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

Bdelloid.JPG

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 transfer multiple segments of DNA at once to fellow species members.

Talk to the Fossils.jpgBut 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 paper notes:

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, including Phytophthora 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 HGT from 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.

Image: Bdelloid rotifer, by Diego Fontaneto [CC BY 2.5], via Wikimedia Commons.

See the rest of the series to date at “Talk to the Fossils: Let’s See What They Say Back.”