Sunday, February 28, 2010

The Real Conflict Between Science and Religion

The supposed conflict between science and religion is not only bad history, it also goes unsupported by on-going polls of the religious beliefs of scientists. As the story goes, empirical science uncovers inconvenient truths that religious people resist in a losing battle. But if there was a conflict between science and religion, and furthermore if science has uncovered findings inimical to religion, then one might expect a small and dwindling fraction of scientists who are religious. But a recent poll showed that a majority of scientists (51%) say they believe in God or a higher power. And that is up from the 42% who responded similarly almost a century ago in 1914.

The problem is not so much that religion conflicts with science as it co-opts science. Evolutionary thinking was mandated by leading theologians and religious thinkers in the Enlightenment and Darwin's arguments for the truth of evolution followed suit. As David Masci, senior researcher at the Pew Forum, writes:

But although evolutionary theory is often portrayed as antithetical to religion, it has not destroyed the religious faith of the scientific community.

Indeed not.

But this is not to say evolutionists are predominantly religious today. For Darwin, as Richard Dawkins famously put it, "made it possible to be an intellectually fulfilled atheist." Ironically, the religiously motivated and justified theory of evolution has fueled atheism and today the camp is split. Here there is a conflict as the atheist evolutionists and theist evolutionists argue about their differences.

But as Henry Kissinger described academia, the battles are so fierce because the stakes are so small. From the outside the conflict between atheist evolutionists and theist evolutionists is rather meaningless. For the atheists, in spite of all their bluster, are no different than the theists in their religious beliefs. They call themselves atheists, but their convictions about god are as strong as anyone's. (see examples here and here).

So yes many evolutionists are atheists, but as usual the theology rules. Evolutionists are either theists who hold strong religious convictions or atheists who hold strong religious convictions. Either way the science suffers. I guess you could say there is a conflict between religion and science after all.

Saturday, February 27, 2010

GATA-1: A Protein That Regulates Proteins

Proteins are the cell’s special machines that perform a variety of tasks. Some of them help to regulate the production levels of other proteins by influencing the transcribing of the DNA genes that code for the proteins. New research is investigating how one such transcription factor, GATA-1, works and, as usual, it isn’t simple.

Looking at baby red blood cells in mice, the research found the genes that GATA-1 influences are positioned together along the DNA molecule. GATA-1 binds to specific locations along the DNA molecule and genes that cluster around those locations tend to be induced or repressed by the binding of GATA-1. Genes not in these clusters are relatively unaffected. So if GATA-1 is to influence the production of certain proteins, then the corresponding genes need to be positioned in these regulatory clusters.

But why are some genes induced while others are repressed? One factor is how close the gene is to the GATA-1 protein. The closer genes tend to be induced whereas the more distant genes tend to be repressed. So the positioning of the genes is even more fine-tuned. Not only are the genes to be influenced found in the regulatory clusters, but their position within the cluster is important.

There are other factors as well. For instance, TAL1 is another transcription factor and when it is absent the nearby genes are usually repressed. This is usually accompanied by a modification of one of the histone proteins around which the DNA is wrapped. Specifically, the 27th amino acid in histone H3, a lysine, is trimethylated (three methyl groups are added to the side chain).

These and other factors help to explain how GATA-1 works to regulate protein production, and why some genes are induced while others repressed. But the observed factors do not fully explain the patterns of protein production. For instance, many repressed genes do not lack the TAL1 transcription factor. There is still more to be learned.

Evolutionists believe these protein regulation mechanisms and factors arose from molecular mishaps that were passed on. Those mishaps that luckily helped out persisted. The gene positionings, GATA-1 design, production and binding sites, TAL1, histone trimethylation machine, and other intricacies just happened to arise by happenstance. And they worked. Religion drives science and it matters.

Friday, February 26, 2010

Garter Snake Immunity, Sodium Channels, and Evolutionary Expectations Dashed Again

Certain species of garter snake are remarkably immune to tetrodotoxin, a deadly compound that paralyzes and kills. That’s fortunate because the newt, one of the snake’s favorite meals, is loaded with the toxin. The resistance of these lucky snakes is due to tiny adjustments in a protein segment which otherwise is highly conserved across a wide range of animals. This high conservation, and the tiny variations in these snakes, constitute one of the many false predictions of evolutionary theory that lie hidden in journal papers. To understand this evolutionary quandary we first need a quick review of sodium channels.

What are sodium channels?

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

Like the many telephone wires wrapped into a cable, 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 electronic impulse travels along the nerve cell tail, it causes the sodium channels to quickly open. 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.

Toxic to evolutionary theory

Sodium channels are a great target for a biological toxin such as tetrodotoxin. Introduce a compound that clogs the channel and nerves and muscles lose function. That brings on paralysis, respiratory failure, and even death. Tetrodotoxin wreaks its havoc by binding to the opening of the sodium channel.

But for all its lethality, tetrodotoxin can be neutralized with merely a few changes to the sodium channel’s amino acid string. In fact, even swapping in a single new amino acid can do the job.

Such minor changes are found in various species, including three garter snakes, Thamnophis atratus, Thamnophis couchii and Thamnophis sirtalis, as detailed in research published last year.

These minor changes are found in segments of the sodium channel gene which otherwise is highly conserved across a wide range of species. From the garter snake to humans, these segments are identical, or nearly so.

For evolutionists, such strong similarity across so many species suggests strong selection at work. That is, very little variation in the amino acid sequence can be tolerated. As the authors explain:

Amino acid sequences within the [sodium channel segment] are nearly invariant across garter snakes and relatives and are almost identical to mammalian sequences, suggesting the locus is under strong purifying selection because of its critical functional role.

But if so little variation can be tolerated, then how did the sodium channel evolve in the first place? Vague evolutionary speculation, such as here and here, of course does not address this awkward question.

Also, how could those three lucky garter snake species survive the few mutations that must have occurred according to evolution. In other words, with evolution we must be believe that one or a few mutations occurred in the sodium channel segment which apparently cannot tolerate such change. These mutations would have been handy when the snake eventually consumed a newt, but in the meantime the mutations should not have been tolerable according to evolution.

Finally, the evidence suggests the multiple mutations work together. Alone, some of the mutations have little affect on helping the snake resist the tetrodotoxin, but together the mutations have a tremendous effect. The weak mutations alone would have been less likely to have been selected and therefore, according to evolution, essentially simultaneous mutations are more likely to have occurred. But this dramatically reduces the likelihood of such an event occurring at all. Religion drives science, and it matters.

Thursday, February 25, 2010

A New Evolutionary Mechanism Based on Inefficient Selection

The origin of complexity is a key problem in evolutionary theory. How did the blind process construct so many precise and elaborate biological designs? The evolutionary expectation has always been that Darwin's process of natural selection is the driving force that creates everything from biosonar to the brain. But new research indicates that much of the complexity found in the higher organisms is due not to natural selection, but rather to limitations on natural selection. It is yet another new evolutionary mechanism in a dizzying list of new, and ever more complex, mechanisms.

It probably should not be surprising that this new mechanism is as circuitous as a Rube Goldberg device. After all, the mechanism just happened to happen, and so is not exactly elegant. In fact, it consists of a rather unlikely series of steps, as follows:

1. Gene are sometimes duplicated, for reasons we don't fully understand (somehow evolution did that even though there was no reason, but it worked really well in the end).

2. Duplicate genes lead to excessive quantities of the protein. (bad)

3. Too many copies of the protein leads to dosage imbalance. (bad)

4. Small population size means inefficient selection. (usually bad, but good in this case)

5. Inefficient selection means the duplicate genes are not deleted quickly. (bad, but later good)

6. The duplicate genes become mutated. (good)

7. Some of these mutations affect expression levels via microRNA interactions, alleviating dosage imbalance. (good)

8. Some other mutations affect the protein structure, causing less compact, and less stable proteins. (bad, but later good)

9. These proteins are fortunately stabilized by binding with other proteins. (good)

10. These protein-protein interactions cause higher complexity. (good)

As you can see the process got off to a bad start. It did not look promising, but evolution has a way of finding a way to produce, one way or another. That's how evolution works--it creates complexity (see Step 10).

In this case, the complexity of the process almost matches the complexity of the designs it created. And interestingly, it dispenses with the outdated idea of natural selection driving the design. As one evolutionist explained:

the origins of some key aspects of the evolution of complexity may have their origins in completely nonadaptive processes.

Fortunately, evolutionists are rapidly determining how everything came about.

Wednesday, February 24, 2010

Early Vision More Complicated

As you read these words a frenzy of activity is taking place as the light entering your eye triggers a dizzying sequence of actions, ultimately causing a signal to be sent to your brain. In fact, even a mere single photon can be detected in your vision system. It all starts with a photon interacting with a light-sensitive chromophore molecule. 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.

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.

Cellular signal transduction design is modular. Its many steps can be modified, or interchanged with alternative steps to provide solutions in other applications, such as the olfactory system. Within the vision system one can, for instance, modify the chromophore's color sensitivity—its action spectrum—so different colors cause their own specific signals.

An example of this is found in the so-called third eye (parietal eye) which is found in a variety of species. This eye is not an image forming eye but rather provides for light sensitivity. This system includes two antagonistic light signaling pathways in the same cell. Blue light causes the hyperpolarizing response as described above, but green light causes a depolarizing response.

How is this done? By the inhibition of the cGMP phosphodiesterase enzyme. Specifically, there are two opsins, one that is sensitive to blue light which activates the cGMP phosphodiesterase enzyme, and another that is sensitive to green light which inhibits the cGMP phosphodiesterase enzyme. It appears that initially these are two separate pathways and they come together at the point of influencing the cGMP phosphodiesterase enzyme.

The molecular components of this fascinating design are elucidated in a 2006 paper. In addition to reporting on their findings of this unique design, the final paragraphs propose an evolutionary explanation for the design. Here the paper turns from empirically based science to unfounded, non scientific speculation. Not surprisingly their evolutionary story begins with the heavy-lifting already accomplished and, in Lamarckian fashion, improvements are implemented as needed:

A G_o-mediated phototransduction pathway might already be present in the ciliary photoreceptors of early coelomates, the last common ancestor of lizard (vertebrate) and scallop (mollusk), because both have this pathway. Later, the ancestral vertebrate photoreceptor acquired a second G protein, either gustducin or transducin, for chromatic antagonism and perhaps other purposes. The parietal photoreceptor evolved subsequently and retained these ancestral features.

One can hardly blame evolutionists for their smuggling in of Lamarckian terminology. It sounds better than the Darwinian just-add-water account which holds that random biological variation produced a phototransduction pathway, and then produced myriad new proteins, which fortunately just happened to include a second G protein, which fortunately just happened to ... well you know the story.

Tuesday, February 23, 2010

Independent Evolution of Eyes

Evolution has to be true, and yet it is not well supported scientifically. If you ask how evolution occurred, you will be told there are various theories grappling with the problem. But if you ask if evolution occurred, you will be told that, without a doubt, it is an unequivocal fact. Evolutionists have metaphysical certainty about the truth of evolution, in spite of the empirical evidence. This is a consistent theme in the evolution genre. Here, for example, is the opening paragraph in a journal paper from last year on the evolution of vision:

The evolution of the eye has focused research interest ever since Darwin identified the eye with its ‘‘inimitable contrivances’’ as a vexing problem for evolutionary theory (1859). Gradual evolution seemed implausible because ‘‘intermediate’’ forms of the eye seemed unlikely to be adaptive and selectable. Since Darwin’s original challenge, however, a surprisingly large number of cases of independent evolution of image-forming eyes have been documented.

Translation: Contrary to evolutionary expectations, biology presents us with a wide variety of vision systems. They are too different to have evolved from a common ancestor. The evolutionary spin on this surprise is that vision must have independently evolved many times (after all, the fact that vision must have evolved, somehow, is not in question).

Furthermore, various living species with completely functional forms of eye organization are now known, which could be viewed as ‘‘intermediate’’ between a simple photoreceptive patch and the complex image-forming eye seen in cephalopods and most vertebrates.

On the other hand, they could not be viewed as intermediate. It all depends on whether we are following the evidence. In fact, the biochemistry of even simple, non image forming, eyes is profoundly complex.

Although the fact of repeated evolution of image-forming eyes, as well as the capacity for functional intermediates, is thus firmly established, the mechanism of the evolutionary process is still speculative.

Translation: We may have to contrive just-so stories to explain evolution, but we will continue repeating that it is a fact.

Monday, February 22, 2010

Hopeful Monsters: An Endless List of Special Cases

Textbook evolutionary theory holds that evolutionary change occurs gradually. It may speed up or slow down but change, when it occurs, takes small steps. But from the fossil record to observed adaptations in the field, biological data do not always cooperate with theory. In fact, populations do respond dramatically to environmental challenges in a time window measured in years—not millions of years—and single mutations or the management of existing genes effect such responses. A review from last week, entitled Revenge of the hopeful monster, summarized the situation as follows:

Experimental evidence has shown that individual genetic changes can have vast effects on an organism without dooming it to the evolutionary rubbish heap. Single-gene changes that confer a large adaptive value do happen: they are not rare, they are not doomed and, when competing with small-effect mutations, they tend to win. But small-effect mutations still matter—a lot. They provide essential fine-tuning and sometimes pave the way for explosive evolution to follow. As the molecular details unfold, theory badly needs to catch up.

For example, consider freshwater sticklebacks which can rapidly adjust their pelvic spine length, from generation to generation, depending on the environment. How does the fish achieve such dramatic body plan modifications?

The answer seems to be that a stretch of DNA that enhances the production of a particular protein is sometimes found to be cut out. The reduced production of the protein explains the reduction or loss of pelvic spine length.

But reduced levels of the protein should also cause all kinds of other nonsensical changes to the fish. Why aren’t they observed? The answer is that this DNA editing occurs only in the pelvis and not elsewhere. The result is a helpful design change rather than chaos. As the review explained:

With expression of [the protein] preserved in all other vital structures, freshwater sticklebacks could lose their pelvic spines without dire repercussions elsewhere.

And this design modification is observed to occur independently, in different stickleback populations.

This example illustrates the general finding of built-in adaptation capabilities in biology. In different species we find different mechanisms to effect design changes. As the review explained:

Large effect or small, evolution begins to look like an endless list of special cases, each a new challenge to Fisherian models.

Evolution as an endless list of special cases? Now we must believe evolution created finely tuned, built-in, design change levers that respond precisely to environmental shifts. And these design changes are supposed to be examples of evolution? Yes, the theory does badly need to catch up. And evolutionists, in their Darwinian Wonderland, are just the ones to fix the problem. You can’t make this stuff up.

Friday, February 19, 2010

A Two-For-One Absurdity: Junk DNA Meets Evolvability

Tandem repeats are short stretches of DNA that are repeated head-to-tail. "At first sight," explains evolutionist Marcelo Vinces, "it may seem unlikely that this stutter-DNA has any biological function." This is an example of how evolutionary thinking harms science. Since life is an accident, biology must be straightforward. If we do not immediately perceive how something works, then evolutionists typically think it is non functional junk. Over and over this evolutionary expectation has turned out wrong. And now again with tandem repeats:

unstable junk DNA allows fast shifts in gene activity, which may allow organisms to tune the activity of genes to match changing environments--a vital principle for survival in the endless evolutionary race.

The tandem repeats allow for swift adaptation to environmental demands, so cells with more repeats stand a better chance. As the evolutionists explain, "Their junk DNA saved their lives."

Of course none of this is impossible. But it calls for a healthy dose of serendipity. We are now to believe that evolution created these DNA sequence patterns which were useless for generations. Nonetheless evolution maintained them in the population. That was fortunate because one day, when the environment presented new challenges, they saved the day.

Or there is the preadaptation explanation. It holds that there are some previous functions that the design performed. Like Darwin's gardener we can't observe them anymore, but we can hypothesize.

Either way the result is that evolution created more evolution. Evolutionists now routinely speak of the evolution of evolvability. In other words, we must believe that evolution created the ability to evolve.

Impossible? Certainly not.

The obvious scientific conclusion? You've got to be kidding.

An undeniable fact? I have a bridge to sell you.

But evolutionists do mandate that it is a fact. And therefore they must conclude that what they thought was junk DNA has now saved the day. Evolutionists are flipping between absurdities in what is increasingly looking like a parody. The evolution literature looks more and more like a spoof. As if sensing the problem, the science writer reporting on the new research hastened to add that it is to be published in a reputable journal.

Thursday, February 18, 2010

Jerry Coyne: Why Embryology Proves Evolution

It seems that evolutionists are forever repeating their refrain that evolution is both theory and fact. And for good reason—evolution is commonly misunderstood. On the one hand, evolution is a mechanistic explanation for the origin of species. That is the theory part of evolution and it is open to substantial revision. A wide variety of explanations are possible and even the venerable natural selection can be discarded if need be. The only requirement, it seems, is that the explanation must be mechanistic. Aside from that, most any explanation, no matter how fantastic, is fair game.

On the other hand, evolution is known to be true. That is the fact part of evolution. So the question of if evolution occurred has been settled, even if the question of how evolution occurred remains open to revision.

And this fact/theory distinction is not particular to evolution. Science is full of ideas that we all agree are true even if we don’t fully understand them. A favorite example is gravity, which physicists are still researching even though no one would doubt it is real. Evolutionists like to say that evolution is as much a fact as is gravity. Indeed, some have said that evolution is even more certain than gravity.

There is, however, an important difference between evolution and gravity. Gravity is a fact because we can observe it. Indeed we can feel it. Not so with evolution. Even evolutionists agree that the adaptation that we can observe is insufficient to explain the large-scale changes evolution needs.

So how do we know that evolution, and especially that large-scale part, is a fact? This is where evolution becomes metaphysical. For the past 350 years a number of theological and philosophical proofs have mandated the truth of evolution.

Evolution is commonly understood to be “just science” because its explanation is strictly mechanistic. But that is the theory part of evolution. The fact part of evolution is metaphysical. Here is an example.

In his book Why Evolution is True, Jerry Coyne explains why embryology proves evolution to be true. It is not that evolution predicted precisely what we observe in the developmental stages of the various species. In fact, evolution does not require what we observe to be true. Evolution could explain a wide variety of observables.

But as Coyne explains, what we observe cannot be explained by alternative, non mechanistic, theories. As Coyne reminds his reader, the facts of embryology “make sense only in light of evolution.” This is equivalent to an IF-AND-ONLY-IF-THEN statement, and it reveals the non scientific, metaphysical, aspect of evolution. Coyne writes:

Embryonic stages don't look like the adult forms of their ancestors, as Haeckel claimed, but like the embryonic forms of ancestors. Human fetuses, for example, never resemble adult fish or reptiles, but in certain ways they do resemble embryonic fish and reptiles. Also, the recapitulation is neither strict nor inevitable: not every feature of an ancestor’s embryo appears in its descendants, nor do all stages of development unfold in a strict evolutionary order. Further, some species, like plants, have dispensed with nearly all traces of their ancestry during development. … Yet we shouldn’t throw out the baby with the bathwater. Embryos still show a form of recapitulation: features that arose earlier in evolution often appear earlier in development. And this makes sense only if species have an evolutionary history.

Now, we’re not absolutely sure why some species retain much of their evolutionary history during development. The “adding new stuff onto old” principle is just a hypothesis—and explanation for the facts of embryology. It’s hard to prove that it was easier for a developmental program to evolve one way rather than another. But the facts of embryology remain, and make sense only in light of evolution. [78-9]

Skeptics argue this is bad science and evolutionists retort that it is good science. But in fact, it is not science at all. Coyne and the evolutionists rely on metaphysical premises to make this argument. Evolutionists say their idea is a fact, and their proofs are always metaphysical.

Wednesday, February 17, 2010

Junk Protein Not so Worthless After All

One problem with evolution is its strong bias toward viewing everything in biology as a kludge. When a newly discovered structure is examined, evolutionists take one look and conclude it is leftover junk. After all, blind, unguided mutations and other processes just happened to produce everything we see. The evolutionist’s going in position is that biology is a fluke. We’re lucky anything works.

As we have seen, this expectation pervades evolutionary thinking, and shows up again and again to be wrong. The once-we-thought-it-was-junk-but-now-we-see-how-it-works is a consistent theme in evolutionary thought. In recent years we've seen the so-called junk DNA turn up performing useful functions. More recently this story has repeated itself at the protein level. Designs that were once considered to be so much junk are now found to be essential. Evolution sure it helpful. Here is how one evolutionist described this latest rags-to-riches story:

Here we have a molecule that serves an important role in how cells function and survive, but it contains these puzzling 'junk' sequences that don't seem to have any apparent purpose. Our work suggests that this disorder is really a way of creating flexibility, allowing the protein to function as a molecular switch, a process that is thought to go wrong in certain diseases.

Evolution has provided researchers with convenient modular structures, areas that are repeated over and over again to make up proteins, and so we tend to dismiss the interspersed disordered sequences that don't seem to have any definable structure. Here we show that the weak molecular interactions in a disorganized protein equence are essential in giving this protein its unique attributes.

Well it is good to see that evolution has been helping researchers by providing convenient modular structures. At least evolution does something right.

Tuesday, February 16, 2010

Integrons: Evolution Creates Itself

The evolutionary expectation was that species adapt by unguided variation. Sometimes, it was thought, this blind process happens to stumble upon an improved design which has a reproductive advantage, and so becomes more prevalent in future generations. This evolutionary model could hardly be more wrong. We now have glimpsed the profound complexity of biology adaptation mechanisms. They are anything but a blind process and recent research adds yet more insight into this fascinating aspect of biology that contradicts evolution.

I've discussed this and other examples of how adaptation reveals an immense, yet unspoken, serrendipity in evolutionary theory. Evolution, so we must believe, just happened to create incredible mechanisms which, in turn, fueled evolution. Even evolutionists admit that these mechanisms are crucial to their story.

The recent research adds to this story by exploring the ability of bacteria to acquire resistance to multiple antibiotics using a genetic "copying and pasting" of resistance genes. Apparently unaware of the theory of evolution, this sophisticated design, as one writer put it, uses the antibiotics themselves to "trigger the synthesis of the bacterial enzyme that captures the resistance genes and enables their expression in the integron."

Unbelievable. Adaptation was always claimed as the no-brainer, empirical evidence for evolution. How can anyone doubt evolution when we can observe it right before our eyes? This claim has always been an absurd equivocation on evolution, for such adaptation has very little in common with the macro evolution narrative. The absurdity is reinforced by this growing body of knowledge revealing the deep complexity of adaptation.

Evolutionists are left scratching their heads, wondering how their know-nothing process was able to devise such a clever adaptation machine. They are left with the silly idea that evolution created the intelligent adaptation machine that then allowed for evolution. But if you won't tell anyone about this, then I won't either. Aren't the emperor's clothes beautiful?

Monday, February 15, 2010

ESEB: Liitle Shop of Fallacies

Ever tire of chasing down all those evolutionary fallacies? Dustin Penn and co workers have solved the problem by collecting them in one place: at the European Society for Evolutionary Biology (ESEB) website. Their goal is to improve public education and understanding of evolution. If that means revealing the various strawmen, mischaracterizations, twisting of science, and other logical fallacies, then they have greatly succeeded.

Of course Penn and helpers are quite enthusiastic about evolution, because after all:

Darwin presented a massive amount of evidence from a wide variety of disciplines to show that evolution is a fact. Species change over time.

There you have it. Species change over time, so evolution must be true. An excellent demonstration of evolutionary logic.

The fact of evolution is no longer debated among scientists, as the evidence for evolution is overwhelming.

And that overwhelming evidence would be? Oh, I forgot already, species change over time. Right.

Penn’s next penetrating revelation is that Darwin’s theory of natural selection “not only explains how the diversity of species has arisen, but also the complex, design-like properties of organisms.” No citation given for that one, but no matter, after all species change over time right? In fact, as Penn summarizes:

For many scientists and scholars, Darwin's theory is “the single best idea that anyone has ever had.”

That one did have a citation. It came from that objective sage Daniel Dennett.

Although you would never know it, Penn and co-workers point out that evolution is the key to just about everything in the life sciences, and even more:

Today, evolution provides the conceptual foundation that integrates all of the biological sciences, including genetics, molecular and cell biology, developmental biology, physiology, behavioral biology, ecology, and paleontology. Evolutionary biology is increasing being integrated into the social sciences, as it is central for efforts to understand human origins and behavior. Evolution has many practical implications and it has contributed to important advances in applied sciences. In the biomedical sciences, evolution plays an increasing role in research on HIV, influenza, and other infectious diseases, and in the discovery of genes that cause disease and treatments. Evolution has been critical for understanding the emergence of bacteria resistant to antibiotics and other drugs. Evolution has contributed to advances in agriculture, such as development of crops and livestock and pest management (the evolution of pesticide resistance). Evolution even influences research in biotechnology, and fields outside of the life sciences, including the development of computer technologies and information sciences (evolutionary algorithms).

Strange that biotechnology developers don’t actually use evolution in their work. But surely the influence must be there.

The discussion also includes the usual evolutionary confusion about theories, laws, facts, and evidence. The reader learns that “evolution is not a theory in the colloquial sense of the word, which implies a mere hypothesis, conjecture, or speculation.” No, Darwin’s theory is “a comprehensive explanation strongly supported by evidence, and useful for making predictions.” No mention that those predictions were false, but that’s an aside.

The reader next learns that “Scientific theories are not less than scientific laws, contrary to what is often assumed.” That’s helpful, particularly in light of the next flash of insight: “Scientific laws describe facts whereas theories explain them.” If this seems confusing, just consider that “Darwin’s Theory, for example, explains the fact of evolution.” That should clarify things, and if it doesn’t, the reader is left with this hilarious attempt at objectivity: “It is crucial to understand that evolution — like all facts in science — remains open to question.”

Right, evolution is open to question, just like those veering atoms were open to question to the Epicureans. Evolution has made so many false predictions we’ve stopped counting, but rest assured, it is always open to question. Its truth is never actually questioned, but it is always open to question.

But what is really amazing is that evolution created science itself:

The most important lesson from this controversy is that science is a precious gift, and the greatest accomplishment of human intellect for solving nature's mysteries.

It’s truly amazing that evolution created the brain by which those evolutionists learn truths like evolution. How precious.

Saturday, February 13, 2010

Happy Birthday: Another False Prediction

We celebrate another Darwin birthday, this time with the false prediction of gradualism. See Section 5.4 here. As always, readers should review Section 1, the introduction, so they understand the purpose and context of the document.

Friday, February 12, 2010

Transposable Elements: From Junk DNA to Evolution Mechanism

Imagine if, back in 1859, Charles Darwin explained that evolution proceeds in fits and starts. Species rapidly appear as if planted there, and then go unchanged for eons. There would have been, as we say today, no bounce. In fact Darwin would have been laughed off the stage, and he knew it. Darwin had to present a narrative of gradualism. Funny thing is, the fits-and-starts narrative is today precisely what evolutionists tell us.

It seems strange that the absent minded process of evolution would leave a trail of contradictory evidence. For instance, evolution has not squared very well with the fits-and-starts pattern of the fossil record. Why should biology's evidence make evolution appear to be unlikely? Is evolution trying to deceive us? Or perhaps it is merely testing our faith. Well now we know. Enter junk DNA.

As I have mentioned before, a few years back evolutionists began to think that retroviruses could play important roles in evolution. This idea has now taken hold in a much bigger way, with the discovery of Genomic Drive. Amazing new research found that transposable elements, comprising about half of our genome and once thought to be so much junk, are the drivers behind evolution itself.

Now it makes sense that species suddenly appear and then don't change for eons. It is because those transposable elements occasionally awaken to action. The once junk DNA has gone from the dog house to the starting lineup. It turns out that transposable elements supply the genomic drive behind biology's wonders. Mutations are out, jumping genes are in.

In fact, this junk DNA is now thought to have a critical role in ensuring the survival of biological lineages. And how do they work their magic? The answer is easy. Transposable elements, they say, "do their survival work by reformatting and rearranging DNA genomes to sometimes create significant adaptive mutations that undergo natural selection." It is amazing that evolution so cleverly created its own Genomic Drive. Now, evolution is even more of a fact.

Thursday, February 11, 2010

Research Into How Science and Evolutionary Beliefs Relate

Michael Reiss has published important new work on the relationship between biology and religion. It's good to see these important religious influences being investigated. Here is a summary of this important relationship and influence:

Belief in evolution is widespread and gaining significance in a number of countries. My research examines the characteristics of science and of evolutionary beliefs and the possible relationship between science and religion. I argue that evolution is sometimes best seen not as a misconception but as a worldview. In such instances, the most to which a science educator (whether in school, college or university) can normally aspire is to ensure that students with evolutionary beliefs understand the scientific position. In the short term, the scientific worldview is unlikely to supplant an evolutionary one for students who are firm evolutionists. We can help students to find their biology courses interesting and intellectually challenging without their being threatening. Effective teaching in this area can help students not only learn about biology but better appreciate the way science is done, the procedures by which scientific knowledge accumulates, the limitations of science, and the ways in which scientific knowledge differs from other forms of knowledge.

The damage from religious beliefs seems to be spreading faster than it can be contained. But there is reason for hope. Such beliefs can be countered with rational thinking and science. Do not give up.

More Accelerated Sequence Evolution

Evolutionists have a wide range of explanatory mechanisms from which to draw when trying to figure out how the species evolved. But sometimes these supposed mechanisms look more like a cover-up than an explanation. For instance, the differences between the human and chimp DNA instructions are not sprinkled, more or less at random, throughout our genome. Rather, these differences are found in clusters. Even more interesting, at these locations the chimp's genome is quite similar to other primates--it is the human that differs from the rest, not the chimp. Evolutionists refer to these clusters as human accelerated regions (HARs) because they believe the human genome evolved from a human-chimp common ancestor. These HARs cause several problems for evolution. For instance, we must believe that evolution magically caused rapid changes to occur right where needed to improve function and eventually create a human. As one evolutionist wrote:

The way to evolve a human from a chimp-human ancestor is not to speed the ticking of the molecular clock as a whole. Rather the secret is to have rapid change occur in sites where those changes make an important difference in an organism’s functioning. HAR1 is certainly such a place. So, too, is the FOXP2 gene, which contains another of the fast-changing sequences I identified and is known to be involved in speech.

This is truly a whopper of a just-so story and you can read more here and here.

Now, evolutionists are again appealing to this accelerated evolution "mechanism" to explain the origin of a toxic protein found in the saliva of a North American shrew. The protein chops up other proteins using a novel mechanism, and evolutionists are saying that it "evolved adaptively via acquisition of small insertions and subsequent accelerated sequence evolution."

There you have it--evolution happens. But that's not all. Evolution implemented the same clever design in a Mexican lizard. Amazing.

This is yet another example of a striking design repeat in biology, but this time it is via accelerated evolution. Evolutionists have not calculated the probability of blind mutations doing this not once but twice, probably because it doesn't matter. After all, evolution is a fact.

Wednesday, February 10, 2010

Placental Evolutionary Tree: Example of Theory Complexity

It has long been understood that elaborate explanations can always be contrived in order to explain observations. But why should we believe they are true? The backward motion of planets can be explained by a series of epicycles, designed specifically to fit the peculiar motion. But with heliocentrism no such adjustments are required—the backward planetary motion is a natural outcome. So while complicated narratives are needed for bed-time stories and soap operas, parsimony is valued in science. Nature, and only nature, should be explained. Scientists become suspicious when a theory becomes increasingly complex to accommodate failed expectations—when particular explanations are needed to adjust to contradictory findings.

Falsifications can also be a sign of problems if they are common. If a theory makes predictions that are consistently wrong, then suspicion again arises. Regardless of how much complexity is needed to explain the contradictory findings, a steady stream of such findings, in itself, can indicate weakness.

Evolution has a long history of false predictions leading to rising complexity. The evolutionist’s claim that all of this is a sign of good science, of learning how evolution actually occurred, is not consistent with evolution’s many falsified predictions and complex adjustments.

One example of this is the evolutionary history of placental mammals. In recent decades this history was investigated by comparing the DNA sequences from different placentals. But the results were conflicting. Now, recent research has once again investigated this evolutionary history, this time using the much touted DNA retroelements which promise to provide a much clearer picture. But again, evolutionists must resort to convoluted explanations in order to fit the data to their theory:

We believe that the most parsimonious interpretation of the current data is that the ancestral placental populations were characterized by severe ancestral subdivisions and rejoinings, leading to a complex mosaic of phylogenetic relationships in recent species. Effects of alternating divergence, hybridization, introgression, and incomplete lineage sorting might complicate our search for a clear dichotomy at the base of this tree and leave us with an indistinct, effective “soft” polytomy, leading sometimes to one or the other solution depending on the size of the data set and the particular markers examined.

Evolution is now its own best parody. Evolutionists think nothing of these sorts of explanations and repeatedly use them when needed. But elaborate explanations can always be contrived in order to explain observations. Why should we believe they are true? As with heliocentrism, evolution erects so many "epicycles" in order to fit the data. Religion drives science and it matters.

Tuesday, February 9, 2010

The Persistence of Saltationism

One of Charles Darwin's predictions was that evolution occurs gradually via variations within populations. His friend Thomas H. Huxley was concerned that Darwin had assumed "an unnecessary difficulty in adopting Natura non facit saltum [nature does not make leaps] so unreservedly." But Darwin's theory would have been much less compelling without it. Imagine if evolution had included the caveat that saltations—rapid leaps—can occur by unknown mechanisms such that new fossil species can appear fully formed. This would have destroyed Darwin's premise that species evolve by natural processes and we wouldn’t be talking about him today. Yes the fossil record suggested that nature does take jumps, but it was safer for Darwin to question the data than to admit them into his theory.

In order for evolution to succeed Darwin would need to steer clear of the supernatural, or anything that could be interpreted as supernatural, and argue for a strictly naturalistic origin of species. Darwin could hardly argue for a naturalistic origin, and then propose a theory that suggested a supernatural interpretation.

In its first century evolution maintained Darwin's hope that the fossil record was incomplete. Aside from a few heretics such as Richard Goldschmidt and his hopeful monsters, most evolutionists carefully avoided the problem of stasis and abruptness in the fossil record. But scientific evidence doesn’t go away.

Today the specter of saltational evolution persists, and probably is here to stay. In recent years evolutionary studies have increasingly appealed to saltational evolution to explain a variety of biology’s wonders. For the angiosperm flower to Cirripedes (a Darwin favorite) and the turtle, evolutionists are saying saltational evolution should be considered in addition to the many other explanatory mechanisms.

Of course the appeal to hopeful monsters is certainly not evolution’s first or only use of one-time or strange events. From history changing endosymbiosis events to meteorite impacts, evolution is the story of contingencies. So why not a saltational event now and then? As evolutionist Ernst Mayr wrote, "Laws and experiments are inappropriate techniques" for explaining evolutionary events and processes. Anything can happen in this theory.

Monday, February 8, 2010

Important New Paper on Evolutionary Explanation

Evolutionist Marc Hauser has an important new paper on: The Origins of Evolutionary Storytelling: Evolved Adaptation or By-Product? The work is, as usual, extremely sophisticated and complex. As a service, here is a summary of the research and findings, without all the big words:

Considerable debate has surrounded the question of the origins of evolutionary storytelling. One proposal views evolutionary storytelling as an adaptation for cooperation, whereas an alternative proposal views evolutionary storytelling as a by-product of evolved, non-storytelling, cognitive functions. We critically evaluate each approach, explore the link between storytelling and mendacity in particular, and argue that recent empirical work in the history of mythology provides stronger support for the by-product approach. Specifically, despite differences in mythological background, individuals show no difference in the pattern of their preference for unfamiliar mythological scenarios in particular, and level of mendacity in general. These findings suggest that evolutionary storytelling evolved from pre-existing mythology and proclivity toward mendacity, but that it may then have been subject to selection, creating an adaptively designed system for solving the classic problem of looking in the mirror.

More Doubts About Primordial Soup

You were probably taught in high school biology class that life arose from a primordial soup--the twentieth century's rendition of Darwin's "warm little pond." Most textbooks show pictorial-type drawings of the early earth as a dynamic environment, full of activity. Sunlight is beaming through the clouds with its all important energy-bearing ultra violet rays; rain is pouring down as lightning strikes bring more needed energy to the surface; volcanic activity creates hot spots with yet more energy and a few stray comets might be seen bringing their organic chemicals to seed the life-giving processes. The evolution machine is revving up its engines. Another figure might have illustrated an experimental arrangement mimicking those early-earth conditions. A primordial soup of various organic compounds brewed as sparks were set off in a gaseous mixture above steaming water. There's only one problem: it doesn't work.

Charles Darwin had speculated that life may have begun in a warm little pond with protein compounds ready to undergo more complex changes. Strangely enough, a century later experiments were found to confirm this vision. It appeared that Darwin just happened to be right and the headlines proclaimed that scientists had created "Life in a test tube."

But a plethora of problems were ignored in the process which textbooks eventually had to acknowledge. The 2004 version of George Johnson's high school text, published by Holt, Rinehart and Winston, for instance, includes the primordial soup section but adds a caveat.

In its Principles of Evolution unit, the student reads the usual narrative of organic molecules forming spontaneously in chemical reactions activated by energy from solar radiation, volcanic eruptions, and lightning. The text recounts the success of primordial soup experiments in synthesizing certain organic compounds and concludes:

These results support the hypothesis that some basic chemicals of life could have formed spontaneously under conditions like those in the experiment.

But this traditional life-in-a-test-tube narrative is then followed by an awkward caveat. As the next section explains,

Recent discoveries have caused scientists to reevaluate [the experiment]. We now know that the mixture of gases used in [the experiment] could not have existed on early Earth. ... Some scientists argue that the chemicals were produced within ocean bubbles. Others say that the chemicals arose in deep sea vents. The correct answer has not been determined yet.

That's a refreshing admission. Now a new evolution paper goes further. As one author put it, commenting on the paper:

Despite bioenergetic and thermodynamic failings, the 80-year-old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup has no capacity for producing the energy vital for life.

"It is time to cast off the shackles of fermentation in some primordial soup," commented another author.

These evolutionists believe deep sea vents are the answer. The vents provide chemical gradients that early life would have used before learning how to create their own gradients. Of course we have no idea, beyond speculation, how this actually could have happened. The cell's energy transfer process (referred to as chemiosmosis), using nutrients to synthesize its own chemical energy (ATP), is astonishingly complex. But no matter, it must have happened:

Far from being too complex to have powered early life, it is nearly impossible to see how life could have begun without chemiosmosis ...

The eighteenth century philosopher and evolutionary thinker David Hume argued that the problem of evil trumped the problem of complexity. Nature may be complex, but it must have evolved because god would not have created this wretched world. Now, two centuries later, complexity is simply dismissed because evolution must have occurred.

Sunday, February 7, 2010

Barbara Herrnstein Smith: A Thoughtful Voice

Barbara Herrnstein Smith’s recent piece in the New York Times on the interaction between religion and science is worth the time. Smith, literary critic at Duke and English professor at Brown, has several thoughtful observations on this often inflammatory topic. For instance, Smith urges that apparent conflicts between science and religion

need not exist in the ongoing lives and experiences of individuals. For neither logic nor rationality requires that all our ideas, impulses, affections, and acts be mutually aligned all the time.

Yet she rightly suspects problems in approaches that compartmentalize religion versus science, or attempt to make them complementary.

The former, as exemplified in Stephen J. Gould’s nonoverlapping magisteria, fails to capture the relation between them and “though seeking to counter views that lead to the dismissal of religion in the name of scientific knowledge, goes some distance to reinforcing them.” Smith continues:

Indeed, I’m inclined to say that Gould’s proposed partition of the territory (that is, facts and accounts of the natural world to science, values and instructions for moral conduct to religion) is, like many political partitions, objectionable in principle and unworkable in practice.

Finally and most seriously, I think that the idea of science and religion as counterpoised monoliths deepens prevailing misunderstandings of both. As I emphasize throughout the book, the kinds of things that can be assembled under the term “religion” are exceptionally diverse. They range from personal experiences and popular beliefs to formal doctrines, priestly institutions, ritual practices and devotional icons — Neanderthal burial rites to Vatican encyclicals. The same can be said of “science,” a term that embraces a wide range of quite different kinds of things — general pursuits and specialized practices, findings and theories, instruments and techniques, ideals and institutions (not to mention a share of devotional icons and ritual practices).

Smith also laments how her thoughtful views (my description, not hers), and the nuanced topic of the interaction between religion and science itself, are so often caricatured. Comments to an earlier column so often missed the point:

A good number consist of off-to-the-races polemics on science and religion having little to do with either the book or column. Others object to my presumed views based on inappropriate surmise.

Welcome to the debate. From newspaper headlines and TV news reports to blog comments, the complexities of both religion and science, not to mention their interaction, are so often lost. But complex they are:

Science and religion, in Gould’s account, are nicely balanced and occupy equally valuable pieces of land, but they remain monoliths — precisely, as one commentator puts it, “rocks of ages.” In “Natural Reflections,” I seek to pulverize both of those rocks, not in order to annihilate them but in order to reveal their complex, copious, varied, and changing composition.

And one of those complexities, so often ignored from the start, is the religion that makes its way into the column labeled as science, and the science that makes its way into the column labeled as religion.

Saturday, February 6, 2010

Do You Believe in Magic? How Evolution Creates Evolution

New research is suggesting yet another twist on how evolution creates itself. The research tells us more about epigenetics, so first we need to review how epigenetics has already falsified much of evolutionary theory. I’ve written this before but it bears repeating. The adaptation of species to environmental pressures would seem like obvious evidence for evolution. But in recent years we have begun to understand the enormous complexity of adaptation. It is not a story of natural selection acting on undirected biological variations (that is, variations that are blind to environmental pressures). This sort of undirected process has been the evolutionary dogma for the past century. In what was known as the Modern Synthesis, biological adaptation was described as resulting from blind variations resulting, for instance, from genetic rearrangements or unguided mutations. No thanks to evolution we are now beginning to understand the real version of biological adaptation. What we are seeing is an incredibly complex adaptation machine that tweaks the designs of organisms in response to environmental pressures.

It is not a simple story as there are a variety of different ways such adaptations can occur. These mechanisms, broadly labeled as epigenetic inheritance, can regulate the expression of genes as well as redesign the genes. The bottom line is that the adaptations are not unguided, they benefit the organism, and they are extremely complex. The evolutionary story is completely wrong. As one evolutionist admitted, the Modern Synthesis:

states that variations are blind, are genetic (nucleic acid-based), and that saltational events do not significantly contribute to evolutionary change. The epigenetic perspective challenges all these assumptions, and it seems that a new extended theory, informed by developmental studies and epigenetic inheritance, and incorporating Darwinian, Lamarckian, and saltational frameworks, is going to replace the Modern Synthesis version of evolution.

A new extended theory? This should be interesting, for it would have to explain how evolution creates mechanisms which, themselves, cause evolution (in the form of adaptation). I sense a just-so story coming on. In fact, evolutionists are already explaining this without losing a step. For instance (from the same paper):

Epigenetic inheritance should be favored in fluctuating environmental conditions that last for more than one generation (but not for very long) and may be particularly important in the type of environments experienced by many microorganisms. In such fluctuating environments, efficient epigenetic inheritance is likely to evolve (i) if the parental environment carries reliable information about the offspring’s environment, (ii) when the response to induction is lengthy and incurs a very high cost, and (iii) when recall is not an option or incurs too high a cost.

See, that was easy. Evolution just happens. So long as there is an advantage to a new design, then it will appear. That's how evolution works.

One of the best known epigenetic mechanisms is DNA methylation in which a methyl group is added to cytosine, one of the four DNA chemical letters. The methyl group is a sort of marker that can help to regulate the expression of genes. DNA methylation is accomplished via the action of a complicated molecular machine (DNA methyltransferase) that adds the methyl group at precisely the right location in the DNA strand.

So evolution configured DNA methyltransferase and the associated molecular information that tells it where to add the methyl group, so that later the organism and its offspring could benefit when certain environmental pressures arose. That's good planning--evolution is almost as smart as evolutionists are.

And to further complicate matters, this molecular marker can, itself, be modified. That is, the mark can be marked, thus adding another layer of information to the epigenetic mechanism. In this case, the methyl group is hydroxylated. And of course a different complicated molecular machine is required for the task, and the information of when and where to go to work is needed.

Evolution must have created all these processes and molecular machines so evolution could occur. But that’s not all. Recently researchers found differing methylation patterns amongst mice from the same litter, reared in the same environment. As was reported:

[Researchers] found regions in the animal's genetic makeup with strikingly different patterns. Moreover, these regions occurred among genes responsible for determining anatomy during early development.

In other words, variably methylated regions of DNA have been discovered, and such variability could lead to increased trait variability. Evolutionists speculate that this could help the population survive:

We're proposing that certain gene variants contribute to heterogeneity in populations. In a fluctuating environment, this gives generations more opportunity to survive.

And perhaps this new capability could help answer long-standing questions about how it is that evolution could work so well. As the article explains:

For more than 100 years, mainstream science has embraced the basic tenets of Darwin's view that characteristics that increase an organism's ability to survive and reproduce will be passed from generation to generation. … Characteristics that affect an organism's ability to adapt and survive in times of environmental change have been thought to arise by chance through random mutations in an organism's DNA. However, this view could not explain how such mutations, which arise only rarely, help organisms of every size and variety adapt quickly enough through time.

We already knew evolution was plenty clever. It created genes, chromosomes and alleles, horizontal gene transfer, introns, DNA methylation, and its additional hydroxyl signal just to name a few structures and processes. Of course there is a dizzying array of molecular machines choreographing this drama at just the right moments. All this so more evolution could occur.

And now we add another miracle to the list: variably methylated regions of DNA so future generations could survive when some unforeseen environmental challenge arises. The levels of absurdity to which evolutionists will go is truly remarkable.

Friday, February 5, 2010

How to Read Darwin

The first two chapters of Origin are on the topic of biological variation. In the first chapter Darwin discusses what breeders had learned (Variation Under Domestication) and the second chapter discusses biological variability in the wild (Variation Under Nature). The two chapters serve as a good summary of what was known at the time, but it's slow going as the material does not seem to advance Darwin's thesis very well. In these chapters Darwin is, among other things, introducing the reader to the idea that what we observe today as distinct species, and the labels we give them, are rather arbitrary. What we are seeing is a snapshot at a particular point in time, but over eons of time the designs of the species are fluid. The boundaries shift and new species emerge as the picture gradually changes. The reading is a bit tedious, but as these first two chapters close Darwin pivots, and makes his first important move.

Darwin ends Chapter 2 with a section entitled Summary, but here he introduces a new, important idea. Yes, he summarizes what he has been discussing, but he provides a new, powerful interpretation:

In genera having more than the average number of species in any country, the species of these genera have more than the average number of varieties. In large genera the species are apt to be closely, but unequally, allied together, forming little clusters round other species. Species very closely allied to other species apparently have restricted ranges. In all these respects the species of large genera present a strong analogy with varieties. And we can clearly understand these analogies, if species once existed as varieties, and thus originated; whereas, these analogies are utterly inexplicable if species are independent creations.

Earlier in the chapter Darwin had made a few comments in passing about creationism, but nothing too significant. But here Darwin introduces the reader to the power behind his long argument. The pattern will repeat many times: long tedious passages followed by the powerful conclusion that nature's evidence falsifies divine creation.

Don't worry if you don't completely follow the observations Darwin discusses in the above quote. Here's what you need to understand. The take home message for evolutionists is that, as usual, there are no viable explanations other than evolution's. The observations may not be fully understood under evolution, but under creation or design the story becomes downright impossible. As Ernst Mayr wrote:

The greatest triumph of Darwinism is that the theory of natural selection, for 80 years after 1859 a minority opinion, is now the prevailing explanation of evolutionary change. It must be admitted, however, that it has achieved this position less by the amount of irrefutable proofs it has been able to present than by the default of all the opposing theories.

Indeed, but the default of those opposing theories is not a scientific conclusion. It was evolutionary metaphysics that dictated the outcome. This is the take home message for everyone else. Darwin's reasoning, such as in the passage above, is metaphysical.

The idea that the patterns Darwin was discussing are "utterly inexplicable if species are independent creations" is not from science. Nor did it come from creationists of the day. Nor was it merely a casual observation, made in passing. Then and today, these are the arguments that make evolution a fact. There is no proof that evolution is a fact that does not entail metaphysics. As Stephen Jay Gould observed:

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.

Religion drives science, and it matters.

Thursday, February 4, 2010

Coyne: Evolutionary Arguments Not Theological

Evolutionists agree that their theory is a fact, every bit as much as gravity is a fact. It is not difficult to find proofs for this claim in the evolution literature. On the Internet, in magazine articles, in popular books, and in textbooks, proofs of the fact of evolution are common. In fact they date back to the beginning of modern science (or even to antiquity if one cares to take it that far). And these proofs are perfectly logical—there is nothing wrong with their reasoning. But a proof contains going-in assumptions, or axioms, and evolution’s axioms are metaphysical. That is, evolution incorporates axioms that do not come from science; rather, they drive the science.

Here’s an example. It has been known since Aristotle that species tend to cluster in a hierarchical pattern and in the eighteenth century Linnaeus saw it as a reflection of the Creator’s divine plan. Obviously this pattern does not force one to embrace evolution. But does it really look like a divine plan? Darwin argued it most certainly did not:

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 argument about divine patterns did not begin with Darwin. It has complex theological roots, and today it continues as one of evolution’s many metaphysical axioms. Fifty years ago evolutionist George Carter explained that “If species are separately created there is no reason why they should be created in large groups of fundamentally similar structure.”

Niles Eldredge agrees that the pattern defies creationism and design:

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?

Likewise Jerry Coyne explains that the appearance of species through time is “far from random” and “no theory of special creation, or any theory other than evolution, can explain these patterns.” [29] And why are species so similar? “There is no reason,” explains Coyne, “why a celestial designer, fashioning organisms from scratch like an architect designs buildings, should make new species by remodeling the features of existing ones.” [54]

Of course this claim about how the species would be designed does not come from science. Nor do the many other metaphysical claims that, over and over, prove evolution.

For instance, another common metaphysical mandate is that god or a designer would never draw up inefficient designs. A favorite example is the recurrent laryngeal nerve which, Coyne explains,

makes no sense under the idea of special creation ... No form of creationism/intelligent design can explain these imperfections …

In fact evolution is drenched in metaphysics. From its early formulations in the Enlightenment years, to Darwin, to today’s refinements, evolution relies on non scientific assumptions. The “fact” of evolution has never been demonstrated without appeal to ultimate truths which are far beyond the halls of science.

Is this enough for us to convict evolution? Actually no, metaphysics is no sin. There’s certainly nothing wrong with holding religious beliefs. And is there anything wrong with viewing the world through the spectacles of one’s beliefs?

Indeed, who says there is anything wrong with allowing one’s beliefs to influence science? Well, in fact evolutionists say this, and herein lies the rub. The problem is not that evolution is a metaphysical theory or that evolutionists promote their metaphysical views. The problem is that evolutionists criticize others for precisely what they do. They even deny what they do. As Jerry Coyne explains, our metaphysics are really not metaphysics at all:

the argument from imperfection — i.e., organisms show imperfections of “design” that constitute evidence for evolution — is not a theological argument, but a scientific one. The reason why the recurrent laryngeal nerve, for example, makes a big detour around the aorta before attaching to the larynx is perfectly understandable by evolution (the nerve and artery used to line up, but the artery evolved backwards, constraining the nerve to move with it), but makes no sense under the idea of special creation — unless, that is, you believe that the creator designed things to make them look as if they evolved. No form of creationism/intelligent design can explain these imperfections, but they all, as Dobzhansky said, “make sense in the light of evolution.”

Should we laugh or cry? According to Coyne the design “makes no sense under the idea of special creation" and this "is not a theological argument, but a scientific one.” Coyne’s misrepresentations and sophistry are astonishing. You can read more about this here. The problem is not that evolutionists are metaphysicians—the problem is that they are in denial, and in the process make a mockery of science. Religion drives science and it matters.

Scientists (Do Not) Find a Fingerprint of Evolution

Did you know that most of the evidence claimed for evolution is actually not evidence for evolution? That's right, remember the mountain of evidence that evolutionists say is supposed to make evolution a fact? Well most of it consists of biological findings that merely have been interpreted according to evolution.

Here is an example that I've discussed before at Evolution News & Views. A prestigious scientific journal, the Proceedings of the National Academy of Sciences, published detailed findings about how DNA information is used to make proteins in our cells. The research team, led by Cold Spring Harbor Laboratory professor Michael Zhang, discovered subtle signals in the DNA that help guide incredibly complex molecular machinery when editing the DNA information. The findings are not in any way evidence for evolution, and yet the headlines proclaimed “Scientists Find a Fingerprint of Evolution Across the Human Genome.”

This was not merely a case of journalistic naivete. One can hardly blame the science writer when the journal paper itself presented the results as elucidating the evolutionary process. The paper's title alone (“RNA landscape of evolution for optimal exon and intron discrimination”) suggests a new finding about evolution, and the paper concludes that human genes seem to have been optimized “during evolution.”

But the “during evolution” part is gratuitous. The key findings are about how the genetic signals work, not that they evolved. There is, in fact, nothing in the findings to indicate evolution. The science writer concluded that “the researchers found signs that evolution rejects some types of mutations,” but there simply was no such finding. What the researchers actually found was the presence of certain subtle signals in the genome. They found no evidence that the signals were produced by evolution.

This dynamic is common and, not surprisingly, influences popular thinking. For reports such as this are taken to be objective, scientific confirmations of evolution. They often find their way into the popular literature, text books, Internet discussions, origins debates and so forth. Because evolution is believed to be a fact, we have lost the ability to rightly evaluate scientific evidence. All evidence must point to evolution, even if it doesn’t. This is yet another way that evolution harms science.

Wednesday, February 3, 2010

Reverend Jerry Coyne: Lanugo and Epistemology

You probably have never seen the words lanugo and epistemology in the same sentence. But to understand the power of evolutionary thinking we need to understand both words. Lanugo is a fine hair we grow about six months after conception and then lose before birth. Epistemology, on the other hand, is the theory of knowledge. How do we know what we know? How can we know that what we know is true? It's a complicated subject and science avoids many of the quandaries by simply positing hypotheses that make predictions. Think of the process as an IF-THEN statement. IF the planets circle the sun, THEN we should observe retrograde motion. Epistemologically speaking, the IF-THEN statement is very safe. It makes no claims about ultimate truth, it simply states that if a particular hypothesis is true, then a particular event should be observed. And if the event is observed then the hypothesis may or may not be true. All we can say is that it has not been falsified. If the event is not observed, on the other hand, then the hypothesis is false or at least needs to be modified. As you can see it is not easy to make progress with the IF-THEN statement. If all we can do is not falsify a hypothesis how can we ever establish any truths? This is where evolutionary thinking comes in.

Evolutionary thinking smashes through the IF-THEN log jam by instead using the IF-AND-ONLY-IF-THEN statement. Here's an example: If and only if it is Friday, then evolutionists play poker. In this example, if we observe evolutionists playing poker then it must be Friday. There is no other possibility. Unlike the IF-THEN statement, the IF-AND-ONLY-IF-THEN statement allows you to establish truths.

Evolutionists have used this powerful technique to establish the truth of evolution. Consider perhaps the most famous phrase in evolution today: "Nothing in biology makes sense except in the light of evolution." This was written by the famous twentieth century evolutionist Theodosius Dobzhansky and the phrase continues to be celebrated by evolutionists today. It is equivalent to claiming that "Everything in biology only makes sense in light of evolution," or in the IF-AND-ONLY-IF-THEN statement format as: "IF-AND-ONLY-IF evolution is true, THEN will we find what we find in biology."

It is all suddenly so simple--of course evolution is true. It is a wonder that creationists ever doubted this obvious truth. From where else can you get that kind of certainty except evolutionary thought?

The power of the IF-AND-ONLY-IF-THEN statement, as you can see, is that it covers the water front. It provides knowledge of all possible explanations. Evolution, and only evolution, can explain biology. No other explanation works.

Philosophers such as Kyle Stanford have worried that science is vulnerable to the problem of unconceived alternatives. How can we really know that no other explanation works? How can we even know what are all the possible alternatives? But as usual philosophers fail to comprehend the power of evolutionary thought.

Evolutionists have powerfully used the IF-AND-ONLY-IF-THEN statement for centuries to prove their ideas. They have provided true-truth like no other tradition in the history of thought. And for that we must thank them gratefully. To fully appreciate the power, and simplicity, of evolutionary thought, here is how the Reverend Jerry Coyne applies this logic to lanugo. Here is the Word of Coyne:

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. [80:1]

As usual Coyne skillfully presents evolutionary truths with a gentle and loving message. How obvious it now is that lanugo can only be explained by evolution (or in other words, IF-AND-ONLY-IF evolution is true, THEN will we have lanugo). Now you can see why evolution is true.