A hostile takeover?

Horizontal Gene Transfer: Sorry, Darwin, It's Not Your Evolution Any More

Denyse O'Leary 

Horizontal gene transfer (HGT), sometimes called lateral gene transfer (LGT), is a profound recent discovery in genetics: Genome mapping has shown that bacteria can acquire genes from the bacteria around them --that is, horizontally -- rather than from a previous generation (vertical transfer), as when a parent cell divides into two daughter cells. They can transfermultiple segments of DNA at once to fellow species members.

But that was hardly the critical finding. This is: Because bacteria are found everywhere and are comparatively simple, they can move newly acquired genes between life forms in the other domains of life. They can produce heritable changes with no recent common ancestor. For example,

-- Some researchers have reported that a massive network of recent gene exchange connects bacteria from around the world, "10,000 unique genes flowing via HGT among 2,235 bacterial genomes," providing the bacteria with genetic information they didn't inherit from their parent cells, including antibiotic resistance.

Microbes were fighting natural antibiotics this way, we are told, from long before humans learned how to invent them. Bacteria from 30,000 years ago that resist today's antibiotics have been found in permafrost (underground frost that never melts). A generalized antibiotic resistance may have been traded between types of bacteria long ago, including some that subsequently got frozen for millennia.

-- Bacteria were assumed to need long, intact strings of DNA to integrate. But it turns out that they can also use discarded DNA. A 2013 PNAS papernotes:

Our surroundings contain large amounts of strongly fragmented and damaged DNA, which is being degraded. Some of it may be thousands of years old. Laboratory experiments with microbes and various kinds of DNA have shown that bacteria take up very short and damaged DNA from the environment and passively integrate it in their own genome. Furthermore this mechanism has also been shown to work with a modern bacteria's uptake of 43,000 years old mammoth DNA.

One is reminded of mechanics who visit wrecking yards to locate reuseable spare parts.

-- Sometimes the microbes' methods of harvesting genes are more sophisticated than we might expect. Bacteria that grow on crustaceans can absorb fragments containing more than 40 genes, using a small "spear." Researcher Melanie Blokesch describes that number as "an enormous amount of new genetic information." That may explain why antibiotic resistance sets in so quickly.

Bacteria just do not play by Darwin's rules.

Neither, it turns out, do plants, animals, or fungi, not when bacteria shuttle between them, absorbing, carrying, and delivering genes that get incorporated into other genomes.

-- Scientific American observes that HGT from bacteria to more complex life forms (eukaryotes) is more common than formerly believed:

Muller and his colleagues scanned the genomes of 149 eukaryotes, and found acdS-like genes in 65 of them -- 61 in fungi and 4 in parasitic microorganisms called oomycetes, includingPhytophthora infestans, the microbe responsible for the Irish potato famine. After analysing the organisms' genetic family trees, the researchers determined that the most likely explanation was that three different kinds of bacterium had donated the gene to the fungi and oomycetes in a total of 15 different horizontal-gene-transfer events.

-- In another study, ferns were found to have adapted to low light via HGTfrom moss-like hornworts from which they diverged 400 million years ago:

"We're actually seeing more and more incidence of horizontal gene transfer in plants"... However neochrome was transferred, it seems to have occurred at just the right moment in ferns' evolutionary history.

-- The giant Rafflesia flower has stolen genes from plants it parasitizes.Genes may even be shared among plants with only a distant ancestral relationship.

-- Animals do it too. Bacteria are known to use horizontal gene transfer by injecting toxins into rival cells. And some species of ticks and mites (relatives of spiders) have been found to acquire these toxins to get rid of the bothersome bacteria.

-- The bdelloid rotifer (pictured above) holds the record for HGT (as of 2013). It dispenses with sex, and at least 8 percent of its genes are considered likely to have been acquired by HGT.

Even vertebrates do it.

-- An article in prestigious Scientist tells us, "Scientists show that horizontal transfer of a particular DNA sequence among a diverse range of vertebrates is more widespread than previously believed."

The results can be surprising. In one gene sequence, cows are closer to snakes than elephants, with shared parasites as a possible vector.

-- One finding could affect lab research: Bacterial DNA pass traits from mouse mother to offspring, which means, among other things that when we study lab mice, we must account for the possibility that inherited bacteria and their genes could influence the trait under study--as opposed to assuming that the Darwinian mechanism of vertical common ancestry is the only possible source of genes.

-- Lastly, in one remarkable case, an invertebrate stole more than a plant's genes: Sea slugs were known to steal chloroplasts from algae (kleptoplasty) since the 1970s. But one question was how the chloroplasts lasted so much longer in the slug than in the algae. A recent finding:

"This paper confirms that one of several algal genes needed to repair damage to chloroplasts, and keep them functioning, is present on the slug chromosome," Pierce says. "The gene is incorporated into the slug chromosome and transmitted to the next generation of slugs." While the next generation must take up chloroplasts anew from algae, the genes to maintain the chloroplasts are already present in the slug genome, Pierce says.

"There is no way on earth that genes from an alga should work inside an animal cell," Pierce says. "And yet here, they do. They allow the animal to rely on sunshine for its nutrition. So if something happens to their food source, they have a way of not starving to death until they find more algae to eat."

The slug did not "evolve" this trait, it hijacked it. One researcher has commented, "The process of evolution just isn't what many evolutionary biologists think it is."

But surely bacteria could not transfer DNA to humans, considering how complex we are? Yes they can, apparently,according to a recent article in the Scientist.

-- For example, we are told in Aeon Magazine, "... in Japan, some people's gut bacteria have stolen seaweed-digesting genes from ocean bacteria lingering on raw seaweed salads."

-- It may not even be rare, say researchers published in Genome Biology:

Lead author Alastair Crisp from the University of Cambridge, UK, said: "This is the first study to show how widely horizontal gene transfer (HGT) occurs in animals, including humans, giving rise to tens or hundreds of active 'foreign' genes. Surprisingly, far from being a rare occurrence, it appears that HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing, meaning that we may need to re-evaluate how we think about evolution."

-- From the Economist, we learn:

Alastair Crisp and Chiara Boschetti of Cambridge University, and their colleagues, have been investigating the matter. Their results, just published in Genome Biology, suggest human beings have at least 145 genes picked up from other species by their forebears. Admittedly, that is less than 1 percent of the 20,000 or so humans have in total. But it might surprise many people that they are even to a small degree part bacterium, part fungus and part alga.

Dr Crisp and Dr Boschetti came to this conclusion by looking at the ever-growing public databases of genetic information now available. They did not study humans alone. They looked at nine other primate species, and also 12 types of fruit fly and four nematode worms. Flies and worms are among geneticists' favourite animals, so lots of data have been collected on them. The results from all three groups suggest natural transgenics is ubiquitous.

So we are a long way from when biochemist Christian de Duve (1917-2013), grudgingly admitted the significance of horizontal gene transfer, noting that it "... has been recognized as a major complication when attempting to use molecular data to reconstruct the tree of life."¹

It certainly has, because where HGT is in play, there just isn't a tree of life. Even popular science writers are beginning to recognize the significance of this fact. New Scientist's Mark Buchanan writes: "Just suppose that Darwin's ideas were only a part of the story of evolution. Suppose that a process he never wrote about, and never even imagined, has been controlling the evolution of life throughout most of the Earth's history."

No need to suppose, actually; it's here. But HGT isn't "controlling the evolution of life." It is simply breaking Darwinism's monopoly on accounting for it.

Some ask, why is HGT bad news for Darwin? Can't Darwinism simply co-opt it? No. Admittedly, some hope it can, sort of. In Aeon Magazine, science writer Ferris Jabr suggests,

The fact that horizontal gene transfer happens among eukaryotes does not require a complete overhaul of standard evolutionary theory, but it does compel us to make some important adjustments...

Ferris, it really does require a complete overhaul.

He goes on to defend Darwinism by personifying the gene:

We did not invent gene transfer; DNA did. Genes are concerned with one thing above all else: self-perpetuation. If such preservation requires a particular gene to adapt to a genome it has never encountered before - if riding a parasite from one species to another turns out to be an extremely successful way of guaranteeing perpetuity - so be it. Species barriers might protect the integrity of a genome as a whole, but when an individual gene has a chance to advance itself by breaching those boundaries, it will not hesitate.

No, no, no. Genes can travel but they have no minds and no desires. When the Dawkinsian metaphysic of the vertical "selfish gene" is used to assign properties of minds to genes, it becomes not only questionable but ridiculous. What Jabr mainly demonstrates is how difficult it is for people raised on Darwin (and Dawkins) to maintain a science-based view of evolution in the face of evident non-Darwinian evolution.

Speaking of Richard Dawkins: For over a century, Darwinism was the "must be" explanation, the only "scientific one." As Dawkins put it (p. 287, Blind Watchmaker, 1986):

My argument will be that Darwinism is the only known theory that is in principle capable of explaining certain aspects of life. If I am right it means that, even if there were no actual evidence in favour of the Darwinian theory (there is, of course) we should still be justified in preferring it over all rival theories.

But Darwinism is not "the only known theory that is in principle capable of explaining certain aspects of life." Claims that were formerly merely preferred must be tested against HGT. True, some of the example findings given above may need revision or replacement. But many more will likely turn up, as research uncovers HGT in many genomes.

Anything HGT does, Darwinian evolution did not do. As more and more pieces are carved out of Darwin's territory, just think of the impact on the vast project of "Darwinizing the culture."

One report boldly alludes to Darwin's plight:

It's a firmly established fact straight from Biology 101: Traits such as eye color and height are passed from one generation to the next through the parents' DNA.

But now, a new study in mice by researchers at Washington University School of Medicine in St. Louis has shown that the DNA of bacteria that live in the body can pass a trait to offspring in a way similar to the parents' own DNA.

The latter explanation involves a major change in thinking because it suggests that traits affected by bacteria can pass from mothers to their offspring in the same manner as traits affected by mouse DNA.

As a major change in thinking, HGT is very bad news for Darwinism.

So we find ourselves in an odd situation: Yes, there is some evidence for evolution, but it provides no help to the publicly funded, widely believed, court-enforced Darwinian theory stoutly defended in media as "evolution."

And things will get stranger still when we look at epigenetics. For now, just suppose a sharply diminished Darwin.

Notes:

(1) Christian de Duve, "Mysteries of Life" , in Bruce L. Gordon and William A. Dembski, The Nature of Nature: Examining the Role of Naturalism in Science(Wilmington, DE: ISI Books, 2011), p. 348.

The future of money?

Yet more on the formalising of the design inference.

Epigenetics vs. Darwin

RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants

The problem with epigenetic mechanisms is that they respond to future, unforeseen, environmental challenges. They don’t work in the present, and so even if random mutations somehow created such mechanisms, they would not be selected for. In other words, epigenetic mechanisms contradict evolutionary theory—there is no fitness improvement at the time of origin by random mutations, so there is no selection. Nor do evolutionists have an explanation for this—they don’t even try. Consider a paper discussing a particular epigenetic mechanism subtitled: “The Evolution of a Complex Epigenetic Pathway in Flowering Plants.”

The paper discusses a complicated cellular process in which different segments of DNA are copied (creating RNA transcripts). The RNAs work together to methylate the DNA at a particular location. The methylation “mark” helps to regulate gene expression. But how did this epigenetic mechanism evolve?

This epigenetic mechanism involves a small army of molecular machines. For instance, the different RNAs are transcribed, from the DNA, by different copying machines. These copying machines consist of a dozen protein subunits. The paper states that two of the copying machines—which are central to the epigenetic mechanism—each evolved from a third copying machine. Why?

The idea of the two copying machines evolving from the third copying machine is problematic because there are significant differences between them. The paper gives no justification for such an unlikely event. It gives no justification because there is none, save for the presupposition that evolution is true. Under evolutionary theory it must have occurred.

In other words, there is no empirical evidence that the two copying machines evolved from the third copying machine and there are enormous problems with the idea. But it is taken as a given because evolution is assumed to begin with.

The point here is that in attempting to explain the evolution of a complex epigenetic pathway the paper presupposed evolution a priori.

Similarly, the paper states that the two copying machines “are evolving rapidly.” Again, where did this come from? Does the science actually show this to be true? Does the science even merely provide any evidence at all for this astonishing claim?

Again, no and no.

Nowhere does the science demonstrate or prove that the two copying machines “are evolving rapidly.” In fact, the science doesn’t even provide any evidence at all for this.

Nada.

What the science shows is that the proteins in the two copying machines have significant differences compared to the corresponding proteins in the third copying machine. The two copying machines are more different from the third copying machine, than would normally be expected if they had evolved from that third copying machine.

But since evolution is assumed to be true to begin with, then those two copying machines must be “evolving rapidly.”

Again, the claim is driven by the belief that evolution is true. There is no empirical evidence that the two copying machines are evolving rapidly, let alone that they even evolved at all.

This is all dogma. There is no science here.

The paper then spends considerable effort attempting to reckon with the various problems that arise when their evolutionary history is assumed. There are duplication events and introns are mysteriously inserted. There are fusion events to explain unexpected differences, and other cases are simply unknown. There must have been a complex series of evolutionary events the reasons for which “remain obscure,” and the evolutionary origin of one gene is “a mystery.”

It is a long sequence of just-so stories. A long sequence of special events just happened to happen, which luckily produced this new epigenetic mechanism.

And then, after all of this, it would not be selected for. All of these events, and the resulting epigenetic mechanism would not improve the evolutionary fitness.

This evolutionary tale is not supported by the empirical evidence. Instead, it is supported by the prior assumption that evolution occurred.

Posted by Cornelius Hunter 

Darwinism's miracles.

Miracles in Evolutionary Theory
Evolution News & Views

Charles Darwin gave science a major step forward in intellectual progress, many assume. He replaced what he considered "miracles" of design by natural processes. His goal seemed noble to many: unifying the disparate organisms of the earth into a unified picture of descent with modification, united by a law of nature he called natural selection. Science was thus rid of miracles. So he thought.

Darwin's law of nature, however, amounted to little more than historical contingency. Variations appear randomly in his view -- without direction or purpose -- at the basis of life which evolutionists today usually locate in the genes. From the "bottom up" view, to avoid looking miraculous, variations had to be small and gradual, barely making a difference to the organism except for some slight increment in a nebulous quality he called "fitness." From the "top down" view, however (the tree of life), many disparate organisms needed to be united by lines of common descent with huge gaps between them. Bringing the bottom-up and top-down pictures together has not been easy. Two recent articles show how modern evolutionists do it by employing miracles -- stretching credibility beyond the breaking point to bring the two pictures together.

In Current Biology, Thibaut Brunet and Detlev Arendt appear excited about the possibility of solving the "hard problem of cartilage origins." Their title, a play on the "hard problem of consciousness" described by David Chalmers, refers here to the origin of hard parts in animal bodies. Can all the disparate animal body plans be united by a common ancestor?

Skeletons are misunderstood. Because of their resistance to decay, bones have become symbols of death; yet, they are intensely alive tissues, undergoing lifelong active remodeling. To the evolutionary biologist, the hard parts of animals are similarly double-faced: their endurance makes them the prime candidates for fossilization and provides paleontologists with a wealth of information on the skeleton of extinct animals. From the paleontologist's view, animal evolution is thus mainly the evolution of hard parts (plus what can be deduced from them). But for the same reason, the origin of the first animal skeletons, and the ancestral structures that gave rise to them in soft-bodied animals, remains mysterious; preservation of soft tissue is too rare to provide a clear-cut solution. For more than a century, morphologists have been debating, with precious little evidence, the hard questions of skeleton origins: When did animal skeletons first evolve? Did they appear once or several times independently? Which ancestral soft tissues first became rigid, and by what molecular mechanisms? A recent study by Tarazona and co-authors, comparing skeleton formation between invertebrates and vertebrates at the molecular level, sheds new light on these questions. [Emphasis added.]
As is common in evolutionary literature, Brunet and Arendt do not ask whether hard parts evolved, but only how they evolved. According to the "rules of science," questioning naturalism is forbidden. By limiting one's explanatory toolkit to unguided natural processes, however, difficulties arise. There's nothing like an appeal to miracles to get around a difficulty. As Finagle advised, "Do not believe in miracles. Rely on them."

The authors admit that "Historical attempts to compare vertebrate and invertebrate skeletons have not fared well." That's why Tarazona's solution appeals to them. That paper found similarities in cartilage formation between a cuttlefish and a horseshoe crab -- very distant creatures in Darwin's ancestral tree, belonging to different phyla. In their thinking, therefore, the common ancestor of both these animals must have had the ability to manufacture cartilage. Brunet and Arendt masterfully illustrate possible evolutionary links between those animals and annelids (earthworms), brachiopods, arthropods, and vertebrates by pointing out similarities between the general organization of their collagen expression sites and the developmental genes that regulate the expression of collagen. Like a magic trick, it looks simple until you probe the details. Consider:

They give no explanation for the emergence of 3 sets of genes that code for collagen. "The ancestral soxD+ soxE+ colA+ ventral mesentery is assumed to have given rise to both the chordate sclerotome and the chelicerate endosternite," they say, 'assuming' that six transcription factor genes and the collagenase gene conspired to create the first hard parts. Either the genes were co-opted from some other function, or emerged on their own. Is that magic? Luck? What else in naturalistic evolution could "give rise" to the improbable?

Collagen is a complex protein, using all 20 amino acids except tryptophan. Wikipedia lists 7 steps in its manufacture inside cells, including the formation of precursors (like "pre-pro-peptide to pro-collagen") followed by extensive post-translational modifications.

The formation of cartilage involves additional complex steps, including a balance between the signal proteins Hedgehog and Wnt. You can't just assume the innovation of collagen is going to automatically lead to cartilage or bone. As for bone, specialized cells (osteoblasts and osteoclasts) build and dissolve bone in a delicate balance of processes.

Hard parts do not appear randomly in cells or on animal body plans, but are specifically arranged for function. Look at the elaborate armor on Cambrian comb jellies (Science Advances), assumed by some evolutionists to be one of the earliest animal phyla. It's not enough to create collagen building blocks. The materials have to be delivered to specific locations during development.

One "miraculous" innovation like collagen would be astonishing, but that's not enough. Collagen makes a "scattered appearance" on the tree of life. The authors invoke even more miracles to explain this: "If so, this would exemplify an often neglected type of independent evolution called 'parallel evolution', in which the same ancestral structure undergoes a similar sequence of modifications in separate lines of descent." Giving an improbable wonder a name like "parallel evolution" does not make it any less "miraculous."

Hard parts appear suddenly in the fossil record. Wave the magic wand for more miracles! "Also, the fossil record suggests that most phyla evolved skeletons in a rapid and parallel fashion during the Cambrian explosion, fuelled by an arms race between the first elaborate predators and their prey." Our readers have heard plenty about all the failed explanations for the Cambrian explosion, so we won't belabor the point here. Suffice it to say that the details do not make belief in "evolutionary innovations" as Darwinians are wont to call them look "natural."

Good Luck, LUCA

An even greater appeal to miracles is found in evolutionary stories about the origin of life, because until reliable self-replication begins, there can be no natural selection. Consequently, evolutionists cannot avail themselves of their favorite hand-waving rescue device and can only appeal only to laws of chemistry and to chance.

The "last universal common ancestor" (LUCA) "is what scientists call the forerunner of all living things," Live Science observes. LUCA must mark the point, therefore, at which natural selection begins, because if natural selection had acted on anything prior (such as speculative "RNA World" replicators), it had no bearing on life as we actually observe it. Anything prior left no record; it is outside empirical science.

As much as evolutionists would like to simplify LUCA, there comes a point at which the organism would not have been able to carry on the necessary functions of metabolism, motility, and reproduction to be called alive. LUCA had to be a "cell" of some sort, with a genetic code and protein machines enclosed in a membrane to keep it together. As we learned in March, Craig Venter's team could not get their synthetic cell simpler than 463 genes. The new study says,

Much about LUCA remains uncertain; while previous research suggested that it was little more than a chemical soup from which evolution gradually built more complex forms, recent work suggested it may have been a sophisticated organism with an intricate structure.
How sophisticated? By comparing millions of prokaryotic genes, researchers at Heinrich Heine University in Düsseldorf, Germany estimated the requirements for LUCA:

The genes the scientists examined were blueprints for proteins. (Some genes are not thought to direct protein-making.) Of the 286,514 protein groups the researchers looked at, only 355 matched the strict criteria that the researchers set for potentially belonging to LUCA. Previous research had uncovered the functions of many of these genes, so they now shed light on LUCA's habitat and lifestyle.
Their paper, published in Nature Microbiology, expects this "forerunner of all living things" to have been able to metabolize hydrogen, fix nitrogen, use transition metals and coenzymes, and much more. It had genomics and epigenomics: "Its genetic code required nucleoside modifications and S-adenosyl methionine-dependent methylations." None of these are simple! Furthermore, the researchers believe that LUCA was a thermophile, living in the harsh conditions of hot springs or hydrothermal vents. The thermophiles we see today have sophisticated mechanisms for repairing and preserving their DNA and proteins from destruction by heat.

Did LUCA arise by chance? Jeff Errington, cell biologist at Newcastle University, doesn't even ask the question. At The Conversation, he speculates about what kind of organism LUCA was, assuming it originated in the high temperatures of hot springs, had enzymes and a genetic code, metabolized hydrogen, and was well equipped for survival. He knows, though, that LUCA had minimum requirements:

Sadly, without a time machine, there is no way to directly verify these results. Nevertheless, this information will now be of great interest, not least to those scientists wishing to use the information to inform their bottom-up experiments in recreating modern forms of primitive life. But it will not be easy, given the requirement for high temperature, nitrogen, carbon dioxide and explosive hydrogen gas.
In Signature in the Cell, building on research by Douglas Axe on protein function, Stephen Meyer calculated the probability of one relatively short protein 150 amino acids in length as being one chance in 10 to the 164th power (10-164, pp. 210-212). In other words, expecting just one protein by chance exceeds the universal probability bound calculated by William Dembski (10-150) by 14 orders of magnitude -- 100 trillionth the chance! The word "miracle" doesn't even come close to belief in such an event. Yet these evolutionists want us to believe that somewhere between 355 and 463 genes or protein products, all working in concert, emerged by chance.

It's time to stop the caricature of ID by evolutionists that the former believe in miracles and the latter do not. It makes better sense to think that the "innovations" we observe were planned for a purpose by an intelligent cause necessary and sufficient to explain them, rather than to trust in sheer dumb luck. Arranging parts for function is not a "miracle" anyway. We do it all the time ourselves against the natural course of things.

Yet another Darwinian bedtime story?

Test Your Evolutionary Storytelling Skills
David Klinghoffer | @d_klinghoffer

Ever notice that some older people sleep less and sometimes more fitfully than younger people? Sure you did. On the other hand, you’ve probably also known old people who sleep in and some middle aged and younger people who complain of sleep problems. I could introduce you to representatives of all these groups from my own family.

Any phenomenon in human life is a suitable subject for evolutionary storytelling, and telling stories about the past is what a team of scientists set out to do. Traveling to Africa, they fitted members of the Hadza people of Tanzania with actigraph devices to monitor their sleep.

The subjects of the experiment are hunter-gatherers who slumber outdoors in small groups in the wild. The study confirmed what you would have guessed: It’s pretty typical for older people to doze and wake and doze and wake more than young people. They wake up earlier too. From Science Daily:

As part of the study, 33 healthy men and women aged 20 to 60 agreed to wear a small watch-like device on their wrists for 20 days, that recorded their nighttime movements from one minute to the next.

Hadza sleep patterns were rarely in sync, the researchers found. On average, the participants went to bed shortly after 10 p.m. and woke up around 7 a.m. But some tended to retire as early as 8:00 p.m. and wake up by 6 a.m., while others stayed up past 11 p.m. and snoozed until after 8 a.m.

In between, they roused from slumber several times during the night, tossing and turning or getting up to smoke, tend to a crying baby, or relieve themselves before nodding off again.

As a result, moments when everyone was out cold at once were rare. Out of more than 220 total hours of observation, the researchers were surprised to find only 18 minutes when all adults were sound asleep simultaneously. On average, more than a third of the group was alert, or dozing very lightly, at any given time.

They always have to put in that they were “surprised.” Otherwise why bother with the study? Anyway, that’s really all you need to know. Now take the challenge: With these facts, tell an imaginative story about human evolution. Think about it for a moment and if you want, write down your answer on some scratch paper.

Here’s a hint: Did you follow Monday’s news story  from Colorado about a 19-year-old camp counselor, sleeping in the open by a lake, who awoke to find a bear sharpening its teeth on his skull? The counselor was camping out with four younger campers. He survived, despite serious lacerations.

OK, what did you come up with? If it’s the following, I wouldn’t be surprised: Long ago, ancient humans slept in the open, like these African hunter-gatherers. Having older people with you improves the likelihood that if hostile animals or people creep up, then someone will be awake to sound the alarm. Evolution selected for this feature. End of story.

We read on:

The findings may help explain why Hadza generally don’t post sentinels to keep watch throughout the night — they don’t need to, the researchers say. Their natural variation in sleep patterns, coupled with light or restless sleep in older adults, is enough to ensure that at least one person is on guard at all times.

…

[The scientists] call their theory the “poorly sleeping grandparent hypothesis.” The basic idea is that, for much of human history, living and sleeping in mixed-age groups of people with different sleep habits helped our ancestors keep a watchful eye and make it through the night.

“Any time you have a mixed-age group population, some go to bed early, some later,” Nunn said. “If you’re older you’re more of a morning lark. If you’re younger you’re more of a night owl.”

If the Colorado bear attack victim had been camping out with his grandparents, it’s possible one of them might have noticed the bear before it could get too close. Same thing if the group had posted a lookout, as I imagine some campers in the area, worried about bears, may do tonight. It’s genuinely surprising the Hadza don’t assign anyone to act as a sentinel. This would make me nervous if I were one of them, and it might even interfere with sleep.

In any event, is this science or storytelling? From the Abstract of the study:

Chronotype variation and human sleep architecture (including nocturnal awakenings) in modern populations may therefore represent a legacy of natural selection acting in the past to reduce the dangers of sleep.

It may or it may not. There are physiological reasons that sleep varies with age. Babies also wake up periodically during the night, while many teenagers have a hard time getting up in the morning. The story about ancient human lifestyles is interesting, but attributing “human sleep architecture” to natural selection is merely what chemist and National Academy of Sciences member Philip Skell, writing in The Scientist, dismissed as evolutionary “narrative gloss.”

Besides needing to say they are “surprised” by the results, the researchers, who published in their work in the  Proceedings of the Royal Society B, are expected to come up with a reason why the findings are of practical usefulness. They oblige:

“A lot of older people go to doctors complaining that they wake up early and can’t get back to sleep,” [Duke University anthropologist Charlie] Nunn said.

“But maybe there’s nothing wrong with them. Maybe some of the medical issues we have today could be explained not as disorders, but as a relic of an evolutionary past in which they were beneficial,” said Nunn.

Some older people are bothered by their irregular sleep patterns. Others aren’t bothered by it. It’s the ones who are bothered that go to the doctor to complain. For them, it is hard to see what help a physician could offer, that would make a difference, by telling an evolutionary bedtime story.

And yet even more on the real world's anti-Darwinian bias.

Math, Computers, and Evolution: Robert Marks on Searches and Artificial Intelligence
Evolution News | @DiscoveryCSC

On a new episode of ID the Future, CSC Director of Communications Rob Crowther talks with Robert Marks, Distinguished Professor of Electrical and Computer Engineering at Baylor University, about Marks’s new book, Introduction to Evolutionary Informatics, which makes an important but esoteric-sounding field accessible to the general reader.

Dr. Marks talks about how he and William Dembski originally connected as researchers, and began working on the subject in 2007, how intelligent design can inform thinking on artificial intelligence, and what a “search for a search” means in evolutionary terms. Download the podcast here, or listen to it here.

Get your copy of Introduction to Evolutionary Informatics  by Winston Ewert, William Dembski, and Robert Marks! More information is at the Evolutionary Informatics Lab’s website,  evoinfo.org — that’s evo info, as Dr. Marks helpfully explains, not evil info. Just so there’s no confusion.

The Royal Society on Darwinism's "explanatory deficits"

Why the Royal Society Meeting Mattered, in a Nutshell

Evolution News | @DiscoveryCSC

We devoted  considerable attention to last month’s Royal Society meeting in London. Otherwise, the three-day conference on “New Trends in Evolutionary Biology” was kept rather quiet in the media.

Oh, there were a few reports. Writing for the Huffington Post,  science journalist Suzan Mazur complained of a lack of momentousness: “[J]ust what was the point of attracting a distinguished international gathering if the speakers had little new science to present? Why waste everyone’s time and money?” On the other hand, a write-up in The Atlantic by Carl Zimmer acknowledged a sense of strain between rival cliques of evolutionists: “Both sides offered their arguments and critiques in a civil way, but sometimes you could sense the tension in the room — the punctuations of tsk-tsks, eye-rolling, and partisan bursts of applause.”

Mild drama notwithstanding, why should anyone care about this meeting?

Despite the muffled coverage, the meeting was still significant in a number of ways. First, remember that the Royal Society is arguably the world’s most august scientific body. Its founders included Robert Boyle and it was later headed for 24 years (1703-1727) by Isaac Newton — a fact that is hard to forget when they have his death mask on prominent display in a glass case. Portraits of Boyle and Newton on the walls look down from above. The historical connections lent a certain weight by themselves to the proceedings.

That such a thoroughly mainstream scientific organization should now at last acknowledge problems with the received neo-Darwinian theory of evolution is also obviously notable. Indeed, from our point of view, though presenters  ignored, dismissed, or mocked ID, not realizing the number of design-friendly scientists in the audience, the proceedings confirmed something ID advocates, including Stephen Meyer and others, have been saying for years.

Consider, for example, Meyer’s provocative claim in the Prologue to Darwin’s Doubt:

The technical literature in biology is now replete with world-class biologists routinely expressing doubts about various aspects of neo-Darwinian theory, and especially about its central tenet, namely the alleged creative power of the natural selection and mutation mechanism.

Nevertheless, popular defenses of the theory continue apace, rarely if ever acknowledging the growing body of critical scientific opinion about the standing of the theory. Rarely has there been such a great disparity between the popular perception of a theory and its actual standing in the relevant peer-reviewed science literature.

The opening presentation at the Royal Society conference by one of those world-class biologists, Austrian evolutionary theorist Gerd Müller, underscored exactly Meyer’s point. Müller opened the meeting by discussing several of the fundamental “explanatory deficits” of “the modern synthesis,” that is, textbook neo-Darwinian theory. (Discovery Institute’s Paul Nelson recounted Müller’s remarks here, on which in part we base the following.) According to Müller, the as yet unsolved problems include those of explaining:

Phenotypic complexity (the origin of eyes, ears, body plans, i.e., the anatomical and structural features of living creatures);

Phenotypic novelty, i.e., the origin of new forms throughout the history of life (for example, the mammalian radiation some 66 million years ago, in which the major orders of mammals, such as cetaceans, bats, carnivores, enter the fossil record, or even more dramatically, the Cambrian explosion, with most animal body plans appearing more or less without antecedents); and finally

Non-gradual forms or modes of transition, where you see abrupt discontinuities in the fossil record between different types.

As Müller has explained in previously published work (with Stuart Newman), although “the neo-Darwinian paradigm still represents the central explanatory framework of evolution, as represented by recent textbooks” it “has no theory of the generative.”1 In other words, the neo-Darwinian mechanism of mutation and natural selection lacks the creative power to generate the novel anatomical traits and forms of life that have arisen during the history of life. Yet, as Müller noted, neo-Darwinian theory continues to be presented to the public via textbooks as the canonical understanding of how new living forms arose — reflecting precisely the tension between the perceived, and actual, status of the theory that Meyer described in Darwin’s Doubt.

Yet, the most important lesson of the Royal Society conference lies not in its vindication of claims that our scientists have made, gratifying as that might be to us, but rather in defining the current problems and state of research in the field. The conference did an excellent job of defining the problems that evolutionary theory has failed to solve, but it offered little, if anything, by way of new solutions to those longstanding fundamental problems.

Much of the conference subsequent to Müller’s talk did discuss various other proposed evolutionary mechanisms. Indeed, the prime movers in the Royal Society event, Müller, along with James Shapiro, Denis Noble, and Eva Jablonka — the “Third Way of Evolution” crowd — have proposed repairing the explanatory deficits of the modern synthesis by highlighting evolutionary mechanisms other than random mutation and natural selection. Much debate at the conference centered around the question of whether these new mechanisms could be incorporated into the basic population genetics framework of neo-Darwinism, thus making possible a new “extended” evolutionary synthesis, or whether the emphasis on new mechanisms of evolutionary change represented a radical, and theoretically incommensurable, break with established theory. This largely semantic, or classificatory, issue obscured a deeper question that few, if any, of the presentations confronted head on: the issue of the origin of genuine phenotypic novelty — the problem that Müller described in his opening talk.

Indeed, by the end of Day 3 of the meeting, it seemed clear to many of our scientists, and others in attendance with whom they talked, that the puzzle of life’s novelties remained unsolved — if, indeed, it had been addressed at all. As a prominent German paleontologist in the crowd concluded, “All elements of the Extended Synthesis [as discussed at the conference] fail to offer adequate explanations for the crucial explanatory deficits of the Modern Synthesis (aka neo-Darwinism) that were explicitly highlighted in the first talk of the meeting by Gerd Müller.”

In Darwin’s Doubt, for example, Meyer emphasized the obvious importance of genetic and other (i.e., epigenetic) types of information to building novel phenotypic traits and forms life. The new mechanisms offered by the critics of neo-Darwinism at the conference — whether treated as part of an extended neo-Darwinian synthesis or as the basis of a fundamentally new theory of evolution — did not attempt to explain how the information necessary to generating genuine novelty might have arisen. Instead, the mechanisms that were discussed produce at best minor microevolutionary changes, such as changes in wing coloration of butterflies or the celebrated polymorphisms of stickleback fish.

Moreover, the mechanisms that were discussed — niche construction, phenotypic plasticity, natural genetic engineering, and so on — either presupposed the prior existence of the biological information necessary to generate novelty, or they did not address the mystery of the origin of that information (and morphological novelty) at all. (Not all the mechanisms addressed were necessarily new, by the way. Niche construction and phenotypic plasticity have been around for a long time.)

Complex behaviors such as nest-building by birds, or dam construction by beavers, represent examples of niche construction  in which some organisms themselves demonstrate the capacity to alter their environment in ways that may affect the adaptation of subsequent generations to the environment. Yet no advocate of niche construction at the meeting explained how the capacity for such complex behaviors arose de novo in ancestral populations, as they must have done if the naturalistic evolutionary story is true.

Rather, these complex behaviors were taken as givens, leaving the critical question of their origins more or less untouched. While there is abundant evidence that animals can learn and transmit new behaviors to their offspring —  crows in Japan for instance, have learned how to use automobile traffic to crack open nuts — all such evidence presupposes the prior existence of specific functional capacities enabling observation, learning, and the like. The evolutionary accounts of niche construction theory therefore collide repeatedly with a brick wall marked “ORIGINAL COMPLEX FUNCTIONAL CAPACITY REQUIRED HERE” — without, or beyond which, there would simply be nothing interesting to observe.

Jim Shapiro’s talk, clearly one of the most interesting of the conference, highlighted this difficulty in its most fundamental form. Shapiro presented fascinating evidence showing, contra neo-Darwinism, the non-random nature of many mutational processes — processes that allow organisms to respond to various environmental challenges or stresses. The evidence he presented suggests that many organisms possess a kind of pre-programmed adaptive capacity — a capacity that Shapiro has elsewhere described as operating under “algorithmic control.” Yet, neither Shapiro, nor anyone else at the conference, attempted to explain how the information inherent in such algorithmic control or pre-programmed capacity might have originated.

This same “explanatory deficiency” was evident in the discussions of the other mechanisms, though we won’t attempt to demonstrate that exhaustively here. We would direct readers, however, to Chapters 15 and 16 of Darwin’s Doubt, where Meyer highlighted the way in which, not just neo-Darwinism, but also newer evolutionary mechanisms, including many discussed at the conference, fail to solve the question of the origin of information necessary to generate novelty. In those chapters, he reviewed a range of proposed fixes to the Modern Synthesis. He acknowledged and described the various advantages that many of these proposals have over neo-Darwinism, but also carefully explained why each of these mechanisms falls short as an explanation for the origin of the biological information necessary to build novel structures and forms of animal life. He quoted paleontologist Graham Budd who has observed: “When the public thinks about evolution, they think about [things like] the origin of wings….But these are things that evolutionary theory has told us little about.”

Many fascinating talks at the Royal Society conference described a number of evolutionary mechanisms that have been given short shrift by the neo-Darwinian establishment. Unfortunately, however, the conference will be remembered, as Suzan Mazur intimated in her coverage, for its failure to offer anything new. In particular, in our judgment, it failed to offer anything new that could help remedy the main “explanatory deficit” of the neo-Darwinian synthesis — its inability to account for the origin of phenotypic novelty and especially, the genetic and epigenetic information necessary to produce it. These are still problems that evolutionary theory tells us little about.

Notes:

(1) Gerd Müller and Stuart Newman, On the Origin of Organismal Form (Cambridge, MA: MIT Press, 2003), p.7.

Nature's navigators v. Darwin.

Getting Around: Animal Migrations Exceed Evolutionary Expectations
Evolution News | @DiscoveryCSC

Why not stay put? In evolutionary terms, that seems an easier option for migrating animals. The evolutionist might argue that animals need to follow the food supply, but since natural selection is supposed to be so clever, why not evolve hibernation or a smaller stomach? Sure, animals need to follow the temperature, but why not just evolve thicker fur or feathers like snowy owls?

For every spectacular case of animal migration, biologists can find other animals that stay put in the cold, like the snowshoe hare, or go into hibernation, like bears or insect pupae, surviving the cold months of winter. Plants stay put whether in the Arctic or the desert. Why should animals travel thousands of miles through precarious weather or trackless seas? It doesn’t make evolutionary sense. Let’s look at some recent findings about animal migration.

Fish: European Eels

   

In Evolution: Evolution: Still a Theory in Crisis, Michael Denton describes the amazing life cycle of European eels. It’s an example of “baroque” design in the animal world, he argues, totally inexplicable by any kind of “selective pressure” that might be alleged to explain it. Since we last wrote about eels in October, more has been learned about the spectacular migration of these freshwater fish out to the salty ocean. We had asked, “Are eels equipped with magnetosensing, like salmon, sea turtles, and Monarch butterflies?”

The answer is, “yes” — researchers at the University of Miami  have found.

Scientists are closer to unraveling the long-standing mystery of how tiny glass eel larvae, which begin their lives as hatchlings in the Sargasso Sea, know when and where to “hop off” the Gulf Stream toward European coastlines to live out their adult lives in coastal estuaries.

In a new study by the University of Miami (UM)’s Rosenstiel School of Marine and Atmospheric Science in collaboration with the Norwegian Institute of Marine Research’s Austevoll Research Station found that these glass eels (Anguilla anguilla) can sense Earth’s magnetic field and use it like a compass controlled by an internal “biological” clock to orient themselves towards the coast. 

Notice that two senses cooperate in this skill: the ability to sense Earth’s magnetic field, and a biological clock to know when to change direction in relation to that field. The discoveries were made by monitoring eel orientations in a test facility where the ambient magnetism could be controlled.

“It is incredible that these small transparent glass eels can detect the earth’s magnetic field. The use of a magnetic compass could be a key component underlying the amazing migration of these animals,” said Cresci, the study’s lead author. “It is also the first observation of glass eels keeping a compass as they swim in shelf waters, and that alone is an exciting discovery.”

Not surprisingly, the paper in Science Advances  doesn’t speculate about how this ability might have evolved. They simply state the design-friendly facts:

Glass eels have a magnetic compass, and their orientation abilities appear to be linked to the tidal phase. This is preliminary evidence that magnetic compass–guided movement behavior could be tuned by an endogenous rhythm in the early life stages of a fish. This compass-guided movement, regulated by an endogenous rhythm, may be present in many migratory species.

Speaking of timing, it appears that salmon like to migrate in groups. Phys.org says that even when conditions are stable, observers don’t see sockeye salmon cueing off environmental conditions individually. Instead, pulses of fish are seen migrating together, perhaps for the added protection of a group.

Birds: Golden Eagles and Shearwaters

Humans aren’t the only beings familiar with a generation gap. Golden eagles have it, too. Bird watchers with the American Ornithological Society found that young and old eagles have “counterintuitive” migration habits. Science Daily  explains the findings:

Migration is tough, and birds do everything they can to optimize it. How do factors like weather and experience affect the strategies they choose? A new study from The Auk: Ornithological Advances shows that older, more experienced Golden Eagles actually migrate in poorer weather conditions and cover less ground than their younger counterparts, but for a good reason — they’re timing their efforts around raising the next generation of eagles.

The authors give a tip of the hat to evolution, saying, “Because of the costs of migration, there is selective pressure to capitalize on variation in weather to optimize migratory performance.” But as we said earlier, selection pressure should work to make the eagles stay put, not make them go through such hardships to reproduce.

The shearwater is a migratory bird that carries with it a travel journal of sorts. Richard Banati, a nuclear physicist in Australia, decided to take a look at the feathers with X-ray fluorescence microscopy, and found something unexpected: bands of zinc, calcium, bromine, copper and iron. He believes these provide clues to this species’ migratory habits as they fly a figure-8 path between the coasts of Siberia, Japan, and Tasmania on a 60,000-km route over open ocean. Writing in  The Conversation, he says:

Like the annual growth rings of trees, birds’ feathers lay down growth bars during their moult. (Moulting is the process of shedding old feathers, making way for new ones to grow.)

While bars simply show growth, the patterns of chemical elements tell us about the bird’s life during the growth period of the feather. They can indicate environmental exposures in a bird population, perhaps before impacts such as illness and death are clear….

The chemistry of feathers might become a tool for watching our environment.

Mammals: Whales

Imagine the surprise of boaters when a blue whale overturned their sightseeing boat off the coast of San Diego (see the video at BBC News). Is this sport to the giant beasts, the largest animals that have ever lived, something like tipping cows to farm boys? Nobody knows what was going through this whale’s mind, but we do know that whales are also master migrators, covering thousands of miles through clear and murky ocean routes. Remember Isabela, the blue whale that clocked a record 5,200 kilometers?

The World Wildlife Fund has been having fun with “whale cams” attached to humpback whales and minke whales,  Live Science reports. This is giving scientists unprecedented views of the social lives and feeding habits of these animals. The whale cams show that migration can be vertical as well as horizontal: “whales will range from rolling lunges near the surface to dives up to 1,148 feet (250 meters) deep to eat krill (small crustaceans), their main food source.”

Another team publishing in  Science Advances found a novel technique to monitor humpback feeding habits: radiocarbon. “While the whales mostly relied on Antarctic-derived energy stores during their annual migration, there was some evidence of feeding within temperate zone waters in some individuals.” Differences in radiocarbon, measured in the whales’ baleen plates and skin, apparently come from different abundances of radiocarbon between polar and temperate waters. The study provided the first evidence that some individuals were supplementing their diet with trips into geographically distant food webs.

Amazing Daily Commuters

Daily migrations can be as interesting as annual migrations. The average human commuter drives about 5 to 13 miles per day, according to National Geographic. Compare that with blue herons, which fly up to 20 miles per day in search of food. A tropical Atlantic fish called the French grunt swims about a kilometer per day. Then there are the golden jellyfish of Palau, which follow the sun each day across a lake to support their photosynthetic algae partners.

One of the most amazing daily commuters, though, is also the smallest: plankton. Reporter Liz Langley calls it the largest vertical migration of its kind, in terms of biomass. An embedded video clip teases, “The world’s largest migration isn’t what you think.” In the video, Dr. Erika Montague says that all the plankton in the world outweigh all other sea animals combined. Tiny jellyfish, shrimp, comb jellies, and other organisms lumped into the collective we call plankton are not just passive drifters; they have the ability to move vertically through the water column. You can see them flapping their fins or pumping their water bells like hard-working swimmers.

Oceanographers estimate that these tiny sea creatures might move as much water as the wind and the tides. “This happens all around the planet, in every ocean,” Montague says. “It’s amazing.” It is.

  

Darwinism's greatest adversary may be Darwinism?

Biologist Laments, “I Want Deeply for [Darwinism] to Make Sense”
David Klinghoffer | @d_klinghoffer

In his important new book, coming out on September 12 from HarperOne, State University of New York biologist J. Scott Turner tells the story about the Christmas pony. As a gift for a child who wants a pony, a poor family could afford only a pile of horse manure. Traipsing downstairs on Christmas morning to behold this well-intentioned mess, the child delightedly squealed and clapped.Her parents asked her why. She answered, “Because I know there’s a pony in there somewhere.”

In evaluating the coherence of Darwinian theory, Dr. Turner finds many of his fellow biologists in much the same mood. Squealing and clapping, they know there’s a coherent theory in there somewhere.

His book,  Purpose and Desire: What Makes Something “Alive” and Why Modern Darwinism Has Failed to Explain It,  underlines that Turner is not an “anti-Darwinist.” On the contrary, he explains that “I want deeply for it” – meaning the modern theory of Darwinian evolution – “to make sense.” The reasons for his disillusion, which he outlines in this fascinating contribution to the evolution debate, turn upon long-ignored problems with the theory, and counterevidence from the mysterious nature of life itself.It is still a couple of months too early for reviews of Purpose and Desire, but Kirkus welcomes it with a pre-publication starred review as an “ingenious mixture of science and philosophy that points out major defects in Darwinism and then delivers heterodox but provocative solutions…a highly thought-provoking book.”

Turner writes:

For the longest time, we’ve been able to fudge these problems, carried along on the faith that, to paraphrase the punch line of an old joke, there had to be a pony in there somewhere. But the dread possibility is beginning to rear its head; what if the pony isn’t there?

The problem for modern Darwinism is, I argue, that we lack a coherent theory of the core Darwinian concept of adaptation.

It all unravels from there, thanks to unexpected insights from Biology’s Second Law – homeostasis – and the great 19th-century French physiologist Claude Bernard, writing just six years after Darwin’s Origin of Species. After some delay, the crisis for the evolutionary biologist is at hand.

Without giving away any more punch lines, I recommend this: Pre-order Purpose and Desire now, because if you do so, for a limited time only, you’ll also get two free e-books to go along with it. The free e-books are Fire-Maker: How Humans Were Designed to Harness Fire and Transform Our Planet, by biologist Michael Denton, and Metamorphosis, which I edited as a companion to the Illustra Media documentary. Find the details here. (Note: When we first pointed out this offer, the web page wasn’t working correctly. It’s now fixed.)

Well. Turner’s book is a great read, and while he’s not a proponent of ID, he turns a fresh new page for the case for design in nature. Promise: We’ll have more to say about his argument in due time.