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.

Is the Current Solar System Evolution Theory Nearing the Next Flip?

The epistemological foundation of evolution is interesting. Evolutionists know that evolution is a fact, but they do not know how evolution happened. In fact there is tremendous uncertainty about how the world could have spontaneously originated all by itself. This extreme epistemological difference between the fact and theory of evolution may seem contradictory but it isn’t. The fact of evolution is not contingent on how it happened. It merely is contingent on the end product. It is, as mathematicians say, path independent. The end product makes evolution a fact because the end product obviously would not have been intended by any intelligent agency otherwise capable of designing and creating the world. So Aristotle had it right with his disinterested and oblivious Prime Mover. Nature must have created itself. This makes for a striking dichotomy between evolutionary apologetics and evolutionary research. The former has no doubt evolution is a fact while the latter is full of doubt about how evolution occurred. In fact, evolutionary theories display an often humorous level of flexibility of explanation. Evolutionary explanation must be strictly natural, but beyond that anything goes, no matter how heroic, unlikely and cartoonish. And when the unlikeliness becomes too extreme even for the evolutionist, he simply calls upon the multiverse to improve the odds. If there is a near-infinity of universes, then anything can happen. An early example of this flexibility of explanation was in the theories of how the solar system evolved which to this day have continued to amass just-so stories. Now it appears the current theory of solar system evolution may be approaching another flip.

A century before Lamarck, Darwin and Wallace were imagining how biological evolution could have occurred, Bernoulli, Kant, Buffon and Laplace were imagining how the solar system could have evolved. In both cases the naturalists were certain evolution had occurred, though they had nothing but unfounded speculation about how it occurred. Bernoulli, Kant and Laplace had proven the solar system evolved with the usual silly evolutionary proofs.

A false dichotomy

Bernoulli’s explanation, that the sun’s atmosphere caused the planetary motions and alignments, was reminiscent of Descartes’ whirlpools. And while Bernoulli’s explanation was later discarded (as most evolutionary explanations eventually are), he introduced a powerful argument that became crucial in evolutionary thought and remains pervasive today.

Bernoulli argued that there are two possibilities: random design or a single mechanistic cause. Like ripples in the sand, patterns that we observe in nature are, according to evolutionists, necessarily a consequence of mechanism. It is yet another evolutionary argument that is difficult to explain because it is so silly. But that is the argument. In this false dichotomy, random design is evolution’s null hypothesis.

It was well known that the planetary orbits were aligned so as to form a striking pattern. Surely this could not have arisen by chance, argued the great mathematician. Bernoulli argued that either the planets fell into their orbits by chance or some mechanism caused their alignment. Bernoulli used a calculation to show the long odds of random design, thus proving beyond a shadow of a doubt that a mechanical cause did the job. He who would deny this, Bernoulli fallaciously concluded, “must reject all the truths, which we know by induction.”

Twenty years later Immanuel Kant elaborated Bernoulli’s argument. Why do planets revolve about the sun in the same direction? “It is clear,” explained the great philosopher, “that there is no reason why the celestial bodies must organize their orbits in one single direction.” If God had directly arranged their orbits then we would expect them to reveal deviations and differences:

Thus, God’s choice, not having the slightest motive for tying them to one single arrangement, would reveal itself with a greater freedom in all sorts of deviations and differences.

Theology was not discarded in the Enlightenment, as is often said, it was internalized. Laplace followed with his version of Bernoulli’s random design null hypothesis calculation, and cosmic evolution increasingly became accepted. The details were yet to be worked out, but it was fast becoming a fact.

Thus Laplace could on the one hand assure Napoleon of his evolutionary theory while, on the other hand, fail to explain new observations such as the anomalous orbits of Uranus’ moons, discovered by William Herschel. Here is how historian Stephen Brush describes it:

Laplace was familiar with Newton’s opinion that the regular motions of the planets proved their divine design. We know he was acquainted with Daniel Bernoulli’s prize essay of 1734 on the subject, since in an earlier paper he had cited Bernoulli’s method for calculating the probability that n bodies all move in the same one of two possible directions if their motions are selected by chance: 2^(–n+1). In that paper Laplace had applied the method to six planets and ten satellites, finding the probabilities to be 2^–15 = 1/32768. By 1796 he had made the coincidence even more unlikely by including the seventh planet, Uranus (discovered by William Herschel in 1781), as well as four more satellites, Saturn’s rings, and the rotations of five planets, the Sun, the Moon, and one of Saturn’s satellites (Iapetus). Thus of the 30 known motions in the Solar System, all are in the same direction. If these motions had been determined by chance, the probability that at least one of them would be different from the rest is extremely high (1–2^–29). [Nebulous Earth, Cambridge, 1996, p. 21]

It is astonishing that thinkers such as Bernoulli and Laplace promoted such metaphysical madness. Brush continues:

Laplace was aware when he first published his theory that Herschel had found the two satellites of Uranus to have orbits in a plane nearly perpendicular to the plane of the ecliptic. In 1798 Herschel announced that the satellites of Uranus have retrograde motion. While this amounted to only a slight revision of his earlier result—the orbit plane is still nearly perpendicular but is tilted in the other direction—it was still [Herschel explained] “a remarkable instance of the great variety that takes place among the movements of the heavenly bodies” since previously all known motions took place in the same direction.

A remarkable instance of the great variety? Even the evolutionary false dichotomy was breaking down. But no matter, the narrative had become too compelling. Laplace simply ignored the anomalies (as evolutionists routinely do today), while including four other satellites announced by Herschel which were never confirmed:

In later editions of the Exposition, Laplace simply ignored the fact that at least two of the Uranian satellites have retrograde orbital motion, even though he added to his total the four spurious ones announced in the same paper by Herschel. Perhaps he considered that an orbit that is nearly perpendicular to the ecliptic should not be counted as retrograde; but I agree with Jaki that his treatment of this case is peculiar. Laplace did express doubt about the existence of the four satellites reported in 1798, and unless they are counted as retrograde (which Herschel did not claim) their inclusion scarcely affects the statistical argument.

In fact Laplace’s treatment of this case is not at all peculiar. Confirmation bias is standard practice in evolutionary apologetics. And that’s after the false dichotomy.

Laplace referred to his theory as the “true system of the world.” Sound familiar? Laplace could assure Napoleon that the God Hypothesis was superfluous not because Laplace had solid scientific details backing up his case—he didn’t—but by virtue of this ridiculous, fallacious line of argument.

Flexibility of explanation

Herschel’s anomalous satellites, with orbits almost perpendicular to expectations, would by no means be the only problem for Laplace’s Nebular Hypothesis. Problems mounted and, as usual, the theory became more complicated.

In Laplace’s Nebular Hypothesis, planet formation is a natural consequence of star formation. In Buffon’s earlier comet theory, planet formation is a separate event and not a consequence of star formation. This fundamental difference defines two categories of theories for the origin of the solar system—the monistic and dualistic categories, respectively. Monistic theories hold that all the major components of the solar system formed together. Dualistic theories hold that stars form by one process and planets form by a different process.

Since Laplace the mounting problems with the Nebular Hypothesis caused a reevaluation and search for alternate explanations. A major problem was that the sun rotates too slowly. The vast majority of the angular momentum in the solar system resides in the planets, a fact that was difficult to reconcile with the Nebular Hypothesis.

And so the twentieth century witnessed a series of monistic and dualistic theories competing to explain the solar system’s origin. There was the dualistic theory of a close encounter with a nearby star proposed by Chamberlin and Moulton and later by Jeans and Jeffreys. But such a close encounter could not reproduce the high angular momentum we observe in the planetary orbits. Also, material ripped from the sun by the encounter would be too hot to condense and form planets.

Russell proposed a new monistic theory calling for a rise in density of the collapsing solar nebula. Also, the idea of magnetic braking was considered as a mechanism for depleting the sun’s angular momentum. This was followed by the dualistic theory of Alfvén and Schmidt, and then the monistic theory of Kuiper and Urey. Schmidt’s dualistic theory was later refined in the Safronov–Wetherill model and after this Cameron promoted the “supernova trigger” hypothesis.

Both monistic and dualistic theories have been repeatedly proposed throughout the twentieth century. In fact, as Brush observes, the time scale for reversing the answer has grown shorter and shorter as we approach the present. Hence the origin of the solar system, says Brush, is an unsolved problem.

Today’s hypothesis

Today’s accepted theory for the origin of the solar system is a complex, cosmic choreography based on the Nebular Hypothesis. It goes something like this (as you read this keep in mind it is a fact because, as Bernoulli and Laplace argued, there obviously is only a single cause):

A large cloud of material, including dust, hydrogen and helium, collapses to form the sun and a surrounding disk. The rotational rate increases as the cloud collapses. It also heats up, especially in the inner region, say within the orbit of Jupiter. In this inner region, only rocky materials can withstand the high temperatures and they collect to form the inner planets, initially as molten blobs. Later they are coated with particles that collect on their surface. These become the crusts of the inner planets.

Between Mars and Jupiter there is no planet but instead we find the asteroid belt. This is because Jupiter perturbed the nascent planets that formed in that region, causing them to collide rather than coalesce. The result is a ring of asteroids, rather than a planet, circling the sun.

In the outer regions of the solar system, where the temperature is lower, icy dust collects to form small planetesimals that later attract the hydrogen and helium gases. Left over planetesimals may be captured as moons or are ejected to the outer reaches of the solar system to become comets. Hence the composition of comets and meteorites should represent the early solar nebula.

Later, the sun’s radiation and solar wind drive any remaining gas out of the solar system, and the sun’s rotation is dramatically slowed by magnetic braking. This is the rendition of Laplace’s Nebular Hypothesis from recent years, but there remain several anomalies to explain. For instance, Venus and Uranus have anomalous spin characteristics. Also, about a third of the more than one hundred moons in the solar system have irregular orbits, revolving about their host planet in the wrong direction for example. And some revolve faster than their host planet spins. This would not occur if they were formed by a condensing cloud. Also, Pluto’s orbit is more elliptical than the other planets, and significantly inclined from the ecliptic.

There is no general explanation for these many anomalies. It could be that huge impacts reversed the spin of Venus and tipped Uranus on its side. Perhaps moons that revolve too fast have dropped from a higher orbit, and thus increased their rate of rotation. Or they may have been captured by rather than formed with the planet.

As for Pluto, one idea is that a large planetesimal passed near Neptune, lost some energy and fell down near Jupiter which ejected it to beyond Pluto. In the process the orbits of Jupiter, Saturn, Uranus and Neptune are all perturbed and Neptune, in turn, perturbs Pluto into its highly eccentric and inclined orbit we observe today.

Another difficulty with today’s theory of the solar system origin is the great size of the outer gaseous planets. In order to accumulate so much light gas they must have formed very quickly because early on the sun’s solar wind would have blown the gas out of the solar system altogether.

One explanation for this is that these planets formed via a faster acting mechanism known as disk instability. But if this works for Jupiter and Saturn, it leaves open the question of why Uranus and Neptune are not so large. If the disk instability mechanism gave Jupiter and Saturn their thick atmospheres, why didn’t it give thick atmospheres to Uranus and Neptune?

One answer is that our solar system formed in a cluster of stars. Perhaps the neighboring stars were so close that radiation heated the gases in the outer reaches of our solar system, making them more difficult for Uranus and Neptune to capture

A new flip?

In recent years the Nebular Hypothesis has met with even more failures. For instance, discoveries of distant planets have revealed star systems that make no sense on the Nebular Hypothesis. As one researcher commented, “These discoveries are making it very difficult to stick to the party line endorsing the so-called standard model.”

And now, new analysis of NASA’s Genesis mission reveals contradictory variations in nitrogen and oxygen isotopes. As one researcher explained:

These findings show that all solar system objects including the terrestrial planets, meteorites and comets are anomalous compared to the initial composition of the nebula from which the solar system formed.

And as another researcher concluded, that raises questions about the Nebular Hypothesis:

The implication is that we did not form out of the same solar nebula materials that created the sun—just how and why remains to be discovered.

Discovered? This has very little to do with scientific discovery. The researcher is confusing metaphysics with science. The reasons for the isotope variations will be explained, not discovered. New epicycles will be applied where needed, and perhaps there will be a flip to a new dualistic theory.

Of course there is nothing wrong with hypotheses about how the world arose. Even circuitous, heroic and unlikely theories are at least worth consideration. There should be no constraint or limit on our imagination. Theories can be posited, tested, evaluated and rejected, as appropriate. But of course evolutionary thinking isn’t about any of this. If it was then the true status of the theories would be admitted.

Evolutionary thinking is about injecting a religious agenda into science that evolutionists insist must be true. Religion drives science, and it matters.

Lethal Membrane Nanotubes

As recently discussed the cell membrane structure provides a barrier between the cell interior and the external environment and includes a great variety of molecular machines attached to the sandwich structure which is formed by phospholipid molecules in tail-to-tail formation. These hydrocarbon tails, sandwiched in the middle of the membrane, make for a very oily membrane interior which contributes to the cell’s protective barrier.

But such membrane structures are not limited to the cell’s outer boundary. They also serve various purposes inside, and even outside, the cell. And new research is helping us to understand better some of these roles. For instance, as a recent research paper explains, membrane structures can be used to form long, thin nanotubes used by immune cells to reach out and destroy harmful cells:

Membrane nanotubes are membranous tethers that physically link cell bodies over long distances. Here, we present evidence that nanotubes allow human natural killer (NK) cells to interact functionally with target cells over long distances. Nanotubes were formed when NK cells contacted target cells and moved apart. The frequency of nanotube formation was dependent on the number of receptor/ligand interactions and increased on NK cell activation. Most importantly, NK cell nanotubes contained a submicron scale junction where proteins accumulated, including DAP10, the signaling adaptor that associates with the activating receptor NKG2D, and MHC class I chain-related protein A (MICA), a cognate ligand for NKG2D, as occurs at close intercellular synapses between NK cells and target cells.

As described above, like the cell membrane, these membrane nanotubes include a variety of specialized, critical molecular machines.

And why are such nanotubes needed? The researchers hypothesized that such nanotubes might be used to maintain contact with target cells that move around too much:

It is well established that T or NK cells receive a “stop” signal when activated by a target or antigen-presenting cell. However, target cells would not receive an equivalent stop signal; therefore, particularly motile target cells may be able to move away from cytolytic NK or T cells before an effector response has been realized. Hence, one speculative role for nanotubes could be to facilitate cytolytic cells being able to sustain an interaction with target cells that are particularly motile (e.g., other lymphocytes).

More research is required to understand these nanotubes better, but what we do understand reveals a most interesting story. How curious it is that the nanotubes are able to recruit important molecular machines in order to function. And how strange that the nanotubes deploy when required and successfully kill the target cell. Are we really to believe that such structures and functions arose via a sequence of mutations? And that each mutation was random with respect to the need and the final design? And this in spite of the fact that no such sequence of mutations is actually known to us?  In fact this seems to be yet another example of nature not cooperating with evolutionary expectations.

Response to Comments: Does Natural Selection Help?

According to the theory of evolution the biological world arose via random biological variation, such as caused by mutations. By “random” evolutionists do not mean completely random. Perhaps mutations occur more often in summer. Or perhaps they occur more often in the daytime, or on Tuesdays. Perhaps mutations occur more often in one part of the genome. Such trends are clearly not random. So what do evolutionists mean by random? They mean that the biological variation is random with respect to need. Mutations are not, for instance, biased in ways that help the organism adapt to environmental challenges.

As an aside, this is yet another evolutionary expectation that has been falsified. We now know, no thanks to evolution, that biological variation very much is not random with respect to need. In fact, we observe rapid, non random, adaptations arising to cope with changing environments. Evolutionists, after resisting the findings, subsumed them within evolution. Such amazing adaptive capabilities, claimed evolutionists, were created by evolution. After all, populations that can rapidly adapt to challenging conditions would be better off, and so preserved by natural selection.

That was not entirely an aside because it raises the question of selection. Given that biological variation is random with respect to need, does natural selection help to explain how those amazing adaptive capabilities, or the other thousands of fantastic biological designs, arose?

According to evolutionists it certainly is. Breeders select for the traits they desire and Darwin argued that nature—by virtue of differential survival rates—effectively selects for the more fit designs.

Evolutionists often refer to selection “pressure” to indicate the powerful and effective role of natural selection in the evolution of biological designs. But in fact there is no such thing as selection pressure. Remember, according to evolution biological variation is random with respect to need. And selection is powerless to change this. It does not coax the needed mutations to occur. Natural selection is merely the consequence of (i) some mutations not working and so disappearing from the population and (ii) others having a neutral or positive effect and so perhaps surviving. We might say that selection kills off the bad designs. It certainly does not induce certain designs to arise.

So if selection pressure is a fiction then what role is there for natural selection? The answer is not much. In fact, starting at that warm little pond almost four billion years ago, evolution must have created humans via a very long sequence of random biological changes. Humans, and everything in between, arose by an astronomically long series of lucky shots. Selection merely eliminated the wrong turns.

Evolutionists are wrong to appeal so strongly to natural selection as the driving force behind evolution’s brilliance. The secret in the soup is evolution’s heroic claim about the nature of chemistry, physics, biology and life itself. Simply put, evolutionists imagine that from a lifeless pond to a human being, there is a long, gradual sequence of tiny, simple changes, each of which confers a slightly positive improvement in the ability to reproduce.

Each of these tiny, simple changes consists of a modest chemical modification, drawn from a small population of possibilities. For example, there are only four letters in the alphabet of DNA. If changing a particular DNA nucleotide to one of the other three letters confers a reproductive enhancement, then is it not likely to occur randomly at some point, and then be selected? Sure, but natural selection is not the key to this story.

The key to the evolution miracle is not natural selection, which itself is relatively uncontroversial, but the unfounded and unspoken assumption that the nature of matter, chemical bonds, chemistry’s periodic table, physic’s universal laws, and all of biology conspire together to form spontaneously a most unlikely thing: life. That is, starting from no life at all, the millions and millions of species and their incredible designs all spontaneously form via gradual, tiny chemical changes that just happen to occur at random. All this because there is an astronomical number of ever improving designs, all linked by those tiny changes. These never-ending lineages of nearly identical species form a myriad of pathways in biology’s immense design space. These pathways lead to each and every species we observe.

This is the heavy lifting behind evolutionary theory, not natural selection. Evolutionists tout selection and selection pressure, but these merely provide cover for the real absurdity. It would be like claiming that jet aircraft could be constructed by a long sequence of intermediates, each of which could fly.

But we need not depend on analogies or intuition. Biology gives us little doubt that there is no such evolutionary magic. Perhaps evolution’s many pathways leading to the many species are real, but there is no scientific evidence for them. Experiments consistently reveal limitations to change, not the sort of biological elasticity evolution requires. Even a mere, single protein molecule cannot be evolved from scratch. And biological designs give us little reason to think they are one in a long line of gradually changing designs, each working a bit better than the previous.

But evolutionists deny the science and insist that with natural selection, evolution becomes feasible. They resist acknowledging the fact that there is no such thing as selection pressure, and that their theory relies on random biological variation coupled with a fanciful notion of life.

For example, an evolutionist recently asked this question:

Let’s have CH clarify: when creationist debaters try to convince people that modern evolutionary theory is a theory of adaptation by pure random mutation, are they misleading their audiences? Is that a problem for CH?

The professor’s concern is that these creationists do not tell their audiences about natural selection and its role in evolutionary theory. Sure, if we want to describe evolution we need to include natural selection. But in that case we need to describe it accurately. We need to explain its limitations. And we need to explain evolution’s unlikely assumptions about the nature of biology and life. If evolutionists are concerned about self-serving, scientifically faulty descriptions of their theory, then perhaps they should look closer to home.

Response to Comments: Avoiding the Obvious Evidence

Inquiring minds occasionally ask me why it is that evolutionists are evolutionists. How is it that a person can become so dogmatic about such a bizarre idea? It is because they are atheists, right? And of course they want to maintain their status in the scientific community, right? They need to publish papers, obtain funding, receive tenure and all these keep evolutionists in line, right?

Wrong. These are not the reasons why evolutionists are evolutionists. True, these can be important influences in science. Science is an endeavor that is, for better or for worse, done by humans. And so social pressures, funding requirements and post modern tendencies can all influence conclusions and beliefs. But if you think these are the key drivers behind evolution then you don’t understand evolution.

The common theme here is that all these reasons amount to ulterior motives. Like conspiracy theorists we imagine ulterior motives because we can’t believe that legitimate reasoning could be involved. But, in fact, that is the reason. Evolutionists are evolutionists because they are absolutely convinced of evolution. They have arguments and evidence, and they have reasoned it out. There are no simple, ulterior, motives driving people from widely differing backgrounds to subscribe to such dogma.

Believe it or not, if you want to understand evolutionists all you need to do is listen to them. If you read the evolution literature you will see why evolutionists are evolutionists. For they have explained it over and over and over again. People from different continents, cultures, and centuries have repeatedly given the arguments and evidences. And though the scientific evidence grows over time, evolution’s themes are quite consistent. Very simply put, evolution wins because the alternatives lose.

Evolution is mandated because the god(s) would never have intended for this world. They must have allowed the world to arise on its own. Perhaps they initiated motion and instituted the natural laws, but like Aristotle’s Prime Mover showed little interest thereafter.

Evolutionists will complain that they don’t recognize this description of their thinking. But when they make the scientific-sounding argument that duplicated errors in different species proves common descent they are, in fact, resting on an enormous metaphysical foundation. This is true of all the arguments and evidences that prove evolution to be a fact. Evolution fails to explain the biological world and is constantly surprised by the scientific evidence. But it must be a fact—our religion demands it.

Evolutionists insist that science must be free of subjective, metaphysical premises. Faulty scientific theories must not be protected, they warn, just because we prefer them. But these are precisely their practices. Evolutionists judge themselves, for they violate their own rules.

Evolution protected from the evidence

Because evolution is underwritten by metaphysical dictates it is not empirically vulnerable. Evolution is robust to contradictory evidence and failed expectations. All of the scientific problems—and they are enormous—are taken to be mere research problems. Evidence cannot question whether evolution occurred, only how it occurred.

Also, because evolution is proven by its underlying metaphysical dictates, it is to those dictates which evolutionists return when challenged. Every argument that proves evolution to be a fact is metaphysically laden. And so if you question the fact of evolution, you will be answered with one form or another of evolution’s metaphysics.

Consider, for example, the recent comments of one evolutionist. I suggested that scientific theories should at some point be discarded if they are excessively faulty. If a theory produces a long list of false predictions, then it should be rejected. Technically it is true that we can know for sure. No matter how many false predictions have been made, theories can always be rescued with patches, reinterpretations of data, and heroic assumptions. But in practice, when the probabilities become low, theories are no longer taken seriously. Certainly scientists are not shy about casting out the flat earth model or geocentrism.

But revealing just how well protected and impenetrable evolution is, the evolutionist appeals to this tiny ray of hope for his theory. And after having thus neutralized the devastating scientific evidence, he returns to his metaphysics. Sure there may be evidential challenges but, he insists, we must judge evolution by comparing it to the alternatives (for example, creation or design ideas):

What Cornelius fails to understand is that this complaint [of false predictions] still fails. To invoke modus tollens, the conclusion has to follow deductively from the premises. Having many predictions that were “probably bad,” would at best make the theory less probable. …

Theories make predictions using a set of several premises. For example:

If theory T and A and B and C and D and E and F then with some probability we expect X.

Not X.

What conclusion can we draw from this?

Is the theory improbable? Perhaps, but this also depends on how sound the premises A-F were. If X didn't happen and we find out that A was a bad assumption then we can now say that T and (new A) and B and C and D and E and F then with some probability we expect Y. In this way, theories can make bad predictions and still remain viable. Would the theory, after a certain number of bad predictions, become false by modus tollens? Obviously not, even though Cornelius likes to pretend so.

What I wrote above might seem like a cop-out, allowing any theory to survive any kind of test and, in a way, this is true. One can continue changing ones premises (but not inventing them out of thin air the way ID would have to do to make predictions) indefinitely and the theory would still not be false by modus tollens. This is why it’s important to COMPARE theories.

So in spite of the evidence evolution is a fact because it is better than the alternatives. After all, we must compare theories, not merely judge them according to the evidence. But evolutionists also say that creation and design theories do not qualify as science because they are not strictly naturalistic. So evolution can only be judged in comparison to the alternatives, and the alternatives are disqualified from the start.

And even if we were to compare evolution with creation and design, the victory would only mean that evolution wins over the particular theories of creation and design that were tested. It would not establish evolution as a fact as evolutionists claim.

Unless, that is, if we knew all the possible theories of creation and design. And in fact, evolutionists do assume just this. For example, when the evolutionist writes:

Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense. —Stephen Jay Gould

he is deeply immersed in his metaphysics. There is nothing wrong with comparing theories. But when such comparisons are used to proclaim the winner to be a fact, then you know metaphysics are at work.

But why stop with comparisons? If even the best theory is scientifically lousy then shouldn’t we think harder about the problem? Shouldn’t we at least be tentative? Should we hide behind philosophical shenanigans or should we face the scientific evidence straight on?

Biological Control of Cell Membrane Structural Properties

You learned about DNA and proteins in your high school biology class, but you may not remember much about the cell’s membrane which is based on a dynamic, fluctuating sandwich structure. This cellular envelope controls what chemicals enter and exit the cell, partly due to molecular machines such as channels and pumps in the membrane, and partly due to the sandwich structure itself. This sandwich structure is a barrier to certain types of chemicals. But the membrane permeability and the operation of the molecular machines depend on the details of the sandwich structure. And as recent research has been finding, contra evolutionary expectations, organisms actively maintain and fine-tune the sandwich structure in response to environmental challenges.

The cell membrane’s sandwich structure consists of two layers facing away from each other. Each layer is made up of an array of phospholipid molecules lined up next to each other. Phospholipid molecules consist of a water-loving (or hydrophilic) head, a phosphate group, and two oily (or hydrophobic) hydrocarbon tails.

The two layers face away from each other in a tail-to-tail arrangement. This creates a very oily, low dielectric, interior of the sandwich. While small oily molecules are able to pass through this membrane structure, it is difficult for any water-loving molecule, including water itself, to pass through the barrier. So when this sandwich structure forms a closed sphere surrounding the cell, the inside compartment is separated and protected from the outer aqueous environment. But the sandwich structure is not a simple, rigid, structure. It fluctuates, and this influences the membrane performance.

At lower temperatures the sandwich structure has a more rigid, gel, phase and at higher temperatures it has a less rigid, fluid phase. As with the freezing and melting of water there is a distinct phase change, between the gel and fluid phases of the sandwich structure, which occurs over a rather narrow temperature range. This melting point temperature is strongly influenced by the degree of attraction between the adjacent phospholipid tails. Depending on the temperature and this degree of attraction, the sandwich structure may be like a gel or like a fluid, and this is important because the phase influences the membrane permeability and the membrane’s molecular machines.

Within the membrane sandwich structure, the phospholipid tails are attracted to each other via the weakest chemical force, van der Waals interactions. Unlike the stronger chemical bonds, van der Waals interactions do not arise from the trading or sharing of electrons. So how do these interactions work?

Consider two neighboring atoms. As the electrons quickly move about, uneven charge distributions can occur across the atom. One side of an atom may temporarily be positively charged, and the other side negatively charged. Such charges influence the neighboring atom. For instance, a negative charge will tend to repel the electrons of the neighboring atom causing an attractive, uneven charge distribution in that atom. The two atoms can then continue with synchronized, fluctuating charge distributions. But all of this depends greatly on the distance between the two neighboring atoms. If they are too far apart (or too close together), the entire interaction, weak as it is, becomes insignificant.

The distance between adjacent phospholipid tails depends on their shape. If the tails have two hydrogen atoms for each carbon atom, then there are no double bonds. Such saturated chains have a consistent, linear, shape and they pack tightly together at the van der Waals preferred distance.

Unsaturated chains, on the other hand, have double bonds which cause structural kinks, loose packing and therefore weaker van der Waals interactions. And the particular location of the double bond is important, as some locations disrupt the van der Waals interactions more than others.

So all of this means that the number and location of hydrogen atoms in the phospholipid tails is an important tuning parameter (there are other tuning strategies as well), determining the phase of the sandwich structure and, in turn, the cell’s membrane performance. This is particularly important for organisms that are subject to greater temperature variations, such as poikilotherms. Such temperature variations can cause unwelcome phase changes in the membrane’s sandwich structure.

Physiological response to temperature change

Years ago it was thought that the various protein machines in the cell’s membrane were more or less randomly distributed. It is yet another example of the influence of evolutionary thinking on biology. If the biological world is a fluke, then aren’t biological designs, such as the cell’s membrane architecture, random?

Now we know better. The cell membrane architecture is anything but random. In fact, the attention to detail is enormous. This includes the phase of the sandwich structure and its tuning mechanisms, such as the degree to which the phospholipid tails are saturated. Here are quotes from representative research papers discussing how organisms monitor and control their membrane fluidity, particularly in response to temperature variations:

E. coli incorporates increasing proportions of saturated and long-chain fatty acids into phospholipids as growth temperature is increased. It was found that this compositional variation results in the biosynthesis of phospholipids that have identical viscosities at the temperature of growth of the cells. [link to paper]

Numerous studies have shown that fluidity is an important factor in the function of biological membranes. Changes in fluidity affect the activity of membrane-bound enzymes and the activity of transporters, as well as the permeability of membranes to nonelectrolytes, water, and cations. Given that temperature has profound effects on membrane fluidity, it is not surprising that poikilotherms adjust the composition of their membranes in ways that defend fluidity in the face of changes in body temperature. …

Although the ways in which membrane composition is altered in response to temperature are not always consistent among species, tissues, cells, or even organelles, a few important trends have emerged. One prominent response to a decrease in the body temperature of poikilotherms is an increase in the percentage of unsaturated fatty acids that make up the phospholipids. … Phospholipids with saturated fatty acids pack readily into bilayers, whereas phospholipids with unsaturated (and therefore, kinked) acyl chains tend to disrupt hydrophobic interactions among acyl chains of adjacent phospholipids. An increase in the proportion of unsaturated fatty acids thus results in an increase in membrane disorder and fluidity, which tends to oppose the ordering effect of a drop in temperature. [link to paper]

The phospholipid composition of plasma membranes from the kidney of rainbow trout, Salmo gairdneri, was determined over a period of 21 days as fish were acclimating between temperatures of 5 and 20 degrees C. Proportions of phosphatidylethanolamine (PE) were significantly higher (29.03 vs. 23.26%) in membranes of 5 degrees C- than 20 degrees C-acclimated trout [link to paper]

Our observations suggest that a physical parallel to the changes of lipid composition is the maintenance of an optimal lipid order in the hydrophobic core of the cytoplasmic membranes. It can be interpreted as a tendency of Bacillus subtilis to keep the lateral pressure in its membranes at an optimal value, independent of the temperature of cultivation. [link to paper]

Not only is the cell membrane intricate and complex (and certainly not random), but it has tuning parameters such as the degree to which the phospholipid tails are saturated. It is another example of a sophisticated biological design about which evolutionists can only speculate. Random mutations must have luckily assembled molecular mechanisms which sense environmental challenges and respond to them by altering the phospholipid population in the membrane in just the right way. Such designs are tremendously helpful so of course they would have been preserved by natural selection. It is yet another example of how silly evolutionary theory is in light of scientific facts.

Response to Comments

The theory of evolution states that the entire biological world is a fluke—it just happened to arise all by itself. Actually, evolutionary thought extends this claim to the entire universe. From a scientific perspective there are, not surprisingly, substantial problems with this view. It is an idea that goes back at least to the ancient Epicureans who believed swerving atoms created the world and today’s version is, frankly, no less ridiculous. But that’s not all. Evolutionists are not merely interested in researching this unlikely idea—they also insist it is a fact. This is where the story takes a turn for the really strange (as if it were not already strange enough). For there literally is no question—at least no rational question—that evolution is not a fact. It would be like saying Santa Claus is a fact. And yet this is what evolutionists steadfastly claim. They are unable to justify the claim, but they are nonetheless quite certain of it and they are unable to see anything wrong with their idea. Here are some recent comments from evolutionists.

I recently explained that the vitamin C pseudogene pattern is not powerful evidence as evolutionists claim. Evolution did not predict it and would not be harmed if there was no such pattern. Given that the pseudogene exists in certain species, it is true that the pattern fits evolution. But this isolated fact does not mean much. For instance, the sun rising fits geocentrism, and a pig with a cold nose fits the theory that pigs can fly. To this an evolutionist explained how the pattern is interpreted according to evolution, and concluded:

Under evolutionary theory we would predict that the loss of function in GULO will result in loss of conservation—the relaxation of purifying selection—and the accumulation of more differences to GULOP sequences than to functional GULO sequences per unit time as inferred in molecular phylogenies. And this is so. Despite this, we would still expect the differences within a clade such as Haplorrhini to match create a nested hierarchy because of the differing times since divergence as predicted by common descent. And they do. Clearly, this is not the same as wet nose/flying pig.

The evolutionist’s comments about the pseudogene pattern and how it fits evolution seem reasonable. But he has missed the larger point. The consistency of the pattern with evolutionary expectations is not strong evidence for evolution. Sure, let’s call it a successful prediction. All kinds of ridiculous theories enjoy successful predictions, such as the theory that pigs can fly. The question here is not whether the evidence is consistent with evolution, but whether this is powerful and compelling evidence for evolution, as they claim. It isn’t. This is important because evolutionists use examples such as these are a sort of proof text for their claim that evolution is a fact.

I also made the point that evolution and common descent lack a plausible mechanism. To this an evolution commented:

As you are aware, the hypothesized pattern of common descent is evaluated independently of any reference to mechanism.

This is the typical defense, but it is not quite true. Common descent does make claims about the expected pattern of designs in biology, and as such it specifies the underlying mechanism of evolution, to a certain degree. For instance, it requires gradualism. Without gradualism common descent could not know what biological patterns to expect. Yet evolutionists routinely turn off gradualism where the data do not fit.

I also explained that, aside from consistent data, evolution and common descent have made so many false predictions. If we are going to evaluate theories according to their predictions, then certainly we must conclude evolution and common descent are false by modus tollens. To this an evolution commented:

No, we must not conclude that at all. I would have thought that by now, you should have realized that the expected observations given a certain hypothesis are probabilistic. Here, let me help you:

This is what you want things to be like: If hypothesis H then observation O. Not O, therefore not H.

This is what things are like: If hypothesis H then there is some sort of probability of observation O. Not O, therefore ... well, definitely not not H via modus tollens.

I would also have thought that by now, you should have realized that there are alternatives to strict Popperian falsification for evaluating theories. …

Common descent didn't come out looking silly at all - unlike your sophistry.

Actually I briefly discuss this issue of predictions and falsification here (Sections 1.1 – 1.4). Contrary to the evolutionist’s complaint here, I did not say that a falsified prediction implies the hypothesis is false. What the evolutionist omitted was the word “many.” This is not a case of one or two failures. Evolution and common descent have generated a plethora of false predictions, including their major predictions. My point was that evolutionists advertise their few successful predictions to be compelling while failing to reckon with their many false predictions.

Indeed, if there is a fallacy here it is not in my suggestion that false predictions be seriously dealt with, but in the evolutionist’s over estimating the power of their successful predictions. Yes, we can agree the vitamin C pseudogene patterns are consistent with evolution and common descent, but this is hardly the strong evidence they claim it to be. This is important because it is precisely this type of mistake that masks the tremendous mistake evolutionists are making. If a few consistent observations make evolution compelling, then its myriad problems can be ignored. After all, evolution must be a fact, so those problems must merely be research problems. It is a case of confirmation bias on steroids.

Next, in my previous post I discussed how evolutionists say that random biological variation, such as caused by mutations, created the entire biological world. I noted that an analogy once used for this claim is that of a room full of monkeys pounding away at typewriters and producing Hamlet. To this an evolution commented:

It is, pardon me, disgraceful. When used by third-rate creationist debaters, it is either a sign of total ignorance of evolutionary biology, or a deliberate attempt to mislead an unwary audience into thinking that evolutionary biology is nothing but a theory of pure mutation, unaided by natural selection. That strikes the audience as an absurd theory. They are not being told of the effect of natural selection.

Why CH, who knows much better, would endorse this absurdity without at least a little embarrassment is a matter for puzzlement.

But I did discuss the role of selection in the evolutionary explanation. I also explained why selection doesn’t solve the problem and that experiments have helped to demonstrate this.

The problem here is not that evolutionists are ill-informed or not smart. They are well educated, intelligent people. But knowledge and intelligence do not ensure wisdom. Very smart people can believe in strange things. This has been repeatedly demonstrated throughout history, and today it is demonstrated no better than in the theory of evolution.

Evolutionist: Our Best Defense Against Anti-Science Obscurantism

Evolutionists say undirected, random events, such as mutations, accumulated to create the entire biological world. An analogy once used for this claim is that of a room full of monkeys pounding away at typewriters and producing Hamlet. Today the analogy needs to be updated from typewriters to computer keyboards, but otherwise remains apropos. When the letters are selected at random, a page (or screen) full of text is going to be meaningless. And the problem is no easier in the biological world. Whether English prose or molecular sequences, the problem is that there are relatively few meaningful sequences in an astronomically large volume of possibilities. Nor does selection help because the smallest sequence that could be selected—such as a small gene—is not very small. All of this is rather intuitive and for centuries evolutionists have been trying to solve the problem. Their latest solution is being called natural genetic engineering.

Heat death

It is obvious that randomly selected letters aren’t likely to form a meaningful message. The exact probability is difficult to compute but it is astronomical. As physicist Gerald Schroeder has pointed out, even a simple Shakespearean sonnet of only 488 letters would never be produced by those monkeys (there are 10^691, or a 1 followed by 691 zeros, different possible transcripts). As Schroeder explains:

Convert the entire 10 to the 56 grams of the universe (forget working with the monkeys) into computer chips each weighing a billionth of a gram and have each chip type out a billion sonnet trials a second (or 488 billion operations per second) since the beginning of time, ten to the 18th seconds ago. The number of trials will be approximately ten to power of 92, a huge number but minuscule when compared with the 10 to power 690 possible combinations of the letters. We are off by a factor of ten to power of 600. The laws of probability confirm that the universe would have reached its heat death before getting one sonnet. We will never get a sonnet by random trials, and the most basic molecules of life are far more complex than the most intricate sonnet.

And the fact that there are many possible sonnets, not just one, does not make a meaningful dent in these astronomical probabilities. Both prose and proteins are not going to arise by chance.

But evolutionists say it is not a matter of chance because natural selection guides the way. Evolution is not required to create a complete organism or even a complete gene, it needs only small victories which natural selection preserves.

Consider the word “selection.” It has 9 letters and for a 26 letter alphabet there are 26^9, or 5 million million different possible combinations of letters. The monkeys would never type out even this single word.

But what if a correct letter, whenever it happens to be typed, is preserved by natural selection? Then the search shrinks from 26^9 to 26*9 different possibilities. The search space reduces from 5 million million to 234 different possible combinations of letters.

From Charles Darwin to Richard Dawkins, evolutionists have elaborated on how natural selection largely removes the random element from evolution and makes the origin of the complex biological world all but inevitable. As Darwin wrote:

Although the belief that an organ so perfect as the eye could have been formed by natural selection, is enough to stagger any one; yet in the case of any organ, if we know of a long series of gradations in complexity, each good for its possessor, then, under changing conditions of life, there is no logical impossibility in the acquirement of any conceivable degree of perfection through natural selection.

Darwin explained that his theory “would absolutely break down” if we found a design that could not possibly have arisen gradually. Not surprisingly Darwin concluded that he could find out no such case. What he didn’t tell the reader is that his falsification criteria was impossible. It is obvious to objective observers that the biological world abounds with such designs, but showing this to an evolutionist is another matter.

Evolving even a single protein under carefully controlled laboratory conditions has proved to be elusive. You can see the details here, here, here, here and here. The problem is that blind gradualism, even with perfect selection, doesn’t magically produce fantastic designs as Darwin, Dawkins and the rest had hoped.

The specific difficulties with their fanciful idea are many. From the rough fitness surfaces to the smallest unit of selection not being small, it is difficult to coax intricate designs from a warm little pond.

Consider again, for example, the word “selection.” It seemed impressive that selection could reduce the search space from 5 million million to 234 different possibilities. But this cannot actually happen because selection cannot select individual letters. What good is an “s”? The word “selection” doesn’t make sense until you have the entire word.

Recognizing these problems evolutionists are now searching for non gradualistic mechanisms to do the job. Proteins must form not by the gradual accumulation of mutations but by sudden rearrangements and new designs may evolve by macromutations.

Perceptive readers will see the obvious problem: replacing gradualism with saltationism does not solve the underlying problem. For instance, from where did the protein modules come? Or from where did the macromutation mechanisms come?

Ultimately, no matter how many thought experiments and just-so stories are brought to bear, the problem remains the same. Evolutionists claim that incredibly complex designs just happened to arise all by themselves.

Natural genetic engineering

This silliness reached new levels in a recent review paper which attempted to summarize this emerging, non gradualistic view of evolution. Even evolutionists admit that biology has turned out to be complex. And this complexity is no less observed at the cellular and molecular levels of biology. As the review paper, for example, explains:

Molecular cell biology has uncovered sophisticated networks in all organisms. They acquire information about external and internal conditions, transmit and process that information inside the cell, compute the appropriate biochemical or biomechanical response, and activate the molecules needed to execute that response. These information-processing networks are central to the systems biology perspective of the new century.

The genome is not like a blueprint as evolution once envisioned, but more like an interactive read-write memory system. The cell’s ability to monitor, detect and repair genome damage is astonishing. But the complexity doesn’t stop there. Yes the genome often needs a repair, but it also sometimes needs a redesign.

The twentieth century discovered that cells can read and write information onto their genomes at several levels. Beyond this, cells can even restructure their genomes to meet environmental challenges. And these redesigns can be passed on to future generations.

All of this means biology possesses incredible capabilities evolutionists never envisioned. And it also means that biological change responds intelligently to the environment. Biological variation is not according to blind, undirected processes such as mutation, as envisioned by evolutionists. Evolutionists thought that such variation was random with respect to need and that adaptation was merely the result of the useful variations surviving via natural selection. This unintelligent process would require long time periods but biology revealed intelligent, fast adaptation.

There was strong resistance to this paradigm in the evolution camp but now evolutionists are increasingly finding it to be a convenient enhancement to the ailing gradualism. If organisms can restructure their genomes to meet environmental challenges, then could they not have evolved via such brilliance? This would remedy the problems with strict gradualism, and fit the abruptness of the fossil record.

Cells redesign proteins by shuffling their modules, and genes are shared between organisms via complex horizontal transfer mechanisms. To these add even greater mechanisms such as cell fusions and whole genome doublings and you have nature’s version of genetic engineering. Is this natural genetic engineering not capable of evolving the species?

Once we were breeders, so evolution was viewed as a natural breeder. Now we are genetic engineers, so evolution is viewed as a natural genetic engineer. Evolution somehow created this marvelous genetic toolkit with which to create the biological world. And fortunately the tools cooperate, working when and where needed, and not when and where not needed.

Now evolutionists can continue to speculate about “the origins of complex adaptive novelties at moments of macroevolutionary change.” For instance, is it not evident that retrotransposons were necessary for the emergence of mammals in evolution?

According to evolutionists, evolution just happened to create the retrotransposons which later just happened to be needed for the emergence of mammals. This and the many other fantastic mechanisms that form the natural genetic engineering toolkit first had to be created by evolution so they then could cause evolution to happen.

Evolutionists ignore such serendipity while they debate the nuances of how evolution occurred, secure in their knowledge that it did occur. As the review summarizes:

Thus, novel adaptations that require changes at multiple locations in the genome can arise within a single generation and can produce progeny expressing all the changes at once. There is no requirement, as in conventional theory, that each individual change be beneficial by itself.

Just as genetic engineering has many advantages over the old breeding techniques, evolutionists find that the new natural genetic engineering version of evolution works so much better than the old breeding version of evolution.

Anti-science obscurantism

Natural genetic engineering is the most recent version of evolutionists’ attempts to explain how the entire biological just happened to arise spontaneously. A fluke that now amazes us.

Evolution is a religiously motivated mandate that, from a scientific perspective, is unlikely. But as Michael Polanyi once explained, they will “come so firmly to uphold this fiction that they will regard it as ‘the scientific view’ of life and condemn anyone challenging this fallacy as an anti-scientific obscurantist.”

Polanyi was often prescient and no less so here. For the evolutionist’s certainty comes not from the science, but from the underlying religion. And crucial to this dogma is the turning upside down of science. The legitimate scientific concerns, that evolution is profoundly improbable, are themselves cast as an anti-scientific obscurantist, just as Polanyi put it. As the review paper concludes:

In other words, our best defense against anti-science obscurantism comes from the study of mobile DNA because that is the subject that has most significantly transformed evolution from natural history into a vibrant empirical science.

It is truly difficult to know whether to laugh or to cry. Evolution is, at once, both hilarious and dangerous. Religion drives science, and it matters.

Evolutionists: Larry Moran Still Correct!

In my previous posts I discussed Larry Moran’s undefendable claim that the vitamin C pseudogene is powerful evidence for evolution and common descent. In response evolutionists continue to comment that I have it all wrong and Moran’s claim is quite correct. Here is what one evolutionist wrote:

Common descent is well supported by the evidence in the broken GULO gene (along with myriad other independent lines of evidence in the haplorhine primates). The fixed mutations in the broken gene form a nested hierarchy that matches phylogenies for functional genes. Interestingly, the substitutions differ from those in guinea pigs, which appear to have had an independent loss of GULO. These threads of evidence amount to more than claiming that common descent is only better than pure chance.

But common descent is, in fact, not “well supported” by this evidence. Evolutionists continue to repeat their mantra, but this evidence does not support common descent anymore than a pig with a cold nose supports the claim that pigs can fly. It is true that if pigs can fly, then we would expect to find pigs with cold noses. But we would hardly conclude that the hypothesis that pigs can fly is strongly supported by pigs with cold noses.

Nor do the “independent lines of evidence” support common descent any better. Indeed, the evidence leaves little doubt that what seemed obvious is, in fact, obvious. Common descent not only is intuitively silly, it is scientifically silly as well.

There is, for starters, that little problem of mechanism. Though they can’t supply the details, evolutionists say that a long, lucky, series of garbled, random mutations and other flukes of variation led to the millions and millions of species with all their incredible designs.

Or again, there is the problem of the biological patterns that don’t fit. From the striking similarities found in distant species to the profound differences in otherwise allied species, the predictions of common descent have been falsified many times over.

If ever there was an idea that doesn’t work scientifically, this is it.

It is true that there are patterns that, when taken in isolation, do fit common descent. The vitamin C pseudogene is an example. But this doesn’t magically dissolve the multitude of scientific problems. Yes, the evidence is consistent with common descent, but so too is the rising sun consistent with geocentrism.

As if sensing a problem the evolutionist, in typical fashion, makes a quick switch to metaphysics with a series of rhetorical questions:

If we were to reject common descent, is there some theory dealing with common design that provides a better explanation for a shared, broken gene in a line of otherwise apparently closely related species?

This is the heart of evolutionary thought. It is not that evolution makes sense (it doesn’t), it is that evolutionists believe it is the only choice. Rhetorical questions such as this one are common with evolutionists. A key to understanding evolution is that evolutionists think this line of reasoning is scientific, that such questions can be answered with a high level of certainty, and that in particular the answer is “no.”

But of course, contra evolutionists, science has no way of making such ultimate truth claims. It cannot know all possible explanations. As such scientists do not make sweeping claims that no such reasonable explanation is possible for observations, such as the vitamin C pseudogene patterns. Evolutionists, on the other hand, do.

Another evolutionist wrote that the vitamin C pseudogene pattern is a prediction of evolution given that it is found in certain species. He writes:

For example, given that humans, gorillas and orangutans all have this pseudogene, common descent predicts that chimps will also have it.

This seems reasonable, but since evolution and common descent have made so many false predictions, then certainly we must conclude they are false by modus tollens. If evolutionists use successful predictions to promote their theory, then shouldn’t the many false predictions mean something?

Religion drives science, and it matters.

Evolutionist: Larry Moran is Correct!

In my previous post I discussed Larry Moran’s undefendable claim that the vitamin C pseudogene is powerful evidence for evolution and common descent. In response an evolutionist in the know commented that I had it all wrong and Moran’s claim is quite correct:

We can calculate the likelihood of those mutations being shared via common ancestry. This likelihood is much higher than the likelihood you get under the hypothesis that the mutations were independently acquired by chance. This is strong support for the common ancestry model in the usual way that statistics are used to support hypotheses throughout all hypotheses in science.

It is worth elaborating on this argument to reveal the depths of evolutionary thinking. For this argument dates back centuries (at least to 1734 when Daniel Bernoulli used it) and hinges on, like all evolutionary arguments, deep metaphysics.

The term “likelihood” here refers to the probability of the evidence (the vitamin C pseudogene patterns in this case) we observe given a hypothesis of how they arose. So the likelihood of common descent, in this case, is the probability of the vitamin C pseudogene patterns given that they arose via the process of common descent.

Now the trick evolutionists use is to compare this likelihood of common descent with the likelihood of random design (or as our elite evolutionist puts it above, “independently acquired by chance”).

Don’t worry if you haven’t understood a word of this explanation. Here is the plain English version: Evolutionists claim that similarities (and in particular similarities that are harmful) between species are powerful evidence for their theory because it is obvious that such similarities did not arise by chance.

This certainly is the Mother of all false dichotomies. When put into plain English it is astonishing.

To be sure, who would disagree that most similarities between species—including the vitamin C pseudogene patterns—probably did not arise by chance? That seems reasonable enough.

But evolutionists then claim that, therefore, their unlikely theory is compelling.

In other words, simply put, it’s either evolution or chance. Those are your choices. That’s it. This argument is prima facie absurd and it is astonishing that evolutionists are serious. But they are, and that makes it important. Until you understand the depths of these fallacies you will not understand evolutionary thought.

Of course what evolutionists have actually shown is that their theory is better than origin by pure chance. That’s what their argument reveals—one silly theory is more likely than another silly theory. And they call this science? Sorry but this does not make evolution a fact. In fact, evolution and common descent still have all the monumental problems they had before evolutionists made the argument. None of those problems went away just because of the non random vitamin C pseudogene patterns.

But this argument is typical, and it speaks volumes. Evolutionary thought is not merely science gone wrong. It is not the consequence of a faulty experiment or flawed theorem. It is an utterly ridiculous mandate, tracing back to antiquity, that the universe and everything in it must have just happened to arise spontaneously. The scientific absurdity of the idea is exceeded only the evolutionist’s certainty it is true. Religion drives science, and it matters.

Larry Moran: Vitamin C Pseudogene is Powerful Evidence

In his on-going criticism of Jonathan Wells’ new book, The Myth of Junk DNA, evolutionist Larry Moran now asserts that the much discussed vitamin C pseudogene is powerful evidence for evolution and common descent:

The main argument of scientists like Ken Miller and Jerry Coyne is not that the GULOP pseudogene exists. It's that the GULOP gene and its pseudogene are at the same location in the genomes of all mammals. In the primate lineage this gene is non-functional due to a number of mutations that make it impossible to produce a functional protein. Some of the same deactivating mutations are found in related species such as humans and chimpanzees. This suggests strongly that the non-functional pseudogene was inherited from a common ancestor.

How did Moran arrive at such a conclusion? Why is the vitamin C pseudogene such strong evidence for inheritance via common descent? Unfortunately, Moran fails to explain his reasoning. He simply asserts this amazing claim.

Evolution and common descent have failed to explain how the original vitamin C gene could have arisen. In fact they fail to explain how any protein could have arisen. They have also failed to explain how all of biology could have arisen.

This is not a good start. So far this evidential claim of Moran’s seems unlikely. But let’s look at the pseudogene in particular. Perhaps there is something about this pseudogene that will make the evidence more obvious. For example, perhaps evolution made a strong, heroic prediction about this pseudogene.

In fact, evolution and common descent made no such prediction.

Well is there, at least, a powerful retrodiction? Again, no. Well perhaps evolution and common descent would absolutely be falsified if there were no such vitamin C pseudogene. Again, the answer is no.

No prediction, no retrodiction, and no falsification. Evolution and common descent do not predict the vitamin C pseudogene, and they are not harmed if there was no such thing. This in addition to the fact that evolution and common descent do not explain how the original gene could have arisen in the first place.

Moran’s assertion that the vitamin C pseudogene is powerful evidence for his unlikely idea appears to be just that, an empty assertion.

The Evolution of Mat-Hugging

Did early multicellular animal life obtain its oxygen from floating microbial mats? Oxygen would have been scarce and this raises questions of how early animal life could have evolved. Evolutionists are now speculating that mats of photosynthetic bacteria might have supplied local high concentrations of oxygen:

Modern atmospheric oxygen levels average around 0.21 atm, but when multicellular life was evolving, levels of around 0.10 atm would have been the norm — too low for most multicellular organisms. "Daily fluctuations in oxygen would have made it very difficult for animals other than simple creatures like sponges to exist," explains Jim Gehling, a palaeontologist at the South Australian Museum in Adelaide.

Gingras and his colleagues propose that the mats had a key role in helping early animals to get the oxygen they needed. "We think that animals used the small but highly oxygenated zones as oases," says Murray.

But even this idea has its challenges. Night time oxygen levels would have been too low and large animals might have had difficulty accessing the oxygen in the narrow mats. Perhaps, Gingras hypothesizes, evolution solved these problems with “mat-hugging behaviours.”

This sort of unfounded speculation is typical in evolutionary theory. It brings a creative, story-telling, element into science, where unlikely scenarios with little empirical support are routinely set forth as though they are genuine scientific explanations.

And, as in this example, these just-so stories often entail substantial serendipity. In this case, the evolution of multicellular animals is made possible by the earlier evolution of particular microbial mats and special mat-hugging behaviors.

Evolution must have first produced the needed lagoons, photosynthetic bacteria, and mat structures to set the stage. Then came multicellularity that just happened to have nearby mats available. Even with all this, however, problems remained. Evolution luckily just happened to produce the much-needed mat-hugging behavior. It was sheer luck (remember, evolution has no brains), but when that behavior happened to arise, it must have been wildly successful.

This, then, is science in the hands of evolutionists—a vehicle for story-telling. Religion drives science, and it matters.

The Education of a Science Writer

Last week science writer John Farrell discussed the genetic evidence for evolution in his Technology article at Forbes. Farrell referenced evolutionist Stan Rice to argue the genome could not have been designed. Not only is it a clumsy design but it is susceptible to terrible, debilitating mutations. Such a design would never have been intended and must have evolved via the mindless play of natural processes.

Farrell’s other source was evolutionist Larry Moran, who has convinced Farrell that Jonathan Wells has it all wrong in his new book, The Myth of Junk DNA. As Farrell summarizes:

From which we are to conclude, the creationist argument goes, that most scientists are knee-jerk ideological Darwinists, and isn’t this another good reason to get a better theory like intelligent design into the public school science classrooms.

But Farrell’s conclusion does not stand up very well to a simple fact check. First, Wells is not a creationist. Second, Wells makes no argument for teaching intelligent design in public school science classrooms. Perhaps Farrell is confused because his source, Larry Moran, makes similarly erroneous claims.

Moran erroneously refers to Wells as a creationist. Moran also makes liberal use of the pejorative term “IDiot.” Why the harsh rhetoric? Let’s have a look.

Moran cries foul when Wells is asked in an interview to explain junk/non-coding DNA “for those who dropped science after Grade Ten.” Here is how Wells answered the question:

“Non-coding” in this context means “non-protein-coding.” An important function of our DNA is to specific the sequences of subunits (amino acids) in the proteins that (along with other types of molecules) make up our bodies. When molecular biologists discovered in the 1970s that about 98% of our DNA does not code for proteins, some biologists called non-protein-coding DNA “junk.”

This is a straightforward, factual response for those “who dropped science after Grade Ten.” But Moran warns that it is misleading. After all, there is non coding DNA, such as regulatory sequences and RNA genes, that we all agree is functional and not junk.

Anyone familiar with the subject matter will recognize this as a canard. Of course Wells is not referring to that small fraction of non coding DNA whose function was known in the 1970s. Wells is not giving a dissertation on the subject. He is giving a brief response, explaining why long stretches of DNA with no known function and not thought to be transcribed (not all non-protein-coding DNA), was considered to be junk DNA by some.

This is why discussions with evolutionists are often tedious. It is tiresome to stretch out explanations with lengthy caveats. And so, like lawyers, evolutionists follow the rule of “least charitable” reading to castigate those who doubt their dogma.

For sympathetic readers who are less familiar with the details of molecular biology, such as many science writers, Moran’s attempt to discredit will seem convincing.

Moran next thinks Wells has wrongly associated junk DNA with selection:

Implying that junk DNA has anything to do with Darwin’s theory of evolution by natural selection is totally wrong. No matter how you define “neo-Darwinism” the fact remains that most biologists who believed in adaptation were very skeptical of junk DNA precisely because it didn’t fit with Darwin’s view of evolution.

But Wells made no such assertion. Wells explanation was thoughtful and circumspect. He explained that “According to Charles Darwin’s theory, all living things are descendants of common ancestors that have been modified solely by unguided natural processes that include variation and selection. In the modern version of his theory—neo-Darwinism— genes control embryo development, variations are due to differences in genes, and new variations originate in genetic mutations.”

In fact, Moran’s assertion that junk DNA can have nothing to do with evolution by natural selection is an overly simplistic, black-white version of the theory. While advocating natural selection Darwin’s book was full of examples of dysteleology, and the same is true of today’s literature. Those who view selection as more important tend to look for adaptive explanations, but that by no means absolutely rules out non adaptive explanations.

Moran also objects to Wells’ reference to Richard Dawkins and the concept of selfish DNA. Moran writes:

Dawkins was writing about selfish DNA when he wrote that passage in The Selfish Gene. Selfish DNA is not junk DNA. It has an adaptive purpose and a function. It is completely wrong to claim that Richard Dawkins was a big fan of junk DNA in the 1970s. Dawkins makes that very clear in The Extended Phenotype when he proposes various explanations for the extra DNA in our genome.

Completely wrong? Selfish DNA is not junk DNA? It has an adaptive purpose and a function? Dawkins proposes various explanations?

Once again, to the uninformed reader this criticism may seem damning. Most readers will not have read The Extended Phenotype and so will trust Moran. But again Moran’s criticisms are obvious canards to those more familiar with the material.

Dawkins does not propose various explanations for the extra DNA in our genome in The Extended Phenotype. He reviews a couple of concepts by way of introducing the selfish DNA concept which, contrary to Moran’s canard, does not have an adaptive purpose. Dawkins writes:

the thing to notice in the present context is that [adaptive explanations] are hypotheses made in the traditional mould; they are based on the idea that DNA, like any other aspect of an organism, is selected because it does the organism some good. The selfish DNA hypothesis is based on an inversion of this assumption: phenotypic characters are there because they help DNA to replicate itself [158]

Dawkins goes on to explain the concept of intragenomic selection that he views as selecting for selfish DNA:

“Intragenomic selection” can therefore lead to an increase in the amount of certain types of meaningless, or untranscribed, DNA, littered around and cluttering up the chromosomes. [161]

In other words, contrary to Moran’s canard, the selfish DNA concept did not include adaptive purpose and Dawkins did not propose various explanations.

These criticisms of Wells are not only unfounded, they come from Moran who, as an evolutionist, believes the world just happened to arise by chance. The entire biological world is a fluke that spontaneously arose. Indeed, Moran believes this is an obvious fact. After all, DNA, and the rest of this world, certainly would never have been designed:

It’s true that well-established bits of junk DNA—like known pseudogenes—have been effectively used to challenge the idea that our genome appears designed. Those examples remain powerful, and true, examples of evolution that cannot be explained by Intelligent Design Creationism. They have not been refuted and they have not been explained by the IDiots.

If it is true that junk DNA is impossible under creationism or design, then sure, they are probably “true” examples of evolution. But how does Moran know such truths? Metaphysical certainty is a dangerous thing. Religion drives science, and it matters.

From Philosopher to Science Writer: The Dissemination of Evolutionary Thought

Last week science writer John Farrell discussed the genetic evidence for evolution in his Technology article at Forbes. Farrell’s sources are evolutionists Larry Moran and Stan Rice. It is an interesting example of how evolutionary thinking is handed down and disseminated.

A strong framework

Three hundred years ago the famous and influential Lutheran polymath Gottfried Leibniz argued strenuously for what today is sometimes called naturalism. The idea that the world arose and operates strictly via the natural laws we observe has, historically, been mandated by a framework of interrelated theological and philosophical arguments.

The theological arguments deal mainly with the nature and attributes of a divine creator. The philosophical arguments, on the other hand, deal mostly with knowledge and how we obtain it. Or simply put, the theological arguments deal with god and the philosophical arguments deal with man.

While some of these arguments trace back to antiquity, the complete framework was developed and refined in the early years of modern science when Christian thought was applied to the growing movement of describing and understanding nature. By the mid eighteenth century—a century before Darwin wrote his book—the framework was largely complete.

As a leading intellectual Leibniz contributed substantially to the emerging framework. For example, Leibniz ruled out divine intervention, for it surely was a sign of a lesser, incompetent, creator whose natural laws were insufficient to do the job.

But Leibniz was by no means the only, or even the central, figure in the construction of this framework. What is interesting is how ubiquitous was the urge for naturalism. It was not confined to one genre of thought. It did not come from a particular discipline, or region or religion. Scientists, philosophers and theologians, on the continent and in Britain, Lutheran, Anglican and Roman Catholic all contributed. And today we could add atheist to the list. As PZ Myers wrote:

We go right to the central issue of whether there is a god or not. We’re pretty certain that if there were an all-powerful being pulling the strings and shaping history for the benefit of human beings, the universe would look rather different than it does.

Believing that god does not exist does not preclude believing things about god. In fact, ironically, atheists often hold their theological views more intensely than do “religious” people.

And not surprisingly, with his Lutheran background, Myers’ religious sentiment is nothing new. The idea that an omniscient, omnibenevolent creator would never have created this world comes right out of that seventeenth century framework for naturalism. Whether god creates via natural laws or whether, with Myers, we dispense altogether with this superfluous Prime Mover, matters little. The basic story line was already told long ago.

Understanding John Farrell (and all of evolution)

This centuries old framework for naturalism is key to understanding evolution today. Science writers such as Farrell report that scientists have discovered, for instance, “just how not-so-intelligently designed the human genome actually is,” but this is not a scientific conclusion. For unlike the target of his criticism (the ID theory) which refers to complexity rather than goodness of design, evolutionary thought and its underlying naturalism framework refer to the design’s metaphysics. As Farrell explains:

Many mutations are neutral, or can be easily overcome by technology. And some of them cause a great deal of psychological suffering, such as the mutation that causes trimethylaminuria, which is physically harmless but causes the victims to smell like rotten fish no matter how clean they are. But many other mutations are deadly or, worse yet, can cause a person to have a lifetime of suffering. Perhaps the most disturbing mutation is the one that causes Lesch-Nyhan syndrome. This one mutation, of a single amino acid in a protein, causes the victim to have an uncontrollable compulsion for self-mutilation: they chew their own lips and fingers, and find sharp objects to stab their faces and eyes. The victims are fully able to feel their pain and they know what they are doing, but cannot control it.

Obviously to argue such mutations are the product of intentional design is to suggest the deity or intelligence responsible, is something of a monster.

Indeed. Leibniz was concerned about the evil in the world, but he had no idea how deeply it runs. It is truly abominable, and it makes for a moving and powerful argument that no good creator who has the power to create a universe would ever create this one.

Whether by the Epicurean’s swerving atoms, or science’s natural laws, the world must have arisen on its own.

How could anyone deny this obvious conclusion? This and other metaphysical arguments leave no room for debate. Evolution must be true. We may not know how it occurred, but it is a fact.

The powerful theory of evolution hangs on this framework of thought that mandates naturalism. The science is weak but the metaphysics are strong. This is the key to understanding evolutionary thought. The weak arguments are scientific and the strong arguments, though filled with empirical observation and scientific jargon, are metaphysical. The stronger the argument, the more theological or philosophical.

Oblivious to this context Farrell continues:

But it’s even more problematic, Rice argues: the very structure of the genome itself—not just the mutations—is inconsistent with the idea that the genome, or the human body, or the world was directly designed by an external agent.

The human genome is full of stuff that interferes with the use of genetic information to produce healthy and functional enzymes and bodies. First, consider the fact that only about 1 percent of human DNA codes for those enzymes. About 68 percent of the DNA consists of non-coding DNA that is between the genes, and about 31 percent of the DNA consists of non-coding DNA that is inside of the genes. This is, at best, a clumsy system, because whenever a cell divides, all of this DNA is copied, not just the DNA that the cell will use. In addition, since each gene is broken into little “exon” fragments by a large amount of internal “intron” DNA, the genetic information must be spliced together in order to be put to use. That is, to get a functional enzyme, the genetic information from lots of exon fragments has to be cobbled together. If it works, there is no problem, but the whole system is so cumbersomely complex that it often fails. Not only are many genetic diseases caused by mutations in the genes themselves, but many genetic diseases are caused by (or also caused by) failures of the cell to deal properly with the non-coding DNA and the splicing.

Science writers are at the end of the dissemination chain. Evolutionary thought began with the theologians and philosophers. Their ideas informed institutions and culture. By the time Darwin developed his theory the ground was well prepared and all his strong arguments were non scientific. Nothing has changed today except the details. Evolutionists continue to issue their scientifically absurd proclamations that everything spontaneously arose by itself. They are absolutely certain of this, and inform us that doubters must be religious fundamentalists. Next historians, philosophers and intellectuals apply these evolutionary truths to their respective fields. The world is explained in terms of evolutionary thought. Finally the science writers regurgitate the dogma that is handed down to them. At this point the story line cannot be changed or questioned. The authorities are too intimidating and institutions too overwhelming. The ridiculous must be true. In fact, it must not even be ridiculous.

Next we’ll look at Farrell’s other source, Larry Moran.