Wednesday, August 31, 2011

A Journalist Gets it Right

Ann Coulter has succeeded where others have routinely failed—in a sentence she has cut to the core of the origins debate:

Intelligent design scientists look at the evidence and develop their theories; Darwinists start with a theory and then rearrange the evidence.

Right or wrong, Intelligent design is an appeal to the evidence. And right or wrong, evolution is an appeal to the convictions. Once again it is empiricism versus rationalism—another round of an age-old debate.

That debate doesn’t progress very far when pundits from George Will to Chris Matthews don’t even understand what it is about. Kudos to one journalist for getting it right.

Monday, August 15, 2011

Saturday, August 13, 2011

Peacefulness, in a Grown Man, That is Not a Good Sign

Evolution is, as Karl Popper once sensed without delving into all the details, a metaphysical research program. That a movement is metaphysical is in itself neither unusual or, in evolution’s case, very interesting. What makes evolution so fascinating, and what Popper did not much explore, is its combination of certainty and denial, of its own metaphysics.

The metaphysics of evolution are most evident not in its explanation of how all of biology has arisen naturalistically, but in its mandate that all of biology must have arisen naturalistically. This is crystal clear in any number of religious claims evolutionists have been making for centuries. Would god have created the mosquito? Of course not, so evolution is the obvious conclusion for evolutionists such as Ken Miller. Or as Stephen Jay Gould explained:

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

And just what is a “sensible god” according to evolutionists? A sensible god, of course, is altogether like an evolutionist. For centuries evolutionists have been issuing their sophmoric metaphysical truth claims with absolute certainty. Like a five year old talking about Santa Claus, the evolutionist’s banality is exceeded only by his certainty.

The IFF statement

These claims of ultimate truth sometime take the form of an IF AND ONLY IF statement, or its linguistic equivalent, which evolutionists consistently use. The IF AND ONLY IF, or IFF, statement is the underlying logic when evolutionists say that only evolution can explain biology. It is another example of the evolutionist’s reasoning by process of elimination. He is certain his idea is correct because the alternatives are wrong.

The rub is that this logic works only if one possesses knowledge of all the alternatives. This may seem to be a minor technicality but it is the crucial, and often unspoken, weak link in the evolutionary calculus. Here is an example from Darwin:

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

Here Darwin claims that structures which are of no particular or “special” use to an organism must have been inherited. In other words, inheritance and only inheritance can explain such structures. Let’s breakdown Darwin’s logic:

1. Organisms have structures that are of no special use.
2. Structures that are of no special use are structures whose origin cannot be explained except by inheritance.
3. Organisms have structures whose origin cannot be explained except by inheritance.

Step 2 is unspoken and, more importantly, metaphysical. For in science we cannot know that only one theory can work for the simple reason that we cannot know all the possible theories. It is the equivalent of an IFF statement which is not scientific.

This method of metaphysical reasoning runs all through the evolution genre. Evolutionists consistently claim only their theory can explain what we observe in biology.

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

If and only if evolution is true, then we would observe such identical mutations in pseudogenes. Here is another example from Coyne of this non scientific logic:

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

According to Coyne our lanugo can only be explained as a consequence of common ancestry. Evolutionists freely issue these metaphysical edicts as though they are scientific findings we all must acknowledge.

The most celebrated example of this non scientific reasoning comes from one of the twentieth century’s leading evolutionists, Theodosius Dobzhansky, who claimed that “nothing in biology makes sense except in the light of evolution.” Though Dobzhansky did not know the details of how all of biology could have spontaneously evolved, he was certain that it did. For over and over he argued that only evolution could explain the biological world.

Evolution’s denial of itself

In the movie Triage a psychiatrist played by Christopher Lee attempts to help a war photographer played by Colin Farrell. Farrell’s character had witnessed too much of the world’s violence and insanity. He finally withdrew into a subtle form of denial symbolized by his very peaceful naps, one of which he is enjoying when Lee visits him for the first time. Lee quickly perceives Farrell’s massive denialism and lays the groundwork for their next meeting as he walks out the door:

Lee: You know you sleep very peacefully, there’s not a movement, not a wrinkle in your face, just like a baby.
Farrell: That's a good thing isn’t it?
Lee: No. If you were thrashing about and muttering to yourself it would mean a problem is close by. But peacefulness, in a grown man, that is not a good sign.

Denial, particularly in the face of massive contradictions, is a fascinating phenomenon. Between their peaceful naps evolutionists are busy contradicting their denials. They issue their many metaphysical and religious edicts, only to sleep through the consequences, denying they ever did any such thing.

Evolutionists routinely tell me they make no undue metaphysical assumptions. They make various theological claims and conclude their scientifically unlikely idea must be a fact, and then deny the whole thing. No script writer could have dreamt this up.

Consider professor Douglas Theobald who wrote a paper that compares several hypotheses for the early phases of evolutionary history and shows how universal common descent, in one variant or another, is the clear winner. After showing that a comparison of 23 proteins—similar versions of which are found in many species—fit the universal common descent hypothesis far better than the hypothesized alternatives, the paper erroneously states that the results are “very strong empirical evidence” for universal common descent. It was yet another example of the non scientific IFF statement type of logic.

Not surprisingly the paper was an instant hit with evolutionists, celebrated everywhere from journals and popular science magazines to the blogosphere. One science newsletter proclaimed:

First Large-Scale Formal Quantitative Test Confirms Darwin’s Theory of Universal Common Ancestry

Scientific American informed its readers that “The Proof Is in the Proteins: Test Supports Universal Common Ancestor for All Life,” and National Geographic added that:

All Species Evolved From Single Cell, Study Finds
Creationism called “absolutely horrible hypothesis”—statistically speaking.

In his blog PZ Myers, who with his Lutheran background believes god would never have created this world, applauded the big numbers that “support evolutionary theory.” And Nick Matzke, who also believes in the evolutionary metaphysics that god would never have designed what we observe in the biological world, was delighted that the new work debunks creationism.

Of course all of this is false. It is junk science at its worst. I asked Theobald about these problems. I reminded him that one hypothesis comparing well against others does not translate into very strong empirical evidence for the hypothesis. But he disagreed. He assured me that his analysis is fundamentally based on modern, cutting edge statistical methods, and that he firmly stands by his conclusions. Indeed, no scientist or statistician would find them to be controversial, he added.

I explained to him that the problem lies not with the statistical methods. But when comparing such scores a scientist or a statistician would merely claim that the hypothesis with the significantly higher score is the winner of the group. That is entirely different than his high claim that the results constitute very strong empirical evidence for the hypothesis. That conclusion is simply false. The hypothesis may be true, it may not be true, but the study does not provide such powerful empirical evidence for it. Unfortunately, such misinformation fuels the kind of reporting we saw above.

But Theobald continued in his denial. You are simply incorrect, he replied. From a model selection perspective, from a likelihood perspective, and from a Bayesian perspective, empirical evidence can only be evaluated relative to other hypotheses. That’s all we have. No hypothesis can be evaluated in isolation—such an idea is impossible and incoherent. This view is not from evolutionary biology—this is the standard non-frequentist statistical view (and even most frequentists have the same view).

It was another fascinating example of denial of the plain facts. I replied that I was amazed. The lengths to which evolutionists must go is incredible. It is always striking to see the certainty with which evolutionists promote their philosophies and metaphysics. You can see it in the history of evolutionary thought, and today it just keeps on coming. They impose their philosophies, as though they were facts, on the world.

I again explained that when one hypothesis beats out others you cannot make the claims he was making. What you have is very strong evidence that the hypothesis beats out the other hypotheses, period. You do not have very strong evidence for the hypothesis, as you are claiming.

And your appeal to the limitations in your confirmation methods doesn’t change the fact that you are making false claims, and celebrating them as valid findings. The fact that “That’s all we have” hardly justifies the publishing and promotion of misinformation. The fact that “That’s all we have” ought to serve to temper the claims, not exalt them.

But contrastive thinking has been at the heart of evolutionary thought for centuries. From Kant to Darwin, and on up, what has always been rather revealing is how evolutionists have presented their proofs as though they were objective, undeniable findings. It is always a bit shocking to see such bold claims made on such faulty logic.

At this point the evolutionist turned the blame on me. We have, he explained, overwhelming evidence that universal common ancestry beats out competing multiple independent ancestry hypotheses. If you don’t consider that as evidence for universal common ancestry, then you are certainly entitled to that opinion. But the rest of us are not required to believe that your opinion makes any sense. Yours is a strange philosophy, to my mind, and I’m sure to most people who will read your words.

Repeatedly I have found that evolutionists are unable to see the problems and fallacies with their theory. And so when you point out those problems, the evolutionist ultimately can only conclude that the problem lies with you. You are an obstructionist, or biased, or anti science, or something.

Theobald was not being judgmental in any personal way. He threw up his hands and concluded that I am the problem, but his response was genuine, not contrived. It was not mean spirited. Just as Bernoulli proclaimed that anyone who would deny the obvious evolutionary conclusions “must reject all the truths, which we know by induction” so too evolutionists ever since can only understand skepticism as, itself, problematic.

Evolution is a metaphysically-driven tradition and like most such traditions has built-in protections against objective critique. The result, unfortunately, is junk science. In spite of monumental scientific problems, evolution is held to be a fact. If we do not acknowledge this obvious truth we must be obstructionists or biased.

Evolution cannot even explain how a single protein first evolved, let alone the massive biological world that ensued. From biosonar to redwood trees, evolution is left with only just-so stories motivated by the dogma that evolution must be true. That dogma comes from metaphysics, but silly science and metaphysics are not what makes evolution interesting. What is fascinating is the denial.

Friday, August 12, 2011

The Cod’s Unlikely Immune System and Evolutionary “Flexibility”

It’s being called “evolutionary flexibility.” Evolution’s effortless incorporation of the cod’s unusual immune system is yet another example of the near infinite plasticity of Darwin’s idea which, ultimately, could make unlikely alliances between everything from gradualism to saltationism, selection to drift, common descent to independent origin, bad designs to good designs, inefficiency to optimality, and so forth. Evolution is the ultimate big tent coalition where everything, save the truth of course, is allowed and flourishes.

Contrary to that quaint evolutionary expectation of similar designs in similar species, new research finds that the Atlantic cod (Gadus morhua) has an “unusual” immune architecture compared to other vertebrates whose genomes have been analyzed.

Unusual is right. In fact, G. morhua is missing the major histocompatibility complex (MHC) II. That’s right, the highly conserved and crucial MHC II is simply not present in the cod. Like the government which loses billions of dollars from time to time, evolution just happens to lose crucial molecular and cellular components now and then.

Needless to say, losing MHC II is not likely under evolution. Aside from the difficulty in simply losing all those genes (genes related to MHC II were also “lost”), such a loss would have left the cod with a crippled immune system—hardly the sort of adaptive change evolutionists are always talking about.

But true to form evolution can always find an explanation. First the hapless cod somehow lost its MHC II and related genes, but then cleverly compensated for the loss with massive additions to its MHC I. In the end all was well, and evolutionists have more puzzles to work on. As one explained, the finding could “challenge our understanding of the evolution and flexibility of the vertebrate immune system.” If only Ripley were alive today.

Tuesday, August 2, 2011

Of and About TEs: How Evolutionists Interpret Transposable Elements

TEs love TEs. That is, theological evolutionists love transposable elements. This is because transposable elements—a type of DNA segment—are powerful evidence for common descent. Transposable elements are often what evolutionists, such as Francis Collins, refer to when they say common descent is compelling. For similar transposable elements are found in similar locations in the genomes of similar species. If they have a common ancestor which also had those transposable elements at those locations in its genome, then would we not expect to see precisely what we are seeing: cousin species with similar transposable elements? This evidence certainly is a successful prediction (or retrodiction) of the theory of common descent. But there’s more.

Transposable elements are not merely a successful prediction of common descent, they are a powerful exhibit of dysteleology—the lack of design. We can hardly imagine that god would have installed these not very useful DNA segments at the same place in cousin species.

As theological evolutionists explain, transposable elements are an example where the design hypothesis fails and there really is no other explanation aside from common descent.

The IFF statement

In other words, this is not the usual case of IF theory X is TRUE, then we should observe Y. Instead, this is a case of IF AND ONLY IF theory X is TRUE, then we should observe Y. Not only does common descent explain transposable elements, but only common descent explains transposable elements.

The IF AND ONLY IF statement, also known as an IFF statement, is different from the usual IF statement in some important ways. First, given IF X THEN Y, it is not true that IF Y THEN X. In other words, a successful prediction does not mean the theory is true. That is the fallacy of affirming the consequent. A successful prediction merely means that the theory has passed a test.

Not so with an IFF statement. Given IFF X THEN Y, it is also true that IF Y THEN X. A successful prediction does mean the theory is true.

Another important difference between the IF statement and the IFF statement is that whereas the IF statement is scientific, the IFF statement is metaphysical. That is, in science a theory can produce predictions. If the theory is true, certain observations are expected. The IF statement is simply a statement about the theory and its predictions.

But the IFF statement is not merely a statement about the theory—it is a statement about all possible theories. The IFF statement is a claim that there does not exist any theory aside from X that can explain observation Y. Such claims are not possible within science.

In the case of transposable elements, evolutionists say god would not allow for the pattern of similarities we observe without common descent being true. This is because the transposable element patterns between species make common descent appear to be true. Therefore if god allowed for this pattern of similarities without common descent being true, it would be deceptive. Since god is not deceptive, only common descent can explain transposable elements. IFF common descent, THEN transposable elements.

IFF statements are common in evolutionary thought. The most famous one comes from one of the twentieth century’s leading evolutionists, Theodosius Dobzhansky, who claimed that “nothing in biology makes sense except in the light of evolution.” If it isn’t already obvious, that claim is equivalent to an IFF statement, as the following sequence of equivalent statements demonstrates:

1. Nothing in biology makes sense except in the light of evolution
2. Everything in biology makes sense only in the light of evolution
3. Only evolution can make sense of anything in biology
4. IFF evolution THEN biology

Dobzhansky justified his claim with a series of theological arguments that god would never had intended for this world.

The problem of unconceived alternatives

The history of science is littered with theories that were believed to be true and yet later dropped. In many cases a theory was held to be true not so much because it was convincing but because the alternatives were considered to be impossible. The theory was later dropped not because one of those alternatives became more palatable, but because an entirely different explanation was discovered. In other words, this reasoning by process of elimination is susceptible to unconceived alternatives.

The evolutionist’s many IFF statements are another example of this reasoning by process of elimination. They are certain their idea is correct because the alternatives must be wrong. As Ernst Mayr, another leading evolutionist of the twentieth century, once admitted, evolution achieved its predominance “less by the amount of irrefutable proofs it has been able to present than by the default of all the opposing theories.”

Just common sense

Now all this talk of theological premises, IFF statement and unconceived alternatives may seem unnecessary and irrelevant. Isn’t all this just an asterisk on what is obvious? As one evolutionist commented, yes it is a theological claim, but it is really amounts to common sense.

Transposable elements and their patterns obviously are not designed no matter how many technicalities one can raise against the clear conclusion. There is a theological claim there, but it is hardly important. It is nothing more than a teensie, tiny part of the reasoning.

This sentiment is typical and reminds us of Whitehead’s brilliant advise not to 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.

Evolutionists know for sure that their idea is a fact. And if all the evidence aligned with their claims then we would join with them. After all, there’s nothing wrong with metaphysics.

The rest of the story

But this the rub. While evolutionists are convinced by evidences such as transposable elements, there are monumental problems with evolution and common descent. As for common descent, biology is full of patterns that, unlike the transposable elements, do not align with the expected pattern.

In fact, if this were about following the evidence, then common descent would have been falsified long ago. Even evolutionists are now admitting the venerable evolutionary tree is falling because the species comparisons are yielding similarities and differences that simply do not match the expectations.

Incredible similarities in distant species and incredible differences in similar species abound. No one knows what kind of pattern may emerge, but it isn’t looking like an evolutionary tree.

So while there are evidences, such as transposable elements, that predominantly support common descent, there are plenty of others that do not. If we want to evaluate common descent we would, like an accountant, tally up the gains and losses—the confirmations and contradictions.

But evolutionists don’t do this. Instead of cooly analyzing the various evidences and their implications, evolutionists are busy making unfounded and undefendable truth claims, and ridiculing those who don’t follow along.

This is where the metaphysics and theology come back to bite us. If we apply theology selectively to the evidence of choice, and conclude common descent must be true, then the rest of the evidence no longer matters. It is relegated to the status of a research problem.

Amazingly, evolutionists often are not even cognizant of contradictory evidences. Over and over they claim that all the evidence unequivocally supports common descent and evolution. That’s just bad science.

Evolution’s track record is that the more we learn about the evidence the more it contradicts evolutionary theory. New evidence is interpreted according to evolution and hailed as new proofs, but as more is learned the proofs turn to questions and finally to contradictions.

Today transposable elements are good evidence for common descent and evolution. Whether they remain that way is difficult to say. But what is clear is that evidences such as transposable elements are counter balanced by monumental problems for both common descent and evolution. And the transposable element evidence does nothing to clear up that conflict.

As it stands, common descent and evolution are not very good scientific theories. The fact that they enjoy the support of certain evidences puts them in the class of blood-letting and the flat earth theory.

Confirmed predictions are not hard to come by in science. The difference is that evolutionists apply religious mandates to the evidence. What is merely a confirmed prediction becomes something far more powerful. Religion drives science, and it matters.