On asking the right questions re:the origin of biological information.

Asking the Right Questions about the Evolutionary Origin of New Biological Information
Casey Luskin 

As we've seen, it's easy to duplicate a gene, but the key missing ingredient in many neo-Darwinian explanations of the origin of new genetic information is how a gene duplicate then acquires some new optimized function. Evolutionists have not demonstrated, except in rare cases, that step-wise paths to new function for duplicate genes exist.

As we saw in an earlier post, Austin Hughes cautions against making "statistically based claim[s] of evidence for positive selection divorced from any biological mechanism."26 In other words, natural selection is invoked to explain the evolution of genes where we do not even know the functional effect of the mutations being asserted. In this regard, Hughes observes that even in one of the more sophisticated studies, "there was no direct evidence that natural selection was actually involved in fixing adaptive changes."27

Hughes also acknowledges a problem inherent in many appeals to natural selection, namely that required mutations may not give any selective advantage when they first arise. He thus writes regarding one study:

For example, a rhodopsin from the Japanese conger eel with λmax ≈ 480 nm achieved this sensitivity through the interaction of three different amino acid replacements (at sites 195, 195, and 292). There does not seem to be any way that natural selection could favor an amino acid replacement that would be of adaptive value only if two other replacements were to occur as well.28
In this case, there was no stepwise advantage gained with each successive mutation. Because no advantage could have been gained until all three mutations were present, Hughes finds it more "plausible" to believe that the first two mutations were "selectively neutral" and became fixed due to random, non-adaptive processes such as genetic drift. Once the third mutation arose it might have provided an advantage, but to paraphrase Scott Gilbert, at best this really only explains the survival of the fittest, not the arrival of the fittest.29

But Hughes' explanation has deep deficiencies: it requires that two mutations become fixed before any selective advantage for the third mutation is gained. This implies that there must be three specific mutations to gain any selective advantage. A key question is thus, Are multiple specific mutational changes likely to appear in the same individual through unguided chance mutations given known mutation rates and population sizes? Even Hughes, despite his exhortations to fellow evolutionary biologists to employ more rigor in their studies, does not address this fundamental question.

A similar example is found when leading paleoanthropologist Bernard Wood critiqued a simplistic model of human cranial evolution on the grounds that too many mutations would be required to gain any functional advantage:

The mutation would have reduced the Darwinian fitness of those individuals. . . . It only would've become fixed if it coincided with mutations that reduced tooth size, jaw size and increased brain size. What are the chances of that? 30
Similarly, Jerry Coyne writes that "It is indeed true that natural selection cannot build any feature in which intermediate steps do not confer a net benefit on the organism."31 This highlights a key deficiency in many neo-Darwinian accounts of the evolution of genes. Namely, they fail to demonstrate that the processes necessary to generate new functionally advantageous genetic information are plausible. As with Hughes's or Wood's examples above, multiple mutations might be necessary to gain any functional advantage. Any account invoking blind, unguided, random mutations to evolve a gene from Function A to Function B must address at least these three questions:

Question 1: Is there a step-wise adaptive pathway to mutate from A to B, with a selective advantage gained at each small step of the pathway?
Question 2: If not, are multiple specific mutations ever necessary to gain or improve function?
Question 3: If so, are such multi-mutation events likely to occur given the available probabilistic resources?
Mathematician David Berlinski considers such questions when critiquing evolutionary accounts of eye evolution. Darwinian processes fail because multiple changes are required for a new function to appear:

If these changes come about simultaneously, it makes no sense to talk of a gradual ascent of Mount Improbable. If they do not come about simultaneously, it is not clear why they should come about at all. 32
Again, the key question is therefore, how hard is it for new functional biological information to arise? Answering this question requires assessing the ability of random mutation and natural selection to generate new functional biological information. But when most evolutionary biologists play the Gene Evolution Game, they do not make such assessments and rarely consider these questions. Instead they typically invoke processes such as gene duplication, natural selection, and rearrangement, without demonstrating that random and unguided mutations are sufficient to produce the information needed. Any explanation that at base is little more complicated than "duplication, rearrangement, and natural selection" is not a demonstration that new functional genes can arise by unguided processes.

Thankfully, some scientists are willing to consider these key questions. They have performed research providing data that offers strong reasons to be skeptical of the ability of mutation and selection to form new functional genetic sequences.

A. Asking Questions 1 and 2:
Molecular biologist Doug Axe has performed mutational sensitivity tests on enzymes and found that functional protein folds may be as rare as 1 in 1077.33 His research shows that the fitness landscape for many enzymes looks like this, making it very unlikely that neo-Darwinian processes will find the specific amino acid sequences that yield functional protein folds:


To put the matter in perspective, these results indicate that the odds of Darwinian processes generating a functional protein fold are less than the odds of someone closing his eyes and firing an arrow into the Milky Way galaxy, and hitting one pre-selected atom.34 To say the least, this exhausts the probabilistic resources available. Such data help us answer the first question: it's not likely that there will be a functional stepwise mutational pathway leading from Function A to Function B.

Douglas Axe is by no means the only biologist to make this observation. A leading college-level biology textbook, Campbell's Biology, observes that "Even a slight change in primary structure can affect a protein's conformation and ability to function."35 Likewise, David S. Goodsell, an evolutionist biologist, writes:

As you might imagine, only a small fraction of the possible combinations of amino acids will fold spontaneously into a stable structure. If you make a protein with a random sequence of amino acids, chances are that it will only form a gooey tangle when placed in water. Cells have perfected the sequences of amino acids over many years of evolutionary selection...36
What Goodsell does not mention is that if "perfected" amino acid sequences and functional protein folds are rare and slight changes can disrupt function, then selection will be highly unlikely to take proteins from one functional fold to the next without traversing some non-functional stage. So how do new functional protein folds evolve? This effectively answers question two, implying that many specific mutations would be necessary for evolving genes to pass through non-functional stages while evolving some new function. Question 3 assesses whether this is likely to happen.

B. Asking Question 3:
In 2004, Michael Behe and physicist David Snoke published a paper in the journal Protein Science reporting results of computer simulations and theoretical calculations. They showed that the Darwinian evolution of a simple functional bond between two proteins would be highly unlikely to occur in populations of multicellular organisms. The reason, simply put, is because too many amino acids would have to be fixed by non-adaptive mutations before gaining any functional binding interaction. They found:

The fact that very large population sizes--109 or greater--are required to build even a minimal [multi-residue] feature requiring two nucleotide alterations within 108 generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.37
According to this data, chance mutations are unlikely to produce even two required non-adaptive mutations in multicellular diploid species within any reasonable timescale. This answers the third question: getting multiple specific non-adaptive mutations in one individual is extremely difficult, and more than two required but non-adaptive mutations are likely beyond the reach of multi-cellular organisms. Studies like this show that the actual ability of random mutation and unguided selection to produce even modestly complex new genetic functions is insufficient.

In 2008, Behe and Snoke's would-be critics tried to refute them in the journal Genetics, but found that to obtain only two specific mutations via Darwinian evolution "for humans with a much smaller effective population size, this type of change would take > 100 million years." The critics admitted this was "very unlikely to occur on a reasonable timescale." 38 In other words, there is too much complex and specified information in many proteins and enzymes to be generated in humans by Darwinian processes on a reasonable evolutionary timescale.

As noted in the comments on the Gene Evolution Game, when neo-Darwinists try to explain the evolution of genes, mere point mutations often are insufficient to account for the gene's sequence. They must therefore appeal to genetic rearrangements such as insertions, deletions, or an alleged process called "domain shuffling" where segments of proteins become shuffled to new positions in the genome. In his book The Edge of Evolution, Michael Behe reviews research that engineered new protein function by swapping domains to change protein function, and found that the intelligently engineered changes required multiple modifications that, in nature, would require too many simultaneous mutational events to yield functional changes:

[Protein engineering research] does not mimic random mutation. It is the exact opposite of random mutation. ... What do the lab results tell us about whether random-yet-productive shuffling of domains "occurs with significant frequency under conditions that are likely to occur in nature"? About whether that is biologically reasonable? Nothing at all. When a scientist intentionally arranges fragments of genes in order to maximize the chances of their interacting productively, he has left Darwin far, far behind. ... [Experiments that engineered proteins by shuffling domains] didn't just splice two genes together in a single step; they took several additional steps as well. ... Remember the more steps that have to occur between beneficial states, the much less plausible are Darwinian explanations. ... Domain shuffling would be an instance of the "natural genetic engineering" championed by James Shapiro where evolution by big random changes is hoped to do what evolution by small random changes can't. But random is random. No matter if a monkey is rearranging single letters or whole chapters, incoherence plagues every step. ... One step might luckily be helpful on occasion, maybe rarely a second step might build on it. But Darwinian processes in particular and unintelligent ones in general don't build coherent systems. So it is biologically most reasonable to conclude that, like multiple brand new protein-protein binding sites, the arrangement of multiple genetic elements into sophisticated logic circuits similar to those of computers is also well beyond the edge of Darwinian evolution. 39
As Behe observes, "No matter if a monkey is rearranging single letters or whole chapters, incoherence plagues every step." Thus, when multiple mutational events--whether point mutations, "domain shuffling," or other types of rearrangements--are required to gain some functional advantage, it seems unlikely that blind neo-Darwinian processes can produce the new biological function.

Unfortunately, few if any advocates of the neo-Darwinian just-so stories investigate whether mutation and natural selection are sufficient to produce new functional genetic information. Instead they believe that finding similarities and differences between genes demonstrates that neo-Darwinian evolution has occurred, and they assume that "positive selection" is a sufficient explanation.

As Hughes cautions, they engage in "use of certain poorly conceived statistical methods to test for positive selection," causing "the literature of evolutionary biology [to become] glutted with extravagant claims of positive selection" resulting in a "vast outpouring of pseudo-Darwinian hype [that] has been genuinely harmful to the credibility of evolutionary biology as a science." 40 Or, as Michael Behe cautions, they confuse mere sequence similarity with evidence of neo-Darwinian evolution. Finally, Michael Lynch warns his colleagues that "Evolutionary biology is not a story-telling exercise, and the goal of population genetics is not to be inspiring, but to be explanatory." 41

With these principles in mind, in the next installment we will assess about a dozen of the just-so stories concerning the origin of genes offered in studies cited by the NCSE.

References Cited:

[26.] Austin L. Hughes, "Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level," Heredity, Vol. 99:364--373 (2007).

[27.] Id.

[28.] Id.

[29.] "The modern synthesis is good at modeling the survival of the fittest, but not the arrival of the fittest." Scott Gilbert, quoted in John Whitfield, "Biological Theory: Postmodern evolution?," Nature, Vol. 455:281-284 (2008).

[30.] Bernard Wood, quoted in Joseph B. Verrengia, "Gene Mutation Said Linked to Evolution," Associated Press, found in San Diego Union Tribune, March 24, 2004.

[31.] Jerry Coyne, "The Great Mutator," The New Republic (June 14, 2007). Coyne asserts he knows of no example where this is the case.

[32.] David Berlinski, "Keeping an Eye on Evolution: Richard Dawkins, a relentless Darwinian spear carrier, trips over Mount Improbable. Review of Climbing Mount Improbable by Richard Dawkins (W. H. Norton & Company, Inc. 1996)," in The Globe & Mail (November 2, 1996) at http://www.discovery.org/a/132

[33.] Douglas D. Axe, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds," Journal of Molecular Biology, Vol. 341: 1295-1315 (2004); Douglas D. Axe, "Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors," Journal of Molecular Biology, Vol. 301: 585-595 (2000).

[34.] See Stephen C. Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design, pg. 211 (Harper One, 2009).

[35.] Neil A. Campbell and Jane B. Reece, Biology, pg. 84 (7th ed, 2005).

[36.] David S. Goodsell, The Machinery of Life, pg. 17, 19 (2nd ed, Springer, 2009).

[37.] Michael J. Behe & David W. Snoke, "Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues," Protein Science, Vol 13:2651-2664 (2004).

[38.] Rick Durrett and Deena Schmidt, "Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution," Genetics, Vol. 180: 1501--1509 (November 2008).

[39.] Michael Behe, The Edge of Evolution: The Search for the Limits of Darwinism, Appendix D, pgs. 272-275 (Free Press, 2007) (emphasis added).

[40.] Austin L. Hughes, "The origin of adaptive phenotypes," Proceedings of the National Academy of Sciences USA, Vol. 105(36):13193--13194 (Sept. 9, 2008) (internal citations removed).

[41.] Michael Lynch, "The frailty of adaptive hypotheses for the origins of organismal complexity," Proceedings of the National Academy of Sciences, Vol. 104:8597--8604 (May 15, 2007).

Who're you calling primitive?

Even Sponges Are Complex Enough to Inspire Architects
Evolution News & Views September 21, 2015 3:22 AM

Sponges are outliers in biology's big bang, the Cambrian explosion. Their embryos appear in Precambrian strata, leading some to consider them primitive. That's an illusion. New studies of how they construct their skeletons with silica "spicules" have revealed design principles remarkable enough to inspire biomimicry.

The punch line first -- here's how a news item from Cell Press concludes:

"This work not only sheds new light on skeleton formation of animals, but also might inspire interdisciplinary studies in fields such as theoretical biology, bioengineering, robotics, and architectural engineering, utilizing mechanisms of self-constructing architectures that self-adjust to their environments, including remote environments such as the deep sea or space," the researchers write.
Goodness! What are these simple animals doing to arouse such commotion? Just watch the video clip in the article of sponge cells at work. Then, look at the Graphical Abstract in the paper in Current Biology and see the steps diagrammed in well-organized stages: (1) spicules are manufactured in specialized cells, then transported to the construction site; (2) the silica spicules pierce the epithelial tissue; (3) they are then raised up into position; (4) the bases are cemented by collagen provided by basal epithelial cells.

This simple animal knows, in short, how to build a house with pole-and-beam architecture in a way that self-adjusts to its environment. That's pretty impressive.

Sponge skeletons, with their unique spicules, have been studied for a long time, but the manner of construction has been a mystery till now. What's new, according to the Japanese researchers, is the identification of specialized "transport cells" that carry and finally push the spicules through the epithelia, and cementer cells that fasten them in place like poles. The process reveals division of labor and an overall plan.

Here we report a newly discovered mode of skeleton formation: assembly of sponges' mineralized skeletal elements (spicules) in locations distant from where they were produced. Although it was known that internal skeletons of sponges consist of spicules assembled into large pole-and-beam structures with a variety of morphologies, the spicule assembly process (i.e., how spicules become held up and connected basically in staggered tandem) and what types of cells act in this process remained unexplored. Here we found that mature spicules are dynamically transported from where they were produced and then pierce through outer epithelia, and their basal ends become fixed to substrate or connected with such fixed spicules. Newly discovered "transport cells" mediate spicule movement and the "pierce" step, and collagen-secreting basal-epithelial cells fix spicules to the substratum, suggesting that the processes of spiculous skeleton construction are mediated separately by specialized cells. Division of labor by manufacturer, transporter, and cementer cells, and iteration of the sequential mechanical reactions of "transport," "pierce," "raise up," and "cementation," allows construction of the spiculous skeleton spicule by spicule as a self-organized biological structure, with the great plasticity in size and shape required for indeterminate growth, and generating the great morphological diversity of individual sponges.
This method of skeleton construction differs greatly from arthropods and vertebrates. It doesn't appear to follow a set of rules or a preordained pattern, but it is very effective for sponges, "whose growth is plastic (i.e. largely depends on their microenvironment) and indeterminate, with great morphological variations among individuals." Nevertheless, design and coordination is evident in the division of labor, the specialization of cells, and the end result that is good enough to inspire architects. If it were so simple, the authors would not have left many questions unanswered:

Many precise cellular and molecular mechanisms still remain to be elucidated, such as how transport cells can carry spicules, or how one end of pierced spicules is raised up. Additionally, one of the further questions that need to be answered is how sponges fine-tune their skeleton construction according to conditions of their microenvironment, such as water flow or stiffness of the substratum, since it is reported that the growth form of marine sponges changes according to the water movement of their environment.
Design is also evident in the self-organizational principles encoded in sponge DNA that make these results successful. Human intelligent designers would like to benefit from this knowledge. The authors conclude, repeating the "punch line":

Intriguingly, our study revealed that the spiculous skeleton of sponges is a self-organized biological structure constructed by collective behaviors of individual cells. A chain of simple and mechanical reactions, "transport-pierce (by transport cells)-raise up (by yet unknown cells and/or mechanisms)-cementation (using collagenous matrix secreted by basopinacocytes and possibly by spicule-coating cells)," adds a spicule to the skeleton, and as a result of the iteration of these sequential behaviors of cells, the spiculous skeleton expands. As far as we know, this is the first report of collective behaviors of individual cells building a self-organized biological structure using non-cellular materials, like the collective behaviors of individual termites building mounds. Thus, our work not only sheds new light on skeleton formation in animals but also might inspire interdisciplinary studies in fields such as theoretical biology, bioengineering, robotics, and architectural engineering, utilizing mechanisms of self-constructing architectures that self-adjust to their environments, including remote environments such as the deep sea or space.
The reference to termite mounds is apt. Science Magazine recently described how these mounds, built by hundreds of individual termites, are able to "breathe" like an "external lung":

Here's how it works: Inside the hill is a large central chimney connected to a system of conduits located in the mound's thin, flutelike buttresses. During the day, the air in the thin buttresses warms more quickly than the air in the insulated chimney. As a result, the warm air rises, whereas the cooler, chimney air sinks -- creating a closed convection cell that drives circulation, not external pressure from wind as had been hypothesized. At night, however, the ventilation system reverses, as the air in the buttresses cools quickly, falling to a temperature below that of the central chimney. The reversal in air flow, in turn, expels the carbon dioxide-rich air -- a result of the termites' metabolism -- that builds up in the subterranean nest over the course of the day, the researchers report online this week in the Proceedings of the National Academy of Sciences.
We know that some caves "breathe" as the temperature changes, but this is different. Termites construct their mounds for a purpose: to control the temperature and remove carbon dioxide for their health. It's a bit like active transport in cells that draws in what the cell needs and removes what it doesn't need, using machines that work against natural concentration gradients.

Intelligent Self-Organization

We all know that some beautiful things can self-organize without programming (snowflakes are a prime example). What we see here, though, are systems working from genetic programs for a purpose. In the case of sponges, its specialized cells cooperate in a plan to build a skeleton that adapts to the environment. In the case of termites, each individual insect's genetic program makes it behave in a cooperative enterprise to build an air-conditioned mound. Such things do not arise by unguided natural forces.

If functional self-organization were simple, why are five European countries taking years "working to design the European Union's first autonomously deployed space and terrestrial habitat"? (see Space.com). The effort, called the "Self-deployable Habitat for Extreme Environments" (SHEE) project, has a goal of programming elements for "autonomous construction" of housing for astronauts on Mars or other hostile locales. It's requiring years of work in design, prototyping, construction, and optimization to get these buildings to "self-deploy" with no humans in the loop.

So when a sponge can do it, we should see intelligent design behind the scenes -- not the sponge's intelligence, which admittedly is miniscule, but intelligence as a cause for the genetic information that allows the sponge to run a program that leads to a functional result.

Those of us who appreciate the spectacular genetic programs that built the Cambrian animals should take note of the level of complex specified information in the lowly sponge. We can also notice that the sponge's mode of construction bears no evolutionary ancestry with the diverse, complex body plans that exploded into existence in the Cambrian strata. Sponges did well. They're still with us.

Napoleon the great?:Pros and cons.

Looking for magical beasts? Just ask your nearest Darwinian apologist.

Prehoda's Goof: Mutational Fitness Effects Cannot Be Predicted
Evolution News & Views 

Last February when we looked into the claims of University of Oregon biochemist Kenneth Prehoda, we saw him pounding Darwin's pulpit with righteous fervor. He practically shouted that you could get instant animals by chance. His team's discovery of a mutation that seemed to allow proteins to interact more easily in a choanoflagellate became the springboard for a sermon envisioning all the marvels of multicellularity without intelligent design.

Indeed, a breathless reporter from the Washington Post gave him credit for explaining human beings with that one random accident: "Every example of cells collaborating that has arisen since -- from the trilobites of 500 million years ago to the dinosaurs, woolly mammoths and you -- probably relied on it or some other similar mutation."

He has toned down the rhetoric a bit in the latest news from his lab. Maybe he didn't want to face another Twitter storm by engaging "the ire of anti-evolutionists" the way he did last time. "We've witnessed evolution," he had said. "Evolution is just a fact, hands down." Even his reviewers had gotten on his case for overstating the implications of his findings. We showed that there were plenty of empirical and logical reasons, not religious reasons, for doubting the significance of his instant-animal mutation.

This time, the news item makes more modest claims:

Just as the course of a drift boat can be irreversibly altered by a log in its path, a single mutation can send life in an entirely new direction.
That scenario, says UO biochemist Ken Prehoda, provides a window on how one mutation sparked a huge jump in the evolutionary course of a protein important for the evolution of animals.

Earlier this year, Prehoda was on a team that found that a random mutation 600 million years ago in a single-celled organism created a new family of proteins that are important for multicellular life. In a new paper, now online ahead of print in the Journal of the American Chemical Society, Prehoda and colleagues describe what the mutation did to the original protein family.

Mutations happen randomly. Most are bad news. But occasionally a mutation is good, helping an organism adapt to environmental changes or advancing overall fitness. Understanding such changes better, Prehoda said, could potentially point to new treatments for human diseases such as cancer.

Ah, yes; evolutionists can score extra points for claiming their otherwise esoteric research "could potentially" lead to cures for cancer. But we don't need to deduct those points; there are enough other vulnerable points at risk of lowering Darwin's score.

Prehoda's basic claim was that a point mutation in an enzyme called guanylate kinase gave it a new protein-interacting domain (PID), launching the GKPID family of enzymes used by all animals. And coincidentally, this mutation happened right when multicellular organisms were first appearing 600 million years ago. Could human beings be far behind?

Prehoda now reveals that all he found was that the mutation "stiffened" the GK enzyme a bit. One might think this to be a disadvantage, but he weaves a story that the stiffening of the enzyme's backbone actually was a good thing.

The mutation, which researchers labeled s36P, set off a cascade of events in which protein interactions took new routes and evolved into more complex multicellular organisms, Prehoda said. The mutation is still conserved in all animals today, he added.
"A lot of the proteins that do the work in our bodies can be thought of as molecular machines," Prehoda said. "They move in a way that is coordinated with function. Each protein spins in a circle or motors along filaments. Our protein, before the mutation, was an enzyme that had certain flexible movements related to its function. This one mutation fixed the protein's backbone, locking the molecule into a shape that is important for its new function."

Incidentally, the spinning machine is ATP synthase, and the motor is most likely kinesin. We find that out in the new paper, published this time not in eLife but in the Journal of the American Chemical Society, which does not include reviewer's comments. For obvious reasons, Prehoda does not try to evolve ATP synthase by single point mutations.

In the paper, Whitney, Volkman and Prehoda mere "suggest" that the mutation that stiffened the GK enzyme "might have been important" for instigating new functions by "tuning" its "conformational flexibility" in some way. Even so, they retain some epistemic modesty in this less audacious hypothesis: "Furthermore, even if flexibility was important in the functional transition from enzyme to PID, we do not know how it was altered or how doing so could lead to such a dramatic change in function."

Unfortunately, a new paper just appeared in the Proceedings of the National Academy of Sciences that undercuts their premise. Prehoda's team assumes that random mutations can be ranked as "good" and "bad" -- as if you can sort them like marbles into green jars and red jars. In this view, good things add up, and bad things get tossed out by natural selection. That was Darwin's view, too:

It may be said that natural selection is daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and in organic conditions of life.
The new PNAS paper by Bank et al., "On the (un)predictability of a large intragenic fitness landscape," takes a serious look at the effects of mutational interactions. Mutations aren't like isolated red and green marbles. They interact in complex ways. "Epistasis" is a term referring to the combinatorial effects of mutations. For instance, two neutral mutations might interact to produce a benefit; that would be a case of positive epistasis. On the other hand, a seemingly beneficial mutation could have negative effects elsewhere in the organism; that's called negative epistasis. It won't improve an organism's fitness, for example, if a mutation for stronger muscles also produces heart attacks.

The point of the study is that epistatic interactions are profoundly unpredictable. By performing one of the largest-ever surveys of epistasis on engineered mutations to Hsp90, a well-known protein, they concluded that it is extremely difficult to predict what will happen. Because their conclusion has far-reaching implications for all evolutionary predictions, it bears quoting in full:

Originally introduced as a metaphor to describe adaptive evolution, fitness landscapes promise to become a powerful tool in biology to address complex questions regarding the predictability of evolution and the prevalence of epistasis within and between genomic regions. Due to the high-dimensional nature of fitness landscapes, however, the ability to extrapolate will be paramount to progress in this area, and the optimal quantitative and qualitative approaches to achieve this goal are yet to be determined.
Here, we have taken an important step toward addressing this question via the creation and analysis of a landscape comprising 640 engineered mutants of the Hsp90 protein in yeast. The unprecedented size of the fitness landscape, along with the multiallelic nature, allows us to test whether global features could be extrapolated from subsets of the data. Although the global pattern indicates a rather homogeneous landscape, smaller sublandscapes are a poor predictor of the overall global pattern because of "epistatic hotspots."

In combination, our results highlight the inherent difficulty imposed by the duality of epistasis for predicting evolution. In the absence of epistasis (i.e., in a purely additive landscape), evolution is globally highly predictable because the population will eventually reach the single-fitness optimum, but the path taken is locally entirely unpredictable. Conversely, in the presence of (sign and reciprocal sign) epistasis evolution is globally unpredictable, because there are multiple optima and the probability to reach any one of them depends strongly on the starting genotype. At the same time, evolution may become locally predictable with the population following obligatory adaptive paths that are a direct result of the creation of fitness valleys owing to epistatic interactions.

The empirical fitness landscape studied here appears to be intermediate between these extremes. Although the global peak is within reach from almost any starting point, there is a local optimum that will be reached with appreciable probability, particular when starting from the parental genotype. From a practical standpoint, these results thus highlight the danger inherent to the common practice of constructing fitness landscapes from ascertained mutational combinations. However, this work also suggests that one promising way forward for increasing predictive power will be the utilization of multiple small landscapes used to gather information about the properties of individual mutations, combined with the integration of site-specific biophysical properties.

From this, we can see that Prehoda's team has taken a leap to think that one mutation in one enzyme would start a path to animals. He has not taken into account the effects of epistasis. Bank et al. say that local fitness peaks would be more likely to strand the animal there, rather than let it progress. Walking right past the "danger" sign, Prehoda engaged in the "common practice of constructing fitness landscapes from ascertained mutational combinations." At best, he should only investigate a "small landscape" around the mutation to see what might happen. Maybe it would help a certain choanoflagellate. Beyond that, he is on dangerous ground making predictions.

Prehoda might have this comeback argument. He could say that his work on "ancestral protein reconstruction" shows that the mutation occurred right at the time multicellularity took off. It's a postdiction, therefore, not a prediction. This argument, however, commits the fallacy of "affirming the consequent" -- i.e., "If P, then Q. Q occurs. Therefore, P." You can't say P caused Q. That overlooks multiple other possibilities for Q. In fact, there could be an infinite number of causes for Q besides P. Prehoda could only argue Q if and only if P: specifically, that the emergence of animals required a specific mutation to guanylate kinase. That would be unwarranted even within neo-Darwinian theory. The best he can say is that the mutation is "consistent with" a scenario in which a stiffer enzyme contributed to new functions useful to multicellular organisms, assuming it avoided negative epistasis in the process.


Such clarification, however, would be unlikely to yield headlines in the Washington Post. Empirically speaking, Bank et al.'s yeast remain yeast, and Prehoda et al.'s choanoflagellates remain choanoflagellates.

Nuclear energy can save the planet?:Pros and cons.

In OOL Science imagination has replaced evidence as a pillar.

Self-Replicating Droplets: Evidence or a Shot in the Dark?
Sarah Chaffee 

When scientists judge explanations for the origin of life that employ strictly chemical means, the evidentiary bar often seems notably low. For example, consider a new  article  on the Chemistry World website, published by the Royal Society of Chemistry. It claims, "Key riddle of life's origin may be answered by primitive protocells that can divide," and references a study in Nature Physics.

Generally, chemical evolution theorists assume that three components must have been necessary for the first living cell: 1) metabolism, 2) RNA/DNA, and 3) a containment structure or primitive cell wall to separate the first two components from the outside world. This study aims to address the third issue.

Researchers found that droplets, when influenced by an energy source, grow by absorbing moisture from their surroundings and then divide when they reach a critical size. Supposedly, if RNA was contained in one of these droplets, the system could have sparked life.

The article goes on to note:

Evolutionary biologist  William Martin  of Heinrich Heine University of Düsseldorf, who advocates the idea that life originated in pores in hydrothermal vents, says: 'It's not clear to me what real biological system based on observations from nature that this might be emulating.' However, he adds: 'If we assume that hydrothermal vents provide a system of organic micro-compartments, and that these have collected hydrophobics, then it's certainly imaginable that there might have been properties of these droplets in the aqueous phase within a hydrophobic phase that might have been relevant. You never know.'

In origin-of-life theories the term "imagine" appears quite often to cover a giant gulf between what can be demonstrated and what is required to produce the first viable cell.

In this case, the differences between a chemical-rich droplet and a functional cell membrane are numerous. For instance, the latter must distinguish between fuel and waste, allowing only the right molecules to pass into the cell and the right molecules to exit. Even the most generous calculations indicate that the likelihood of droplets coalescing with the needed properties around an extremely rare (nonexistent?) RNA molecule are essentially nil.


In contrast, the appearance of a fantastically improbable set of molecules carefully configured together to achieve a function goal shows the unmistakable signs of intelligent design, a source of  causation we know well from daily experience. Design, unlike unguided chemical processes, requires no strenuous exercise in imagination.

The gentleman thief talks cognitive bias.

When scientists attack?

Why Scientific Polarization? A Case Study
David Klinghoffer | @d_klinghoffer

Here’s a scientific war that’s rending the fabric of polite disagreement. Scientists are divided against themselves, choosing sides in a highly polarized environment, charging each other’s “lobby” with denying or distorting evidence.

As the European Journal for Philosophy of Science summarizes, “The two sides of the controversy have never seen eye to eye, but over the past decade, the accusations and counter accusations have become increasingly belligerent and entrenched.” It’s not merely a scientific but a “legal and political battleground.”

Yes, it’s the bitter scientific dispute over…evolution? Nope. Climate change? No, silly, over Lyme disease! 

Debate and Death Threats

The specific issue is the existence and treatment of “chronic Lyme disease.” Our friend Alex Berezow at the American Council on Science and Health notes, “The man who discovered Lyme disease, Allen Steere, was skeptical of the chronic Lyme diagnosis as well as long-term antibiotic therapy. So, he started receiving death threats from patients who were convinced he was wrong.” The aforementioned journal article takes this debate, previously unknown to me, as a model of how disagreement arises even among scientists — you know, those models of cool, rational deliberation — and tends increasingly toward irrational polarization. Berezow writes:

The authors employ a mathematical model to show that, even when scientists are acting in good faith over the correct interpretation of evidence, polarization is still a likely outcome. How so?

Suppose a scientist believes that Hypothesis X is more likely to be correct than Hypothesis Y. He may perhaps come to believe that other scientists who also accept Hypothesis X are slightly more reliable than scientists who accept Hypothesis Y. Over time, this slight initial bias against data provided by scientists who believe Hypothesis Y can morph into outright distrust. Once that happens, a stable state of polarization develops, in which neither side can “win” the debate, even if the facts clearly support one hypothesis over the other.

The authors reach a rather disturbing conclusion:

“We do not need to suppose that anyone is a bad researcher (in our models all agents are identical), or that they are bought by industry, or even that they engage in something like confirmation bias or other forms of motivated reasoning to see communities with stable scientific polarization emerge. All it takes is some mistrust in the data of those who hold different beliefs to get scientific polarization.”

In other words, everybody acting in good faith can result in a society in which we cannot agree on a common set of facts.

Berezow cites the parallel of our contemporary political scene where Left and Right often appear not just to hold different opinions but to live in alternative universes. You can compare these, dizzyingly, by switching rapidly back and forth between Fox News and CNN.

Strengths and Weaknesses

I would add that the evolution debate presents another illustration, equally stark. Berezow again: “Over time, this slight initial bias against data provided by scientists who believe Hypothesis Y can morph into outright distrust. Once that happens, a stable state of polarization develops, in which neither side can ‘win’ the debate, even if the facts clearly support one hypothesis over the other.”

I honestly don’t think that most advocates of intelligent design are unable to recognize merits in the other side’s case. If we were unable, we wouldn’t speak of the alternative neo-Darwinian theory’s “strengths and weaknesses.” Yes, it has strengths. In explaining the emergence of biological novelties, the choice between Darwin and design is not a no-brainer.

This most sound unfair if you know little about the evolution debate. However, from long experience, I do believe that many evolution proponents are so committed to their view with its unacknowledged philosophical underpinnings, so mistrustful of other interpretations, that arguing with them is likely a waste of time. 

A friend explained recently that this appears to be so, not least, with theistic evolutionists of a certain profile. See “No Escape from Theistic Evolution?” When we do argue with these people, the purpose is not to convince them, which is probably hopeless, but to persuade the unpersuaded who, we know, are listening or reading.

Denis Noble says time to rebuild rather than repair Darwinism.

Denis Noble: Why talk about replacement of Darwinian evolution theory, not extension?
Posted by News under Darwinism, Evolution, Intelligent Design

In  new book on the Royal Society’s  Public Evolution Summit,, Oxford’s Denis Noble explains,

The reasons I think we are talking about replacement rather than extension are several. The first is that the exclusion of any form of acquired characteristics being inherited was a central feature of the modern synthesis. In other words, to exclude any form of inheritance that was non-Mendelian, that was Lamarckian-like, was an essential part of the modern synthesis. What we are now discovering is that there are mechanisms by which some acquired characteristics can be inherited, and inherited robustly. So it’s a bit odd to describe adding something like to the synthesis ( i.e., extending the synthesis). A more honest statement is that the synthesis needs to be replaced.

By “replacement” I don’t mean to say that the mechanism of random change followed by selection does not exist as a possible mechanism. But it becomes one mechanism amongst many others, and those mechanisms must interact. So my argument for saying this is a matter of replacement rather than extension is simply that it was adirect intention of those who formulated the modern synthesis to exclude the inheritance of acquired characteristics. (p. 25)

That’s why the fat’s in the fire and smoking hot. Darwinism (or whatever the term du jour is) has been a totalistic system, enforced as such. But the evidence today simply doesn’t support it.

Reading Mazur’s book, I was struck by two things:

The genuinely interesting nature of alternative evolution proposals contrasts sharply with the science media release where fairly dull researchers have come up with a casuistical explanation of how Darwinism can account for various phenomena. And one realizes that for those individuals, that is evolution. That is science. Science is about reaffirming and finding evidence for the teachings of the Great One. And deploring or attacking anyone who doubts his teachings, irrespective of the state of the evidence.

The new approach is not exclusive or totalistic. It does not behave, as Darwinism does, as a metaphysic. Among many assemblies of evidence, some will naturally prevail, as more persuasive than others. But for once, evidence exists to understand living things better rather than to understand Darwin better.

Ladies and gentlemen, place your bets. This’ll be fun.

Russia's tattered reputation re: religious liberty regresses to full blown dumpster blaze

Mass Arrests and Detentions Continue in Russia

During the month of October 2018, local and federal police raided more than 30 homes throughout western Russia. Six brothers and two sisters were arrested and sentenced to pretrial detention for so-called extremist activity. Consequently, there are now 25 brothers and sisters unjustly imprisoned, and 18 others are under house arrest.

October 7, Sychyovka, Smolensk Region—Local police and masked special forces searched four homes and arrested two sisters, 43-year-old Nataliya Sorokina and 41-year-old Mariya Troshina. Two days after their arrest, the Leninsky District Court sentenced our sisters to pretrial detention through November 19, 2018. Then, on November 16, 2018, the Leninsky District Court extended the sisters’ pretrial detention for an additional three months, that is, until February 19, 2019.

October 9, Kirov, Kirov Region—At least 19 homes were raided. Five congregation elders were arrested and later sentenced to pretrial detention. Four of the brothers (Maksim Khalturin, Vladimir Korobeynikov, Andrey Suvorkov, and Evgeniy Suvorkov) are Russian nationals, and one, Andrzej Oniszczuk, is a Polish citizen. Brother Oniszczuk is the second foreigner, after Dennis Christensen from Denmark, to be unjustly detained in Russia for his Christian beliefs.

October 18, Dyurtyuli, Republic of Bashkortostan—Police raided at least 11 homes and seized money, bank cards, photographs, personal letters, computers, SIM cards, and cell phones. Anton Lemeshev, an elder, was arrested and then sentenced to pretrial detention for two months. On October 31, 2018, he was released from prison and transferred to house arrest, where he remains at present.

Despite the ongoing threat of raids and unlawful seizure of their belongings, local brothers and sisters continue to pray for those imprisoned and to provide them and their families with practical help when possible. Until the situation is resolved, our international brotherhood will supplicate Jehovah in behalf of all his faithful servants in Russia, even mentioning some by name.—Ephesians 6:18.

Darwinism's glass jaw and the Cambrian explosion's challenge.

In Cambrian Explosion Debate, ID Wins by Default
Evolution News | @DiscoveryCSC

Sometimes you win a game by default. The loser might not acknowledge losing, but fails to show up. 

Picture a world champion prize fighter who has command of the media. He hears a challenger who claims to have a knockout punch, but refuses to get into the ring with him. Instead, he runs to the media and tells them there is indeed a big challenge, and it “might” be winnable. That’s it. Reporters run with the story and report, “The Fight Might Be Winnable.” Nothing is said about the challenger or his knockout punch. Question: under these circumstances, who wins the fight?

This is the impression you get reading the mainstream media regarding the debate about the Cambrian explosion. Stephen Meyer offered a big challenge in Darwin’s Doubt, claiming that Darwinian evolution is not only incapable of explaining the Cambrian event, but that the hierarchical information required to explain almost 20 new body plans that appeared suddenly in Cambrian layers gives positive evidence of intelligent design. His challenge was not lost on Darwin proponents. The book created a strong backlash by evolutionists in blogs, but only one Darwinian got into the ring with Meyer, so to speak, but at least by taking on his challenge. That was “heavyweight” paleontologist Charles Marshall, and a gentlemanly interchange resulted. Meyer answered the response by demonstrating that it did not explain the main point: the origin of the information required to create hierarchical body plans (see Debating Darwin’s Doubt, Section III). The challenge stood.

Still Waiting Engagement

The rest of Debating Darwin’s Doubt responded to various critics who had taken potshots outside the ring. None of them defeated Meyer’s challenge. Paul Nelson wrote in Chapter 34, “Still Waiting Engagement”: 

Thus, at the end of the day, it really doesn’t matter whether the contemporary evolutionary theorists that Meyer discusses in Darwin’s Doubt are attempting to supplement neo-Darwinian theory, replace it with something fundamentally new, or replace some, but not all, parts of the theory. What matters is whether any of these theories can explain what needs to be explained: the origin of novel animal body plans and the biological information necessary to produce them. 

That was in 2015. In the four years since, evolutionists have had plenty of opportunity to “engage” and offer their explanation, yet every paper reported here at Evolution News has simply dodged the issue. They pretend the challenge doesn’t exist. Instead, they mutter among themselves that “the fight might be winnable,” and give the media the impression that Darwin remains the world champion in the heavyweight category of scientific explanation.

The latest is an essay by Michael S. Y. Lee and James B. Dorey in Current Biology, “Evolution: Dampening the Cambrian Explosion.” Lee and Dorey practice all the same old moves that failed before. They rely on two recent papers, one already addressed by Evolution News: the one by Deline et al: and another by Graham Budd, who has been cited several times in these pages, most recently here.

A List of Moves

Here’s a list of the moves in the new Current Biology paper. This is the latest response by Darwinians about the Cambrian explosion. Keep your eye on the right hook (the origin of biological information) and see if they are ready for it.

The Small Explosion move: “Cambrian diversity was not greater than living diversity — at least for arthropods, the most diverse group of animals then and now.”

The Soft Touch: Sure, arthropods and vertebrates developed hard parts that accelerated their diversification, but “most phyla have either soft bodies (e.g. annelids, nematodes) or simple and relatively inert skeletons (mollusks, brachiopods), and remain largely confined to aqueous environments.”

The Distraction: The Burgess Shale Cambrian animals failed to fit into living phyla, but “when viewed from the perspective of the Cambrian explosion, modern birds and beetles would appear even more bizarre.”

The “Got All Day” feint: “Animal disparity is still increasing, and the extent of post-Cambrian innovation rivals the Cambrian explosion, though admittedly occurring over a longer timeframe.”

The Promise-to-Fight Later tactic: “more complex phyla indeed have larger genomes” —a result from analysis that “should therefore provide fertile ground for further testing.”

The Churchill Strategy: “History is written by the victors,” Churchill said. Twisting this principle in support of Darwin, they allege that “focusing only on living taxa can give a very distorted view of the dynamics of evolutionary radiations.” What we see as an explosion might just be an artifact of having only survivors in the record. Darwin was as busy at the beginning as he is now!

Punch at random: “Budd and Mann further speculate that if speciation rates are correlated with rates of morphological and molecular change — an association which has been much debated  — then surviving clades would also exhibit elevated rates of phenotypic evolution and genetic change, again due to chance alone.”

That’s it. Did you see any response to the origin of biological information for new body plans? There’s a lot of punching at the air, and hitting at the soft gloves of the sparring partner. Basically, they reaffirm Darwin as the undisputed champion, even without a fair fight. Here’s the ending paragraph. They acknowledge a big challenge is afoot, but they tell the media not to overestimate it, promising them that “the fight might be winnable.”

While there is little doubt that the Cambrian explosion represented a massive and rapid proliferation of animal forms and lineages, the two studies caution against overestimating its magnitude [i.e., Meyer “might” be a pushover.] The empirical work of Deline and colleagues demonstrates that the Cambrian did not represent the zenith of animal diversity, and that major innovation continues to this day, while the theoretical study of Budd and Mann suggests that elevated rates in speciation at the base of such radiations might be at least partly attributable to stochastic upswings rather than unusual evolutionary mechanisms.

“Innovation” or Chance Miracles?

You can always trust Darwin to be the world champion eventually, they promise. In Darwinspeak, “innovation” refers to chance miracles, like new body plans appearing suddenly. Those miracles evidently happen more quickly in periods of “stochastic upswings” within the “usual evolutionary mechanisms” (you know: sheer dumb luck). Sometimes, by chance, sheer dumb luck runs faster!

Most amusing in this paper is a suggestion that actually handicaps Darwin more. It’s the idea that there might have been even more body plans at the Cambrian that we don’t see! This makes perfect sense — if you believe that blind chance has infinite creative power. Since Darwin is always on the move, they speculate, and since history is written by the victors, the explosive evidence in the fossil record might just be an artifact of what survived. Logical, right? Commenting on the Deline paper, they say:

In a major challenge to the view of unsurpassed Cambrian diversity, all Cambrian fossils fall near (between or within) living phyla: for instance, the famously bizarre Anomalocaris helps link modern velvet worms and arthropods. Thus, at least some gaps between the different body plans of modern phyla are artefacts of extinction of ‘intermediate’ taxa, rather than fundamental evolutionary discontinuities. 

How this will help Darwin in the “major challenge” he admittedly faces (Darwin called the Cambrian explosion “the most obvious and serious objection which can be urged against the theory”) is anyone’s guess.

Furthermore, the morphospace occupied by Cambrian forms is much smaller than the morphospace occupied by living forms, even after accounting for non-preservation of soft features in most fossils.

But again, that is not the challenge Meyer makes. It’s about disparity, not diversity. They can call it small, but the morphospace includes at least 20, and up to 30, new body plans, each distinctive, bearing complex systems like muscles, nerves, digestive systems, sensory systems, locomotion, and reproductive systems with no precursors in the Precambrian. They all appear suddenly. Where are the “intermediate taxa”? They are nowhere in the rock record, 158 years after Darwin had hoped they would be found.

So that’s the situation going on six years after Meyer’s challenge. Marshall tried a few practice punches after the book came out, but then left. Bloggers have hooted and hollered from the stands, nothing more. Meyer still stands alone in the ring. He wins by default.