Response to Comments: Proteins Did Not Evolve Even According to the Evolutionist’s Own Calculations but so What, Evolution is a Fact

Evolutionists say they just don’t know how to discern miracles. They might begin by looking at a protein. Proteins, according to science, are not likely to have evolved. And when I say “not likely,” I mean the chances are astronomically against such evolution. I may as well simply say: Proteins, according to science, did not evolve. To review, very briefly, here are some of the reasons:

1. Not enough time. New genes are found in species which allow only for a few million years for protein evolution.

2. Too important. These new genes are not functionally less important, as they should be if they recently evolved.

3. Wrong patterns. Protein sequences provide plenty of violations of evolution’s expected pattern, and the violations are not merely evolutionary “noise.”

4. Inflexible. Experiments show that proteins do not tolerate mutations very well. They rapidly lose their function with only a few mutations, so the evidence indicates that to evolve to a protein you need to start very close to it.

5. Not searchable. The protein design space is astronomically large and experiments show it provides no guidance as to where the fully functioning proteins are in the space. Like looking for a needle in a haystack, the hay provides no guidance.

I have discussed this issues here, here, here, here and here. Now if you already believe evolution is true and you don’t mind ignoring the obvious scientific evidence and you don’t restrict yourself to plausible explanations then, yes, you can explain all of the many issues with protein evolution using a variety of non scientific, just-so stories.

But for those who respect science, the evidence we currently have is clear. In fact, unlike most of the evolution narrative which appeals to a great many contingencies over a great many years in the past, protein evolution is more amenable to scientific experimentation. The just-so stories give way to the raw data of experiments which, not surprisingly, clearly show protein evolution to be unlikely.

Of course evolutionists attempt to spin the results of these experiments to favor their theory. They ignore monumental assumptions and use calculations that unrealistically favor evolution. But even then—even giving evolution every advantage—protein evolution is nonetheless unlikely.

For instance, in one case evolutionists concluded that the number of evolutionary experiments required to evolve their protein (actually it was to evolve only part of a protein and only part of its function) is 10^70 (a one with 70 zeros following it). Yet elsewhere evolutionists computed that the maximum number of evolutionary experiments possible is only 10^43. Even here, giving the evolutionists every advantage, evolution falls short by 27 orders of magnitude.

The theory, even by the evolutionist’s own reckoning, is unworkable. Evolution fails by a degree that is incomparable in science. Scientific theories often go wrong, but not by 27 orders of magnitude. And that is conservative.

How conservative? In order to educate readers about the science, as opposed to the evolution mythology, I wanted to explain not only the 27 orders of magnitude shortfall, but also why even that estimate is grossly under valued.

So I explained the several evolutionary assumptions involved. For instance, the evolutionists computed that a maximum of 10^43 evolutionary experiments are possible by assuming a time span of 4 billion years. But that is unrealistic.

Even evolutionists agree that evolutionary innovations, including proteins, arise rapidly, on the order of some tens of millions of years, or in some cases even in just a few million years. So their time span was two to three orders of magnitude too long.

In response to this, one professor made this comment:

The "evolutionist" authors to whom Dr Hunter refers (Dryden, Thomson and White, 2008), assumed a time-frame for the biological activities of bacteria on earth of four billion (4*10^9) years (a commonly accepted value).

An order of magnitude is a factor of 10, so Dr Hunter proposes that a more realistic value for the duration of existence of bacteria on earth is 100- to 1,000-fold less than 4*10^9 years, or between 4*10^7 and 4*10^6 years. That's between 40 million and 4 million years! (Faithful readers may recall Dr Hunter's previous essay on a Cambrian fossil that was dated to ~515 million years ago!)

What was he thinking?

Again, it is unrealistic to use the entire time span of bacteria on earth. Proteins must have evolved much faster than that. Indeed, the bacteria themselves are full of proteins. So giving the bacteria a four billion year time frame leaves much less time to evolve their proteins.

In another example, the evolutionists computed the maximum of 10^43 evolutionary experiments are possible by assuming a protein size of 50 amino acids. I pointed out that this is extremely small as very few proteins are this short. Indeed, the vast majority of protein domains are far longer than 50 residues. Single domain proteins, and domains in multiple-domain proteins are typically in the hundreds of residues.

In response to this, the professor made this comment:

On the contrary:

"The size of individual domains also varies widely (Fig. 6C), from 36 residues in E-selectin (lesl) (Graves et al., 1994), a two-domain protein, to 692 residues in lipoxygenase-1 (2sbl, chain B) (Boyington et al, 1993), also a two-domain protein. However, very large domains are the exception. The distribution peaks at around 100 residues per domain and 80.3% of the domains are comprised of less than 200 residues. Very similar distributions have been observed in smaller non-redundant data sets. Siddiqui and Barton (1995), using DOMAK to assign domains for a data set of 230 protein chains, found that 90% of domains comprised less that 200residues. Holm and Sander (1994) using PUU on a dataset of 330 protein chains, also observed a domain size distribution that peaked at 100 residues."

Domain assignment for protein structures using a consensus approach: Characterization and analysis

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143930/pdf/9521098.pdf

Of 787 proteins studied, 370 (47%) had domains smaller than 100 residues (Fig 6C).

Here the professor simply reinforces my point. As the graph below shows, the protein domain sizes range from about 50 to about 700 and the majority (approximately two-thirds) are longer than 100 residues. The evolutionists used the extremely short value of 50 to try to improve their chances, but that is unrealistic.

The 27 orders of magnitude estimate, as miraculous as it is, is a ridiculously low-ball figure. The problem is so complicated we don’t have a good understanding of what the right number is, but a conservative estimate is 10^100 (100 orders of magnitude). For a typical protein of 250 amino acids, its gene has about 10^450 different possible sequences and the protein has about 10^325 different possible sequences. Thus this 10^100 estimate is an incredibly tiny fraction of the theoretical total.

What the right figure is no one knows, but the evidence we do have is clear. Protein evolution is profoundly unlikely. So why don’t evolutionists simply acknowledge this conclusion? Why don’t evolutionists go by the science? The answer, of course, is that this never was about the science in the first place. Religion drives science, and it matters.

Response to Comments: Astonishing But Typical p53 Comment Illustrates Evolutionary Thinking

I described here how the Human Genome project and high throughput technologies have revealed levels of complexity evolutionists hadn’t even dreamed of, revealing yet another monumental failure of evolutionary theory. One example of the discovery of new levels of complexity is the “guardian of the genome,” protein p53 which binds to thousands of DNA sites to control transcription, processes RNA, binds to proteins to modify activity, and undergoes alternative splicing to take on nine different forms:

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.

The p53 protein is encoded by about 1200 nucleotides in the TP53 gene which spans about 20,000 nucleotides. The 1200 nucleotides are divided amongst several exons (coding regions) which are separated by introns (non coding regions). To create p53 the cell transcribes the TP53 gene, edits the transcript, and translates the edited transcript into the corresponding sequence of about 400 amino acid according to the genetic code.

Evolutionists do not know how the highly skilled p53 protein evolved. How did one protein gain all those different functions? Evolutionists do not know. In fact they don’t know how proteins, in general, could have first evolved. Evolutionists also don’t know how genes, in general, evolved. Nor do they know how introns evolved. Nor do they know how the fantastic process of protein synthesis (gene transcription, transcript editing and translation) evolved. They don’t know how the DNA code evolved.

p53 is just one example of biology’s complexity that defies evolution. And yet this is how evolutionists typically respond:

Well, one could predict that if TP53 is involved in so many systems / pathways that are fundamental to a host of cellular processes including (but probably not limited to) cell cycle regulation, apoptosis and senesence, then it had to have originated around the time that the simplest forms of multi-cellular life emerged and therefore would be present in the simplest of life forms as well as the most complex. One could also predict that the separate genetic changes that may have affected this gene as different lineages diversified would allow scientists to generate some sort of phylogeny maybe? Perhaps, TP53 may even be part of a larger 'super-family' of genes that have homologs and orthologs throughout multi-cellular life forms that also, through genetic analyses, appear to form some sort of hierarchy... If only scientists could find such a thing huh.

Oh yeah, the p53/p63/p73 superfamily. Highly conserved genes found all the way up from C.elegans to H.sapiens.

http://cshperspectives.cshlp.org/content/2/7/a001131.full

I'd post more links but don't see the point. The info is out there for those who wish to see it. No amount of linking to primary data or peer-reviewed journal articles will help those that don't want to.

CH, p53 is not a good example if you want to poke a stick at the ToE.

In other words, if TP53 has so many fundamental functions then it must have originated early in evolutionary history. And indeed it is found everywhere from worms to humans. And if TP53 has been evolving all this time then it should roughly fit the expected evolutionary pattern. And it does. And finally, such a widespread and important gene should be part of a super family of genes. And indeed it is. So the science is obvious, isn’t it? We can acknowledge the data, or willfully ignore the obvious.

It is frightening how intelligent, knowledgeable, well-educated people can be so self assured about bad science. In fact these three predictions mentioned by the evolutionist are phony. If genes did not appear in super families evolution would be perfectly happy. Likewise, if genes fell into unexpected, contradictory patterns it would pose no problem. And if TP53 was not ubiquitous evolution would be unharmed.

How do I know this? Because it happens all the time. These predictions are more like Lakatos’ auxiliary hypotheses. Convenient explanations of the data that are gratuitous and may be forfeited. They are the protective belt that shield the theoretical core. Serviceable as “proofs” when correct, the stuff of good solid scientific research when incorrect.

This response above is typical. These soft “predictions” are touted as no-brainer, compelling proof-texts of evolution. But in fact these “predictions” are repeatedly falsified.

And even if they were true the reasoning amounts to the fallacy of affirming the consequent. Geocentrism isn’t true because the sun traveled across the sky today.

What is perhaps most astonishing, however, is the steadfast faith of evolutionists in the face of utter failure. Forget about evolution’s soft “predictions” that are consistently wrong, or the evolutionist’s faulty logic. Those breakdowns are minor compared to evolution’s inability to provide anything beyond sheer speculation on just how life is supposed to have arisen by itself.

As stated above, the Human Genome project and high throughput technologies revealed levels of complexity evolutionists hadn’t even dreamed of. Not that this was new news—even in Darwin’s day it was clear biology was fantastically complex. Darwin provided no plausible rationale for its evolution, and nothing has changed since 1859.

Evolution is an utterly ridiculous, religiously-motivated notion that has no scientific standing. This is not hyperbole but rather a simple description of the facts. Religious proofs underwrite the theory in spite of the obvious scientific evidence. Evolution is not a minor error. It is not a theory that merely needs some tweaks and adjustments. It is an absurdity that is obvious to anyone with common sense. Religion drives science and it matters.

Response to Comments: Detecting Miracles and Digging Holes

Evolutionists say they cannot reckon with miracles. They don’t know how to determine if naturalistic explanations don’t work. Therefore science must be limited to naturalism and, indeed, anything else is a science stopper according to evolutionists.

But the fact that evolutionary science can only reckon with naturalistic explanations does not mean that only those explanations are true. This would be like an automobile mechanic claiming that jet aircraft cannot be real because, after all, he does not possess the knowledge or tools to work on them. Evolutionists say they lack the tools to test and evaluate theories that are not strictly naturalistic, but this does not mean such theories are necessarily false.

The irony here is that evolutionists make naturalism unscientific according to their own criterion of testability. This is because naturalistic explanations are the only explanations that are allowed. Imagine if the species were designed. What if the DNA code, the bat’s sonar system and the many other biological wonders were created by a miracle. If this were true, it would not be allowed within evolutionary science. Evolutionists would forever be trying to figure out how such marvels evolved. And they would continue to insist that evolution is a fact.

Of course evolutionists are not fooling anyone but themselves. When you hear an evolutionist claim that evolution is a fact you know there is an commitment to naturalism underwriting the claim.

Digging holes

But it doesn’t help to point out these problems to evolutionists, as I did here and here. They just dig themselves in deeper and deeper. One evolutionist in the know made this comment:

Why don’t you just explain, in simple language, why scientists should adopt your view (which is to insert miracles wherever you don’t understand something),

In simple language, that is not my view. Evolutionists make metaphysical arguments for why evolution is a fact, and when you point out their logical fallacies and scientific errors they blame you for introducing the metaphysics. It seems the evolutionist always blames you for what they do.

In fact I discussed two legitimate ways evolutionists can do science without sacrificing their commitment to naturalism. But as usual, the evolutionist rejects them for they strip away his metaphysics. It’s no fun following the rules if you can’t have your way. The evolutionist continues:

Oh, and please give us some method for including/excluding miracles in science. We're still waiting.

As I’ve already explained, it is not necessary to include/exclude miracles (using Rene Descartes approach, for example). The evolutionist continues:

Without that all you are giving us is meaningless complaining.

Meaningless complaining? Evolutionists violate scientific logic, you point it out, and its dismissed as meaningless complaining. As I pointed out here, the evolutionary claims are not scientific. Evolutionists can modify their approach and join science, or just blame the messenger and continue with their metaphysics.

Surprise, Human Genome Didn’t Solve All the Mysteries: Life is Complicated and Evolution Fails Yet Again

Here is a Nature News Feature that speaks volumes about the state of evolutionary theory. It explains how the Human Genome project and high throughput technologies have revealed levels of complexity evolutionists hadn’t even dreamed of. It is yet another monumental failure of evolutionary theory, even though we all know evolution is a fact.

Not that long ago, biology was considered by many to be a simple science, a pursuit of expedition, observation and experimentation. At the dawn of the twentieth century, while Albert Einstein and Max Planck were writing mathematical equations that distilled the fundamental physics of the Universe, a biologist was winning the Nobel prize for describing how to make dogs drool on command.

And yet life scientists such as Joseph LeConte were absolutely certain evolution was true. They did not have the foggiest notion of how the biological world could have arisen on its own. In fact they didn’t understand much about the biological world period. But that never got in the way of their certainty.

The molecular revolution that dawned with the discovery of the structure of DNA in 1953 changed all that, making biology more quantitative and respectable, and promising to unravel the mysteries behind everything from evolution to disease origins. The human genome sequence, drafted ten years ago, promised to go even further, helping scientists trace ancestry, decipher the marks of evolution and find the molecular underpinnings of disease, guiding the way to more accurate diagnosis and targeted, personalized treatments. The genome promised to lay bare the blueprint of human biology.

Few predicted, for example, that sequencing the genome would undermine the primacy of genes by unveiling whole new classes of elements — sequences that make RNA or have a regulatory role without coding for proteins. 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.

Translation: Evolution’s simplistic, gene-centric, just-add-water view of biology led researchers to believe that sequencing the entire genome would lead to great breakthroughs. That naïve view became yet another failed evolutionary expectation.

Instead, as sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude. Delving into it has been like zooming into a Mandelbrot set — a space that is determined by a simple equation, but that reveals ever more intricate patterns as one peers closer at its boundary.

With the ability to access or assay almost any bit of information, biologists are now struggling with a very big question: can one ever truly know an organism — or even a cell, an organelle or a molecular pathway — down to the finest level of detail?

I once debated an evolutionist who said the purpose of science is to explain, and that evolution explains biology. False. As usual it is the exact opposite. Evolution does not explain biology. Evolution is constantly surprised by scientific findings.

"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."

Isn’t evolution amazing?

"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."

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.

In the past few years the story of regulation has become profoundly more complex than evolutionists ever imagined. Needless to say, there is no credible, scientific, explanation for how it all evolved.

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.

Indeed. It is also “incredibly naïve” to insist we know how such complexity arose.

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 reported3 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.

Of course beyond just-so stories, evolutionists have no idea how such complexity evolved. And yet p53 is just one example of biology’s complexity that defies evolution.

And reading further it is good to see a point of agreement:

The p53 story is just one example of how biologists' understanding has been reshaped, thanks to genomic-era technologies. Knowing the sequence of p53 allows computational biologists to search the genome for sequences where the protein might bind, or to predict positions where other proteins or chemical modifications might attach to the protein. That has expanded the universe of known protein interactions — and has dismantled old ideas about signalling 'pathways', in which proteins such as p53 would trigger a defined set of downstream consequences.

"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."

Indeed, those networks of information are “infinitely more complex” than expectations. That is hardly surprising given that those expectations came from evolutionary theory. What the data are revealing is nothing like what evolution expected.

But even with the deluge of data being provided by high-throughput technologies and the power of super computers will not easily solve biology’s infinite complexity:

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.

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."

A certain amount of naivety? But if all of biology arose from those random mutations and the like, shouldn’t biology be easy to understand?

Some, such as Hiroaki Kitano, a systems biologist at the Systems Biology Institute in Tokyo, point out that systems seem to grow more complex only because we continue to learn about them. "Biology is a defined system," he says, "and in time, we will have a fairly good understanding of what the system is about."

So biology’s complexity is just an illusion of too much knowledge. Once we figure all this out we’ll see how simple it actually is. Sounds like another prediction of evolution. Will it follow the trend of its failed predecessors?

Mina Bissell, a cancer researcher at the Lawrence Berkeley National Laboratory in California, says that during the Human Genome Project, she was driven to despair by predictions that all the mysteries would be solved. "Famous people would get up and say, 'We will understand everything after this'," she says. "Biology is complex, and that is part of its beauty." She need not worry, however; the beautiful patterns of biology's Mandelbrot-like intricacy show few signs of resolving.

Yet another failed prediction.

The notion that all of this evolved into existence is outrageous. It violates both simple common sense and detailed analysis, and makes mockery of science. When will taxpayers stop funding this religious drivel?

Of Gaps, Fine-Tuning and Newton’s Solar System

New research is providing a fascinating new perspective on fine-tuning and a three hundred year old debate. First for the context. When Isaac Newton figured out how the solar system worked he also detected a stability problem. Could the smooth-running machine go unstable, with planets smashing into each other? This is what the math indicated. But on the other hand, we’re still here. How could that be?

According to the Whig historians, Newton, a theist, solved the problem by invoking a divine finger. God must occasionally tweak the controls to keep things from getting out of control. It explained why the solar system hasn’t come to ruin, and it provided a role for divine providence which, otherwise, might not be needed for the cosmic machine that ran on its own.

About a century later, Whig history tells us, the French mathematician and scientist Pierre Laplace solved the stability problem when he figured out that Newton’s bothersome instabilities would iron themselves out over the long run. The solar system was inherently stable after all, with no need of divine adjustment, thank you.

Newton’s sin was to use god to plug a gap in our knowledge. What a terrible idea. First, using god to plug gaps is a science-stopper. Why investigate further if god fixes the tough problems? And second, it damages our faith when science eventually solves the problem and the divine role is further diminished. The key to avoiding this problem is to sequester religious thinking to its proper role. Science and religion must be separated lest both be damaged.

That’s the Whig history. Now for what actually happened. Instead of Newton being wrong and Laplace being right it was, as usual, the exact opposite. Newton was right and Laplace was wrong, though the problem is far more complex than either man understood.

And Newton was not the doctrinaire and Laplace was not the savior as the Whigs describe. Again, the truth would be closer to the exact opposite. Newton was more circumspect than is told, and Laplace didn’t actually solve the problem. True, he thought he had solved the problem, but his claim may indicate more about evolutionary thinking than anything to do with science.

And Newton’s allowing for divine creation and providence never shut down scientific inquiry. If that were the case he never would have written the greatest scientific treatise in history.

After Newton, the brightest minds were all over the problem of solar system stability (though it is a difficult problem and would take many years to even get the wrong answer). And no one’s faith was shattered when Laplace produced his incredibly complicated calculus solution because they were banking on some Newtonian interventionism.

But what did raise tempers was the very thought of God not only creating a system in need of repair, but then stooping so low as to adjust the controls of the errant machine. The early evolutionary thinker and Newton rival, Gottfried Leibniz found the idea more than disgraceful. The Lutheran intellectual accused Newton of disrespect for God in proposing the idea the God was not sufficiently skilled to create a self-sufficient clockwork universe.

The problem with Newton’s notion of divine providence was not that it is a science stopper (if anything such thinking spurs on scientific curiosity) or a faith killer when solutions are found. The problem is that it violates our deeply held gnosticism, which is at the foundation of evolutionary thought.

Darwin and later evolutionists have echoed Leibniz’ religious sentiment time and again. Everyone knew what the “right answer” was, and this was the cultural-religious context in which Laplace worked.

Indeed, Laplace’s “proof” for his Nebular Hypothesis of how the solar system evolved came right out of this context and was, not surprisingly, metaphysical to the core. You can read more about that here.

Today the question of the solar system’s stability remains a difficult problem. It does appear, however, that its stability is a consequence of some rather fine-tuning. Fascinating new research seems to add to this story. The new results indicate that the solar system could become unstable if diminutive Mercury, the inner most planet, enters into a dance with Jupiter, the fifth planet from the Sun and the largest of all. The resulting upheaval could leave several planets in rubble, including our own.

Using Newton’s model of gravity, the chances of such a catastrophe were estimated to be greater than 50/50 over the next 5 billion years. But interestingly, accounting for Albert Einstein’s minor adjustments (according to his theory of relativity), reduces the chances to just 1%.

Like so much of evolutionary theory, this is an intriguing story because not only is the science interesting, but it is part of a larger confluence involving history, philosophy and theology.

600 Genes Involved in Fundamental Cell Division

The regulation of cellular processes occurs at many levels. Gene expression, where the DNA is transcribed into an RNA molecule, is exquisitely controlled but so are the many downstream actions as well. For instance, the new RNA molecule can be inactivated by an incredible process referred to as RNA interference. This sophisticated process targets specific genes, and as usual nature’s own tools provide researchers with excellent means to investigate and harness biology. For instance, researchers have used RNA interference to turn off one gene at a time in the human cell to determine its function.

One of their findings is that about 600 genes are involved in the fundamental process of cell division. As one researcher put it, without this type of cell division “nothing happens in life, really.”

It is not surprising that hundreds of genes are involved given how complex is cell division. You can read more about it here, here, here and here. It is also not surprising that evolutionists attempts to explain how it evolved are nothing more than embarrassing stories. You can read more about that here. The hundreds of genes are involved in an absolutely fundamental biological process is yet another example of evolution’s failure to explain biology.

Response to Comments: The Problem With Miracles

Imagine if a police detective was told his theory had to be strictly natural. The evidence at the crime scene was obvious, but the boss wants no criminals indicted. The cause of the crime must be limited to the wind, rain, earthquakes, polar shifts, whatever. Absurd you say? Welcome to evolution.

Evolutionists say we must be limited to strictly natural explanations, and they then turn around and says they’ve figured out how all of life arose—by mutations and the like. They’re not exactly sure how those mutations could possibly produce the brain and everything else, but they are sure that’s how it happened. After all, we must limit ourselves to strictly natural explanations. Those explanations may not work very well, but they are all we have insist the evolutionists.

Of course this makes no sense, but when you point this out, as I did here, evolutionists just become even more sure of themselves. Here is what one evolutionist in the know said:

Cornelius -- please tell us your method for detecting/testing/refuting miracles, or else scientists have no reason to listen to you.

His point is that in science we just can’t deal with miracles. We can’t detect them, test for them, refute them, and so forth. So no matter what the evidence, evolutionists will forever continue to restrict their answer to naturalism. Show them a code, a machine or a molecular repair kit, it won’t matter.

No matter how badly evolution fares—most of its fundamental predictions have turned out false—evolutionists will always continue to insist it is a fact. This is not science, it is dogma.

In fact, if the evolutionist’s concern is simply that science can’t deal with miracles, then fine. Don’t deal with them. You can limit science to those problems where science works well, as Francis Bacon advocated. Or you can drop the “fact” claim, as did Rene Descartes.

But of course this isn’t the concern at all. We all know what is really going on here. We all know, because evolutionists have written and talked about this ad nauseam. The problem is not that they cannot discern any miracles—the problem is that they do not want to discern any miracles.

From theology (e.g., Christian Wolff), to philosophy (e.g., David Hume), to astronomy (e.g., Gottfried Leibniz), to geology (e.g., Charles Lyell) to biology (e.g., Charles Darwin), evolutionary thinkers have filled libraries with why there shouldn’t be any miracles.

Let’s admit it, science is done by people, and people have biases. Evolutionists pretend they have discovered an important new finding—the world just happened to happen, they proclaim.

Balderdash, people have been saying that ever since there were people. And the idea is contradicted today by high-tech science just as much as it was eons ago by simpler science. The idea is beyond ridiculous—it isn’t even wrong.

In fact, when evolutionists are not busy making their bogus warnings about miracles and claims about facts, they are hard at work attempting to refute the non strictly naturalistic Intelligent Design idea. Evolutionists know perfectly well how to deal with miracles when they think it suits their needs.

Let’s drop the game-playing, silly maneuvering and ridiculous truth claims, and instead deal honestly with the data.

Flax: More Falsifications of Evolution and the Real Warfare Thesis

The headline says it all: “Environs Prompt Advantageous Gene Mutations as Plants Grow; Changes Passed to Progeny.” It could also have read: “Lamarck Was Correct, Evolution is False.” Of course this is not new news. For the umpteenth time we hear about the inheritance of acquired characteristics—the catch phrase most often associated with the pre Darwin naturalist Jean-Baptiste Lamarck—which evolutionists desperately opposed for so many years until it could no longer be suppressed so now they say it was their idea all along. Yes there is indeed a battle against science, it’s just not the one evolutionists want you to believe.

For years scientists have observed that organisms intelligently respond to environmental threats and challenges. The usual examples, such as altitude acclimatization, are biological adjustments not observed to be passed on to offspring. But there are also plenty of examples that are passed on to the next generation. It is yet another falsification of a fundamental tenet of evolutionary theory which, in this case, holds that biological change is random with respect to need and helpful changes persist only via natural selection.

The latest paper deals with flax plants which, when grown under stressful conditions, modify their genome. The genomic changes help the plant to thrive under the new conditions, and the changes are passed on to the progeny.

The flax plant’s genomic changes are not just a lucky strike—the same precise additions, in the same precise location, occur when the experiment is repeated. For the changes are “the result of a targeted, highly specific, complex insertion event.” Sounds just like evolution doesn’t it.

Remember evolution is that clever idea that everything happened for no particular reason. Biology, and everything else for that matter, is a fluke. All biological variation arose from random events such as mutations. Yes all biological variation. With evolution there are no intelligent biological variations—no design, no teleology, no final causes. Just random events. Somehow this world arose on its own. Everything around us just happened to happen. As one paper explained:

Mutation is the central player in the Darwinian theory of evolution – it is the ultimate source of heritable variation, providing the necessary raw material for natural selection. In general, mutation is assumed to create heritable variation that is random and undirected.

What would we do without evolutionists?

Targeted, highly specific, complex insertion events that directly and instantly respond to environmental shifts is not exactly what today’s Epicureans had in mind. But that is not all. For the flax plant’s thousands of new DNA nucleotides are just that, new. At the very least evolutionists needed the DNA additions merely to be rearrangements of existing segments. That would still leave much unexplained, but as it is biology does not even leave evolution with that consolation. The plant creates a new DNA segment, as needed. As one evolutionist admitted:

the evidence for some kind of massive programmed rearrangement upon environmental induction in flax is unequivocal. Inheritance of acquired changes has been an anathema to evolutionary biologists ever since Darwin’s time, but that is because claims of Larmarckian inheritance were never accompanied by plausible mechanisms. However, in the case of flax at least, we may not be far from meeting this requirement.

Plausible mechanisms? You’ve got to be kidding. It is always humorous to hear evolutionists insist on “plausible mechanisms.” Trust me, the lack of mechanism is not why evolutionists vehemently oppose Larmarckian inheritance. If they required plausible mechanisms then by definition they wouldn’t be evolutionists.

Swift and precise adaptation to environmental shifts, such as observed in flax, is not evolution. Instead of evolution’s long, slow arduous process of random mutations that eventually, somehow against all odds, happen to find a helpful change, what biology reveals is instantaneous adjustment. Like shifting gears when you encounter a hill, biology adjusts designs in real-time. You can read more examples of such epigenetic change here, here, here, here, here, here, here and here.

As is typical evolutionists have resisted the science. As one report explains, due to the controversy surrounding the flax plant adaptability findings, “many scientists are hesitant to accept them as true.” Hesitant to accept scientific findings?

According to a paper, “The role of the environment in generating adaptive mutations is still a contentious subject.” For as one evolutionist admitted, “The really heretical thing to say is that the environment could be pushing the epigenetic information in a direction that is beneficial … that raises the hackles.” Evolutionists are at war with science.

The real Warfare Thesis

Ironically, while evolutionists have constructed a Warfare Thesis (which historians have explained is contrived) in an attempt to enlist the history of religion and science, these evolutionists actively engage in their own religious war against science. Once again, evolution is, if anything, hypocritical.

Darwin’s religiously-motivated theory was scientifically unlikely when he first proposed it, and since then it has become even worse. Evolution has repeatedly been contradicted by science. This has left evolutionists battling science every step of the way. Scientific results cause controversy and “raise the hackles,” because they refute the evolutionist’s religious mandates. And so evolutionist’s make a mockery of science as they invert findings to support their ridiculous dogma. Religion drives science, and it matters.

What Evolutionists Don’t Understand About Methodological Naturalism

OK let’s try this again. One more time, this time with pictures. In their celebrated volume  Blueprints, evolutionists Maitland Edey and Donald Johanson argued that “What God did is a matter for faith and not for scientific inquiry. The two fields are separate. If our scientific inquiry should lead eventually to God … that will be the time to stop science.” Similarly for evolutionist Niles Eldredge, the key responsibility of science—to predict—becomes impossible when a capricious Creator is entertained:

But the Creator obviously could have fashioned each species in any way imaginable. There is no basis for us to make predictions about what we should find when we study animals and plants if we accept the basic creationist position. … the creator could have fashioned each organ system or physiological process (such as digestion) in whatever fashion the Creator pleased. [The Monkey Business, p. 39, Washington Square Press, 1982.]

Or again, evolutionist Paul Moody explains that:

Most modern biologists do not find this explanation [that God created the species] satisfying. For one thing, it is really not an explanation at all; it amounts to saying, “Things are this way because they are this way.” Furthermore, it removes the subject from scientific inquiry. One can do no more than speculate as to why the Creator chose to follow one pattern in creating diverse animals rather than to use differing patterns. [Introduction to Evolution, p. 26, Harper and Row, 1970.]

Likewise Tim Berra warns that we must not be led astray by the apparent design in biological systems, for it “is not the sudden brainstorm of a creator, but an expression of the operation of impersonal natural laws, of water seeking its level. An appeal to a supernatural explanation is unscientific and unnecessary—and certain to stifle intellectual curiosity and leave important questions unasked and unanswered.” In fact, “Creationism has no explanatory powers, no application for future investigation, no way to advance knowledge, no way to lead to new discoveries. As far as science is concerned, creationism is a sterile concept.” [Evolution and the Myth of Creationism, pp. 66, 142, Stanford University Press, 1990.]

In his undergraduate evolution text Mark Ridley informs the student that “Supernatural explanations for natural phenomena are scientifically useless,” [Evolution, p. 323, Blackwell, 1993] and commenting on the Dover legal decision Eugenie Scott of the National Center for Science Education explains that supernatural explanations:

would be truly a science stopper, because once we allow ourselves to say, “Gee, this problem is so hard; I can’t figure out how it works—God did it,” then we stop looking for a natural explanation; and if there is a natural explanation, we’re not going to find it if we stop looking.

Over and over evolutionists today agree that science must strictly be limited to naturalistic explanations. One finds this throughout the evolutionary literature and it is a consistent refrain in discussions and debates about evolution.

But this sentiment by no means arose with today’s evolutionists. In 1891 UC Berkeley professor Joseph LeConte argued strenuously for this philosophical mandate:

The origins of new phenomena are often obscure, even inexplicable, but we never think to doubt that they have a natural cause; for so to doubt is to doubt the validity of reason, and the rational constitution of Nature. So also, the origins of new organic forms may be obscure or even inexplicable, but we ought not on that account to doubt that they had a natural cause, and came by a natural process; for so to doubt is also to doubt the validity of reason, and the rational constitution of organic Nature.

Likewise Darwin argued that whether one “believes in the views given by Lamarck, by Geoffroy St. Hilaire, by the author of the ‘Vestiges,’ by Mr. Wallace or by myself, 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 open to him for further inquiry.”

Explanations needed to be naturalistic for scientific inquiry. And as usual the foundations for this evolutionary mandate long predate 1859. Miracles were increasingly eschewed by leading thinkers and a century before philosopher David Hume had made persuasive arguments against miracles. Much of Hume’s material came from theological debates earlier in the century. On the continent leading Lutherans had already discarded the supernatural.

Method, completeness and realism in pictures

So when an evolutionist today insists that science must be naturalistic he is standing on a deep foundation of ideas. But setting aside this history for a moment, what about this argument? Remember that these same evolutionists claim their idea is also a fact. Is there not something curious about these tandem claims? I was once in a debate where the evolutionists claimed that we know evolution is a fact, and that it also is necessary in order to do science. How did they know that? Let’s have a look.

First, imagine the set of all possible explanations, as represented by the blue area below:

Because the blue area contains all possible explanations, it includes false as well as true explanations, lousy as well as good explanations, aesthetic and clumsy ones, and natural and non natural ones. It is every possible explanation in one set.

Now consider the set of all solutions that are according to a particular method, such as naturalism, as illustrated in the orange area below. All explanations that are strictly naturalistic are in the yellow area, and all other explanations are outside the orange area. Because the blue area contains all possible explanations, the orange area is a subset—it is wholly within the blue area.

Next consider the set of all true explanations as represented by the green circle below. These true explanations provide realistic models of nature. Again, this set of explanations must be wholly within the blue area, but otherwise we don’t know just where this green circle is. It could be in the orange area, it could be outside the orange area, or it could overlap. We don’t know what the true solutions all are, which is why we do science.

I have drawn the green circle above as partly inside and partly outside the orange area merely to illustrate the possibilities. But we don’t know where it is, and therefore whenever we mandate, a priori, a method such as naturalism, we automatically exclude a set of explanations that might be true.

In the early days of modern science philosophers were keen to this issue. Francis Bacon, for instance, wanted science only to pursue true explanations. But Bacon also wanted science to restrict itself to naturalistic explanations. Bacon realized that the restriction to naturalism would exclude any realistic, true, explanations that were not strictly naturalistic.

Bacon said that such non naturalistic phenomena should not be pursued by science. So Bacon insisted on naturalism and realism, but forfeited completeness. Science would not investigate all things. The thick black line below illustrates how this position limits itself to explanations that are both realistic and naturalistic, while potentially forfeiting some true explanations (depending on where exactly the green circle really is).

Like Bacon, another early philosopher, Rene Descartes, also insisted on naturalism. But he didn’t like the idea of forfeiting completeness. Descartes wanted science to be able to investigate all phenomena. But what if some realistic, true, explanations fall outside of naturalism? So what.

Descartes solution was to forfeit realism. Science, according to Descartes, would occasionally produce untrue explanations that otherwise could very well be useful. This approach is illustrated by the thick line below that encompasses all the naturalistic explanations, but misses some of the true explanations. Science might produce useful fictions along the way. Descartes mandated method and completeness, but in doing so had to forfeit realism.

After Descartes several scientists did not like this idea of forfeiting realism, as Descartes did, or forfeiting completeness, as Bacon did. These empiricists were interested in true solutions for all phenomena. This approach is illustrated below with the thick line encompassing the true solutions. But in order to maintain such realism and completeness, this approach cannot guarantee what method would be necessary. They might require non naturalistic explanations, for instance. So this approach provides realism and completeness, but forfeits any guarantee of method, such as naturalism.

Bacon, Descartes and the empiricists represent three different approaches to doing science. All are logically consistent. And who knows, the different methods might yield different insights—let a thousand flowers bloom.

But of course all three approaches have a limitation. Like the Heisenberg Uncertainty Principle, you cannot have realism, completeness and method all in one. You cannot have your cake and eat it too.

This brings us back to the evolutionists. Unlike Bacon, Descartes and the empiricists, evolutionists do have their cake and eat it too. They claim evolution is a fact, they mandate naturalism, and their science knows no limits. They have realism, method, and completeness all together. How can this be?

The answer is simple. One cannot have realism, method, and completeness simultaneously without some extra, non scientific, knowledge. Evolution’s gnosis is, of course, that true solutions are, indeed, naturalistic. This is illustrated below by the thick line that encompasses all true explanations, but it is also wholly naturalistic. How so? The trick is that the green circle has been moved. It is completely within the orange area. Knowing the location of the green circle, even before doing the science, is evolution’s gnosis—their secret knowledge.

It is this secret knowledge the evolutionists possess that allows them to have their cake and eat it too, and this brings us back to the history of the idea. There is no great mystery here, for evolutionists have for centuries made strong theological arguments that the world must have arisen naturalistically. The true explanations are all naturalistic. Therefore it is little wonder that, while not knowing how the world could have evolved, evolutionists are sure it did evolve. Evolution, one way or another, is a fact.

It is here that many fail to appreciate evolution’s conundrum. They often criticize evolution’s method mandate. Have not evolutionists been wrong to insist on methodological naturalism? No, such a method is perfectly fine.

The problem with evolution is not its insistence on method, but on its underlying theology. By insisting on method and realism and completeness, evolutionists are literally not equipped to consider other legitimate possibilities. They have already made a metaphysical commitment, without knowing whether or not it is true. They have confined themselves to a box. For when problems are encountered there is no way to tell whether the correct naturalistic solution has simply not yet been found, or whether the phenomenon itself is non natural. Of course evolutionists must always opt for the former, no matter how absurd the science becomes.

So the problem with evolution is not that the naturalistic approach might occasionally be inadequate. The problem is that evolutionists would never know any better. The evolutionists truth claims, and the underlying theology, have immense consequences. Religion drives science, and it matters.

Sober: Religion Isn’t Science, Except When it Is

In his book Evidence and Evolution Elliott Sober chastised those silly creationists for deducing that god created the species. “If this simple formula were enough to explain the observations in question,” the evolutionary philosopher warned, “there would be no need for science. Not only would Darwin’s own theory be unnecessary; there would be no need for theories in any other area of science, either.” Darwin’s theory unnecessary? Unthinkable. The “god did it” hypothesis is strictly unscientific. In fact Sober applauds Darwin’s refutation of creationism in proving evolution. In a PNAS paper Sober writes:

One of the main objections to Darwin’s theory, both when the Origin was published and in the minds of many present-day Creationists, is the idea that species (or “fundamental kinds” of organism) are separated from each other by walls. No one doubted, then or now, that natural selection can cause small changes within existing species. The question was whether the process Darwin described can bring about large changes. Maybe a species can be pushed only so far. …

If we focus just on natural selection, it is hard to see why Darwin had the more compelling case. However, if we set natural selection aside and consider instead the idea of common ancestry, the picture changes. Darwin thought he had strong evidence for common ancestry. This is enough to show that insuperable species boundaries (and insuperable boundaries between “kinds”) are a myth; if different species have a common ancestor, the lineages involved faced no such walls in their evolution. And the case for common ancestry does not depend on natural selection at all. ...

Two of the facts mentioned earlier—that humans and monkeys have tailbones, and that human fetuses and fish have gill slits—are evidence for common ancestry precisely because tailbones and gill slits are useless in humans.

I know, tailbones are not useless and human embryos don’t have gill slits. Right now we’re ignoring evolution’s abuse of science and focusing on the theological argument. One fallacy at a time, please.

Now back to the argument. So why are (supposedly) useless or deleterious structures such strong evidence for common ancestry? Would not evolution have done away with such disasters? No, it was busy doing other things.

Nature’s malignant mechanisms prove common ancestry by virtue of refuting separate ancestry. If separate ancestry is false, then what’s left? Exactly, common ancestry is proved by the process of elimination.

And why is it, again, that these mistakes refute separate ancestry? Why that’s simple. As Sober explains, under separate ancestry it would mean that the mistake was made twice (or even multiple times), whereas under common ancestry it was only made once, a much more reasonable and probable conclusion.

Take that creationists. No creator would make a mistake twice. Like the Addam’s Family, nature’s monsters must all be related. There must be no fundamental kinds. The “god did it” hypothesis is not only unscientific, it is obviously wrong. We know because god didn’t do it. That’s just the Stuff of Good Solid Scientific Research.

Glycolysis and the Citric Acid Cycle: The Control of Proteins and Pathways

Automobiles have incredible engines, cooling systems, drive trains, and so forth, but all of this must be controlled. The accelerator, gears and brakes are essential in automobile design. This is even more true in biology where regulation and control at all levels is crucial and incredibly complex, particularly since so much of the control is performed automatically. At the cellular level, the cell’s machines—the proteins—are controlled at several levels. As one leading textbook describes:

A living cell contains thousands of enzymes, many of which operate at the same time and in the same small volume of the cytosol. By their catalytic action, these enzymes generate a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. In this maze of pathways, there are many branch points where different enzymes compete for the same substrate. The system is so complex that elaborate controls are required to regulate when and how rapidly each reaction occurs.

Regulation occurs at many levels. At one level, the cell controls how many molecules of each enzyme it makes by regulating the expression of the gene that encodes that enzyme. The cell also controls enzymatic activities by confining sets of enzymes to particular subcellular compartments, enclosed by distinct membranes. The rate of protein destruction by targeted proteolysis represents yet another important regulatory mechanism. But the most rapid and general process that adjusts reaction rates operates through a direct, reversible change in the activity of an enzyme in response to specific molecules that it encounters.

So the cell controls its proteins by controlling how many it creates and destroys, and by confining them to certain compartments. But most directly it controls them directly, as one controls an automobile with the accelerator and brake.

Glycolysis and the citric acid cycle

A great example of all this is the nearly universal glycolysis pathway and citric acid cycle which team up to process food intake. In the glycolysis pathway about a dozen protein enzymes break down the six-carbon sugar known as glucose into two three-carbon molecules. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme. If just one of the enzymes is not present or otherwise not functioning then the entire process doesn’t work.

In addition to breaking down glucose, glycolysis also produces energy-carrying molecules called ATP. These are in constant demand in the cell as they are used wherever energy is needed. Like most pathways, glycolysis is interconnected with other pathways within the cell. The molecular products of glycolysis are used elsewhere and so the rate at which the glycolysis pathway proceeds is important. Too fast and its products won’t be useful, too slow and other pathways have to slow down.

Glycolysis is regulated in a number of ways. The first enzyme in the glycolysis pathway is regulated by its own product. This enzyme alters glucose to form an intermediate product, but if the rest of the pathway is not keeping up then the intermediate product will build up, and this will cause the enzyme to shut down temporarily. The enzyme is designed to be controlled by the presence of its product.

Two other enzymes in the pathway have even more sophisticated regulation. They are sensitive to a number of different molecules which either increase or decrease the enzyme activity. For example, these enzymes are partly controlled by the energy level of the cell. This makes sense since glycolysis helps supply energy to the cell. A good indicator of the cell’s energy level is the relative concentrations of ATP and spent ATP. High levels of ATP indicate a strong energy supply. Hence the enzyme activity is inhibited (and therefore the glycolysis pathway is slowed) when ATP is abundant. But high levels of spent ATP counteract this effect.

How do these molecules control enzyme activity? The molecules are tiny compared to the big enzymes they control. Just as a small key is used to start up and turn off a big truck, so too these small molecules have big effects on their target enzyme. And just as the truck has an ignition lock that can be turned only by the right key, so too the enzyme has several docking sites that are just right for a particular small molecule, such as ATP.

Not only does ATP fit just right into its docking site, but it perturbs the enzyme structure in just the right way so as to diminish the enzyme activity. There is another docking site that only a spent ATP will fit into. And if this occurs then the enzyme structure is again perturbed just right so as to encourage activity and reverse the ATP docking effect.

Glycolysis and the rest of the cell

Glycolysis and the citric acid cycle do not merely create energy for the cell. Just as an oil refinery also produces a range of petroleum products, glycolysis and the citric acid cycle, in addition to producing energy, spin off a series of essential biochemical components needed by the cell. This figure illustrates how these pathways produce nucleotides, lipids, amino acids, cholesterol and other molecules.

In fact glycolysis and the citric acid cycle exist within a complex web of chemical pathways within the cell. These many pathways interaction with each other in many ways, as shown in this wire chart (glycolysis and the citric acid cycle are shown in red).

Sometimes a three dimensional view, that can be rotated, helps to understand the interactions between these many pathways.

This design is complex at many levels. At the molecular level, there is the precise control of the protein enzymes. At the pathway level, there is the interaction between the enzymes. And at the cellular level there is interactions between the different pathways. And all of this has nothing in common with evolution’s naïve, religiously-driven, dogma that biology must be one big fluke. As one evolutionist admitted (one of the textbook authors):

We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naive as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB—and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. … But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. […]

Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like the machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts. Within each protein assembly, intermolecular collisions are not only restricted to a small set of possibilities, but reaction C depends on reaction B, which in turn depends on reaction A—just as it would in a machine of our common experience. […]

We have also come to realize that protein assemblies can be enormously complex. … As the example of the spliceosome should make clear, the cartoons thus far used to depict protein machines vastly underestimate the sophistication of many of these remarkable devices. [Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell 92 (1998): 291-294.]

But the dogma remains. Evolutionists insist that evolution must be a fact and they use dozens of religious arguments to make their case. In the next moment they turn around and insist it is all about science. The result is pathetic science, such as the journal paper that tried to explain the citric acid cycle as “evolutionary opportunism.” Religion drives science, and it matters.

Response to Comments: Natural Selection Doesn’t Help, Gradualism is Out, and so is Evolution

When Charles Darwin presented his theory of evolution one of the main objections was that he had no credible explanation for how biology, with its many designs and intricacies, could have arisen on its own. Darwin’s main argument, for which he presented many powerful evidences, was that biology did not appear to be designed. From its different patterns to its inefficiencies, the design perspective seemed to be badly failing. But this leaves us with evolution in name only. What were the details? How did the world of biology arise on its own? Inefficient or not, biology nonetheless was not trivial. How could it have evolved?

A never ending dialectic?

In the ensuing century and a half evolutionary explanations did not improve very much. The problem in 1859, that evolution did not seem to be capable of producing the biological world, has only grown worse. In fact, while much has been learned since Darwin, the data inevitably are recruited to service the same old arguments.

For skeptics, the new findings simply reinforce biology’s incredible complexity. But for evolutionists, the new data, like the old data, is often irrational, disproving design and so mandating evolution

It’s Cleanthes versus Philo all over again. For every Paley touting complexity there is a Hume ridiculing the backwardness or inefficiency of the design. The design argument is a great challenge, but it is neutralized by the evil in the world. “I needed all my skeptical and metaphysical subtlety to elude your grasp,” admitted Philo, but “Here I triumph.”

Will this dialectic never end? Will all of this thesis versus anti thesis never lead to a synthesis? Like Sisyphus forever pushing the stone up the hill only to have it roll back down, are we doomed to a never ending cycle of complexity versus dysteleology? Cleanthes versus Philo? Paley versus Hume? Perhaps not.

New molecular evidence

One problem with evolution is that since it deals with low probability events taking place over eons of time in the distant past via a long list of candidate mechanisms, it is difficult to test. Darwin tried to put his theory up for a test, but it was nearly impossible. He wrote:

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.

Darwin may sound generous here, allowing that his theory would “absolutely break down,” but his requirement for such a failure was close to impossible. For how could one can show that an organ “could not possibly” have been formed in such a way?

It appeared that Darwin had constructed a theory sufficiently malleable to avoid falsification. This has been highlighted in recent years by the use of the multiverse to explain low probability events. If you have a near infinity of universes from which to draw you can explain just about anything. Astronomically unlikely events suddenly become probable.

But the story does not end here, in futility. In fact an entirely new type of evidence has arisen since Darwin’s day that is much more amenable to detailed, quantitative analysis which cannot be swept under the rug of deep time. It is a result of the twentieth century’s revolution in molecular biology, and it already has provided ample demonstrations of the sort Darwin discussed. It may not be too bold to think that an Hegelian synthesis is nigh.

One good example of a complex “organ” which could not possibly have been formed by numerous, successive, slight modifications is the typical protein. Short of a multiverse, evolution simply does not explain their origin. I have discussed this here, here, here and here. Here are the salient points:

1. DNA and protein sequences provide plenty of violations of evolution’s expected pattern. Importantly, these violations are not “in the noise.” Beyond vague speculation evolutionists cannot explain these as the vagaries of their random process.

2. Although proteins were once thought to be flexible in their design, and so perhaps not so difficult to evolve, we now understand protein design better. Their designs are not very flexible. They cannot tolerate many mutations, and this means evolving a gene from scratch is not feasible, as it was once thought.

3. Given this lack of flexibility, it is not surprising that attempts to evolve real proteins from scratch have failed. Literally millions of millions of attempts are required to stumble upon even the weakest and simplest of partial functions. But even this many evolutionary experiments does not provide natural selection with a stepping stone, for the partial, weak, function provides no useful fitness improvement. Evolutionists who tried to evolve a more realistic, useful protein (but even in that case it was only part of a protein) concluded it is not possible via gradual change. They appealed to non gradualistic mechanisms, such as homologous recombination.

So to summarize, in addition to proteins violating evolution’s expected pattern in important ways, proteins cannot be evolved via gradualistic mechanisms. Do you remember your biology teacher’s lecture on gradualism and how crucial it was to evolutionary theory? Well forget it. It is out. Gradualism doesn’t evolve proteins.

But that is precisely what Darwin set forth as a crucial test of evolution. Remember, “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.”

Well forget it. Gradualism is out, and with it Darwin’s falsification criterion has been met. Evolution has been falsified.

But when I explain these things evolutionists cry foul. One professor wrote:

Nonsense. You assume that evolution must search randomly through (half of) 10^100 states to find a specific protein. That is plain wrong. Evolution is not a random search. It is plainly misleading to say so.

When presented with their own claims evolutionists consistently reject them. Evolutionists are their own judge. Yes, evolution must indeed search randomly. There is no such thing as selection “pressure.” That is a euphemism evolutionists use to refer to scenarios where selection could potentially work. But the design change needed must arise without selection’s guidance. No hints allowed.

When critics are not around evolutionists are busy telling the world that evolution is unguided. There is no logic, no design, no teleology in evolution. It does not have a goal in mind as it meanders mindlessly.

Evolution must indeed “search randomly” before selection can work. This is the problem that was intuitively understood in 1859, and today the quantitative example of proteins illustrates why. The professor continues:

It has been shown experimentally [1] that fitness can be increased substantially by local moves alone. We have discussed that here. In that particular instance, a randomly scrambled system reached 52% of its original fitness through single substitutions. Nonlocal moves are required to move through the rugged landscape at the top, but evolutional variations do include nonlocal moves. Frame shifts and duplications to name a few.

[1] Y. Hayashi et al., "Experimental Rugged Fitness Landscape in Protein Sequence Space," PLoS ONE 1, e96 (2006); doi:10.1371/journal.pone.0000096.

Once again the evolutionary version of the evidence is riddled with misrepresentations. In this experiment, to which the professor refers, only a fraction of a protein machine was randomized and then mutations in the randomized segment were evaluated for their improvement to the overall machine performance. Not surprisingly some mutations helped. But the improvements were minor, not “substantial.” The “improved” machine was still far less functional than the native version. The difference in productivity in the experiments was enormous.

But to make the results appear more hopeful evolutionists divide the logarithms of the productiveness of the native and evolved machines. Imagine a salesman who sells only 100 cars a year while his co-worker sells 1000 cars. Would his boss buy his argument that the difference is really just 50%? In fact the difference is 900.

In fact even the evolutionists who did the research admitted that gradualistic evolution cannot do the job. They estimated that 10^70 [a one followed by 70 zeros] evolutionary experiments would be required to break the logjam, and even then the machine nonetheless would not be fully function.

And of course this was when only a fraction of the machine was randomized. The remainder of the machine was assumed to be fully evolved and assembled. And a functional biological environment was assumed to be in place in which the protein machine could be tested and evolved.

Even given all these advantages gradualistic evolution failed. 10^70 evolutionary experiments is completely unrealistic, so the evolutionists appealed to non gradualistic mechanisms, such as homologous recombination. But homologous recombination isn’t available. It comes after proteins, not before. And furthermore, even if some magical non gradualistic mechanism just happened conveniently to be available, it wouldn’t help anyway. All that does is start the experiment over again. Remember, evolution has no foresight.

Imagine a toddler trying to climb Mt. Everest. He walks a few hundred feet and realizes he will never make it to the top. His solution? Start over again. This is what the evolutionists are telling themselves.

As if sensing a problem, another professor came to the rescue. He wrote:

Probability calculations such as this depend on the model being proposed. Dr Hunter’s calculation is based on the arbitrary assumption that the entirety of protein sequence space must be randomly sampled to yield functional proteins.

No, I’m assuming no such thing. As I have explained several times, evolution need not search the entire protein sequence space, not even close. But it nonetheless must explore an astronomically large space, well beyond its means.

The professor continues:

But the incorporation of some limiting factors into the model yields a different outcome:

“We suggest that the vastness of protein sequence space is actually completely explorable during the populating of the Earth by life by considering upper and lower limits for the number of organisms, genome size, mutation rate and the number of functionally distinct classes of amino acids. We conclude that rather than life having explored only an infinitesimally small part of sequence space in the last 4 Gyr, it is instead quite plausible for all of functional protein sequence space to have been explored and that furthermore, at the molecular level, there is no role for contingency.”

How much of protein sequence space has been explored by life on Earth?
David T.F Dryden, Andrew R Thomson and John H White

http://rsif.royalsocietypublishing.org/content/5/25/953.long

This paper the professor refers to is, unfortunately, another example of how evolution has damaged science. It presents several obviously flawed arguments that have no place in a scientific journal. But the reviewers of the paper are evolutionists and approved of the pseudo science.

The paper attempts to make two general points. First that evolution can succeed with a much smaller protein sequence space and second, that evolution can easily search the entire protein sequence space. Both conclusions are scientifically ridiculous and are inconsistent with what we do understand about proteins.

But why should that matter, for the paper is written from an evolutionary perspective. In other words, evolution is assumed to be true, and so proteins must have evolved somehow. Let’s have a look at the arguments.

Evolution can succeed with a much smaller protein sequence space

For the first claim, the evolutionists argue for a smaller protein sequence space because:

A. “the actual identity of most of the amino acids in a protein is irrelevant” and so we can assume there were only a few amino acids in the evolution of proteins, rather than today’s 20.

B. Only the surface residues of a protein are important.

C. Proteins need not be very long. Instead of hundreds of residues, evolution could have used about 50 for most proteins.

For Point A, the evolutionists use as support a series of simplistic studies that replaced the actual protein three-dimensional structure and amino acid chemistries with cartoon, two-dimensional lattice versions.

The evolutionists next used the fact that a type of protein can be found in different species with very different amino acid sequences. So doesn’t that mean the amino acid identities don’t matter very much? No, this is yet more evolutionary blowback. Evolutionists conclude this because they believe the proteins all evolved from a common ancestor. But science tells us that proteins, generally, do not tolerate amino acid substitutions very well.

As I have explained before, the amino acid sequence is not merely “along for the ride.” Because the evolutionists believe the proteins evolved, they mistakenly confuse sequence variation (which is observed) with sequence irrelevance (which is not generally observed).

Likewise Point B is at odds with science, and again is an unwarranted extrapolation on a simplistic lattice study.

For Point C, the evolutionists note that many proteins are modular and consist of self-contained domains “of as few as approximately 50 amino acids.” But the vast majority of protein domains are far longer than 50 residues. Single domain proteins, and domains in multiple-domain proteins are typically in the hundreds of residues.

While it is true that one can envision a smaller amino acid alphabet, and that shorter proteins can sometimes work, the evolutionists stretch the science far beyond its reasonable extrapolation point.

Evolution can easily search the entire protein sequence space

To defend their second claim, that evolution can easily search the entire protein sequence space, the evolutionists present upper and lower bound estimates of the number of different sequences evolution can explore.

Their upper bound estimate of 10^43 (a one followed by 43 zeros) is ridiculous. It assumes a four billion year time frame with 10^30 bacteria constantly testing out new proteins. First, even for an upper bound estimate their time frame is about two to three orders of magnitude too large. And furthermore, from where did these bacteria come? Bacteria need thousands of, yes, proteins. You can’t use bacteria to explain how proteins first evolved when the bacteria themselves require an army of proteins.

The lower bound of 10^21 is hardly any more realistic. The evolutionists continue to use the four billion year time frame. And they also continue to rely on the pre existence of an earth filled with a billion species of bacteria (with their many thousands of pre existing proteins).

So with these two claims in hand, the evolutionists conclude that the evolution of new proteins is no big deal. “We hope,” they explain, “that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention.”

This shifting of attention to “divine intervention” does not remedy their several scientific errors. The scientific fact is that the numbers are big. This isn’t a “game.”

For instance, consider an example protein of 300 residues (many proteins are much longer than this). With 20 different amino acids to choose from, there are a total of 10^390 different amino acid sequences possible. Now let’s simplify and assume only four different amino acids are needed. This reduces the problem to 10^180 different sequences.

Next let’s assume that only 50% of the residues are important. At the other 50%, any amino acid will do. That is, fully half of the amino acid sequence is inconsequential. These are extremely aggressive and unrealistic assumptions, yet nonetheless we are left with a total of 10^90 sequences. 90 may not appear to be a big number, but a one followed by 90 zeros is. It is completely impractical for evolution.

And if you don’t agree with my example, then we have the evolutionary experiments, described above, which concluded that 10^70 tries would be required. And even that was only for a fraction of the protein machine, and it assumed a pre existing biological world with its many proteins already in place.

So let’s take the evolutionist’s own numbers at face value, giving them every advantage. The number of experiments required is 10^70 and the number of experiment possible is 10^43. Even here, giving the evolutionists every advantage, evolution falls short by 27 orders of magnitude.

The theory, even by the evolutionist’s own reckoning, is unworkable. Gradualistic evolution—the test that Darwin himself set forth—or non gradualistic evolution, it does not matter. Evolution fails by a degree that is incomparable in science. Scientific theories often go wrong, but not by 27 orders of magnitude. And that is conservative.

The ghost of Hume

But it all comes back to the Humean rebuttal. Those big numbers are impressive, but “Here I triumph.” Evolutionists will never adhere to the science, because this never was about science in the first place. From the Epicureans to the evolutionists, it is about the failure of design. We must not have divine intervention for this gritty world. As Lucretius put it:

That in no wise the nature of all things
For us was fashioned by a power divine-
So great the faults it stands encumbered with.

Religion drives science, and it matters.