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.

The OOL re:the design debate.

Why OOL apart from design is a non-starter.

A clash of Titans. LXVIII

The fossil record v. Darwin (again)

Bechly: The “Explosive” Pattern in the Fossil Record, and What It Means
David Klinghoffer | @d_klinghoffer

“There’s no reasonable way to get from bacteria to mammals via evolutionary processes.” So says notable German paleontologist Günter Bechly, for a variety of reasons. One reason he describes in really interesting detail in a new ID the Future episode is the puzzling pattern of explosive radiation events in life’s long history. Those include the Avalon explosion producing the bizarre Ediacaran biota, some 574 million years ago, the great Ordovician biodiversification event perhaps 470 million years ago, aka “life’s second Big Bang,” several abrupt appearances in the Triassic, from 251 to 240 million years ago, in which dinosaurs and proto-mammals enter the scene, and many more.

This is all apart from the granddaddy and most familiar of all life’s explosions, the enigmatic Cambrian event. The pattern is not at all what Charles Darwin expected from the fossil record.

Dr. Bechly talks with Sarah Chaffee about what the pattern means for the theory of unguided evolution, and the idea of universal common descent compared with a polyphyletic view. Can the two be reconciled? Bechly discusses his chapter co-written with Steve Meyer in the recent book Theistic Evolution: A Scientific, Philosophical, and Theological Critique. And he describes fresh turns his thinking has taken more recently, since the book was completed. That’s right, the theory of intelligent design, in the hands of scientists like Bechly, is still a work in progress with intellectual ferment, twists and turns, ongoing as we write here. Unlike the more traditional evolutionary view, ID hasn’t assumed the shape of a living fossil from an antique age.


That’s one thing that makes conversations like this so fascinating.  Listen to the podcast or download it here.

On the historicity of the scriptures:The Watchtower society's commentary.

A “Pim” Testifies to the Bible’s Historicity

THE word “pim” occurs only once in the Bible. In the days of King Saul, the Israelites had to get their metal tools sharpened by Philistine smiths. “The price for sharpening proved to be a pim for the plowshares and for the mattocks and for the three-toothed instruments and for the axes and for fixing fast the oxgoad,” states the Bible.​—1 Samuel 13:21.

What was a pim? The answer to that question remained a mystery until 1907 C.E. when the first pim weight stone was excavated at the ancient city of Gezer. Bible translators of earlier dates had difficulty translating the word “pim.” The King James Version, for example, rendered 1 Samuel 13:21: “Yet they had a file for the mattocks, and for the coulters, and for the forks, and for the axes, and to sharpen the goads.”

Scholars today know that a pim was a weight measure averaging 7.82 grams, or approximately two thirds of a shekel, the basic Hebrew unit of weight. A pim measure of silver scrap was the price the Philistines charged the Israelites for sharpening their tools. The shekel weight system went out of use with the fall of the kingdom of Judah and its capital, Jerusalem, in 607 B.C.E. So how does the pim measure testify to the historicity of the Hebrew text?

Some scholars argue that the texts of the Hebrew Scriptures, including the book of First Samuel, date to the Hellenistic-Roman era, even as late as from the second to the first century B.C.E. It is claimed, therefore, that “they are . . . ‘unhistorical,’ of little or no value for reconstructing a ‘biblical’ or an ‘ancient Israel,’ both of which are simply modern Jewish and Christian literary constructs.”

Referring to the pim measure mentioned at 1 Samuel 13:21, however, William G. Dever, professor of Near Eastern archaeology and anthropology, says: “[It] cannot possibly have been ‘invented’ by writers living in the Hellenistic-Roman period several centuries after these weights had disappeared and had been forgotten. In fact, this bit of biblical text . . . would not be understood until the early 20th century A.D., when the first actual archaeological examples turned up, reading pîm in Hebrew.” The professor continues: “If the biblical stories are all ‘literary inventions’ of the Hellenistic-Roman era, how did this particular story come to be in the Hebrew Bible? One may object, of course, that the pîm incident is ‘only a detail.’ To be sure; but as is well known, ‘history is in the details.’”

On Samson's Naziriteship:The Watchtower society's commentary.

How could Samson touch dead bodies that he had slain and still remain a Nazirite?

In ancient Israel, an individual could voluntarily make a vow and become a Nazirite for a certain length of time.* One of the restrictions resting upon the one making this vow stipulated: “All the days of his keeping separate to Jehovah he may not come toward any dead soul. Not even for his father or his mother or his brother or his sister may he defile himself when they die.” What if someone “should die quite suddenly alongside him”? Such an accidental touching of a dead body would defile his Naziriteship. Thus, it was stated: “The former days will go uncounted.” He would need to go through a purification ceremony and start the Nazirite period over again.​—Numbers 6:6-12.

Samson, though, was a Nazirite in a different sense. Before Samson’s birth, Jehovah’s angel told his mother: “Look! you will be pregnant, and you will certainly give birth to a son, and no razor should come upon his head, because a Nazirite of God is what the child will become on leaving the belly; and he it is who will take the lead in saving Israel out of the hand of the Philistines.” (Judges 13:5) Samson took no vow of Naziriteship. He was a Nazirite by divine appointment, and his Naziriteship was for life. The restriction against touching a corpse could not apply in his case. If it did and he accidentally touched a dead body, how could he start over a lifelong Naziriteship that began with his birth? Evidently, then, the requirements for lifetime Nazirites differed in some ways from those for voluntary Nazirites.

Consider Jehovah’s commandments to the three lifelong Nazirites​—Samson, Samuel, and John the Baptizer—​mentioned in the Bible. As noted earlier, Samson was required not to cut the hair of his head. Concerning her yet to be conceived child​—Samuel—​Hannah made the vow: “I will give him to Jehovah all the days of his life, and no razor will come upon his head.” (1 Samuel 1:11) In the case of John the Baptizer, Jehovah’s angel said: “He must drink no wine and strong drink at all.” (Luke 1:15) Moreover, “John had his clothing of camel’s hair and a leather girdle around his loins; his food too was insect locusts and wild honey.” (Matthew 3:4) None of these three individuals were commanded not to come near a dead soul.

Though a Nazirite, Samson was among the judges whom Jehovah raised up to save the Israelites out of the hand of their pillagers. (Judges 2:16) And in fulfilling this assignment, he came in contact with dead bodies. On one occasion, Samson struck down 30 Philistines and stripped off their outfits. Later, he went smiting the enemy, “piling legs upon thighs with a great slaughter.” He also took a moist jawbone of an ass and killed a thousand men with it. (Judges 14:19; 15:8, 15) Samson did all of this with Jehovah’s favor and backing. The Scriptures refer to him as a man of exemplary faith.​—Hebrews 11:32; 12:1.

Does the statement that Samson ripped apart a lion “just as someone tears a male kid in two” suggest that the tearing apart of young goats was a common practice in his day?

There is no evidence that in the time of Israel’s Judges, it was common for people to tear apart young goats. Judges 14:6 states: “Jehovah’s spirit became operative upon [Samson], so that he tore it [a maned young lion] in two, just as someone tears a male kid in two, and there was nothing at all in his hand.” This comment likely is an illustration.

The expression “he tore it in two” could have two meanings. Samson either tore apart the jaws of the lion or tore the lion limb from limb in some way. If the former is meant, then doing the same thing to a young goat is conceivably within human power. In this case, the parallel illustrates that conquering a lion with his bare hands was no more difficult for Samson than had the lion been a mere male kid. However, what if Samson killed the lion by tearing it limb from limb? The comment then can hardly be taken as anything more than a simile. The point of the simile would be that Jehovah’s spirit empowered Samson to perform a task that required extraordinary physical strength. In either case, the comparison drawn at Judges 14:6 illustrates that with Jehovah’s help, a powerful lion proved to be no more ferocious to Samson than a male kid would be to the average person.

[Footnote]

The length of time for Naziriteship was left up to the individual making the vow. According to Jewish tradition, however, the minimum length for the vow was 30 days. It was thought that anything less would make the vow commonplace.

The thumb print of Jehovah under the microscope.

Why the sun god cannot save Darwinism.

Steven F.Hayward V. Settled Science.

On the circus that is human origins theory.

Adam and the Genome and Hominid Fossils
Evolution News | @DiscoveryCSC

In his book Adam and the Genome, which we’ve been considering here, biologist Dennis Venema attempts to show that a traditional Adam and Eve did not exist. Instead, humans evolved, like any other species:

The evidence thus suggests that our lineage over the past 4 million years passed through an Ardipithecine-like species, on to an Australopithecine-like species, and then through various shades of Homo until our species is first preserved in the fossil record 200,000 years ago.

(Adam and the Genome, p. 59)

But in Science and Human Origins, Casey Luskin reviewed the fossil evidence including Ardipithecus and Australopithecus and showed:

Hominin fossils generally fall into one of two groups: ape-like species and human-like species, with a large, unbridged gap between them. Despite the hype promoted by many evolutionary paleoanthropologists, the fragmented hominin fossil record does not document the evolution of humans from ape-like precursors.

(Science and Human Origins, p. 45)

Adducing numerous authorities, the book showed that hominid fossils

…fall into two basic categories: ape-like fossils, and Homo-like fossils. This discontinuity between fossil types is well-known. Nonetheless, the hominin fossils have been interpreted as historical, physical evidence of our common ancestry with apes. Ernst Mayr, a well-known evolutionary biologist, acknowledged both the gap and the story-telling in his book What Makes Biology Unique:

“The earliest fossils of Homo, Homo rudolfensis and Homo erectus, are separated from Australopithecus by a large, unbridged gap. How can we explain this seeming saltation? Not having any fossils that can serve as missing links, we have to fall back on the time-honored method of historical science, the construction of a historical narrative.”

(Science and Human Origins, p. 17)

As for Ardipithecus, a fossil noted by Venema, Luskin cites authorities pointing out that this fossil was highly fragmented. This condition makes it difficult to establish whether it walked upright like humans, and, indeed, quite a few authorities believe it was not on the line that led to humans. Moreover, Luskin lists many differences between the australopithecines and our genus Homo, and he cites many authorities who have recognized this gap. Our old friend Casey documented all this and more in a range of articles online:

Ardipithecus as an unlikely human ancestor:

• “The Fragmented Fossil Record of Early Hominins”
• “Another Scientific Paper Challenges Ardi’s Place as a Bipedal Human Ancestor”
• “Nature Publishes Paper Critical of Ardi’s Status as Human Evolutionary Ancestor”
• “Is ‘Ardi’ All Washed Up? (Updated)”

For problems with citing the australopithecines as human ancestors or intermediates:

• “Later Hominins: The Australopithecine Gap”
• “My Pilgrimage to Lucy’s Holy Relics Fails to Inspire Faith in Darwinism”

The abrupt appearance of humans:

• “A Big Bang Theory of Homo”
• “Professor Who Indoctrinates Students on Human Evolution Pushes Them Away from Science”

Casey Luskin has a more extensive treatment of this subject in a chapter, “Missing Transitions: Human Origins and the Fossil Record,” in the recent book Theistic Evolution: A Scientific, Philosophical, and Theological Critique. 

There, he writes:

The standard evolutionary view of human origins — generally accepted by theistic evolutionists — holds that our species, Homo sapiens, evolved from apelike species through apparently unguided evolutionary processes like natural selection and random mutation. Theistic evolutionists and other evolutionary scientists often claim the fossil evidence for this Darwinian evolution of humans from ape-like creatures is incontrovertible. But their viewpoint is not supported by the fossil evidence. Hominin fossils generally fall into one of two groups: ape-like species and human-like species, with a large, unbridged gap between them. Virtually the entire hominin fossil record is marked by fragmented fossils, especially the early hominins, which do not document precursors to humans. Around 3 to 4 million years ago, the australopithecines appear, but they were generally ape-like and also appear in an abrupt manner. When our genus Homo appears, it also does so in an abrupt fashion, without clear evidence of a transition from previous ape-like hominins. Major members of Homo are very similar to modern humans, and their differences amount to small-scale microevolutionary changes. The archaeological record also shows an “explosion” of human creativity about thirty to forty thousand years ago. Despite the claims of evolutionary paleoanthropologists and the media hype surrounding many hominin fossils, the fragmented hominin fossil record does not document the evolution of humans from ape-like precursors, and the appearance of humans in the fossil record is anything but a gradual Darwinian evolutionary process. … [T]wo top paleoanthropologists have admitted that “the evolutionary sequence for the majority of hominin lineages is unknown.” With the fossil evidence for human evolution so weak, why should our theistic evolutionist brothers and sisters insist that the church must adopt their viewpoint?

So, despite Dennis Venema’s statements to the contrary, there is no clear-cut lineage of fossils leading from ape-like hominids to modern humans. Want to learn more? A good place to start is here: “Human Origins and the Fossil Record: What Does the Evidence Say?”

Something fishy about Darwin splainin'?

A Smell Test for Design v. Evolutionary Explanations
Evolution News | @DiscoveryCSC

If you’ve ever experienced sharing your home or kitchen with cockroaches, you know that these unpleasant critters seem to multiply faster than your can of Raid will spray, and they get into everything. Nevertheless, it’s good to report that some scientists have seen the value of trying to understand them and figure out why they are so successful. What they found is quite astonishing — and a good test case for comparing Darwinian with design explanations. The researchers published their work in Current Biology under the title, “Spatial Receptive Fields for Odor Localization.”

One of the reasons cockroaches are so successful is their keen sense of smell. Like many insects, including the more pleasing butterflies we all love, roaches smell with their antennae. We saw some micrographs of a butterfly antenna in  Metamorphosis — an intriguing structure, to be sure, but loaded with more complexity than apparent even at that level. The cockroach antenna is called a flagellum, which just means any whip-like thing. But this is no ordinary whip. It is loaded with complex specified information in the form of olfactory sensory neurons (OSNs). The authors focused, on just one odorant, a molecule that is one ingredient of the roach sex pheromone odor cocktail. Male roaches need to follow the “odor plume” of periplanone-B to find a female, even in the dark. They come well equipped. The authors estimate there are some 36,000 OSNs for this odorant on the antenna.

Animals rely on olfaction to navigate through complex olfactory landscapes, but the mechanisms that allow an animal to encode the spatial structure of an odorous environment remain unclear. To acquire information about the spatial distribution of an odorant, animals may rely on bilateral olfactory organs and compare side differences of odor intensity and timing or may perform spatial and temporal signal integration of subsequent samplings. 

In other words, having 36,000 sensors is not enough. A male roach will be out of luck if he hangs around where the odor plume used to be. To track his beloved’s perfume, he needs to localize its source as she is moving. Previous studies had shown that the male tends to navigate to the edge of the plume rather than race to the center of highest concentration, a strategy that may serve to amplify spatio-temporal changes. But that strategy is not going to work without having a battery of high-tech instruments and software to interpret it. Again, the roach olfactory system comes well equipped.

PNs’ terminals are broadly distributed in the MB, a neuropil involved in processes such as multimodal sensory integration and associative learning. Here, we have shown that S-PNs’ terminals display a stereotyped distribution, suggesting that the spatial information encoded in the MG can be relayed to the MB….

Whoa, what? That’s the trouble with reading papers on olfaction. The jargon tends to be specialized and dense. So rather than try to define projection neuron, Kenyon cell, mushroom body and other unfamiliar terms, let’s keep it simple. Even the mouthful “macroglomerulus” comes from Latin meaning “big ball of twine.” Let’s give ordinary names to the important parts, based on analogies with familiar things (that’s what the original name-inventors did, anyway; “mushroom body” looks like a mushroom but doesn’t taste like one. Scholars can wade through the open-access paper with its specialized jargon to their heart’s content). We can call the macroglomerulus the string ball. It receives twangs from the triggers on the whip (flagellum, that is), carried on waves by strings. What we want to follow is the process, not the nomenclature. That’s where the real fascination is.

So we discover 36,000 strings plucked by the pheromone, reaching out to the string ball, carrying waves of “encoded information” (they do use that term) from up and down the whip. Let’s add some more complexity now. The whip looks like a guitar neck with frets along its length. Just as a guitarist changes the pitch by position, the information coming from the whip encodes spatial information: the strings at the tip “sound” different from those at the base. And just as the strings each have their own character, the scientists found 12 different kinds of strings responding to this one odorant molecule.

It’s like having a 12-string guitar, but there’s more. There are thick strings and thin strings. All of them plug into the string ball at very specific points. It might be best to shift analogies here, and compare the string ball to a mixing console with lots of plug-in inputs. The scientists found that the thin strings plug into distinct layers around one another in the mixing console, and the thick strings plug into overlapping inputs. The thick strings “sound” pretty much the same from along the guitar neck, but the thin strings have more specificity. In fact, the thin strings can even inhibit the twangs, something like a guitarist performing a “stop” action to produce overtones. They apparently do this to maximize resolution. The scientists found that this gives the thin strings a response area to plucking as fine as 1 millimeter.

As any sound engineer knows, the point where you plug in an input is very important. Also important is how you send the sounds down the line to submixes and mains, to get the proper blend of sounds. The scientists wanted to know if this spatial information was maintained in the next devices in the chain. Sure enough, the submixes found in the mixing board also are identifiable in the mushroom body, which we can call the program console. We’ve all seen the control rooms at TV stations where dozens of consoles line the wall. The program engineer selects between these inputs with split-second decisions to present a unified TV show to the viewer. In the case of olfaction, something similar happens. The brain can’t afford to get swamped by TMI (too much information) when what it is interested in is whether to follow the female this way or that. And remember, the program engineer is not just monitoring this one screen about this one pheromone signal. He’s got thousands of other inputs responding to other odors. It’s like having thousands of other instruments each sending their strings of information in real time down to their own mixing boards and on to the program manager’s console.

This spatial information has to be preserved, but it’s constantly changing. Each mixing board is updating its signal constantly. If you watched the “Pacific Salmon’s sense of smell” animation in Living Waters, it’s like that, and even more complex than shown. The proof of its effectiveness is the behavior: the salmon loses the scent on one tributary, and turns around to follow it up the adjacent one. The roach loses the odor plume in one direction, so it continually adjusts its steps to adjust to the constantly changing signal. The reason the roach follows the edge of the odor plume is because that’s where the concentration gradient and the dynamical information is likely to be greatest, giving the strings more nuance These animals respond faster than a program engineer does for TV. It’s amazing. Are you getting a little more respect for those household pests?

At the risk of overkill, let’s pile on more design by mentioning that all this complexity is constructed during development from a single egg. Furthermore, it has to be upgraded and improved, without breaking anything, during the 11 molts the cockroach goes through on its way to adulthood.

Let’s miniaturize it some more. News from the University of California, Riverside describes olfaction in fruit flies and mosquitoes, which are much tinier than cockroaches, yet just as responsive to odors. Here’s all you need to hear:

Odor receptors are proteins that festoon the antennae and sensory appendages on the heads of fruit flies. Odorant molecules plug into them like a key into a lock, activating the odor-detecting machinery in the fly brain to trigger behaviors such as homing in on ripe fruit. Deciphering the odor-detecting machinery has been incredibly difficult, said Ray, because the fly has more than 100 different odor receptor proteins, which feed into an even more complex odor-processing circuitry in the brain.

If you’re getting the idea that olfaction is a challenge to evolution, you’re right. That’s why Illustra took time to show it in Living Waters. That’s why it was (and still is) one of the most difficult senses to figure out. Even with our simplified analogies, the half is not being told. It remains an active area of research, and attempts to build “electronic noses” have been about as minimally successful as artificial intelligence. One thing we know is that every time we see a functioning system with similar complexity, we know it came from an intelligent cause.

So now, for our grand finale: let’s hear the evolutionary explanation! How will they tackle the following observations:

The use of highly specialized sub-compartment of the cockroach olfactory circuit as a model system has been instrumental in revealing a fine mechanism for the acquisition of spatial information on the olfactory surroundings. The direct correspondence of the antennal surface with a stereotyped antennotopic structure within the brain, coupled with continuous active sensing of the surrounding air space, provides the neuroanatomical means to generate an internal representation of the pheromone distribution.

The Darwin spokesperson steps up to the microphone to explain how this originated. Get ready: get set…

The distribution of [specialized neurons] within the macroglomerulus have [sic] evolved through hundreds of millions of years of selective pressure to efficiently localize the sexual mate and increase individual fitness.

All of this simply…“evolved.” That’s it? That’s it? Yes, that’s it. Simple as that.

On Darwinian trickery.

Evolution a Creative Trickster? Heretic Bioengineer Says No
Jonathan Witt

headline at Science Daily announces, “Evolution Plays Many Tricks against Large-Scale Bioproduction.”The headline paints evolution as a creative wunderkind, a mischievous Br’er Rabbit brilliantly outsmarting the Br’er Bear of industrial bioproduction.

There is mischief here, but it’s the vandal kind, not the creative sort.

“Ultra-deep DNA sequencing of thousands of cells uncovers many competing mechanisms of evolution as a threat to efficient scale-up of biobased chemicals production,” the article reports. “Evolution plays an underestimated role in bioprocesses and limits yields much more than previously anticipated.”

I passed this along to my Heretic co-author, distinguished Finnish bio-engineer Matti Leisola. When he wrote back, he said the instability of bio-engineered strains in such cases is a well-known problem. He encountered it years ago at Cultor, an international bio-engineering company where he served for several years as a research director before returning to academic life. He said:

We had in Cultor two 350 cubic meter (17 m high) and ten 50 cubic meter reactors. We were at that time the largest producer of glucose isomerase enzyme used by ADM to produce high-fructose corn syrup. The bacterial strain we used had over 100 copies of the needed gene but lost the extra copies during the fermentation process almost completely, and we had to start every new production process with an original freeze-dried engineered strain.

Leisola was underwhelmed by the Science Daily article’s talk of evolution in action:

The story is actually really funny. The word evolution is used to mean degeneration, as is so often done. This is how they describe it: “We discovered that a wide diversity of genetic disruptions turned producing cells into non-producing when we deep-sequenced thousands of production organisms over time.”

That’s a crucial point. Modern evolutionary theory purports to explain how fundamentally new biological machines and other forms originated. But many of the oft-cited examples of evolution in action involve devolution. In each such case, an organism or molecular machine devolves in a way that gives it a niche advantage, but at the cost of overall fitness.

Michael Behe describes some examples in The  The Edge of Evolution (e.g., antibiotic and malaria resistance). And in this ID the Future conversation, he discusses another example, polar bears. David Klinghoffer summarizes the podcast as a conversation “about evolution’s dark secret: When we can show it at work, in the lab or in the wild, evolution is very often engaged in breaking things, not building them.”

Leisola said there is ample evidence that in competing environments microbes tend to lose unnecessary genes that are only an extra load for them. In a 2014 Bioscience article,“For Microbes, Devolution is Evolution,”writer Marcia Stone describes some of that evidence, and quotes J. Jeffrey Morris, a member of Richard Lenski’s famed Michigan State University lab. “Species are in a ‘race to the bottom,’” Morris said, “deleting the genes for as many costly functions as they can get away with.”

Even when evolution has a small, step-by-step path to a modest complexity advance, that pathway may be foreclosed by a more attractive devolutionary path. Matti and I discuss this in  Heretic: One Scientist’s Journey from Darwin to Design:

It is generally assumed that a multi-step mutational evolutionary path is possible if all the intermediary steps are functional and can each be reached by a single mutation. The activity produced in this way may, however, be so weak that the cell must over-express the hypothetical newly formed enzyme — in other words, produce too much of the enzyme, causing a huge strain on the cell because it has to use extra synthetic capacity for this. Therefore it is likely that the cell would shed such a weak side-activity. The modest benefit wouldn’t be worth the strain caused by the overproduction.

 Ann Gauger and her colleagues studied what happened in such a case under laboratory conditions. They introduced a mutation that partially interfered with a bacterial cell’s gene for the synthesis of the amino acid tryptophan. Then they introduced a second mutation into the gene that completely abolished the ability to synthesize tryptophan. Cells with the double mutant could, theoretically, regain weak tryptophan synthesizing ability with only one back-mutation. Given more time, cells with the one back-mutation might then undergo one more back-mutation to regain full tryptophan-synthesizing ability. This might demonstrate how a cell could gain a new function with just two mutations. But this did not happen. Instead, cells consistently acquired mutations that reduced expression of the doubly mutated gene. The experiment suggests that even if the cell could acquire a weak new activity by gene mutation, it would get rid of it because weakly performing functions of this sort exact too heavy an energy burden.