Daniel Sarewitz: Bias is Like a Magnetic Field That Pulls Iron Filings Into Alignment

Kudos to Daniel Sarewitz for his must-read comment on the problem of bias in scientific research where he discusses mounting evidence that bias in science is not random. If it were then multiple studies would serve to cancel it out. Instead false positive results persist and to make matters worse, science’s attempts at internal controls, such as conflicts of interest disclosure, are not keeping up with the problem. Sarewitz points out that industry teams, who seek actually to implement scientific findings, are consistently unable to confirm what were thought to be “landmark” findings. As John Ioannidis has put it, “claimed research findings may often be simply accurate measures of the prevailing bias.”

The causes of scientific bias are both complex and yet, in retrospect, rather obvious. As Sarewitz explains:

All involved benefit from positive results, and from the appearance of progress. Scientists are rewarded both intellectually and professionally, science administrators are empowered and the public desire for a better world is answered. The lack of incentives to report negative results, replicate experiments or recognize inconsistencies, ambiguities and uncertainties is widely appreciated — but the necessary cultural change is incredibly difficult to achieve.

One reason bias persists, and is so harmful, is that in the moment it is not perceived as bias. In many settings, when a research study begins there are certain outcomes which are acceptable and others which are not. But such a priori commitments are most likely to be perceived as nothing more than a reflection of what science has so far revealed. And most often that is true. But not always.

Sarewitz uses a powerful metaphor of how a magnetic field aligns iron filings—something every freshman learns—to illustrate how scientific bias aligns outcomes into its preconceived framework.

Commentators such as Sarewitz and Ioannidis tend to focus on the field of biomedical research which not only is so important but as an experimental science has the virtue of being, at least in principle, more amenable to verification. But if the experimental sciences are experiencing such problems with bias, one wonders how the historical sciences are faring. As Sarewitz warns, “It would therefore be naive to believe that systematic error is a problem for biomedicine alone.”

As Ioannidis warns, it appears that it is more likely for a research claim to be false than true. And so should we really accept uncritically the evolutionist’s claim that the world spontaneously arose as a consequence of chance events?

If there ever was a scientific field subject to cultural influence and bias this would be it. From the ancient Epicureans to today’s evolutionists, there has always been right answer and a wrong answer. Spontaneous origins is the right answer and, in spite of scientific problems, is now known to be a fact. Is that just a coincidence?

An Extraordinary New Carnivorous Sponge

The deep sea harp sponge has a series of vertical vanes that maximize surface area for passive suspension feeding. As one report explains:

Scientists believe the harp sponge has evolved this elaborate candelabra-like structure in order to increase the surface area it exposes to currents, much like sea fan corals. … “C. lyra is an extraordinary example of the kind of adaptations that animals must make in order to survive in such a hostile environment.”

Apparently these “scientists” do not understand evolution very well for in evolution nothing happens for any reason. It may sound good, but no species “has evolved” anything “in order to increase” anything else.

In fact, everything occurs spontaneously, for no reason. Random chance events, such as mutations, collectively just happened to construct the harp sponge (no, natural selection never designed anything).

The harp sponge was created by a long series of random mutations and the like which just happened to happen, and just happened to create and continue to improve a living, eating, reproducing population that ultimately led to the harp sponge.

Selection, nor anything else, caused those mutations to occur. And selection certainly did not cause certain, more effective, mutations to occur. Evolutionists cannot tell you what that sequence of mutations was. They cannot even determine a hypothetical, candidate sequence of mutations that could have created the sponge. But they know there was such a sequence. Why? Because they know evolution is a fact.

Soft Inheritance Differences Between Human and Chimp Genomes

Human and chimpanzee genomes are highly similar. Protein coding genes in the two species are usually practically identical. This led to some rather silly conclusions by evolutionists trying to make sense of the evidence that showed their gene-centric view made no sense.

In fact, there are substantial molecular differences between humans and chimps, the differences just aren’t typically in the gene sequences. For instance, there are big differences in the regulation of those genes. And many of those differences are types of soft inheritance, involving not DNA differences but chemical markers influencing gene expression. As one report explains:

They found that the distinct gene expression patterns of the three species can be explained by corresponding changes in genetic and epigenetic regulatory mechanisms that determine when and how a gene's DNA code is transcribed to a messenger RNA (mRNA) molecule.

Dr. Gilad also determined that the epigenetics process known as histone modification also differs in the three species. The presence of histone marks during gene transcription indicates that the process is being prevented or modified.

The human and chimp genomes reveal substantial differences in their gene expression patterns. Those differences are due not only to differences in the DNA regulatory sequences but also to differences in the epigenetic markers.

So soft inheritance falsifies evolution’s expectation that acquired changes are not inherited, and soft inheritance’s origin is not explained by evolution, and now evolution must explain how it constructed different soft inheritance strategies in the human and chimp genomes.

Evolutionist: Sub Hypotheses of Evolution Need Not Be Testable

Though evolutionists often cite testability as a criterion for acceptance, this apparently is not required when the theory is one of their own. The mutational-hazard (MH) hypothesis is difficult to test but, as one evolutionist reminds us, that is no reason to reject it:

Given its broad phylogenetic perspective across species with widely different features, the MH hypothesis is admittedly difficult to test with comparative data. … Unfortunately, the procurement of direct estimates of Ne remains dauntingly difficult [40], and until this problem is solved, it will remain difficult to obtain unbiased estimates of the key parameter Neu. However, there is no justification for rejecting a theory based on its accessibility to formal hypothesis testing.

Evolutionists insist on strictly naturalistic explanations. That makes evolution—broadly construed as the origin of species via natural laws and processes—the right answer. Evolution can be modified by rejecting old sub hypotheses and erecting new ones, but the core idea cannot be wrong. Now even evolution’s sub hypotheses can also be untestable.

Whitney Tilson’s Diatribe Explains Why Science (Still) Doesn’t Matter

The conviction that the world must have arisen spontaneously dates back to antiquity and is no less strong today. Its contemporary label is evolution and if you want your funding, or just respectability, you must accept it. Skepticism of the power of spontaneity is not allowed as this latest post from investor and all-around smart-guy Whitney Tilson makes clear:

Even if Romney is a pragmatic centrist, I question his ability to act independently of a party that I fear has become beholden to people I view as extremists – anti-intellectuals who are hostile to women, minorities, the poor, immigrants, and gays, and who don’t believe in evolution, diplomacy, protecting the environment, equality for women, global warming, and gun control.

Can you imagine doubting evolution in the company of elites such as Tilson? You would automatically qualify, in their view, as an extremist. To question whether all of biology could have somehow arisen by itself makes you an anti-intellectual. On the other hand the evolutionist’s insistence that they hold the truth is the intellectual approach.

For evolutionists, their views are true and good and anyone who so much as doubts is automatically linked to all manner of nefarious thoughts and deeds.

Ironically all this comes after Tilson complains that “the political environment has become very toxic.” So while pointing the finger and castigating those who don’t silently go along with their dogma, evolutionists simultaneously bemoaning the toxic environment.

Religion drives science and it matters.

In a Few Minutes Felix Baumgartner Will Jump

In a few minutes Felix Baumgartner will jump from his capsule at an altitude of 120,000 feet.

Mohamed Noor: Evolution is True Because We Say So

Today’s first set of lectures in Mohamed Noor’s Introduction to Genetics and Evolution course would seem downright bizarre to anyone not familiar with evolutionary thinking. Noor is teaching this course via through the coursera on-line service and the Earl D. McLean Professor and Associate Chair of Biology at Duke University is maximizing accessibility to his material by minimizing the course prerequisites. Non specialists are welcome and many newcomers to evolutionary thought, now seeing what it is—or should we say what it isn’t—have sunk back in their chairs with blank stares wondering what in the world evolutionists such as Noor are thinking.

Framing the debate

This first day of class was mostly about evolution and why it is a no-brainer. Noor repeatedly and triumphantly declared evolution to be true. With such a startling claim students naturally had their interest piqued and expectations raised. What secrets would the confident professor unveil to make good on his incredible claim. How does he know evolution to be true?

Things turned strange however, at least for those not familiar with evolution, when Noor attempted to justify his heroic claim. Noor began with the usual equivocation when he defined evolution as “change through time” that occurs over multiple generations. We’ve seen this fallacy many times before as it is standard amongst evolutionists (see here, here, here and here and here). So red flags were raised as students sensed a canard. Was Noor’s celebration merely about “change through time”?

As if to confirm suspicions Noor next used an absurd example of a population of light and dark colored moths. Due to industrial pollution the predominant color in the population shifted from light to dark due to predation by birds. Eyes rolled as even newcomers could see this had nothing to do with evolution’s claim that millions of species arose from a warm little pond or deep sea vent.

Next Noor took the absurdity one step further. Noor claimed confidently and unequivocally that evolution is “a mathematical inevitably.” There is no way to avoid having evolution by natural selection, Noor assured the students, if some very simple conditions are met.

And what are those simple conditions? Students were astonished as Noor presented a cartoon example of a population of squirrels, some of which feared asphalt and so avoided being run over by automobiles, and the rest which did not fear asphalt and so were not able to leave as many offspring. In all seriousness Noor worked through this trivial example as though it actually proves evolution to be “a mathematical inevitably.”

Things turned from bad to worse when the students next had to endure yet another round of evolution’s whig history. Noor began with the mandatory retelling of the mythical 1925 Scopes Monkey Trial which the professor was only too happy to propagate. And it ended with Noor’s scolding of the people of Kansas who have had the audacity to request that the science be taught in their schools without first presuming evolution to be true.

Noor’s next canard was the typical equating of evolution with antibiotic resistance. Harmful bacteria gain resistance to antibiotics so new antibiotics are then designed and the bacteria then follow in turn, gaining yet more resistance. For evolutionists such as Noor, it is all part of the evolutionary lore. How could we possibly understand this critical public health issue without his truth that all of biology spontaneously arose?

It’s called framing the debate. Before evolutionists present their evidence, they frame the theory and its evidences in a cultural mandate. First and foremost, evolution is true from the start. Next evolution is cast as objective science in pursuit of the good. And skeptics are cast as forces of ignorance and darkness. It is the standard presentation of evolution that is full of bad science and bad history.

The evidence for the truth of evolution

When professor Noor finally arrived at the evidence for evolution it was, not surprisingly, a let down. In fact, Noor did not even attempt to show that the evidence demonstrates evolution to be true.

He simply continued to insist it is true while proceeding through a list of evidences, making various unscientific and fallacious claims as he went and ignoring monumental scientific problems.

For instance, Noor claimed that evolution’s prediction that early life should be simple has been confirmed. The professor is apparently unaware of life science research showing the enormous complexity that must have existed in early life if evolution is true. From our brain to vision, DNA repair mechanisms, the last universal common ancestor (LUCA), the genome and the proteome, high complexity is ubiquitous and must have existed early in evolutionary history. As one report explained:

Simple cells like bacteria are supposed to be, well, simple. They might have transformed Earth because of their unimaginable numbers, but they’re little more than tiny, solitary bags of chemicals. Or so we thought. Here, New Scientist looks at the growing number of exceptions to the rules. The most recent discoveries are challenging our ideas about the nature of early life.

For instance, evolutionists have been forced to conclude that the last common ancestor of eukaryotes must have had not only the vast majority of the complex DNA replication, RNA splicing and interference, and protein translation machinery, it was also capable of advanced movement and was equipped with versatile energy conversion systems. Or as one evolutionist conceded, it is the “Incredible Expanding Ancestor of Eukaryotes.” Incredibly, evolutionists now view the origin of the amoeba as a giant step, and of man a small step.

Indeed, even the LUCA must have possessed incredible complexity. As one evolution admitted, “In short, then, the last common ancestor of all life looks pretty much like a modern cell.” Or as another report explained:

It is commonly believed that complex organisms arose from simple ones. Yet analyses of genomes and of their transcribed genes in various organisms reveal that, as far as protein-coding genes are concerned, the repertoire of a sea anemone—a rather simple, evolutionarily basal animal—is almost as complex as that of a human.

You can read more about these here, here, here, here, here, here, here, here, here, here and here.

But Noor’s blunder did not stop there. Not only has the science falsified evolution’s prediction that early life is simple, Noor next explained that “only later would more ‘modern’ forms appear.” That, of course, is a tautology. Species that come later are more “modern” to evolutionists because they come later.

From there Noor moved to naïve falsificationism, explaining to the student that “There are no rabbits in the Precambrian era.” This is a famous low hurdle that evolutionists like to set for themselves, and Noor used it to commit the fallacy of affirming the consequent as he explained:

That [the rabbit] has not been found, so there has not been an observation to refute the truth of evolutionary common ancestry.

There are no rabbits in the ancient strata so therefore “there has not been an observation to refute the truth of evolutionary common ancestry”?

Evolutionists are known for sloppy logic and fallacious reasoning, but with this statement jaws were dropping. “Refute the truth of evolutionary common ancestry”?

Noor next wanted to demonstrate evidence of species gradually changing. Amazingly the best he could do was to show the horse lineage—an example that has endured much evolutionary abuse. Indeed, what the horse lineage shows is long periods of stasis and abrupt appearance of new species—precisely the opposite of what Noor sought to demonstrate.

For transitional forms Noor showed a feathered dinosaur and the whale lineage, ignoring the actual data and instead showing a clean, sanitized lineage of creatures leading to the modern whale. The empirical evidence looks more like a bush, but evolutionists carefully draw the best lineage they can and carefully edit out the rest of the bush, giving the student an entirely false impression of the scientific data.

Next the professor proclaimed that vestigial organs are “very difficult to explain except in the context of common ancestry.” What he didn’t explain is that the term “vestigial” presupposes that said organs are evolutionary leftovers. In other words, evolution is assumed in the very interpretation of the organs. Noor’s question-begging did not stop there as his next topic was “vestigial” genes.

Noor followed this with examples from biogeography. Oceanic islands have many native birds and insects, but lack native mammals, amphibians, and freshwater fish. And new species introduced to the islands competed very well. Also, these islands often have species that are similar to those on the nearest mainland.

At this point Noor’s presentation was increasingly incoherent. He didn’t attempt to provide predictions or otherwise explain how this biogeographical evidence confirmed evolution as he claimed it did. He finished up with an equally bizarre discussion of inefficient designs, using the laryngeal nerve as his example.

There was no explanation of how inefficient designs and the other evidences prove evolution to be a fact. There were no prior or conditional probabilities, no treatment of contradictory evidences, not even a discussion of how one would, in principle, prove evolution to be a fact.

It was all just an obvious truism to Noor for which the details could be left up to the student. Noor simply threw up a sequence of evidences—oblivious to their warts and fallacies—and at the end was as certain evolution is true as he was at the beginning. The evidence really didn’t matter. If it did Noor wouldn’t be an evolutionist.

And what are we to learn from this exercise in banality? A top professor at a top university gave a lecture on how something comes from nothing and how he knows it is true. In the process he exposed evolutionary thought for all to see. There were fallacies and misrepresentation galore and it was downright embarrassing. Students who wanted to understand the gist of evolution got what they paid for.

Evolutionists Now Claim Directed Adaptation is Evolution in “Real Time”

If you remove the caterpillars from an evening primrose population, the plants will adjust, and adjust fast. Within even a few generations intelligent changes arise reflecting the absence of the predator. For instance, in plots protected from insects, the flowering time and defensive chemicals against the insects adjust. The plant’s resistance to insects is reduced, which makes sense since the insects are no longer attacking the plant. And in exchange, the plant’s competitive ability is improved. In other words, remove a threat that the plant had to defend against, and the plant population immediately and intelligently exploits the opportunity. It is yet another fascinating example of biology’s many built-in adaptation capabilities. Yet evolutionists claim it demonstrates evolution occurring in “real time.” To understand this move we need to begin with three underlying concepts: deep time, the definition of evolution and blowback.

Deep time

When Darwin was developing his theory, the age of the earth was not well understood. Darwin himself advocated a 400 million year or more age for the earth, which he considered to be required for the new species to evolve. Not surprisingly, arguments that the earth must be younger were one of Darwin’s “sorest troubles.” As Cherry Lewis of the University of Bristol has explained, “The age of the Earth was hugely important for people like Darwin who needed enormous amounts of time in which evolution could occur. As Thomas Huxley, Darwin’s chief advocate said: ‘Biology takes its time from Geology’.”

Eventually those arguments fell by the wayside and in the twentieth century the age of the earth was extended into the billions of years. All was well as evolution had its much needed deep time. You can read more about this here. The point is that because evolution is based on random chance, it would require a very long time to construct biology’s many wonders.

But a century later the story is changing. What science reveals is remarkable changes can come about in only a few years time as populations respond to environmental shifts and challenges. The reason such change can arise quickly because it is not by chance. It is not brought about by random mutations undergoing natural selection. Instead, it is directed by complex adaptation mechanisms, built-in to the species.

Amazingly, the response of evolutionists has been to claim this is yet more proof of evolution. They do this by equivocating on evolution.

The definition of evolution

As we have pointed out before the word evolution can take on different meanings. Probably the most concise definition of evolution is: the origin of species by strictly natural means. More generally evolution refers to cosmological origins as well as biological origins. In other words, the naturalistic origin of everything.

For centuries now theologians, philosophers and scientists have insisted upon the truth of this naturalistic origin of the world for religious reasons. Today we simply say that evolution is a fact. The problem, however, is that the origin of species by strictly natural means runs afoul of the science. Over and over evolution’s explanations and expectations turn up false or unlikely. One problem, such as with the evening primrose, is that the biological change we do observe tends to be in the form of rapid and effective directed adaptations to environmental changes brought about by built-in sophisticated mechanisms.

Not only is this change not caused by chance events such as random mutations, but evolution does not explain scientifically how such sophisticated adaptation mechanisms could have evolved in the first place.

So one strategy evolutionists have adopted is simply to redefine evolution merely as change over time, or as changes in allele frequencies over time. You can see examples of this here, here, here and here.

Of course such definitions are vacuous and trivial. Indeed they would render creationism as a form of evolution. But they make evolution undeniably true. And they immediately transform contradictory findings, such as directed adaptations, from problems to confirmations. This brings us to the problem of evolutionary blowback.

Evolutionary blowback

Evolution is motivated and justified by theological concerns. As such evolution is a vector for religious influence and control of science. But the harm does not stop there. To absorb and sustain science’s many refutations of their dogma, evolutionists equivocate on evolution and redefine it as the unfalsifiable concept of change over time. Consequently all new findings, no matter how contradictory, are simply interpreted as some new form of evolution, no matter how absurd.

In the evening primrose study, evolutionists now use the term real-time evolution as a euphemism for the observed rapid adaptation. As one report explained, “evolution can happen more quickly than was previously assumed, even over a single generation.” The report also included explanations from evolutionist Marc Johnson making clear the equivocation:

Johnson says that evolution, which is simply a change in genotype frequency over time, was observed in all plots after only a single generation. … “What this research shows is that changes in these plant populations were not the result of genetic drift, but directly due to natural selection by insects on plants,” says Johnson. “It also demonstrates how rapidly evolutionary change can occur -- not over millennia, but over years, and all around us.”

It is the ultimate form of blowback. Evolution is redefined as mere genetic change over time and so then mere genetic change over time becomes yet more confirmation of evolution. The evening primrose response to the lack of insects is not interpreted scientifically as an adaptation, but rather as a demonstration of evolution, even real-time evolution.

Of course there is nothing in these new findings to suggest the adaptations of the evening primrose could somehow accumulate to provide the large-scale changes evolution requires to explain the origin of species. Indeed evolutionists have no scientific explanation for such large-scale and complexity occurring spontaneously, as they claim it must have.

But none of that matters because evolution is now genetic change over time. When it comes to confirming evolution, evolutionists point to the trivial. And then when it comes interpreting evolution, evolutionists insist it is a fact that the biological world arose by itself. Should we laugh or cry?

Religion drives science, and it matters.

Evolution (Not) Crucial in Antibiotics Breakthrough: How Science is Actually Done

Where is the best place to find low-cost, easy-to-produce, natural, robust and non toxic antibiotics? Easy, in our own bodies. Nature so often provides the solutions we are looking for and, as an aside, that is why the preservation of species from extinction is so important. In this case the solution is natural antibiotics which University of California at Berkeley researchers have confirmed to exist in the tails of certain proteins called cytokeratins. These proteins help our eyes, for example, ward off infections. The eye’s cornea is remarkably free of pathogens and the research reveals something about how these wonderful proteins work. Once again, however, the research was not motivated by evolutionary theory.

Proteins consist of a long chain of amino acids, attached one after the other. This chain, or backbone, is usually tightly coiled into a helix shape or stretched out into a strand shape. Occasionally the backbone folds back on itself and so adopts a turn shape. Proteins that are inserted into the cell membrane are usually helices for the helix shape can have a more oily surface to match the oily interior of the membrane.

The Berkeley researchers found that the cytokeratin tails apparently insert into the membrane of pathogen cells. The cytokeratin tails they investigated were 13 to 26 amino acids long and are rich in the simplest amino acid, glycine. Here, from the paper, are the sequences and their properties:

Glycine’s side chain is nothing but a mere hydrogen atom and as such it is the most flexible amino acid. So not surprisingly the cytokeratin tails do not adopt a fixed helix or strand shape, but rather a looser, less common, coil shape. It appears that the insertion of the tail into the pathogen’s membrane not only serves to immobilize the foreign cell, it also creates a pore in the membrane. Such pores are harmful to cells because they serve to neutralize the all-important chemical and electrical properties of the cell.

This new research is important for what it tells us about antibiotics and for what it tells us about science. Rationalists maintain that scientists must operate from a theory of origins in order to do science and that, in particular, that theory must be evolution. But science itself demonstrates that there is no such requirement.

Beyond the Power of Accident

Just over a century ago a gracefully aging scholar quietly left the world with these wise words:

A young bird makes us laugh. When its feathers have grown, the same bird makes Shelley write an immortal ode. Such is the wonder of feathers. And how do they grow? Evolution can explain a great deal; but the origin of a feather, and its growth, this is beyond our comprehension, certainly beyond the power of accident to achieve. … The scales on the wings of a moth, have no explanation in Evolution. They belong to Beauty, and Beauty is a spiritual mystery. Even Huxley was puzzled by the beauty of his environment. What is the origin of Beauty? Evolution cannot explain.

Was this man a fundamentalist resisting the inexorable progress of science? No, this was evolution’s co-founder Alfred Wallace who believed evolution to be a good, but limited, hypothesis. Once again wisdom is justified by all her children for now, a century later, Wallace’s simple yet profound observations have been fulfilled. There is no scientific explanation for the origin of feathers, wings of moths, or untold other biological designs. Evolution is a fact, but not because it explains the origin of species.

Here’s That New Paper Showing the Genetic Regulation Hiearchy

Ever since Mendelian genetics was incorporated into Darwinism, evolutionists have believed that the gene is king. Genes, they thought, determine an organism’s design or, in technical jargon, the genotype specifies the phenotype. This fit their view that the species originated from the natural selection of biological change which did not arise initially as a consequence of need but rather as a consequence of random, spontaneous events. Those random, spontaneous, events were, for example, mutations in the genes. And later when the genetic code, which translates the information in those genes into proteins, was found to be essentially universal throughout biology, the story seemed complete. For if the species were designed why would their genetic codes be identical? But today, so many problems with this story have emerged it is difficult to keep track. And new research continues to add yet more problems.

Aside from the non scientific claims underlying evolution’s metaphysics (what scientific experiment informed evolutionists that independently created species would necessarily have different genetic codes?), the empirical science has contradicted evolution’s story at every turn. Genes are not king, mutations show no sign of creating biology’s marvels in spite of evolutionist’s many attempts to coax them to show off their power, the genetic code has special properties and shows no sign of having been a “frozen accident,” and all kinds of new codes have been discovered that are not universal but instead are lineage-specific.

One interesting part of this on-going contradiction of evolutionary theory is the role of proteins referred to as transcription factors which help to regulate the expression of genes. The elaborate genetic regulation processes are fascinating and you can read more here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here and here. It highlights yet another chicken-or-the-egg conundrum, for proteins are produced from the information in genes, and yet proteins are required in that very production process.

One of the types of proteins involved are the  transcription factors which help to turn genes on or off. They bind to nearby DNA regions that flank the genes to influence the genetic copying machine. The DNA sequences in those flanking regions as well as the transcription factors are important in determining the genetic regulation.

But the action of these transcription factors is not universal or consistent across species but rather are lineage-specific. Evolutionists were surprised when transcription factor binding was found to be not conserved between mice and men, between various other vertebrates, and even between different species of yeast.  If a universal code confirms evolution then a non universal code contradicts evolution.

But there are more ways in which transcription factors and their associated DNA regions contradict evolution. For instance, those DNA regions have special properties that evolution must have somehow accidentally created. In fact, as one evolutionist explained, evolution must have created these DNA regions “which may allow evolutionary adaptation to novel conditions.”

In other words, evolution created special DNA regions so that evolution could then occur.

Another such complication is that transcription factors can not only start and stop the RNA polymerase copy machine, they can also pause the machine after it has begun. And other transcription factors turn off the pause, so the transcription process may continue. So astonishingly, evolution must have created these profound complexities from random mutations so they could then be selected.

Now new research adds to this story with a massive study of the interactions between transcription factors and DNA. The study found that the action of transcription factors falls into three distinct, hierarchical, categories. There are interactions that specify the basic cell type (muscle, skin, nerve, and so forth). Then there are interactions that specify the cell’s sub-identity (the particular type of muscle cell, for example). And finally there are interactions that specify the cell’s response to the current environmental challenges.

Of course evolutionists have no explanation, beyond vague speculation, of how such a hierarchy of mechanisms could have arisen spontaneously. But for now no such explanation is needed. Evolution is known to be a fact and so we can be confident that future research will explain all these apparent contradictions. That’s how evolutionary theory works.

You Are What You Your Mother Eats

New research continues to reveal biology’s complex adaptation capabilities broadly referred to as epigenetics. Simply put, individuals not only respond physiologically to environmental challenges by modifying their DNA, they also pass such adaptations on to their progeny. It is, by any other name, the inheritance of acquired characteristics, a concept evolutionists have resisted for almost a century. Now researchers studying mice have found that a mother’s diet not only during pregnancy, but before pregnancy, causes intelligent adaptations to occur that are passed on to the offspring—a finding that once was cause for blackballing. Now, molecular machines that (i) sense environmental shifts, (ii) produce the desired response, and (iii) pass that response on to offspring arose by chance, and were later selected. What was once unacceptable anathema is now becoming orthodoxy in what we know to be the fact of evolution. As Darwin explained:

Whether the naturalist believes in the views given by Lamarck, by Geoffroy St. Hilaire, by the author of the ‘Vestiges,’ by Mr. Wallace and myself, or in any other such view, signifies extremely little in comparison with the admission that species have descended from other species, and have not been created immutable; for he who admits this as a great truth has a wide field opened to him for further inquiry.

It isn’t that we know how life has arisen so much as we know how life has not arisen. That’s how science works sometimes.

Here’s an Example of Evolution’s Unavoidable Anti Realism

Though evolutionists think of themselves as realists—ruthlessly objective investigators interested only in truth—their naturalistic constraint ultimately leaves them with only anti realism. This is because any a priori restriction of the answer might exclude the true answer. If I decide my math homework must contain only odd numbered answers, then I’ll be wrong on those problems whose correct answer is an even number. I can round up, approximate, truncate, contort or whatever to obtain an odd number, but I will be wrong. For such problems, the only way to be right is to remove the a priori restriction. But evolutionists cannot do this. Foundational to their thinking is that the world must have arisen by itself, strictly via natural laws and processes. What most evolutionists do not grasp is that their extreme rationalism leads at best to anti realism, and at worst to skepticism.

Evolutionary theory has produced so many false predictions—and as a consequence has become so complex—that it is difficult to keep track. Evolutionists have approximated, truncated, contorted or whatever to obtain their mandated answer. The fact that evolution is a fact is underwritten by the rationalistic a priori constraint rather than the scientific results. The former has precedence because the latter is always a work in progress. Scientific results can change, so given enough time and contorting we may yet find that the science supports the rationalism.

In the meantime this commitment to method can lead to awkward moments, such as when the student asks how evolution created life and all its species, how it created such complexity, how it created such variation where it shouldn’t be, or how it created such similarity where it shouldn’t be, and so forth.

While brow-beating, intimidation, delegitimization, dismissal, mockery and funding threats are usually sufficient to check any such challenges, some evolutionists find safety in the ultimate defense: evolution’s latent anti realism. Scientific problems don’t matter because evolution need not track reality in the first place. It is simply a brute fact.

Descartes introduced the specter of anti realism to evolutionary thought in the seventeenth century when he advocated for naturalism regardless of truth. For when the true cause is unknown, “it suffices to imagine a cause which could produce the effect in question, even if it could have been produced by other causes and we do not know which is the true cause.” For Descartes, a theory could be fictional, but still useful.

Today, evolutionists dismiss scientific failure as inconsequential. Evolution need not produce true explanations, just useful explanations. The evolutionary tree has failed, for example, but as Joel Velasco explains, though evolutionary processes may not be tree-like, nonetheless the evolutionary tree model helps us to understand the world better:

Phylogenetic trees are meant to represent the genealogical history of life and apparently derive their justification from the existence of the tree of life and the fact that evolutionary processes are tree-like. However, there are a number of problems for these assumptions. Here it is argued that once we understand the important role that phylogenetic trees play as models which contain idealizations, we can accept these criticisms and deny the reality of the tree while justifying the continued use of trees in phylogenetic theory and preserving nearly all of what defenders of trees have called “the importance of tree-thinking.” …

We have seen that phylogenetic trees are ubiquitous in biology. The justification for the use of trees has traditionally been that evolutionary processes are in fact tree-like. This justification is faulty. Attempting to interpret phylogenetic trees in a literal way leads to the view that these trees entail many falsities about evolutionary history. Attacks on the universal tree of life thus appear to be justified. The goal of this paper is to argue that these attacks are not in conflict with the continued and justified use of trees and tree-thinking in biology. The use of phylogenetic trees can often be completely justified even if they are not entirely accurate representations of the world. Instead, these trees are models which contain idealizations. These models are used to better understand the world. Sometimes, for some purposes, a tree model is inappropriate. But often, trees are entirely appropriate and perhaps even the best models we have.

Modeling and idealizations are widespread throughout the sciences. There is no particular reason to think that systematics should be any different. Evolutionary history is complicated. It is a sign of the advancement of the science of systematics that we not only take advantage of standard modeling practices from other disciplines, but that we understand that this is what it is that we are doing. It is true that belief in the existence of the tree of life as the big, universal, grand unifying, scale-free representation of all of the history of life should probably go away (if indeed biologists ever did believe there was such a tree). Whether we can still talk about the tree of life as some modified version of this idea is, I think, an open question. Whether the problems with the universal tree extend to smaller trees as well will depend on the particular details of the case in question. But whatever the outcome of these debates, phylogenetic trees and the importance of tree-thinking are here to stay. The future of tree-thinking is bright as long as we can recognize the importance of tree-thinking without the tree.

Evolution’s predictions have consistently failed and the species do not form an evolutionary tree. These are yet more manifestations of evolution’s underlying anti realism. But evolution remains a fact.

Crab and Locust Bones Optimized For Their Respective Functions

New research on the bone designs of crabs and locusts—whose skeletons are on the outside—has found that their high-tech composite bone material known as cuticle is formed into optimal geometries for their respective uses. The crab bone which the researchers analyzed undergoes both bending and compression and the bone’s design was found to be “an ideal compromise to resist these two types of loading.” The locust bone that was analyzed, on the other hand, mostly undergoes bending and was found to be “optimized for this loading mode.” Endoskeleton bones, on other hand, were not found to be optimized for these structural functions.

Self-Refuting Belief Systems

Relativism states that there are no absolute truths, but if true then that statement is an absolute truth. Likewise the statement that evolution is a fact, if true, means that we cannot know evolution to be a fact. Why? Because with evolution our minds are nothing more than molecules in motion—an accidental biochemistry experiment which has yielded a set of chemicals in a certain configuration. This leads to what Darwin called “the horrid doubt”:

But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind.

Today evolutionists agree that while a random collection of chemicals doesn’t know anything, nonetheless over long time periods and under the action of natural selection, phenomena which we refer to as knowledge, will and consciousness will spontaneously emerge. And how do we know this? Because evolution occurred and we know that it occurred. Therefore evolution must have created the phenomena of knowledge. The proof is left to the student.