Tuesday, June 30, 2015

Vaccine Study Finds No Harmful Association, But Wait …

A Foregone Conclusion

A recent large vaccine study found no evidence of harmful association between the measles-mumps-rubella (MMR) vaccine and autism spectrum disorders (ASD). That good news was celebrated everywhere from the health care trade journals to the mainstream media. “The vaccine for measles, mumps and rubella,” reported CNN, “doesn't bring an increased risk of autism, according to a new study of more than 95,000 children.” In a related interview on the same webpage, CNN medical correspondent Sanjay Gupta argued that while “We don’t know what causes autism, but we know that vaccines do not.” Gupta went on even to suggest that “vaccines have been protective against autism.” That was, amazingly, precisely the most statistically-significant finding in the new study. That’s right, for one of the groups studied, receipt of the MMR vaccine was strongly associated with reduced autism risk. There is only one problem: it was yet another example of bogus Warfare Thesis science.

Historians have tried for years to disabuse us of the Warfare Thesis mythology. But their efforts have largely been in vain. The Warfare Thesis myth has always served as a powerful context for evolutionary theory and, false or not, evolutionists show no signs of forfeiting this powerful narrative.

Similarly, statisticians have tried for years to bring discipline to their field which too often uses statistics to “discover” a desired conclusion. One journal, Basic and Applied Social Psychology, recently even went so far as to ban altogether null hypothesis significance testing. But biostatisticians at Johns Hopkins rightly point out that ridding science of shoddy statistics will require scrutiny of every step, not merely the last one.

I point out the Warfare Thesis and statistical inference not as disparate examples of scholarship gone wrong, but rather as two very related problems. You might say statistical inference is one of the Warfare Thesis’ preferred tools, and this new vaccine study is a good example.

The study’s most significant finding was that the MMR vaccine is associated with reduced autism risk. The authors were right to seek some sort of confounding variables to explain this unlikely result. But this result, even if explained away, hints at the underlying challenges and problems in such a research study.

One problem is that the we are dealing with people. Different parents have different levels of concern. And diagnoses may be influenced by various factors. Second, autism spectrum disorders include a variety of symptoms and conditions. Statistical comparisons may be complicated by such factors.

Nonetheless, the authors concluded that “receipt of the MMR vaccine was not associated with increased risk of ASD.” While that is technically true, the opposite is also true. That is, receipt of the MMR vaccine was not associated with an absence of increased risk either. In other words, the uncertainty of their results is such that they are consistent with both no increased risk, or some increased risk. Either could be true, within reasonable levels of statistical confidence.

What the results do show is that the MMR vaccine is not associated with a dramatic increased risk of ASD. Receipt of the vaccine was not likely associated with a doubling of the risk, for example. But again, those results are subject to the caveats discussed above (which may be overriding factors).

The bottom line is that the study’s conclusions are false and irresponsible. And they led to yet more false and irresponsible proclamations in the media, with commentators such as Sanjay Gupta making demeaning comments about parents struggling with this difficult decision.

One might ask how papers such as this survive peer review? The answer is that the paper said exactly what the peer reviewers were looking for. You see, like all literature, the scientific literature comes in a genre, and today that genre is the Warfare Thesis. This is made clear at the very beginning of the paper, long before the data are considered:

Two doses of measles-mumps-rubella (MMR) vaccine are currently recommended for children in the United States: the first at age 12 to 15 months and the second at age 4 to 6 years. Although a substantial body of research over the last 15 years has found no link between the MMR vaccine and autism spectrum disorders (ASD), parents and others continue to associate the vaccine with ASD. Parents cite vaccinations, especially MMR, as a cause of ASD and have deferred or refused vaccinations for their children as a result. Lower vaccination levels threaten public health by reducing both individual and herd immunity and have been associated with several recent outbreaks of measles, with most cases occurring among unvaccinated individuals.

There you have it. Science has revealed the truth yet resistance to the undeniable facts continues, posing threats to us all. There was no question where the paper was headed—the results were a foregone conclusion. There is no way the researchers were going to discover anything wrong with vaccines. Those were the ground rules that readers must understand.

And once the beachhead is established the media’s heavy artillery can be brought to bear, proclaiming how the science had once again debunked the recurrent myths of the ignorant, as commentators such as CNN’s Jake Tapper shake their head in disgust.

These new truths then, in turn, lead to laws such as the California law mandating vaccines for all public school students which Governor Jerry Brown signed into law today. The law forces parents to violate their conscience or lose their tax monies to a public school system they are not allowed to use. Brown is a good leader but this new law is unfair and a mistake.

Does any of this mean that vaccines are not a great public health success, or that they should be avoided at all costs? No, of course not. Vaccines hold great promise and have conferred great health benefits. But the choice of whether or not to vaccinate is not simply a scientific question.

The problem is not that this is a difficult decision for some. That’s life. The problem is that evolution’s Warfare Thesis has resulted in both faulty science and an environment of discrimination against and vilification of parents struggling with legitimate decisions.

h/t; Little John

Antinomian Fervor: The Ten Commandments Must Go

“Do not think that I came to destroy the Law”

In yet another in-your-face ruling, another high court, the Oklahoma Supreme Court in this case, has ruled that a Ten Commandments statue must be removed from outside of the state capitol because, after all, it is religious. Rulings such as this have much broader implications. The sixth commandment is, for example, “You shall not murder,” and is a good example of how our entire judicial system is, in fact, “religious.” Of course we are not going to do away with the entire canon, but nine tenths of the law is not so much the laws that are in place but how those laws are interpreted and respected. Unfortunately, ours is a world where laws are treated like items on a cafeteria menu. We select what we like and ignore the rest. That’s antinomianism.

Tania Lombrozo on Evolutionary Belief and Cultural Factors

Here I Triumph

When an article begins with the statement that “The theory of evolution by natural selection is among the best established in science,” you know the author won’t be defending that claim but rather will be assuming it as a given. You also know the author, in this case psychology professor Tania Lombrozo at the University of California, Berkeley, is sufficiently distant from evolutionary theory such that facts won’t confuse the message. Even committed evolutionists have long since admitted that natural selection, at best, can only be one of several modes of evolutionary change. In fact biological adaptations we can observe are dominated by rapid, directed change in response to environmental challenges, not slow, random change accumulated via natural selection as evolutionary dogma had insisted.

Lombrozo’s article discusses ideas and theories about why some people accept evolution while others do not. Cultural factors and religious beliefs are at play, but there is something more:

But in the last 20 years or so, research in psychology and the cognitive science of religion has increasingly focused on another factor that contributes to evolutionary disbelief: the very cognitive mechanisms underlying human cognition.

So there are cognitive mechanisms underlying human cognition that influence our failure to accept evolution. While that seems to make sense it reminds us of that thorny problem, of which Lombrozo is happily oblivious, that these cognitive mechanisms (as well as everything else for that matter) must have been created by evolution.

In other words, Lombrozo’s belief in evolution is, according to her own account, simply a consequence of mechanistic actions in her head and the resulting molecular states, all of which just happened to arise spontaneously by the blind interplay of chance events and natural law.

How can Lombrozo be confident of any of her Epicurean assertions? Nonetheless she forges ahead:

Researchers have argued that a variety of basic human tendencies conspire to make natural selection especially aversive and difficult to understand, and to make creationism a compelling alternative. For instance, people tend to prefer explanations that offer certainty

Preferences for certainty? Is the Berkeley professor familiar with Rene Descartes and his need for certainty? Is she aware that Thomas Huxley acknowledged the great rationalist as foundational to evolutionary thought because, if not, she should know she’s soaking in it or, in this case, him (please click on video above to understand the full extent of Lombrozo’s predicament).

Lombrozo speaks of cultural factors as though she transcends them. In fact her belief that the world spontaneously arose is drenched in such cultural factors.

In fact, there's evidence that individuals vary in the extent to which they favor purpose and exhibit other relevant cognitive tendencies, and that this variation is related to religious belief — itself a strong predictor of evolutionary belief.

Indeed, evolutionary belief is a religious belief. There is no science behind spontaneous origins, rather it is mandated by our convictions about what a good god would and would not do. From a scientific perspective evolution is absurd. From a religious perspective it is a fact.

Lombrozo is hardly alone in her confusion over evolution’s epistemology, or lack thereof. Darwin himself made the same blunder in his famous July 3rd, 1881 letter to philosopher and political economist, William Graham. With less than a year left to promote his message, the elderly Darwin admitted that Graham made good points against chance but, in classic Petitio Principii style, Darwin turned the obvious evidence on its head:

Nevertheless you have expressed my inward conviction, though far more vividly and clearly than I could have done, that the Universe is not the result of chance. But then with me the horrid doubt always arises whether the convictions of man's mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey's mind, if there are any convictions in such a mind?

In other words, while evolution’s chance construction (yes, it is chance, the supposed natural selection merely kills off the bad designs, it does not coax good designs to arise—every mutation must have occurred by chance according to evolution) calls Graham's scientific judgments into question, thus protecting Darwin's modern-day Epicureanism, evolution’s chance construction by no means harms our theological convictions that God never would have created this world. Therefore evolution must be true.

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

So there you have it. The theory of evolution by natural selection is among the best established in science.

Sunday, June 28, 2015

Jeff Sachs Goes There: Anti-Vaxxers Go To Jail

Don’t Pass Go, And Don’t Collect $200

Given the dominance and confluence of the Warfare Thesis, its resulting scientism, and evolution’s apparently unceasing thirst for control over people, I kick myself for not predicting Jeff Sachs’ latest we-would-laugh-except-this-is-real threat that parents who do not vaccinate their children are committing a crime [1:50]. It is not enough that this past week the California legislature passed a new law that prohibits parents, who avoid the risk of vaccination, from sending their children to the public schools while nonetheless taxing those same parents to pay for the public school system which they are not allowed to use. These parents are a small minority and so are an easy target. But if Sachs has his way, unfair taxation will be the least of these parents’ concerns as they will be convicted as criminals for their choice to protect their children. Undoubtedly the state would also take their children from them.

Given the strong language from global warming (AGW) advocates about how those who don’t agree with them should be incarcerated, Sachs’ move is not too surprising. Please see this post , where I concluded that this vigilante justice could jump to other issues:

What we are seeing are classic defamation tactics. Evolution’s Warfare Thesis has lit all kinds of fires and emotions are running high. With evolution there is no law, just narrative. Today it focuses on climate, but it could jump to any number of issues.

According to Sachs, vaccination should be one of those issues. That fits nicely into the nineteenth century, mythical Warfare Thesis which was erected by evolutionists to protect their theory. One of the many targets of the Warfare Thesis were those anti-vaccination rascals. To this day evolutionists rally around vaccinations as another support for their scientism.

The fact is that vaccinations have done a world of good and there are plenty of reasons to vaccinate, but they also carry low-probability risk. Those are generalizations and the details are different for each vaccine and each patient.

The bottom line is that vaccinations often present a classic risk-reward tradeoff. They provide helpful protections, but they can present a very low risk of both short-term and long-term illness and death. Recently more than two dozen children in Mexico were hospitalized and two died after receiving vaccines. Authorities halted vaccinations temporarily. Tragedy has also struck in this country, such as in the case of Lorrin Kain, popularized in a recent book, who eventually died from her vaccination injuries. Even the official vaccine court acknowledged the vaccine injury, though the reparations were not nearly adequate.

For most people the risks are tolerably low, and the tradeoff favors the vaccination. But this isn’t a scientific analysis. Not only are the exact probabilities unknown (mostly because the Warfare Thesis has served to cloud and corrupt the science of properly evaluating the vaccine risk), but even if they were known, the risk-reward tradeoff cannot be set to a formula. It is a choice each parent must make for each vaccine, in consultation with their doctor.

None of this is controversial, yet evolutionary thinking demands a very different approach. It demands that while parents must have the choice to kill their unborn child, they ought not have the choice to make the vaccine risk-reward decision. What about the risk? Evolutionists deny the risk because, after all, correlation does not imply causation.

When I explained this evolutionists attacked me with their usual demagoguery. One evolutionist explained the problem is that I don’t accept the basic principles of science because, after all, unlike him I am skeptical that the species arose naturalistically:

The fact that the author of this post is a dedicated anti-evolutionist for whom no amount of evidence is enough to make him even question his convictions, and who has now apparently become an anti-vaxer is not surprising: if you don't accept the basic principles of science, then any application of science to human welfare is, by foregone conclusion, definitely negative

Note the dismissive language. Doubting that the species arose naturalistically makes me a “dedicated anti-evolutionist for whom no amount of evidence is enough” who does not “accept the basic principles of science.” And pointing out that the benefits of vaccines are accompanied by risks makes me “an anti-vaxer.” It’s all Warfare Thesis.

Another evolutionist attacked my post, making the absurd suggestion that the Lorrin Kain’s injuries may have been a mere coincidence, and threatening that he had “Saved and tweeted [the post] for posterity.”

It is disappointing that rational discussion is not possible, but this is the environment that the Warfare Thesis has created. The above Jeff Sachs video in which he calls for the criminalization of parents choosing not to vaccinate, for example, appears at Business Insider under the heading: “Watch Jeff Sachs destroy the anti-vaccine movement in under two minutes.” It is all about attacking the “deniers.” Meanwhile unlikely hypotheses are insisted to be fact, and anyone who doesn’t go along will incur their wrath, and maybe their indictments.

Friday, June 26, 2015

What Does Jeb Bush Have in Common With Stephen Jay Gould?


Evolution, a headline from earlier this month explained, “is unpredictable and irreversible, biologists show.” This was hardly a new thought for evolutionists. Stephen Jay Gould popularized the notion that if one could “replay the tape” of history the world would, as Eckels unfortunately discovered, turn out differently. It is contingency rather than law that governs history. Evolutionary events are “unique, unrepeatable, and irreversible” in the words of the famous evolutionist Theodosius Dobzhansky. Or as Harvard’s Ernst Mayr wrote, “Laws and experiments are inappropriate techniques” for explaining evolutionary events and processes. The world turns not according to Newton’s firm and unchanging laws but by particular, unique events which are for us to explore and explain. And as Phillip Johnson described, exploring and explaining, rather than following nature’s laws, gives us control. Given a lever and the law Archimedes could move the world, but given extension and motion Descartes’ could construct the world.

Antinomianism isn’t limited to theological debates. Whether in religion, science or politics, the law stands in our way. It blocks our control and so we reject it. By contrast the psalmist delights in the law. The book begins with the man who is blessed, for “his delight is in the law of the Lord.” Likewise Jesus explained that “till heaven and earth pass away, one jot or one tittle will by no means pass from the law till all is fulfilled.”

This ancient law is now the basis of our current legal system and it is every bit as important to us. Yet it is routinely rejected. Descartes and the evolutionists reject natural law in favor of absurd notions of the world spontaneously arising by creating itself. And in politics, equally silly notions are not hard to find. Leading presidential candidate Jeb Bush, for example, advocates warrantless surveillance. That’s fine if he can make it legal, but Bush rejects any such requirement. He states that there is not a shred of evidence that such surveillance has violated the rights of any American. Does he also believe there is not a shred of evidence that bank robberies have resulted in theft? Of course bank robberies have resulted in theft, otherwise they wouldn’t be bank robberies. Warrantless surveillance, by definition, is a violation of rights—it is illegal.

For Christians the law is precious and antinomianism, in any form, is to be avoided.

Wednesday, June 24, 2015

Evolutionist: Abortion Can Improve Life and Prevent Harm


So much of our mythology, as George Orwell pointed out, relies on the creative use of language in order to fool ourselves into believing. Evolution is said to “find” biological solutions, as though the evolutionary process is an intelligent agent. The new law that forces consumers to make purchases is called the “affordable” care act. And abortion is said to help people. An article published this week by an abortion “doctor” provides yet more examples of such Orwellian newspeak. She wrote that “Abortion can improve life and prevent harm; pro-choice, to me, does not mean anti-life.” How is it that the killing of innocent babies serves to “improve life and prevent harm”? And if this is not “anti-life,” then what is? Of course it is anti-life, but it is precisely this sort of upside down, euphemistic terminology that allows us to continue in the myth.

Monday, June 15, 2015

Evolution Makes No Sense on This Molecular Clock Problem

This One is a Mess

Evolutionary thought did not begin nor end with Charles Darwin. To be sure Darwin was its most important exponent, but evolutionary thinking goes back centuries before 1859 when Darwin first published his book on evolution, and it continued to develop long after Darwin. For example, for all his theorizing Darwin had little idea how biological variation—a crucial, fundamental component of evolutionary theory—actually occurs. How do species change to begin with? About half a century later evolutionists constructed neoDarwinism which added to Darwin’s theory the idea that random genetic mutations provided the needed biological variation which occasionally hit upon improvements and would be preserved via natural selection. Indeed, according to evolution, whales, oak trees, and humans all must have been created by an incredibly long series of random mutations. The theory did not work very well for a number of reasons. For example, mutations don’t slowly add up to arrive at complex biological structures and mechanisms, and biological change is rapid and directed, not slow and random. Those are merely two of a great many false predictions generated by evolutionary theory. One of them is the concept of a molecular clock.

Given the evolutionary (neoDarwinian) hypothesis that evolution is driven by a steady diet of random mutations, evolutionists believed that they could compute evolutionary time by counting mutations. In other words, the number of DNA differences, for example in a particular gene, between two different species could be used to compute how long it has been since they diverged from a common ancestor.

This notion of a molecular clock became extremely popular and certain amongst evolutionists. Study after study used genetic differences to map out the supposed evolutionary tree. But this area of work eventually ran into substantial contradictions and other problems which you can read about here. Simply put, the data did not fit the theory.

A recent article entitled “DNA mutation clock proves tough to set” in the top science publication in the world, continued to reinforce the dramatic failure of this evolutionary notion. The article focuses on the mutation rate—a fundamental parameter in the molecular clock—in humans. Simply put, the mutation rate can be estimated (i) from theory-neutral measurements or (ii) from theory-laden measurements, and the two don’t match. In fact, they’re not even close. They differ by a factor of two.

The theory-laden measurements are based on evolutionary theory. The theory-neutral measurements do not entail evolutionary thinking. In other words, making measurements based on evolutionary theory leads to problems. The resulting DNA mutation rates are not even close to what we can measure more directly, free from theoretical assumptions.

As is often the case, these discrepancies between the evidence and the theory leave evolutionists unsure and of differing opinions. As one evolutionist admitted:

The fact that the clock is so uncertain is very problematic for us, It means that the dates we get out of genetics are really quite embarrassingly bad and uncertain.

Given problems such as this, evolutionists’ insistence that their idea is a fact beyond all reasonable doubt reveals that is isn’t about the science.

Wednesday, June 10, 2015

Miracles are a Glaring Problem for Evolution, and Here’s Why

Begging the Question

A commenter recently reminded me of one of the many fundamental fallacies of evolutionary thought. When I point out problems with evolution, and make arguments against evolutionary thought, it is not because I am against the idea or want it to be false. Life would be much easier if the evidence simply supported evolution, if evolutionary thought was a stellar example of intellectual progress, if—to put it simply—evolution was an undeniable scientific fact, just as evolutionists insist. But it’s not. Evolution is not any of those. Evolution is not supported by the empirical evidence, it is not a rational, intellectual movement, and it is not a scientific fact, undeniable or otherwise. I’m not grinding a personal ax here, I’m simply pointing out the obvious. It makes no difference to me if evolution is true, false, or somewhere in between. But it does make a difference when we lie to ourselves.

One of the lies we tell ourselves is about miracles and how they relate to evolution. Specifically, evolutionists have been making arguments against miracles for centuries. A convenient starting place is seventeenth century church history, when Roman Catholic and Protestant elements of the church argued with each other, and between themselves, about miracles. It is a long story, but the upshot was that miracles were increasingly viewed with disdain for several reasons.

By the time David Hume arrived in the mid eighteenth century, the dust was settling. Hume is well known for his arguments against miracles, but he was largely repackaging sentiment that had long since been expressed.

Some arguments were epistemological. Others were theological, philosophical or ontological. But the short version is that evolutionary thought emerged in a milieu in which miracles were on the way out, both as explanatory mechanisms and as historical reality. Darwin contemporary David Friedrich Strauss, and his Life of Jesus, is but one of many examples of this broad, robust movement.

The movement against miracles was, not surprisingly, influential in the natural sciences. Simply put, if we’re not to appeal to miracles, then the world must have arisen naturalistically. This had a profound effect on the critical thinking, or lack thereof, of the time. Speculative hypotheses, with little basis in fact, enjoyed serious consideration and triumphant acceptance.

The bar was placed exceedingly low for such theories as pure conjecture became acceptable and celebrated science. Monumental scientific problems with the notion of spontaneous origins went ignored and evolutionary theories (from cosmological to biological) soon became “fact.”

Today strictly naturalistic, evolutionary, theories are a given. They simply are accepted as true, or as true as anything in science can be. And it also is a given that miracles are false. But what evolutionists prefer to overlook is that there is a causal relationship here. The latter made way for, and mandated, the former.

What an incredible coincidence it would be if, on the one hand, miracles were known to be false and, on the other hand, the empirical evidence turned out to prove a naturalistic origins. Theology, philosophy and science would have converged on the same truth.

But there is no such convergence.

The “convergence” that occurred is artificial. It is artificial because the empirical scientific evidence was interpreted according to the cultural mandate. Science was told what to do.

Indeed, from an objective, theory neutral, perspective, evolution is unlikely. It is not good science. In fact it is an outstanding example of bad science, breaking all the rules of what the textbooks tell us about how science is supposed to work. The idea that the multitude of species, the cosmos, consciousness and, well, everything, arose spontaneously by the interplay of chance contingencies of history and natural laws is silly. And that is being kind.

The problem of miracles is another example of the failure of evolutionary thought. Religion drives science, and it matters.

Saturday, June 6, 2015

Forget the Micro Flies, See These Micro Frogs

Impossible Miniaturization

Remember those micro flies which are practically invisible? Well perhaps even more amazing are the micro frogs from the island of New Guinea which at their largest are about three-quarters of a centimeter. There are about two and half centimeters per inch. So these micro frogs are not much more than a quarter inch long.

Tuesday, June 2, 2015

About That Squid and its RNA editing …

Molecules Gone Wild

We recently reported that the common squid, Doryteuthis pealeiirecodes, uses massive, tissue-specific, RNA editing to modify many of its proteins. One evolutionary explanation for this apparent intelligent design would be that the editing machinery is merely an uncontrolled, random process. This would be in keeping with evolution’s view of life as a train off the tracks. Indeed, many past findings were initially described as vestigial or junk, until the design could no longer be denied. One current example is the finding that most of the human genome is transcribed. Apparently it is functional, and so isn’t mostly junk. But one evolutionary explanation that continues to have currency is that the transcription machinery is uncontrolled and has gone wild.

Well this “Molecules Gone Wild” explanation won’t work this time, for several reasons. First, the RNA editing is not only tissue specific, but also is protein specific. Certain proteins, such as those working on the squid nervous system, undergo much more editing than the other proteins. This doesn’t look like a random, uncontrolled, editor.

Furthermore, the RNA edits cause changes to the resulting protein amino acid sequence at a rate far higher than would be expected from random edits. And, just as striking, that non random rate is highly correlated with the editing level of the RNA site. In a given RNA transcript, some sites are found to be edited more often than others. The level of editing can range from a percent up close to 100%. And as that editing level increases, the rate at which the edits deviate from the randomly expected rate of changing the resulting protein amino acid sequence increases as well. The correlation is striking, as the graph below shows.

The horizontal red line shows the rate of amino acid sequence change that would result from random RNA edits. As you can see, for those sites that are more consistently edited, the rate increasingly rises above that red line. Something very non random is going on there, and evolution has no explanation for it aside from, “Wow, an incredibly complex design happened to arise by chance, and then it was maintained by natural selection.” That’s not science.