On that(perennially missing)missing link

The Human-Ape Missing Link — Still Missing
Evolution News | @DiscoveryCSC

Here is a long, substantive, and interesting article from the BBC —  “We still have not found the missing link between us and apes.”  It is interesting for two reasons.

It admits that we haven’t found anything that resembles the last common ancestor (LCA) between humans and apes, what author Colin Barras calls the “missing link.”

It admits that it’s hard to even agree on what the LCA might have looked like.

What it doesn’t do is admit the even bigger problem: that  we don’t even have transitional forms between Australopithecus and Homo.  This is a major omission.

That having been said, Barras raises a lot of interesting issues relevant to problem (2) above. Scientists can’t agree on what the LCA looked like because humans share different similarities with different primates. It’s hard to decide which primate we’re most closely related to. This shows that the phylogenetic tree of primates isn’t as clear-cut as we’re often told — humans share similarities and differences with many primates in a pattern that doesn’t makes a nice, clear-cut tree.

The article does a good job of discussing this. It states, for example:

Primates in general (particularly monkeys) are often relatively small-bodied, and they scamper around in forest canopies by running along branches. But apes are unusual primates. Most have big bodies with extraordinarily long arms. They often get around by swinging below branches rather than running along the top of them – a form of locomotion called “brachiation”.

According to many of these early researchers, the LCA was a large-bodied, long-armed, brachiating ape.

By the late 1960s, researchers were fleshing out the LCA even further. An anthropologist called Sherwood Washburn pointed out that chimpanzees, and particularly gorillas, actually spend significant amounts of time moving around on all fours on the forest floor.

Both apes use their arms in an idiosyncratic way when they walk: they flex their fingers so that their weight bears down on the knuckles. To Washburn it made sense that the LCA “knuckle-walked” too. The behaviour could even be seen as a stepping-stone on the way to walking upright on two legs, he wrote.

But it would be wrong to think that everyone was on board with these ideas of a brachiating, knuckle-walking, chimp-like LCA. In fact, almost from the moment that Huxley first put pen to paper, a minority of scientists were arguing that the earliest human ancestors — and the LCA — was decidedly not chimp-like.

For instance, just a decade after Huxley’s book, biologist St George Mivart argued that humans shared many features in common with monkeys or even lemurs. Meanwhile, from 1918 onwards an anatomist called Frederic Wood Jones argued that humans had a lot more in common with tarsiers than with chimpanzees or gorillas.

… [H]uman arms, hands, legs and feet are not as highly specialised as we might assume.

“In these characters man finds his counterparts not in anthropoid apes [gorillas, chimpanzees, and orangutans] but in animals that are clearly regarded… as more primitive,” wrote [anatomist William] Straus.

What Straus and a few others were really getting at is that humans show none of the specialised features that allow other apes to swing through the trees. It made sense to at least consider the possibility that humans split apart from other primates before the apes evolved brachiation, or knuckle-walking for that matter. Straus could not say exactly which species should be recognised as our sister. But the LCA could well have been a relatively small-bodied primate that ran along branches rather than swinging beneath them.

This disagreement continued for several more decades, says Nathan Young at the University of California in San Francisco. In fact, even into the 1980s it was not clear from anatomical features alone exactly where humans slotted into the primate evolutionary tree.

So what made them finally ditch the idea that humans are most closely related to “lower” primates in favor of believing that humanity’s closest relative is the chimp? As the article explains, human DNA turned out to be most similar to chimp DNA. So the drift of opinion turned to chimps as our closest cousin.

The kicker, however, is this: We’re constantly told that both our genes and our morphology are very similar to chimps. But as this article concedes, some major aspects of our morphology are more like other primates than they are like chimps. So our morphology isn’t necessarily entirely chimp-like.

Thus, we get this really interesting passage in the article:

The story should end there, but it does not. Surprisingly, the last 15 years have actually seen popular opinion begin to swing away from the idea of a chimp-like LCA, and towards a model closer to that argued by people like Straus in the 1940s.

There are several factors that explain the recent rethink. A more thorough understanding of chimp and gorilla anatomy helped.

There had been murmurings for some time that gorillas and chimpanzees (and bonobos) might not knuckle-walk in quite the same way. In 1999, Mike Dainton and Gabriele Macho at the University of Liverpool, UK, looked at the idea more formally. From subtle differences in the way gorilla and chimpanzee wrist bones change as the apes grow from juveniles to adults, Dainton and Macho concluded that the two may have evolved knuckle-walking independently.

Over the following decade, other researchers reported similar findings. By 2009, Tracy Kivell — now at the University of Kent, UK — and Daniel Schmitt at Duke University in Durham, North Carolina, were arguing that humans did not evolve from a knuckle-walking LCA.

Strikingly, the article even notes that molecular biologists are willing to question whether the LCA links humans most closely to chimps:

Of course, only if and when fossils of the LCA itself come to light will the debate finally draw to a close. But the search for those crucial fossils is no longer quite as straightforward as it once seemed. In the last five years, some geneticists have begun to question whether the molecular clocks they use to estimate when the LCA lived are being read correctly. It is possible, they say, that the LCA might actually have lived 13 — not seven — million years ago.

The author notes other skeptics of the molecular data linking us to chimps:

There are also a few researchers who take a completely different view.

For instance, [University of Pittsburgh’s Jeffrey] Schwartz is adamant that it is orangutans, not chimpanzees, that are our sister species. It is an idea he first developed in the 1980s — before, he says, anthropologists “caved in” and conceded that molecules and not anatomy were the ultimate arbiters of the shape of the ape family tree.

Schwartz thinks DNA is not the infallible witness on evolution many assume it to be, and that there are many anatomical and behavioural similarities between humans and orangutans that should not simply be ignored.

For instance, both have thick layers of enamel on their teeth, and female orangutans (like women) do not “advertise” to males when they are most fertile — something biologists call oestrus. “Orangs are the only other mammal I know of that don’t have oestrus,” says Schwartz.

To be clear, few researchers agree with Schwartz. But even putting his ideas to one side, it is clear that there is not yet universal agreement on the LCA.

The article promotes Ardi as a possible candidate for LCA. But it notes why this proposal is not widely accepted:

[T]he Ardi analysis was not uncontroversial. One of the implications of their interpretations was that all sorts of anatomical features shared by gibbons, orangutans, chimps and gorillas must have evolved independently in each of these apes.

“I think they took it a little too far,” says Kivell. “Their model means that there is a lot of parallel evolution across all apes. I still think comparative studies with chimps and other African apes can provide a lot of insight into our own evolution.”

In the end, it’s clear that the entire field is a mess:

It is true that, today, some researchers have a well-thought-through idea of what the LCA looked like and how it behaved. The trouble is that other researchers have equally well-reasoned models that suggest an LCA that looked and behaved in a completely different way. And that puts the research community in a bit of a quandary.

In short, there are so many morphological similarities and differences between humans and other primates that it’s very difficult to draw a phylogenetic tree showing how these species are related. This makes it very difficult to infer what the common ancestor of humans and apes might have looked like.

Part of the difficulty, as well, is that we’re not as chimplike as we’re often told. The article doesn’t put it in exactly those terms, but that’s what’s going on. And now you understand.

How new words acquire respectability.

Yet More shifting of the goalposts by Darwinists.

Darwinists in a Muddle: Do Lenski's Microbes Show "Why Evolution Is True," or Not?
David Klinghoffer


Jerry Coyne is ticked off that readers are attributing significance in the wider evolution debate to Michael Behe's current paper in the Quarterly Review of Biology, explicating the results of viral and bacterial evolution studies -- notably the famous long-term study of Richard Lenski:

As I predicted, the IDers completely ignore the limitations of this paper (see my analyses here and here), and assert, wrongly, that Behe has made a powerful statement about evolution in nature.
What Coyne "completely ignores" is that Darwinists have accustomed themselves to waving Lenski as a banner that makes "a powerful statement about evolution in nature." In The Greatest Show on Earth, Richard Dawkins devoted an ecstatic and detailed discussion to Lenski's work, enthusing:
Creationists hate it. Not only does it show evolution in action; not only does it show new information entering genomes without the intervention of a designer, which is something they have all been told to deny is possible ("told to" because most of them don't understand what "information" means); not only does it demonstrate the power of natural selection to put together combinations of genes that, by the naïve calculations so beloved of creationists, should be tantamount to impossible; it also undermines their central dogma of "irreducible complexity." So it is no wonder they are disconcerted by the Lenski research, and eager to find fault with it.
Coyne himself in his book Why Evolution Is True adduces the evidence of Richard Lenski, showing us "genuine evolutionary change."
So which is it, gentlemen? Is Lenski relevant to the broader debate, or not?

Remember how Darwinists assured us that there was no link Between Darwin and Hitler?Really?

Darwinian Biologist Endorses Killing Handicapped Babies Who “Suffer”
Michael Egnor

This odious stuff never ends. Darwinist biologist Jerry Coyne  endorses euthanasia for severely handicapped infants. Here are Coyne’s arguments, with my replies.

The question of whether one should be able to euthanize newborns who have horrible conditions or deformities, or are doomed to a life that cannot by any reasonable light afford happiness, has sparked heated debate.  Philosopher  Peter Singer has argued that euthanasia is the merciful action in such cases, and I agree with him. If you are allowed to abort a fetus that has a severe genetic defect, microcephaly, spina bifida, or so on, then why aren’t you able to euthanize that same fetus just after it’s born?  I see no substantive difference that would make the former act moral and the latter immoral.

I agree with Coyne that there is no moral difference between aborting a handicapped fetus and killing a handicapped baby. I believe that both are profoundly immoral. Coyne condones such killing.

After all, newborn babies aren’t aware of death, aren’t nearly as sentient as an older child or adult, and have no rational faculties to make judgments (and if there’s severe mental disability, would never develop such faculties).

Many people aren’t “aware of death” — normal infants and toddlers, people with severe traumatic brain damage, people with Alzheimer’s disease. Heck, people who are sleeping aren’t aware of death at the moment. How does that justify killing them? A severely handicapped newborn wouldn’t be aware of rape either.

Just how is it that “unawareness” of an evil act justifies the act? If anything, unawareness makes the victim more vulnerable, and ought to spur those of us who are aware to offer innocents greater protection, not less protection.

It makes little sense to keep alive a suffering child who is doomed to die or suffer life in a vegetative or horribly painful state. After all, doctors and parents face no legal penalty for simply withdrawing care from such newborns, like turning off a respirator, but Singer suggests that we should be allowed, with the parents’ and doctors’ consent, to painlessly end their life with an injection. I agree.

There are situations in which continuation of heroic medical treatment (surgery, respirators, antibiotics, etc.) merely prolongs the process of dying, and in which it is ethical to withdraw such heroic care. I have done it many times (I’m a pediatric neurosurgeon). But the purpose of the withdrawal is not to cause death, but to cease interfering with the natural course of a disease, when no good can come of heroic treatment. That is a very different thing, morally and legally, from deliberately killing a child by injecting him with a lethal dose of potassium or a barbiturate.

The Doctors Trial

Coyne goes on to recount the uproar over Singer’s endorsement of the Groningen protocol, which is a legal innovation employed in Holland for killing handicapped infants.

For these views Singer has been demonized by disability rights advocates, who have called for his firing and disrupted his talks (see my post about that here). All for just raising a reasonable ethical question that should be considered and discussed!

Most of the “disability rights advocates” who have protested Singer’s endorsement of killing handicapped infants are handicapped adults who, as infants, were the very people Singer proposes killing. Disrupting a talk is rude, but if there’s ever a justification for it, it would seem that disrupting the talk of a highly regarded philosopher who advocates killing you as a baby might count as justified.

One imagines that Coyne and Singer would not sit with equanimity through a lecture in which the speaker advocated killing atheist biologists and philosophers in the crib.

After all, fifty years ago the same kind of opprobrium would have been leveled at those calling for voluntary euthanasia (assisted suicide) of terminally ill adults, but now that’s legal in several places in the world; as Wikipedia notes, “As of June 2016, human euthanasia is legal in the Netherlands, Belgium, Colombia, and Luxembourg. Assisted suicide is legal in Switzerland, Germany, Japan, Canada, and in the US states of Washington, Oregon, Colorado, Vermont, Montana, Washington DC, and California.”

It’s true that many of the euthanasia policies that are becoming more accepted today were verboten fifty years ago. I use “verboten” deliberately, as one prominent example of disapproval of euthanasia in that era was the decision by the judges in the Nazi Doctors Trial in 1946. Sixteen doctors were convicted of crimes against humanity, and seven were hanged. Some of those convictions were for euthanizing handicapped children.

Note to Dr. Coyne: When your rationalizations for killing handicapped children were used by defense counsel in the Nazi Doctors Trial, it’s time to rethink your ethics.

This change in views about euthanasia and assisted suicide are [sic] the result of a tide of increasing morality in our world…

What? Reintroducing medical practices for which Nazi doctors were hanged is “a tide of increasing morality in our world”? Goodness gracious.

It’s time to add to the discussion the euthanasia of newborns, who have no ability or faculties to decide whether to end their lives. Although discussing the topic seems verboten now, I believe some day the practice will be widespread, and it will be for the better.

I too suspect that killing handicapped people will become more widespread. This will not be “for the better.”

 After all, we euthanize our dogs and cats when to prolong their lives would be torture, so why not extend that to humans? Dogs and cats, like newborns, can’t make such a decision, and so their caregivers take the responsibility. (I have done this myself to a pet, as have many of you, and firmly believe it’s the right thing to do. Our pain at making such a decision is lessened knowing that dogs and cats, like newborns, don’t know about death and thus don’t fear it.)

We do all sorts of things to pets — we euthanize them, we cage them, we buy and sell them, we neuter and spay them, we breed them. If Coyne’s analogy to animals allows killing of handicapped children just like we kill sick pets, why wouldn’t the analogy justify caging, buying and selling, neutering and breeding children as well?

The reason we don’t allow euthanasia of newborns is because humans are seen as special, and I think this comes from religion — in particular, the view that humans, unlike animals, are endowed with a soul.

Both humans and animals have souls. Humans have spiritual souls, created in God’s image, which distinguishes them from animals. Coyne dismisses theology and philosophy, of which he is ignorant.

It’s the same mindset that, in many places, won’t allow abortion of fetuses that have severe deformities. When religion vanishes, as it will, so will much of the opposition to both adult and newborn euthanasia.

The world is replete with dead ideologies that died waiting for religion to “vanish.”

Just the Beginning

Certainly, Christian morality is on the wane in the West (it is surging in Africa and Asia). The waning of Christian morality, and Christian respect for life in its sanctity, will have horrendous consequences, of which killing handicapped children is just the beginning.

My view, then, aligns with Singer’s: a child falling in any of the classes above should be considered as a subject for euthanasia, and it should be legal if the doctors and parents concur. As for the “slippery slope” argument — that this will lead to Nazi-like eugenics — well, this hasn’t come to pass in places where assisted suicide or euthanasia of adults is legal. Since the newborn can’t decide, it’s up to the parents, with advice (and maybe consent) of the doctors.

Killing handicapped children because their lives are unworthy of life  won’t lead to Nazi medical practice. It is Nazi medical practice.

The pain of these newborns, and of making these decisions, is evident in a piece in yesterday’s New York Times’ “The Stone” section (a philosophy column), provocatively called “You should not have let your baby die.” (What the author means is that “you should have killed your baby.”) It describes the situation of parents whose baby was born with “trisomy 18”: three rather than the normal two copies of chromosome 18. Trisomy 21, three copies of the smaller 21st chromosome, is what produces Down Syndrome. But unlike the Down case, trisomy 18, involving imbalance of a larger chromosome, produces a severe condition, with most children dying horrible deaths soon after birth. A few, though, can live into their 20s and 30s.

Therein lies the dilemma. Should you take that chance? The child described by author Gary Comstock, a philosophy professor at North Carolina State University, was in dire shape, forced to breathe on a respirator and unable to survive without one. The odds that that child could live in a decent state were nil. After agonizing over what to do, the parents decided to take the legal course of withdrawing care: removing the respirator. The child slowly suffocates.

The notion that handicapped children intractably suffer is a lie. I’ve treated thousands of these kids. Most of the conditions that cause severe neurological impairment aren’t painful and don’t inherently cause physical suffering. Spina bifida, holoprosencephaly, various trisomies and anencephaly don’t “hurt,” and in fact the children afflicted are often quite content babies. They are loved by their families, and they can enjoy life in accordance with their physical limitations.

Most people with spina bifida go to school, get a job, and many get married and have families. More severely disabled children (such as those with anencephaly) can live for several years, and can be quite happy. Anencephaly does not mean “brain death” — these kids have profound developmental limitations, but they clearly can feel things and experience emotions.

I cared for a little girl with anencephaly for several years. Her mother brought her to my office for regular check-ups. The child was content, loved to be held and fed by her mother (who always dressed her beautifully), and her mother loved her dearly. She died at 4 years of age from an infection, but she didn’t suffer particularly. If anything, her life seemed happier than most, from her perspective.

Encroaching Materialism and Darwinism

Some people with severe handicaps at birth can achieve quite a bit in life. My friend Karin Muraszko was born with spina bifida and needed extensive surgery and a brain shunt as a child. I met her when I was a medical student. She wasn’t a patient — she was a resident in neurosurgery, and I followed her on rounds and learned from her. She is now Professor and Chairman of Neurological Surgery at the University of Michigan, and she has professorships in pediatrics, communicable diseases, and plastic surgery. She has served on the American Board of Neurological Surgery, and is one of the most respected clinicians and researchers in my field.

She is married and has two kids, and she is director of the Shunt Project, which is an organization devoted to providing medical care for children (like her) with severe neurological handicaps in poor countries.

To propose, as Dr. Coyne does, that she should have been killed at birth because of her “suffering” is a particularly odious example of the encroachment of materialist and Darwinist philosophy on our culture. It should be resisted, with every bit of our strength.

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.