Tuesday, September 20, 2011

Independent Evolution of Complex Designs in Molluscs: Why the Explanations are in Need of Explaining

To the modern student Aristotle’s physics and cosmology are likely to seem bizarre. His final causes, geocentrism, and sublunar and superlunar realms seem to have no correspondence with reality. But Aristotelianism makes more sense when one understands the historical context of ancient Greek thought. In fact Aristotle’s physics and cosmology describe and explain what we observe in nature. This is attested to by the fact that it was well accepted and influential for a millenium and a half. Eventually, however, as scientific understanding progressed, the Aristotelian explanations became increasingly strained. Aristotelianism became more of a tautology, as whatever was observed was described according to the ancient system. Fire, for example, had the quality of dryness and heat. But is this not simply a tautology? As Descartes put it: “If you find it strange that … I do not use the qualities called ‘heat,’ ‘cold,’ ‘moistness,’ and ‘dryness,’ as do the philosophers, I shall say to you that these qualities appear to me to be themselves in need of explanation.” Aristotelianism failed to explain the physical action causing the effects. Today Darwin’s theory of evolution follows a similar denouement. To modern scientists it seems strange, but Darwin had good reasons for his theories of common descent and evolution. In the final acts, however, evolution is more of a tautology. Like Aristotelianism, evolution is a superfluous explanatory device rather than a value added. The difference is that evolution is running its course over a couple of centuries, rather than a couple of millenia.

Mollusca: A case study

Molluscs are mostly slugs and snails, but they also include larger, more advanced creatures, including the giant squid whose over-sized nerve cells have helped make it possible to study the physics and electrical properties of neurons.

The squids, along with others such as the octopus and cuttlefish make up the brainy side of the phylum and one would think (at least an evolutionist would think) that their more sophisticated central nervous systems would fall into the usual common descent pattern.

New research, however, suggests otherwise. It is a plot line that has played out over and over. Evolutionists arrange the species according to common descent, but when we look under the hood the species don’t cooperate. Contradictory differences in the supposedly closely-related cousins, and contradictory similarities in the supposedly distantly-related neighbors, betray evolutionary expectations.

In this case we now must believe that these advanced central nervous systems evolved independently, not once, but several times. Here is how one report summarized the new findings:

The findings, which rely on advanced statistical analyses, fundamentally rearrange branches on the mollusc family tree. In the traditional tree, snails and slugs (gastropods) are most closely related to octopuses, squid, cuttlefish and nautiluses (cephalopods), which appears to make sense in terms of their nervous systems: both groups have highly centralised nervous systems compared with other molluscs and invertebrates. Snails and slugs have clusters of ganglia – bundles of nerve cells – which, in many species, are fused into a single organ; cephalopods have highly developed central nervous systems that enable them to navigate a maze, use tools, mimic other species, learn from each other and solve complex problems.

But in Kocot's new family tree, snails and slugs sit next to clams, oysters, mussels and scallops (bivalves), which have much simpler nervous systems. The new genetic tree also places cephalopods on one of the earliest branches, meaning they evolved before snails, slugs, clams or oysters.

All this means that gastropods and cephalopods are not as closely related as once thought, so they must have evolved their centralised nervous systems independently, at different times.

That's a remarkable evolutionary feat. "Traditionally, most neuroscientists and biologists think complex structures usually evolve only once," says Kocot's colleague Leonid Moroz of the University of Florida in Gainseville.

"We found that the evolution of the complex brain does not happen in a linear progression. Parallel evolution can achieve similar levels of complexity in different groups. I calculated it happened at least four times."

Once again evolutionary expectations are at odds with reality, and once again the uncooperative empirical data are force fit to the theory. As with Aristotelianism, evolution does not add scientific knowledge. It does not tell us what to look for, and where to look for it. Quite the opposite, it is consistently turning up wrong. And yet the theory simply morphs to encompass the new, uncooperative results. No matter what is found, evolution is assumed to have created it. As one evolution remarked, concerning these new results, “This is more evidence that you can get complexity emerging multiple times.”

If you find it strange that I do not use the explanations of evolution, I shall say to you that these explanations appear to me to be themselves in need of explanation.

Religion drives science, and it matters.

Monday, September 19, 2011

What Michele Bachmann and Charles Darwin (Don’t) Have in Common

In a recent political debate presidential hopeful Michele Bachmann raised the topic of vaccines. She accused Rick Perry, governor of Texas, of abusing his authority when he imposed vaccine mandates. What does this have to do with Charles Darwin? Darwin was also concerned about vaccines. But the so-called Father of Modern Biology had a different sort of concern. Darwin erroneously worried that vaccines preserved the lives of those who otherwise would have succumbed. “Thus,” warned the Sage of Kent, “the weak members of civilized societies propagate their kind.” And that, he ominously concluded:

must be highly injurious to the race of man. It is surprising how soon a want of care, or care wrongly directed, leads to the degeneration of a domestic race; but excepting in the case of man himself, hardly any one is so ignorant as to allow his worst animals to breed.

The aid which we feel impelled to give to the helpless is mainly an incidental result of the instinct of sympathy, which was originally acquired as part of the social instincts, but subsequently rendered, in the manner previously indicated, more tender and more widely diffused. Nor could we check our sympathy, even at the urging of hard reason, without deterioration in the noblest part of our nature. The surgeon may harden himself whilst performing an operation, for he knows that he is acting for the good of his patient; but if we were intentionally to neglect the weak and helpless, it could only be for a contingent benefit, with an overwhelming present evil. Hence we must bear without complaining the undoubtedly bad effects of the weak surviving and propagating their kind; but there appears to be at least one check in steady action, namely the weaker and inferior members of society not marrying so freely as the sound; and this check might be indefinitely increased, though this is more to be hoped for than expected, by the weak in body or mind refraining from marriage.

It is little wonder that fifteen years later Nietzsche proclaimed that “The invalids are the great danger to humanity, not the evil men.” The rest, as they say, is history. Let’s hope it stays that way.

Religion drives science, and it matters.

Rosenberg: Evolution Produces Awareness of Evolution

One of the amazing things about evolution, aside from spontaneously creating everything, is its creation of conscious automata which in turn figured out that they, and everything else, had evolved. As Duke’s Alex Rosenberg informs New York Times blog readers:

“On the Origin of Species” revealed how physical processes alone produce the illusion of design. Random variation and natural selection are the purely physical source of the beautiful means/ends economy of nature that fools us into seeking its designer. Naturalists have applied this insight to reveal the biological nature of human emotion, perception and cognition, language, moral value, social bonds and political institutions. Naturalistic philosophy has returned the favor, helping psychology, evolutionary anthropology and biology solve their problems by greater conceptual clarity about function, adaptation, Darwinian fitness and individual-versus-group selection.

There you have it. Rosenberg reveals that he is the result of physical processes alone which he then became aware of. And fortunately naturalists have applied this insight to reveal the source of emotion, morality and everything else. That’s just the Stuff of Good Solid Scientific Research.

Infra Dig: What Goes Around Comes Around and Why Evolution is a Fact

re•li•gion [ri-lij-uhn], noun: A set of beliefs concerning the cause, nature, and purpose of the world, especially when considered as the creation of a god or gods.

The view that God should work according to natural laws rather than direct providence has always been attractive to religious believers. These believers prefer a more distant God for many reasons. For instance, is it not obvious that God would not have directly created such an evil world? Instead, God must have created the laws and went away. Like Aristotle’s Prime Mover, God is removed from the evil and not culpable. But there are several other theological traditions that argue just as strongly against divine intervention, and for creation by natural law. One is that the world, especially the lowly things of the world, are beneath God’s dignity.

In the era of modern science the infra dignitatem argument, or infra dig for short, traces at least back to the Cambridge Platonists in the seventeenth century. The idea was that God would not, as the Anglican botanist John Ray put it, “set his own hand as it were to every work, and immediately do all the meanest and trifling’st things himself drudgingly, without making use of any inferior or subordinate Minister.”

The subordinate minister or agent was Plastic Nature which, unlike the Creator, was not infallible or irresistible. Instead, Plastic Nature had to contend with the ineptitude of matter. The results were those “errors and bungles” of nature.

Such gnostic tendencies by no means ceased with the seventeenth century. Indeed, this view seemed to have a divine sanction. After all, to control the world exclusively through natural laws—God’s secondary causes—required an even greater God. In 1794 Darwin’s grandfather Erasmus Darwin wrote this Gnostic-sounding vision of how natural history should be viewed:

The world itself might have been generated, rather than created; that is, it might have been gradually produced from very small beginnings, increasing by the activity of its inherent principles, rather than by a sudden evolution by the whole by the Almighty fiat. What a magnificent idea of the infinite power of the great architect! The Cause of Causes! Parent of Parents! Ens Entium! For if we may compare infinities, it would seem to require a greater infinity of power to cause the causes of effects, than to cause the effects themselves.

A striking example of these gnostic tendencies in Darwin’s time arose when John Millais’ painting Christ in the house of his parents was first exhibited at the Royal Academy in 1850. In the painting, the boy Jesus had injured his hand in his father’s carpentry shop. Mother Mary attended to the boy while Joseph continued with his work. Outside the door sheep patiently awaited their future savior. The scene was both symbolic and realistic, with wood scraps lying all about and workers going about their duties.

But the Victorians emphasized God’s wisdom, power and transcendence. Could he really have bruised his hand in a messy carpenter’s shop? The Times complained that the painting was revolting, for its “attempt to associate the holy family with the meanest details of a carpenter’s shop, with no conceivable omission of misery, of dirt, even of disease, all finished with the same loathsome meticulousness, is disgusting.” Blackwood’s Magazine said “We can hardly imagine anything more ugly, graceless and unpleasant,” and Charles Dickens called the painting “mean, odious, revolting and repulsive.”

The gnostics could not believe God became a man for the same reasons they could not believe God directly created the world—they could not envision God involved in a world so fraught with misery. Similarly, just as the Victorians were troubled by Millais’ depiction of the human side of Jesus, they also would have trouble with the idea that God so lowered himself to create the messy and detailed biological world, so full of not only of useless bloodshed but of anomalies and particulars. It was all beneath God’s dignity.

A few years earlier the Reverend Baden Powell had insisted that physical and moral problems had completely separate foundations and should have nothing to do with one another. God’s works and God’s word were separate and moral and physical phenomena were completely independent. He wrote in 1838:

Scientific and revealed truth are of essentially different natures, and if we attempt to combine and unite them, we are attempting to unite things of a kind which cannot be consolidated, and shall infallibly injure both. In a word, in physical science we must keep strictly to physical induction and demonstration; in religious inquiry, to moral proof, but never confound the two together. When we follow observation and inductive reasoning, our inquiries lead us to science. When we obey the authority of the Divine Word, we are not led to science but to faith. The mistake consists in confounding these two distinct objects together; and imagining that we are pursuing science when we introduce the authority of revelation. They cannot be combined without losing the distinctive character of both.

The message here is that religion and science are to be kept separate. God is retained to supply the former, but it would never do to consider him in the latter. So it is not too surprising that in his 1844 book Vestiges, Robert Chambers reissued the infra dig argument:

How can we suppose an immediate exertion of this creative power at one time to produce the zoophytes, another time to add a few marine mollusks, another to bring in one or two crustacea, again to crustaceous fishes, again perfect fishes, and so on to the end. This would surely be to take a very mean view of the Creative Power.

Divine providence could engage in the noble activity of impressing laws upon matter, but not grovel in the muck of nature.

Alfred Wallace agreed. Evolution’s cofounder argued that the universe was self-regulating according to its general laws and in no need of continual supervision and rearrangement of details. “As a matter of feeling and religion,” concluded Wallace, “I hold this to be a far higher conception of the Creator of the Universe than that which may be called the ‘continual interference hypothesis’.”

Darwin, for his part, was keen to the implications of this modern gnosticism. If God was not intimately involved in the world, then was He involved at all? In a letter Darwin challenged his American friend Asa Gray to think this through:

I see a bird which I want for food, take my gun and kill it, I do this designedly. An innocent and good man stands under a tree and is killed by a flash of lightning. Do you believe (and I really should like to hear) that God designedly killed this man? … If you believe so, do you believe that when a swallow snaps up a gnat that God designed that that particular swallow should snap up that particular gnat at that particular instant? I believe that the man and the gnat are in the same predicament. If the death of neither man nor gnat are designed, I see no good reason to believe that their first birth or production should be necessarily designed.

Many argue about whether Darwin believed in God, but Darwin certainly held strongly to the popular beliefs about God. It was reasonable for Darwin to argue that God would not be personally involved in the swallow’s attack on the gnat and then leverage his theological principle to conclude that all of biology arose on its own. Evolution is the right conclusion given a gnostic starting point. God and matter don’t mix, so life wasn’t created. If Archimedes needed only a place to stand to move the world, Darwin needed only a theological ledge.

Not surprisingly Darwin also used gnostic ideas to defend his theory against the problem of complexity. Darwin pointed out that 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.

The Victorians could not believe that the boy Jesus actually labored in his earthly father’s carpentry shop. Likewise, it was reasonable for Darwin to argue that complex organs were not likely shaped by God because that would mean he works as man does.

These Gnostic tendencies remain with us today. Evolutionist Stephen Jay Gould, for example, admiringly recounted the Darwin-Gray correspondences. The problem, according to Gould, is not the religious motivation in Darwin’s supposedly scientific theory, but rather that Darwin’s position can be depressing. Gould wrote a book on how we are supposed to understand this new gnosticism. He believed that science and religion do not overlap and are non-overlapping magisteria.

Likewise Niles Eldredge takes the position that “religion and science are two utterly different domains of human experience” and Bruce Alberts, writing for the National Academy of Sciences, informs us that:

Scientists, like many others, are touched with awe at the order and complexity of nature. Indeed, many scientists are deeply religious. But science and religion occupy two separate realms of human experience. Demanding that they be combined detracts from the glory of each.

Similarly Salman Khan at the Khan Academy explains that an all-powerful God would not design the particular. God, if there is one, would use simple laws to create a complex world. Khan concludes:

That to me is a better design.

And isn’t that all that matters?

These are just a few of the many examples of modern gnosticism within evolutionary thought. God must be disjoint from creation and any attempt to force-fit them together is bound to be awkward. Or again, how is it that God could create the universe but have nothing to do with science? The answer of course is that God did not create the world, at least not directly—the world evolved. The historian’s assessment of gnosticism could just as easily apply to evolution:

The cardinal feature of gnostic thought is the radical dualism that governs the relation of God and world … The deity is absolutely transmundane, its nature alien to that of the universe which it neither created nor governs and to which it is the complete antithesis … the world is the work of lowly powers. [Hans Jonas, quoted in: Philip J. Lee, Against the Protestant Gnostics, p. 16, Oxford University Press, 1987.]

The gnostic’s hope in “lowly powers” was fulfilled in evolution’s natural selection. And the acceptance of evolution, in turn, reinforced gnosticism in modern thought. Darwin gave form to the gnostic’s vision, but that brought with it a movement towards gnosticism. The influence of gnostic thought today is not often acknowledged or understood. It is, according to Harold Bloom, the most common thread of religious thought in America. He calls it the American Religion, and he finds it “pervasive and overwhelming, however it is masked, and even our secularists, indeed even our professed atheists, are more Gnostic than humanist in their ultimate presuppositions.”

It is perhaps one of the great enigmas in religious thought that one can profess to be an agnostic, skeptic, or even atheist regarding belief in God yet still hold strong opinions about God. Evolution may breed skepticism, but its adherents have continued to make religious proclamations. Indeed, those proclamations are really no different than those made by Darwin and his fellow Victorians.

Religion drives science, and it matters.

Sunday, September 18, 2011

The Khan Academy Promotes Theological Naturalism

A friend pointed out that over at the Khan Academy, Salman Khan, while assuring his students he is not taking sides, seems to have been channeling such luminaries as John Ray and Alfred Wallace as he informs them that god would never design or create the particulars of this world. Khan—who has four degrees from MIT and Harvard and is certain that evolution and its natural selection created the entire biological world—assures the viewer that “You can ask any engineer” and they will tell you that simple laws underlying a complex design, as exemplified by the Mandelbrot set, is the better way. Of course non of this comes directly from Ray or Wallace—what this illustrates is not a homologous doctrine, but rather the independent origin and persistence of theological traditions. The infra dignatatum argument appears and reappears in the history of thought not because it derives from a single teacher, but because we like it. Here then, we present the 21st century’s version of this age-old tradition within theological naturalism:

[4:19] A belief in god would not point to a god who—a belief in a universal, all-powerful god, would not point to a god who designs the particular—who designs each particular. And even more, the imperfections we see around us—and especially because we see variation and they’re being selected for—we can’t just focus on the eye, we’d have to focus on viruses and cancers and it would have to speak to a god who is designing one-off every version of every sequence of DNA. Because if someone talks about designing the eye, we know the eye is the by product of DNA, and we know that DNA is a sequence of base pairs, ATGCA, billions and billions of them, and so when we talk about design, we would be talking literally about designing the sequence, and we even know there is some noise in there, that comes from primitive viruses in there deep in our past. So the argument I’m making here is that in order to give credit to the all-powerful, at least to my mind, a system that comes from very simple, elegant and basic ideas—like natural selection and variations; in our DNA we call those mutations, but the laws of physics and chemistry, from those simple and elegant and basic ideas, for complexity to emerge. …

This speaks to a higher form of design, this speaks to a more profound design. …

This idea of the laws of physics and chemistry and natural selection … This is a very profound design, and it speaks to the art of the designer. As opposed to designing each of these entities, one off. And what is even more profound about the design is that it is adaptive. If there is environmental stress, then the other variations survive more frequently. … That to me is a better design.

Religion drives science, and it matters.

Saturday, September 17, 2011

He’s Baaaack: Evolution Professor Walks it Back, Then Forward, Then Back, Then …

When I explained how astronomically unlikely protein evolution is, a professor complained that I had it all wrong. When he saw evolution’s ridiculously long odds he figured I must be assuming that the entire protein sequence space must be randomly sampled to yield functional proteins.

Of course that’s not true and my calculations were, in fact, on the optimistic side for evolution.

Next the professor recommended a paper that would clear it all up by explaining that only a very limited fraction of the protein sequence space actually need be searched.

But of course the paper didn’t help. Even though its assumptions were completely ridiculous (e.g., protein evolution is explained by first assuming the earth is loaded with bacteria which are each chocked full of, yes, proteins), the paper nonetheless proved how unlikely is protein evolution. Even with their ridiculous assumptions, and giving evolution every advantage (e.g., assuming only part of a protein need be evolved, with the other parts already, somehow, evolved), protein evolution is 27 to 49 orders of magnitude from reality. That puts it somewhere between a myth and a fairy tale.

So next the professor explained that protein evolution—even though the subject of massive evolutionary assaults—is actually not part of evolution at all. “Evolutionary theory,” he said, “makes no claims about the origin of life.”

This is a favorite trick of evolutionists. Biology is incredibly complex and defies evolutionary musings, so evolutionists say that incredible complexity actually occurred in the beginning, when life first formed. Evolution proper, they say, took the helm at that point. It is another evolutionary shell game that reveals their desperation.

Next the professor said I was playing a “numbers game.” That was similar to what the paper said:

We hope that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention.

As usual divine intervention was the target. It must, of course, be ruled out. After all, that’s not scientific and evolution is a fact.

Next the professor said such “numbers games” are futile because there is too much uncertainty:

The frivolity is in his probability calculations. Such calculations depend on such questionable assumptions that they are scientifically useless - though they seem to be useful to anti-evolution apologists.

I pointed out that I was using assumptions from the paper which he had recommended. Why was he now disparaging the assumptions as “questionable” and “scientifically useless”?

Now the professor says that he did not disparage the paper but rather my use of the paper. But all I did was use the results from the paper.

But since I pointed out that those results were ridiculously optimistic, the professor now says we shouldn’t use those results because “probability calculations are only as good as the qualifying assumptions behind them.”

So let’s see, evolutionists provide the results, those results show evolution to be astronomically unlikely, but since the results, as bad as they are, are nonetheless unrealistically optimistic toward evolution, we should just drop the whole thing.


I’m not sure if this is just the Stuff of Good Solid Scientific Research or if the ball bearings are rolling.

Religion drives science, and it matters.

Friday, September 16, 2011

How the Protein Amyloid State Once was a Good Thing: Evolution’s Lurking Anti-Realism

If there were the equivalent of a “Most favored nation” status in science, evolution would be granted it. If there was an Emperor of science, evolution would be it. If there was a “Get Out of Jail” card in science, evolution would have it. For evolution is special. It can lack the evidence and still be a fact. It can fail and still be true. It can get it all wrong, and still be right.

It is not uncommon for scientists to use false ideas. The flat earth model, for example, is often used. In that case everyone knows the model is wrong. In other instances the status of the model or theory may not be so obvious. Four centuries ago different cosmological theories competed. Did the cosmos revolve about the earth or the sun? Such radically different models could, both, produce reasonably accurate predictions. So it was well understood that a scientific model could be accurate but not true, and that scientists could develop and use a theory with no claim of realism.

In science there is a long history of using models and theories and have limited or no correspondence with reality. Theories fill the spectrum from realism to anti realism and everything in between. For instance, realism may be intended in one part of a model but not another part.

Scientists know the difference and have no difficulty juggling different ideas with different levels of realism. Scientists don’t become confused and make truth claims for theories that have no basis in reality.

Evolution, on the other hand, is different. Evolutionists routinely devise all manner of mechanisms and processes that have no correspondence with reality while simultaneously making high truth claims.

For instance, evolutionists say that the important, information-bearing, DNA molecule was once not so. Instead, they say it was an RNA world. According to this idea the RNA molecule held and processed the information. There is a wealth of information missing from this story. This is not too surprising since it has no correspondence with reality.

Or again, evolutionists say that there was a time when biological cells exchanged genetic information on a massive level, in sophisticated networks using never-observed processes. Evolution, they say, was more horizontal than vertical. But these processes are far beyond anything actually observed in biology.

Evolutionists also say that there was a time when evolution experimented with different DNA codes. What is observed today, on the other hand, is that the DNA code is robust. New and different codes do not easily evolve.

Evolutionists also say that there was once a time when the amyloid state of proteins was a good thing, which evolution made use of. Did not the self-complementary stickiness of short segments of proteins turn them into useful building blocks?

That is in sharp contrast to what is actually observed. Only a relatively small set of particular proteins stick together normally. Usually protein aggregation is harmful and cells have a range of sophisticated strategies to eliminate any such possibility.

Unlike most theories, evolution is special. It can employ any number of just-so stories which have no basis in reality. Like a good bed-time story, the narrative can take any turn at any time, with no need for justification. For as evolutionists say, their theory is a given.

Religion drives science, and it matters.

What the Science Really Says: The Theory of Evolution Versus the Fact of Evolution or Science Versus Religion

While evolutionists consistently state that evolution is a fact beyond all reasonable doubt, the empirical evidence consistently states otherwise. One can see examples of this in the scientific journals, where articles assume evolution is true from the beginning, but then also present the scientific evidence which point in the other direction. It is interesting to see this manifestation of science versus religion buried in the depths of research papers. Here is one paper that tries to explain how evolution works, but must admit that “we know little about the fundamental principles of phenotypic variability that permit new phenotypes to arise.”

In other words, our convictions mandate that evolution is true even though after centuries of trying, we can’t force-fit the facts to the theory. But we’ll keep on trying anyway because we have no other choice.

Religion drives science, and it matters.

Thursday, September 15, 2011

The Amyloid Threat, Big Numbers Game and Quote Mining: Protein Evolution and How Evolutionists Respond to the Empirical Evidence

Even by the evolutionist’s own numbers protein evolution has failed by somewhere between 27 to 49 orders of magnitude. And those estimates—which make evolution unquestionably the worst theory in science—are optimistic. They are based not on the evolution of a protein, but only part of a protein. But even worse, those estimates assume, believe it or not, the prior existence of proteins. That’s right, when evolutionists estimated the number of searches evolution could have made for those elusive protein sequences, they assumed billions of bacteria were available to do the job. But to synthesize a protein, bacteria need hundreds of different types of, yes, proteins. Indeed, to be bacteria, they need an army of proteins. So we cannot sneak in billions of bacteria when trying to show that evolution can create proteins. If we are going to argue that X could have evolved, we are not allowed to assume the prior existence of X. Nonetheless the evolutionists did just that, and concluded:

We hope that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention.

As usual divine intervention is the target and ruling it out is the motivation for the pseudo science. For evolution’s theoretical core, as Lakatos would put it, is not gradualism or selection, but naturalism.

Gradualism and selection are two of the many explanations of how evolution occurred, a topic that is always up for grabs because evolution is so unlikely. But despite its many scientific problems, evolutionists insist that evolution must have occurred. It is a fact, no question about it. Divine intervention is strictly disallowed, for otherwise we would be faced with all those unthinkables. The problem is not with the “divine,” it is with the “intervention.” That’s a no-no. So much for the separation of church and state.

Another problem: Protein aggregation

But science knows none of this. It continues on its inexporable march toward truth. One finding long hypothesized, that further aggravates the problem of protein evolution, is that what seem to be perfectly good proteins, in fact, have a propensity to stick to each other and form fibrils. Like a crystal, multiple copies of a protein can attach and form a growing and dangerous amyloid fibril.

The cell’s solution to this that the sticky patches on proteins, which cause the proteins to aggregate, are conveniently tucked away in the protein’s interior when it folds up. Furthermore, the cell is equipped with a variety of mechanisms to guard against aggregation, and detect and destroy fibrils when they do occur.

All of this simply creates more problems for the evolution narrative. Not only are proteins unlikely to evolve, but even if evolution somehow performs miracle after miracle, it must also ensure those sticky patches are not exposed, and evolution will rapidly need those additional safeguard mechanisms, with the hundreds of, yes, proteins they require.

Reader comments

But evolutionists will have none of this. As usual they are unfazed by empirical evidence. One evolutionist in the know commented:

Cornelius Hunter, 2011, paraphrased (blogpost): "It is too easy for proteins to evolve to bind to each other. Therefore, evolution is impossible."

Michael Behe, 2007, paraphrased (Edge of Evolution): "It is too hard for proteins to evolve to bind to each other. Therefore, evolution is impossible."

That’s funny, and perhaps more tongue-in-cheek than serious, but to be clear the amyloid state is caused by the binding of short, self-complementary protein sequences which have a relatively high propensity to stick to themselves. These self-complementary sequences are fairly common. The quaternary binding surfaces to which Behe refers, on the other hand, are far more elusive and difficult to generate at random.

Another evolutionist continued with the “numbers game” criticism:

The kinds of numbers games that Dr Hunter likes to play may be amusing to some, but they are futile at our current state of ignorance. … To disparage evolution for not being able to offer an explanation for every event in the history of life is a cheap shot, much favored by creationists.

Evolutionists insist that science completely and unequivocally confirms evolution, but when the evidence is presented to them they appeal to our ignorance and future resolution of the problems.

Of course no one knows what the future findings will reveal. That is the nature of science. But when we claim a theory is a fact, we are referring to our current knowledge. Evolutionists cannot claim their idea is a fact, beyond a shadow of a doubt, while simultaneously denying the empirical evidence. The evolutionist later continued:

The frivolity is in his probability calculations. Such calculations depend on such questionable assumptions that they are scientifically useless - though they seem to be useful to anti-evolution apologists.

Actually, while the evolutionist’s assumptions are “questionable,” as discussed above, even these estimates from the evolutionists themselves show how severely the evidence contradicts evolution. The evolutionary shortfall is between 27 orders of magnitude and 49 orders of magnitude, according to the evolutionist’s own numbers. So these probabilities do not come from me, they come from evolutionists. In fact, this same evolutionist had once recommended the paper which he now disparages. So what an evolutionist writes is good science. But when repeated by a skeptic, it becomes a frivolous “numbers game.”

Another evolutionist denied that contrary evidence is important:

Saying that something is unlikely really doesn't mean anything on it's own. A hypothesis can be extremely unlikely and still be correct. This is a point that Cornelius simply refuses to understand.

Actually I agree with this point. My point is not that evolution is false, as this evolutionist seems to think. The problem is not so much with the idea of evolution, which is empirically unlikely, but with the evolutionist’s insistence that it is a fact.

As I have explained many times, this “fact” claim is an epistemological claim. It is a claim about the state of our knowledge. I do not know whether evolution occurred or not. But I do know that it is not a fact. The protein evolution evidence discussed above is one example of why it is not a fact. So contrary to this evolutionist’s claim, saying that something (such as evolution) is unlikely really does mean something. It means it is not a fact.

Another evolutionist said that I was ignoring an obvious solution to the problem:

[T]hat's why so many of us have problems with CH's lack of honesty. The paper CH continually cites shows nothing of the sort. It says the protein couldn't evolve in that time frame by adaptive walking only. But then the paper goes on to add that adaptive walking isn't the only mechanism at work, that there are other known mechanisms such as homologous recombination that greatly shorten the timeline. So there's no huge time problem.

CH loves to quote-mine the first part of the summary but always forgets to include the later explanation.

Here is the quote this evolutionist refers to:

Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination.

I have discussed this several times, such as here and here. Homologous recombination is a complex genetic mechanism assisted by, yes, finely-tuned proteins. As with the bacteria example above, it is circular to recruit such a mechanism for the initial evolution of proteins—for no such mechanism is likely to have existed.

And even if homologous recombination could somehow have been in play, it wouldn’t help anyway. For while this is a clever mechanism for the swapping of nature’s protein modules, it does not help when used with sequences that are nowhere close to solving the problem. Jumping from one local peak in sequence space to another doesn’t improve the odds in finding the astronomical, one-in-10^70, longshot.

Finally, an evolutionist attacked a common strawman:

The "amyloid threat" that you mention poses a challenge to science only if you assume that the functional state of a protein must be its most thermodynamically stable state. But this is not a valid assumption since evolution does not aim for the all-time best possible protein structure in terms of stability but one that is stable enough to perform the intended function.

It is true that the “amyloid threat,” as he puts it, poses no threat to science. I never made such a claim. It does pose yet another problem, however, for evolution. And none of this assumes that the functional state of a protein must be its most thermodynamically stable state. Indeed, it may not be for many proteins, but that is a separate issue. He continued:

The error in your thinking is a common one, that of assuming that evolution must somehow aim toward an ideal situation (in this case thermodynamically most stable structure). The reality is that evolution can only work on what already exists, which often is far from being the best possible set of solutions.

Except that I made no such assumption.

Evolution, even with extremely optimistic assumptions, is easily the worst scientific theory. One can find theories that may be unlikely, but evolution’s shortfall, of 27 orders of magnitude (and that is assuming a biosphere teeming with life already exists), is extreme.

That does not mean future findings won’t somehow reverse our current knowledge. Nor does it mean that our current knowledge falsifies evolution. Though most scientists would drop a theory with such astronomically unlikely probabilities, low probability—even incredibly low probability—cannot insure that an idea is false.

What all this does tell us is that evolution is not a fact. It is not beyond all shadow of a doubt. But this is what evolutionists claim. And when presented with the science, you can see above how they react.

Religion drives science, and it matters.

Monday, September 12, 2011

The Amylome: More Constraints on Protein Design and Evolution

According to evolutionists scientific problems don’t count for much. They believe evolution is a fact that science will confirm. Scientific problems with evolution, therefore, are more indicative of gaps in our knowledge rather than any fault of their convictions. Hence they view scientific critiques as based on gaps or ignorance, rather than any direct evidence against evolution. This is a good example of how the religion that drives evolutionary thought harms science. In this case evolutionists make science vulnerable to just-so stories. If scientific problems don’t matter then anything goes. In fact, there are substantial empirical problems with evolution. Not only have most of evolution’s fundamental predictions failed, the science shows the idea to be highly unlikely. Consider, for example, the area of protein evolution where recent findings make the theory even more unlikely.

Review: Not enough evolutionary experiments possible

Unlike most of the evolution narrative which appeals to speculative hypotheses about the distant past that cannot be tested, protein evolution is more amenable to scientific experimentation. For instance, in one case evolutionists concluded that the number of evolutionary experiments required to evolve a protein is 10^70 (a one with 70 zeros following it).

Yet elsewhere evolutionists computed that the maximum number of evolutionary experiments possible is only 10^43. So the number of evolutionary experiments required is 27 orders of magnitude greater than the number of evolutionary experiments possible.

Furthermore, both these estimates are optimistic. The number of evolutionary experiments required was estimated using only part of a protein and only part of its function was considered.

And the number of evolutionary experiments possible was estimated assuming a four billion year time frame and assuming the preexistence of an earth full of bacteria. The time frame is two to three orders of magnitude too large (proteins come early, not late in the history of life). And bacteria need thousands of, yes, proteins. You can’t use bacteria to explain how proteins first evolved when the bacteria themselves require an army of proteins.

The evolutionists did provide a more conservative estimate of the number of evolutionary experiments possible, reducing the number from 10^43 to 10^21. This increases the evolutionary shortfall from 27 orders of magnitude to 49 orders of magnitude. But even in this more conservative estimate the evolutionists continued to use the four billion year time frame and the pre existence of bacteria (with their many thousands of pre existing proteins).

Evolution, even by the evolutionist’s own reckoning, is unworkable. The theory fails by a degree that is incomparable in science. Scientific theories often go wrong, but not by 27 to 49 orders of magnitude. And that is conservative. The problem is too complicated for precise estimates, but the evolutionary shortfall is probably in the hundreds of orders of magnitude.

Another problem: Protein aggregation

Even if evolution could somehow create proteins, another problem that awaits is the propensity of proteins to stick to each other and form fibrils. As one researcher explained, “The amyloid state is more like the default state of a protein, and in the absence of specific protective mechanisms, many of our proteins could fall into it.”

The problem is that short protein segments of say half a dozen amino acids can be self-complementary and sticky. If these sticky patches are on the exterior of a protein, then multiple copies of the protein can attach and form a growing and dangerous amyloid fibril.

Not surprisingly the cell has several mechanisms to protect against protein fibrillation. The sticky patches may be particularly exposed when proteins are initially synthesized and folding. So other molecules, such as the so-called chaperone proteins, help to ensure proteins fold correctly and avoid the amyloid state. Other cellular mechanisms recognize and destroy amyloids that do form, and proteins that are particularly susceptible may be sequestered in their own compartments. In all there are hundreds of genes that help to protect against the amyloid threat.

Beyond these protective mechanisms, the proteins themselves tend to have their sticky patches safely hidden away in the protein interior. As one evolutionist hypothesized, “Most proteins have evolved to fold in a way that effectively conceals their amyloid-prone segments.”

If that is true, then it is yet another hurdle for evolution. Not only is there the conservative estimate of a 27 to 49 orders of magnitude shortfall just for evolution to create a protein, but now we have the problem of avoiding the amyloid threat. It is not good enough for the protein merely to fold and function. Its sticky patches need to be buried in the interior. And then the cell needs those hundreds of genes for all the additional protective mechanisms.

The scientific problems with evolution do count for those not committed a priori. But religion drives science, and it matters.

Sunday, September 11, 2011

They’ll Always Blame it on You: Response to Comments

It’s the oldest trick in the world. Tell your lies and then blame it on the other guy. After centuries (millennia actually if you care to go back that far) of proclaiming religious truths and mandating their pseudo science, evolutionists blame it on you.

They insist the world must have spontaneously arisen because, after all, “Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread.” They can’t provide the details, but they’re absolutely certain evolution is a fact. And if you doubt any of this—if you point out the sham—then you get the blame.

Here is a typical response from an evolutionist. When I explained the evidence of DNA repair, the reader blamed me:

I share Dr Hunter's awe at the beauty of biology as science has been revealing it. I don't share his presupposition that the origin of life or its subsequent history are dependent on an imaginary supernatural creator.

I am also in awe at the scale of the Universe as science has been revealing it. I don't share his religiously inspired presupposition that the scale of the Universe necessarily required supernatural creation.

Burn me at the stake.

So after constructing a religious theory based on centuries of theological dogma and ruining the careers of those who dare to question the pseudo science, evolutionists turn it around and point the finger at the dissenters. Those who question evolution, they must be the ones with the religious presuppositions. They are the ones who persecute.

I couldn’t care less if the evolutionist’s silly ideas are true or not. Given the evidence it would be remarkable if evolution is anywhere close to the mark. But there is some evidence for evolution, and perhaps its many problems will be resolved in the future. If the evidence shifts to support the idea, that’s fine by me. For the idea of evolution is not the problem. The problem is the evolutionist’s misrepresentation that evolution is a fact.

From the misrepresentations of the science, to the bogus truth claims, to the blackballing, to the legal canards, evolutionists have perpetrated not one long argument, but one long misrepresentation. It is a sordid tale that even Hans Christian Andersen could never have imagined.

Religion drives science and it matters.

DNA Repair and the Choices We All Must Make

When you repair a broken pipe, shattered window or cracked sidewalk, you first remove the broken pieces and establish a starting point. Likewise when a break occurs in DNA, the automatic repair machines must first remove the broken, dangling molecules and establish a starting point. It is another fantastic capability of the cell’s DNA repair kit.

Your genome is under constant attack. Radiation and carcinogens from the outside and even the cell’s own chemicals can damage and break the flimsy DNA molecule. When only one of the strands of the double helix breaks, the repair job can take advantage of the complementary strand. Just as DNA is replicated by using one strand as a template, so too the repair job can rebuild the broken DNA by using the unbroken, complementary strand.

But when both DNA strands break the repair job is much more difficult. Like a bridge that has lost a section in an earthquake, you now have two DNA helices floating freely which need to be rejoined. And like the bridge which has broken rebar and chunks of cement dangling off the edge which need to be cleared, the DNA helices have pieces of broken nucleotides which need to be removed.

A repair job begins by cleaning away the damage. And so the proteins that repair DNA breaks begin by cleaning up the damaged site. They first remove the pieces of the broken nucleotides. New research is showing that the protein that so efficiently searches and identifies DNA breaks also performs this clean up job.

This research adds to the other wonders of the cell’s DNA repair kit, such as discussed here, here and here, which make no sense on evolution. The problem is DNA (and RNA) repair is at once complex and necessary. And so we must imagine that evolution created such capabilities very early in the history of life.

And imagine they do. Evolutionists imagine a gradual build up of capability, or they imagine early proteins that were far more versatile. These ancient proteins handled many tasks and, as luck would have it, RNA and DNA repair was one of them.

But there is no avoiding the fact that evolution fails to provide a plausible explanation for how random mutations just happened to create fantastic machines. In this case—as is often the case—the problem is aggravated by the fact that the astonishing complexity had to arise fast and early in the history of life. In fact, in this case, evolution must have been astonishingly fast since most life forms that we know of require these repair kits.

It is not that these DNA repair kits, or the myriad other empirical evidences from biology, by themselves falsify evolution. Such a feat is elusive given evolution’s low specificity and high malleability. Indeed, natural selection has produced a modern creation narrative—the theory of evolution—which is as hardy as any virus. But the narrative does not comport with reality.

Evolution is required to satisfy our metaphysics. Even the mere questioning of evolution immediately raises the specter of those unthinkables. Evolution must be true.

But on the physical evidence, evolution makes no sense. There may be test tubes and Bunsen burners in the laboratories, but believe me, this is all about metaphysics.

Each of us must make a choice and our decision has consequences. We can follow the evidence, or we can follow the dogma. Evolutionists have made their choice. Religion drives science, and it matters.

Thursday, September 8, 2011

More Insertion Site Preferences: A Reminder of Evolutionists Having it both Ways

New research is showing that P transposable elements have some interesting insertion site hotspots. Specifically, in the fly genome these transposons often show up in the promoter region of a few hundred seemingly unrelated genes. One common theme, however, is that many of the P element target sites serve as starting points for the DNA replication process that creates a duplicate copy of the genome prior to cell division. So there is a correlation, in this case, between the transposon insertion site preference and DNA replication. This finding has implications for how the P elements spread through a population. And it is yet another indication of, in contrast to evolution’s it’s-all-just-a-random-fluke view, how much really goes on under the hood. But this new twist on insertion site preferences also reminds us of evolution’s pretzel logic.

One way evolutionists try to avoid the many problems with their theory is to compare evolution with an alternative. Elliott Sober explains this in his book Evidence and Evolution, and you can see examples here, here and here.

The idea is to show how much more likely common descent is than the alternative. But in making this comparison, what evidence does Sober and the evolutionists use, and what alternative do they use?

Would you be shocked to learn that Sober and the evolutionists are highly selective? They avoid the many evidences that contradict common ancestry. And they use a strawman alternative which, for example, has no common mechanisms.

Not surprisingly the verdict of this kangaroo court is that common descent is a no-brainer—it is beyond a shadow of a doubt.

When challenged evolutionists say their strawman allows for no common mechanisms because—notwithstanding findings such as the transposon insertion site preferences discussed above—we don’t have evidence for common mechanisms on such a massive level.

True enough but if evidence of mechanisms were required then common ancestry would have been ruled out as well. In fact, evolutionists repeatedly explain that their proof does not entail explanations of exactly how common ancestry is supposed to have worked. The details, for the purposes of the proof, are not required. Regardless of the mechanics, evolutionists say common descent can be evaluated against the evidence, and compared to the alternative. But when it comes to hypothesizing an alternative, only known, fully established, mechanisms are allowed.

It is another example of the evolutionist’s pretzel logic. In order to prove common descent he has it both ways. The many contradictions to common descent are ignored, and a strawman alternative serves as the foil.

Religion drives science, and it matters.

Does Huntsman believe in evolution?

Once again politicians are discussing evolution, this time at the Republican presidential debate Wednesday night held at the Ronald Reagan Presidential Library in Los Angeles exurb Simi Valley. The comments, made by moderate Jon Huntsman, former Utah Governor and US Ambassador to the PRC, seemed to be more about politics than science, but perhaps not. Here is what Huntsman had to say:

Listen, when you make comments that fly in the face of what 98 out of 100 climate scientists have said, when you call into question the science of evolution, all I’m saying is that in order for the Republican party to win, we can’t run from science, … And by making comments that basically don’t reflect the reality of the situation, we turn people off.

Huntsman is a politician, and speaking here qua politician his comments make some sense. Huntsman is merely pointing out that, in his view, Republicans need to acknowledge and respect the leading scientific opinions. Otherwise they risk losing votes. In other words, it seems he is talking about political strategy, not scientific realism.

There is of course the philosophical and ethical question that politicians always face. Should politicians “sell out” for votes? How many lies and absurdities should one tolerate to gain office?

But beyond this, one wonders if Huntsman’s remarks go beyond political gamesmanship. When the Palo Alto High dropout speaks of “the science of evolution” it almost sounds as though he is speaking as an evolutionary realist who believes evolution is true, or approximately true.

Adding to this speculation, Huntsman speaks of “the reality of the situation.” Does he mean the political reality of the situation, or the scientific reality of the situation?

Unfortunately Huntsman has never had the question put directly to him: Does he believe evolution is a fact?

Paying homage to evolution for political reasons, as low as that may seem, is an understandable political strategy. Believing in the absurd religious theory that the world spontaneously arose, is quite another.

Wednesday, September 7, 2011

An Electric Face: A Rendering Worth a Thousand Falsifications

From electron microscopes to earth-orbiting observatories, scientists use a variety of instruments to study nature by measuring, observing and yes, rendering. Measurements are graphed and fitted with mathematical models. Renderings, on the other hand, are not so easily quantified. This can make them less useful for the business of building quantitative models and making predictions. But renderings can, in an instant, convey a powerful message. A picture, as they say, is worth a thousand words.

Consider, for instance, ribonuclease A, an enzyme that voraciously chops up RNA molecules. In the mid twentieth century scientists figured out how to determine the structure of such proteins using X-rays, and then later using other techniques as well. A protein sample is carefully crystallized and then exposed to an X-ray beam. The X-rays diffract as they pass through the sample and create a complex pattern which indicates the positions of the various atoms in the protein. Here is what the 124 amino acid ribonuclease A protein structure looks like when its many atoms are rendered in a three-dimensional graph:

As you can see, a graph of a protein’s individual atoms doesn’t tell you very much. It looks like, well, a bunch of atoms. But if we step back and consider the protein’s amino acids we see something very different. In a protein, the amino acids are sometimes wound tightly in a helix. Or they can be stretched out into a strand. These two patterns can be detected from the atomic locations and graphed. Here is the ribonuclease A structure again, but this time with these amino acid patterns rendered and their individual atoms left off the graph:

Suddenly a coherent structure is apparent.

Because ribonuclease A is such a voracious eater it sometimes needs to be turned off. Enter the ribonuclease inhibitor. Here are some different renderings of this beautiful horse-shoe shaped protein:

The ribonuclease inhibitor is shaped to dock with ribonuclease A and bring it to a halt. Here are renderings of the two proteins docked together:

Such renderings provide an immediate peek at the phenomena at work. They provide higher level information than do mere measurements. And it is interesting that these renderings were made with graphing tools that know nothing of ribonuclease A or ribonuclease inhibitors, in particular. Computer scientists have developed these powerful rendering tools based on general principles of protein structure. But these tools do nothing without the structural data provided by measurement techniques, such as X-ray diffraction.

So as with electron microscopes and astronomical observatories, these molecular tools create impressive, beautiful and meaningful renderings that are completely dependent on the measurements. The computer scientist creates the tool, but has no idea what rendering might emerge after the raw data are input.

A recent example of the power of rendering, and the importance of stepping back and choosing the right perspective, is the frog embryo’s electric face. If that sounds strange read on, for as one researcher said, “electric face” is the perfect description.

The body electric

Electricity is not just for engineers, it is crucial in biology as well. For instance, a cell contains various ionic compounds which give the cell interior a net charge. And the difference between the intracellular charge and that of the the external environment causes a voltage across the cell membrane. This membrane voltage is crucial in cellular biology. For instance, a wide variety of membrane proteins, such as channels that allow chemical in and out of the cell, are controlled by the membrane voltage. Change the voltage and you suddenly change the state of those proteins and their various actions.

Yes electricity is important in biology, but when Dany Adams left her digital camera and microscope apparatus running overnight, she had no idea what stunning electrical patterns would emerge on the frog embryo she was studying. Watch this video to learn more:

Here is a shorter video of just the embryo:

The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.”

The frog’s electric face is one of those renderings worth a thousand words. We could make detailed protein measurements showing that evolution cannot even explain how a single protein could have arisen. In fact there are 27 orders of magnitude between evolution’s expectations and reality. And that is going by the evolutionist’s own reckoning (in reality it is 100+ orders of magnitude). Or we could make detailed measurements of mutations and show that unicellular organisms are not likely to evolve spontaneously into elephants.

But the frog’s electric face, in an instant, reminds one of the utter absurdity of evolution. Religion drives science, and it matters.

* Hat tip to bornagain77

Animals Found a the Bottom of the Sea With No Oxygen

As you remember from high school biology plants take in carbon dioxide and give off oxygen, and animals take in oxygen and give off carbon dioxide. But what about the recently discovered loriciferans—tiny animals at the bottom of the ocean where oxygen is hard to come by? The loriciferans, living two miles under the surface of the Mediterranean Sea, apparently spend their entire existence in anoxic conditions.

Most animals use oxygen when metabolizing food to produce the crucial ATP molecules—the body’s ubiquitous fuel pellets. But these creatures have a different type of organelle that does the job with oxygen.

So evolution just happened to import or produce a completely different energy system in these creatures, along with several other adaptations, so they could relocate to the bottom of the sea. Or perhaps the creatures happened to explore the depths first, and then luckily evolution provided the massive changes needed.

And how many random biological design changes were needed (yes, they are random with respect to what counts) to do the job? As evolutionists like to say, “That would be: a lot.”

And why did the loriciferans hang around waiting all that time? Or if they didn’t then why were the changes selected? As evolutionists like to say, “Evolution is a contingent process.” It happened because it happened (and other tautologies). That’s just good solid scientific research.

Remember, evolution is a fact, Judge Jones said so. Religion drives science, and it matters

Tuesday, September 6, 2011

Message Are Not Only in Bottles: What’s in an Egg?

Everyone knows that eggs contain nourishment, but eggs also contain messages. As one researcher explained:

We’ve known for about twenty years that maternal substances in the egg can influence how chicks develop, but the common assumption is that they are a means by which mothers manipulate their offspring in a way that suits the mother more than the chick.

What we’ve shown is the reverse: these substances are actually there to suit the chick. If we muck up the message in the egg experimentally, it is the chick that is penalized directly rather than the mother.

So let’s see, a whole bunch of mutations created birds and a whole bunch of mutations created eggs (not sure which came first, but evolutionists have that all figured out), and then a bunch of mutations created the capability to insert messages into eggs. That didn’t help, but a another bunch of mutations created the capability to interpret those messages and, Eureka!, evolution did it again. That’s just good solid scientific research.

DNA Signals Too: Findings Unexpected But Not to Worry

You know the drill, scientific findings refute evolution’s everything-is-just-a-fluke expectations, evolutionists are flabbergasted, evolutionists re-engineer their theory for the (n+1)th time, evolutionists sing the praise of Darwin, saying their theory explains the evidence so well, and the findings become yet another proof text for our creation myth. This time the finding is that DNA does more than sit at the center of everything like Jabba the Hutt. Evolution’s geno-centric, DNA-is-king myth expects DNA—which is supposed to hold the keys to the phenotype (remember how DNA mutations were supposed to create the dinosaurs, and everything else?)—to receive care and feeding from its various cyto-servants. Remember selfish and greedy DNA?

According to evolution those cellular slaves attended to DNA and sent requests to the double-helix majesty indicating what gene products might or might not needed. Now we find DNA can be just another messenger. DNA has moved off its throne to be part of the cellular signaling chain. As one researcher explained:

It’s a basic change in our way of thinking about cell signaling—that all signals go into the nucleus and dead-end at DNA, that they point to chromatin and stop. Our data show that’s not the case. We have a new fundamental aspect of cellular regulation that we need to now explore.

Next we’ll be hearing how this is a new proof of evolution. Remember when the DNA difference between chimps and humans was found to be only about 2%? A few amino acid swaps per protein does not magically produce Johannes Brahms. Unless, that is, you are a doctrinaire evolutionist. Soon their absurdity became the new normal, and the 2% difference became the latest apologetic, once again proving evolution without a doubt.

Religion drives science, and it matters.

Transgenerational Epigenetic Inheritance (Shhhh, It’s NOT Lamarckism!)

Funny thing about scientific evidence, it doesn’t go away. After a century of playing whack-a-mole with Lamarckians, the evolutionist’s worst nightmare keeps reoccurring. Like Bill Murray forever waking up to I Got You Babe by Sonny and Cher, evolutionists are continually reminded that the science isn’t going anywhere soon.

Of course one trick, after rejecting Lamarckism for a century, is to appropriate it and say you knew it all along, as evolutionists did with Paul Kammerer. After driving him to suicide they then realized he was right and so called him an evolutionist. With friends like that who needs enemies?

The dumbest trick is to just deny the whole thing and keep shouting “(and again, it’s NOT Lamarckism!),” like Lutheran PZ Myers does.

But the best trick is to rename it and hope they’ll forget about the whole thing, like this paper does. Let’s just call it “transgenerational epigenetic inheritance” OK?

Whatever happened to those random mutations that “occur without reference to their possible consequences or biological uses,” as heir to the throne Julian Huxley so dogmatically put it?

Religion drives science, and it matters.

Monday, September 5, 2011

The World Through Evolutionary Eyes: Theological Naturalism, Hypocrisy and Response to Comments on the CSC Case

The theoretical core of evolutionary thought is naturalism. Evolutionists dogmatically insist that the world must have arisen strictly via 100% naturalistic processes. This extreme position is in the minority, but it dominates academia today and is now taken as a given by elites and opinion makers. Not surprisingly this extreme position on naturalism has fueled atheism. If creation arises on its own, then what need is there for a creator? But ironically naturalism arose not from atheism, but from the exact opposite: theism. In fact it is the underlying religious ideas that give evolutionists their strong convictions. This is why evolutionary thought and the Enlightenment arose from the highly religious culture of 17th century western Europe, and it is why religious people do most of the evolutionary apologetics, even today. From the Roman Catholic Ken Miller to the protestant Francis Collins, religious people are insistent that evolution must be a fact. Atheists such as Richard Dawkins and PZ Myers help out on the fringes, but even their arguments are religious. They have been fooled by religion. When it comes to evolution, there is no difference between the theist and atheist. Hence when we speak of the naturalism that drives evolutionists, we are speaking of theological naturalism. Here is how I described theological naturalism in my book Science’s Blind Spot:

There were many religious influences within science in centuries past. In fact, theological concerns often guided and constrained scientific ideas and thought. A variety of such concerns were raised by different thinkers at different times. This makes them both easy to see but not necessarily easy to trace out. These ideas were prevalent but complex—there was no single religious tradition, no single theological concern, no leading thinker or even school of thought, at the interface between religion and science. What was the motivation for these religious ideas, how were they related, and importantly exactly what influence did these religious ideas have on science?

The answers to such questions are not simple but, on the other hand, they are not beyond our reach. There are strong connections between religion and science and recurring themes are obvious. Theological premises do not merely suggest possibilities or stimulate thinking—they are at times crucial in framing scientific thought. This book traces out these connections and their effects.

We begin in Chapter Two with a survey of several common religious influences in the seventeenth through nineteenth centuries. Most of them fall into four distinct categories: greater God theology, religious rationalism and deism, the problem of evil, and theological opposition to miracles. These categories are overarching. None of them represent a single tradition or concern, but rather a family of similar concerns. And these categories do not capture the totality of religious thought impinging on science. Other concerns that we will see in later chapters include the warning against anthropomorphizing God, the God of the gaps warning, and the intellectual necessity.

This history and framework gives helpful structure to the religion-science interface. As we shall see, these different theological traditions would circumscribe scientific activity by defining what types of solutions were, and were not, acceptable. Indeed, these theological mandates are common in the scientific literature.

There are, as it were, theological ground rules imposed on science. And although these theological concerns are varied, they all funnel toward a similar consequence. Put simply, the theological ground rules are that scientific explanations must be purely naturalistic. The term "naturalism" can take on different meanings when used by historians and philosophers of science. Here it is used to refer to this restriction of science to naturalistic explanations for religious reasons. We use a new term, theological naturalism, to clarify this and avoid ambiguity.

This term theological naturalism reminds us that the assumption of naturalism in science is neither a result of atheistic influence nor an empirically-based scientific finding. It is a consequence of metaphysical reasoning, and the implications for science are profound. Theological naturalism provides science with well defined universal criteria to which it conforms. Instead of merely following the data where ever it may lead, science has a framework already in place. The answer, to a certain extent, is already in place. This is a move toward rationalism and away from empiricism. The result is that science has a powerful philosophy of science but, as we explore in Chapter Three, it does not come without cost. Theological naturalism brings with it a blind spot.

A fascinating aspect of theological naturalism is that, on the one hand, it is obvious, but it can also be very subtle. Here is an example of how obvious theological naturalism can be:

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

This is a powerful argument that resonates with many. So powerful, in fact, that it seems to be in no need of defending. Is it not obvious and undeniable that “odd arrangements and funny solutions” disprove design? Is it not obvious that identical mutations in sister species must have arisen in a common ancestor? Is it not obvious that death and destruction in the biological world would have be part of an all-good divine plan?

The metaphysics seems so compelling and obvious that it goes overlooked. Evolutionists are convinced they are doing “just science.” And so the obvious theological naturalism becomes subtle. Darwin’s book on evolution was one long religious argument. Over and over he made religious claims about how the creator would never have created this creation. Evolution was the only answer.

But Darwin never felt the need to explain, justify or defend any of his religious claims. They were bare assertions, presented as simple and undeniable truths. And, importantly, his readers felt the same way. Even sophisticated challengers, such as Princeton’s Charles Hodge, weren’t quite able to pinpoint the message.

So evolutionists make their metaphysical claims casually, with no hesitation or concern. In the next breath they insist they are all about science. Here is an example from a leading textbook:

However, there are some homologies that do look positively disadvantageous. One of the cranial nerves goes from the brain to the larynx via a tube near the heart. In fish this is a direct route. But the same nerve in all species follows the same route, and in the giraffe it results in an absurd detour down and up the neck, so that the giraffe has to grow maybe 3-5 meters more nerve than it would with a direct connection. The “recurrent laryngeal nerve,” as it is called, is surely inefficient. It is easy to explain such an efficiency if giraffes have evolved in small stages from a fish-like ancestor; but why giraffes should have such a nerve if they originated independently … well, we can leave that to others to try to explain. …

In the scientific version of the theory which we are concerned with here, supernatural events do not take place … [Mark Ridley, Evolution, Blackwell, p. 50, 57, 1993]

Notice how easily the textbook slips into metaphysics. A scientific text, discussing scientific evidence, suddenly is doing metaphysics without warning or justification, as though it all is obviously true.

This is typical. Evolutionists insist evolution is a fact, and they arrive at this lofty conclusion via metaphysical proofs. As Alfred North Whitehead once advised, do not question someone on what he feels he needs to defend, but rather on what he takes for granted. The popular version goes like this: It isn’t what a man doesn’t know that scares me, but what he knows for sure.

The corollary to evolution’s theological naturalism is that those who do not adhere to their religious claims are, in fact, the religious ones. After all, such skeptics are allowing that god might have designed this obviously undesigned world. Isn’t that an obvious religious belief? So while evolutionists assert religious claims, those who are make no such claims are, according to evolutionists, religious. For the evolutionists, such fundamentalism is obviously not scientific and must be censored. This is the Alice-in-Wonderland world of evolution.

The CSC case

And so it is not surprising that evolutionists brand any skepticism, such as in the Darwin’s Dilemma film, as “religious.” The specter of its showing at the California Science Center’s IMAX theater prompted USC professor Hilary Schor to be “less troubled by the freedom of speech issues than why my tax dollars which support the California ‘Science’ Center are being spent on hosting religious propaganda.”

So where exactly is the “religious propaganda” in the Darwin’s Dilemma film? Of course there is none. Here is how one commenter here described the film:

I watched the documentary online and found it very scholarly and well presented. The narrator was very professional and I actually found the lack of creationism refreshing, because if in fact it was there, it would have been tough to mask. Most creationism films spend more time attacking Evolutionists than dealing with the science and of course most Evolutionist propaganda films do likewise.

I think the fact that it WAS well written and presented from the standpoint of asking logical skeptical scientific methodical questions instead of religiously accepting religious story telling is what actually infuriates the Darwin crowd. It's not a matter of allowing intelligent people to honestly ask for real world factual proofs [minus the massive amounts of story invention] as it is a matter of being skeptical and actually asking questions in the first place and not accepting through blind faith that the self-promoting geniuses have it right. As history has shown through the ages around the Earth, religious Ecclesiastical Hierarchies hate being questioned.

In fact there are no religious claims in the movie, those are in evolutionary thought. There are no metaphysical mandates or theological dictates. Again, those are in evolutionary thought. Evolutionists openly and consistently make religious claims and then blame it on the skeptics who are looking at the evidence. It is the height of hypocrisy.

But meanwhile an evolutionist accused me of misrepresenting the CSC case:

Let's look at what the press release actually said

"The debate over Darwin will come to California on October 25th, when the Smithsonian Institution's west coast affiliate premieres Darwin's Dilemma: The Mystery of the Cambrian Fossil Record, a new intelligent design film which challenges Darwinian evolution."


By 'Smithsonian Institution's west coast affiliate' the AFA obviously meant the CSC. But the CSC wasn't premiering the film, the AFA was. The CSC and Smithsonian had nothing to do with the film save renting building space.

That's the sort of blatant dishonesty we've come to expect from the IDiots and the professional liars at the DI. You want to defend the wording of the press release CH?

As is typical, the evolutionist manipulates the evidence. He quotes from the first paragraph of the press release and cries foul. But only two sentences later the press release explicitly states who is sponsoring and hosting the event:

The screening is sponsored and hosted by the American Freedom Alliance.

The evolutionist uses a selective reading of the press release and then jumps to the usual ridicule and false accusations.

This is how evolutionists treat those who are not theological naturalists. This is how they treat those who do not, as they do, insist on religious truths that all must follow. This is how they treat those who are interested in the evidence, rather than dogma.

Religion drives science, and it matters.

Sunday, September 4, 2011

The CSC Case and Evolution: More Than Just Bad Science

When Darwin’s Dilemma, a film that examines evolution in light of the scientific evidence, was booked at the California Science Center’s IMAX theater two years ago, evolutionists from around the country were furious. They made sure the booking was cancelled. So while the CSC censored the film, their censorship was by no means an independent action. The CSC was at the tip of the spear, but evolutionists near and far drove that spear home. And those evolutionists were by no means limited to life scientists. For evolutionary thought is about much more than merely the origin of species. Consider, for example, Hilary Schor, Professor of English, Comparative Literature, Gender Studies and Law at the University of Southern California.

Schor is co-director of the Center for Law, History, and Culture at USC, sponsored in part by the Gould School of Law. When not studying feminist theory and gender studies, Schor’s research interests include “law and literature.”

Schor’s view of the law, however, seems to be rather selective. Regarding the CSC case, as she explained, she was “less troubled by the freedom of speech issues than why my tax dollars which support the California ‘Science’ Center are being spent on hosting religious propaganda.”

Schor characterizes Darwin’s Dilemma as “religious propaganda.” And why would that be? The film, which is shot on location in southern China, the Canadian Rockies, and Great Britain, explores the Cambrian Explosion and how the rapid appearance of so many species compares with the theory of evolution. The film includes interviews of both evolutionists (Simon Conway Morris of Cambridge University and James Valentine of the University of California at Berkeley) and skeptics.

So where exactly is the “religious propaganda”? Of course there is none. There are no religious claims in the movie, those are in evolutionary thought. There are no metaphysical mandates or theological dictates. Again, those are in evolutionary thought. It is curious how evolutionists openly and consistently make religious claims and then blame it on the skeptics who are looking at the evidence. It is the height of hypocrisy.

The result is Schor is not too concerned about trampling on freedom of speech rights. As always, the law is only as good as the people behind it. When the elite single out particular groups as not deserving of protection under the law, then the law is not universal. It protects only the preferred groups.

So evolution misrepresents science, biases education, manipulates justice and tramples on constitutional rights. What’s next?

Religion drives science, and it matters.