An Open Letter to Ard Louis

Dear Professor Louis:

You have presented the view that from a theological perspective evolution is not objectionable. You explained, for instance, that we ought not to confuse mechanism with meaning. If the creator used evolution as a creation tool, that need not detract from the meaning of the creation. And you thoughtfully defended Leibniz’s arguments that occasional divine intervention demeans God’s craftsmanship and that God doesn’t do miracles to satisfy the wants of nature, but rather those of grace.

But have you considered what theology has to say about scientific realism? Solomon, for example, wrote that “It is the glory of God to conceal a matter, But the glory of kings is to search out a matter.” Is there not a theological mandate that science ought to adhere to the evidence and data?

I ask the question because evolution is so often at odds with the scientific evidence. For instance, science suggests that the evolution of even a single protein is highly unlikely. One study concluded that the number of evolutionary experiments required to evolve a protein is 10^70 while another study concluded that the maximum number of evolutionary experiments possible is only 10^43. So the number of evolutionary experiments required is 27 orders of magnitude greater than the number of evolutionary experiments possible.

By any reasonable measure a 27 order of magnitude shortfall is at least tantamount to “highly unlikely.” In fact, this estimate is conservative for several reasons. First, these studies were performed not by skeptics but by evolutionists.

Second, these studies were not carefully selected to magnify the problem but on the contrary, are optimistic. The conclusion that the number of evolutionary experiments required to evolve a protein is 10^70 was arrived at using only part of a protein and only part of its function was considered. Also, other pre existing proteins were used in the experiment.

And the conclusion that the number of evolutionary experiments possible is 10^43 was computed by making every assumption as optimistic as possible. The evolutionists computed a range of values, and 10^43 was the upper end of their range. It was computed assuming a four billion year time frame and assuming the preexistence of an earth full of bacteria. The time frame is two to three orders of magnitude too large (proteins must have evolved in a matter of millions, not billions, of years). And bacteria need thousands of, yes, proteins. So even to compute the number of evolutionary experiments available to evolve a protein, it was again necessary to assume the pre existence of proteins.

The evolutionists did provide a more conservative estimate of the number of evolutionary experiments possible, reducing the number from 10^43 to 10^21. This increases the evolutionary shortfall from 27 orders of magnitude to 49 orders of magnitude. But even in this more conservative estimate the evolutionists continued to use the four billion year time frame and the pre existence of bacteria (with their many thousands of pre existing proteins).

Therefore according to today’s science the evolution of even a single protein, by the evolutionist’s own reckoning, is unworkable. This is, of course, one particular example in a consistent trend. Science presents substantial problems with the theory of evolution. Is this not a matter we should search out?

NT Wright Versus Karl Giberson

NT Wright has cogently argued that evolutionary thinking did not begin in 1859 and Darwin was not an intellectual revolutionary who single-handedly illuminated a new truth. In fact, the evolutionary foundation and framework were already in place “long before Darwin got in a boat and went anywhere.”

Wright is keenly aware that the origins debate and the greater science-religion landscape holds much more than the caricatured positions often presented. In the video below, Wright gives this solemn warning at the 3:04 mark:

Let’s put this thing on a broader canvas and let’s lighten up and have the proper discussion, instead of assuming that we already know, as soon as anyone mentions any scientific evidence for anything, “oh, they’re a Darwinian, they’re a liberal, they’re this that and the other.” Or, when somebody says they believe in God, “Oh, well you must be anti science then.” These are both trivial—actually childish reactions and we need to grow up.

Compare Wright’s wise cautionary words with Karl Giberson’s stereotypical attack on “Evangelicals” from the New York Times op-ed this week.

The rejection of science seems to be part of a politically monolithic red-state fundamentalism, textbook evidence of an unyielding ignorance on the part of the religious.

For Giberson, those who question the metaphysically-laden theory of evolution are guilty of a “rejection of science.” But Giberson sees hope, which in his world means some of those anti-intellectual fundamentalists are coming around to his position:

There are signs of change. Within the evangelical world, tensions have emerged between those who deny secular knowledge, and those who have kept up with it and integrated it with their faith. Almost all evangelical colleges employ faculty members with degrees from major research universities — a conduit for knowledge from the larger world. …

Scholars like Dr. Collins and Mr. Noll, and publications like Books & Culture, Sojourners and The Christian Century, offer an alternative to the self-anointed leaders. They recognize that the Bible does not condemn evolution and says next to nothing about gay marriage. They understand that Christian theology can incorporate Darwin’s insights and flourish in a pluralistic society.

Secular knowledge? For Giberson there is this thing called secular knowledge. It is a neutral, objective source of truth, free of metaphysical influence. It gives us things like “Darwin’s insights.” Then there is religious belief which must accommodate that “secular knowledge.” And of course to question evolution is to “deny secular knowledge.”

Giberson’s caricatures stand in stark contrast to Wright’s plea for more understanding. Ironically the Wright video above was produced by Giberson’s Biologos organization. Perhaps Giberson should watch it.

Gene Expression Evolution: Your Daily Teleology …

Here is a new paper that claims to show the rate of gene expression evolution in a range of different mammalian species. Of course the paper shows no such thing. What it does show are gene expression rates in extant species. And what they found is that those rates are all over the map. The rates are often similar, but in other cases the rates not only vary between species, they also vary between organs and even chromosomes. As usual, the evolutionists describe the findings using teleological language to cover over what evolution really says:

We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation.

Of course there is no such thing as “selective pressure.” This phrase is commonly used to envision an active process that responds to environmental challenges. If natural selection shapes and designs the species according to need, then it sounds more plausible. In reality, all natural selection does is kill off the bad designs.

Although gene expression evolution in mammals was strongly shaped by purifying selection, …

Translation: The evolutionists found that many cases similar genes have similar expression rates.

we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals.

In other words, the evolutionists also found some similar genes that have significantly different expression rates. So the evolutionists must infer a new kind of evolution. Instead of mutations grinding away which, on rare occasion, provide a slightly better design (in terms of reproduction of course), the new kind of evolution states that the genes and their regulation mechanisms are generally already in place. What changes is their expression rates. So evolution created all these genes and regulation mechanisms, no knowing that it had just created the building blocks for all massive biological complexity. All that was needed was some expression rate changes.

Aside from being unlikely, evolution calls for massive serendipity. As usual, it is presented in teleological terms.

Transcription Factors: More Species-Specific Biology

Evolutionists say that molecular biology has provided resounding confirmations of the fact of evolution. But actually the new molecular data reveal many contradictions. Far from confirming evolution, molecular biology has revealed yet more problems with the “fact.” For example, we find variations between species that are at odds with evolutionary expectations. One such example is in the transcription factors—proteins that bind to DNA and influence which genes are expressed.

Last year I discussed a study of how transcription factor binding is not conserved between mice and men. Evolutionists were surprised to find that similar transcription factors in human and mouse embryonic stem cells bind in very different DNA locations. In fact, the binding sites are often so-called “lineage-specific,” meaning that the transcription factor binds to a section of DNA that is unique to that species. As one writer explained:

Remarkably, many of these RABS [repeat-associated binding sites] were found in lineage-specific repeat elements that are absent in the comparison species, suggesting that large numbers of binding sites arose more recently in evolution and may have rewired the regulatory architecture in embryonic stem cells on a substantial scale.

Rewired the regulatory architecture on a substantial scale? In other words, evolutionists must believe that although evolution had provided, in a common ancestor to mice and men, perfectly good transcription factors and perfectly good binding sites for those transcription factors to attach to, nonetheless this was all “rewired.”

They call this species-specific or lineage-specific biology, which simply means that evolution’s predictions don’t work. Evolution doesn’t help explain the findings, it is a gratuitous, unparsimonious layer added to the science. Rather then the theory guiding the science and elucidating the findings, it is the science that is contradicting the theory.

Such divergence between transcription factor binding sites even shows up in very similar species, such as different species of yeast. As one paper explains, “most of these sites have diverged across these species, far exceeding the interspecies variation in orthologous genes.” And as usual the evolutionists did not miss a step in reinventing their theory to accommodate the contradictory findings:

Transcription factor binding sites have therefore diverged substantially faster than ortholog content. Thus, gene regulation resulting from transcription factor binding is likely to be a major cause of divergence between related species.

In other words, the unexpected findings between different species become a causal mechanism for the evolutionists. The right mutations just happened to occur in both the genes that code for the transcription factors, and in the DNA to create new binding sites which just happened to drive evolutionary change to fantastic new designs. Saying this is unlikely is putting it kindly.

Another study found “large interspecies differences in transcriptional regulation” between different vertebrates which the evolutionists claimed “provide insight into regulatory evolution” and reveal “the evolutionary dynamics of transcription factor binding.” But of course the findings reveal no such thing. There were no “evolutionary dynamics” revealed by the transcription factor binding differences. That is a multiplied entity based on the dogma that evolution is a fact. Here is how one writer described the findings:

Researchers from Cambridge, Glasgow and Greece have discovered a remarkable amount of plasticity in how transcription factors, the proteins that bind to DNA to control the activation of genes, maintain their function over large evolutionary distances.

The text books tell us that transcription factors recognise the genes that they regulate by binding to short, sequence-specific lengths of DNA upstream or downstream of their target genes. It was widely assumed that, like the sequences of the genes themselves, these transcription factor binding sites would be highly conserved throughout evolution. However, this turns out not to be the case in mammals.

[…]

In all tested species, the transcription factors CEBPA and HNF4A are master regulators of liver-specific genes. By mapping the binding of CEBPA and HNF4A in the genomes of each species and comparing those maps, they found that in most cases neither the site nor the sequence of the transcription factor binding sites is conserved, yet despite this, these transcription factors still manage to regulate the largely conserved gene expression and function of liver tissue.

[…]

"By studying changes in transcription factor binding, we can understand the evolution of gene regulation," said Duncan Odom from Cancer Research UK Cambridge Research Institute and coauthor on the paper.

Once again the evolutionary textbooks are wrong, but no matter, evolution is a fact. Religion drives science and it matters.

New Research Continues to Point to a Super Progenitor

Everyone knows biology is full of complicated designs, but evolutionists think it arose spontaneously, as a result of the play of natural laws. In other words, it happened to happen. First there was nothing, then there was something, then that something became very complicated. All this just happened to happen.

There are many problems with this evolutionary narrative. One is that we can’t explain how such complexity could have arisen on its own. Another is that if evolution is true, then complexity must have somehow formed early in evolutionary history. In fact, evolutionists sometimes use this fact to dodge the failure of their idea. They say that immense complexities, such as molecular machines and codes, are not really a problem because they occurred so early in evolutionary history. That early history, these evolutionists say, falls under the origin of life (OOL) phase, not evolution proper. So with a wave of the hand, they dismiss major failures of their idea.

But the failure of the evolutionary expectation of simple beginnings will not go away so easily. One such example in the news is the last universal common ancestor (LUCA) to all life. If evolution is true, then this ancient progenitor of all life must have been extremely complex. Here is what I wrote ten years ago in my book Darwin’s God:

[T]he next step was to piece together what the progenitor would have looked like by comparing the genetic differences and similarities of the three lineages. But the task became confusing due to the wide variety of genes between and amongst the three lineages. No clear picture of a simple progenitor emerged. Instead the only solution seemed to be a super progenitor that already had most of the highly complex traits found in each of the three lineages. The super progenitor would have been as complex as modern cells yet would have somehow arisen in a short time.

This story has not changed and recent research continues to point to a mythical “super progenitor.”

Last Universal Common Ancestor More Complex Than Previously Thought

New evidence suggests that LUCA was a sophisticated organism after all, with a complex structure recognizable as a cell, researchers report. Their study appears in the journal Biology Direct.

The study builds on several years of research into a once-overlooked feature of microbial cells, a region with a high concentration of polyphosphate, a type of energy currency in cells. Researchers report that this polyphosphate storage site actually represents the first known universal organelle, a structure once thought to be absent from bacteria and their distantly related microbial cousins, the archaea. This organelle, the evidence indicates, is present in the three domains of life: bacteria, archaea and eukaryotes (plants, animals, fungi, algae and everything else).

The existence of an organelle in bacteria goes against the traditional definition of these organisms, said University of Illinois crop sciences professor Manfredo Seufferheld, who led the study.

"It was a dogma of microbiology that organelles weren't present in bacteria," he said. But in 2003 in a paper in the Journal of Biological Chemistry, Seufferheld and colleagues showed that the polyphosphate storage structure in bacteria (they analyzed an agrobacterium) was physically, chemically and functionally the same as an organelle called an acidocalcisome (uh-SID-oh-KAL-sih-zohm) found in many single-celled eukaryotes.

Their findings, the authors wrote, "suggest that acidocalcisomes arose before the prokaryotic (bacterial) and eukaryotic lineages diverged." The new study suggests that the origins of the organelle are even more ancient.

So even given evolutionary assumptions, this evidence indicates an early organelle and with it, early complexity.

"There are many possible scenarios that could explain this, but the best, the most parsimonious, the most likely would be that you had already the enzyme even before diversification started on Earth," said study co-author Gustavo Caetano-Anollés, a professor of crop sciences and an affiliate of the Institute for Genomic Biology at Illinois. "The protein was there to begin with and was then inherited into all emerging lineages."

But the evolution of even a single protein is astronomically unlikely, even according to evolutionist’s unrealistically optimistic assumptions.

The study lends support to a hypothesis that LUCA may have been more complex even than the simplest organisms alive today, said James Whitfield, a professor of entomology at Illinois and a co-author on the study.

"You can't assume that the whole story of life is just building and assembling things," Whitfield said. "Some have argued that the reason that bacteria are so simple is because they have to live in extreme environments and they have to reproduce extremely quickly. So they may actually be reduced versions of what was there originally. According to this view, they've become streamlined genetically and structurally from what they originally were like. We may have underestimated how complex this common ancestor actually was."

Early complexity is yet another example of evolutionary expectations gone wrong. Religion drives science, and it matters.

Two-Fold Fragile Codons and Amino Acids

If you read Brian Cusack’s paper (discussed here) you may have wondered why the evolutionists did not distinguish the two-fold fragile codons from the single-fold fragile codons. Perhaps I missed it, but I saw no mention of this distinction. The evolutionists define as “fragile” those codons that can be changed into a STOP codon with a single substitution. They are shaded gray in the table below (from Figure 1 in the paper):

For instance, TCG, which codes for the amino acid serine (Ser), becomes a STOP if the cytosine (C) at the second position is replaced with an adenine (A). As the table shows, there are 18 such codons (shaded in gray).

But of these 18 “fragile” codons, five of them are two-fold fragile. That is, there are two different substitutions that can change the codon into a STOP. The other 13 codons are single-fold fragile in that one and only one substitution can effect the change to a STOP.

The two-fold fragile codons are: TTA, TCA, TAT, TAC and TGG. The first two code for the amino acids leucine (Leu) and serine, respectively. The next two both code for tyrosine (Tyr), and the final one codes for tryptophan (Trp).

This leads to another distinction. The evolutionists also point out that there are six amino acids that are coded for exclusively by fragile codons. They are also shaded in gray in the figure (Tyr, Gln, Lys, Glu, Cys and Trp). These are the “fragile amino acids.”

But Tyr and Trp—both aromatic hydrophobics and the two largest amino acids—are coded for exclusively by two-fold fragile codons. We might call them the “two-fold fragile amino acids.”

The theme of the evolutionists’ paper is that these fragile codons appear less frequently where transcriptional error correction mechanisms are less effective. Fewer fragile codons means there will be fewer erroneous STOP signals in regions where they are more likely to go uncorrected.

All that makes sense, but why didn’t the evolutionists mention the two-fold fragile codons and the amino acids that are coded for exclusively by them? Would they not have expected the correlation with the correction mechanisms to be even stronger? Am I missing something, or could this be yet another case of evolutionary confirmation bias by the authors and reviewers?

Nature: Life is Complicated

According to the theory of evolution the biological world arose spontaneously. Evolutionists, however, prefer to use teleological language to explain how biology came to be. “Natural selection,” they explain, “has evolved a strategy.” Teleological language is needed to cover over the awkwardness of evolution. For evolutionists have no choice. Inspite of the data, evolutionists must dogmatically insist that they are right. It must be a fact that the most complex designs arose all by themselves. And complex they are. In fact, in spite of having been created by nothing and arising all by themselves, biological designs are too complex for our best scientists. Armies of the world’s smartest researchers using the most powerful supercomputers available still cannot figure out how it all works. As one article from last year explained, “Life is complicated.”

Non-coding DNA is crucial to biology, yet knowing that it is there hasn't made it any easier to understand what it does. "We fooled ourselves into thinking the genome was going to be a transparent blueprint, but it's not," says Mel Greaves, a cell biologist at the Institute of Cancer Research in Sutton, UK.

Instead, as sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude.

Complexity growing by orders of magnitude? This is precisely what was not expected.

"It seems like we're climbing a mountain that keeps getting higher and higher," says Jennifer Doudna, a biochemist at the University of California, Berkeley. "The more we know, the more we realize there is to know."

Biologists have seen promises of simplicity before. The regulation of gene expression, for example, seemed more or less solved 50 years ago. In 1961, French biologists François Jacob and Jacques Monod proposed the idea that 'regulator' proteins bind to DNA to control the expression of genes. Five years later, American biochemist Walter Gilbert confirmed this model by discovering the lac repressor protein, which binds to DNA to control lactose metabolism in Escherichia coli bacteria. For the rest of the twentieth century, scientists expanded on the details of the model, but they were confident that they understood the basics. "The crux of regulation," says the 1997 genetics textbook Genes VI (Oxford Univ. Press), "is that a regulator gene codes for a regulator protein that controls transcription by binding to particular site(s) on DNA."

Indeed, for evolutionists all of biology is a fluke. It just happened to arise, so isn’t it simple?

Just one decade of post-genome biology has exploded that view. Biology's new glimpse at a universe of non-coding DNA — what used to be called 'junk' DNA — has been fascinating and befuddling. Researchers from an international collaborative project called the Encyclopedia of DNA Elements (ENCODE) showed that in a selected portion of the genome containing just a few per cent of protein-coding sequence, between 74% and 93% of DNA was transcribed into RNA.

Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. "Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things — such as how a cell turns on and off — is incredibly naive," says Joshua Plotkin, a mathematical biologist at the University of Pennsylvania in Philadelphia.

But wait, did not the non-coding DNA, like everything else, spontaneously arise by itself? How could we be so “incredibly naïve” about all of this?

Even for a single molecule, vast swathes of messy complexity arise. The protein p53, for example, was first discovered in 1979, and despite initially being misjudged as a cancer promoter, it soon gained notoriety as a tumour suppressor — a 'guardian of the genome' that stifles cancer growth by condemning genetically damaged cells to death. Few proteins have been studied more than p53, and it even commands its own meetings. Yet the p53 story has turned out to be immensely more complex than it seemed at first.

In 1990, several labs found that p53 binds directly to DNA to control transcription, supporting the traditional Jacob–Monod model of gene regulation. But as researchers broadened their understanding of gene regulation, they found more facets to p53. Just last year, Japanese researchers reported that p53 helps to process several varieties of small RNA that keep cell growth in check, revealing a mechanism by which the protein exerts its tumour-suppressing power.

Even before that, it was clear that p53 sat at the centre of a dynamic network of protein, chemical and genetic interactions. Researchers now know that p53 binds to thousands of sites in DNA, and some of these sites are thousands of base pairs away from any genes. It influences cell growth, death and structure and DNA repair. It also binds to numerous other proteins, which can modify its activity, and these protein–protein interactions can be tuned by the addition of chemical modifiers, such as phosphates and methyl groups. Through a process known as alternative splicing, p53 can take nine different forms, each of which has its own activities and chemical modifiers. Biologists are now realizing that p53 is also involved in processes beyond cancer, such as fertility and very early embryonic development. In fact, it seems wilfully ignorant to try to understand p53 on its own. Instead, biologists have shifted to studying the p53 network, as depicted in cartoons containing boxes, circles and arrows meant to symbolize its maze of interactions.

Did all of this spontanously arise via random biological change, such as caused by mutations?

"When we started out, the idea was that signalling pathways were fairly simple and linear," says Tony Pawson, a cell biologist at the University of Toronto in Ontario. "Now, we appreciate that the signalling information in cells is organized through networks of information rather than simple discrete pathways. It's infinitely more complex."

Evolution’s predictions routinely turn out to be false. Evolutionists are constantly surprised because their theory is always pointing in the wrong direction.

"In many cases you've got high-throughput projects going on, but much of the biology is still occurring on a small scale," says James Collins, a bioengineer at Boston University in Massachusetts. "We've made the mistake of equating the gathering of information with a corresponding increase in insight and understanding."

A new discipline — systems biology — was supposed to help scientists make sense of the complexity. The hope was that by cataloguing all the interactions in the p53 network, or in a cell, or between a group of cells, then plugging them into a computational model, biologists would glean insights about how biological systems behaved.

In the heady post-genome years, systems biologists started a long list of projects built on this strategy, attempting to model pieces of biology such as the yeast cell, E. coli, the liver and even the 'virtual human'. So far, all these attempts have run up against the same roadblock: there is no way to gather all the relevant data about each interaction included in the model.

In many cases, the models themselves quickly become so complex that they are unlikely to reveal insights about the system, degenerating instead into mazes of interactions that are simply exercises in cataloguing.

No way to gather all the relevant data about each interaction? But according to evolution the creative force behind biology is, well, nothing. So how could there be such mazes of interactions?

In retrospect, it was probably unrealistic to expect that charting out the biological interactions at a systems level would reveal systems-level properties, when many of the mechanisms and principles governing inter-and intracellular behaviour are still a mystery, says Leonid Kruglyak, a geneticist at Princeton University in New Jersey. He draws a comparison to physics: imagine building a particle accelerator such as the Large Hadron Collider without knowing anything about the underlying theories of quantum mechanics, quantum chromodynamics or relativity. "You would have all this stuff in your detector, and you would have no idea how to think about it, because it would involve processes that you didn't understand at all," says Kruglyak. "There is a certain amount of naivety to the idea that for any process — be it biology or weather prediction or anything else — you can simply take very large amounts of data and run a data-mining program and understand what is going on in a generic way."

From where did that “naivety” come, and will they learn from their mistakes? It seems not:

For example, transcription factors encoded in the urchin embryo's genome are first activated by maternal proteins. These embryonic factors, which are active for only a short time, trigger downstream transcription factors that interact in a positive feedback circuit to switch each other on permanently. Like the sea urchin, other organisms from fruitflies to humans organize development into 'modules' of genes, the interactions of which are largely isolated from one another, allowing evolution to tweak each module without compromising the integrity of the whole process. Development, in other words, follows similar rules in different species.

"The fundamental idea that the genomic regulatory system underlies all the events of development of the body plan, and that changes in it probably underlie the evolution of body plans, is a basic principle of biology that we didn't have before," says Davidson. That's a big step forwards from 1963, when Davidson started his first lab. Back then, he says, most theories of development were "manifestly useless".

In other words, the massive biological change change evolution brought about was based on the genomic regulatory system which, of course, evolution had just happened to have already created. That was fortunate.

This article is worth revisiting because the problem with all of this is not merely that mistakes were made. Nor is there anything wrong with a theory that doesn’t work out. This happens all the time in science. The problem is that evolution is driven by theological and philosophical convictions that won’t be overturned by scientific evidence. Religion drives science, and it matters.

Brian Cusack’s Latest: Anti Parsimonious, Teleological, Petitio Principii, Cum Hoc Ergo Propter Hoc and Misrepresentations—Other Than That It’s Perfect

Or should we say, it is perfect, for creatively finding new ways to cram as many fallacies as possible into a single paper is precisely what “scientific” evolutionism seems to be all about. Cusack’s latest peer-reviewed contribution to the evolution literature, Preventing Dangerous Nonsense: Selection for Robustness to Transcriptional Error in Human Genes, is perfectly typical. But alas, due to the strict page limits of Darwin’s God, we are only able to provide a mere brief overview.

Background

When a gene is used to synthesize a protein, error checking and prevention is performed all along the way. An important and dangerous error is the so-called nonsense error in which the code for an amino acid is erroneously replaced with a stop signal. This causes the protein synthesis process to be halted in mid stream, leaving a half-baked and useless segment of protein. Cell’s have various processes to check for and correct such nonsense errors, but another way around the problem is to avoid the genetic coding that is particularly susceptible to nonsense errors.

Anti parsimonious

The main contribution of Cusack’s paper is its elucidation of how these correction and prevention mechanisms often complement each other nicely. In particular, the error correction mechanisms have their limitations. One of the correction mechanisms usually doesn’t work for genes that are written out in one, single continuous region. And for genes that are divided into several separate regions, that mechanism often doesn’t work for the final region.

It is in these particular regions—where the error correction is more limited—that the prevention is stronger. In these regions, the particular genetic coding that is susceptible to nonsense errors is diminished. It would be like having a spell-checker that cannot check a certain page, but that page doesn’t have any long words to begin with.

This and other examples need nothing more than common sense to understand. Looking at the design of the error correction and prevention mechanisms, it makes perfect sense that where the error correction is less effective, there would be more error prevention. Nonetheless, the evolutionists break every rule of parsimony to impose their evolutionary framework. They multiply entities and construct superfluous causes. From Occam to Einstein we know not to do this, but evolutionists must have their theory. Here are two examples from the paper:

Given the high rate of transcriptional errors in eukaryotes, we hypothesized that natural selection has promoted a dual strategy of “prevention and cure” to alleviate the problem of nonsense transcriptional errors. A prediction of this hypothesis is that [the error correction’s] inefficiency should leave a signature of “transcriptional robustness” in human gene sequences that reduces the frequency of nonsense transcriptional errors.

[…]

Interestingly, one group of genes falls entirely outside of the range of [the error correction’s] surveillance. Replication-dependent histones contain neither introns in their coding sequences nor polyA-tail in their mRNAs. Therefore, histone genes represent a blind-spot for both mammalian [the error correction] pathways. According to our hypothesis histone genes should represent the most transcriptionally robust genes in the mammalian genome since PTC-containing transcripts of their genes will not be recognized and degraded before translation.

Evolution adds nothing to the science here. These are yet more examples of how evolution is a gratuitous explanation, adding nothing but “multiplied entities” as Occam put it. We may as well say, with the Aristotelians, that fire is hot because it has the quality of heat.

Teleological

Evolution adds little to the science beyond gratuitous explanation, and furthermore that explanation is awkward. The theory states that the entire biological world just happened to arise all by itself.

Not surprisingly evolutionists never describe it this way. Nor do they use equally accurate but more detailed explanations, such as that blind mutations just happened to create complex, interdependent designs while natural selection killed off the bad designs. Such accurate explanations of the theory are not used because they make obvious the absurdity of the whole project.

Instead evolutionists craft clever explanations that cast evolution and its natural selection in the active role of a designer. The theory sounds so much more plausible when natural selection responds to a need by creating a new design. And so there is an underlying, latent Lamarckianism running through the evolution genre. Out of one side of their mouth they rail against teleology while from the other they appeal to it over and over. Here are typical examples from the paper:

we hypothesized that natural selection has promoted a dual strategy of “prevention and cure” to alleviate the problem of nonsense transcriptional errors.

[…]

Nonsense errors are potentially highly toxic for the cell, so natural selection has evolved a strategy called Nonsense Mediated Decay (NMD) to “cure” such errors.

[…]

Moreover, these “prevention and cure” strategies are used interchangeably …

Natural selection has promoted a dual strategy to alleviate a problem? Strategies are used interchangeably? Of course evolutionists do not mean any of this to be true. Their teleology is rhetorical. They need it to avoid the literal.

Petitio principii

The evolutionists force-fit the evidence into their theory, and the fit isn’t very good. Cusack’s flawed thesis is that evolution predicts how the error correction and prevention methods complement each other. But as usual the project depends on the pre existence of biology’s wonders. In this case, the evolutionists believe that evolution just happened to create the genetic code, which conveniently just happened to have some stop signals.

Evolution also just happened to create genetic information, including stop signs at the appropriate places, and the incredible molecular machines to read, copy and translate that genetic information, and to stop at the stop signs.

But sometimes errors occurred which inserted stop signs somewhere in the middle of a copy of a gene. Fortunately, evolution just happened to create incredible molecular machinery and mechanisms to check for and correct for such errors. The likelihood of all (or any) of this happening is of course beyond ridiculous. The theory isn’t even wrong.

The only way to avoid evolution’s massive contradictions is simply to assume it is true. Having swallowed such lunacy the evolutionists are now in a position to declare that the new evidence is yet another fulfilled prediction of, yes, evolution. Evolution is true, therefore evolution is true.

Cum hoc ergo propter hoc

A common evolutionary fallacy is to confuse correlation with causation. In this case Cusack and the evolutionists find a good correlation between the correction and prevention mechanisms. Simply put, where the correction is weaker, the prevention is stronger. And so they assume the former is the cause of the latter via the evolutionary process:

We observe that single-exon genes have evolved to become robust to mistranscription, because they show a significant tendency to avoid fragile codons relative to robust codons when compared to multi-exon genes.

[…]

Depletion of fragile codons is due primarily to inactivity of EJC–dependent NMD but also to reduced efficiency of PABP–dependent NMD.

[…]

We show that variable NMD efficiency also leaves its signature in the coding sequences of human genes and in the amino-acid content of the proteins they encode.

When will evolutionists learn that correlation does not imply causation. The answer of course is that they will learn this only when they learn to stop corrupting science with their religious dogma. That may sound harsh, but that is precisely what evolutionists are doing. Their metaphysics mandates evolution to be true. Therefore such correlations must be assumed to be the result of evolutionary causation.

Misrepresentations

No evolutionary treatise would be complete without misrepresentations of the science. If there is any common thread to scientific evolutionism it is the very bizarre interpretations of the scientific evidence which, to put it kindly, amount to misrepresentations. Such misrepresentations run all though the genre, from the popular works on down to the technical papers. Consider these misrepresentations from Cusack’s paper:

In contrast, gene expression errors are not inherited and have tended to be disregarded in evolutionary studies. Here we show how human genes have evolved a mechanism to reduce the occurrence of a specific type of gene expression error—transcriptional errors that create premature STOP codons (so-called “nonsense errors”).

But of course the paper showed no such thing. It did not “show how human genes have evolved a mechanism …” That is an incredibly unlikely, religiously-driven hypothesis that makes little scientific sense. The paper continues:

Nonsense errors are potentially highly toxic for the cell, so natural selection has evolved a strategy called Nonsense Mediated Decay (NMD) to “cure” such errors. However this cure is inefficient. Here we describe how a preventative strategy of “transcriptional robustness” has evolved to decrease the frequency of nonsense errors.

These are yet more blatant misrepresentations of the science. The paper does not “describe how a preventative strategy of ‘transcriptional robustness’ has evolved to decrease the frequency of nonsense errors.” The paper not only did not describe how such a strategy evolved, it did not even show that it evolved.

Religion drives science, and it matters.

Independent Evolution of Complex Designs in Molluscs: Why the Explanations are in Need of Explaining

To the modern student Aristotle’s physics and cosmology are likely to seem bizarre. His final causes, geocentrism, and sublunar and superlunar realms seem to have no correspondence with reality. But Aristotelianism makes more sense when one understands the historical context of ancient Greek thought. In fact Aristotle’s physics and cosmology describe and explain what we observe in nature. This is attested to by the fact that it was well accepted and influential for a millenium and a half. Eventually, however, as scientific understanding progressed, the Aristotelian explanations became increasingly strained. Aristotelianism became more of a tautology, as whatever was observed was described according to the ancient system. Fire, for example, had the quality of dryness and heat. But is this not simply a tautology? As Descartes put it: “If you find it strange that … I do not use the qualities called ‘heat,’ ‘cold,’ ‘moistness,’ and ‘dryness,’ as do the philosophers, I shall say to you that these qualities appear to me to be themselves in need of explanation.” Aristotelianism failed to explain the physical action causing the effects. Today Darwin’s theory of evolution follows a similar denouement. To modern scientists it seems strange, but Darwin had good reasons for his theories of common descent and evolution. In the final acts, however, evolution is more of a tautology. Like Aristotelianism, evolution is a superfluous explanatory device rather than a value added. The difference is that evolution is running its course over a couple of centuries, rather than a couple of millenia.

Mollusca: A case study

Molluscs are mostly slugs and snails, but they also include larger, more advanced creatures, including the giant squid whose over-sized nerve cells have helped make it possible to study the physics and electrical properties of neurons.

The squids, along with others such as the octopus and cuttlefish make up the brainy side of the phylum and one would think (at least an evolutionist would think) that their more sophisticated central nervous systems would fall into the usual common descent pattern.

New research, however, suggests otherwise. It is a plot line that has played out over and over. Evolutionists arrange the species according to common descent, but when we look under the hood the species don’t cooperate. Contradictory differences in the supposedly closely-related cousins, and contradictory similarities in the supposedly distantly-related neighbors, betray evolutionary expectations.

In this case we now must believe that these advanced central nervous systems evolved independently, not once, but several times. Here is how one report summarized the new findings:

The findings, which rely on advanced statistical analyses, fundamentally rearrange branches on the mollusc family tree. In the traditional tree, snails and slugs (gastropods) are most closely related to octopuses, squid, cuttlefish and nautiluses (cephalopods), which appears to make sense in terms of their nervous systems: both groups have highly centralised nervous systems compared with other molluscs and invertebrates. Snails and slugs have clusters of ganglia – bundles of nerve cells – which, in many species, are fused into a single organ; cephalopods have highly developed central nervous systems that enable them to navigate a maze, use tools, mimic other species, learn from each other and solve complex problems.

But in Kocot's new family tree, snails and slugs sit next to clams, oysters, mussels and scallops (bivalves), which have much simpler nervous systems. The new genetic tree also places cephalopods on one of the earliest branches, meaning they evolved before snails, slugs, clams or oysters.

All this means that gastropods and cephalopods are not as closely related as once thought, so they must have evolved their centralised nervous systems independently, at different times.

That's a remarkable evolutionary feat. "Traditionally, most neuroscientists and biologists think complex structures usually evolve only once," says Kocot's colleague Leonid Moroz of the University of Florida in Gainseville.

"We found that the evolution of the complex brain does not happen in a linear progression. Parallel evolution can achieve similar levels of complexity in different groups. I calculated it happened at least four times."

Once again evolutionary expectations are at odds with reality, and once again the uncooperative empirical data are force fit to the theory. As with Aristotelianism, evolution does not add scientific knowledge. It does not tell us what to look for, and where to look for it. Quite the opposite, it is consistently turning up wrong. And yet the theory simply morphs to encompass the new, uncooperative results. No matter what is found, evolution is assumed to have created it. As one evolution remarked, concerning these new results, “This is more evidence that you can get complexity emerging multiple times.”

If you find it strange that I do not use the explanations of evolution, I shall say to you that these explanations appear to me to be themselves in need of explanation.

Religion drives science, and it matters.

What Michele Bachmann and Charles Darwin (Don’t) Have in Common

In a recent political debate presidential hopeful Michele Bachmann raised the topic of vaccines. She accused Rick Perry, governor of Texas, of abusing his authority when he imposed vaccine mandates. What does this have to do with Charles Darwin? Darwin was also concerned about vaccines. But the so-called Father of Modern Biology had a different sort of concern. Darwin erroneously worried that vaccines preserved the lives of those who otherwise would have succumbed. “Thus,” warned the Sage of Kent, “the weak members of civilized societies propagate their kind.” And that, he ominously concluded:

must be highly injurious to the race of man. It is surprising how soon a want of care, or care wrongly directed, leads to the degeneration of a domestic race; but excepting in the case of man himself, hardly any one is so ignorant as to allow his worst animals to breed.

The aid which we feel impelled to give to the helpless is mainly an incidental result of the instinct of sympathy, which was originally acquired as part of the social instincts, but subsequently rendered, in the manner previously indicated, more tender and more widely diffused. Nor could we check our sympathy, even at the urging of hard reason, without deterioration in the noblest part of our nature. The surgeon may harden himself whilst performing an operation, for he knows that he is acting for the good of his patient; but if we were intentionally to neglect the weak and helpless, it could only be for a contingent benefit, with an overwhelming present evil. Hence we must bear without complaining the undoubtedly bad effects of the weak surviving and propagating their kind; but there appears to be at least one check in steady action, namely the weaker and inferior members of society not marrying so freely as the sound; and this check might be indefinitely increased, though this is more to be hoped for than expected, by the weak in body or mind refraining from marriage.

It is little wonder that fifteen years later Nietzsche proclaimed that “The invalids are the great danger to humanity, not the evil men.” The rest, as they say, is history. Let’s hope it stays that way.

Religion drives science, and it matters.

Rosenberg: Evolution Produces Awareness of Evolution

One of the amazing things about evolution, aside from spontaneously creating everything, is its creation of conscious automata which in turn figured out that they, and everything else, had evolved. As Duke’s Alex Rosenberg informs New York Times blog readers:

“On the Origin of Species” revealed how physical processes alone produce the illusion of design. Random variation and natural selection are the purely physical source of the beautiful means/ends economy of nature that fools us into seeking its designer. Naturalists have applied this insight to reveal the biological nature of human emotion, perception and cognition, language, moral value, social bonds and political institutions. Naturalistic philosophy has returned the favor, helping psychology, evolutionary anthropology and biology solve their problems by greater conceptual clarity about function, adaptation, Darwinian fitness and individual-versus-group selection.

There you have it. Rosenberg reveals that he is the result of physical processes alone which he then became aware of. And fortunately naturalists have applied this insight to reveal the source of emotion, morality and everything else. That’s just the Stuff of Good Solid Scientific Research.

Infra Dig: What Goes Around Comes Around and Why Evolution is a Fact

re•li•gion [ri-lij-uhn], noun: A set of beliefs concerning the cause, nature, and purpose of the world, especially when considered as the creation of a god or gods.

The view that God should work according to natural laws rather than direct providence has always been attractive to religious believers. These believers prefer a more distant God for many reasons. For instance, is it not obvious that God would not have directly created such an evil world? Instead, God must have created the laws and went away. Like Aristotle’s Prime Mover, God is removed from the evil and not culpable. But there are several other theological traditions that argue just as strongly against divine intervention, and for creation by natural law. One is that the world, especially the lowly things of the world, are beneath God’s dignity.

In the era of modern science the infra dignitatem argument, or infra dig for short, traces at least back to the Cambridge Platonists in the seventeenth century. The idea was that God would not, as the Anglican botanist John Ray put it, “set his own hand as it were to every work, and immediately do all the meanest and trifling’st things himself drudgingly, without making use of any inferior or subordinate Minister.”

The subordinate minister or agent was Plastic Nature which, unlike the Creator, was not infallible or irresistible. Instead, Plastic Nature had to contend with the ineptitude of matter. The results were those “errors and bungles” of nature.

Such gnostic tendencies by no means ceased with the seventeenth century. Indeed, this view seemed to have a divine sanction. After all, to control the world exclusively through natural laws—God’s secondary causes—required an even greater God. In 1794 Darwin’s grandfather Erasmus Darwin wrote this Gnostic-sounding vision of how natural history should be viewed:

The world itself might have been generated, rather than created; that is, it might have been gradually produced from very small beginnings, increasing by the activity of its inherent principles, rather than by a sudden evolution by the whole by the Almighty fiat. What a magnificent idea of the infinite power of the great architect! The Cause of Causes! Parent of Parents! Ens Entium! For if we may compare infinities, it would seem to require a greater infinity of power to cause the causes of effects, than to cause the effects themselves.

A striking example of these gnostic tendencies in Darwin’s time arose when John Millais’ painting Christ in the house of his parents was first exhibited at the Royal Academy in 1850. In the painting, the boy Jesus had injured his hand in his father’s carpentry shop. Mother Mary attended to the boy while Joseph continued with his work. Outside the door sheep patiently awaited their future savior. The scene was both symbolic and realistic, with wood scraps lying all about and workers going about their duties.

But the Victorians emphasized God’s wisdom, power and transcendence. Could he really have bruised his hand in a messy carpenter’s shop? The Times complained that the painting was revolting, for its “attempt to associate the holy family with the meanest details of a carpenter’s shop, with no conceivable omission of misery, of dirt, even of disease, all finished with the same loathsome meticulousness, is disgusting.” Blackwood’s Magazine said “We can hardly imagine anything more ugly, graceless and unpleasant,” and Charles Dickens called the painting “mean, odious, revolting and repulsive.”

The gnostics could not believe God became a man for the same reasons they could not believe God directly created the world—they could not envision God involved in a world so fraught with misery. Similarly, just as the Victorians were troubled by Millais’ depiction of the human side of Jesus, they also would have trouble with the idea that God so lowered himself to create the messy and detailed biological world, so full of not only of useless bloodshed but of anomalies and particulars. It was all beneath God’s dignity.

A few years earlier the Reverend Baden Powell had insisted that physical and moral problems had completely separate foundations and should have nothing to do with one another. God’s works and God’s word were separate and moral and physical phenomena were completely independent. He wrote in 1838:

Scientific and revealed truth are of essentially different natures, and if we attempt to combine and unite them, we are attempting to unite things of a kind which cannot be consolidated, and shall infallibly injure both. In a word, in physical science we must keep strictly to physical induction and demonstration; in religious inquiry, to moral proof, but never confound the two together. When we follow observation and inductive reasoning, our inquiries lead us to science. When we obey the authority of the Divine Word, we are not led to science but to faith. The mistake consists in confounding these two distinct objects together; and imagining that we are pursuing science when we introduce the authority of revelation. They cannot be combined without losing the distinctive character of both.

The message here is that religion and science are to be kept separate. God is retained to supply the former, but it would never do to consider him in the latter. So it is not too surprising that in his 1844 book Vestiges, Robert Chambers reissued the infra dig argument:

How can we suppose an immediate exertion of this creative power at one time to produce the zoophytes, another time to add a few marine mollusks, another to bring in one or two crustacea, again to crustaceous fishes, again perfect fishes, and so on to the end. This would surely be to take a very mean view of the Creative Power.

Divine providence could engage in the noble activity of impressing laws upon matter, but not grovel in the muck of nature.

Alfred Wallace agreed. Evolution’s cofounder argued that the universe was self-regulating according to its general laws and in no need of continual supervision and rearrangement of details. “As a matter of feeling and religion,” concluded Wallace, “I hold this to be a far higher conception of the Creator of the Universe than that which may be called the ‘continual interference hypothesis’.”

Darwin, for his part, was keen to the implications of this modern gnosticism. If God was not intimately involved in the world, then was He involved at all? In a letter Darwin challenged his American friend Asa Gray to think this through:

I see a bird which I want for food, take my gun and kill it, I do this designedly. An innocent and good man stands under a tree and is killed by a flash of lightning. Do you believe (and I really should like to hear) that God designedly killed this man? … If you believe so, do you believe that when a swallow snaps up a gnat that God designed that that particular swallow should snap up that particular gnat at that particular instant? I believe that the man and the gnat are in the same predicament. If the death of neither man nor gnat are designed, I see no good reason to believe that their first birth or production should be necessarily designed.

Many argue about whether Darwin believed in God, but Darwin certainly held strongly to the popular beliefs about God. It was reasonable for Darwin to argue that God would not be personally involved in the swallow’s attack on the gnat and then leverage his theological principle to conclude that all of biology arose on its own. Evolution is the right conclusion given a gnostic starting point. God and matter don’t mix, so life wasn’t created. If Archimedes needed only a place to stand to move the world, Darwin needed only a theological ledge.

Not surprisingly Darwin also used gnostic ideas to defend his theory against the problem of complexity. Darwin pointed out that while it is tempting to see God as the master engineer who crafted complex organs such as the eye, this would make God too much like man.

Darwin agreed that the perfection of the eye reminds us of the telescope which resulted from the highest of human intellect. Was it not right to conclude that the eye was also the product of a great intellect? This may seem the obvious answer but Darwin warned against it, for we should not “assume that the Creator works by intellectual powers like those of man.” Better to imagine the eye as the result of natural selection’s perfecting powers rather than having God too much involved in the world.

The Victorians could not believe that the boy Jesus actually labored in his earthly father’s carpentry shop. Likewise, it was reasonable for Darwin to argue that complex organs were not likely shaped by God because that would mean he works as man does.

These Gnostic tendencies remain with us today. Evolutionist Stephen Jay Gould, for example, admiringly recounted the Darwin-Gray correspondences. The problem, according to Gould, is not the religious motivation in Darwin’s supposedly scientific theory, but rather that Darwin’s position can be depressing. Gould wrote a book on how we are supposed to understand this new gnosticism. He believed that science and religion do not overlap and are non-overlapping magisteria.

Likewise Niles Eldredge takes the position that “religion and science are two utterly different domains of human experience” and Bruce Alberts, writing for the National Academy of Sciences, informs us that:

Scientists, like many others, are touched with awe at the order and complexity of nature. Indeed, many scientists are deeply religious. But science and religion occupy two separate realms of human experience. Demanding that they be combined detracts from the glory of each.

Similarly Salman Khan at the Khan Academy explains that an all-powerful God would not design the particular. God, if there is one, would use simple laws to create a complex world. Khan concludes:

That to me is a better design.

And isn’t that all that matters?

These are just a few of the many examples of modern gnosticism within evolutionary thought. God must be disjoint from creation and any attempt to force-fit them together is bound to be awkward. Or again, how is it that God could create the universe but have nothing to do with science? The answer of course is that God did not create the world, at least not directly—the world evolved. The historian’s assessment of gnosticism could just as easily apply to evolution:

The cardinal feature of gnostic thought is the radical dualism that governs the relation of God and world … The deity is absolutely transmundane, its nature alien to that of the universe which it neither created nor governs and to which it is the complete antithesis … the world is the work of lowly powers. [Hans Jonas, quoted in: Philip J. Lee, Against the Protestant Gnostics, p. 16, Oxford University Press, 1987.]

The gnostic’s hope in “lowly powers” was fulfilled in evolution’s natural selection. And the acceptance of evolution, in turn, reinforced gnosticism in modern thought. Darwin gave form to the gnostic’s vision, but that brought with it a movement towards gnosticism. The influence of gnostic thought today is not often acknowledged or understood. It is, according to Harold Bloom, the most common thread of religious thought in America. He calls it the American Religion, and he finds it “pervasive and overwhelming, however it is masked, and even our secularists, indeed even our professed atheists, are more Gnostic than humanist in their ultimate presuppositions.”

It is perhaps one of the great enigmas in religious thought that one can profess to be an agnostic, skeptic, or even atheist regarding belief in God yet still hold strong opinions about God. Evolution may breed skepticism, but its adherents have continued to make religious proclamations. Indeed, those proclamations are really no different than those made by Darwin and his fellow Victorians.

Religion drives science, and it matters.

The Khan Academy Promotes Theological Naturalism

A friend pointed out that over at the Khan Academy, Salman Khan, while assuring his students he is not taking sides, seems to have been channeling such luminaries as John Ray and Alfred Wallace as he informs them that god would never design or create the particulars of this world. Khan—who has four degrees from MIT and Harvard and is certain that evolution and its natural selection created the entire biological world—assures the viewer that “You can ask any engineer” and they will tell you that simple laws underlying a complex design, as exemplified by the Mandelbrot set, is the better way. Of course non of this comes directly from Ray or Wallace—what this illustrates is not a homologous doctrine, but rather the independent origin and persistence of theological traditions. The infra dignatatum argument appears and reappears in the history of thought not because it derives from a single teacher, but because we like it. Here then, we present the 21st century’s version of this age-old tradition within theological naturalism:

[4:19] A belief in god would not point to a god who—a belief in a universal, all-powerful god, would not point to a god who designs the particular—who designs each particular. And even more, the imperfections we see around us—and especially because we see variation and they’re being selected for—we can’t just focus on the eye, we’d have to focus on viruses and cancers and it would have to speak to a god who is designing one-off every version of every sequence of DNA. Because if someone talks about designing the eye, we know the eye is the by product of DNA, and we know that DNA is a sequence of base pairs, ATGCA, billions and billions of them, and so when we talk about design, we would be talking literally about designing the sequence, and we even know there is some noise in there, that comes from primitive viruses in there deep in our past. So the argument I’m making here is that in order to give credit to the all-powerful, at least to my mind, a system that comes from very simple, elegant and basic ideas—like natural selection and variations; in our DNA we call those mutations, but the laws of physics and chemistry, from those simple and elegant and basic ideas, for complexity to emerge. …

This speaks to a higher form of design, this speaks to a more profound design. …

This idea of the laws of physics and chemistry and natural selection … This is a very profound design, and it speaks to the art of the designer. As opposed to designing each of these entities, one off. And what is even more profound about the design is that it is adaptive. If there is environmental stress, then the other variations survive more frequently. … That to me is a better design.

Religion drives science, and it matters.

He’s Baaaack: Evolution Professor Walks it Back, Then Forward, Then Back, Then …

When I explained how astronomically unlikely protein evolution is, a professor complained that I had it all wrong. When he saw evolution’s ridiculously long odds he figured I must be assuming that the entire protein sequence space must be randomly sampled to yield functional proteins.

Of course that’s not true and my calculations were, in fact, on the optimistic side for evolution.

Next the professor recommended a paper that would clear it all up by explaining that only a very limited fraction of the protein sequence space actually need be searched.

But of course the paper didn’t help. Even though its assumptions were completely ridiculous (e.g., protein evolution is explained by first assuming the earth is loaded with bacteria which are each chocked full of, yes, proteins), the paper nonetheless proved how unlikely is protein evolution. Even with their ridiculous assumptions, and giving evolution every advantage (e.g., assuming only part of a protein need be evolved, with the other parts already, somehow, evolved), protein evolution is 27 to 49 orders of magnitude from reality. That puts it somewhere between a myth and a fairy tale.

So next the professor explained that protein evolution—even though the subject of massive evolutionary assaults—is actually not part of evolution at all. “Evolutionary theory,” he said, “makes no claims about the origin of life.”

This is a favorite trick of evolutionists. Biology is incredibly complex and defies evolutionary musings, so evolutionists say that incredible complexity actually occurred in the beginning, when life first formed. Evolution proper, they say, took the helm at that point. It is another evolutionary shell game that reveals their desperation.

Next the professor said I was playing a “numbers game.” That was similar to what the paper said:

We hope that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention.

As usual divine intervention was the target. It must, of course, be ruled out. After all, that’s not scientific and evolution is a fact.

Next the professor said such “numbers games” are futile because there is too much uncertainty:

The frivolity is in his probability calculations. Such calculations depend on such questionable assumptions that they are scientifically useless - though they seem to be useful to anti-evolution apologists.

I pointed out that I was using assumptions from the paper which he had recommended. Why was he now disparaging the assumptions as “questionable” and “scientifically useless”?

Now the professor says that he did not disparage the paper but rather my use of the paper. But all I did was use the results from the paper.

But since I pointed out that those results were ridiculously optimistic, the professor now says we shouldn’t use those results because “probability calculations are only as good as the qualifying assumptions behind them.”

So let’s see, evolutionists provide the results, those results show evolution to be astronomically unlikely, but since the results, as bad as they are, are nonetheless unrealistically optimistic toward evolution, we should just drop the whole thing.

Right.

I’m not sure if this is just the Stuff of Good Solid Scientific Research or if the ball bearings are rolling.

Religion drives science, and it matters.

How the Protein Amyloid State Once was a Good Thing: Evolution’s Lurking Anti-Realism

If there were the equivalent of a “Most favored nation” status in science, evolution would be granted it. If there was an Emperor of science, evolution would be it. If there was a “Get Out of Jail” card in science, evolution would have it. For evolution is special. It can lack the evidence and still be a fact. It can fail and still be true. It can get it all wrong, and still be right.

It is not uncommon for scientists to use false ideas. The flat earth model, for example, is often used. In that case everyone knows the model is wrong. In other instances the status of the model or theory may not be so obvious. Four centuries ago different cosmological theories competed. Did the cosmos revolve about the earth or the sun? Such radically different models could, both, produce reasonably accurate predictions. So it was well understood that a scientific model could be accurate but not true, and that scientists could develop and use a theory with no claim of realism.

In science there is a long history of using models and theories and have limited or no correspondence with reality. Theories fill the spectrum from realism to anti realism and everything in between. For instance, realism may be intended in one part of a model but not another part.

Scientists know the difference and have no difficulty juggling different ideas with different levels of realism. Scientists don’t become confused and make truth claims for theories that have no basis in reality.

Evolution, on the other hand, is different. Evolutionists routinely devise all manner of mechanisms and processes that have no correspondence with reality while simultaneously making high truth claims.

For instance, evolutionists say that the important, information-bearing, DNA molecule was once not so. Instead, they say it was an RNA world. According to this idea the RNA molecule held and processed the information. There is a wealth of information missing from this story. This is not too surprising since it has no correspondence with reality.

Or again, evolutionists say that there was a time when biological cells exchanged genetic information on a massive level, in sophisticated networks using never-observed processes. Evolution, they say, was more horizontal than vertical. But these processes are far beyond anything actually observed in biology.

Evolutionists also say that there was a time when evolution experimented with different DNA codes. What is observed today, on the other hand, is that the DNA code is robust. New and different codes do not easily evolve.

Evolutionists also say that there was once a time when the amyloid state of proteins was a good thing, which evolution made use of. Did not the self-complementary stickiness of short segments of proteins turn them into useful building blocks?

That is in sharp contrast to what is actually observed. Only a relatively small set of particular proteins stick together normally. Usually protein aggregation is harmful and cells have a range of sophisticated strategies to eliminate any such possibility.

Unlike most theories, evolution is special. It can employ any number of just-so stories which have no basis in reality. Like a good bed-time story, the narrative can take any turn at any time, with no need for justification. For as evolutionists say, their theory is a given.

Religion drives science, and it matters.