Dr. Moreau would be proud.

David Barash’s Proposal — Something Wicked This Way Comes
Ann Gauger

If you want to see something creepy, read the article in  Nautilus by David Barash, that Wesley Smithand Richard Weikart have already noted. The face that stares out is a chimp/human chimera, thankfully still fictional. But if David Barash, emeritus professor of psychology at the University of Washington, has his way, chimeras will soon be a reality.

Human/animal chimeras are not new. Human pluripotent stem cells have been added to mouse, cow, and pig embryos already, and the results were published in the journal Cell in 2017. In the biggest experiment, the researchers successfully created pig/human chimeras and implanted them in female pigs. They terminated them after 28 days because of ethical concerns.

Indeed, there is an instinctive abhorrence about mixing animal and human cells. Letting such a part-human creature come to term would be monstrous. “The idea of having an animal being born composing [sic] of human cells creates some feelings that need to be addressed,” Izpisua Belmonte told Hannah Devlin at The Guardian.

Why do this research at all? Lead researcher Izpisua Belmonte said, “This provides us with an important tool for studying species evolution, biology and disease, and may lead ultimately to the ability to grow human organs for transplant.” That does not make it moral, however.

No restrictions exist in federal law. Fortunately, the U.S. National Institutes of Health do have a regulation in place. Barash says, “Currently prohibited — and likely to remain so — is funding for studies that involve injecting human stem cells into embryonic primates, although inserting such cells into adults is permissible…. All sorts of things can be done; whether they should, is another question.” (Emphasis added.)

That sounds like a reasonable point of view. But in the very next paragraph, he says:

I propose that generating humanzees or chimphumans would be not only ethical, but profoundly so, even if there were no prospects of enhancing human welfare. How could even the most determinedly homo-centric, animal-denigrating religious fundamentalist maintain that God created us in his image and that we and we alone harbor a spark of the divine, distinct from all other life forms, once confronted with living beings that are indisputably intermediate between human and non-human? 

David Barash wants to see chimp/human chimeras brought face to face with humanity to force us to acknowledge that humans are not in any way exceptional. His rage against religion is clear:

…the nonsensical insistence that human beings are uniquely created in God’s image and endowed with a soul, whereas other living things are mere brutes has not only permitted but encouraged an attitude toward the natural world in general and other animals in particular that has been at best indifferent and more often, downright antagonistic, jingoistic, and in many cases, intolerably cruel…. It is only because of this self-serving myth that some people accord the embryos of Homo sapiens a special place as persons-in-waiting, magically endowed with a notable humanity that entitles them to special legal and moral consideration unavailable to our nonhuman kin.

Perhaps not surprisingly, Richard Dawkins has said equally strong things about human exceptionalism. The Guardian reproduced the results of “Edge.org’s annual New Year challenge to the world’s leading thinkers.” The question was, “What will change everything?” and his answers included “successful hybridization between a human and a chimpanzee.”

Our ethics and our politics assume, largely without question or serious discussion, that the division between human and ‘animal’ is absolute. ‘Pro-life’, to take just one example, is a potent political badge, associated with a gamut of ethical issues such as opposition to abortion and euthanasia…

In the minds of many confused people, a single-celled human zygote, which has no nerves and cannot suffer, is infinitely sacred, simply because it is ‘human’. No other cells enjoy this exalted status.

But such ‘essentialism’ is deeply un-evolutionary.

Dawkins expands on the ways human exceptionalism can be shown to be wrong. I will list only the first three:

The discovery of relict populations of extinct hominins such Homo erectus and Australopithecus. Yeti enthusiasts notwithstanding, I don’t think this is going to happen. …

A successful hybridisation between a human and a chimpanzee. Even if the hybrid were infertile like a mule, the shock waves that would be sent through society would be salutary. …

An experimental chimera in an embryology lab, consisting of approximately equal numbers of human and chimpanzee cells.

Indeed, Barash’s justification for his belief in the viability of chimeras is similar: evolutionism.

There is an immense pile of evidence already demonstrating continuity, including but not limited to physiology, genetics, anatomy, embryology, and paleontology, but it is almost impossible to imagine how the most die-hard advocate of humans having a discontinuously unique biological status could continue to maintain this position if confronted with a real, functioning, human-chimp combination.

Despite Barash’s claims, the likelihood of being “confronted with a real, functioning, human-chimp combination” is low because full-fledged human/chimp embryos are unlikely to develop.Varki and Altheide report a 4 percent difference in the DNA sequences of chimps and humans, with many of those differences being significant, especially in the brain Another study estimates as much as 17.4 percent of gene networks in the cortex of the brain are specific to humans compared to chimps, significantly more than would be expected from a simple 4 percent DNA difference. Then there are cell surface differences, differences in infant development, differences in reproduction, physiology, and the immune system, just to name a few. In fact,  chimps do not make a good medical model for human beings, for we do not get the same major diseases.

Is Barash ignorant of studies like these, or is he so convinced of the justice of his position that he rejects anything that does not fit his paradigm? He continues his campaign, in any case:

It is only because of this self-serving myth [of human exceptionalism] that many people have been able to deny the screamingly evident evolutionary connectedness between themselves and other life forms.

Barash thinks his is a noble cause — to make us see the truth about our selves, that we are only animals. But does he see the truth about himself? In a very telling paragraph he explains why making chimeric human/chimp creatures in the lab is all right.

But what about those presumably unfortunate individuals thereby produced? Neither fish nor fowl, wouldn’t they find themselves intolerably unspecified and inchoate, doomed to a living hell of biological and social indeterminacy? This is possible, but it is at least arguable that the ultimate benefit of teaching human beings their true nature would be worth the sacrifice paid by a few unfortunates.

In Barash’s own words, chimeras could be “intolerably unspecified and inchoate, doomed to a living hell of biological and social indeterminacy.” But it would be worth their sacrifice to teach us all a lesson.

What about the lessons learned at Dachau and Auschwitz? One of the Mengele twins, victims of Nazi experimentation said this:

We were treated like animals — we were his guinea pigs. But it hurts 10 times more today to realize that some American scientists and doctors want to use this data regardless of the pain and suffering paid by the victims. The advocates for the use of the data claim they want to save human lives. It is obnoxious to me that some of the advocates are so magnanimous with other peoples’ lives and suffering.

This might very well be the attitude of any chimera created solely because of David Barash’s agenda.

Surprisingly, Barash himself is not unaware of the dangers. He opens his article by recounting the lesson of Mary Shelley’s Frankenstein. “Haven’t we learned that Promethean hubris leads only to disaster, as did the efforts of the fictional Dr. Frankenstein?” Barash asks. Answering himself, he says it will still be worth Promethean hubris to teach us we have no souls. I think David Barash has learned the wrong lesson.

Darwinian spin 101.

Answering Simplistic Presentations of Darwinism
Evolution News | @DiscoveryCSC

Every once in a while, popular science writers feel the need to re-educate their readers about the fact of evolution, lest the readers be swayed by certain fringe elements. It’s like the need for a booster shot against tetanus; just re-inoculate the public with the same medicine, and they will be safe for another year. The booster shot usually includes some of the following elements:

Evolution is a fact. It’s obvious. Things change, don’t they?

Charles Darwin was the greatest scientist who ever lived. He wrote the greatest book in the history of science.

Darwin was wrong about some things, but those have all been corrected now.

Natural selection is one of the best-tested laws of nature. It explains everything.

The evidence for evolution is overwhelming: whales, antibiotic resistant bacteria, and human sexual behaviors.

No serious scientist doubts evolution.

Some fringe groups like those intelligent design rascals don’t understand evolution. They can be ignored, like creationists.

Evolution is not against religion. You can be very religious and still accept the fact of evolution.

Controversy? What controversy?

These talking points are so predictable, they seem to come from the same source every time. Perhaps the reporter consults TalkOrigins or the National Center for Science Education. The reporter feels no need to consult actual ID sources, because nobody should consult fake science from discredited groups. Just ask the NCSE.

A good example of this booster-shot reporting is Ker Than’s article for Live Science, “Darwin’s Theory of Evolution: Definition & Evidence.”

The theory of evolution by natural selection, first formulated in Darwin’s book “On the Origin of Species” in 1859, is the process by which organisms change over time as a result of changes in heritable physical or behavioral traits. Changes that allow an organism to better adapt to its environment will help it survive and have more offspring.

Evolution by natural selection is one of the best substantiated theories in the history of science, supported by evidence from a wide variety of scientific disciplines, including paleontology, geology, genetics and developmental biology. 

The article uses all nine talking points plus a few others. It’s notable that most of the piece is not neo-Darwinian, but old-style Darwinism: universal common descent by natural selection on variations:

The theory has two main points, said Brian Richmond, curator of human origins at the American Museum of Natural History in New York City. “All life on Earth is connected and related to each other,” and this diversity of life is a product of “modifications of populations by natural selection, where some traits were favored in and environment over others,” he said.

More simply put, the theory can be described as “descent with modification,” said Briana Pobiner, an anthropologist and educator at the Smithsonian Institution National Museum of Natural History in Washington, D.C., who specializes in the study of human origins.

The theory is sometimes described as “survival of the fittest,” but that can be misleading, Pobiner said. Here, “fitness” refers not to an organism’s strength or athletic ability, but rather the ability to survive and reproduce.

The article does not point out the meaninglessness of this formulation of natural selection. Norman Macbeth and Tom Bethell are among many observers who find a tautology here. When fitness is defined in terms of reproduction, then reproduction is a measure of fitness by definition. Such a vacuous thought can explain anything. There’s no way to test it. If it’s fit, it survives. If it survives, it’s fit.

For evidence, Mr. Than appeals to both microevolutionary and macroevolutionary change. He sees evolution in the common human dilemma of seeking to date an appropriate person. Yet surely he would never claim that those who do succeed in dating Mr. or Miss Right are evolving into a new species in the Darwinian sense.

The article’s biggest evidential appeal is to whale evolution. The whale sequence shown is comparable to the “Parade of Man” icon that has been roundly debunked by evolutionists. All that is needed to explain the sequence, Mr. Than implies, is natural selection. What we see in microevolution changing hair color or size can be extrapolated endlessly. Time is the hero of the plot:

But natural selection is also capable of much more. Given enough time and enough accumulated changes, natural selection can create entirely new species, known as “macroevolution.” It can turn dinosaurs into birds, amphibious mammals into whales and the ancestors of apes into humans.

In Living Waters, Richard Sternberg pointed out the need for coordinated mutations to arrive on time to make complex systems work. His calculations, using standard population genetics equations, show that getting just two coordinated mutations would require vastly more time than evolutionists think the entire alleged whale sequence occurred. Yet Live Science weaves a just-so story bordering on the magical, where coordinated mutations happen all over the place:

Random genetic changes resulted in at least one whale having its nostrils placed farther back on its head. Those animals with this adaptation would have been better suited to a marine lifestyle, since they would not have had to completely surface to breathe. Such animals would have been more successful and had more offspring. In later generations, more genetic changes occurred, moving the nose farther back on the head.

Other body parts of early whales also changed. Front legs became flippers. Back legs disappeared. Their bodies became more streamlined and they developed tail flukes to better propel themselves through water.

Moving a nostril farther back on the head overlooks numerous coordinated changes that would have to occur, so that the animal could breathe, swallow, and perform echolocation. Without the coordination, the animal would be less fit. The assertions in that second paragraph are more Lamarckian than Darwinian. The article overlooks all these problems.

But natural selection isn’t the only mechanism by which organisms evolve, she said. For example, genes can be transferred from one population to another when organisms migrate or immigrate, a process known as gene flow. And the frequency of certain genes can also change at random, which is called genetic drift.

All three of those processes, lateral transfer, gene flow, and genetic drift, have nothing to do with progressive evolution — the kind Darwin envisioned, where a four-footed animal becomes a whale. Random changes to complex systems degrade information. Mr. Than equivocates here, making “evolution” any kind of genetic change. With that kind of definition, the Darwinist can’t lose: a species going extinct becomes evidence for Darwinian evolution.

Brian Richmond of the American Museum of Natural History caps off the article with a prediction:

Evolution is well supported by many examples of changes in various species leading to the diversity of life seen today. “If someone could really demonstrate a better explanation than evolution and natural selection, [that person] would be the new Darwin,” Richmond said.

This implies that the scientific community would immediately jump on the new alternative with gusto. Would that were true, because intelligent design scientists have made a case that not only undermines Darwinism, but offers a more logical and evidence-based alternative. They have the advantage of not taking one side’s talking points on faith, because many of them were evolutionists before they began critically evaluating the theory.

Recently, Evolution News humorously advised scientists on how to write a first-class biology paper.  Similar rules apply to writing science news stories for the popular media. They are sure to get published if the reporter follows the same rules for the Introduction, “Start by stating confidently that evolution is true,” and the Conclusion, “Evolution is true.”

For those who prefer a more balanced view of evolution, here are the most recent books where you will get a real debate looking at both sides:  Heretic, by Matti Leisola; Undeniable, by Douglas Axe; Darwin’s House of Cards, by Tom Bethell, and Zombie Science, by Jonathan Wells.

On eternal punishment v. eternal punishing.

“Punishment” and the Polysemy of Deverbal Nouns
by Chris Date ·

In the opening statement from my recent debate  I had said,

What we disagree on is the meaning of punishment. Traditionalists see it as suffering forever, whereas annihilationists see it as the everlasting effect of being executed. Linguists call this a deverbal result noun, a noun referring to the results of its corresponding verb, and it’s a phenomenon found both in Scripture and in modern language.

This was recently misunderstood by pseudonymous blogger TurretinFan, and understandably so—excuse the pun—because it didn’t come across quite right. I did not mean to say that linguists call “punishment” a deverbal result noun; I meant that they call the object to which I was referring—namely, a noun that refers to the results of its corresponding verb—a deverbal result noun. What’s more, I neither said nor implied that “punishment” is in every case a deverbal result noun, but that it is in the case of Matthew 25:46.

Nevertheless, TurretinFan argued that the “noun ‘punishment’ is a deverbal noun, but it is not a deverbal result noun” (emphasis his), going on to seemingly argue that this is inherent in the meaning of the noun. Let us examine this claim.

First, it should be noted that many deverbal nouns are polysemous, ambiguous between a process or result meaning. For example, the phrase, “The translation of the book took ten years,” means that the process of translating lasted ten years. The phrase, “The translation has been published recently,” on the other hand, means that the translation that resulted from, or was the outcome of, the translating process was recently published. Building may refer to the process (e.g., “building a house”) or to the result (e.g., “a beautiful building”); the word construction is similarly ambiguous. Isolation may refer to the process (e.g., “gene isolation”) or to the result (e.g., “forced into isolation”). Other ambiguous examples include separation, banishment, performance, subjugation, imprisonment, and many more.

TurretinFan cited Roget’s Thesaurus on “punishment” in support of his contention that “‘punishment,’ like ‘walk,’ is a manner noun, not a ‘result’ noun.” I do not dispute that “punishment” does sometimes—even often—refer to the process of punishing. But since such deverbal nouns are often polysemous, it does not follow that therefore “punishment” carries a process meaning every time it’s used. “Punishment” may often describe “a manner of treatment, not the result of that treatment,” but this is not always the case.

The Oxford English Dictionary (OED) includes a definition of punishment that describes a process, namely, “The infliction of a penalty or sanction in retribution for an offence or transgression” (emphasis mine), but it immediately follows this first definition with, “(also) that which is inflicted as a penalty.”1 This distinction, between the infliction of a penalty and the penalty which is inflicted, can serve to illustrate the difference between “punishment” as a process noun and “punishment” as a result noun.

One of the synonyms TurretinFan cites is “amercement,” for example, which the OED defines as “a discretionary penalty or fine.”2 The punishment of a fine certainly isn’t the infliction of the fine—the process of paying it—but rather the resulting absence of that money from the offender’s bank account. Consider “confiscation,” also included in the list of synonyms TurretinFan cites. The punishment of confiscation certainly isn’t the infliction of it—the process of having one’s property confiscated—but rather the resulting lack of something previously owned. Examples of punishments whose measure is in their process obviously exist, but they are not the only kinds of punishment.

Perhaps there is no better example of a punishment which does not fit TurretinFan’s conclusion than that of capital punishment. After all, what is the nature of capital punishment? Is it suffering as part of the process of death? And how is it measured? Is it measured in the amount of time it takes to die? TurretinFan’s insistence that “‘punishment’ [is] about the process” would render a lengthy prison sentence a greater punishment than a quick and painless execution, such as death by lethal injection. And yet capital punishment, by any means, is reserved for the most serious of crimes.

Saint Augustine rhetorically asked, “As to the award of death for any great crime, do the laws reckon the punishment to consist in the brief moment in which death is inflicted, or in this, that the offender is eternally banished from the society of the living?”3 TurretinFan alleged that my reference to Augustine misses the point: “Capital punishment is severe regardless of its duration, because of the kind of punishment it is. But ‘eternal punishment’ is specifically a comment on the duration of the punishment.” But I suspect it may be TurretinFan who misses the point.

Did we not see Augustine explicitly stating that the measure of capital punishment is not in the duration of the punishing, but rather in the duration of the consequent lifelessness? And the context of his statement is those punishments which last longer than the time it takes to commit a crime. In fact, he includes death in a list of such punishments, rhetorically asking again, “Is there any one of these which may be compressed into a brevity proportioned to the rapid commission of the offence, so that no longer time may be spent in its punishment than in its perpetration, unless, perhaps, reparation?”4 If it is not possible to compress the punishment of death into the amount of time it takes to commit a crime worthy thereof, then the duration of the punishment of death must be measured in the result, rather than the process, of being executed.

It seems to me that those critical of conditionalism cannot appeal to the phrase “eternal punishment” by itself, for it may refer to the everlasting effect of being punished by death. So Jonathan Edwards, arguing against annihilationists who posit a very extended period of suffering prior to annihilation, writes,5

For, if it be owned, that Scripture expressions denote a punishment that is properly eternal, but that it is in no other sense properly so, than as the annihilation, or state of non-existence, to which the wicked shall return, will be eternal; and that this eternal annihilation is that death which is so often threatened for sin, perishing for ever, everlasting destruction, being lost, utterly consumed … If this be all that these expressions denote, then they do not at all signify the length of the torments, or long continuance of their misery; so that the supposition of the length of their torments is brought in without any necessity, the Scripture saying nothing of it, having no respect to it, when it speaks of their everlasting punishments; and it answers the scripture expressions as well, to suppose that they shall be annihilated immediately, without any long pains, provided the annihilation be everlasting.

You see, Edwards’ argument is not that the language of eternal punishment works against annihilationism. Quite the contrary, he argues that annihilation answers the “scripture expressions” of eternal punishment well, but that if that’s what these expressions refer to, there remains no biblical justification for a lengthy period of penal suffering prior to annihilation. In Edwards’ mind, while there may be many reasons for rejecting annihilationism, the phrase “eternal punishment” is not in and of itself one of them.

Traditionalists would do well to recognize what Edwards recognized. Scripture has a lot to say about final punishment, and this vast wealth of biblical testimony cannot be read through the lens of this single, solitary, polysemous phrase in Matthew 25:46. Apparently, upon further thought, TurretinFan agreed. He wrote,

even if Date were correct that “punishment” were a deverbal result noun, he would have to argue that the context favors a result interpretation, not an event/process/manner interpretation…Words can have a range of meanings, known as the “semantic range” of the word. When there is a question about which meaning of the range of meanings applies, the very best clue to that meaning is the immediate context.

This is precisely what I argued in my opening statement. I said, “The question, then, is what is the nature of eternal punishment?…And the answer is clear from Jesus’ reference to the ‘eternal fire,’ a phrase found in two other places in the New Testament.” And then I went on to my make case from those uses of the phrase, which I’ll make in the future here at Rethinking Hell.

TurretinFan, however, appears to insist on a different element of the local context as the means by which we must determine whether “punishment” in Matthew 25:46 is a result or a process noun. He writes, “when ‘eternal punishment’ is placed in parallel with ‘eternal life,’ we are given an unmistakable clue that the ‘event’ or ‘manner’ sense is intended.” In other words, what determines one noun’s reading is that of its nearest neighbor. But this is not true. If a mechanic were to repair the engine of one’s car, guaranteeing that both the parts and labor will last for a year, one would naturally understand that while the parts themselves would function properly for a year, the laboring would not; the outcome of the labor would last for that period of time. TurretinFan’s test would render the guarantee nonsensical.

Were TurretinFan to object on the grounds that in this example one noun is deverbal and the other is not, another example could be brought to bear. If two people were to enter into an agreement that lasts for the duration of their lives, since the deverbal noun “agreement” refers to the result of agreeing, applying TurretinFan’s test would require that the deverbal noun “lives” refers to the time during which the agreeing takes place. Yet, clearly this is not the case. The result of agreeing would last for as long as these hypothetical partners live. And so, whether one deverbal noun has a process or result meaning is not what determines whether its neighbor carries the same meaning.

Thus the parallel between “eternal life” and “eternal punishment” in Matthew 25:46 does certainly indicate that “eternal” means “for eternity” in both cases, but the deverbal nouns described as “eternal” need not carry the same reading. The phrase Jesus uses a mere verses earlier, “eternal fire,” carries a certain meaning elsewhere, which along with the rest of Scripture must be the lens through which we interpret “eternal punishment,” rather than the other way around.

punishment, n. Oxford English Dictionary, Third edition, September 2007; online version June 2012; accessed 19 June 2012 [↩]

amercement, n.  Oxford English Dictionary, Third edition, March 2008; online version June 2012; accessed 19 June 2012 [↩]

St. Augustine (2011-10-04). The City of God - Enhanced (Kindle Locations 16804-16805). Kindle Edition. [↩]

Ibid. (Kindle Locations 16792-16794). [↩]

Edwards, Jonathan. The Works of President Edwards: With a Memoir of His Life (G. & C. & H. Carvill, 1830), 401. [↩]

An ancient witness adds to the testimony in favor of the Holy Scriptures

Most ancient Hebrew document since the Dead Sea Scrolls deciphered – it's Leviticus
3D scanning and advanced digital imaging enable verses from Leviticus in burned, 1,500-year-old scroll to be deciphered.

Advanced technology has enabled researchers from the Israel Antiquities Authority to decipher parts of a burnt scroll unearthed in 1970 at the ancient Ein Gedi synagogue.

Scientists have dated the parchment scroll to the late sixth century C.E. The verses that have been deciphered are from the beginning of the Book of Leviticus, making it the most ancient Torah scroll found since the Dead Sea scrolls and the most ancient ever found in a synagogue.

The synagogue, along with the entire Ein Gedi settlement, was destroyed by fire in the sixth century, toward the end of the Byzantine Era. The residents did not return to the site after the fire, leaving the Torah scroll, a bronze menorah, a collection of 3,500 coins and other relics to be discovered by archaeologists. The synagogue was excavated in the 1960s.

Researchers, headed by Dr. Sefi Porath, believe the fire and subsequent destruction resulted from an attack by Bedouin raiders or as a result of a confrontation with Byzantine authorities.

Charred scroll fragments were found in what the archaeologists believe was most likely the Holy Ark of the synagogue. One of them was a roll that looked like a cigar. Initial attempts to decipher it, including efforts by the police forensics unit, were unsuccessful. Eventually, it was put in storage in the Israel Museum.

Scientists returned to the scroll recently, using new methods developed to scan and decipher ancient scrolls. High-resolution 3D scans of the scroll were sent to Professor Brent Seales at the University of Kentucky, developer of digital imaging software which allows the scroll to be virtually unrolled and the text visualized, according to an announcement by the authority.

The text that was rendered legible by the software is substantial parts of the first eight verses of Leviticus. From the initial reading, there are no major differences between the text and the traditional text recognized today.

The oldest biblical text ever found in a synagogue. Photo by Reuters

Deciphering the scroll allowed researchers to declare that they had discovered the oldest Torah within a synagogue excavation. The next oldest scroll is the 10th-century Aleppo Codex.

Pnina Shor, curator and director of the Antiquities Authority’s Dead Sea Scroll Projects, said that the plan is to continue deciphering the rest of the scroll’s layers and additional fragments in similar condition.

“The discovery absolutely astonished us; we were certain it was just a shot in the dark but decided to try and scan the burnt scroll anyway,” she said. “Now, not only can we bequeath the Dead Sea Scrolls to future generations, but also a part of the Bible from a Holy Ark of a 1,500-year-old synagogue.”

“The historic discovery before us is fascinating and important,” said Culture Minister Miri Regev, who was at the press conference on Monday in which the Antiquities Authority revealed the discovery. “It is instructive about the Jewish people’s deep connection to its country and homeland.”

“The finding reflects a tradition of thousands of years, which I am glad encountered the professional determination of Antiquities Authority workers who utilized all the existing scientific capabilities to present the world with this wonderful find,” said Israel Hasson, the authority’s director, who was also at the press conference.

DNA v. Darwin.

DNA as Architect as Well as Librarian: Structural Functions of the Double Helix
Evolution News | @DiscoveryCSC

An assortment of words can do little without the structure of books to arrange them. And an assortment of books can do little without the structure of a library to organize it. The structures may not comprise the information content of the words, but they could be described as informational structures by nature of their ability to organize and present the coded information where it is needed. Could much of what was once dismissed as “junk DNA” function in that fashion?

Modern libraries are increasingly organized by machines that catalog, sort, and position information for readers. In the same way, DNA relies on a host of machines that read the strands, repair the strands, modify the transcripts, and send them where needed in the cell. Wouldn’t it be cool if the same DNA molecule that stores conceptual information also functions as a building block for the walls and buildings of the library? That’s what scientists are finding.

The DNA Balloon

Researchers at the University of California, San Diego, found for DNA “an unexpected role in cell architecture” that’s exciting enough to throw a party over. It pumps up the spore of a bacterium like a balloon.

As a basic unit of life, the cell is one of the most carefully studied components of all living organisms. Yet details on basic processes such as how cells are shaped have remained a mystery. Working at the intersection of biology and physics, scientists at the University of California San Diego have made an unexpected discovery at the root of cell formation.

As reported in the journal Cell on Feb. 8, 2018, biologists Javier Lopez-Garrido, Kit Pogliano and their colleagues at UC San Diego and Imperial College in London found that DNA executes an unexpected architectural role in shaping the cells of bacteria.

Studying the bacterium Bacillus subtilis, the researchers used an array of experiments and technologies to reveal that DNA, beyond serving to encode genetic information, also “pumps up” bacterial cells. [Emphasis added.]

The scientists found that if DNA is not translocated into the spore, the forespore fails to inflate. Is this a unique example of DNA acting as a structural element? The first author, Javier Lopez-Garrido, thinks not. “DNA is best known for being the molecule with genetic information,” he says, “but it’s becoming more and more obvious that it does other things that are not related to that.” The press release says that their work has relevance for human cells, for instance, “in terms of how they are generated and shaped, as well as aid explanations of basic mechanical processes and the structure of the nucleus and mitochondria.” It appears this structural role applies widely in many cells, beyond the specific instance they studied regarding spore formation in this one species of bacterium.

“Biologists tend to think of cell growth as following normal, biosynthetic pathways, but we found a pathway that is not normal, as it does not depend on processes normally required for growth,” said Pogliano, a professor in the Section of Molecular Biology and the paper’s senior author. “All you need for this cell to grow is to inflate it with DNA and its associated positively charged ions, and the ability to make more membrane so the cell can get bigger. Nothing else seems to be required.”

The discovery is a game changer. The observation that DNA has an architectural role opens up all kinds of research opportunities to find even more structural design in cells mediated by DNA.

“It’s amazing how we are just beginning to scratch the surface of how physics impacts living organisms,” said Pogliano. “This is a unique example of a very simple biophysical property impacting cell shape and it illustrates the value of physicists working closely with biologists. Understanding how physics and biology intersect is a huge area for future growth.”

The Chromosome Looper

The last time we mentioned the protein condensin,the “DNA wrapper,” we learned that scientists were trying to find out if it works as a molecular motor. “Yes,” was the answer last November. Molecular biologists also found that it was fast, and they knew that it caused DNA to form loops. But is it a loop extruder? Boy, is it! A picture is worth a thousand words.

It’s so impressive: a living cell is able to neatly package a big jumble of DNA, over two meters in length, into tidy, tiny chromosomes while preparing for cell division. For over a century, it has been clear that a cell can do so, but scientists have been puzzled for decades on how the process works. Researchers from the Kavli Institute of Delft University and EMBL Heidelberg now managed for the first time to isolate and film the process, and witnessed — in real time — how a single protein complex called condensin reels in DNA to extrude a loop. By extruding many such loops in long strands of DNA, a cell effectively compacts its genome so it can be distributed evenly to its two daughter cells. The scientists published their findings online in Science First Release on 22 February.

Moving at 1,500 base pairs per second but using only a “modest” amount of ATP fuel, condensin turns a spaghetti mess of DNA into a compact organization.

Structure as a Switchboard

In a final case of DNA structure with function, we see how the packaging of DNA in a cell helps it act like a giant switchboard. News from the Huntsman Cancer Institute at the University of Utah describes how proteins and DNA work in harmony to “orchestrate development.”

Researchers demonstrated that the hundreds of genes important for controlling embryonic development are all packaged in a unique manner in the early embryo — and even as far back as the paternal sperm — and that this packaging helps control how, when, and where different genes are expressed in the embryo. The findings, published today in the journal Cell, have significant implications for understanding how early development is orchestrated, and provides a mechanism for how parental environment might impact the expression of these genes in the offspring.

The findings make it clear that DNA structure is part of its function. It’s not merely a string of code. The way its genetic information is arranged in 3-D space matters. In a real sense, there is a structural code behind the informational code. This helps explain the large stretches of non-coding DNA that confused scientists when the human genome was first deciphered:

They demonstrated that DNA segments (genes) important for controlling development are packaged in physical structures that help turn ‘on’ and ‘off’ genes at different stages of development. These physical structures serve as platforms that help activate or poise these genes, as needed, for normal development. The researchers also identified the protein machines that place these physical structures into the genome, and the proteins that remove them, to ensure their proper placement and function.

Contrary to the old “Central Dogma” that pictured DNA calling all the shots, we now see that the “genetic code” really consists of both DNA and its protein machinery working “in harmony” as a team. This helps explain why a zygote is totipotent — able to generate all the cell types of the adult. A big part of that transformation relies on heritable structures, platforms, and switches in which both DNA and protein machines participate. The physical state of the decision-making genes, they found, determines their role in different cell types. Some of the structural information is inherited apart from DNA, they note:

Researchers have long sought to better understand whether and how genes from mom and dad might be packaged in a manner that influences expression and development in the embryo, and how those packaging states are maintained or reprogrammed during the development process. This study identifies that packaging — termed histone variant H2AFV — and provides a mechanism for inheriting gene packaging, and therefore has important implications for developmental potential and inheritance. Remarkably, although the initial packaging of genes in the paternal sperm differs somewhat from packaging in the maternal egg, the maternal packaging was shown to reprogram to the same packaging state of the paternal genome, thus harmonizing the packaging states from the parents in the early embryo to arrive at the same cellular development state.

These are exciting times for molecular biology. You know you’re on the right track when your expectation of more functional information in the “junk” keeps coming true.

Another stake through the heart of one of Darwinism's Zombies?

Finch Varieties in New Guinea Undercut Iconic Galápagos Finch Story
Evolution News | @DiscoveryCSC

Look at these photos of colorful finches found in New Guinea via  Boston University. What amazing variability we see: coloration patterns so different, a taxonomist would readily categorize them into different species. Now read this from Michael Sorenson, who with Katie Stryjewski catalogued 301 finch species in New Guinea:

Sorenson discovered that the entire group of New Guinea finch species was more genetically similar than is typical for the birds within a single African finch species.

It may take a re-reading of that sentence for its significance to sink in. Ever since Darwin, evolutionists have made a fuss about the 13 or so species of finches on the Galápagos Islands, which vary only slightly by millimeter-size differences in their beaks. Numerous books, papers, and seminars have been held about “Darwin’s Finches” as demonstrations of natural selection and the origin of species. Peter and Rosemary Grant have spent decades deciphering their significance. We were told that those small variations took millions of years for natural selection to create.

And now, all of a sudden, we have an even greater population of finches in another island community that tells a whopping different story. Does Sorenson’s research advance the Darwin finch story, or fly in its face?

Michael Sorenson, a professor of biology, explains that the birds are an evolutionary anomaly: Despite their striking coloration differences, all 11 species are extremely closely related, suggesting that they evolved quickly and recently (evolutionarily speaking), even faster than the famous Darwin’s finches of the Galapagos.

This points to an “extraordinarily recent and rapid radiation” occurring over tens or hundreds of thousands of years (compared to millions of years for most bird species).

Something is going on here that could change the whole evolutionary spiel. If you can get more variability in less time by non-selection processes, then Darwin’s finch icons may be going out of style. Biologists should flock to New Guinea for better insight into biological change.

But how and why did these close relatives end up looking so different? And how did they evolve so quickly into different species? Biologists have long wondered exactly how new species form, but generally assume that new genetic mutations account for the changes in form and function that ultimately make each species unique. However, that may not always be the case, and studying unusual groups like the finches of New Guinea helps biologists better understand other ways new species emerge, revealing more about evolution as a whole.

They have just abandoned the classical neo-Darwinian mutation/selection mechanism to explain these finch varieties. By extension, they could repudiate it for the Galápagos finches as well, seeing as how those finches show even less variability. So what is their new explanation? First, Sorenson feels it necessary to pledge allegiance to evolution, lest he become suspect:

“Speciation is the process by which the incredible diversity of life on earth came into being — including humans,” Sorenson says. “It is not only one of the most fundamental processes in evolutionary biology, but is central to understanding the history of life on earth.”

Sorenson just saluted the talking points of Darwinism: evolution is a fact, it accounts for the origin of species, and nothing in biology makes sense except in the light of evolution. No creationism to see here. No intelligent design. Having blown the all-clear whistle, he can say what he really thinks.

First, he and Stryjewski establish their credentials as empirical scientists. They showed impressive rigor in bird collection and genetic sequencing.

To understand how this extraordinary group of finches evolved, Katie Stryjewski… collected birds throughout New Guinea and carefully preserved blood, feather, and tissue samples, with Sorenson joining her on the last of four trips. Then Stryjewski used genome sequencing to peer deep inside the birds’ genetic codes.

Photos of some of Stryjewski’s carefully written data cards and notebooks leave no doubt. Sorenson, too, having sampled many finches in natural history museums, polishes his credentials:

“My career has been a somewhat less-than-coherent series of studies on out-of-the-ordinary examples of behavior and evolution in birds,” he says. “The unifying theme, however, is an interest in understanding not only the evolution of new species, but also the diversity of behavior and morphology observed in different species.”

If he wanted out-of-the-ordinary examples of evolution in birds, he clearly has that on his hands. As he said, these New Guinea finches, despite their diverse color patterns, have more genetic similarity than individuals within a single African finch species! Some birds from overlapping regions maintain distinct plumage patterns.

Sorenson was intrigued. “Which genes are involved? And how many genes does it take to build this species versus that species?” he says. “The profound genetic similarity of these species provided the perfect opportunity to answer these questions.”

Their field work was impressive: trips to remote regions by river, living with villagers, setting up mist nets, taking samples and making taxidermy specimens, and keeping diligent notes. It’s like the grand voyages of discovery, using some of the old methods of Darwin himself on the Beagle. But this time, the two had a new tool to add to the mix: genetic sequencing. And therein lays a new emerging picture. Comparing genes of different finches revealed a new mode of speciation:

Stryjewski and Sorenson identified about 20 genes that differed among finch species, half a dozen of which are known to control coloration in other organisms, including humans. Different combinations of genes were mixed and matched among species, “as opposed to new mutations cropping up,” Stryjewski says. “Each version of a gene is like a different little thing you could put on a Mr. Potato Head doll, and each bird is collecting a different set of them, and so they all end up looking different.”

A startling conclusion! Very different from the typical evolutionary story. The new scenario shows finches shuffling existing traits, as if playing Mr. Potato Head together.

Sorenson adds that “the birds’ genes likely interact with each other in complex ways, making the plumage that results from a particular combination of genes something more than the sum of the parts.” Sorenson thinks that occasional interbreeding between species that live in the same area … likely how different versions of genes moved from population to population over time.

The result of this mixing of already-present genetic information? Profound differences in appearance. Look at the 11 species of finches shown in their paper in Nature Ecology & Evolution: the vastly different color patterns are astonishing. There are beak size differences, too.

Darren Irwin, a zoologist at the University of British Columbia, praises the research for its “elegant analysis of a particularly interesting recent and rapid avian radiation.” He adds that scientists usually think of new species as arising from a single species splitting into two, but “this study provides a great example of how new forms arise in part through mixing genes from other populations.”

If Sorenson’s goal was “to advance general understanding of how evolution works,” he has advanced it in a very un-Darwinian direction! In the paper, Sorenson and Stryjewski call it “collateral evolution” and compare it to the Galápagos case:

The precise history of allelic variants at individual outlier loci is also difficult to reconstruct, but differential selection on retained ancestral polymorphisms and/or lateral transfer of adaptive alleles via introgression must have been involved in generating the mosaic patterns we observed. These processes comprise two forms of ‘collateral evolution’, defined as the parallel evolution of ancestral genetic variants in independent lineages and recognized as an important mechanism for convergent evolution. In Darwin’s finches, for example, ancestral alleles at two loci are associated with changes in bill morphology across multiple species. Likewise in the munias [New Guinea finches] ancestral alleles may underlie convergent components of each species’ unique phenotype, but we suggest that collateral evolution also contributed to phenotypic diversification by generating new combinations of alleles across a relatively small set of potentially interacting colour genes and other functionally relevant loci. The role of ancestral variation and collateral evolution in producing phenotypic novelty and diversity may be under-appreciated.

The variations do not require mutations culled by natural selection over millions of years. They can arise quickly by recombining already-existing genes in complex ways. Intelligent design theory can handle that. In addition, because of epistasis, pleiotropy and recombination, and possibly epigenetics, even more heritable variations on the theme can be generated from the information bank. Variations would tend to radiate outward, but not upward.

To be clear, the authors affirm neo-Darwinism: “Natural selection and recombination combine to produce heterogeneous patterns of genomic divergence between nascent and recently evolved species,” they say. But their own work does not require mutation and selection. All these colorful birds came about by recombining genes in different ways — genes that already existed, and still exist in humans.

Our results suggest that differential selection on ancestral genetic variation and lateral transfer of alleles via introgression have contributed to the phenotypic diversification of the Lonchura munias by generating unique combinations of alleles across a relatively small set of phenotypically relevant genes.

These scientists did not observe “ancestral genetic variation.” They observed different combinations of genes. Might this shed light on other cases of so-called “adaptive radiation” like Caribbean anole lizards, South American Heliconius butterflies, and even human beings? After all, we humans inhabit vastly different environments around the world, many of them overlapping. No biologist would dare classify us as different “species” based on hair color, or skin color, or body build, which can differ dramatically. We share pre-existing genes by lateral gene transfer, too. Often groups tend to isolate themselves by social preferences — not by mutation and selection. The differences in Homo sapiens are arguably as pronounced as those in the finch study. What’s Darwinism got to do with it? We’re all just playing Mr. Potato Head and having fun. Even Neanderthals played the game, because we all have Neanderthal genes.

Despite the authors’ pledge of allegiance to Darwinian evolution, the new finch study puts a very different spin on biological change. “Collateral evolution” looks more like a bush than a tree. The bush grows out from the center, as different combinations of existing genes create variations, but Mr. Potato Head does not evolve into something completely different. The authors had very little to say about mutation and natural selection in their paper: certainly nothing about its ability to create novelty from scratch.

Nobody would claim that “collateral evolution” can account for all the variability in the living world, but the new work on finches opens up possibilities for explaining a great deal of variability within groups, apart from neo-Darwinian mechanisms. It certainly casts doubt on neo-Darwinism as a progressive, creative force leading to a great branching tree of common ancestry. As Darwin stands over there scratching his head, those Galápagos finches don’t look so good anymore as icons of evolution. And neither do peppered moths, horses, or hominids.

By the way, in his update to the Darwin’s finches story in  Zombie Science, pp. 67-70, Jonathan Wells makes a similar case for the varieties on the Galápagos. He cites evidence of extensive interbreeding and hybridization between the supposed 13 “species” of finches, noting that it is “far from obvious why we should consider them separate species at all.”