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.”

The death of moral clarity?

Should EMTs Save a Human or a Dog First?
Wesley J. Smith

Bioethicists never cease to entertain — if some of the dangerous views pushed by this mainstream movement can be considered “entertaining.”

But this entry into the discourse sort of takes the cake. Over at  bioethics.net, “maintained by the editorial staff of The American Journal of Bioethics,” a DePaul University PhD named Craig Klugman worries that EMT responders won’t give pets mouth-to-mouth resuscitation out of fear that saving Fido could be considered practicing veterinary medicine without a license. (!!!)

Really? Well, if EMTs need liability protection when rescuing our pets, then by all means, grant them the protection.

Klugman then ponders a situation in which both a human and an animal need CPR. Which, he asks, should the EMT help first?

Before you read his answer below about flipping a coin and decision-making by “aesthetics,” realize that Klugman understands his readership. Many bioethicists would brand an automatic response, “the human,” to be “speciesism” — i.e., discrimination against animals  — which those who hold such misanthropic views deem akin to racism. (Ditto, animal-rights activists.)

Now, to Klugman. From “Snout to Mouth: The Age of PET CPR Requires Pet POLSTS” (my emphasis):

Having EMS able to give pet CPR does raise some intriguing bioethical issues. From a resource perspective, if an EMT arrives on scene where a human needs CPR and a dog needs CPR, which one should the EMT assist first (assuming that only one EMT is available)? Most people would probably respond, “the human, of course” because although we care deeply for our pets, our society still values human life over that of animals (rightly or wrongly).

If we viewed both lives as equal, then perhaps the EMT should flip a coin.

However, the ethics of aesthetics are probably at play in developing this prioritization since a headline that says “EMT saves human; dog dies” is less likely to be litigious than “EMT saves dog while not treating human.”

Yikes. Talk about not taking a stand!

And what if Fido doesn’t have a quality of life worth living? Advance directives!

Where first responders offer pet-CPR, it may be important to have POLST documents for Fluffy and Spot (though legally these may not be enforceable). You may want to add a DNR dogtag (yes these are meant for people, but are available and are not too large) as part of your dog’s tags.

That’s bioethics for you, folks! Good grief.