to employ more rigor in their studies, does not address this fundamental question.

A similar example is found when leading paleoanthropologist Bernard Wood critiqued a simplistic model of human cranial evolution on the grounds that too many mutations would be required to gain any functional advantage:

The mutation would have reduced the Darwinian fitness of those individuals. . . . It only would've become fixed if it coincided with mutations that reduced tooth size, jaw size and increased brain size. What are the chances of that? 30
Similarly, Jerry Coyne writes that "It is indeed true that natural selection cannot build any feature in which intermediate steps do not confer a net benefit on the organism."31 This highlights a key deficiency in many neo-Darwinian accounts of the evolution of genes. Namely, they fail to demonstrate that the processes necessary to generate new functionally advantageous genetic information are plausible. As with Hughes's or Wood's examples above, multiple mutations might be necessary to gain any functional advantage. Any account invoking blind, unguided, random mutations to evolve a gene from Function A to Function B must address at least these three questions:

Question 1: Is there a step-wise adaptive pathway to mutate from A to B, with a selective advantage gained at each small step of the pathway?
Question 2: If not, are multiple specific mutations ever necessary to gain or improve function?
Question 3: If so, are such multi-mutation events likely to occur given the available probabilistic resources?
Mathematician David Berlinski considers such questions when critiquing evolutionary accounts of eye evolution. Darwinian processes fail because multiple changes are required for a new function to appear:

If these changes come about simultaneously, it makes no sense to talk of a gradual ascent of Mount Improbable. If they do not come about simultaneously, it is not clear why they should come about at all. 32
Again, the key question is therefore, how hard is it for new functional biological information to arise? Answering this question requires assessing the ability of random mutation and natural selection to generate new functional biological information. But when most evolutionary biologists play the Gene Evolution Game, they do not make such assessments and rarely consider these questions. Instead they typically invoke processes such as gene duplication, natural selection, and rearrangement, without demonstrating that random and unguided mutations are sufficient to produce the information needed. Any explanation that at base is little more complicated than "duplication, rearrangement, and natural selection" is not a demonstration that new functional genes can arise by unguided processes.

Thankfully, some scientists are willing to consider these key questions. They have performed research providing data that offers strong reasons to be skeptical of the ability of mutation and selection to form new functional genetic sequences.

A. Asking Questions 1 and 2:
Molecular biologist Doug Axe has performed mutational sensitivity tests on enzymes and found that functional protein folds may be as rare as 1 in 1077.33 His research shows that the fitness landscape for many enzymes looks like this, making it very unlikely that neo-Darwinian processes will find the specific amino acid sequences that yield functional protein folds:


To put the matter in perspective, these results indicate that the odds of Darwinian processes generating a functional protein fold are less than the odds of someone closing his eyes and firing an arrow into the Milky Way galaxy, and hitting one pre-selected atom.34 To say the least, this exhausts the probabilistic resources available. Such data help us answer the first question: it's not likely that there will be a functional stepwise mutational pathway leading from Function A to Function B.

Douglas Axe is by no means the only biologist to make this observation. A leading college-level biology textbook, Campbell's Biology, observes that "Even a slight change in primary structure can affect a protein's conformation and ability to function."35 Likewise, David S. Goodsell, an evolutionist biologist, writes:

As you might imagine, only a small fraction of the possible combinations of amino acids will fold spontaneously into a stable structure. If you make a protein with a random sequence of amino acids, chances are that it will only form a gooey tangle when placed in water. Cells have perfected the sequences of amino acids over many years of evolutionary selection...36
What Goodsell does not mention is that if "perfected" amino acid sequences and functional protein folds are rare and slight changes can disrupt function, then selection will be highly unlikely to take proteins from one functional fold to the next without traversing some non-functional stage. So how do new functional protein folds evolve? This effectively answers question two, implying that many specific mutations would be necessary for evolving genes to pass through non-functional stages while evolving some new function. Question 3 assesses whether this is likely to happen.

B. Asking Question 3:
In 2004, Michael Behe and physicist David Snoke published a paper in the journal Protein Science reporting results of computer simulations and theoretical calculations. They showed that the Darwinian evolution of a simple functional bond between two proteins would be highly unlikely to occur in populations of multicellular organisms. The reason, simply put, is because too many amino acids would have to be fixed by non-adaptive mutations before gaining any functional binding interaction. They found:

The fact that very large population sizes--109 or greater--are required to build even a minimal [multi-residue] feature requiring two nucleotide alterations within 108 generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.37
According to this data, chance mutations are unlikely to produce even two required non-adaptive mutations in multicellular diploid species within any reasonable timescale. This answers the third question: getting multiple specific non-adaptive mutations in one individual is extremely difficult, and more than two required but non-adaptive mutations are likely beyond the reach of multi-cellular organisms. Studies like this show that the actual ability of random mutation and unguided selection to produce even modestly complex new genetic functions is insufficient.

In 2008, Behe and Snoke's would-be critics tried to refute them in the journal Genetics, but found that to obtain only two specific mutations via Darwinian evolution "for humans with a much smaller effective population size, this type of change would take > 100 million years." The critics admitted this was "very unlikely to occur on a reasonable timescale." 38 In other words, there is too much complex and specified information in many proteins and enzymes to be generated in humans by Darwinian processes on a reasonable evolutionary timescale.

As noted in the comments on the Gene Evolution Game, when neo-Darwinists try to explain the evolution of genes, mere point mutations often are insufficient to account for the gene's sequence. They must therefore appeal to genetic rearrangements such as insertions, deletions, or an alleged process called "domain shuffling" where segments of proteins become shuffled to new positions in the genome. In his book The Edge of Evolution, Michael Behe reviews research that engineered new protein function by swapping domains to change protein function, and found that the intelligently engineered changes required multiple modifications that, in nature, would require too many simultaneous mutational events to yield functional changes:

[Protein engineering research] does not mimic random mutation. It is the exact opposite of random mutation. ... What do the lab results tell us about whether random-yet-productive shuffling of domains "occurs with significant frequency under conditions that are likely to occur in nature"? About whether that is biologically reasonable? Nothing at all. When a scientist intentionally arranges fragments of genes in order to maximize the chances of their interacting productively, he has left Darwin far, far behind. ... [Experiments that engineered proteins by shuffling domains] didn't just splice two genes together in a single step; they took several additional steps as well. ... Remember the more steps that have to occur between beneficial states, the much less plausible are Darwinian explanations. ... Domain shuffling would be an instance of the "natural genetic engineering" championed by James Shapiro where evolution by big random changes is hoped to do what evolution by small random changes can't. But random is random. No matter if a monkey is rearranging single letters or whole chapters, incoherence plagues every step. ... One step might luckily be helpful on occasion, maybe rarely a second step might build on it. But Darwinian processes in particular and unintelligent ones in general don't build coherent systems. So it is biologically most reasonable to conclude that, like multiple brand new protein-protein binding sites, the arrangement of multiple genetic elements into sophisticated logic circuits similar to those of computers is also well beyond the edge of Darwinian evolution. 39
As Behe observes, "No matter if a monkey is rearranging single letters or whole chapters, incoherence plagues every step." Thus, when multiple mutational events--whether point mutations, "domain shuffling," or other types of rearrangements--are required to gain some functional advantage, it seems unlikely that blind neo-Darwinian processes can produce the new biological function.

Unfortunately, few if any advocates of the neo-Darwinian just-so stories investigate whether mutation and natural selection are sufficient to produce new functional genetic information. Instead they believe that finding similarities and differences between genes demonstrates that neo-Darwinian evolution has occurred, and they assume that "positive selection" is a sufficient explanation.

As Hughes cautions, they engage in "use of certain poorly conceived statistical methods to test for positive selection," causing "the literature of evolutionary biology [to become] glutted with extravagant claims of positive selection" resulting in a "vast outpouring of pseudo-Darwinian hype [that] has been genuinely harmful to the credibility of evolutionary biology as a science." 40 Or, as Michael Behe cautions, they confuse mere sequence similarity with evidence of neo-Darwinian evolution. Finally, Michael Lynch warns his colleagues that "Evolutionary biology is not a story-telling exercise, and the goal of population genetics is not to be inspiring, but to be explanatory." 41

With these principles in mind, in the next installment we will assess about a dozen of the just-so stories concerning the origin of genes offered in studies cited by the NCSE.

References Cited:

[26.] Austin L. Hughes, "Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level," Heredity, Vol. 99:364--373 (2007).

[27.] Id.

[28.] Id.

[29.] "The modern synthesis is good at modeling the survival of the fittest, but not the arrival of the fittest." Scott Gilbert, quoted in John Whitfield, "Biological Theory: Postmodern evolution?," Nature, Vol. 455:281-284 (2008).

[30.] Bernard Wood, quoted in Joseph B. Verrengia, "Gene Mutation Said Linked to Evolution," Associated Press, found in San Diego Union Tribune, March 24, 2004.

[31.] Jerry Coyne, "The Great Mutator," The New Republic (June 14, 2007). Coyne asserts he knows of no example where this is the case.

[32.] David Berlinski, "Keeping an Eye on Evolution: Richard Dawkins, a relentless Darwinian spear carrier, trips over Mount Improbable. Review of Climbing Mount Improbable by Richard Dawkins (W. H. Norton & Company, Inc. 1996)," in The Globe & Mail (November 2, 1996) at http://www.discovery.org/a/132

[33.] Douglas D. Axe, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds," Journal of Molecular Biology, Vol. 341: 1295-1315 (2004); Douglas D. Axe, "Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors," Journal of Molecular Biology, Vol. 301: 585-595 (2000).

[34.] See Stephen C. Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design, pg. 211 (Harper One, 2009).

[35.] Neil A. Campbell and Jane B. Reece, Biology, pg. 84 (7th ed, 2005).

[36.] David S. Goodsell, The Machinery of Life, pg. 17, 19 (2nd ed, Springer, 2009).

[37.] Michael J. Behe & David W. Snoke, "Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues," Protein Science, Vol 13:2651-2664 (2004).

[38.] Rick Durrett and Deena Schmidt, "Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution," Genetics, Vol. 180: 1501--1509 (November 2008).

[39.] Michael Behe, The Edge of Evolution: The Search for the Limits of Darwinism, Appendix D, pgs. 272-275 (Free Press, 2007) (emphasis added).

[40.] Austin L. Hughes, "The origin of adaptive phenotypes," Proceedings of the National Academy of Sciences USA, Vol. 105(36):13193--13194 (Sept. 9, 2008) (internal citations removed).

[41.] Michael Lynch, "The frailty of adaptive hypotheses for the origins of organismal complexity," Proceedings of the National Academy of Sciences, Vol. 104:8597--8604 (May 15, 2007). 

And still yet more on reality's antiDarwinian bias

“Shared Error” Argument: Olfactory Receptor Genes Prove Common Descent?
Cornelius Hunter

We have seen that a new book, Adam and the Genome, co-authored by theistic evolutionists Dennis Venema and Scot McKnight is influenced by the mythical Warfare Thesis (here and here) and makes erroneous arguments that the fossils and echolocation support evolution (here and here). I’ll now move on to another topic: broken genes, or pseudogenes.

This is a popular argument amongst evolutionists and Venema uses as his example the olfactory receptor genes. The idea here is that, in different species (such as the human and chimpanzee), the same damaging mutation can be found in the same pseudogenes. When we find the same strange spelling mistake in the homework of different students we conclude that plagiarism occurred. It is more likely that the mistake had one source, rather than occurred twice, independently.

Likewise, the same mutation in different species points to a single source in a common ancestor — common descent. Furthermore, we don’t see mutations that violate the expected pattern. Clearly common descent is the obvious, most parsimonious explanation. As Venema concludes, common descent is “overwhelmingly supported.”

This is a powerful argument for evolution that has influenced many people. There’s only one problem: It fails historically, philosophically, and scientifically.

First, the olfactory system is profoundly complex. Odors entering the nose interact with finely tuned receptor proteins (created from the olfactory receptor genes), setting off an incredible cascade of events in the cell, resulting in an electrical signal sent to the brain. Studies have found that each cell expresses only a single olfactory receptor gene, and so is sensitive to a particular odor. At the brain, the signals are grouped and organized by odor. In other words, for all the cells in the nose expressing the same olfactory receptor gene (and thus sensitive to the same odor), their signals spatially converge as they feed into the brain area.

And of course, as with all the senses, these incoming signals are providing mere electrical information. There is no odor, or light, or sound entering the brain via these nerve cells. Instead, a bunch of electrical signals are entering the brain via these nerve cells. The brain, by itself, has no way of knowing what these electrical signals mean. It must somehow be given the source and meaning of these incoming signals. It then processes and interprets these signals and the end result is that we are conscious of images reported by our eyes, sounds reported by our ears, smells reported by our nose, and so forth. All of this defies evolution, and should give us pause.

Second, the evolutionist’s contention that common descent is needed to explain those shared mutations in different species contradicts the most basic biology. Simply put, similarities across species that cannot be explained by common descent are rampant in biology. The olfactory system is no exception. Its several fundamental components, if evolution is true, must have evolved several times independently. The level of independent origin that evolutionists must admit to (variously referred to as convergent evolution, parallel evolution, recurrent evolution, cascades of convergence, and so forth depending on the pattern) is staggering and dwarfs the levels of similarities in the olfactory receptor genes. To cast those relatively few similarities as mandates for common descent, while ignoring the volumes of similarities that violate common descent, constitutes the mother of all confirmation biases.

Third, the strength of this evolution argument is lack of function, but that renders it fallacious. As lawyers know, if you can’t convict the defendant on the facts, you decry how horrifying the crime is. In this case, the entire argument hinges on the utter uselessness of the broken genes. As Venema explains, they are “damaged,” “defective,” “mess[ed] up,” “wrong,” and “ruin[ed].” Clearly, according to Venema, these genes are useless — that’s why they are called pseudogenes. This is crucial because, for evolutionists, it means they would only arise by chance (what designer would implement useless designs?).

All of which means that evolutionists have a very simple formulation: Either those crippling mutations arose once in a common ancestor, or they just happened to arise by chance, coincidentally, multiple times. Clearly the former is much more likely, and this points to common descent. It is, as Venema concludes, “overwhelmingly supported.”

However, this powerful argument comes at a cost. There is no free lunch.

The conclusion that common descent is “overwhelmingly supported” utterly depends on our knowing the pseudogenes are useless. Disutility underwrites the assumption of chance as the only alternative to common descent. And chance as the only alternative is crucial. It is why the argument is so powerful, because the chance hypothesis is so unlikely.

Restricting the problem to a contest between evolution and chance makes evolution the obvious winner, but amidst the celebration we forget the weak link. We forget that the entire edifice resides on our certainty of disutility. This, it turns out, is a very weak link.

The history of evolutionary thought, going back to the Epicureans, is full of predictions of disutility gone wrong. It is, quite literally, a theory of gaps. When gaps in our scientific knowledge leave us with ignorance about function, evolutionists routinely assume there is no function. After all, if the world arose by chance, it should be full of aimless, useless “designs,” if they can even be called that.

But as those gaps close with the inexorable march of scientific progress, it seems we inevitably learn of function. Evolutionists claim disutility at brand new findings, only to be proved wrong, again and again. Look no further than the seemingly endless parade of “We thought it was junk, but now…” stories.

Ultimately, the long history of disutility claims is informed by the theory rather than the evidence. This is a classic example of what philosophers refer to as theory-laden observations.

None of this means there are no truly useless structures in biology. There may well be plenty of them. But the supposition has a terrible history.

Furthermore, regardless of the history, disutility is very difficult to know. As with the proverbial “proving a negative,” proving that a pseudogene, or anything else in biology for that matter, actually is useless, is a very difficult undertaking.

From introns to transposons, initial claims of uselessness have given way to a steady stream of findings of function. And, yes, the olfactory receptor “pseudo”-genes are no exception. They are now being called pseudo-pseudogenes because all those evolutionary claims of uselessness are rapidly fading. As one recent paper concluded, “such ‘pseudo-pseudogenes’ could represent a widespread phenomenon.”

This is yet another example in a long history of failed disutility predictions. Clearly, the assumption that we know that olfactory receptor pseudogenes are useless is unfounded. Even the name (pseudogenes) will serve future generations of scientists as a constant reminder of this evolutionary foible.

The story does not end here, though, for even if something like pseudogenes could somehow be proven useless, this would not justify the evolutionary formulation of random chance origin as the only other alternative.

Evolution fails to explain how even a single gene could evolve, let alone the entire olfactory system. In fact the presence of supposedly useless structures, such as pseudogenes, is hardly a plus for evolution. As Elliott Sober has pointed out, there is nothing about this story that provides a positivistic argument for evolution.

The argument, with all its strength, hinges entirely on the refutation of the alternative. This is a proof by the process of elimination. Hence it becomes utterly crucial that the alternatives be carefully and exhaustively considered. In particular, all possible alternatives must be known, understood, evaluated, and disproved.

Do you see a pattern here?

This powerful evolutionary argument not only crucially depends on knowing that the pseudogenes are useless, it also crucially depends on knowing that a simple random chance model is the only alternative to evolution for their origin.

Not only is this philosophically problematic (how do we know that the random chance model is the only alternative?), historically it has a terrible track record. As Kyle Stanford has shown, the history of science is full of theories that were advocated with this type of contrastive reasoning (disproving a perceived alternative), only later to fail because the assumed alternative was wrong.


To summarize, this highly influential and popular argument, from similar structures that appear to be useless, lies in ruins. It is a disaster. It should never have been used in the first place, for its scientific failure was entirely predictable from both the history and philosophy of science.

Yet more on Venezuela's meltdown

An altruistic society is a pipe dream?:Pros and cons.

Russia's international reputation re:religious liberty left in tatters.

State Dept. Condemns Russian Religious Clampdown
By Curt Mills, 

The U.S. State Department has condemned the Russian ban on Jehovah's Witnesses.


"The United States is extremely concerned by the Russian government's actions targeting and repressing members of religious minorities, including Jehovah's Witnesses, under the pretense of combating extremism," Acting State Department spokesman Mark C. Toner told U.S. News by email late Thursday night.Earlier Thursday, the Russian Supreme Court called the pacifist religious sect extremist and ordered the shuttering of more than 300 chapters in the country.

"We call on the Russian authorities to ensure that Russia's anti-terrorism and anti-extremism legislation is not misused to target members of peaceful religious minorities, including the Jehovah's Witnesses," Toner said. "The prosecution of peaceful religious minority groups for 'extremism' creates a climate of fear which itself undermines efforts to combat the threat of radicalization."

Russian prosecutors had argued in court that the group is "a threat to the rights of the citizens, public order and public security." 
The Justice Ministry showed pamphlets from the group that it argued posed "a threat to health."

But the U.S. questioned the legal underpinning of such a ban.

"Freedom of religion is critical to a peaceful, inclusive, stable, and thriving society. All religious minorities should be able to enjoy freedom of religion and assembly without interference, as guaranteed by the Russian Federation's constitution," Toner said.The Jehovah's Witnesses say they will appeal, within the appellate division of the Russian Supreme Court, and possibly to the European Court of Human Rights. 

Stalinism redux? II

Russia Bans Jehovah’s Witnesses, Calling It an Extremist Group
By ANDREW HIGGINS

MOSCOW — Russia’s  Supreme Court on Thursday declared Jehovah’s Witnesses, a Christian denomination that rejects violence, an extremist organization, banning the group from operating on Russian territory and putting its more than 170,000 Russian worshipers in the same category as Islamic State militants.

The ruling, which confirmed an order last month by the Justice Ministry that the denomination be “liquidated” — essentially eliminated or disbanded — had been widely expected. Russian courts rarely challenge government decisions, no matter what the evidence.

Viktor Zhenkov, a lawyer for the denomination, said Jehovah’s Witnesses would appeal the ruling. He said it had focused on the activities of the organization’s so-called administrative center, a complex of offices outside St. Petersburg, but also branded all of its nearly 400 regional branches as extremist.

“We consider this decision an act of political repression that is impermissible in contemporary Russia,” Mr. Zhenkov said in a telephone interview. “We will, of course, appeal.”

An initial appeal will be made to the Supreme Court’s appellate division, Mr. Zhenkov said, and if that fails, Jehovah’s Witnesses will take the case to the European Court of Human Rights, in Strasbourg, France.

Hard-line followers of Russia’s dominant faith, the Orthodox Church, have lobbied for years to have Jehovah’s Witnesses outlawed or at least curbed as a heretical sect, but the main impetus for the current campaign to crush a Christian group active in Russia for more than a century seems to have come from the country’s increasingly assertive security apparatus.


Founded in the United States in the 19th century, Jehovah’s Witnesses has its worldwide headquarters in the United States and, along with all foreign-led groups outside the control of the state, is viewed with deep suspicion by Russia’s post-Soviet version of the KGB: the Federal Security Service, or F.S.B.Summing up the Justice Ministry’s case against the denomination, the ministry’s representative, Svetlana Borisova, told the Supreme Court on Thursday that Jehovah’s Witnesses had shown “signs of extremist activity that represent a threat to the rights of citizens, social order and the security of society.”

During six days of hearings over two weeks, lawyers and witnesses for the religious group repeatedly dismissed the extremist allegation as absurd, arguing that reading the Bible and promoting its nonviolent message could in no way be construed as extremist.

Human Rights Watch, in a statement issued in Moscow, condemned the court ruling as “a serious breach of Russia’s obligations to respect and protect religious freedom.”

Rachel Denber, the human rights group’s deputy director for Europe and Central Asia, said the decision delivered “a terrible blow to freedom of religion and association in Russia.”

Jehovah’s Witnesses shuns political activity and has no record of even peaceful — never mind violent — hostility to the Russian authorities. But it has faced growing hostility from the state since President Vladimir V. Putin of Russia began his third term in 2012 and put the Orthodox Church at the center of his push to assert Russia as a great military and moral power.

The denomination suffered relentless persecution by the KGB during the Soviet era, and after more than a decade of relative peace following the collapse of Communism in 1991, it again became a target for official harassment under a 2002 anti-extremism law. That law makes it illegal for any group, other than the Orthodox Church and other traditional religious institutions, to proclaim itself as offering a true path to religious or political salvation.

Stalinism Redux?

Russia’s Supreme Court Rules Against Jehovah’s Witnesses

NEW YORK—After six days of hearings over the last two weeks, the Supreme Court of the Russian Federation today upheld the claim submitted by the Ministry of Justice to liquidate the Administrative Center of Jehovah’s Witnesses in Russia and 395 Local Religious Organizations (LROs) used by Witnesses throughout Russia. The ruling goes into effect immediately.

“We are greatly disappointed by this development and deeply concerned about how this will affect our religious activity,” states Yaroslav Sivulskiy, a spokesman for Jehovah’s Witnesses in Russia. “We will appeal this decision, and we hope that our legal rights and protections as a peaceful religious group will be fully restored as soon as possible.”


Jehovah’s Witnesses in Russia have 30 days to submit their appeal for consideration by a three-person panel.

Media Contacts:

International: David A. Semonian, Office of Public Information, +1-845-524-3000


Russia: Yaroslav Sivulskiy, +7-911-087-8009