File under "Well said" LI

He that falls in love with himself, will have no Rivals.

BENJAMIN FRANKLIN,

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.