Evolutionist: I Follow the Evidence

Really?

Evolutionist Matt Ridley rightly pointed out last week that the scientific consensus does not exactly have a stellar track record:

There was once widespread agreement about phlogiston (a nonexistent element said to be a crucial part of combustion), eugenics, the impossibility of continental drift, the idea that genes were made of protein (not DNA) and stomach ulcers were caused by stress, and so forth—all of which proved false. Science, Richard Feynman once said, is “the belief in the ignorance of experts.”

So why is Ridley an evolutionist? “I agree with the majority view on evolution,” explains the British scientist and author, “not because it is a majority view but because I have looked at evidence. It’s the data that convince me, not the existence of a consensus.”

Looked at evidence? This reminds us of Thomas Huxley’s sentiment that one ought to “Sit down before fact as a little child, be prepared to give up every preconceived notion, follow humbly wherever and to whatever abysses nature leads.”

Every preconceived notion? Well not exactly. Not the preconceived notion that evolution must be true. Other than that, one can follow the evidence.

As for Ridley, here is how he “Looked at evidence”:

We can read in the genes exactly the whole history of life. And we’re gradually understanding all of that, and it absolutely confirms there’s descent with modification with natural selection, and all these things that Darwin said. There’s plenty of room for disagreement about the details. It’s not one dogmatic theory, there’s a whole bunch of theories.

The first thing they should do when they see a consensus is try and shoot it down. But there is no question that all creatures on this planet are [evolutionarily] related. We can see that in the genes. They all share the same genetic code—it looks like a frozen accident. There’s no rhyme or reason why we have the particular genetic code we do. But bacteria have it, we have it, plants have it—it’s all connected.

Exactly the whole history of life? no question?

Of course there are questions. And no, the genes do not reveal the whole history of life. Not if you don’t presuppose evolution to begin with. Yet Ridley is absolutely sure of himself. With evolution, the deviation from the evidence is exceeded only the certainty with which the theory is held.

Here is Carl Sagan’s Proof of Evolution

More Than Meets the Eye

Carl Sagan once responded to an evolution skeptic with a response that Sagan obviously had given some thought to. You can listen to the question and Sagan’s summary beginning at the [0:24] mark:

Skeptic: How do you explain the switch from asexual reproduction to sexual reproduction?

Sagan: First off, let me say that, that in no way challenges the validity of biological evolution, whether we’re able or unable to explain the fact that many species, by no means all, reproduce sexually today. The Darwinian concept of evolution and natural selection is profoundly verified, not just by the fossil record, not just by the clear experience of artificial selection, but by the record in the nucleic acids, which is obtained by DNA sequencing, in which we can see the similarities and differences of organisms, and trace their evolutionary past—their history.

Sagan begins by explaining that the failure to explain basic and important productions of evolution cannot challenge the validity of evolution. Philosophers call this theory-protectionism. If basic, important theoretical failures can do no harm, then the theory is not falsifiable.

Next Sagan provides three evidences for evolution: fossils, artificial selection and DNA comparisons. Even if all these evidences were as evolution predicted they would not prove evolution. In that case, Sagan’s claim that evolution is “profoundly verified” by these evidences amounts to the fallacy of affirming the consequent.

But it gets worse. For in all three cases, the evidence is not even what evolution expects, but instead contradicts the evolutionary prediction. The fossils do not form an evolutionary tree, but rather reveal abrupt diversity explosions followed by a winnowing due to extinctions. The expected evolutionary tree is turned upside down.

Likewise artificial selection, and the experience of breeders, reveals that species do not simply extrapolate indefinitely as evolution expects. Breeders can be bring about change, but only so much. Darwin had to say that natural selection had something that artificial selection did not. There is no evidence for that, but for our purposes that is irrelevant. The point is that artificial selection does not provide the evidence Sagan claimed it did.

Finally, like the fossil record, the DNA sequences also do not form an evolutionary tree, but instead contradict it. Evolutionists have to prefilter the sequence data, and perform several other intellectual twists, to force fit the data into a tree.

Sagan claimed such arguments profoundly verify evolution. Instead the evidence reveals a host of problems for evolutionary theory.

Classic Quotes: “The Cosmos is all that is, or ever was, or ever will be.”

Where Evolution Becomes Crystal Clear

Every once in a while evolutionists distill their thoughts into pithy statements that profoundly summarize what it’s all about for them. Carl Sagan’s 1980 Cosmos video is chocked full of such statements, but non better than his classic opening line: “The Cosmos is all that is, or ever was, or ever will be.” [Please click to see] Obviously that is a truth claim, but it does not come from science. Truth claims that do not come from science are nothing new. What is new, however, is the presentation of such truth as science. And so while there is nothing wrong with evolutionists proclaiming what they believe. There is everything wrong with their insistence that it is what everyone else must believe as well. That their personal religious beliefs, not open to scientific scrutiny, are scientific facts. Evolutionists may be correct about origins, but they are not scientific.

Here is a small, representative sampling of such claims over the past three centuries.

“We think him a better Artist that makes a Clock that strikes regularly at every hour from the Springs and Wheels which he puts in the work, than he that hath so made his Clock that he must put his finger to it every hour to make it strike.” Thomas Burnet, 1681

“Newton and his followers also have a very odd opinion regarding God’s workmanship. According to them, God’s watch—the universe—would stop working if he didn’t re-wind it from time to time! He didn’t have enough foresight to give it perpetual motion. This machine that he has made is so imperfect that from time to time he has to clean it by a miraculous intervention, and even has to mend it, as a clockmaker mends his work. The oftener a clockmaker has to adjust his machine and set it right, the clumsier he must be as a clockmaker!” Gottfried Leibniz, 1715

God would not “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.” John Ray, 1717

It is most appropriate to the wisdom of God that the cosmic structures “develop themselves in an unforced succession out of the universal laws.” Immanuel Kant, 1755

“A perpetual war is kindled amongst all living creatures,” and nature is so arranged so as “to embitter the life of every living being.” David Hume, 1779

“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.” Erasmus Darwin, 1794

“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.” Robert Chambers, 1844

“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. On such principles the whole superstructure of rational geology entirely reposes; to deny them in any instance would be to endanger all science. … The event [the introduction of new species] 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.” Baden Powell, 1855

“these analogies are utterly inexplicable if species are independent creations.” Charles Darwin, 1859

“The strange springs and traps and pitfalls found in the flowers of Orchids cannot be necessary per se, since exactly the same end is gained in ten thousand other flowers which do not possess them. Is it not then an extraordinary idea to imagine the Creator of the Universe contriving the various complicated parts of these flowers as a mechanic might contrive an ingenious toy or a difficult puzzle? Is it not a more worthy conception that they are some of the results of those general laws which were so co-ordinated at the first introduction of life upon the earth as to result necessarily in the utmost possible development of varied forms?” –Alfred Wallace, 1870

“If whales were made at once out of hand as we now see them, is it conceivable that these useless teeth would have been given them?” –Joseph Le Conte, 1891

“What we do not know today we shall know tomorrow.” Alexander Oparin, 1924

“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.” Stephen Jay Gould, 1980

“The Cosmos is all that is, or ever was, or ever will be.” Carl Sagan, 1980

Would God “really want to take credit for the mosquito?” Ken Miller, 1999

“There are too many deficiencies, too much cruelty in the world of life. To assume that they have been explicitly created by God amounts to blasphemy. I believe God to be omniscient and benevolent. The ‘design’ of organisms is not compatible with such beliefs.” Francisco Ayala, 2002

These claims are not from science, but they drive science. They determine what is acceptable and not acceptable. They inform science and constrain it the “right” answers. As was said so long ago, theology is the queen of the sciences. Imagine for a moment that you believed these things. Then you would be an evolutionist.

Meet Professor Pedersen: Turning Science on its Head

The Real Warfare Thesis

In his Computational Molecular Evolution course professor Anders Gorm Pedersen states that “evolutionary theory is the conceptual foundation of biology” and that “A phylogenetic [evolutionary] tree will almost always help you think more clearly about your biological problem.” That might seem strange since evolutionary theory’s fundamental predictions have turned out to be false and the species do not fit into an evolutionary tree. But all is clear when Pedersen approvingly quotes what is practically evolution’s official motto from Theodosius Dobzhansky: “Nothing in biology makes sense except in the light of evolution.”

This statement is diametrically opposed to empirical science, for it is a universal truth claim that is impossible in science. To better understand that you can first restate the motto to its logical positive equivalent: “Everything in biology only makes sense in light of evolution.” A scientist would never, and indeed could never, claim that evidence X can only be explained by theory Y. That’s because a scientist cannot know of all possible theories and explanations. Such knowledge simply is not available within science.

Aside from the minor problem that most of biology does not make sense in light of evolution (and that problem really is the minor one in this case), there is no scientific experiment or rationale that can inform us of all possible explanations for the origin of the world, let alone how well they explain the evidence.

But evolution never was about science in the first place. In evolutionary theory, the science is like window dressing. It comes after the fact that evolution is true. If you don’t believe me just read the literature. Dobzhansky’s non scientific statement is like a chant for evolutionists. It is the continual drumbeat in the background of evolutionary thought. It appears everywhere from the popular literature to peer-reviewed research papers to classroom material such as in Pedersen’s course.

Evolutionists could not be more clear about their beliefs and their non scientific claims. This is not a minor or tangential aspect of evolutionary thought. For evolutionists this is their core position. They are at war with empirical science. A theory that continually contradicts the evidence is declared to be a fact because, well, it must be.

Religion drives science, and it matters.

When I Pointed Out the Problem of Moralizing Evolutionists Gave Me Pushback

More Moralizing

What is intriguing about evolution is not so much the idea itself but what comes along with the idea. Evolution’s idea—that the world arose spontaneously—is certainly enough to raise eyebrows since it goes against so much of what we know from science. But anti realism is not necessarily a bad thing in science, for science needs speculative ideas. What comes along with this particular speculative idea, however, is much more interesting and important. For evolutionists insist their idea is a fact. That claim—so at odds with the empirical evidence—indicates that there is something more to evolution than scientific theorizing. There is an underlying nonscientific foundation of evolution that mandates its certainty. This “fact” of evolution is, for evolutionists, so obvious and necessary that anyone who does not acknowledge it is, in their eyes, suspect. Evolutionists cannot understand how skeptics can have a legitimate argument—there must be ulterior motives at work. Skeptics must be up to no good. They are abusing science and they must be stopped. Evolutionists do not hesitate to cast aspersions on, judge and blackball skeptics. So along with the idea that the world arose strictly naturalistically, evolution brings epistemological and ethical claims which are as strongly held as they are unsupported. Unfortunately this combination of anti realism reinforced by moralizing seems to spreading.

Last week, in their ruling against the Defense of Marriage Act, the Supreme Court engaged in just this sort of moralizing. The court said that those who disagree with them are out to “disparage,” “injure,” “degrade,” “demean,” and “humiliate” our fellow human beings and citizens who are homosexual.

Of course the court holds no such monopoly on ethics. How could it when it did not even provide an alternative which the supposed bigots are to accept? Is one automatically a bigot for not agreeing to toss out the existing definition of marriage when no alternative is offered and to solve a tax problem?

One may agree or disagree with the existing definition of marriage, and that definition may change in the future as society sees fit. But erroneous blanket accusations of bigotry do not advance the discussion and are reminiscent of how evolutionists argue for their theory.

When we pointed this out evolutionists doubled down on their moralizing. Rather than realize the fallacy, they insisted that even our mere pointing this out, itself, constitutes bigotry. In other words, regardless of one’s position on the issue of marriage, acknowledging any legitimacy to the existing definition constitutes bigotry. Amazing.

This sort of hyper critical judgment is typical of evolutionists. The evolutionist’s combination of certainty and self-righteous moralizing is toxic to reasoned debate. Unfortunately it seems to be spreading.

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.

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.

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.

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?

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.

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.

Contradictory Trees: Evolution Goes 0 For 1,070

Whif

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.

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.