Sunday, June 30, 2013

DOMA and Evolution’s Dangerous Cocktail

A Witch’s Brew

Evolution is, if anything, a negative theory. We don’t know how life started in a warm little pond or anywhere else for that matter. We don’t know how fish evolved, or how they transformed into amphibia, reptiles, birds, mammals and all the rest. In short, beyond vague speculation, we don’t know how the species arose. But we do know how they did not arise. The species were not created or designed in any sort of intentional sense. You can see right off that this is a peculiar scientific theory. It arrives at an unlikely conclusion without much of an explanation or justification except that the alternative must be false. But that’s not all. Along with this non empirical, rationalistic, formulation comes two important corollaries: certainty and self-righteousness. It is a dangerous mix in a scientific theory and this week it emerged in American jurisprudence as well.

Evolutionists are certain that evolution is a fact. For if creation and design are false, then one way or another, the species must have evolved. Evolution, they say, is beyond all reasonable doubt. Evolutionists like to compare their theory with gravity, the roundness of the Earth and heliocentrism.

Given this level of certainty, it is not surprising that evolutionists do not suffer dissent gladly. In fact for evolutionists, those who disagree are typically viewed as undermining science and up to no good. This leads to value judgments and the assigning of motives of those who are skeptical of evolution.

So it is not surprising that evolutionists have no compunction about blackballing dissent. Evolution is good and right, and anyone who disagrees has nefarious motives. Here is how one philosopher described this dynamic (speaking of rationalism in general):

The typical rationalist will believe that theories that meet the demands of the universal criterion are true or approximately true or probably true … The distinction between science and non-science is straight-forward for the rationalist. Only those theories that are such that they can be clearly assessed in terms of the universal criterion and which survive the test are scientific … The typical rationalist will take it as self-evident that a high value is to be placed on knowledge developed in accordance with the universal criterion. This will be especially so if the process is understood as leading towards truth. Truth, rationality, and hence science, are seen as intrinsically good. [A. F. Chalmers, What is this thing called science? 2d ed., (Indianapolis, IN.: Hackett Publishing Company, 1982) 102.]

What is dangerous here is the tendency to identify ones theory, not merely as an explanation of the natural world and as explaining certain evidences, but with righteousness. And so those who doubt that the world spontaneously arose, by chance and on its own, are routinely subject to everything from innuendo and silent discrimination to ridicule and blackballing.

All this for an allegation which is patently false. Evolution may be true, but skeptics are certainly not surreptitiously attempting to undermine science. It would be laughable except evolutionists have ruined so many careers and misdirected so many textbooks and students. And like the Witch Trials, once blame has been assigned there is no acceptable defense except to admit to the imagined wrong-doing and accept the sentence.

Such high moralizing, unfortunately, is not limited to the life sciences. Its familiar pattern is too common in today’s cultural disputes and this week it appeared in the Supreme Court’s ruling on the Defense of Marriage Act.

The ruling was, in part, a response to pro traditional marriage propositions that were passed in California. The first one was declared unconstitutional by a judge, so the second (Proposition 8) made the necessary change to the state constitution. It too was overruled, this time by a gay judge in San Francisco.

In his decision the judge accused Californians who had voted for the proposition of bigotry. With the motives of millions of voters determined the judge was confident of his decision. Gay marriage was good and Proposition 8 supporters were bad.

In science there is an old saying, initiated by physicist Wolfgang Pauli, for theories that are not merely incorrect, but make no sense. Such theories are said to be “not even wrong.” The judge’s overturning of Proposition 8 was a legal ruling that was not even wrong. What was amazing was that the judge was oblivious to his own erroneous moralizing.

This week that bizarre opinion not only went uncorrected, but was reinforced when the Supreme Court doubled-down on such high moralizing, this time in its decision on DOMA. Not only did the high court strike down DOMA, it determined that those who disagree with them are out to “disparage,” “injure,” “degrade,” “demean,” and “humiliate” our fellow human beings and citizens who are homosexual.

This ruling was not from a lone judge in a lower court but from five of the top judges in the land with a small army of clerks on their staffs. It is astonishing they could produce a judgment so irrational and false. Again, gay marriage was good and DOMA supporters were bad. It would be difficult to imagine a better example of out of touch elites pronouncing judgments from on high.

The status and definition of marriage is no doubt a complex legal issue. But this is not about technical legal details. Evolution’s negative theorizing and moralizing has set a pattern that now seems to be prevalent. What is frightening is that these prosecutors actually believe their charges. Whether we are talking about a scientist or a judge, whatever the color of the robe, they are certain and they are self-righteous.

Sunday, June 23, 2013

Evolutionists Demonstrate Profound Influence of Natural Selection in Human Evolution

There’s Only One Problem …

Adam Siepel’s laboratory at Cornell University has now shown that natural selection played a crucial role in human evolution. And while that may seem to be an incredible finding there is one minor problem: They assumed evolution to begin with. Their new research paper is entitled “Genome-wide inference of natural selection on human transcription factor binding sites,” but their “inference” is based on the assumptions of evolution in general, that humans and chimpanzees share a common ancestor in particular, and that “nucleotides within a transcription factor binding site evolve by a mixture of four selective modes: (i) neutral drift, (ii) weak negative selection, (iii) strong negative selection and (iv) positive selection.”

So the paper’s conclusion that it has “shown that natural selection has indeed exerted substantial influence on transcription factor binding sites in the human genome” is not really true. They showed no such thing since the entire exercise was predicated on the truth of evolution.

This is not to say that circular reasoning in science is necessarily worthless. Sometimes it can make sense to assume the truth of a theory. But of course one must not forget that initial assumption when advertising the results.

Furthermore, in this case, the assumed theory is that, err, the species arose spontaneously. And the resulting finding is that humans evolved from an ancient primate mostly by changing the expression levels of preexisting proteins.

That is a finding that has been contemplated for years and takes evolution’s serendipity to a whole new level.

Imagine a factory that produces automobiles. Do you think that by changing the quantities of the various parts the factory would then produce rocket ships? Those automobile parts just happened to be what was needed for a rocket ship.

What evolutionists are now forced to say is that it just so happened that the proteins required to make humans evolved millions of years ago in far less fit species. The main difference was the quantities of those various proteins. Evolution merely needed to adjust those expression levels to produce a far more capable species. Right.

So to summarize, evolutionists are now advertising a circular finding based on the scientifically unlikely idea that the entire biological world spontaneously arose and the finding has evolutionists believing in ridiculous levels of serendipity.

Religion drives science, and it matters.

Photosynthesis Relies on Quantum Coherence

When Will They Cry Uncle?

It is no secret that nature’s process of photosynthesis—which harnesses the energy in sunlight—is astonishingly efficient. And researchers have known for years that quantum mechanisms play a role in the protein antenna farms deployed in these marvelous molecular machines. Now new research, based on a experimental technique that tracks these proteins at the femtosecond level (there are a million billion femtoseconds in a second), elucidates some of these quantum mechanisms and, as usual, the results are surprising.

Photosynthesis begins with special proteins that capture and transmit the energy from sunlight. The new research shows that these proteins use specific energy-transfer pathways that apparently are adaptive to the current conditions. These pathways are protein-specific and time-varying.

And part of the reason why these energy-transfer processes are so efficient is that they are coordinated. This quantum coherence is long-lived, persisting for hundreds of femtoseconds. As one of the researchers put it:

These results show that coherence, a genuine quantum effect of superposition of states, is responsible for maintaining high levels of transport efficiency in biological systems, even while they adapt their energy transport pathways due to environmental influences.

It would be an abuse of science to say the evolution of such systems is a fact, or likely. I don’t care if evolution is true or not, but from a strictly scientific perspective (which is not how the theory is motivated or evaluated), the idea is, to be frank, just silly.

These new results continue to make that clear.

Monday, June 17, 2013

Here is That New, Unique, Fluorescent Protein

More Lineage Specific Biology

Some proteins are fluorescent—shine a light on them and they glow. And as usual nature gives us all kinds of variations including different colors. These proteins are wonderful tools for molecular biologists who use them to tag and track molecular machines at work in the cell. Now another type of fluorescent protein has been discovered. Not only is it from a vertebrate (the Japanese eel), but its fluorescence mechanism is different (it uses bilirubin, the four-ring molecule that we shouldn’t have too much of). As one researcher put it, “It’s totally different. There’s not anything you can point to that’s the same.”

This new protein is another example of the incredible genius and creativity we find in biology, and it appears to be another example of the lineage-specific biology which runs counter to the expectations of common descent.

Saturday, June 15, 2013

That Yeast Study is a Good Example of How Evolutionary Theory Works

The Subtleties of Science

In 1846 astronomers in Europe discovered the planet Neptune. It wasn’t the first time Neptune had been seen, but it was the first time the object was identified as a planet. And how did the astronomers know where to look, and know that the object was Neptune? Because the position of Neptune had been computed and predicted. So they looked, and sure enough, there was Neptune. In fact similar predictions had been made independently by different scientists. The predictions were based on observations indicating that the next closest planet, Uranus, did not quite follow its expected orbit. Was Newtonian physics wrong? Perhaps Newton’s Law of Gravity broke down at longer distances. Or perhaps there was a perturbing force from another planet. It was the latter and Newtonian physics survived a strong test.

In this example of the discovery of Neptune, the initially false prediction of Uranus’ orbit eventually led to a greater understanding of the solar system. We discovered a planet. But sometimes false predictions reveal a problem with the theory. About fifty years later scientists began to doubt Newtonian physics not at long distances, but at short distances. The result was quantum mechanics and the understanding that Newtonian physics is incomplete. Quantum mechanics, which is important at the atomic level, was needed to complete the picture.

So false predictions can advance science in different ways. They can teach us about the world or they can teach us about the theory. Either way they lead to a greater understanding of nature.

This greater understanding might also be that a theory is false. This is where science becomes more art than science. For what is the difference between a theory needing adjustment and a theory being false? In principle a theory can always be adjusted to accommodate false predictions? With geocentrism—the idea that the Earth is at the center of the universe—we would expect the planets to follow simple orbits around the Earth. But sometimes they go in reverse. The great astronomer Ptolemy had to introduce dozens of epicycles into the theory where the planets followed strange, contorted trajectories rather than circles. It worked, Ptolemy’s theory described planetary motion very accurately. But was it true?

The theory of evolution has generated a long list of false predictions. Consequently the theory is constantly being revised. Is this good scientific progress or is the idea that the world arose on its own wrong?

One way to evaluate what these false predictions are telling us is to consider the reaction. Just how is the theory of evolution being revised? Is it more like quantum mechanics or geocentrism’s epicycles?

Recently we reported on a false prediction of evolution and gave some of the details. Evolution predicts that different kinds of genes, each found within a group of species, should tell the same story about evolution. They should produce similar evolutionary trees. Evolutionists have touted this fact of nature, and how it confirms a key prediction of evolution, for years. They call it a consilience of independent evidences. But increasingly, as we look under the hood and examine the details, we find there is more contradiction than consilience. The new study provided yet another, systematic and more in-depth, confirmation of these contradictions, or what are called incongruence. Evolutionists were a bit shocked.

What is interesting is how this false prediction was accommodated. The evolutionists tried to fix the problem with all kinds of strategies. They removed parts of genes from the analysis, they removed a few genes that might have been outliers, they removed a few of the yeast species, they restricted the analysis to certain genes that agreed on parts of the evolutionary tree, they restricted the analysis to only those genes thought to be slowly evolving, and they tried restricting the gene comparisons to only certain parts of the gene.

These various strategies each have their own rationale. That rationale may be dubious, but at least there is some underlying reasoning. Yet none of these strategies worked. In fact they sometimes exacerbated the incongruence problem. What the evolutionists finally had to do, simply put, was to select the subset of the genes or of the problem that gave the right evolutionary answer. They described those genes as having “strong phylogenetic signal.”

And how do we know that these genes have strong phylogenetic signal. Because they give the right answer.

This is an example of a classic tendency in science known as confirmation bias. You search for the evidence that confirms your hypothesis, and ignore or explain away the rest. This is what happens when the theory is in control. The theory determines the right answer. One way or another, the study will arrive at the right answer, no matter what is required.

Methods will be attempted, data will be filtered, results will be selected and in the end you will have the right answer. Of course if evolution is true then all of this is warranted. If the world spontaneously arose as a consequence of random events and natural law—chance and necessity—then we need to search for how that could have happened. This is, of course, what evolutionists do. But do their studies reveal evolution to be a fact, as evolutionists claim they do?

Thursday, June 13, 2013

Here Are Those Incongruent Trees From the Yeast Genome

Case Study

We recently reported on a study of 1,070 genes and how they contradicted each other in a couple dozen yeast species. Specifically, evolutionists computed the evolutionary tree, using all 1,070 genes, showing how the different yeast species are related. This tree that uses all 1,070 genes is called the concatenation tree. They then repeated the computation 1,070 times, for each gene taken individually. Not only did none of the 1,070 trees match the concatenation tree, they also failed to show even a single match between themselves. In other words, out of the 1,071 trees, there were zero matches. Yet one of the fundamental predictions of evolution is that different features should generally agree. It was “a bit shocking” for evolutionists, as one explained: “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 yeast.”

In fact, as the figure above shows, the individual gene trees did not converge toward the concatenation tree. Evolutionary theory does not expect all the trees to be identical, but it does expect them to be consistently similar. They should mostly be identical or close to the concatenation tree, with a few at farther distances from the concatenation tree. Evolutionists have clearly and consistently claimed this consilience as an essential prediction.

But instead, on a normalized scale from zero to one (where zero means the trees are identical), the gene trees were mostly around 0.4 from the concatenation tree with a huge gap in between. There were no trees anywhere close to the concatenation tree. This figure is a statistically significant, stark falsification of a highly acclaimed evolutionary prediction.

Wednesday, June 12, 2013

Helicase Animation and Why the Genetic Code Evolved

This is Amazing

In order for a biological cell to give birth to daughter cells, its genome must be replicated. And in order to replicate the DNA molecule, its two strands must first be unwound and separated. Enter the so-called helicase enzymes such as those illustrated in this animation (please click above). And how did all of this evolve? It is, of course, a fact that helicases (and everything else in the world) spontaneously arose from nothing. That may sound strange until you realize that something, namely the universe, came from nothing. So obviously helicases must have come from nothing.

The details of how all that evolving actually happened are another thing altogether. In fact, not only is the evolution of helicases a mystery, but the origin of protein synthesis and the genetic code is another “one of the major mysteries of evolution.” Fortunately, one cutting-edge researcher might be able to take care of both these mysteries with one hypothesis:

I propose that protein synthesis appeared as a side product of helicase activity. The first templates for protein synthesis were functional RNAs (ribozymes) that were unwound by the helicase, and the first synthesized proteins were of random or non-sense sequence. I further suggest that genetic code emerged to avoid this randomness.

This is another example of evolutionary science at work. Only from an evolutionary perspective could a researcher gain such keen insight and realize that the genetic code probably emerged to avoid all that randomness in early cells. That randomness was probably terribly difficult to work with, so of course the genetic code evolved. In hindsight, it was practically inevitable.

So we may not understand everything about the helicase enzymes you watch above. But one thing we know for certain, they evolved. That is a fact.

Tuesday, June 11, 2013

Contradictory Trees: Evolution Goes 0 For 1,070


One of evolution’s trade secrets is its prefiltering of data to make it look good, but now evolutionists are resorting to postfiltering of the data as well. Evolutionists have always claimed that the different species fall into a common descent pattern forming an evolutionary tree. That is, the various traits—from the overall body plan down to the DNA molecular sequences—from the various species, consistently reveal the same evolutionary pattern. If one gene shows species A and B are closely related and species C is more distantly related, then the other genes will reveal the same pattern. Evolutionists call this consilience. In practice however, this consilience is superficial. There are profound contradictions between the different traits, and in a new attempt evolutionists just set a new record for failure: out of 1,070 genes, every single one contradicted the hoped for evolutionary tree, as well as each other. 1,070 different genes and 1,070 different evolutionary trees. Consequently evolutionists are now manipulating the data even more than before to obtain the desired results.

These days when evolutionists compare species they usually use molecular sequence data, such as genes. But what if a particular type of gene is found in species A but not in species B? Obviously this constitutes a big difference between these two species. It is not as though the gene merely is different to some extent. It is altogether missing from one of the species. Nonetheless, the typical strategy in such cases is simply to drop that particular gene from the data set. That big difference is, in a stroke, eliminated from the analysis. This is one type of prefiltering evolutionists use.

Prefiltering is often thought of merely as cleaning up the data. But prefiltering is more than that, for built-in to the prefiltering steps is the theory of evolution. Prefiltering massages the data to favor the theory. The data are, as philosophers explain, theory-laden.

But even prefiltering cannot always help the theory. For even cleansed data routinely lead to evolutionary trees that are incongruent (the opposite of consilience). As one study explained, the problem is so confusing that results “can lead to high confidence in incorrect hypotheses.” And although evolutionists thought that more data would solve their problems, the opposite has occurred. With the ever increasing volumes of data (particularly molecular data), incongruence between trees “has become pervasive.”

This problem became all the more obvious in a new study that examined 1,070 different genes found in a couple dozen yeast species (yes, the data were prefiltered). All those genes taken together produced one evolutionary tree, but each of the 1,070 different genes produced a different tree—1,070 plus 1 different trees. It was, as one evolutionist admitted “a bit shocking.”

Or as another evolutionist put it, “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 [types of] yeast.”

Clearly something is amiss and for evolutionists it cannot be the theory. That means it must be the data. The solution is postfiltering, to go along with the prefiltering. Whereas evolutionists once assured themselves that their problems would go away when more data became available, they now are headed in exactly the opposite direction.

What is needed now is less data. Specifically, less contradictory data. As one evolutionist explained, “if you take just the strongly supported genes, then you recover the correct tree.” And what are “strongly supported” genes? Those would be genes that cooperate with the theory. So now in addition to prefiltering we have postfiltering. We might say that the data now are theory-laden-laden. Evolutionists will be eliminating the uncooperative genes and retaining those genes with what evolutionists euphemistically refer to as “strong phylogenetic signals.”

Then they can tell us again that evolution is a fact because the evidence says so. That’s just the stuff of good solid scientific investigation.

Here Is How Gnosticism Informs Evolution

More Religion in Science

Evolution professor John Avise ends his book, Inside the Human Genome, with a gnostic crescendo. The National Academy of Sciences member writes:

This welcome sentiment—that the evolutionary sciences and religion both have important and complementary roles to play in philosophical discussions about the human condition—has been expressed in many notable statements

Avise then provides several quotes, including this from Michael Zimmerman’s The Clergy Letter Project:

We ask that science remain science and that religion remain religion, two very different, but complementary, forms of truth.

And this from Francis Collins:

Science’s domain is to explore nature, God’s domain is the spiritual world, a realm not possible to explore with the tools and language of science. It must be examined with the heart, the mind, and the soul.

Gnosticism is sometimes viewed as an ancient belief, but the division of the material and the spiritual into separate realms is alive and well in evolutionary thought.

Nor is this merely a recent fad. Avise could have quoted from, for example, Baden Powell, mathematician at Oxford and Anglican priest who wrote In 1838 that scientific and revealed truth are of different natures, and any attempt to combine and unite them would “infallibly injure both.”

And of course if the spiritual world is so isolated from the material world, then the latter, including the species, must have arisen without any help from the former. In other words, the world must have arisen naturally, as Powell explained in 1855, a few years before Darwin published his book:

No inductive inquirer can bring himself to believe in the existence of any real hiatus in the continuity of physical laws in past eras more than in the existing order of things; or to imagine that changes, however seemingly abrupt, can have been brought about except by the gradual agency of some regular causes. … But however little we know of the laws or causes of these changes, one thing is perfectly clear, the introduction of new species was a regular, not a casual phenomenon; it was not one preceding or transcending the order of nature; it was a case occurring in the midst of ordinary operations going on in accordance with ordinary causes. The introduction of a new species (however marvellous and inexplicable some theorists may choose to imagine it) is not a solitary occurrence. It reappears constantly in the lapse of geological ages. It recurs regularly in connexion with those changes which determined the peculiar characters we now distinguish in different formations. It is part of a series. But a series indicates a principle of regularity and law, as much in organic as in inorganic changes. The event is part of a regularly ordained mechanism of the evolution of the existing world out of former conditions, and as much subject to regular laws as any changes now taking place.

But, as Avise explains, there is a problem. This gnostic truth may be firmly in hand, but there remain those who won’t go along—those who allow for the spiritual and material to intersect. These evolutionists conveniently label as fundamentalists and warn that in fundamentalism, religion has overstepped its bounds. And so in the final paragraph Avise makes his plea:

The evolutionary-genetic sciences thus can help religion to escape from the profound conundrums of Intelligent Design and thereby return religion to its rightful realm—not as the secular interpreter of the biological minutiae of our physical existence but rather as a respectable philosophical counselor on grander matters including ethics and morality, the soul, spiritual-ness, sacredness, and other such matters that have always been of ultimate concern to humanity.

Again, the sentiment is nothing new as Avise could have been quoting from Andrew Dickson White, cofounder of Cornell University who in the late nineteenth century targeted those "mediaeval conceptions of Christianity" (evolutionists had not yet hit upon the “fundamentalism” label). Once this “dogmatic theology” is excised, White explained, the separation of God and nature will be complete, and all will be well:

My belief is that in the field left to them—their proper field—the clergy will more and more, as they cease to struggle against scientific methods and conclusions, do work even nobler and more beautiful than anything they have heretofore done. And this is saying much. My conviction is that Science, though it has evidently conquered Dogmatic Theology based on biblical texts and ancient modes of thought, will go hand in hand with Religion; and that, although theological control will continue to diminish, Religion, as seen in the recognition of “a Power in the universe, not ourselves, which makes for righteousness,” and in the love of God and of our neighbor, will steadily grow stronger and stronger, not only in the American institutions of learning but in the world at large.

Today’s evolutionists express the same thoughts and concerns as their forbearers. This is not because today’s evolutionists are mining the literature from centuries past but rather because there are consistent threads of belief that run through time. Evolution is a genre in the history of thought. And one of its cornerstones is Gnosticism.

Try to imagine that you believed in this Gnosticism. Then you too would be an evolutionist. Religion drives science, and it matters.

Saturday, June 1, 2013

Being An Evolutionist

Masatoshi Nei and Evolution’s Hard Core

Do you think the world arose spontaneously? No one would agree with that, not even an evolutionist. But that is, in fact, what evolutionists believe. Indeed they say it is a fact. A fact as much as gravity or the round Earth. There must be no design, no final causes, no teleology. The world must have arisen by itself—spontaneously. And no, natural selection does not change that. There is no magic ratchet or feedback loop to make the hypothesized evolutionary process not a spontaneous process. And in any case natural selection is finally meeting its long-awaited demise, thus confirming even more so what it is to be an evolutionist.

Here’s a test. When I give you a word, you tell me the first thing that comes to mind. Here’s the word: Evolution. Answer: Natural selection, right? If your biology teacher could have used only one idea to describe evolution it probably would have been natural selection. It was practically synonymous with evolution.

But that was then and this is now.

The concept of natural selection always had problems and in recent years they have only grown stronger. So strong that evolutionists, one by one, are slowly admitting that selection could not be the important, primary force it was held to be for so long.

Consider, for example, Masatoshi Nei’s new book, Mutation-Driven Evolution. The term “mutation-driven” means that mutations not only are supposed to provide the raw materials for evolutionary change, but that they also are supposed to cause evolutionary change without the help of the venerable natural selection.

You might be crying foul if you remember all the times you were told that neoDarwinism—evolution by random mutation and natural selection—was a fact. If evolutionists such as Nei are now so easily discarding that once vaunted “fact” then why should we believe their new version? Particularly when the new version is even more unlikely than the old version, if that were possible.

But be careful. Evolutionists never really meant that neoDarwinism was a fact. I know that is what they said, and quite forcefully. But they said that only because neoDarwinism was the current version of evolutionary theory. What they really meant was that evolution, broadly construed, is a fact. NeoDarwinism, like all particular hypotheses of evolution, was always forfeitable.

Hypotheses of evolution can be thrown under the bus at any time. What cannot be questioned is evolution broadly construed, or as Ernst Mayr used to put it, evolution per se. And what is evolution per se? That the species arose according to random events and natural law—chance and necessity. Biology had no guiding hand, no design or final causes. It must have arisen spontaneously. That, as Lakatos would have put it, is evolution’s hard core.

And that is what it is to be an evolutionist.