Thursday, June 30, 2011

New Cambrian Arthropod Vision System: No More Shudders

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Myers follows this circular reasoning with yet more question begging:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Wednesday, June 29, 2011

Composite Multilayered Fish Armor Provides Protection Design Ideas

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

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

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

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

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

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

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

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

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

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

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

Tuesday, June 28, 2011

Response to Comments: Natural Selection Doesn’t Help

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

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

And from those primal germs came all life:

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


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


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

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

That in no wise the nature of all things
For us was fashioned by a power divine-
So great the faults it stands encumbered with
First, mark all regions which are overarched
By the prodigious reaches of the sky:
One yawning part thereof the mountain-chains
And forests of the beasts do have and hold;
And cliffs, and desert fens, and wastes of sea
(Which sunder afar the beaches of the lands)
Possess it merely; and, again, thereof
Well-nigh two-thirds intolerable heat
And a perpetual fall of frost doth rob
From mortal kind. And what is left to till,
Even that the force of Nature would o'errun
With brambles, did not human force oppose,-
Long wont for livelihood to groan and sweat
Over the two-pronged mattock and to cleave
The soil in twain by pressing on the plough

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

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

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

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

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

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

Monday, June 27, 2011

Response to Comments: Flexibility of Explanation in Action

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

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

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

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

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

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

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

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

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

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

Sunday, June 26, 2011

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.

Friday, June 10, 2011

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.

Thursday, June 9, 2011

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.

Wednesday, June 8, 2011

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?

Sunday, June 5, 2011

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.

Thursday, June 2, 2011

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.