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.

New Cambrian Arthropod Vision System: No More Shudders

Years ago physicist Riccardo Levi-Setti became fascinated with trilobites. He wrote a book about them and at one point called their 500 million year old eyes “an all-time feat of function optimization.” They were, as evolutionists admitted, “an impressive feat of early evolution.” But now a new finding shows evolution to be even more impressive.

Charles Darwin considered the eye to be an “organ of extreme perfection.” Even after writing Origins he confessed it gave him a cold shudder. He needed to focus on his theory’s fine gradations to give himself comfort. But one hundred and thirty four years later, in 1994, evolutionists laid the problem to rest. The evolution of the eye was finally understood. It turned out such evolution was no big deal after all. In fact the eye could rather easily evolve.

The only catch to the conclusion was that it was made by evolutionists. Remember that evolutionists insist evolution must be a fact for religious reasons. As such their objectivity is sometimes wanting, as in this case. With evolution taken as a fact, whether or not vision systems evolved was no longer in question—they did. The only question was how they have evolved. The 1994 paper explained that although Darwin “anticipated that the eye would become a favorite target for criticism,” the problem “has now almost become a historical curiosity” and “the question is now one of process rate rather than one of principle.” The evolutionists estimated this rate by first assuming that the eye indeed evolved. They wrote:

The evolution of complex structures, however, involves modifications of a large number of separate quantitative characters, and in addition there may be discrete innovations and an unknown number of hidden but necessary phenotypic changes. These complications seem effectively to prevent evolution rate estimates for entire organs and other complex structures. An eye is unique in this respect because the structures necessary for image formation, although there may be several, are all typically quantitative in their nature, and can be treated as local modifications of pre-existing tissues. Taking a patch of pigmented light-sensitive epithelium as the starting point, we avoid the more inaccessible problem of photoreceptor cell evolution. Thus, if the objective is limited to finding the number of generations required for the evolution of an eye’s optical geometry, then the problem becomes solvable.

The problem becomes solvable? The evolutionists skipped the entire evolution of cellular signal transduction and the vision cascade. That would be like saying you have showed how motorcycles evolved although you took the engine, drive train and wheels as your starting point.

The evolutionists then skipped all of the major problems that arise after you have a signal transduction system in place, such as the incredible post processing system and the creation of the machinery to construct the vision system. The problem they ended up solving is sometimes affectionately referred to as a “cartoon” version of the real world problem.

The research, if you can call it that, did not serve as evidence for evolution. Yet the paper became a favorite reference for evolutionists wanting to suppress scientific skepticism of evolution. Eye evolution, they insisted, was now known to be straightforward. Here, for instance, is how our tax dollars are used by PBS to promote this abuse of science:

Zoologist Dan-Erik Nilsson demonstrates how the complex human eye could have evolved through natural selection acting on small variations. Starting with a simple patch of light sensitive cells, Nilsson’s model “evolves” until a clear image is produced.

With such mythology now internalized in evolutionary lore, evolutionists will believe practically anything, including a new finding of even greater evolutionary wonders. The new paper reports on complex vision in early arthropods long predating most of the trilobites. But in order to properly “educate” the reader and prepare them for the findings, the paper begins with, yes, a reference to that 1994 Nilsson paper:

Despite the status of the eye as an “organ of extreme perfection,” theory suggests that complex eyes can evolve very rapidly. … Here we report exceptionally preserved fossil eyes from the Early Cambrian (~515 million years ago) Emu Bay Shale of South Australia, revealing that some of the earliest arthropods possessed highly advanced compound eyes, each with over 3,000 large ommatidial lenses and a specialized “bright zone.” … The eyes are more complex than those known from contemporaneous trilobites and are as advanced as those of many living forms. They provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event.

With the mythological framework properly in place, the findings could then safely be presented as confirmations of evolution. As the journal’s editor added:

Charles Darwin thought that the eye, which he called an “organ of extreme perfection,” was a serious challenge to evolutionary theory — but he was mistaken. Theory predicts that eyes can evolve with great speed, and now there is support for this prediction from the fossil record.

Support for this prediction? You’ve got to be kidding. A cartoon version of reality, taking the myth of evolution as true, is considered a “prediction” and amazing early complexity in the fossils then becomes a “support for this prediction”?

What the new fossils revealed is an early Cambrian, highly advanced vision system more elaborate than any so far discovered. Its compound eyes have more then 3,000 lenses optimally arranged in the densest and most efficient packing pattern. As the paper explains:

The extremely regular arrangement of lenses seen here exceeds even that in certain modern taxa, such as the horseshoe crab Limulus, in which up to one-third of lenses deviate from hexagonal packing.

All of this is presented to the reader as merely another demonstration of how fantastic designs just happen spontaneously to arise:

The new fossils reveal that some of the earliest arthropods had already acquired visual systems similar to those of living forms, underscoring the speed and magnitude of the evolutionary innovation that occurred during the Cambrian explosion.

Ho-hum, yet more evolutionary innovation. For evolutionists it is just another day in the office. As PZ Myers explains, we already knew that complex animals appear rapidly. After all, that is why they call it the “Cambrian explosion.” Evolutionists have written “whole books on the subject.”

Myers follows this circular reasoning with yet more question begging:

The sudden appearance of complexity is no surprise, either. We know that the fundamental mechanisms of eye function evolved long before the Cambrian, from the molecular evidence;

Of course there is no “molecular evidence” that gives us such knowledge. But if you assume evolution is true to begin with, as do evolutionists who analyze the molecular patterns, then Myers’ fictional, question begging, world makes sense.

Myers follows these circular arguments with a more subtle type of fallacy. He explains that these particular findings are no big deal because both this finding and the trilobite vision systems require cellular signal transduction, development machines and so forth:

It is also the case that the measure of complexity here is determined by a simple meristic trait, the number of ommatidia. This is not radical. The hard part in the evolution of the compound eye was the development of the signal transduction mechanism, followed by the developmental rules that governed the formation of a regular, repeating structure of the eye. The number of ommatidia is a reflection of the degree of commitment of tissues in the head to eye formation, and is a quantitative difference, not a qualitative one.

Setting aside the usual evolutionary speculation about how easily designs evolve, the problem here is that the cellular signal transduction, development machines and so forth are themselves problems for evolution. Indeed, even the simplest of light detection systems sport such incredible designs for which evolution has no explanation beyond vague speculation.

Next Myers is back to question-begging. In typical fashion he attempts to shore up the evolution position with the usual reference to the mythical 1994 Nilsson paper:

And finally, there’s nothing in the data from this paper that implies sudden origins; there can’t be. If it takes a few hundred thousand years for a complex eye to evolve from a simple light sensing organ, there is no way to determine that one sample of a set of fossils was the product of millions of years of evolution, or one day of magical creation.

Next is the fallacy of credulity. If you present an evolutionist with the scientific failures of his theory, he will accuse you of basing your skepticism on your own failure to imagine a solution. As Myers puts it:

It’s a logical error and a failure of the imagination to assume that these descriptions are of a population that spontaneously emerged nearly-instantaneously.

Failure of the imagination? Indeed, we just need to do more imagining, that’s the problem.

Finally Myers reiterates the flawed Darwinian argument that whatever abruptness you see in the fossil record is, after all, merely a consequence of all those gaps in the fossils:

Darwin himself explained in great detail how one should not expect fine-grained fossil series, due to the imperfection of the geological record.

When in doubt, doubt the data. Paleontologists agree that the fossil record reveals abrupt appearances, but when convenient evolutionists can always protect their theory with those gaps in the fossil record.

Evolutionary thinking is remarkable. I am reminded of John Earman’s remarks about Hume’s arguments. For it is astonishing how well evolution is treated, given how completely the confection collapses under a little probing. And yet evolutionists are supremely confident they are right.

Evolutionists such as Myers are very book smart, but the wisdom and common sense is lacking. The evolutionist’s confidence is exceeded only by the absurdity of his theory. Religion drives science and it matters.

Jonathan Dudley: It’s the Stuff of Good Solid Scientific Research

In The Big Chill Jeff Goldblum plays a writer for People Magazine who, not altogether seriously, laments his less than intellectual writing assignments. But when someone quizzically asks where, in fact, they come up with all those stories, Goldblum’s deadpan and incredulous rebuke is that “It’s the stuff of good solid investigative journalism.” I’m reminded of this every time an evolutionist explains, as did Jonathan Dudley this week in his Huffington Post blog, that evolution is the stuff of good solid scientific research. In fact evolution is mandated and justified by religious claims that go back centuries. Dudley demonstrates yet again this hilarious hypocrisy in evolutionary thought when he informs his readers that Christians must accept evolution because it is the result of careful scientific investigation. Don’t we understand that to reject evolution is to reject science? He then demonstrates what evolution is all about with an extended rant against creationism. If I only had a nickel for every time …

Composite Multilayered Fish Armor Provides Protection Design Ideas

In recent years engineers have found breakthrough design secrets in biology and a recent example is the protective armor of certain fish species. A recent study of Polypterus senegalus, of the Polypteridae family, provides a mechanical model for armor that might be useful in both body and vehicle protection.

P. senegalus has a protective armor coat of scales, but this armor is not simply a single material. The scales are interlocking, and constructed with four layers of nanocomposite materials. In all the armor coat is about 400 micrometers (a bit less than half a millimeter) thick. On the outside is a thin layer (about 8 micrometers) of the very strong and hard ganoine. This is followed by layers of the softer dentine and isopedine. These layers are each about 50 micrometers, and they are followed by a 300 micrometer layer of bone.

The objective of structural designs is often to meet the requirement while minimizing weight. In this case, the armor should provide protection against attacks, such as sharp teeth bites, without adding more weight than necessary to the fish. This unique multilayered composite design does just that.

The researchers modeled P. senegalus’ armor using the finite element method and calibrated the mechanical properties of the four layers to experimental observations (such as from atomic force microscopy). They could then use their model to make design conclusions.

Perhaps the main conclusion is that the unique four-layer approach works well. For instance, it provides a 20% weight reduction compared to two-layer models the researchers tested. One reason for this is that the different layers work together to absorb attacks:

In conclusion, here we report on the fascinating, complex and multiscale materials design principles of ancient fish armour in the context of its specific primary environmental threat (penetrating biting attacks) and mechanically protective function. One overarching mechanical design strategy is the juxtaposition of multiple distinct reinforcing layers, each of which has its own unique deformation and energy dissipation mechanisms. As the stiff ganoine transfers load through the ganoine–dentine junction, the underlying softer, more compliant dentine layer dissipates energy via plasticity (at high enough loads). The ganoine thickness was selected (1) to simultaneously access the advantageous mechanical properties of the ganoine (hardness, stiffness) and underlying dentine (energy dissipation), (2) to reduce weight while maintaining the required mechanical properties and (3) to promote the advantageous circumferential cracking mechanism (S22 > S11), rather than disadvantageous radial cracking.

But there is more to the design than the mere use of these four different materials together. For instance, the order is important:

The material layer sequence is also critical; for example, reversing the ganoine and dentine layers in a virtual microindentation leads to magnified interfacial tensile normal and shear stresses, promoting delamination

Also, the ganoine and dentine layers are not uniform, but have mechanical properties that very across the cross section. Furthermore, there are geometrically corrugated junctions between the layers, that provide transitions between the mechanical properties of the different layers. These junctions are a crucial part of the design:

The junctions between material layers are clearly ‘functionally graded’, that is, they possess a gradual spatial change in properties motivated by the performance requirements and are able to promote load transfer and stress redistribution, thereby suppressing plasticity, arresting cracks, improving adhesion and preventing delamination between dissimilar material layers. Last, the corrugated junction between the layers is expected to lead to spatially heterogeneous stresses and a higher net interfacial compression, also resisting delamination. Such multiscale materials principles may be incorporated into the design of improved engineered biomimetic structural materials.

There is, of course, no explanation from evolutionists for such designs. That is not surprising because random events don’t create exquisitely designed multi-layered nanocomposite structures. Nor do they create the manufacturing facilities required to construct such designs. Nor do they create the instructions required to create such facilities. Evolutionists are left only with empty rebuttals. Religion drives science, and it matters.

Response to Comments: Natural Selection Doesn’t Help

According to evolution the millions and millions of species in the world all arose from a long, long sequence of random events. It began with random events that somehow assembled the first living cell. And these random events continued to produce different kinds of cells, multicellular forms, plants, fish, amphibians, reptiles, mammals and so forth. From a lifeless warm little pond, cheetahs, redwood trees and humans were all created by a long series independent, random events (such as mutations) that just happened to occur for no particular reason. It sounds very much like the Epicureans of old. For as Lucretius explained, not by counsel did the primal germs:

'Stablish themselves, as by keen act of mind,
Each in its proper place; nor did they make,
Forsooth, a compact how each germ should move;

And from those primal germs came all life:

Thus then the new Earth first of all put forth
Grasses and shrubs, and afterward begat
The mortal generations, there upsprung-
Innumerable in modes innumerable-
After diverging fashions

[…]

How merited is that adopted name
Of earth- "The Mother!"- since from out the earth
Are all begotten.

[…]

Wherefore, again, again, how merited
Is that adopted name of Earth- The Mother!-
Since she herself begat the human race,

The human race just happened to arise. For Lucretius from Mother Earth and for evolutionists from mutations. Either way it is a euphemism for blind chance. And as with today’s evolutionary theory, Lucretius’ certainty was not from science, but from religion. Is it not obvious that this faulty and mostly useless world must have arisen on its own:

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.
First, mark all regions which are overarched
By the prodigious reaches of the sky:
One yawning part thereof the mountain-chains
And forests of the beasts do have and hold;
And cliffs, and desert fens, and wastes of sea
(Which sunder afar the beaches of the lands)
Possess it merely; and, again, thereof
Well-nigh two-thirds intolerable heat
And a perpetual fall of frost doth rob
From mortal kind. And what is left to till,
Even that the force of Nature would o'errun
With brambles, did not human force oppose,-
Long wont for livelihood to groan and sweat
Over the two-pronged mattock and to cleave
The soil in twain by pressing on the plough.

The sentiment is from antiquity, but it is no different than today’s evolutionary thought. It is mythology built on metaphysics.

But evolutionists will complain, for we have left out natural selection. Does it not provide a guiding hand? Evolutionist Joe Felsenstein agrees that biology’s DNA sequences, for example, are unlikely. But so what? He writes:

I can show you how to—regularly and repeatably—get a sequence of events that is extremely improbable. Every time. Just take a coin and toss it 100 times. The resulting sequence of Heads and Tails has a probability of only 1 part in the 100th power of 2. Which is about 1 part in 10-to-the-30th. Wow, that is really improbable. Yet you can do it every time! I guess that shows that people who toss coins are making unreasonable assumptions ...

In other words, biology’s astronomically unlikely designs are not a problem because all designs are unlikely. Strange that all those evolutionary experiments can’t generate good proteins from scratch. Can’t we just throw together a sequence like evolution did?

The problem with this utterly foolish logic is that not all designs work. In fact, the vast majority don’t work. When I say “vast majority” I mean, for all practical purposes, all of them. For a typical protein you would need more than 10^100 (a one followed by one hundred zeros) evolutionary experiments to create it. And no, we don’t find there to be convenient pathways evolution could use to gradually build-up the protein. Natural selection doesn’t help. That’s the case with most designs, biological or otherwise. You don’t magically have gradual pathways consisting of a long, long sequence of ever so slightly different intermediates, all leading to a fantastic final design.

Evolution is a modern-day myth. No better than Zeus up in the sky, throwing down lightning bolts. But today we should know better. At least Lucretius and the Epicureans can claim scientific ignorance. Today’s version of the myth, evolutionary theory, is a religiously-driven mockery of science. The religion is explicit in the evolutionary literature, as is the mockery of science. Religion drives science, and it matters.

Response to Comments: Flexibility of Explanation in Action

What if an astronomer told you that the retrograde motion of the planet Mars is confirmation of geocentrism? “What? That’s crazy!” would be the appropriate response. Retrograde motion is one of the reasons that geocentrism needed to be patched with those dozens and dozens of epicycles. Retrograde motion is hardly a confirmation of geocentrism. It is, rather, contradictory evidence that needed to be explained away. But once those epicycles were added, the geocentric model did indeed predict the retrograde motion. So for a desperate geocentrist apologist, the backward motion of Mars does indeed become a confirmed prediction. This is an abuse of science. If you need to patch your theory by multiplying entities, then you shouldn’t get credit for those patches. But this is exactly what evolutionists want.

In a recent post I explained some of the history behind evolutionary theories of the solar system. As with biological evolution, this cosmological evolution was declared to be a fact based on observed patterns, even though very little was understood about how the solar system could actually spontaneously arise.

The claim that the evolution of the solar system is a fact was metaphysically loaded and it hinged on the claim that there was a single mechanical cause. But as with biological evolution, this cosmological evolution is repeatedly contradicted by empirical science, and so a great variety of patches were required to save the theory. The specter of a single cause was lost a long time ago.

But those past failures are conveniently forgotten and, again as with biological evolution, today there is a tremendous flexibility of explanation for the origin of the solar system. In my post I listed several just-so stories used today to patch the theory. There are many which I did not mention and one set of patches deals with isotope heterogeneities. As a new paper explains, both (i) “exotic” material and (ii) complex isotope-selective chemistries have been used to explain the heterogeneities:

Thus, the discovery that high-temperature minerals in carbonaceous chondrite meteorites are enriched preferentially in 16O compared to 17O and 18O relative to the abundances in terrestrial samples was considered evidence for the presence of exotic material that escaped thorough mixing and thereby retained a memory of its distinct nucleosynthetic history. Later findings of the widespread nature of very large oxygen isotopic heterogeneities among meteoritic materials and the lack of correlation of these oxygen isotopic compositions with those of presolar components led to various proposals that the oxygen isotopic anomalies were instead generated by complex isotope-selective chemistry within a homogeneous nebula.

New findings from the Genesis spacecraft reveal even more “extreme” nitrogen isotope heterogeneities, as well as oxygen isotope heterogeneities, which I cited as yet more challenging observations for the current theory of solar system evolution. In response to this an evolutionist disagreed:

the ratio of the isotopes measured by Genesis was expected to be different from the average for the solar nebula. The effect was predicted by Clayton in a 2002 paper (Reference 6) and observed in other molecular clouds. The new data present no problem for the solar nebula model, they confirm it!

Sure the isotope heterogeneities were expected. Heterogeneities had already been observed. What the professor does not mention in his comment is that the referenced paper predicted oxygen isotope heterogeneities using a just-so story (isotope-selective self-shielding during ultraviolet photolysis of carbon monoxide), and that heterogeneities were already known to exist.

In other words, like the claim that retrograde motion confirms geocentrism, this claim that the observed oxygen isotope heterogeneities confirm the solar system evolution model is ridiculous. The solar system evolution model was highly augmented with a detailed patch designed to explain the heterogeneities (complex isotope-selective chemistries), and now new observations of oxygen isotope heterogeneities are claimed as a confirmation.

Sure this is a valid prediction, but hardly of the significance the professor claims. This is yet another example of how evolutionary thinking harms science by introducing fallacious reasoning used to protect evolution.

The Vision Cascade is Initiated Not by Isomerization but by Force Field Dynamics

As you read these words a frenzy of activity is taking place as the light entering your eye triggers a highly detailed sequence of actions, ultimately causing a signal to be sent to your brain. In fact, even a mere single photon can be detected in your vision system. It all starts with a photon interacting with a light-sensitive chromophore molecule known as retinal. The interaction alters the retinal molecule and this, in turn, influences the large, trans-membrane opsin protein to which the chromophore is attached. This is just the beginning of the cellular signal transduction cascade. In the next step the opsin causes the activation of hundreds of transducin molecules. These, in turn, cause the activation of cGMP phosphodiesterase (by removing its inhibitory subunit), an enzyme that degrades the cyclic nucleotide, cGMP.

A single photon can result in the activation of hundreds of transducins, leading to the degradation of hundreds of thousands of cGMP molecules. cGMP molecules serve to open non selective ion channels in the membrane, so reduction in cGMP concentration serves to close these channels. This means that millions of sodium ions per second are shut out of the cell, causing a voltage change across the membrane. This hyperpolarization of the cell membrane causes a reduction in the release of neurotransmitter, the chemical that interacts with the nearby nerve cell, in the synaptic region of the cell. This reduction in neurotransmitter release ultimately causes an action potential to arise in the nerve cell.

New research is now helping to explain the details of the first step in this Rube Goldberg machine. What happens when the photon interacts with the retinal molecule? And how does this influence the opsin protein? It had been thought that the key step was a change in the structural configuration of the chromophore. This photoisomerization is caused by the photon and was thought to be how the chromophore influences the opsin.

The new research, however, found that when isomerization is disabled the vision cascade continues to function normally. It seems that a key step, occurring before isomerization, is a shift in the electron distribution of the chromophore. This shift modifies the electric field surrounding the molecule, and this in turn influences several amino acids of the opsin protein, which in turn leads to the activation of the transducin molecules.

An argument from ignorance?

As is typical these new findings do not bode well for evolution. Think of it, evolution designing force fields. But evolutionists cry foul. “You are arguing,” they say, “that since you can’t imagine how evolution could have created such a design that evolution therefore is false. That is nothing more than an argument from ignorance.”

You will be told you don’t understand how science really works and that such findings don’t harm evolution at all. In fact, they open new avenues for understanding how evolution works. Far from a problem for evolution, they enlarge our understanding of what has long since been known to be a fact.

A big design space

Well is it fallacious to think such findings are problematic for evolution? A key issue is the design space. Imagine that a mutation occurs somewhere in a segment of DNA. And imagine that a particular residue within that DNA segment needs to be a certain base, say cytosine. There are a total of four possible bases (adenine, guanine, thymine and cytosine). So the design space for that residue has a total of four possible choices, and the needed design constitutes 25% (one in four) of the design space. It won’t require too many mutations to luckily obtain the needed cytosine. In this case evolution seems reasonable.

But real-world, biological designs require a great deal more than the specification of a single DNA residue. Proteins, for instance, require a great many DNA residues to be specified. Even a single, typical protein requires more than 10^100 (a one followed by one hundred zeros) evolutionary experiments to find. This is an astronomical problem that is well beyond evolution’s capabilities. See here, here, here and here for more details.

In other words, for a typical protein the design space is large and the number of selections, within that design space that work, is relatively small. Instead of a 25% chance of success as we saw in the above simple example, it is many many billions and billions of times less likely. Even optimistic estimates of how many evolutionary experiments are possible fall many orders of magnitude short of what is needed to evolve a protein. Evolutionary theory simply doesn’t work.

Does evolution shape force fields?

The new research presents a different problem for evolution. In addition to designing the opsin protein, evolution must now design the electric field surrounding the chromophore, and how it responds to photon interaction. And while it is busy with that task, it must also specify the correct amino acids at the correct locations within the opsin, that will be influenced by the chromophore’s dynamic electric field.

This massive design problem involves what is known as an n-body solution. That is, the various sub atomic particles in the opsin amino acids and the chromophore, including the chromophore’s flowing electrons which respond to the photon, all contribute to the environmental force fields.

Modeling these force fields and how molecules respond to them is a major problem in molecular dynamics studies. Both the modeling of the force fields, and the molecular dynamics is challenging and computationally intensive. For instance, each particle influences each of the other particles. And as a particle moves, all of its influences change. But other particles are moving as well, so the dynamics quickly become extremely complicated.

The previous model, which had evolution designing the chromophore and its photoisomerization, was complicated enough. Now evolution must also design force fields and their dynamics caused by electron flow within the chromophore. The design space just took another quantum leap.

An argument from ignorance or theory protectionism?

Needless to say evolutionists have only the usual hand-waving speculation to explain the evolution of such designs. The problem is not that skeptics cannot explain how evolution can create such designs, the problem is that evolutionists cannot explain it. Skepticism of evolution is not a consequence of ignorance, it is a consequence of the theory falling far short of its claims. The fact is evolutionary theory doesn’t work and evolutionary cover-ups are nothing more than theory protectionism. Religion drives science and it matters.