Thursday, November 25, 2010

Eugene Koonin: The Pot Calls the Kettle Black

A paper written by an evolutionist from earlier this year, erroneously claiming to confirm common descent, has now been rebuked by other evolutionists. Unfortunately this is not a healthy sign of evolutionists turning to science, for the new paper is just as unscientific as the first.

In the new paper, entitled “The common ancestry of life,” evolutionists Eugene Koonin and Yuri Wolf state that “the evidence in support of [Universal Common Ancestry] provided by comparative genomics is overwhelming.” This non scientific claim is typical in the evolution literature. Evolutionists have plenty of arguments to back it up, and these arguments illustrate the metaphysics which run deep in evolutionary thought.

One of the chief problems with the original paper was its claim to have complete knowledge of all possible explanations for the origins of a set of proteins it analyzed. That is, of course, a non scientific claim. It is one of those little known, unspoken and unseen claims with huge ramifications. If I can make up a list of all possible solutions to a problem, and conveniently all are clearly false except my favorite, then I can claim my favorite to be the right answer—a fact.

This type of contrastive argument runs all through the evolutionary genre. It assumes there are no alternatives of which I have not conceived. And it is not limited to evolutionary thought. Philosopher Kyle Stanford has shown the importance of this problem of unconceived alternatives.

Evolutionists can present scientific-sounding results that prove beyond a shadow of a doubt that they’re right. And they are right, if their claim is true. But that takes us outside of science, right where evolutionary thought began.

In committing itself to this metaphysic, the original paper falls squarely within evolutionary thought. And the new paper by Koonin and Wolf, though critical of the first paper, not surprisingly makes the same metaphysical commitment. Evolutionists argue amongst themselves about specks while missing the beam. Here is the relevant passage from the Koonin and Wolf paper:

The alternative to UCA [Universal Common Ancestry] is convergent evolution of highly similar sequences of the universal proteins … Several lines of evidence indicate that convergence is not a viable explanation for the extensive sequence similarity that is observed among universal proteins. First, … We believe that together this evidence makes convergent evolution of the highly similar sequences in over 100 proteins that are confidently traced back to the putative Last Universal Cellular Ancestor (a highly conservative estimate) a virtual impossibility.

There you have it. The only alternative to universal common ancestry is convergent evolution which is a virtual impossibility. No matter that universal common ancestry repeatedly generates false predictions and calls for natural laws to perform all manner of heroics. It must be the right answer. After all, convergent evolution is even worse. As philosopher Elliot Sober admits in his explanation of, as he puts it, Darwin’s Principle, it is not that the likelihood of common descent is high, but rather that the likelihood of the alternative is so low. Religion drives science, and it matters.

Wednesday, November 24, 2010

The Fly’s Adaptive Aerodynamics

Recent experiments have revealed that when perturbed in flight, a fruit fly can recover its heading to within 2 degrees in less than a tenth of a second. Here’s how the researchers describe the results:

Just as the Wright brothers implemented controls to achieve stable airplane flight, flying insects have evolved behavioral strategies that ensure recovery from flight disturbances.

This is yet another example of evolutionary euphemism. Recovery from flight disturbances is a complex, fine-tuned capability integrating sensors, algorithms and actuators. Not the stuff of random mutations. So the evolutionary euphemism compares it with the Wright brothers and their flying machines.

Pioneering studies performed on tethered and dissected insects demonstrate that the sensory, neurological, and musculoskeletal systems play important roles in flight control.

Indeed, sensory, neurological, and musculoskeletal systems need to be tightly coordinated.

High-speed video and a new motion tracking method capture the aerial “stumble,” and we discover that flies respond to gentle disturbances by accurately returning to their original orientation. These insects take advantage of a stabilizing aerodynamic influence and active torque generation to recover their heading to within 2 degrees in less than 60 ms. To explain this recovery behavior, we form a feedback control model that includes the fly’s ability to sense body rotations, process this information, and actuate the wing motions that generate corrective aerodynamic torque.

The fly’s sensors are tiny sensors known as halteres, structures that evolutionists have considered to be rudimentary—evolutionary leftovers. Now we’re told they just happened to evolve fantastic gyroscopic sensing capabilities, which just happened to be sent to the fly’s neurological circuits, which just happened to compute meaningful flight control maneuvers, which just happened to be sent to the fly’s musculoskeletal system. No wonder evolutionists resort to euphemisms.

Thus, like early man-made aircraft and modern fighter jets, the fruit fly employs an automatic stabilization scheme that reacts to short time-scale disturbances.

An automatic stabilization scheme for short time-scale disturbances that just happened to arise? Religion drives science, and it matters.

Tuesday, November 23, 2010

Chickens Have Cellular Sunglasses

When light enters your eye it triggers a sequence of actions, ultimately causing a signal to be sent to your brain. 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. The interaction causes the chromophore to change configuration and this, in turn, influences the large, trans-membrane rhodopsin protein to which the chromophore is attached. This is just the beginning of the cellular signal transduction cascade. But before any of this begins, in some species the incoming light has already been filtered and focused.

The chromophore photoisomerization is the beginning of a remarkable cascade that causes action potentials to be triggered in the optic nerve. In response to the chromophore photoisomerization, the rhodopsin 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.

All this because a single photon entered into the fray. In short order, this light signal is converted into a structural signal, more structural signals, a chemical concentration signal, back to a structural signal, and then back to a chemical concentration signal leading to a voltage signal which then leads back to a chemical concentration signal. There is, of course, a wealth of yet more detail which makes the information conversion process far more complicated.

Optical oil drops

And there is a seemingly endless stream of variations on this cascade. One fascinating variation is the use of special oil to filter and focus the incoming light before it ever reaches the first step of exciting the light-sensitive chromophore molecule. In chickens, for example, these brightly colored oil droplets seem to improve color discrimination as they focus the light toward the target chromophore molecules.

And these droplets are not just any kind of oil. The oil and its optical properties are finely tuned and specific to the different types of light sensitive cells. In fact the oil provides a convenient method for determining the cell type, which allowed researchers to map the optimal pattern the different cell types fall into. It is all part of what one writer called “a masterpiece of biological design.”

Evolutionists describe this as a consequence of evolutionary pressure:

Our results indicate that the evolutionary pressures that gave rise to the avian retina’s various adaptations for enhanced color discrimination also acted to fine-tune its spatial sampling of color and luminance.

Evolutionary, or selective, pressure is an internal contradiction in evolutionary thought. One can hardly blame evolutionists for their use of such action themes. It sounds better than the just-add-water account which holds that random biological variation produced nature’s marvels. But in fact there can be no such pressure in evolution’s the-world-is-a-fluke hypothesis.

The whole idea in evolutionary theory is that random mutations are, well, random. Biological variation is random with respect to need. There can be no “pressure” to produce any smart designs. And the evolutionist’s hole card, natural selection, doesn’t help. It only kills off the failures (of which there must have been a great many). Every mutation, one after the other, leading to nature’s gems such as the fine-tuned oil droplet in light sensitive cells, must have occurred for no reason. Only after they occurred could natural selection appreciate the brilliance of these random events. And that’s a fact. Religion drives science, and it matters.

Sunday, November 21, 2010

Ethics and the Evolution of the Synapse

Scientific mistakes are no sin, but it would be a mistake to think there is no ethical dimension to the theory of evolution. The ethical aspects of evolution are most obvious in its misrepresentation of science. Even evolutionists agree scientists are responsible for the accurate transmission of scientific knowledge to the public. And yet evolutionists consistently misrepresent science, claiming evolution is an undeniable fact. It would be irrational, they say, to think otherwise. What is striking is the degree of this misrepresentation. We’re not talking about a minor mistake or two that led to an error in the third decimal point. We’re not talking about a subtle blunder that could easily go undetected. Consider, for example, the evolution of the synapse.

In my previous post I discussed the brain and an evolutionist wrote to me about this paper. Does it not reveal solid hypotheses for the evolution of the brain’s circuitry? Before we answer this question we need briefly to review the biology involved.

Our nervous systems contains a great many nerve cells, or neurons. Like wires in a machine, neurons carry electrical signals. And just as wires pass electricity to other wires, so too neurons pass their electrical signals to other neurons. Also, just as wires ultimately connect to a motor, or a sensor, or some other device, neurons ultimately connect not to another neuron, but to tissue. But this is where the similarity ends. The closer we look at neurons and their connections, the more profound are the discoveries we make. So first let’s review how the signal travels down the neuron and how it is transmitted.

Nerve cells have a long tail which carries an electronic impulse, called an action potential. The tail can be several feet long and its signal might be passed to another neuron, stimulate a muscle to action, control a gland, or report a sensation to the brain.

Like a cable containing thousands of different telephone wires, nerve cells are often bundled together to form a nerve. Early researchers considered that perhaps the electronic impulse traveled along the nerve cell tail like electricity in a wire. But they soon realized that the signal in nerve cells is too weak to travel very far. The nerve cell would need to boost the signal along the way for it to travel along the tail.

After years of research it was discovered that the signal is boosted by membrane proteins. First, there is a membrane protein that simultaneously pumps potassium ions into the cell and sodium ions out of the cell. This sets up a chemical gradient across the membrane. There is more potassium inside the cell than outside, and there is more sodium outside than inside. Also, there are more negatively charged ions inside the cell so there is a voltage drop (50-100 millivolt) across the membrane.

In addition to the sodium-potassium pump, there are also sodium channels and potassium channels. These membrane proteins allow sodium and potassium, respectively, to pass through the membrane. They are normally closed, but when the action potential travels along the nerve cell tail, it causes the voltage-controlled sodium channels to open quickly. Sodium ions outside the cell then come streaming into the cell down the electro-chemical gradient. As a result the voltage drop is reversed and the decaying electronic impulse, which caused the sodium channels to open, is boosted as it continues on its way along the nerve cell tail.

When the voltage goes from negative to positive inside the cell, the sodium channels slowly close and the potassium channels open. Hence the sodium channels are open only momentarily, and now with the potassium channels open, the potassium ions concentrated inside the cell come streaming out down their electro-chemical gradient. As a result the original voltage drop is reestablished.

This process repeats itself until the impulse finally reaches the end of the nerve cell tail. Although we’ve left out many details, it should be obvious that the process depends on the intricate workings of the three membrane proteins. The sodium-potassium pump helps set up the electro-chemical gradient, the electronic impulse is strong enough to activate the sodium channel, and then the sodium and potassium channels open and close with precise timing.

How, for example, are the channels designed to be ion-selective? Sodium is about 40% smaller than potassium so the sodium channel can exclude potassium if it is just big enough for sodium. Random mutations must have struck on an amino acid sequence that would fold up just right to provide the right channel size. That is an astronomical long shot.

The potassium channel, on the other hand is large enough for both potassium, and sodium, yet it is highly efficient. It somehow excludes sodium almost perfectly (the potassium to sodium ratio is about 10000), yet allows potassium to pass through almost as if there were nothing in the way. The solution seems to be in the particular amino acids that line the channel and their precise orientation. For potassium, moving through the channel is as easy as moving through water, but sodium rattles around—it fits in the channel but it makes less favorable interactions with the amino acids. Again, the amino acid sequence of the potassium channel is fine-tuned for the job.

Next, when the action potential reaches the end of the neuron it is passed on. First, the action potential causes voltage-controlled calcium channels, located at the end of the tail, to open. Positive calcium ions on the outside stream into the neuron through the open channels. The calcium ions influence special proteins just inside the neuron, which in turn cause small bubbles to dock with the cell membrane. The bubbles contain a neurotransmitter chemical which is released to the outside of the cell.

Very close to this end of the neuron is the other cell with which the neuron communicates. The tight junction between the two is called the synapse. In this case, the neurotransmitter chemical floats across the gap between the cells, and attaches to the other cell, setting off the desired action, which is another story. Again, we’ve left out many details. There are literally thousands of proteins working behind the scenes. As one writer explained:

The human brain is truly awesome. A typical, healthy one houses some 200 billion nerve cells, which are connected to one another via hundreds of trillions of synapses. Each synapse functions like a microprocessor, and tens of thousands of them can connect a single neuron to other nerve cells. In the cerebral cortex alone, there are roughly 125 trillion synapses, which is about how many stars fill 1,500 Milky Way galaxies.

Needless to say, this whole process occurs with great reliability and speed. Nerve cells are constantly firing off in your body. They control your eyes as you read these words, and they send back the images you see on this page to your brain. They, along with chemical signals, control a multitude of processes in our bodies. And new research continues to peel back the layers of this profound design. As one scientist recently explained:

One synapse, by itself, is more like a microprocessor—with both memory-storage and information-processing elements—than a mere on/off switch. In fact, one synapse may contain on the order of 1,000 molecular-scale switches. A single human brain has more switches than all the computers and routers and Internet connections on Earth.


Now, having reviewed the biology, let us consider the evolutionist’s paper. It is a review of the origin and evolution of synapses. Given the molecular biology of synapses, the neuron, action potentials, and associated machinery, you might think random mutations and the like creating all this would be unlikely. And indeed the paper has its share of caveats and uncertainties. Here are some examples:

It is conceivable that the first protein–protein interaction that led to synaptogenesis would be homophilic.

we postulate that these molecules originated before the evolution of synapses …

Cadherins may therefore be important for cytoskeletal rearrangement in choanoflagellates and may represent a precursor to synapse formation.

heterophilic transynaptic protein interactions probably evolved later.

… implying that they may form a protosynaptic complex involved in sensing environmental stimuli and that they could represent an evolutionary precursor to synaptic sites.

But this is only the beginning. In fact nowhere does the paper explain in scientific detail how the synapse and associated machinery could have arisen on its own. How did the massive protein machines, with their intricate and fine-tuned functions arise? How did evolution establish the right ionic concentrations inside and outside of the cell? How did the finely-tuned action potential initiation and transmission mechanisms evolve? How did the neurotransmitter chemical concentrations, complete with bubbles and associated proteins arise? And none of this would function without the finely-tuned receptors on the receiving cell. It also would not function without the right mechanisms for replenishing the neurotransmitter chemical, as well as the calcium, potassium and sodium concentrations. And how did evolution bundle the neurons, and connect them to the right receptors, implementing trillions of synapses. How did evolution provide both memory-storage and information-processing elements to the synapse?

Aside from vague speculation the paper provides no such details. Instead, such problems are, in typical fashion, pushed back. The protein machines, for instance, are said to have “originated before the emergence of classical morphological synapses and have been co-opted for synaptic roles.”

Indeed synapse designs are so widespread amongst the species that the paper must conclude that “Many mammalian synaptic components existed before the appearance of synapses.”

High detail

It is not surprising that evolutionists would be unable to provide scientific details for the evolution of the synaptic components. But when not failing to provide such foundational data, the paper is decidedly confident and certain. It states in no uncertain terms that evolutionary studies “point to an ancestral molecular machinery in unicellular organisms — the protosynapse — that existed before the evolution of metazoans and neurons”

Similarly, the reader learns that this protosynapse consists of “synaptic components that were present before the emergence of synapses.” Were present? It is remarkable that evolutionists can know such details.

Here is another example of how the paper confidently presents detailed evolutionary histories as fact:

In general terms, the evolution of synaptic genes at the eukaryote–metazoan and metazoan–chordate boundaries preceded their expression in different populations of neurons and synapses and thereby allowed diversity of function in nervous systems that have emerged later, in evolutionary terms, and that are generally larger.

Again, these evolutionary conclusions are amazing. What powerful scientific methods do evolutionists possess that can yield such detail and certainty?

A breach of ethics

The answer, it seems, is none. Reading further we see only weak justifications for these sweeping conclusions. In fact the paper’s conclusions are largely based on various genetic comparisons. Here is an example:

If we can deduce the composition of the last common ancestor of all synapses, the ursynapse, then we should be in a position to address the question of how and why the first synapse originated. We approach the question of the composition of the ursynapse by taking synaptic proteins identified in vertebrate model organisms and searching for orthologues in the genomes of two categories of organism.

Searching for orthologues? That may sound sophisticated, but it amounts to nothing more than searching for similar genes in different species. That’s it. Evolutionists search for these and other genetic similarities, and from those make sweeping conclusions and present them as new truths.

One of the ever-present themes in the evolution genre is that similarity mandates evolutionary relationship. If two species share a common design, such as similar genes, it must have arisen from a common ancestor. This is not a scientific premise, and it is an example of how metaphysics makes its way into science under the guise of the scientific method. Searching for orthologues certainly sounds scientific. But in the hands of evolutionists it is religiously-driven science.

Evolutionists insist that evolution is a scientific fact every bit as much as is gravity or the roundness of the earth. That is a misrepresentation of science that goes far beyond a simple mistake. For centuries evolutionary thinkers have issued unlikely speculation as undeniable truth, and the gap is only becoming wider. Today, the certainty they insist upon is prima facie absurd. Evolution has degraded to a religiously-driven junk science making, what are frankly, silly claims. But the manipulation of science is no joke. Misleading the public with inexcusable misrepresentations is a serious breach of ethics. Religion drives science, and it matters.

Wednesday, November 17, 2010

More Switches Than the Internet

Array tomography, yet another new biological imaging technology, is yielding early results. Click here, for example, to see a video rendition of a mouse cortex. Here’s how one writer described the new results:

The human brain is truly awesome. A typical, healthy one houses some 200 billion nerve cells, which are connected to one another via hundreds of trillions of synapses. Each synapse functions like a microprocessor, and tens of thousands of them can connect a single neuron to other nerve cells. In the cerebral cortex alone, there are roughly 125 trillion synapses, which is about how many stars fill 1,500 Milky Way galaxies.


Researchers at the Stanford University School of Medicine have spent the past few years engineering a new imaging model, which they call array tomography, in conjunction with novel computational software, to stitch together image slices into a three-dimensional image that can be rotated, penetrated and navigated.


They found that the brain’s complexity is beyond anything they’d imagined, almost to the point of being beyond belief, says Stephen Smith, a professor of molecular and cellular physiology and senior author of the paper describing the study:

And as Smith explains:

One synapse, by itself, is more like a microprocessor—with both memory-storage and information-processing elements—than a mere on/off switch. In fact, one synapse may contain on the order of 1,000 molecular-scale switches. A single human brain has more switches than all the computers and routers and Internet connections on Earth.

Evolutionists are certain, however, that all of this—and all the rest of biology by the way—just happened to arise on its own. They can’t explain how, but they’re absolutely certain it is a fact. After all, any other explanation is not scientific and in any case chimpanzees and humans have way too much in common. Anyway the world is too evil and god never would have made all those beetles, so evolution must be true. With evolutionists, it's all about philosophy and theology. Religion drives science and it matters.

Tuesday, November 16, 2010

How the Eukaryote Got its Mitochondria

If someone tossed an important part onto their car’s engine, and slammed down the hood, you wouldn’t expect it to work. And if it did work you’d be suspicious. The claim is either absurd or rigged.

The power plant of eukaryote cells is the mitochondria and evolutionists say these marvels first arose when an early pre-eukaryote cell swallowed up a bacteria which then morphed into a mitochondria.

The story may not be as unlikely as it first appears as cells are able to import, one way or another, all kinds of molecular debris. And sometimes the flotsam turns functional.

To be sure turning an early bacteria into the finely-tuned mitochondria, and integrating it within a host cell, does not seem to be an easy task. One way the mitochondria interacts with the cell around it is via its importing of protein machines from the cell’s cytoplasm. But how did its protein importing mechanisms arise?

As evolutionists wrote earlier this year, those importing mechanisms may be been donated from the host cell, or they may have come from within:

How did the process of protein import in mitochondria—which facilitated the evolution of this organelle, and thus, eukaryotic cell evolution—arise? Was the process driven by the ancestral host cell or by the prokaryotic endosymbiont, or by both? … [In the former], to capitalize on energy production by the ancestral endosymbiont, a protein sorting and importing mechanism was necessary to relocate host cell proteins to the endosymbiont.

To capitalize on energy production? Very clever.

Once established [at the outer membrane], host proteins could then gain access to the intermembrane space and the inner membrane in an “outside-to-inside” trajectory of evolution.

More cleverness, but it was all built into previous designs:

In support of this view, some characteristics of host cell proteins appear to have served as “preadaptations” for mitochondrial protein import.

On the other hand, maybe it all happened in the reverse order:

An alternative viewpoint favors an active role of the endosymbiont in establishing key elements of the protein import pathway. We suggest that both the TOM complex in the outer membrane and the transporter in the inner membrane (TIM complex) were derived from ancestral bacterial proteins—that is, proteins originally encoded by the bacterial endosymbiont’s genome. This evolutionary tinkering—constructing a new molecular machine from existing parts—inside the ancestral bacterium is in line with Jacob’s proposition for the evolution of new cellular functions, which states that new pieces of cellular machinery arise ad hoc, often cobbled together from pieces (proteins) already available in other guises.

But here too evolution is ingenious, constructing amazing mechanisms from chewing gum and baling wire.

Who knows, perhaps the eukaryote did obtain its mitochondria by hijacking a bacteria and capitalizing on its ill-gotten gain. But in that case we must believe evolution just happened to create all kinds of parts, not to mention the bacteria and the means for it to be swallowed by the eukaryote, that fortuitously came together to produce the much needed mitochondria.

These various parts and mechanisms would have to have arisen for other reasons. They could not have been selected to form the mitochondria.

Perhaps the chances of the mitochondria evolving were high. Perhaps the brilliant eukaryotic power house is a no-brainer. But if so do not evolutionists think twice about their story? When they claim that the evolution of some marvel is easy, they are just bumping the problem back a few spaces where it is out of sight.

Monday, November 15, 2010

Insects Compute Optimal Flight Plans

Anyone who travels much by air knows that pilots try to ride the wind. Flights may even deviate substantially from the shortest-distance route if the wind is strong enough elsewhere. But of course the wind is not likely moving exactly toward your destination. Add to this the fact that the wind also varies with altitude, and the problem of designing the optimal route of flight becomes highly complex. It is a problem in the calculus of variations (optimizing functionals rather than mere functions) and is analogous to the optics problem of predicting the path of light through a medium with variant refractive index. But this approach requires analytical wind fields, described with functions, rather than numerically derived winds described, for instance, on a grid. In practice the optimal routing problem is solved using various iterative methods. Amazingly, migratory insects also solve this type of problem.

Research using entomological radar has found that migratory insects such as butterflies and moths perform their own flight planning in order to optimize their flights across continents. They select the right time to ride the wind, and they determine the right altitude and flight heading to reach their destination (rather than where the wind is going). As one of the researchers explained:

Migratory butterflies and moths have evolved an amazing capacity to use favourable tailwinds. By flying at the heights where the wind currents are fastest, migratory moths can travel between their summer and winter grounds in just a few nights.

And what is the evidence that this amazing capacity evolved? What mutations produced it? And how did evolution create the ability of the insects know when to start their journey and where they should go? You know the answer: “We’re not sure but we know they evolved because evolution is a fact.” Religion drives science and it matters.

Friday, November 12, 2010

Allele-Specific DNA Methylation and the World of Epigenetics

The ability of species to adapt to changing and challenging conditions is remarkable and due to a wide variety of molecular mechanisms. Many of these mechanisms fall into the broad category of epigenetics of which we are still learning the details.

One of the best known epigenetic mechanisms is DNA methylation in which a small molecule (a methyl group) is added to the DNA macromolecule at particular locations. Like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on. This DNA methylation is accomplished via the action of a protein machine that adds the methyl group at precisely the right location in the DNA strand.

The methylation occurs at certain target sites along the DNA sequence where specific short DNA sequences appear. These sequences are found by protein machines as they move along the DNA. The protein machines search for these sequences and add a methyl group to the appropriate DNA base.

The protein machine binds to the DNA, twists the helix so the DNA base rotates into a precisely shaped pocket in the protein, and the protein then facilitates the transfer of the methyl group from a short donor molecule to the DNA base.

In bacterial studies it has been found that the short donor molecule does more, however, than just supply a methyl group. It also helps to control the protein. First, the short donor molecule binds to the pocket of the protein so the methyl group is ready for transfer. But the donor molecule also binds to another site on the protein. This binding serves to alter the structure of the protein, enhancing its function. So the protein is designed to do its job when it is charged with a donor molecule.

But not all of the DNA target sequences are methylated. This complex DNA methylation function doesn’t occur if the target sequence is protected by another protein that binds to the sequence. This protein binds to some of these DNA target sequences but not all. The result is a particular DNA methylation pattern which influences which genes are expressed.

Mark the marker

Furthermore, the methyl group marker can, itself, be modified. That is, the mark can be marked, thus adding another layer of information to the epigenetic mechanism. For instance, the methyl group can be hydroxylated. And of course a different molecular machine is required for the task, and the information of when and where to go to work is needed.

All of this makes for a complex DNA methylation pattern which is superimposed on the DNA macromolecule. In fact, this encoding of epigenetic information varies substantially across different regions of the DNA and it varies between the two alleles of a given gene and this allele-specific methylation can be tissue-specific.
DNA methylation is also transmitted across generations, but in the embryonic stages of development can be erased by yet another protein machine.


In addition to the DNA macromolecule, methyl groups are also used to tag the histone proteins about which the DNA is wrapped. The histones have a hub, around which the DNA wraps, and a tail that sticks out on which chemical markers are attached. As with DNA, these markers are signals for the protein machinery. And like DNA, these tags are removed as well. Such modifications and removal of these chemical tags means that these codes are dynamic, and there are protein inspectors that double-check these complex encodings.

These subtle codes are also context dependent. In one type of cell a histone modification may turn off a gene whereas in another type of cell the same histone modification may turn on the gene.

In addition to methylation, histones can also vary by tiny differences in their amino acid sequence. This histone sequence variation serves as yet another type of tag used for gene regulation.

Furthermore, histone variants are not merely static sign posts that influence gene expression. These variants are moved, by other proteins, between different locations in the genome, resulting in migration patterns that occur in the embryonic development phases.

Did epigenetics evolve?

Evolutionists do not think twice about the question of whether the epigenetic world evolved. Of course it did. Evolution is a fact, and so all of biology is its handiwork. This despite the “hint at an unimagined complexity of the genome” as one science writer admitted.

With evolution we must be believe that levels of complexity we could never have dreamed of, and which contradict evolution’s predictions, arose from random mutations (no, natural selection doesn’t change that fact, the mutations are still random). And as those complex machines and mechanisms arose, we must either believe there would be no use for them, or just luckily there would be some intermediate use for them that they happened to fulfill, while waiting for a later time for their epigenetic functions to be realized.

In fact, beyond sheer speculation, there is no explanation for how the epigenetic world evolved. The conviction that it did evolve is not a scientific conclusion—it comes from the belief that evolution is a fact.

Of course none of this means that the epigenetic world absolutely could not have evolved. But there certainly is no justification for taking up positions at the other end of the spectrum. There is no scientific justification for proclaiming that evolution, including the evolution of the epigenetic world, is an undeniable fact, as evolutionists insist.

It is unfortunate that we stake out such hard-edged, dogmatic positions that can be defended only by shouting down and blackballing dissent. In spite of the science, evolution must be true and all who disagree must be rejected.

Evolutionists are not the first, and undoubtedly won’t be the last, to engage in religious narrow-mindedness and parochial intolerance, in defiance of the facts. Religion drives science, and it matters.

Thursday, November 11, 2010

Did Horizontal Gene Transfer Create Evolution?

It is common knowledge that evolution is supposed to be caused by random biological variation that helps with reproductive success. By definition such biological variation is more likely to be passed on to later generations and eventually to become established in a population. And, according to the theory, if such variation accumulates it leads to all kinds of biological novelties. One problem, however, is that biological variation is not for free. It arises as a consequence of sophisticated molecular machinery and this forces evolutionary theory to violate science’s dictum of simplicity. Scientific explanations should not consist of a series of coincidences and lucky strikes. In Darwin’s day the knowledge of biology was sufficiently rudimentary that this free lunch problem could be overlooked. But the twentieth century dispelled any such notion that biological variation is a freebie. And recent research has made the problem even worse.

For decades evolutionists have mostly characterized the massive biological variation their theory depends on as a consequence of genetic changes. One example everyone remembers from their high school biology class is mutations, but there are many others as well. But these changes and rearrangements depend on the preexistence of elaborate and complex molecular structures and machines. The DNA macromolecule is just one player in this profound micro choreography. With evolution, what we must believe is that this molecular world somehow evolved, and then as luck would have it the various biological variation mechanisms, that evolutionists place so much faith in, became possible. In other words, evolution produced evolution.

That is quite a bit of serendipity that has been built into evolutionary theory. But that’s not all.

In recent years an even more elaborate source of biological variation has been recognized to be important in biology. It is called lateral or horizontal gene transfer to indicate that genetic material is transferred between individuals rather than vertically between generations. In other words, genes can move from one individual to another, and even between species.

Horizontal gene transfer doesn’t just happen. It is not for free. As with other forms of biological variation it rides on a train of elaborate mechanisms and just-right molecular properties.

And evolutionists are now depending on increasingly heroic versions of horizontal gene transfer to explain what science is telling us. One example is how evolutionists use horizontal gene transfer to explain the origin of biology’s molecular machines.

For example, the universal genetic code has for half a century now been used as powerful evidence for evolution. After all, all species share essentially the same code. It is the ultimate homology running through all of biology. Is it not obvious that the species have inherited the code from an early ancestor via evolution, as the code remained unchanged for eons?

But if that’s so obvious, then how did the code arise in the first place. In fact, the code has remarkable properties useful for the higher eukaryote species. How did such a profound design happen to arise so long ago? The evolutionary explanation that it was a “frozen accident” not only seems rather facile, but does little to help our understanding.

More recently evolutionists have found that attempts to simulate the evolution of the genetic code via traditional evolutionary mechanisms leads to failure. As one report explained:

Starting with a random initial population of codes being used by different organisms—all using the same DNA bases but with different associations of codons and amino acids—they first explored how the code might evolve in ordinary Darwinian evolution. While the ability of the code to withstand errors improves with time, they found that the results were inconsistent with the pattern we actually see in two ways. First, the code never became shared among all organisms—a number of distinct codes remained in use no matter how long the team ran their simulations. Second, in none of their runs did any of the codes evolve to reach the optimal structure of the actual code. “With vertical, Darwinian evolution,” says Goldenfeld, “we found that the code evolution gets stuck and does not find the true optimum.”

Enter horizontal gene transfer. To remedy their failures, the evolutionists built their computer world on a super horizontal gene transfer capability. In this HGT-on-steroids world, species not only could readily and successfully exchange genetic material, but in such a way that they could swap parts of the genetic code as well. In other words, the evolutionists constructed an algorithm to evolve the code:

The results were very different when they allowed horizontal gene transfer between different organisms. Now, with advantageous genetic innovations able to flow horizontally across the entire system the code readily discovered the overall optimal structure and came to be universal among all organisms.

Like a Newton-Raphson search, the algorithm nicely tracked to more advantageous codes. Of course there is no evidence that the world so long ago just happened to provide for such an algorithm. But that has never stopped evolutionists. After all, if evolution is true then it must have happened somehow:

Goldenfeld admits that pinning down the details of that early process remains a difficult task. However the simulations suggest that horizontal gene transfer allowed life in general to acquire a unified genetic machinery, thereby making the sharing of innovations easier. Hence, the researchers now suspect that early evolution may have proceeded through a series of stages before the Darwinian form emerged, with the first stage leading to the emergence of a universal genetic code. “It would have acted as an innovation-sharing protocol,” says Goldenfeld, “greatly enhancing the ability of organisms to share genetic innovations that were beneficial.”

Perhaps so, but what we do know for certain is that these evolutionists are good with computers.

We also now know that evolution relies on an even greater degree of serendipity. Biological variation has always been slipped in through the back door, but now the free lunch is even more obvious. The story now calls for an elaborate innovation-sharing protocol world to have arisen which, in turn, just luckily constructed another vertical evolution world. Once again, evolution creates evolution. Religion drives science and it matters.

Wednesday, November 10, 2010

Abusing Science

When confronted with their own religious doctrine, evolutionists are quick to deny any such thing. Evolution is based on religious claims, but after making these claims evolutionists insist their religious beliefs are entirely gratuitous. Their religious claims, evolutionists explain, are merely criticisms of design and creation. After all, we need to explain to the creationists why their ideas are not scientifically supported. The fact of evolution, on the other hand, is simply a scientific conclusion. But this evolutionary rendition is, as usual, at odds with the facts.

Darwin's theory of evolution was motivated and justified by on-going theological and philosophical concerns. Though these concerns were spread across different continents, religions and centuries, there is a particular religious perspective at work. And naturally it is from this perspective that evolutionists argue. Their religious arguments are not merely sidebar rebukes of creation.

Consider, for example, Darwin's argument that the pattern, or classification, which the different species fall into would never have resulted if they had been created:

The several subordinate groups in any class cannot be ranked in a single file, but seem clustered round points, and these round other points, and so on in almost endless cycles. If species had been independently created, no explanation would have been possible of this kind of classification.

This is, of course, a metaphysical claim. If the species were independently created then, so the reasoning goes, they would have no pattern of similarities. After all, independently created species must have independent designs. And since we find similar designs, the species must not be created. Instead, they must be derived one from the other. For there can only be two possibilities: created with independent designs or evolved with design similarities.

It is not that the species obviously morph into other species, but rather that they do not appear to have been created. The reasoning, as always, is metaphysical.

And this metaphysical claim is distinctly evolutionary. It is not representative of design or creation. Indeed, Linneaus had constructed his hierarchy revealing the classification described by Darwin. But Linneaus believed god created the hierarchical classification. For Linneaus, independent creation certainly did not imply independent design. And this is no trivial example—Linneaus was the leading scientist of his day, and his views were tremendously influential. The evolutionist Darwin was not so much addressing creationism as it was commonly understood, but rather creationism as it was understood by Enlightenment theology.

Nor was Darwin's religious claim a trivial example. It has been repeatedly proclaimed ever since. As Niles Eldredge more recently explained:

Could the single artisan, who has no one but himself from whom to steal designs, possibly be the explanation for why the Creator fashioned life in a hierarchical fashion—why, for example, reptiles, amphibians, mammals, and birds all share the same limb structure?

Of course not. To say that the Creator came up with such a pattern makes no sense according to the evolutionists. Evolution is driven by religious belief. This world is not what we would expect from a creator or designer, and so evolution is mandated.

If this is how evolutionary thought works, then we would expect evolutionists to make truth claims about their theory. If my beliefs dictate that this world is not created or designed, then I will conclude it arose naturalistically, on its own.

Therefore we can make a prediction about evolutionary thought. If it is driven by religious beliefs, then we should find these sorts of truth claims in the literature. This prediction has been fulfilled a great many times over. It would be difficult to tally up the multitude of such truth claims made by evolutionists, both before and after Darwin, in addition to Darwin himself.

The eighteenth century Scottish philosopher David Hume, for example, argued against design. His antagonist Cleanthes made a powerful design argument. The protagonist Philo admitted the argument was a great challenge for him, but it was neutralized by the evil in the world. “I needed all my skeptical and metaphysical subtlety to elude your grasp,” admitted Philo, but “Here I triumph.”

Hume's triumph was not merely that Cleanthes’s metaphysics were wrong. It was that the evolutionary metaphysics of naturalism were right.

Likewise when Darwin argued against his version of special creation he did not merely conclude against that particular view. He believed that that version of special creation was the version of special creation. We might say he believed in that view. If god created the world, then it wouldn't look this way. Therefore evolution must be true. Darwin's religious beliefs allowed him to make a far more comprehensive conclusion. Here is an example:

We cannot believe, that the similar bones in the arm of the monkey, in the fore-leg of the horse, in the wing of the bat, and in the flipper of the seal, are of special use to these animals. We may safely attribute these structures to inheritance.

Darwin does not merely conclude against his particular brand of creation. He concludes against creation in general. Creation must be false, period. And so inheritance must be the explanation.

This method of metaphysical reasoning runs all through the evolution genre. Evolutionists consistently claim their theory is an undeniable fact. And they prove it to be so. But their proofs are always religious.

Pseudogenes for example are sometimes found to be disabled by identical mutations in cousin species. In typical fashion evolutionist Jerry Coyne concludes they wouldn't have been designed that way and that “Only evolution and common ancestry can explain these facts.” [Why Evolution is True, 68]

This is an example of how this religious reasoning is often in the form of an if-and-only-if statement. In this case, if and only if evolution is true, then we would observe such identical mutations in pseudogenes. Here is another example of this non scientific logic:

One of my favorite cases of embryological evidence for evolution is the furry human fetus. We are famously known as "naked apes" because, unlike other primates, we don't have a thick coat of hair. But in fact for one brief period we do--as embryos. Around sixth months after conception, we become completely covered with a fine, downy coat of hair called lanugo. Lanugo is usually shed about a month before birth, when it's replaced by the more sparsely distributed hair with which we're born. ... Now, there's no need for a human embryo to have a transitory coat of hair. After all, it's a cozy 98.6 degrees Fahrenheit in the womb. Lanugo can be explained only as a remnant of our primate ancestry: fetal monkeys also develop a coat of hair at about the same stage of development. Their hair, however, doesn't fall out, but hangs on to become the adult coat. And, like humans, fetal whales also have lanugo, a remnant of when their ancestors lived on land. [Why Evolution is True, 80]

The religion that motivates and justifies evolution is not an afterthought response to those pesky creationists. It is front and center. It is at the inner core of evolutionary thought. It is what makes evolution a fact. As Stephen Jay Gould explained:

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.

Evolution is not about science. But when a mirror is held up and evolutionists are confronted with their own words, they suddenly cry foul. Like Captain Renault, they are shocked, shocked to find religion is going on in here. Evolutionists are their own judge.

Tuesday, November 9, 2010

Back to School Part 7

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, (3) making the grossly false statement that the fossils themselves are a factual observation that macroevolution has occurred here and here, (4) making a series of misrepresentations by carefully selecting the evidence to provide to the student and protecting it with circular reasoning here, (5) misrepresenting the molecular evidence here, (6) presenting the student with a blatantly false history of evolutionary theory here and (7) introducing the usual if-and-only-if evolutionary reasoning here.

Johnson and Losos’ next move is to make what is probably the most enduring and powerful metaphysical proof for evolution: biology’s bad designs would not have been intended. In a rebuke to the intelligent design argument, they write:

As you can see in the blown-up image in figure 17.9, the receptor cells are actually facing backward to the stimulus (light). No intelligent designer would design an eye backwards! [302]

Although this non scientific mandate for naturalism goes back to antiquity, it was particularly strong in the early days of modern science leading into the Enlightenment. Theologians and philosophers led the way, but early scientists also agreed. They were on the continent as well as in Britain, including Lutherans, Roman Catholics and Anglicans. By the nineteenth century the reasoning was often accepted with little question.

Darwin’s book was full of arguments from bad design. They were the powerful arguments for his theory. People who do not share the premise (that a bad design would not have been intended) fail to appreciate the power of the argument. The premise does not sway them, so they have difficulty understanding the point. The key here is to assume the evolutionary perspective. Pretend you are an evolutionist for a moment. Pretend you genuinely believe the premise: a bad design would not have been intended.

The argument then becomes clear. And its power is obvious. If you believe in this metaphysical premise, then of course, some sort of evolution must be true. As Darwin argued in his book:

We cannot believe, that the similar bones in the arm of the monkey, in the fore-leg of the horse, in the wing of the bat, and in the flipper of the seal, are of special use to these animals. We may safely attribute these structures to inheritance.

QED: evolution must be true. Bad designs, inefficient designs, even designs not of "special use" must not have been intended—they must have evolved. We may not understand how it occurred (the theory), but we know that it did occur (the fact). As Stephen Jay Gould more recently put it:

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.

Our textbook authors could not have demonstrated evolutionary thinking any more clearly. If a designer—who is capable of designing the vast and complicated biological world—would never have designed our backward receptor cells, then of course evolution is a no-brainer. It must be a fact, one way or another.

Evolution is at bottom a non scientific, religious, theory. It states that new forms emerge from biological variation undergoing natural selection—an idea that repeatedly has failed on the empirical science. But no matter, it must be true. Religion drives science, and it matters.

Friday, November 5, 2010

David Hume: Here I Triumph

The three fictional characters in David Hume’s eighteenth century Dialogues Concerning Natural Religion were more than archetypes of the day. Cleanthes, Demea and Philo represent timeless metaphysical viewpoints on creation that long predate the Enlightenment and remain common today.

Cleanthes, who in part represented English natural theologians in Hume’s day, argued not only that the complexity of the world proved that it was designed, but that the world was a happy place and this was evidence for god.

Hume had an easy time ridiculing this view. Philo, who represented Hume, as well as Demea agreed that “A perpetual war is kindled amongst all living creatures,” and that nature is arranged so as “to embitter the life of every living being.”

If the natural theologian’s god would have the world be happy, and yet the world is not happy, then we must seek a different god. Philo concluded, against Cleanthes, that god does not will the happiness of man nor animal.

Cleanthes’s design argument was powerful. Philo admitted the argument was a great challenge for him, but it was neutralized by the evil in the world. “I needed all my skeptical and metaphysical subtlety to elude your grasp,” admitted Philo, but “Here I triumph.”

For Philo, the world’s evil indicated a more distant and mystical god. He charged Cleanthes with anthropomorphizing god. Cleanthes, said Philo, made god out to be too much like His human creatures. For example, the natural theologians were fond of comparing the human body with machines such as clocks. No one doubts that a clock was designed, so why not the body as well? Hume, through his character Philo, used the problem of evil to negate this argument. Better to view god as distant and unknowable, and a creation that somehow arose on its own.

Hume had no problem with god being infinitely powerful and wise, but he must also be transcendent and incomprehensible:

But as all perfection is entirely relative, we ought never to imagine that we comprehend the attributes of this divine being, or to suppose that his perfections have any analogy or likeness to the perfections of a human creature. Wisdom, thought, design, knowledge; these we justly ascribe to him; because these words are honorable among men, and we have no other language or other conceptions by which we can express our adoration of him. But let us beware, lest we think that our ideas anywise correspond to his perfections, or that his attributes have any resemblance to these qualities among men. He is infinitely superior to our limited view and comprehension; and is more the object of worship in the temple, than of disputation in the schools.

In other words, while we may have faith in god, we must not think we understand him well enough to infer his actions in the material world. He may be the god of our hearts, but not of our heads. As Darwin would later argue, while it is tempting to see god as the master engineer who crafted complex organs such as the eye, this would make god too much like man.

Darwin agreed that the perfection of the eye reminds us of the telescope which resulted from the highest of human intellect. Was it not right to conclude that the eye was also the product of a great intellect? This may seem the obvious answer but Darwin warned against it, for we should not “assume that the Creator works by intellectual powers like those of man.” Better to imagine the eye as the result of natural selection's perfecting powers rather than having god too much involved in the world.

This anthropomorphic warning and the problem of evil were by no means Hume’s only arguments for a purely naturalistic origins story. There was, for example, the problem of dysteleology:

And what surprise must we entertain, when we find him a stupid mechanic, who imitated others, and copied an art, which, through a long succession of ages, after multiplied trials, mistakes, corrections, deliberations, and controversies, had been gradually improving? Many worlds might have been botched and bungled, throughout an eternity, ere this system was struck out: Much labour lost: Many fruitless trials made: And a slow, but continued improvement carried on during infinite ages of world-making.

Here Hume converts metaphysical arguments against design into an anticipation of Darwinian evolution and even the multi-verse. The eighteenth century Linnean hierarchy was revealing a biological world of repeated designs. Was this not the sign of “a stupid mechanic, who imitated others, and copied an art”? As Niles Eldredge recently explained:

Could the single artisan, who has no one but himself from whom to steal designs, possibly be the explanation for why the Creator fashioned life in a hierarchical fashion—why, for example, reptiles, amphibians, mammals, and birds all share the same limb structure?

Hume also argued that the design argument raised a fatal infinite regress. Divine creation explains the world’s complexity and evidence of design as the result of the creator. The world is complex so it must have been created. But doesn’t this mean that the creator is also complex, and so must have been created? Using this logic we would then need to ascribe the intelligence of the creator to an even greater creator, and so on. Divine creation leads to an infinite regress of creators.

“How therefore shall we satisfy ourselves,” asked Hume, “concerning the cause of that being, whom you suppose the author of nature?” Is it not arbitrary to stop at the first Creator? “If we stop, and go no farther; why go so far?  Why not stop at the material world?  How can we satisfy ourselves without going on ad infinitum? And after all, what satisfaction is there in that infinite progression?”

Or as one recent evolutionary textbook put it:

Omnipotent beings are themselves well-designed, adaptively complex, entities. The thing we want to explain has been built into the explanation. Positing a god merely invites the question of how such a highly adaptive and well-designed thing could in its turn have come into existence.

These are but a few of the metaphysical arguments that called for an evolutionary narrative in the Enlightenment years. And they did not begin, nor end, with the Enlightenment. Hume marshaled several of the powerful and timeless arguments that laid the foundation for Darwin. From a scientific perspective it could not be more obvious that evolution is a stretch. The biological world just happened to arise all on its own? And this is said to be an undeniable fact, as much as is gravity? It is astonishing that grown men engage in such folly.

But from a philosophical and theological perspective, evolution is compelling. If the evolutionists are correct about even just one of their many metaphysical arguments, then evolution must be true. The uncertain details, as evolutionists like to say, deal with how it happened, but there must be no question that it happened. Religion drives science, and it matters.

Thursday, November 4, 2010

Adaptive Robots: Yet More Evidence for Evolution

Not only do biological organisms adapt before our eyes, but in recent years researchers have developed robots that adapt via Darwinian selection. As one recent research paper explained:

Darwin suggested that adaptation and complexity could evolve by natural selection acting successively on numerous small, heritable modifications. But is this enough? Here, we describe selected studies of experimental evolution with robots to illustrate how the process of natural selection can lead to the evolution of complex traits such as adaptive behaviours. Just a few hundred generations of selection are sufficient to allow robots to evolve collision-free movement, homing, sophisticated predator versus prey strategies, coadaptation of brains and bodies, cooperation, and even altruism.

Can robots illustrate how complex traits evolved? Yes they certainly can, the paper concludes. According to the authors, such experiments provide “a spectacular demonstration of the power of natural selection.” Is that true?

Joseph Raphson was a seventeenth century English mathematician who is most famous for devising a numerical method that was also devised, independently, by Isaac Newton. Newton derived the method years earlier but it, as with so much of his work, went unpublished for decades. Therefore Raphson’s work was his own and he rightly is credited alongside the great Newton. Of course standing alongside a giant often means one is overlooked. Today the method is usually referred to simply as Newton’s method, sometimes as the Newton-Raphson method, but never as Raphson’s Method.

The Newton-Raphson method is a relatively simple iteration for finding where a curve has a value of zero. This root finding algorithm is a handy way of calculating difficult formulas, such as the square root of a number. The idea is to temporarily replace the complex curve with a simple straight line. The straight line, which approximates the curve but is far easier to work with, takes you closer to the answer and allows you to generate a new, better, straight line approximation. After only a few iterations you have a an answer that is good to a few decimal places.

An important property of the Newton-Raphson method is that it works with no knowledge of the overall curve. It needs to know only the shape of the curve locally, at the current approximate answer.

Today’s numerical methods are more complex and sophisticated, but the Newton-Raphson method remains an excellent pedagogical tool as well as a useful method in many practical applications. It is also a simple example of the connection between numerical methods and evolutionary theory.

The Newton-Raphson method’s ignorance of the overall curve is analogous to evolution’s ignorance of a population’s overall fitness surface. The Newton-Raphson method nicely converges to a mathematical solution just as evolution is proposed to nicely find biological solutions. Neither knows anything more than the local shape of the curve, but this is sufficient to locate the roots.

In fact certain branches of numerical methods have used biological and evolutionary concepts to explore new approaches. Genetic algorithms and neural networks are computational methods that use concepts such as fitness, genes, chromosomes and selection.

Not surprisingly evolutionists have interpreted the success of these numerical methods as yet more compelling evidence for evolution. Do not these computational algorithms demonstrate the underlying feasibility of Darwin’s idea?

Of course not. Such fallacious logic has it backwards. Clearly Darwin’s idea is mathematically tractable. That is, if fitness landscapes are relatively smooth and reasonably shaped, and if an initial population just happens to appear, and if biological variation just happens to arise and accumulate, and if populations do not resist such change, then of course species can evolve to new designs. Indeed evolutionists often refer to Darwin’s idea as a truism. It necessarily follows from the premises.

And so it is hardly surprising that we can develop numerical methods that solve problems in this manner. Indeed, Newton and Raphson’s work predates Darwin by almost two centuries. By the nineteenth century there was no question that, given the right properties, iterative numerical solutions could move toward a solution in a stepwise manner. And today our methods are all the more sophisticated. But none of this justifies the evolutionary premises.

Consider the robot research in the paper referenced above. The evolutionary robot experiments took place in an engineered environment. Most of the experiments were computer simulations. That is, the experiments took place in computers created by people, developed in programming languages developed by people, running on electricity provided by people, and interpreted by people. Some of the experiments used actual robots in a testing environment that reflected the computer simulations.

Furthermore, the robot’s capabilities were pre arranged and provided. The algorithms that provided the instructions for the robots, as well as the robot configurations, evolved. But such evolution was within the context of the provided capabilities.

For instance, the algorithms that provided the instructions for the robots are controlled by weighting factors and these weighting factors are varied in the experiments to “evolve” the robot behavior. The weighting factors alone do nothing. They rely on the advanced algorithms and software to have their effect.

And sophisticated sensors were supplied that provided the inputs to the algorithms. In turn, the algorithm outputs controlled electronic motors that set the robot into motion. Then the experimenters provided simple criteria (which they referred to as the robot fitness) to select the best designs at each iteration. Just as the Newton-Raphson method iterates toward a solution, the robots were iterated toward their solutions. Here is how the paper described one experiment:

The sensors were connected to eight input neurons that were connected to two output neurons, which each controlled the direction and speed of rotation of one of the wheels. The genome of the robots consisted of a sequence of bits encoding the connection weights between input and output neurons. Mutations allowed the strengths of connections between neurons to change over generations. Experimental selection was conducted in three independent populations each consisting of 80 individuals. The performance of each robot was evaluated with a fitness function describing the ability of the robot to efficiently move in the maze.

It may have been a nifty bit of engineering work, but this is hardly evolution in action. If you randomize aspects of pre supplied functionality, and select for certain outcomes, then you will end up with those outcomes. Here is how the authors described one outcome:

the best evolved individuals across all replicates moved in the direction corresponding to the side with the highest number of sensors. This was because individuals initially moving in the direction with fewer sensors had higher probability of colliding into corners and thus had lower probability of being selected for reproduction.

It seems to have been a fine piece of work, and such approaches are undoubtedly useful in robot design, training and control. But this has very little in common with biological evolution.

And the experimenters even solved the problem of large-scale change by designing a “gene” to supply different algorithmic topologies:

The genome of each robot consisted of two chromosomes, one encoding the topology of a neural network and the other encoding the shape of a body composed of rigid blocks linked by controllable articulations. This led to the coevolution of different types of robots capable of moving towards the cube and preventing access to its opponent. For example, some robots consisted of a cubic block with two articulated, arm-like structures, which were used for moving on the ground and holding the cube. Other robots were composed of only two articulated worm-like segments where one segment was so large and heavy that, once placed over the cube, it prevented the opponent from displacing it.

Given these engineering heroics it is hardly surprising that the experiments worked so well:

Just a few hundred generations of selection are sufficient to allow robots to evolve collision-free movement, homing, sophisticated predator versus prey strategies, coadaptation of brains and bodies, cooperation, and even altruism.

Yes the robots evolved in this engineered environment, but it is simply a misrepresentation to claim this is evidence of biological evolution. Nonetheless this is precisely what the authors claimed:

these experiments revealed how the coevolution between brain and body morphologies can produce various types of adaptive behaviour and morphologies. … These examples of experimental evolution with robots verify the power of evolution by mutation, recombination, and natural selection.

Verify the power of evolution? A spectacular demonstration of the power of natural selection? This is, to put it diplomatically, a non scientific misrepresentation. Unfortunately this is what we can expect from evolutionists. If there is anything spectacular here, it is the steady stream of myth-like claims made by evolutionists. When not overtly religious, the evidence they produce for their theory is, frankly, absurd. Religion drives science and it matters.