Sunday, August 29, 2010

Bug With Bifocals Baffles Biologists

Take a close look at this organism—a very close look. Now answer these questions: Are you an evolutionist? Was this bug created by random mutations? Is it a Lucretian concoction? For evolutionists the answer is yes, all organisms must be such concoctions, and in so saying they are their own accuser—this is not about science.

And the retorts of evolutionists make matters worse. This indictment, they exclaim, is nothing but an argument from incredulity. Evolutionists have so twisted science that in their minds anything goes so long as it adheres to their religious dictates, and skepticism of their bizarre dogma becomes the enemy.

And then there is the complaint that those mutations really aren’t random. So the mutations knew what to design? Of course not, but, but …

But what? Of course the mutations are random with respect to the design. And that is the issue at hand.

Or there is the retort that natural selection remedies all. Those mutations aren’t random at all, they have been selected by a reproductive differential. But of course this after the fact selection does not dictate which mutations should occur. All selection does is kill off the useless mutations. The fact that most mutations don’t work doesn’t help matters as evolutionists imagine, it just reduces the chances of evolution’s miracle stories. The mutations are still random, there are simply fewer (far fewer) of them to work with because most don’t survive.

There’s no magic here that is going to pull amazing designs, such as this insect, out of the Darwinian hat. But to try to convince themselves of their foolish ideas evolutionists tell each other that natural selection creates these biological marvels.

In this case, it is not only a phenomenally complex insect, it is a bug with bifocals:

University of Cincinnati researchers are reporting on the discovery of a bug with bifocals -- such an amazing finding that it initially had the researchers questioning whether they could believe their own eyes.

"To the best of our knowledge, this is the first demonstration of truly bifocal lenses in the extant animal kingdom," the researchers state …

But evolutionary theory was supposed to be the only legitimate way to do science. Didn’t all of biology just happen to arise on its own?

The article explains that using two retinas and two distinct focal planes that are substantially separated, the larvae can more efficiently use these bifocals, compared with the glasses that humans wear, to switch their vision from up-close to distance -- the better to see and catch their prey, with their favorite food being mosquito larvae.

"In addition, we think that within the principle eyes, separate images of the same object could be focused on each of the two retinas, allowing each eye to function as 'two eyes in one,'" the researchers reveal in the article. The tubular-shaped eyes with the bifocals allow them to efficiently focus onto their two retinas, says Annette Stowasser, a UC biology doctoral student and first author on the paper.

Two eyes in one, that is incredible. Natural selection surely must have amazing powers. In fact such a concept could lead to new imaging breakthroughs:

"We're hoping this discovery could hold implications for humans, pending possible future research in biomedical engineering," Buschbeck says. "The discovery could also have uses for any imaging technology," adds Stowasser.

But in fact evolutionary theory contributes little to such findings:

As the researchers zeroed in on how the multiple eyes of this insect worked, they did even more research to try to disprove what they saw. They first used a microscope to look through the lenses of the two eyes detailed in the research article. They saw how the lens could make a second image grow sharper -- something that could only happen with a bifocal. "It was my first research project, and I seriously thought I made a mistake, and then we did additional research to try to kill the hypothesis," says Stowasser. However, their findings were confirmed with more research in addition to observing the operation of the lens and the two focal planes via a microscope. They saw the bifocal again when they used a method to project a narrow light beam through the lens. "Our findings can only be explained by a truly bifocal lens," write the researchers.

Such stories abound in science. The life sciences are full of such design marvels. Yet evolutionary dogma is completely unaffected. Indeed, evolutionists insist that evolution must be true—a fact every bit as much as the fact that the earth is round, that the planets circle the sun, or even gravity. Yes, there must be no question about evolution. Religion drives science, and it matters.

Monday, August 23, 2010

MAVs and Fruit Flies: Unguided Evolution Smarter Than Top Scientists

Autonomous air vehicles are finding increasing use and the Air Force is interested in micro versions:

Micro Air Vehicles (MAVs) typically UAVs with wingspan on the order of 15cm or less are fast becoming commonplace for meeting a wide range of current and future military missions.

But there are tremendous technical challenges:

A typical sensor suite for a MAV consists of GPS, MEMs-based linear accelerometers, angular rate sensors, magnetometers, and barometric-altimeters. While this is adequate for waypoint navigation, the potential of MAVs to replicate the flight agility of natural fliers (e.g., birds, bats, insects) remains elusive, especially in complex terrain such as city streets or forests.

For hints at how to solve such problems designers are looking at nature’s solutions:

The desire to engineer the agility of natural fliers has led researchers to the study of flying organisms to learn how animals combine sensory input with control output to achieve flight maneuverability. Biologists are beginning to understand how visual information is integrated with mechanosensory information in biological systems for flight stabilization, landing, and prey/mate pursuit. Studies are also underway to discover how proprioceptive sensory feedback is used for fine-scale control the movement of wings, legs, etc. during aggressive maneuvers (e.g., obstacle or collision avoidance). These sensory modalities are combined with olfactory or auditory information for predator avoidance and prey/mate pursuit.

Fortunately evolution has created highly advanced flight systems:

The fact that animals such as fruit flies exhibit such remarkable flight agility with many sensory inputs and modest onboard processing suggests a particular kind of coupling between sensing, control and dynamics altogether qualitatively different from that of engineered systems. Advancements in flow control have made it possible to control the separation of flow around wings, either to inhibit separation for higher cruise lift-to-drag ratios or to promote it for large transients in aerodynamics loading for aggressive maneuvers. Natural flyers have anatomic features which probably act as flow control devices (e.g., covert flaps) and may act as aerodynamic sensors.

But understanding evolution’s marvels remains a research challenge:

Rigorous system modeling that can accurately capture the vehicle dynamics, sufficiently accounting for uncertainties in aerodynamic and structural models, remains primitive even for engineered vehicles, let alone for natural flyers. Uncertainty arises both in the veracity of particular models in describing a given flow or dynamics phenomenon, and in unknowns in the inputs, such as wind gusts and their time-dependent effect on the vehicle. While on-going research efforts are addressing some of the critical limitations in this area, significant uncertainties in the dynamics models of MAVs are unlikely to be completely eliminated.

How do random mutations produce such brilliant designs? Answering such questions is, of course, what science is all about. As Darwin explained, evolution opens up wide areas of scientific research. But now we know it also gives top scientists hints to their toughest problems.

Saturday, August 21, 2010

The Gene Myth

Biological variation is, in part, transmitted from parent to progeny. Tall individuals tend to have tall offspring, fast individuals tend to have fast offspring, and so forth. This transmission process is key to the action of natural selection. Those trait variations that are successful in transmitting themselves to the next generation, by definition, survived while those that failed would disappear from the population. So long as traits are transmitted, evolutionists argue that natural selection is inevitable.

In other words, whatever it is that determines your traits is also transmitted to your offspring. Therefore, if you have evolutionarily successful traits then you will have more offspring, and they will receive your successful traits.

But how are the traits defined and transmitted? Darwin didn’t quite know how but in the twentieth century it seemed obvious—via the genes. According to the merger of modern genetics and evolution, it was all in the genes. They determined your traits and they were passed on to your offspring. This view fit evolutionary theory and was quickly accepted as an unquestionable scientific fact.

There is only one problem: it is false.

The fact that our genes are practically identical with the chimpanzees genes should have been a sign to evolutionists that their gene-centric view was problematic. How could the chimp and human be so different if their genes are so similar? Nonetheless, evolutionists proclaimed the great similarity as evidence that there must be an evolutionary relationship between humans and chimps.

In fact the biological evidence is clear: genes are only part of a far more complicated story than what evolution envisioned. As Stuart Newman explains:

Genes, which are composed of DNA, directly specify the sequences of RNA molecules and indirectly, the amino acid sequences of proteins. Before there were multicellular forms, single-celled organisms evolved for as much as two billion years driven, in part, by genetic change, as well as by establishment of persistent symbiotic relationships among simpler cells. During this entire period no cellular structure or function was specified exclusively by a cell’s genes. The protein and RNA molecules produced by cells associate with each other in a context-dependent fashion or, in many cases, catalyze chemical reactions (generating lipids, polysaccharides and other molecules), whose rates depend on the temperature and composition of the external environment. So the population of molecules inside the cell can vary extensively even if the genes do not.

It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true—the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous influence over their functions.

The deployment of information in the genes, moreover, is itself dependent on the presence of certain RNA and protein molecules in the cell. Since, as described above, the composition of the cell’s interior and the activity of many of its proteins depend on more than just the genes, the portion of the genes’ information content that is actually used by the cell is determined, in part, by non-genetic factors. So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent.

As Newman explains, the gene is nothing close to how evolution envisioned it. The gene myth is yet another example of evolution’s failed expectations. It seems that inevitably evolution’s interpretations turn out to be wrong as it has produced a steady stream of false predictions. Evolution is certainly the best counter indicator in the life sciences.

The Law of Compensation (Addendum)

Evolutionists make religious and metaphysical claims that mandate the truth of evolution. Fundamental predictions of their theory turn out to be false. And evolutionists use fallacious reasoning to argue for their theory. These are facts.

Consider, for example, Darwin's circular reasoning in his "Compensation and Economy of Growth" section in Chapter 5 of Origins. In my previous post I explained that Darwin begged the question. Darwin argued that natural selection could bring about change which he presupposed had evolved. Here is his argument broken out into the four points Darwin made:

1. when a cirripede is parasitic within another cirripede and is thus protected, it loses more or less completely its own shell or carapace. This is the case with the male Ibla, and in a truly extraordinary manner with the Proteolepas: for the carapace in all other cirripedes consists of the three highly-important anterior segments of the head enormously developed, and furnished with great nerves and muscles; but in the parasitic and protected Proteolepas, the whole anterior part of the head is reduced to the merest rudiment attached to the bases of the prehensile antennae.

2. Now the saving of a large and complex structure, when rendered superfluous, would be a decided advantage to each successive individual of the species; for in the struggle for life to which every animal is exposed, each would have a better chance of supporting itself, by less nutriment being wasted.

3. Thus, I believe, natural selection will tend in the long run to reduce any part of the organisation, as soon as it becomes, through changed habits, superfluous, without by any means causing some other part to be largely developed in a corresponding degree.

4. And, conversely, that natural selection may perfectly well succeed in largely developing an organ without requiring as a necessary compensation the reduction of some adjoining part.

Or, simply put:

1. Many species have undergone significant loss of components.

2. Such loss can be advantageous, and so increase fitness.

3. Therefore natural selection will select such loss.

4. In the same way, natural selection develops new components. That is, natural selection can add components as well as remove components.

Notice that in Step 1, Darwin takes as his premise that the male Ibla and Proteolepas have undergone evolutionary change. That is, he assumes that they have lost their carapace. His conclusion, that natural selection brings about such change, is presupposed in his premise.

Furthermore, notice that in Step 4, Darwin equates loss of components with addition of components. But there is no basis for this assumption.

This reasoning is fallacious, and therefore not scientific (science requires logical reasoning). Yet every time evolutionists are presented with their own fallacies, they deny there is any such problem.

The Law of Compensation

Are there constraints to how species can vary? A generation before Darwin the German polymath Johann Goethe and French naturalist Etienne Geoffroy Saint-Hilaire formulated their teleological law of compensation in which biological variation occurred according to functional needs. Darwin argued that the law did not apply to organisms in their natural environments. “With species in a state of nature,” Darwin argued that the law of compensation was true to a certain extent for domestic productions, “it can hardly be maintained that the law [of compensation] is of universal application,” even though “many good observers” believed it to be true.

Darwin then cited two particular species which he claimed supported his position. Most readers were probably impressed with the wealth of biological details that Darwin presented in his argument, but his logic was circular.

Darwin argued that the unique features of these two species show that the law of compensation does not hold in the wild because, after all, such unique features must have evolved. Darwin presupposed the truth of evolution in order to find evidence for evolution.

Let’s have a look at Darwin’s argument. Cirripedia, a class in the crustacea phylum, are sessile and highly unique barnacles upon which Darwin had completed a major systematic study. Over against Goethe and Geoffroy, Darwin argued that natural selection, rather than any internal law of biology, could bring about changes he argued were evident in two species named Ibla and Proteolepas:

If under changed conditions of life a structure, before useful, becomes less useful, its diminution will be favoured, for it will profit the individual not to have its nutriment wasted in building up a useless structure. I can thus only understand a fact with which I was much struck when examining cirripedes, and of which many analogous instances could be given: namely, that when a cirripede is parasitic within another cirripede and is thus protected, it loses more or less completely its own shell or carapace. This is the case with the male Ibla, and in a truly extraordinary manner with the Proteolepas: for the carapace in all other cirripedes consists of the three highly-important anterior segments of the head enormously developed, and furnished with great nerves and muscles; but in the parasitic and protected Proteolepas, the whole anterior part of the head is reduced to the merest rudiment attached to the bases of the prehensile antennae. Now the saving of a large and complex structure, when rendered superfluous, would be a decided advantage to each successive individual of the species; for in the struggle for life to which every animal is exposed, each would have a better chance of supporting itself, by less nutriment being wasted.

Thus, I believe, natural selection will tend in the long run to reduce any part of the organisation, as soon as it becomes, through changed habits, superfluous, without by any means causing some other part to be largely developed in a corresponding degree. And, conversely, that natural selection may perfectly well succeed in largely developing an organ without requiring as a necessary compensation the reduction of some adjoining part. [Origins, 6th Ed]

Darwin was not simply applying his theory to a set of observations. He was not illustrating how evolution might have formed these species. Rather, Darwin was building an argument for natural selection. But in constructing his argument, he presupposed that the species had evolved.

Darwin was unquestionably an expert on barnacles, and he could present a detailed example of highly-modified species that most people have never even heard of. But Darwin begs the question when he says that the unique structures of the Ibla and Proteolepas evolved and therefore natural selection can effect such changes.

Thursday, August 19, 2010

Science's Blind Spot

A friend of mine likes to invest in stocks. He understands computer companies so he trades only those stocks. This limitation makes for a simple and straightforward investing strategy. Evolutionists also limit themselves. They investigate only those phenomena that are the result of strictly natural causes. This limitation makes for a simple and straightforward research strategy, though it does create a blind spot.

An investor who buys only computer company stocks can easily identify those companies. He can find companies that build computers, computer components, computer software, and so forth. But how can evolutionists know whether the causes of a past event are strictly natural? How can evolutionists decide which phenomena fall into their research program?

The answer is they can't. Evolutionists have no test for naturalism. They have no way of knowing whether a phenomenon is the result of strictly natural causes.

Imagine an evolutionist using natural laws and processes to describe a phenomenon that does not follow such laws and processes. By searching and searching, he may find a partial fit. So he may have some success, but there are always unexplained observables—data anomalies for which the naturalistic explanation cannot account. Naturalistic explanations will always be problematic. More data will be collected, further analysis will be done, and theories will be modified or replaced altogether. All good scientific research and—in this hypothetical example of a non natural phenomenon—wrong.

When problems are encountered there is no way to tell whether the correct naturalistic solution has simply not yet been found, or whether the phenomenon itself is non natural. Non natural phenomenon can be confused with natural ones, and science has no tools for detecting this, for there is no mechanism within science to detect non natural phenomenon.

Consider the following example. What if it were found that a code existed in all living species and that, within each organism, complicated machinery was used to read vast amounts of stored information via the code? The machinery was so complicated that it automatically (i) read the information, (ii) used the code to interpret the information, and (iii) acted on the instructions.

And what if, after decades of research, no naturalistic explanation could be found for how the code and machinery arose? Even in this example, scientists could not know if naturalistic explanations have been exhausted. There are many problems with naturalistic explanations for the existence of the code and associated machinery. The problem seems to defy naturalistic explanation. But there could be a plausible explanation for how the code arose which has not yet been discovered. And how could anyone prove otherwise? To prove that a plausible explanation does not exist is far more difficult than simply continuing the search for such explanations. For to prove that no explanation exists requires knowledge about all possible explanations.

And what if there were hundreds of other such problems for which naturalistic explanations offered little more than speculation and were consistently falsified?

The answer is, of course, "so what?" Evolutionists cannot consider the possibility that there is no naturalistic explanation. This is science's blind spot. If a theory of natural history has problems—and many of them have their share—the problems are always viewed as research problems and never as paradigm problems.

Evolutionists continue to search for naturalistic explanations for hard problems because they must. Like Sisyphus forever pushing the stone up the hill, they must pursue naturalistic explanations no matter how unlikely. Imagine if they did not. What if, at some point, they were to give up? If they did, then they might miss an undiscovered solution. They might have been on the cusp of a stunning new discovery. One cannot stop trying because the problem seems too difficult—this would be stopping science in its tracks.

Consider the problem of the planet Uranus. After its discovery Uranus did not seem to orbit the sun correctly. Could there be an unknown force perturbing the planet? Uranus's orbit could be explained by the presence of yet another planet. This was one idea to explain the strange orbit of Uranus, and it led to the discovery of the next planet, Neptune.

Imagine if astronomers had considered that Uranus's anomalous path was due to non naturalistic causes. Perhaps an invisible giant was blowing on the planet. Then the prediction and subsequent discovery of Neptune would not have occurred. Deciding on non naturalistic causes can be a science stopper.

How can we decide when a scientific problem is not a research problem, but a paradigm problem? Naturalism has no criteria, no set of rules by which to make such a judgment. And no one wants to turn science's attention away from the future discoveries. In fact, phenomena that are more daunting for naturalism are also more tantalizing, for their explanations will be more surprising and dramatic. Not only does science have a blind spot, not knowing if it has stumbled upon an unsolvable problem, but there is a certain allure of such problems. No one knows what will be science's next "Neptune."

This helps to explain the hesitancy of scientists to admit that non natural phenomena might exist. In science we follow Descartes' prescription and approach everything using naturalistic explanations. It also helps to explain the tolerance for improbable theories. Historical theories, no matter how erroneous they may seem, could be just a "Neptune" away from falling into place.

All of this helps to explain how such an implausible theory as evolution persists. It is underwritten not only by theological conviction that natural causes must suffice, but by a philosophy of science that cannot abide any other possibility, no matter how implausible evolution becomes.

Back to School, Part 4

We continue to examine the work of authors George Johnson and Jonathan Losos in their biology textbook, The Living World ((Fifth Edition, McGraw Hill, 2008). In their chapter on evolution and natural selection, these accomplished evolutionists begin by (1) misrepresenting the relationship between microevolution and macroevolution and biological variation here, (2) making a non scientific, metaphysical, truth claim that mandates the truth of evolution here, (3) making the false statement that the fossils themselves are a factual observation that macroevolution has occurred here and here, and (4) making a series of misrepresentations by carefully selecting the evidence to provide to the student and protecting it with circular reasoning here.

Johnson and Losos’ next move is to distort the molecular evidence. They write:

A series of evolutionary changes thus implies a continual accumulation of genetic changes in the DNA. From this you can see that evolutionary theory makes a clear prediction: organisms that are more distantly related should have accumulated a greater number of evolutionary differences than two species that are more closely related.

But how are species judged to be “distantly related”? By what measure are species compared? The answer, of course, is by the similarities and differences in their visible anatomy. So what exactly is this powerful evolutionary prediction? It is that genetic differences between species are proportional to the differences in their visible anatomy. If two species look alike, then their genomes should be similar. If they look very different, then their genomes should be very different. This is by no means a heroic prediction.

There is, however, another problem with this prediction. Aside from not being heroic, it is false. By now the authors have established a trend of misrepresentation and distortion, and predictably the trend continues:

This prediction is now subject to direct test. Recent DNA research, referred to in section 15.3, allows us to directly compare the genomes of different organisms. The result is clear: for a broad array of vertebrates, the more distantly related two organisms are, the greater their genomic difference.

Here the distortion is mainly one of omission. Like saying that geocentrism’s prediction that the planets should travel across the sky is true without mentioning retrograde motion, Johnson and Losos fail to mention important deviations from this pattern that have even evolutionists acknowledging the evolutionary expectation has failed.

Yes, there is a broad pattern of correlation between visible anatomy and molecular sequences, but there are inescapable and significant deviations which are far outside evolution’s “noise” level. If evolution predicts that “organisms that are more distantly related should have accumulated a greater number of evolutionary differences than two species that are more closely related” then evolution is false, end of story.

The authors next discuss the protein evidence, and in like manner continue their distortion:

This same pattern of divergence can be clearly seen at the protein level. Comparing the hemoglobin amino acid sequence of different species with the human sequence in figure 17.7, you can see that species more closely related to humans have fewer differences in the amino acid structure of their hemoglobin. … Again, the prediction of evolutionary theory is strongly confirmed.

Again, this prediction is not only not “strongly confirmed,” it is in fact false. Yes, hemoglobin and many other proteins fall into the non heroic pattern, but other proteins do not. These are well known to scientists, but evolution has unfortunately compromised science.

Johnson and Losos end this misleading section on the molecular evidence for evolution with yet another fallacious icon of evolution, the molecular clock.

In science theory evaluation is a critical skill. It is crucial to take a neutral, unbiased perspective and be willing to acknowledge both pros and cons of even one’s cherished theories. Unfortunately evolutionists don’t follow this scientific dictum. Yes there is plenty of evidence for evolution, but there are problems as well. But one would never know it from reading the evolution genre. Don’t count on evolutionists to give a scientifically accurate evaluation of their theory. Religion drives science, and it matters.

Wednesday, August 18, 2010

Fossil Find: Fungus Controlled Ant Just Like Today

The fossil record cannot usually tell us about the soft body parts or the behavior of its specimens. For these, we look to the extant species. But now a clever finding reveals an odd behavior in carpenter ants from the distant past.

Nature is full of designs and behaviors not easily preserved in the fossils. Consider the bat, certain types of which map out objects around it as small as a mosquito by sensing the echoes of its own squeaks—a system known as echolocation. The bat emits a high-pitch squeak, well beyond the range of human hearing, up to 2,000 times per second. Next it determines both range and direction to the tiny mosquito by sensing the echo while filtering out echoes from the squeaks of nearby bats. Or consider fish that use underwater electric fields either passively or actively to sense objects around them, including other fish.

It is difficult to determine such details from the fossil record, but they reveal how unlikely is the theory of evolution. Anyone familiar with today’s sonar or radar systems knows the immense complexity involved with such systems: the problems of sensing the echo in the presence of the transmitted signal which can be billions of times stronger, of filtering out spurious signals such as echoes of older transmissions, of combining the echo information with knowledge of your own motion, and so forth. Yet the bat’s detection abilities are superior to those of the best electronic sonar equipment.

It is also difficult to determine complex behaviors from the fossil record. Consider certain Hydra species, a small underwater creature, that develop nematocysts—stinging cells which eject a tiny poisoned hair. A planarian worm known as the Microstomum, consumes Hydra but passes the nematocysts through its digestive system and positions them on its surface. The Hydra meal serves to arm the Microstomum, and when fully equipped the Microstomum omits the Hydra from its diet, resuming again after discharging its ill-gotten arsenal.

For evolution to have formed this system, certain Microstomum must have happened to have selectively digested the Hydra, leaving the nematocysts untouched. Then they also happened to have vectored the nematocysts to the surface and positioned it there. Then certain Microstomum happened to have a feedback loop installed to regulate its diet.

Or consider a sheep parasite known as the brainworm:

The brain worm that reproduces in sheep uses ants to get back into a sheep. The worms get into ants by infecting snails that eat sheep feces. The snails expel tiny worm larvae in a mucus that ants enjoy, and some dozens of worms take up residence in an ant. But this would do them no good if the ant behaved normally; too few ants would be eaten by sheep. Consequently, while most of the worms make themselves at home in an ant’s abdomen, one finds its way to the ants brain and causes the ant to climb up a grass stem and wait to be eaten by a sheep. Ironically, the worm that programs the ant is cheated of happiness in the sheep’s intestine; it becomes encysted and dies.

The whole procedure seems unnecessary. Why do the worm eggs defecated by the sheep not simply hatch and climb up the grass stem to await being eaten by a sheep instead of making the hazardous trip through snail and ant? How could they become adapted to being carried by the ant unless the ant were already programmed to make itself available to be eaten by a sheep?

The list, of course, goes on and on. There is the decoy-fish with its detachable dorsal fin that mimics a smaller fish complete with a dark spot resembling an eye and notch resembling a mouth. The decoy-fish becomes motionless except for the decoy which moves from side to side, causing the “mouth” to open and close. And there is the owl with ears tuned to different frequencies, to better track its prey, and the rattlesnake with heat-sensitive (infrared) sensors to image its prey at night.

Now, a new fossil finding shows just how persistent nature's odd behaviors can be. A carpenter ant (Camponotus leonardi) can be infected by the fungus Ophiocordyceps. Sensitive to the forest temperature and humidity, the fungus must be up off the ground but lower than the forest canopy. It arrives at the desired height by taking over the ant it infects:

The fungus cannot grow high up in the canopy or on the forest floor, but infected ants often die on leaves midway between the two, where the humidity and temperature suit the fungus. Once an ant has died, the fungus sprouts from its head and produces a pod of spores, which are fired at night on to the forest floor, where they can infect other ants.

Scientists led by Hughes noticed that ants infected with the fungus, Ophiocordyceps unilateralis, bit into leaves with so much force they left a lasting mark. The holes created by their mandibles either side of the leaf vein are bordered by scar tissue, producing an unmistakable dumb-bell shape.

It is another fascinating parasitic action that, it would seem, could never be found in the fossil record. But a team of intrepid researchers found a way:

Writing in the journal, Biology Letters, the team describes how they trawled a database of images that document leaf damage by insects, fungi and other organisms. They found one image of a 48m-year-old leaf from the Messel pit that showed the distinctive "death grip" markings of an infected ant. At the time, the Messel area was thick with subtropical forests.

"We now present it as the first example of behavioural manipulation and probably the only one which can be found. In most cases, this kind of control is spectacular but ephemeral and doesn't leave any permanent trace," Hughes said.

And how did evolution design such a Rube Goldberg device? Who knows:

"The question now is, what are the triggers that push a parasite not just to kill its host, but to take over its brain and muscles and then kill it."

He added: "Of all the parasitic organisms, only a few have evolved this trick of manipulating their host's behaviour.

Evolution is truly amazing. It creates in ways we cannot even figure out.

Religion drives science and it matters.

Tuesday, August 17, 2010

Back to School, Part 3

We continue to examine the work of authors George Johnson and Jonathan Losos in their biology textbook, The Living World ((Fifth Edition, McGraw Hill, 2008). In their chapter on evolution and natural selection, these accomplished evolutionists begin by (1) misrepresenting the relationship between microevolution and macroevolution and biological variation here, (2) making a non scientific, metaphysical, truth claim that just happens to mandate the truth of evolution here, and (3) making the grossly false statement that the fossils themselves are a factual observation that macroevolution has occurred here and here.

With this as their start, Johnson and Losos next make a series of misrepresentations of the evidence. First, in an inset story on whale evolution, they show the student a highly selective graphic of the fossil sequence leading to the modern whale. In typical fashion the abundant fossil species that reveal how complicated is the evolutionary hypothesis are omitted. It is as though half a dozen fossils which unambiguously lead to the whale were discovered and nothing else.

Next the authors discuss vertebrate embryos with a graphic showing a reptile, bird and human embryo. They point out that all vertebrate embryos have pharyngeal pouches and a long bony tail. Also, the human embryos "even develops a coat of find fur!" They then inform the student that:

These relict developmental forms strongly suggest that all vertebrates share a basic set of developmental instructions.

But there are significant differences between the embryonic stages of the different vertebrates which the authors fail to mention. If similarities suggest common developmental instructions, then surely the many differences reveal developmental instructions that are not in common. And in any case, why is it that a common set of instructions, to whatever extent they do exist, are evidence for evolution? The authors reveal only selective evidence to the student and make an unjustified claim.

Johnson and Losos next make the circular argument that vertebrates have the same bones:

As vertebrates have evolved, the same bones are sometimes still there but put to different uses, their presence betraying their evolutionary past.

Here Johnson and Losos transition from presenting evidence for evolution to asserting evolution and interpreting the evidence according to the theory. Their phrase "As vertebrates have evolved," marks this unspoken move in the indoctrination. The student is no longer fed evidence for the theory, but instead the truth of the theory has become a given.

Hence the bones in different vertebrates are "the same." After all, they arose from a common ancestor. And since they are "the same," they betray "their evolutionary past." It all makes perfect sense to evolutionists.

And what about those similarities that could not have arisen from a common ancestor? Conveniently, those too are somehow evidence for evolution:

Similarly, in the lower portion of the figure, the marsupial mammals of Australia evolved in isolation from placental mammals, but similar selective pressures have generated very similar kinds of animals.

So similar structures in related vertebrates count as evidence because, after all, they arose from a common ancestor. And similar structures in distant vertebrates count as evidence because, after all, they arose independently from similar selective pressures. Got it (except that selective "pressures" don't generate anything, but don't tell the students that).

Next Johnson and Losos present those structures that have "no use at all!" Back to their whale example, they continue the theme of circular reasoning:

In living whales, which evolved from hoofed mammals, the bones of the pelvis that formerly anchored the two hind limbs are all that remain of the rear legs, unattached to any other bones and serving no apparent purpose.

That, of course, is not an empirical finding but a conclusion based on the assumption that evolution is true. In fact the whale pelvis probably helps in copulation. But so what? After all, whales "evolved from hoofed mammals."

Their next circular example is that vestigial organ, the human appendix. In the great apes it helps with digestion but "The human appendix is a vestigial version of this structure that now serves no function in digestion." So the appendix is evidence for evolution because it is vestigial, and we know it is vestigial because evolutionists say it is.

Unfortunately most students will not be aware of the indoctrination they are receiving. Not will they be aware of the substantial scientific omissions and errors that the text is riddled with. Regarding the appendix, the evolutionary expectation once again failed. As one researcher commented:

Maybe it's time to correct the textbooks. Many biology texts today still refer to the appendix as a 'vestigial organ.'

Indeed, many biology texts do because the science has been compromised by evolution. Religion drives science and it matters.

Monday, August 16, 2010

Jerry Coyne: Simplistic Renderings of Evolutionary Thought

Evolutionist's come in a wide variety of religious flavors. Even in the Christian wing of evolution-dom, the details of how God and evolution are to be understood vary. There is, for example the bottom-up view where God controls the world via sub-atomic particles all working together to effect macro events. Or, at the other end of the spectrum, there is the top-down view where God controls events in a way analogous to the way humans perceive their willed actions. From my perspective, I simply move my arm. I do not initiate nerve impulses in order to activate muscle contractions leading to appendage movement. It's almost difficult to find a view that doesn't fit into the spectrum somewhere. But once again evolutionist Jerry Coyne demonstrates what can be done when facts don't matter.

Evolutionists who are Christian hold to a variety of views of how God used evolution. But there is one view to which they do not hold. They do not believe God used evolution in the way that a sculptor uses a chisel. They do not believe that God precisely and exactly controlled the evolutionary process to achieve a preconceived design. For that would mean that God intended for this gritty world.

As Roman Catholic Nicholas Malebranche hypothesized in the early days of modern science, God limited divine action to secondary causes--creation's natural laws. God preferred the simplicity of such blunt creation instruments to more complex, detailed intervention, even if it meant inefficiencies and evil. Better to believe in divine self limitation than in a God who would create this contemptable world.

Malebranche's seventeenth century system was one of several traditions (mostly Anglican and Lutheran) mandating a strictly naturalistic creation narrative which laid the foundation of modern evolutionary thought.

Creationists view evolutionary thought as atheism is disguise, and atheists such as Coyne view it as creation in disguise. It is neither.

Evolutionists who are Christian hold to a variety of views, but they are not creationists in disguise. Nonetheless, Coyne manages to conclude that evolutionists such as Kenneth Miller, Karl Giberson and Francis Collins are creationists. Of them he writes:

Yes, they do accept that our species changed genetically over time, but they see God as having pulled the strings. That’s not the way evolution works. The graph labels these 48% as believers in intelligent design, and that’s exactly what they are, for they see God as nudging human evolution toward some preconceived goal. We’re designed. These people are creationists: selective creationists.

To count them as allies means we make company with those who accept evolution in a superficial sense but reject it in the deepest sense. After all, the big revolution in thought wrought by Darwin was the recognition that the appearance of design—thought for centuries to be proof of God—could stem from purely natural processes. When we cede human evolution to God, then, we abandon that revolution. That’s why I see selective creationists like Kenneth Miller, Karl Giberson and Francis Collins as parting company with modern biological thought.

One consequence of the naturalistic mandate in evolutionary thought is that divine action cannot be scientifically detectable. As Coyne writes, the appearance of design can stem from purely natural processes. How, and whether or not, God worked via those laws becomes irrelevant. "Let each man hope and believe what he can," as Darwin put it.

But what they may not believe is that design is detectable. They may believe in design, but not that it is detectable. Blinded by his atheistic zeal, Coyne misses this subtlety.

Divine intention is the crux of the argument. If God did not intend for the specifics of this world, but rather merely created natural laws which act on their own, then God is justified and design is not detectable. But if design is detectable, then by definition natural laws are insufficient to explain creation. That means God controlled the process more precisely than we can accept.

Darwin brought forth example after example of designs that made no sense. They must have evolved, and evolution must be true. Today, the story from molecular biology is the same. Junk DNA, regardless of whether some oddball function is found, for evolutionists simply makes no sense on design.

The evolutionary drumbeat that Darwin's idea must be a fact is not a scientific conclusion based on empirical findings in a metaphysical vacuum. Yes there are plenty of empirical findings, but they are viewed through evolutionary spectacles, with all of its rich metaphysical history. It isn't atheism, it isn't creationism, it isn't design, and it isn't empirical science.

Miller, Giberson, Collins and rest are not intelligent design advocates or selective creationists, as Coyne erroneously describes them. Though specifics vary, these Christians are very much in the evolutionary traditions from the Enlightment and before. Today's dominant paradigm did not begin in 1859 and Coyne's new finding that theism is not allowed is absurd. It is also hypocritical since, in typical fashion, Coyne relies on those same theistic arguments (you can see examples here, here, here, here and here).

Sunday, August 15, 2010

No Imagination Shortage

In his piece Reclaiming the Imagination, Oxford's Timothy Williamson argues for more imagination in science. As part of his introduction, the Wykeham Professor of Logic considers our ability to imagine:

Why did humans evolve the capacity to imagine alternatives to reality? Was story-telling in prehistoric times like the peacock’s tail, of no direct practical use but a good way of attracting a mate?

Here Wykeham inadvertently undercuts his premise. There is no shortage of imaginative story-telling in evolutionary thought. Asking evolutionists to reclaim the imagination would be like telling five year olds they need more play time, or telling alcoholics that they need more cheap wine. Yes, imagination is a good thing, but let's start with some realism.

Saturday, August 14, 2010

Of Mice and Men: Unconserved Transcription Factors Binding

You probably learned in high school biology class that the new DNA data has powerfully confirmed evolution. Take any gene and it reveals differences between the species exactly as we would expect. And this sentiment is not limited to high school textbooks. As the Chair of a university Biology department once wrote to me, “DNA sequences provide an absolute and irrefutable record” that evolution is a fact. “Virtually every single gene sequence we examine,” he explained, “can be seen to be represented in closely related species and in more distantly related species with increasing numbers of nucleotide changes as we look at more distant species.” It was, he concluded, “absolute proof, in hard copy, reiterated in every single gene of every single organism.” That is an unfortunately common misrepresentation of the data but the story doesn’t end there. The DNA evidence has falsified several other evolutionary predictions.

Vast stretches of identical DNA segments are found in distant species. Multitudes of differences are found in the DNA of cousin species. Retroviruses that were so often considered to be junk now must be viewed crucial to evolutionary history if Darwin was right. These are some obvious surprises that DNA offered up to evolutionists, but there are more subtle contradictions. One of them, which shows up repeatedly, is the way DNA interacts with proteins.

Consider a recent study of how transcription factor binding is not conserved between mice and men. Transcription factors are proteins that bind to DNA and influence which genes are expressed (transcribed). You may recall that proteins are created by first transcribing genes. So in this complex regulatory network, genes are transcribed to create transcription factor which then return to regulate gene expression.

Evolutionists believe their theory is crucial to biology. Nothing in biology makes sense, they say, except in the light of evolution. We know what questions to ask and where to look only because we have Darwin’s powerful ideas guiding and motivating our research. But transcription factors in the mouse and human do not follow the evolutionary pattern.

Not only do these transcription factors often bind to retrovirus sections of DNA—which evolutionists so often considered to be nothing more than worthless junk—they also usually do not bind in the same DNA locations in spite of their importance. As one commentary explained:

Remarkably, they find that the genomic locations of binding sites for two key regulatory proteins (OCT4 and NANOG) are poorly conserved across species, despite their functional importance in mammalian embryonic stem cell biology. […]

Unexpectedly, only ~5% of binding sites for the two transcription factors OCT4 and NANOG were found in orthologous positions in human and mouse ES cells, suggesting major differences in genome-wide binding profiles between species.

And the story becomes even more contradictory with many of the binding sites were found in non conserved junk DNA:

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

Furthermore, even those genes with conserved transcription factor binding often revealed more detailed differences in the particular binding location:

However, among genes whose OCT4 dependence was conserved between human and mouse, most of the OCT4 binding sites identified were not directly conserved. Instead, the disappearance of a binding site in one species was compensated for by the emergence of a new binding site for the same transcription factor nearby.

The commentary concludes that these findings are consistent with other recent lineage-specific findings:

The notion that some regulatory networks have substantially changed in evolution is also supported by recent independent observations of lineage-specific network rewiring in vertebrate preimplantation embryos and adult liver tissue.

Of course there have been no observations of "network rewiring," lineage-specific or otherwise. This is yet another unfortunate misrepresentation of science. Yes, the new findings are consistent with other recent findings that species differ in subtle yet dramatic ways. But none of this was expected by evolutionary theory. As the paper explains:

Together, these results suggest that many genes have been rewired into the core regulatory network of human embryonic stem cells following the insertion of transposable elements.

So species-specific studies are required:

In contrast, OCT4 and NANOG have very different binding profiles in human and mouse embryonic stem cells, with only ~5% of their sites being homologously occupied. The fact that there is also a limited concordance between regions experimentally observed to be bound and conserved elements, as determined from multispecies sequence alignments, implies that in vivo maps in the relevant species will be important in the study of many mammalian systems. Moreover, to help explain the vast occupancy differences, we showed that species-specific transposable elements have been an important source of new sites in both species.

In other words, evolution doesn’t help explain the findings. What is remarkable is how evolutionists are able to fit even contradictory evidence into their thinking:

we were also able to identify a group of human-specific target genes that show evidence of having been added to the core regulatory network of human embryonic stem cells via the insertion of transposable elements. Although we do not expect all binding events to directly influence gene expression, this data adds important support to a seminal hypothesis on the impact of repeats on the evolution of transcription regulation.

A seminal hypothesis? That is how evolutionists describe unfounded speculation that invokes serendipity to explain unexpected findings.

Genes added to the core regulatory network via the insertion of transposable elements? This is a remarkable example of how evolution has compromised both science and the peer review process. They conclude:

Our results reveal the striking plasticity of the core regulatory network of mammalian embryonic stem cells and the importance that transposable elements have had in facilitating this functional turnover.

This is what happens when evolution is mandated as true. Religion drives science and it matters.

Tuesday, August 10, 2010

Survival of the Fittest or Altruistic Suicide?

Like engineers carefully blowing up a bridge, cells have intricate, programmed suicide mechanisms. The signal is sent and an apparatus of destruction is activated. But suicide hardly fits the evolutionary narrative. Wasn’t this all about survival, reproductive advantages and leaving more offspring? Why would a cell evolve intricate and complex suicide machinery?

The answer is that suicide at the cellular level doesn’t kill the whole organism. Such self destruction serves a range of purposes, from guiding development to keeping cancer at bay. In short, cell death in a multicellular organism can be a good thing.

But if cell suicide in multicellular organisms passes the evolutionary test, what about recent findings of suicide in unicellular organisms? New genome data from the Great Barrier Reef demosponge (Amphimedon queenslandica) reveals high levels of unexpected complexity, for this lowly sponge has an impressive complement of genes. As one evolutionist put it, “This flies in the face of what we think of early metazoan evolution.”

Another evolutionist asked perhaps an even more telling question. “What I want to know now,” he asked, “is what were all these genes doing prior to the advent of sponge?”

That’s a good question because some of those genes are for programmed suicide. What this sponge genome apparently tells us is that programmed cell death would have to have arisen in single-cell organisms. Suicide at the cellular level did kill the whole organism—and that doesn’t make evolutionary sense.

With evolution what we must believe is that programmed cell death did not arise in multicellular species, but in unicellular species. In other words, an intricate, highly complex, set of tools and signals somehow arose and, rather than leading to enhanced survival as evolution calls for, they led to destruction. Evolutionists will need yet another one of their just-so stories to rationalize this.

Monday, August 9, 2010

Butterflies and Flashlights

I once met a fellow who was an aficionado of, believe it or not, flashlights. It seemed rather mundane until I saw all the neat designs using LEDs (light emitting diodes). These semiconductor devices have been greatly improved in recent years and are finding a wide range of uses. But as is so often the case, these technological advancements were there all along in the biological world. In this case, certain butterfly species have their own elaborate optical emission system in their wings. As one researcher put it, “Who knows how much time could have been saved if we'd seen this butterfly structure 10 years ago.”

Up until a few years ago the problem with LEDs was that most of the light was not emitted. This inefficiency was resolved with two-dimensional crystals and layered reflectors called distributed Bragg reflectors (DBRs). And like these high-emission LEDs, scales on the wings of African Swallowtail butterflies make up a two-dimensional photonic crystal enhanced by a three-layer, cuticle-based DBR. The photonic crystal is infused with highly fluorescent pigment and contains an array of hollow air cylinders arranged in a pattern of triangular symmetry. As one paper further explains:

As in ultra–high-efficiency LEDs, these Butterflies’ DBRs support a spectral stop band that matches the peak emission from the structure above it. The DBRs reflect upwardly the downward-emitted fluorescence concurrently with non absorbed longer wavelengths pass through the PCS. The spatial separation between the DBR and PCS minimizes losses via coupling to guided modes in the DBR. Excitation for this fluorescent material appears to be optimized for the radiance from blue skylight, which peaks around 420 nm. Additionally, because the alpha-absorbance band of rhodopsin dominates the green wavelength photosensitivity of Papilio vision, the spectral form of this absorption is ideally placed for stimulation by fluorescence from conspecific wings. As with some shrimps and birds, this enhances signaling, because absorption of visually less productive short wavelengths leads to the emission of longer wavelengths that trigger photoreception.

As the passage explains, the butterfly’s optical emission system is tuned to use sunlight and to maximize visibility. Here is a less technical description of the system:

The trouble with this mechanism is that while half the fluorescent light radiates away from the butterfly, the other half radiates into the wing structure. That half of the light would be lost were it not for the extraordinary structure of the scales.

Vukusic discovered that the base of each scale is a highly efficient three-layered mirror—a structure known as a distributed Bragg reflector. Light from the pigment bounces between these layers, interferes constructively, and then escapes in the direction it came from.

Distributed Bragg reflectors are not perfect, however; some light always becomes trapped on the surface of the reflector and is lost. But the butterfly has another neat trick to get around this. Vukusic and his colleague Ian Hooper discovered that in each scale, sitting just above the mirror, is a slab of material filled with hollow cylinders of air that run perpendicular to the mirror. These cylindrical holes channel the light away from the reflector, preventing it from getting trapped. The slab, says Vukusic, is what optical physicists call a photonic crystal.

The end result is a highly specialized structure that converts skylight into blue-green light, captures this light, and finally channels it out to act like plumage to attract female butterflies.

Was this remarkable system constructed by the blind interplay of natural processes? Evolutionists think so. In fact they are certain it was, though beyond vague speculation they don’t know how.

Evolutionists speculate that perhaps these marvels happened to arise luckily via random mutations. Or perhaps self-assembly and mechanical processes such as buckling, cracking and splitting are important factors. In fact, perhaps pre existing cellular structures serendipitously provide a manufacturing framework. Could it be that “the highly complex inverse opal-type structures could appear ‘suddenly’ in evolutionary time (without having to evolve stepwise)”? Amazingly this is what one finds in evolutionary theory--unfounded speculation underwritten by dogmatic certainty.

Perhaps flashlights also appeared suddenly. Religion drives science, and it matters.