Between physics and abiogenesis an unbridgeable chasm?

The Origin of Life, Self-Organization, and Information
Brian Miller

In an  article here yesterday, I described the thermodynamic challenges to any purely materialistic theory for the origin of life. Now, I will address one of the most popular and misunderstood claims that the first cell emerged through a process that demonstrated the property known as self-organization.

As I mentioned in the previous article, origin-of-life researchers often argue that life developed in an environment that was driven far from equilibrium, often referred to as a non-equilibrium dissipative system. In such systems, energy and/or mass constantly enters and leaves, and this flow spontaneously generates “order” such as the roll patterns in boiling water, the funnel of a tornado, or wave patterns in the Belousov-Zhabotinsky reaction. The assertion is that some analogous type of self-organizational process could have created the order in the first cell. Such claims sound reasonable at first, but they completely break down when the differences between self-organizational order and cellular order are examined in detail. Instead, the origin of life required complex cellular machinery and preexisting sources of information.

The main reason for the differences between self-organizational and cellular order is that the driving tendencies in non-equilibrium systems move in the opposite direction to what is needed for both the origin and maintenance of life. First, all realistic experiments on the genesis of life’s building blocks produce most of the needed molecules in very small concentrations, if at all. And, they are mixed together with  contaminants, which would hinder the next stages of cell formation. Nature would have needed to spontaneously concentrate and purify life’s precursors. However, the natural tendency would have been for them to diffuse and to mix with other chemicals, particularly in such environments as the bottom of the ocean.

Concentration of some of life’s precursors could have taken place in an evaporating pool, but the contamination problem would then become much worse since precursors would be greatly outnumbered by contaminants. Moreover, the next stages of forming a cell would require the concentrated chemicals to dissolve back into some larger body of water, since different precursors would have had to form in different locations with starkly different initial conditions. In  his  book on Origins, Robert Shapiro described these details in relation to the exquisite orchestration required to produce life.

In addition, many of life’s building blocks come in both right and left-handed versions, which are mirror opposites. Both forms are produced in all realistic experiments in equal proportions, but life can only use one of them: in today’s life, left-handed amino acids and right-handed sugars. The  origin of life would have required one form to become increasingly dominant, but nature would drive a mixture of the two forms toward equal percentages, the opposite direction. As a related but more general challenge, all spontaneous chemical reactions move downhill toward lower free energy. However, a large portion of the needed reactions in the origin and maintenance of life move uphill toward higher free energy. Even those that move downhill typically proceed too slowly to be useful. Nature would have had to reverse most of its natural tendencies in any scenario for extended periods of time. Scientists have never observed any such event at any time in the history of the universe.

These challenges taken together help clarify the dramatic differences between the two types of order:

Self-organizational processes create order (i.e. funnel cloud) at the macroscopic (visible) level, but they generate entropy at the microscopic level. In contrast, life requires the entropy at the cellular size scale to decrease.

Self-organizational patterns are driven by processes which move toward lower free energy. Many processes which generate cellular order move toward higher free energy.

Self-organizational order is dynamic — material is in motion and the patterns are changing over time. The cellular order is static — molecules are in fixed configurations, such as the sequence of nucleotides in DNA or the structure of cellular machines.

Self-organizational order is driven by natural laws. The order in cells represents specified complexity — molecules take on highly improbable arrangements which are not the product of natural processes but instead are arranged to achieve functional goals.

These differences demonstrate that self-organizational processes could not have produced the order in the first cell. Instead, cellular order required molecular machinery to process energy from outside sources and to store it in easily accessible repositories. And, it needed information to direct the use of that energy toward properly organizing and maintaining the cell.

A simple analogy will demonstrate why machinery and information were essential. Scientists often claim that any ancient energy source could have provided the needed free energy to generate life. However, this claim is like a couple returning home from a long vacation to find that their children left their house in complete disarray, with clothes on the floor, unwashed dishes in the sink, and papers scattered across all of the desks. The couple recently heard an origin-of-life researcher claim that order could be produced for free from any generic source of energy. Based on this idea, they pour gasoline on their furniture and then set it on fire. They assume that the energy released from the fire will organize their house. However, they soon realize that unprocessed energy creates an even greater mess.

Based on this experience, the couple instead purchase a solar powered robot. The solar cells process the energy from the sun and convert it into useful work. But, to the couple’s disappointment the robot then starts throwing objects in all directions. They look more closely at the owner’s manual and realize they need to program the robot with instructions on how to perform the desired tasks to properly clean up the house.

In the same way, the simplest cell required machinery, such as some ancient equivalent to ATP synthase or chloroplasts, to process basic chemicals or sunlight. It also needed proteins with the proper information contained in their amino acid sequences to fold into other essential cellular structures, such as portals in the cell membrane. And, it needed proteins with the proper sequences to fold into enzymes to drive the metabolism. A key role of the enzymes is to  link reactions moving toward lower free energy (e.g. ATP → ADP + P) to reactions, such as combining amino acids into long chains, which go uphill. The energy from the former can then be used to drive the latter, since the net change in free energy is negative. The free-energy barrier is thus overcome.

However, the energy-processing machinery and information-rich proteins were still not enough. Proteins eventually break down, and they cannot self-replicate. Additional machinery was also needed to constantly produce new protein replacements. Also, the proteins’ sequence information had to have been stored in DNA using some  genetic code, where each amino acid was represented by a series of three nucleotides know as a codon in the same way English letters are represented in Morse Code by dots and dashes. However,  no identifiable physical connection exists between individual amino acids and their respective codons. In particular, no amino acid (e.g., valine) is much more strongly attracted to any particular codon (e.g., GTT) than to any other.  Without such a physical connection, no purely materialistic process could plausibly explain how amino acid sequences were encoded into DNA. Therefore, the same information in proteins and in DNA must have been encoded separately.

In addition, the information in  DNA is decoded back into proteins  through the use of ribosomes, tRNAs, and special enzymes called aminoacyl tRNA sythetases (aaRS). The aaRSs bind the correct amino acids to the correct tRNAs associated with the correct codons, so these enzymes contain the decoding key in their 3D structures. All life uses this same process, so the first cell almost certainly functioned similarly. However, no possible connection could exist between the encoding and the decoding processes, since the aaRSs’ structures are a result of their amino acid sequences, which happen to be part of the information encoded in the DNA. Therefore, the decoding had to have developed independently of the encoding, but they had to use the same code. And, they had to originate at the same time, since each is useless without the other.

All of these facts indicate that the code and the sequence information in proteins/DNA preexisted the original cell. And, the only place that they could exist outside of a physical medium is in a mind, which points to design.

Actually,it is rocket science.

Rocket Science in a Microbe Saves the Planet
Evolution News & Views

Anammox. It's a good term to learn. Wikipedia's first paragraph stresses its importance:

Anammox, an abbreviation for ANaerobic AMMonium OXidation, is a globally important microbial process of the nitrogen cycle. The bacteria mediating this process were identified in 1999, and at the time were a great surprise for the scientific community. It takes place in many natural environments... [Emphasis added.]

And now, the news. A team of European scientists found something very interesting about the bacteria. Publishing in Nature, the researchers tell how they have ascertained the structure of a molecular machine that performs chemical wizardry using rocket science.

Anaerobic ammonium oxidation (anammox) has a major role in the Earth's nitrogen cycle and is used in energy-efficient wastewater treatment. This bacterial process combines nitrite and ammonium to form dinitrogen (N2) gas, and has been estimated to synthesize up to 50% of the dinitrogen gas emitted into our atmosphere from the oceans. Strikingly, the anammox process relies on the highly unusual, extremely reactive intermediate hydrazine, a compound also used as a rocket fuel because of its high reducing power. So far, the enzymatic mechanism by which hydrazine is synthesized is unknown. Here we report the 2.7 Å resolution crystal structure, as well as biophysical and spectroscopic studies, of a hydrazine synthase multiprotein complex isolated from the anammox organism Kuenenia stuttgartiensis. The structure shows an elongated dimer of heterotrimers, each of which has two unique c-type haem-containing active sites, as well as an interaction point for a redox partner. Furthermore, a system of tunnels connects these active sites. The crystal structure implies a two-step mechanism for hydrazine synthesis: a three-electron reduction of nitric oxide to hydroxylamine at the active site of the γ-subunit and its subsequent condensation with ammonia, yielding hydrazine in the active centre of the α-subunit. Our results provide the first, to our knowledge, detailed structural insight into the mechanism of biological hydrazine synthesis, which is of major significance for our understanding of the conversion of nitrogenous compounds in nature.

Dinitrogen gas (N2) is a tough nut to crack. The atoms pair up with a triple bond, very difficult for humans to break without a lot of heat and pressure. Fortunately, this makes it very inert for the atmosphere, but life needs to get at it to make amino acids, muscles, organs, and more. Nitrogenase enzymes in some microbes, such as soil bacteria, are able break apart the atoms at ambient temperatures (a secret agricultural chemists would love to learn). They then "fix" nitrogen into compounds such as ammonia (NH3) that can be utilized by plants and the animals that eat them. To have a nitrogen cycle, though, something has to return the N2 gas back to the atmosphere. That's the job of anammox bacteria.

Most nitrogen on earth occurs as gaseous N2 (nitrogen oxidation number 0). To make nitrogen available for biochemical reactions, the inert N2 has to be converted to ammonia (oxidation number −III), which can then be assimilated to produce organic nitrogen compounds, or be oxidized to nitrite (oxidation number +III) or nitrate (+V). The reduction of nitrite in turn results in the regeneration of N2, thus closing the biological nitrogen cycle.

Let's take a look at the enzyme that does this, the "hydrazine synthase multiprotein complex." Rocket fuel; imagine! No wonder the scientific community was surprised. The formula for hydrazine is N2H4. It's commonly used to power thrusters on spacecraft, such as the Cassini Saturn orbiter and the New Horizons probe that went by Pluto recently. Obviously, the anammox bacteria must handle this highly reactive compound with great care. Here's their overview of the reaction sequence. Notice how the bacterium gets some added benefit from its chemistry lab:

Our current understanding of the anammox reaction (equation (1)) is based on genomic, physiological and biochemical studies on the anammox bacterium K. stuttgartiensis. First, nitrite is reduced to nitric oxide (NO, equation (2)), which is then condensed with ammonium-derived ammonia (NH3) to yield hydrazine (N2H4, equation (3)). Hydrazine itself is a highly unusual metabolic intermediate, as it is extremely reactive and therefore toxic, and has a very low redox potential (E0′ = −750 mV). In the final step in the anammox process, it is oxidized to N2, yielding four electrons (equation (4)) that replenish those needed for nitrite reduction and hydrazine synthesis and are used to establish a proton-motive force across the membrane of the anammox organelle, the anammoxosome, driving ATP synthesis.

We've discussed ATP synthase before. It's that rotary engine in all life that runs on proton motive force. Here, we see that some of the protons needed for ATP synthesis come from the hydrazine reaction machine. Cool!

What does the anammox enzyme look like? They say it has tunnels between the active sites. The "hydrazine synthase" module is "biochemically unique." Don't look for a common ancestor, in other words. It's part of a "tightly coupled multicomponent system" they determined when they lysed a cell and watched its reactivity plummet. Sounds like an irreducibly complex system.

The paper's diagrams of hydrazine synthase (HZS) show multiple protein domains joined in a "crescent-shaped dimer of heterotrimers" labeled alpha, beta, and gamma, constituted in pairs. The machine also contains multiple haem units (like those in hemoglobin, but unique) and "one zinc ion, as well as several calcium ions." Good thing those atoms are available in Earth's crust.

Part of the machine looks like a six-bladed propeller. Another part has seven blades. How does it work? Everything is coordinated to carefully transfer electrons around. This means that charge distributions are highly controlled for redox (reduction-oxidation) reactions (i.e., those that receive or donate electrons). The choice of adverbs shows that their eyes were lighting up at their first view of this amazing machine. Note how emotion seasons the jargon:

Intriguingly, our crystal structure revealed a tunnel connecting the haem αI and γI sites (Fig. 3a). This tunnel branches off towards the surface of the protein approximately halfway between the haem sites, making them accessible to substrates from the solvent. Indeed, binding studies show that haem αI is accessible to xenon (Extended Data Fig. 4c). Interestingly, in-between the α- and γ-subunits, the tunnel is approached by a 15-amino-acid-long loop of the β-subunit (β245-260), placing the conserved βGlu253, which binds a magnesium ion, into the tunnel.

We would need to make another animation to show the machine in action, but here's a brief description of how it works. The two active sites, connected by a tunnel, appear to work in sequence. HZS gets electrons from cytochrome c, a well-known enzyme. The electrons enter the machine through one of the haem units, where a specifically-placed gamma unit adds protons. A "cluster of buried polar residues" transfers protons to the active center of the gamma subunit. A molecule named hydroxylamine (H3NO) diffuses into the active site, assisted by the beta subunit. It binds to another haem, which carefully positions it so that it is "bound in a tight, very hydrophobic pocket, so that there is little electrostatic shielding of the partial positive charge on the nitrogen." Ammonia then comes in to do a "nucleophilic attack" on the nitrogen of the molecule, yielding hydrazine. The hydrazine is then in position to escape via the tunnel branch leading to the surface. Once they determined this sequence, a light went on:

Interestingly, the proposed scheme is analogous to the Raschig process used in industrial hydrazine synthesis. There, ammonia is oxidized to chloramine (NH2Cl, nitrogen oxidation number −I, like in hydroxylamine), which then undergoes comproportionation with another molecule of ammonia to yield hydrazine.

(But that, we all know, is done by intelligent design.)


So here's something you can meditate on when you take in another breath. The nitrogen gas that comes into your lungs is a byproduct of an exquisitely designed, precision nanomachine that knows a lot about organic redox chemistry and safe handling of rocket fuel. This little machine, which also knows how to recycle and reuse all its parts in a sustainable "green" way, keeps the nitrogen in balance for the whole planet. Intriguing. Interesting. As Mr. Spock might say, fascinating.

Why the quest to reduce biology to chemistry is doomed.

The White Space in Evolutionary Thinking

Ann Gauger 

When certain biologists discuss the early stages of life there is a tendency to think too vaguely. They see a biological wonder before them and they tell a story about how it might have come to be. They may even draw a picture to explain what they mean. Indeed, the story seems plausible enough, until you zoom in to look at the details. I don't mean to demean the intelligence of these biologists. It's just that it appears they haven't considered things as completely as they should. Like a cartoon drawing, the basic idea is portrayed, but there is nothing but blank space where the profound detail of biological processes should be.

Let me give an example. This week Discovery Institute released a pair of videos ("How to Build a Worm" and "Switched on Worms") featuring Fellow and philosopher of biology Paul Nelson and a lowly nematode called C. elegans. Its development is precise and intricately patterned, like a Bach fugue that splits and weaves many voices into one. The final cadence is the newly hatched larva. Not coincidentally, the videos use music by Bach throughout.

Old CW chance and necessity did it/New CW gremlins did it

Evolution: The Fossils Speak, but Hardly with One Voice

Denyse O'Leary 

Editor's note: We are delighted to inaugurate a new series, "Talk to the Fossils," by our friend and colleague Denyse O'Leary. See here for her Introduction.

University of Chicago biochemist James Shapiro, not a design theorist,offers in one of his lectures four kinds of rapid, evolutionary change that Darwin "could not have imagined": horizontal DNA transfer, symbiogenesis, genome doubling, and built-in mechanisms of genome restructuring. His approach is in sharp contrast to the "defend Darwin" strategy usually championed in the academy. So it is no surprise that he is a controversial figure. But is he right in saying that many possible mechanisms of evolution owe little or nothing to Darwin's theory, the only concept of evolution most of us hear about?

It is reasonably estimated that there are 8.7 million species today (excluding bacteria), but that only about 14 percent have been identified -- and only 9 percent of ocean life forms. Our picture of Earth's life forms might change radically if we had more information about all the others. For example, an entire kingdom of life, the Archaea, was only identified in the 1970s.

How did all these life forms get to be where they are? As we examine some evidence-based mechanisms, we should keep in mind a critical question: How does a given mechanism fit our current picture of evolution? And how much change can it account for?

The welter of data coming back from paleontology, genome mapping, and other studies presents a challenging picture. With so much new information, the history of life begins increasingly to resemble the history of human civilizations. There is peril in that, principally to older ideas that depended on less information and more overarching theory.

Overarching theories often falter when evidence replaces speculation. Darwinian evolution is, despite legislative protection, certainly one of the victims. By contrast, discarded and ridiculed theories like Lamarck's (inheritance of characteristics acquired in life by the parents) may turn out to have some basis in epigenetics.

So, to start this series, instead of contemplating yet another picture derived from grand theories, let us assemble, under eight headings, some of what we have learned in past decades that we did not expect. That might help us evaluate theories, new and old.

1. First, how reliable is the fossil record? It's really a question of what we don't know that would make a difference. Some sense of the difficulty may be gleaned from a comment offered by University of Bristol's Michael Benton:

Paleontologists are right to be cautious about the quality of the fossil record, but perhaps some have been too cautious. The sequence of fossils in the rocks more or less tells us the story of the history of life, and we have sensible ways of dealing with uncertainty. Some recent work on "correcting" the fossil record by using formation counts may produce nonsense results.

But which results are nonsense? How will we know?

2. Are there patterns in evolution? Yes, probably, at least two: Larger size and growing complexity (partly a function of multicellular body plans). Over the last 542 million years, marine animals' mean size has increased by 150 times. As it happens, the largest animal that has ever lived, so far as we know, is today's blue whale.

That said, patterns we assume to exist may not hold up. A classic evolutionary doctrine, "Dollo's law," claims that traits once lost can never be regained. But bone worms, for one example, seem to break this law, in that the males are roughly the same size as the females, instead of being the usual thousands of times smaller for their type of worm. Frogs, snapdragons, and snakes, among other life forms, apparently also break the law with impunity. From The Smithsonian, we learn that evolution is indeed reversible:

Some mites have returned to their free-roaming ways after countless millennia living on animal hosts. And a tree frog from South America lost its lower teeth only to re-evolve them after 200 million years.

We don't actually know how rare reversal is. And we can't fill in large chunks of time with patterns when there are no verified patterns. Some say Dollo's law is due for retirement. But others aver, using computer models, that evolution is both irreversible and unpredictable. If evolution is indeed unpredictable, there is no pattern.

Some, like science writer Philip Ball, claim nonetheless that there is a "strange inevitability of evolution." At Nautilus, he reports:

"Darwin's theory surely is the most important intellectual achievement of his time, perhaps of all time," says evolutionary biologist Andreas Wagner of the University of Zurich. "But the biggest mystery about evolution eluded his theory. And he couldn't even get close to solving it.

But wait! If the biggest mystery in evolution eluded Darwin's theory, why his theory "the most important intellectual achievement of his time, perhaps of all time"? How are we supposed to get anywhere if we are expected to venerate such a non-explanatory grand theory?

In reality, patterns in life forms are often wrongly interpreted when Darwinism is used as a frame. For example, current evolutionary theory provides no clear basis for interpreting a relationship between longevity and fertility. Thus, some researchers claimed that women undergo menopause but chimpanzees do not, that "menopause is not a part of the life cycle of living apes but has been uniquely derived in the human lineage."

Darwinian explanations for that are, of course, on offer. For example, men triggered menopause (by preferring younger women). Or women's selfish genes cause them to forego future breeding in order to invest in the survival of their existing selfish genes (children), sometimes called the grandmother hypothesis. That thesis assumes, of course, that older women are an asset to a group. Sometimes they are, sometimes not.

Despite all such claims, chimpanzees do undergo menopause, as a carefully researched 2012 paper on captive chimpanzees notes. But she-chimps do not typically live long after menopause. A recent article in Naturesummarizes the fact that current evolution theory provides no basis for interpretation of the relationship between longevity and fertility in life forms.

3. Life forms sometimes survive in ways we did not imagine, let alone predict.Some bacteria eat electrons, demonstrating "the almost miraculous tenacity of life." If some life forms live on pure energy, one wonders, will we one day discover life forms that live on pure information? Don't count it out.

And some life forms defy classification: The ancient (chancelloriid) "balloon animal" from over 500 mya doesn't seem to fit in with anything living today. And in a Chinese fossil trove from 570 mya, it is hard to decide whether the fossils are animals or bacteria. To quote a researcher, "What isn't widely appreciated is that the Doushantuo rock formation contains billions of microfossils, many of which have no traits that are diagnostic of any living group and contain features that are not of biological origin."

Another mysterious giant fossil that "seems to defy all known groups of organisms" is 450 million years old. Similarly, a billion-year-old microorganism is not apparently a fungus, alga, parasite, plant, or animal, so classifiers just called it "protozoa" (first life). Not that we know it was the first life, as the name implies.

Even when life forms can be classified, they may still present conundrums rather than gaps filled. For example, when a 60-million-year-old shrew-like mammal fossil turned up, a researcher noted, "The new dryolestoid, Cronopio, is without a doubt one of the most unusual mammals that I have seen, extinct or living."

Might there be life forms out there that are permanently unclassifiable using our present system? Maybe using a genetic code we don't understand? FromMotherboard, we learn, "There's already some evidence that something weird and undiscovered exists out there. Highly novel (and large) viruses, with weird strings of DNA (for a virus) have been discovered that seem to have strings of DNA from seemingly archaeal and eukaryotic genomes." If we take the ID approach seriously -- that DNA is a language -- the DNA might use different elements to form the instructional words, as long as they are functional in a given context.

Even when we can classify life forms, we are always finding forms that don't fit. Consider a recently discovered vegetarian relative of T. rex, an "evolutionary muddle of a beast," the size of a small horse, whose numbers dominated Patagonia 145 million years ago." We are promised "plenty of headaches for paleontologists hoping to place the animal in the dinosaur family tree." Also dubbed the platypus dinosaur, it mainly demonstrates that evolution studies don't feature much predictive power.

One could say the same of a huge, recently discovered North American dinosaur that could terrorize early tyrannosaurs 100 mya. "Contemporary tyrannosaurs would have been no more than a nuisance to Siats, like jackals at a lion kill."

So a whole narrative of late Cretaceous ecology got started entirely in ignorance of this top predator? That is like trying to understand the northern wilderness without knowing about the existence of bears. Or wolf packs. Similarly, the DNA of some ocean bacteria crucial to ecosystem healthdefies explanation, and "contradicts nearly all accounts of free-living microbial genome architectures to date."

Even when life forms do fit our beliefs, they don't always do what we say they must: A theory of animal origin, that complex life evolved because atmospheric oxygen levels began to rise about 630-635 million years ago, was challenged recently by the discovery that some early animals, including common sea sponges, need almost no oxygen.

Other life forms do things we assumed they could not: A living wasp has an ovipositor partially metal-plated with zinc. Why? "It must be hard but flexible so that the female wasp can curve and bore it through the fig. And the wasp must be able to use it repeatedly and efficiently without it wearing down or fracturing."

4. Beyond this, we keep discovering new life forms that we did not expect or predict. A newly discovered Pacific Northwest spider, announced in 2012, represents a hitherto unknown family, according to conventional classification, not just a new genus or species. Recently discovered mushroom-shaped sea creatures turn out to be neither jellyfish nor comb jelly, and could be related to groups thought to be extinct for over half a billion years. Or possibly a newly discovered branch on the tree of life.

We also keep finding new life forms that change the picture. A mystery mammal's tracks, found alongside those of dinosaurs, belong to a raccoon-size animal at a time (118 mya) when most mammals are thought to have been no bigger than a rat. Similarly, a new fossil find from 130 mya in Chinafeatures "not a parade of galumphing giants, but an assemblage of quirky little creatures like feathered dinosaurs, pterosaurs with advanced heads on primitive bodies, and the Mesozoic equivalent of a flying squirrel."

Yet despite all this, so far as our research can tell, non-life never exploits any strategy to become life. So one thing is still true: Pasteur's dictum, "Omne vivum ex vivo" ("All life comes [only] from life").

5. Far too much attention may be given to genes and DNA. So much current evolution thinking, including questionable fields like evolutionary psychology, depends on the alleged power of the gene. Does anyone remember that fellow who said in the early 90s that a CD of your genome is "you"?

Not even close. From the New Statesman: "According to a growing number of researchers, the standard story of the influence of genes is overblown. So many other factors influence how we turn out as individuals and how we evolve as a species that the fundamentals of biology need a rewrite." "This is no storm in an academic tearoom," a group of biologists wrote in the journalNature recently: "It is a struggle for the very soul of the discipline."

The gene isn't even necessarily what we think. Diverse genomes can exist in a single person: Mothers' cells may remain in their children and children's cells in their mothers decades after childbirth. So that CD of your genome is both you and your mom?

There are some relatively new genes. There are also "hidden" genes that don't show in current populations but might later. Some genes are not "junk" but also not strictly necessary either: "In the late 1990s a team of researchers at Stanford University created around 6,000 mutants of brewer's yeast, each of them lacking a different single gene, and found that many of them thrived just as well as the unmutated yeast did." No surprise there; successful life forms would feature redundant systems.

Some life forms can edit their genes extensively. Squid can, apparently. A researcher noted, "It was astonishing to find that 60 percent of the squid RNA transcripts were edited." The iconic fruit fly is thought to edit only 3 percent of its makeup.

Some species can have more than one genetic origin. Polyploidy, which means that the species has two complete sets of chromosomes, has been identified in a mimulus plant in Scotland. We learn that polyploids "are common among plants, as well as among certain groups of fish and amphibians. For instance, some salamanders, frogs, and leeches are polyploids." and "Mimulus peregrinus is an example of how some branches can come back together again and spawn new species that are in part the combination of their ancestors."

Basic claims about inheritance principles are also coming under fire. Researchers recently found that Mendel's "law of segregation" (an equal probability of inheriting each of two copies of each gene from both parents)doesn't always hold. We now learn, "For years, scientists had evidence that this law was being broken in mammals, but they didn't know how." Apparently, female mice pass on one copy of the R2d2 gene more frequently than the other copy. This finding, if it holds, matters because the probability of heritable illness is calculated by doctors assuming Mendel's Law. But maybe it's not a law.

Not surprisingly, some respected researchers now question the amount of attention given to the gene as such. A recent Royal Society paper denotes genes as "merely a means of specifying polypeptides." Whether the researchers are right or wrong, they add to a growing chorus against the vision of evolution that started with Darwin and was revived by Mendelian genetics, as natural selection acting on random mutation of genes to create the world of life we see around us.

6. Some data that garner attention in the pop science media sound counterfactual. For example, we are told by some researchers that evolution favors the collapse of cooperation, according to game theory:

"It's a somewhat depressing evolutionary outcome, but it makes intuitive sense," said [Joshua] Plotkin, a professor in Penn's Department of Biology in the School of Arts & Sciences, who coauthored the study with [Alexander] Stewart, a postdoctoral researcher in his lab. "We had a nice picture of how evolution can promote cooperation even amongst self-interested agents and indeed it sometimes can, but, when we allow mutations that change the nature of the game, there is a runaway evolutionary process, and suddenly defection becomes the more robust outcome."

Does it make intuitive sense? How is it that many of the most durable species are adept at co-operation, whether we are talking about humans, bees, or Canada geese? And do we know that a high-observed level of co-operation existed back in the Cambrian?

7. Some claims sound either trivial or politically sourced. For example, we are told, "Some species are evolving far more quickly than Darwin ever imagined." How? "Mosquitoes that colonized the London Underground in 1863 are now so different they can no longer mate with their above-ground relatives. Chinook salmon from Alaska to California needed just a human generation to become smaller and shorter-lived after an increase in commercial fishing in the 1920s. Adaptation is happening right under our noses, in our lifetimes." But all of this can be accounted for, assuming mere loss of information. It is gain in information that matters in evolution.

Then there is the assertion that human-caused climate change will spur the evolution of new species in an evolutionary surge, and that new species are beginning to emerge already. At last! A claim we can verify. What and where are these species?

More problematic are widely publicized false claims about "throwbacks" to earlier human evolutionary time. Some readers may recall the Turkish family that walks on all fours, as a supposed instance of "backward evolution" (along with human tails that turn out to be Photoshopped). But, contradicting earlier claims, a careful study showed that the family members do not walk in a diagonal pattern like apes or monkeys. They walk on all fours as other humans would, if asked to do so (laterally). Their unusual mobility is a response to an untreated human disorder, Uner Tan Syndrome (UTS). Many distressing conditions only come to attention when a person seeks modern medical diagnosis. Urban legends about "evolution" are an unwelcome distraction in such a case.

8. Evolution is often spoken of as if it were a deliberating intelligence, though the idea is considered a heresy. "Evolution," we are told by one respected source, has been "experimenting" with different types of early humans, based on the fact that skeletons show more diverse features than expected. That prompts two questions: If all the passengers in a subway car in a large, multicultural city met a mishap and were fossilized, how many "different species" would be identified today, using current methods? Second, is evolution (Evolution?) an intelligent agent? If it is not possible to speak of evolution's course without resort to the language of agency, is that a defect in human intelligence or an apprehension of fact?

Recently, the Washington Post ran a story about ten fossils that explain life on Earth. They only "explain" life on Earth if you think that ten disconnected headlines constitute an explanation.

Along those lines, we are now told at PBS that we must try thinking harder so that we will come to "believe in" evolution. But what specifically ought we to believe in? And is that really a way to approach science?

Instead, let us take a whirlwind tour of ways evolution is known to occur, as opposed to how grand theories say it occurs, and see what we can find out.

Image: La Brea Tar Pits, Los Angeles, by Charles Robert Knight [Public domain],via Wikimedia Commons.

The thinking planet?

Earth's Biosphere Is Awash in Information

Evolution News & Views 

Visualize an exoplanet far away: dynamic, comfortable, yet lifeless. It has water, plate tectonics, volcanoes, an atmosphere and all the ingredients for life -- but no life. What would be the primary factor distinguishing it from Earth? A new paper in PLOS Biology suggests that its chief drawback, all things being equal, would be a lack of complex specified information.

In this remarkable paper, Landenmark, Forgan, and Cockell of the United Kingdom Centre for Astrobiology at the University of Edinburgh attempt "An Estimate of the Total DNA of the Biosphere." The results are staggering:

Modern whole-organism genome analysis, in combination with biomass estimates, allows us to estimate a lower bound on the total information content in the biosphere: 5.3 × 1031 (±3.6 × 1031) megabases (Mb) of DNA. Given conservative estimates regarding DNA transcription rates, this information content suggestsbiosphere processing speeds exceeding yottaNOPS values (1024Nucleotide Operations Per Second). Although prokaryotes evolved at least 3 billion years before plants and animals, we find that the information content of prokaryotes is similar to plants and animals at the present day. This information-based approachoffers a new way to quantify anthropogenic and natural processesin the biosphere and its information diversity over time.

As a side note, they never explain their odd distinction between "natural" and "anthropomorphic" (are humans not natural?). Their last sentence just says, "This approach may help us understand the changing complexity of the biosphere over time and to predict in new ways, both anthropogenic and natural, future changes in the biosphere." Apparently even typical astrobiologists have an intuitive sense of human exceptionalism.

But returning to the topic of interest, let's ponder the scale of this information content and processing speed. A yottaNOPS is a lotta ops! Each prefix multiplies the prior one by a thousand: kilo, mega, giga, tera, peta, exa, zetta, yotta. A "yottabase" doesn't even come close to the raw information content of DNA they estimate: 1031 megabases. That's the same as 1037 bases, but a yottabase is only 1024 bases (a trillion trillion bases). This means that the information content of the biosphere is 50 x 1013 yottabases (500 trillion yottabases). They estimate that living computers perform a yottaNOPS, or 1024 nucleotide operations per second, on this information.

You can pick yourself off the floor now.

This is a profound indication of the priority of information to life. It's not just the rocks, water, and elements that characterize Earth, but the astonishing amount of information and information processing that goes on all around us. That's why we have fish, birds, insects, bacteria, mammals, and people.

But how does a scientific materialist account for this incredible computing power? Let's see what the three astrobiologists do with it. First, they keenly recognize the similarity of DNA processing to computer processing:

Biodiversity and habitat loss is recognised as a global issue. In response, substantial research effort has been invested in genome sequencing and the preservation of vulnerable species and habitats. However, despite these remarkable advances, to our knowledge, there is still no estimate of the total information content of the biosphere. Using available DNA sequencing and genome data, combined with large-scale surveys of biomass, we present an alternative way of quantifying and understanding biodiversity. This is accomplished by adopting an information view of biodiversity, in which the total amount of information in the biosphere is represented by the available amount of DNA (Fig 1). In this way, the biosphere can be visualised as a large, parallel supercomputer, with the information storage represented by the total amount of DNA and the processing power symbolised by transcription rates. In analogy with the Internet, all organisms on Earth are individual containers of information connected through interactions and biogeochemical cycles in a large, global, bottom-up network. By combining data on genome size, spatial diversity, and mass from different prokaryotes, eukaryotes, and the viruses, we estimate the total biomass for each group and then derive a first-order, lower-bound approximation for the total DNA content of each group.

Figure 1 in their paper, reproduced above, illustrates their main point, summarized by the caption: "Storing the total amount of information encoded in DNA in the biosphere, 5.3 × 1031 megabases (Mb), would require approximately 1021 supercomputers with the average storage capacity of the world's four most powerful supercomputers."

How much land surface would be required for 1021 supercomputers (a "zetta-computer")? The Titan supercomputer takes up 404 m2 of space. If we assume just 100 m2 for each supercomputer, we would still need 1023 square meters to hold them all. Universe Today estimates the total surface of Earth (including the oceans) at 510 million km2, which equates to 5.1 x 1014 m2. That's 9 orders of magnitude short of the zetta-computer footprint, meaning we would need a billion Earths to have enough space for all the computers needed to match the equivalent computing power life performs on DNA!

That calculation included the ocean surface for comparison, since much life is in the ocean. Although life occupies multiple levels in the ocean, land, and air, the biosphere represents a very thin veneer of the Earth's overall volume. It's certainly unreasonable to expect every square meter of a planet's surface to contain computers; where would the power come from? It only requires one planet -- not a billion -- to hold all the DNA processors, because life is so miniaturized and efficient, using energy from the sun.

The implications of this "information-based view of the biosphere" are not lost on the astrobiologists. They dismiss Gaia but leave a door open for intelligent design:

We note that the approach that we propose here (and the analogy of supercomputers) does not necessarily imply a global, Gaia-like superorganism. We merely observe that ultimately all organisms interact with each other and the environment. Thus, theinformation being processed in the biosphere is interlinked in a large mass of organisms, however one chooses to conceptualise this. It does not have to be considered as a single, self-regulating organism. The manner in which the total information in the biosphere is processed, and the degree to which it is coordinated and interlinked in feedback processes, is another matter, but one that could be investigated using an information-based approach.

The rest of the paper discusses how the researchers arrived at their numbers and how the values might have varied over time. (They estimated that the information content in prokaryotes, the simplest organisms, is similar to that of higher organisms -- within two orders of magnitude, which they found surprising.) They also include caveats about assumptions and uncertainties in their measurements and offer suggestions for answering future questions. The whole paper is very interesting.

But the damage is done. Even if their estimates need to be revised by a terabase or two some day, they have made it clear that our biosphere is awash in information. Though clearly evolutionists, they have presented a significant challenge to scientific materialism to account for all this processing power. Simultaneously, they demonstrate the fruitfulness of an information-based approach to the investigation of life.

Might we suggest they take a look at Being as Communion by William Dembski in their spare time.

Stalinism redux? III

Russia’s Supreme Court Ruling Has Negative Impact on Jehovah’s Witnesses

Russia’s Supreme Court decision of April 20, 2017, is having a severe nationwide impact on Jehovah’s Witnesses. Authorities are violating the Witnesses’ fundamental freedoms and criminalizing their religious activities. At the same time, some Russian citizens interpret the decision as a license to discriminate against the Witnesses and even to subject them to hate crimes.

Russian Government Abuses and Restrictions on Human Rights

Criminal Charges Against Ministers of Jehovah’s Witnesses

On May 25, police raided the religious services of the Oryol Congregation of Jehovah’s Witnesses. The police arrested Dennis Christensen, a Danish citizen and an elder of the Oryol Congregation. Mr. Christensen is being held in pretrial detention until July 23 while the prosecutor attempts to build a case against him for “extremist activity.” If convicted, Mr. Christensen could be sentenced to a six-to-ten-year prison term.

Official Warnings Issued to Local Religious Organizations

On May 4, the prosecutor’s office issued a warning to the chairman of the Krymsk Local Religious Organization (LRO). The warning stated that the chairman and the members of the LRO can be subject to administrative and criminal liability for holding religious services.

Since the Supreme Court ruling, at least five other LROs have received similar warnings.

Police Raids on Religious Services

On April 22, police entered the Witnesses’ house of worship in Dzhankoy, Republic of Crimea, as religious services were concluding. The officers insisted that after the Supreme Court decision, the Witnesses had no right to meet together for worship. They searched the building and then sealed it to prevent its use for religious meetings.

Since the Supreme Court decision, there have been at least five other instances where police interrupted religious services of the Witnesses, one of which was held in a private home.

“I’m deeply concerned by this unwarranted criminalization of the peaceful activities of members of the Jehovah’s Witnesses communities in Russia. . . . I urge the Russian authorities to ensure that rights to freedom of religion or belief, freedom of opinion and expression, freedom of peaceful assembly and association of individuals belonging to the Jehovah’s Witnesses community are upheld, in compliance with the obligations of the country under international human rights law and OSCE [Organization for Security and Cooperation in Europe] commitments.”—Michael Georg Link, Director of the OSCE Office for Democratic Institutions and Human Rights.

Witness Schoolchildren Targeted

On April 24, in the village of Bezvodnoye, Kirov Region, a teacher humiliated two young students whose mother is one of Jehovah’s Witnesses. The teacher justified her actions by stating that the Witnesses are banned in Russia.

On May 17, in the Moscow Region, a school principal issued a written warning to the parents of an eight-year-old student who had spoken about God to a classmate. The document referred to the Supreme Court decision and prohibited on school grounds “all actions that do not relate to the educational process.” The principal threatened to report the matter to the police and “to raise the issue of transferring the child to another form of training.”

Witness Men Denied Alternative Civilian Service

On April 28, the Conscription Commission of the Cheboksary and Marposadskiy regions rejected the application of one of Jehovah’s Witnesses for alternative service. The Commission stated that Jehovah’s Witnesses are “extremist” and cannot be granted alternative service.

At least two other male Witnesses similarly had their applications for alternative civilian service denied.

Philip Brumley, general counsel for Jehovah’s Witnesses, noted the contradiction in the government’s stance: “On the one hand, the government refuses alternative civilian service to young Witnesses because they are ‘extremists,’ while on the other hand, it demands that these ‘extremists’ be inducted into the army. Does it make sense that the government would allow ‘extremists’ to be in the army?”

Societal Abuses and Discrimination

Acts of Violence Against Witnesses

On April 30, in Lutsino, Moscow Region, the home of a Witness family was burned to the ground, along with the adjoining home of their elderly parents. The arsonist had first expressed his hatred for the family’s religion and then started the fire.

On May 24, in Zheshart, Komi Republic, arsonists caused significant damage to a building used by Jehovah’s Witnesses for religious services.

Kingdom Hall in Zheshart damaged by arson

At least nine other houses of worship have been vandalized since the Supreme Court decision of April 20, 2017.

On April 26, one of Jehovah’s Witnesses in Belgorod was leaving his home when an attacker yelled, “You have been banned!” and then he beat the Witness.

On May 11, a group of men interrupted the religious services of Jehovah’s Witnesses in Tyumen and, using obscene and insulting language, threatened to harm the attendees.

Witnesses Dismissed From Employment

On May 15, the management of a chemical factory in Dorogobuzh, Smolensk Region, dismissed all of its employees who are Jehovah’s Witnesses. The management explained that they had received an order from the FSB to dismiss all of the Witnesses because “extremists” cannot work at the factory.

In at least three other incidents since the Supreme Court decision, Witness employees have been threatened with dismissal because they belong to an “extremist” religion. In the village of Yashkino, Kemerovo Region, the police pressured one Witness, but she refused to divulge information on other Witnesses. The officers said that it was unlawful to be a member of a banned religion and likened Jehovah’s Witnesses to ISIS terrorists.

Concern for the Welfare of Jehovah’s Witnesses in Russia

In the ten years leading up to the Supreme Court decision, Jehovah’s Witnesses in Russia were  victims of a government-sponsored attack against their religious freedom that subjected them to much harassment. Now in the aftermath of the decision, their security is even less certain. The decision vilifies the Witnesses and has emboldened some individuals and government officials to inflict further harm, as exemplified by these recent incidents. Jehovah’s Witnesses worldwide are greatly concerned about what will happen to their fellow Witnesses in Russia if the Appellate Chamber of the Supreme Court upholds the decision when it considers the case on July 17, 2017.

Mr. Brumley stated: “No one has presented any evidence that even remotely links Jehovah’s Witnesses with extremism. The alleged danger that the Witnesses are accused of posing to society is in no way commensurate with the persecution they have already endured. Russia needs to rethink its actions against Jehovah’s Witnesses in light of its constitution and its international agreements that guarantee religious freedom.”