Here’s Why Homoplasy (And Other Contradictions) Isn’t a Problem For Evolution

Evolution and common descent expect the species to fall into a tree-like pattern. Species on the same branch should be similar, whether one is looking at their visible features or the microscopic cellular and molecular features. On the other hand, species on very distant branches should be different, again whether one is looking at their visible features or the microscopic cellular and molecular features. And while this expected pattern has some flexibility that is allowed, the observed pattern reveals far more significant contradictions. Allied species that look like they belong to the same branch reveal profound differences upon closer inspection. And different species that look like they belong to distant branches reveal profound similarities. One might think evolutionists would go easy on their truth claims about evolution being overwhelmingly supported by the evidence and a compelling fact. But they don’t, not in the light of these contradictions or in the light of the many other contradictions. Here is a recent paper that shows exactly how evolutionists respond to these evolutionary tree contradictions. First for some background:

Understanding the diversification of phenotypes through time—“descent with modification”—has been the focus of evolutionary biology for 150 years.

And next for the statement that reveals how evolutionists handle contradictions. They don’t consider the possibility that evolution may not be a fact. Rather, they search for evolutionary explanations:

If, contrary to expectations, similarity evolves in unrelated taxa, researchers are guided to uncover the genetic and developmental mechanisms responsible. 

And while that might seem reasonable, one problem is that while the search is on there is no acknowledgment that evolutionary theory has problems. Evolution racks up problem after problem, and still no such acknowledgment. For those problems are interpreted as research problems which deal with the theory of evolution and have no influence on the fact of evolution. Such research is taken as a sign of good science at work.

So while there is nothing wrong with doing research, the years pass by with no acknowledgment of the actual state of the science. This brings us to the second problem, which is that evolution is sufficiently malleable that it always seems to have at least some sort of explanation, albeit unlikely, to service the contradictions. To wit, the paper continues:

Similar phenotypes may be retained from common ancestry (homology), but a phylogenetic context may instead reveal that they are independently derived, due to convergence or parallel evolution, or less likely, that they experienced reversal. 

In this case, the contradictions can be explained by various combinations of common ancestry, convergence, parallel evolution and reversal, to name a few. They could have included unique selection scenarios, accelerated evolution, and other mechanisms to account for those profound differences found amongst otherwise allied species.

In any case, one way or the other the contradictions will be explained by some mechanisms, no matter how speculative or unlikely. And the whole exercise will be cast as an investigation of how evolution really works.

Such examples of homoplasy present opportunities to discover the foundations of morphological traits. A common underlying mechanism may exist, and components may have been redeployed in a way that produces the “same” phenotype. New, robust phylogenetic hypotheses and molecular, genomic, and developmental techniques enable integrated exploration of the mechanisms by which similarity arises.

Components may have been redeployed? Evolutionists will try hard to explain the findings, but don’t expect an objective, theory-neutral, scientific evaluation of their idea.

This Video Shows Hummingbirds in Super-Slow Motion

You have to click on the image to see this beautiful video.

Evolutionists Caught Again—But They Still Believe

Remember how evolutionists said random mutations created all the species? Then when their genes were compared that random mutation model didn’t always work so well. Those random mutations must have varied considerably both over time and over the genomes. Evolutionists even had to say that evolution had actually created machines and mechanisms to control the mutations themselves. Evolution was causing and directing evolution. If that wasn’t incredible enough, now the story has become even worse. As a new paper now explains, under evolution we must believe that mutations rates have been “evolutionarily optimized.” That is, evolution is now so brilliant that it created the means to not only control, but to optimize the actual mutation rates. First for an introduction:

A central tenet in evolutionary theory is that mutations occur randomly with respect to their value to an organism; selection then governs whether they are fixed in a population. This principle has been challenged by long-standing theoretical models predicting that selection could modulate the rate of mutation itself. However, our understanding of how the mutation rate varies between different sites within a genome has been hindered by technical difficulties in measuring it.

Next the paper introduces the new study, in which a new technical approach is used:

Here we present a study that overcomes previous limitations by combining phylogenetic and population genetic techniques.

And finally, the results are summarized. The first result is that if evolution is true, we must believe that the basic mutation varies by more than an order of magnitude in different bacteria:

Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases. 

The next result is that, under evolution, the variation between different mutation rates must not be random, but rather must follow a rational pattern:

Importantly, the variation is not random: we detect a lower rate in highly expressed genes and in those undergoing stronger purifying selection.

And so, given evolution, we must conclude that evolution has optimized the mutation rate:

Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations.

Of course there is no known mechanism that could do this:

Current knowledge of factors influencing the mutation rate—including transcription-coupled repair and context-dependent mutagenesis—do not explain these observations, indicating that additional mechanisms must be involved. 

But evolutionists will think of something, no matter how speculative.

The findings have important implications for our understanding of evolution and the control of mutations.

These findings have important implications for our understanding of evolution? Well sure, if by that they mean how absurd are evolution truth claims. Evolutionists have been caught again. Round up the usual suspects.

Evolution For Dummies (in 750 words)

As we saw in the previous post, the consensus position among evolutionists is that evolution is a fact, every bit as much as gravity, the round Earth and heliocentrism are facts. But the scientific evidence does not show evolution to be a fact, so what’s going on? For example, evolutionists refer to the fossil record, but the fossils reveal what species existed in the past, not how they got there. Minor adaptations in lineages are suggested in the fossils, but large-scale evolutionary change must be inferred to occur between different fossil species. In fact, the fossil record shows bursts of diversity and new forms appearing abruptly.

Evolutionists also refer to comparative anatomy. But again, these do not tell us how the species arose. Similarity between species does not imply an evolutionary relationship. In fact, comparative anatomy commonly reveals contradictory patterns. Distant species share the same designs, and sister species show very different designs.

Evolutionists also refer to small-scale adaptation we can observe. But we don’t know that these adaptations generally accumulate to create large scale change evolution requires. In fact even evolutionists have agreed this is doubtful, and that some other, unknown, mechanism is required. In fact, these adaptations are produced as a consequence of profoundly complicated molecular structures and mechanisms, whose origin evolution does not explain.

Is there evidence for evolution? Sure, there is plenty of evidence for evolution. But there are significant problems with evolution. There is plenty of evidence for evolution just as there is plenty of evidence for geocentrism. But the science does not bode well for either theory.

So the evidence for evolution follows this general pattern: Even at its best, it does not prove evolution to be a fact. And furthermore, the evidence reveals substantial problems with evolution.

So how can evolutionists proclaim evolution to be a fact with such fervor? There seems to be a glaring mismatch between the evidence and the truth claims of evolutionists. The answer is that evolutionists use contrastive reasoning. Evolution is not claimed to be a fact based on how well it fits the evidence, but rather on how poorly the alternative fits the evidence. Evolution is proved by the process of elimination.

For example, evolutionists explain that nature’s apparently useless or harmful designs make no sense except on evolution. Such harmful designs are actually not predicted by evolution. They are low probability on evolution, but such harmful designs are at least understandable given evolution’s lack of planning. The designs may be low probability, but not altogether impossible.

But if the species were intelligently designed, then these useless or harmful designs make no sense. So we might say that evolution is proved not by positive evidences, but by negative evidences. And in fact the worse the evidence, the better for evolution, because such negative evidences are even worse for the alternative.

Indeed, there are no demonstrations of the fact of evolution that do not appeal to such contrastive reasoning. Evolutionists have a great many proofs for the fact of evolution, but they always entail some form of this contrastive reasoning. Here is how philosopher Eliott Sober explains contrastive reasoning:

This last result provides a reminder of how important the contrastive framework is for evaluating evidence. It seems to offend against common sense to say that E is stronger evidence for the common-ancestry hypothesis the lower the value is of [the probability of E given the common-ancestry hypothesis]. This seems tantamount to saying that the evidence better supports a hypothesis the more miraculous the evidence would be if the hypothesis were true. Have we entered a Lewis Carroll world in which down is up? No, the point is that, in the models we have examined, the ratio [the probability of E given the common-ancestry hypothesis divided by the probability of E given the separate-ancestry hypothesis] goes up as [the probability of E given the common-ancestry hypothesis] goes down. … When the likelihoods of the two hypotheses are linked in this way, it is a point in favor of the common-ancestry hypothesis that it says that the evidence is very improbable. [Evidence and Evolution, p. 314]

These evolutionary arguments and conclusions are very powerful. It seems that the evolutionist’s argument is compelling. The species must have arisen spontaneously via evolutionary mechanisms. But in all of this there is a catch.

Science cannot know all the alternative explanations for the origin of the species. When evolutionists conclude evolution is a fact via the process of elimination, they are making a subtle but crucial non scientific assumption—that they know all the alternative explanations.

So all of these powerful evolutionary arguments for the fact of evolution are non scientific. In other words, evolution has extremely powerful and compelling arguments, but the cost of building such a powerful case is that the idea is not scientific.

Without these powerful proofs, evolution would lie exposed to the many scientific problems and contradictions. The idea that the world, and all of biology, spontaneously arose is, from a strictly scientific perspective, extremely unlikely. But evolution is shielded from such problems by its powerful non scientific proofs.

This non scientific aspect of evolution is immense and would be difficult to underestimate. It has dramatically altered the very perception of science and its evidence. For given the fact of evolution, all of biology is interpreted according to the idea. The many scientific problems with evolution become more friendly “research problems.” And the theory becomes immune to scientific skepticism.

You Won’t Believe What Evolutionists Believe

Evolutionists argue about many things but one thing they agree on is that their idea is a scientific fact. It is the one, definite, consensus position within evolutionary thought. Evolutionists say their idea is as much a fact as is gravity, the roundness of the Earth and heliocentricity. These claims began shortly after Charles Darwin’s book on evolution was published, and they have only grown stronger since. These claims are like a flashing red light indicating a problem. For, of course, evolution is not a scientific fact. Indeed there are tremendous scientific problems with the notion that something comes from nothing, or in the case of biological evolution, that nature’s millions and millions of species, with their profound designs, arose spontaneously strictly according to natural law. Evolution, in one form or another, may somehow be true. It is a difficult question, for who really knows how the world and all of biology actually arose? What isn’t a difficult question, however, is whether the idea is a scientific fact. For the claim that evolution is a fact is not a claim about the distant past, it is a claim about our knowledge of the distant past. We may not know with certainty what happened in the distant past, but we do know for certain what we know about it. And we do not know evolution to be a fact. Not even close. If anything, we know that the idea is greatly challenged by science. It certainly is not a scientific fact. And so the evolutionist’s certainty that evolution is a fact is a sign of the underlying metaphysics. When people believe in things that they don’t understand and, furthermore, insist they are right and everyone else is wrong, and anyone who dares to question must be blackballed, then there is a problem. Unfortunately, that precisely describes evolution. Here then is a small sampling of the evolutionist’s “fact” claims which you won’t believe.

About 30 years after Darwin’s book was published evolution professor Joseph Le Conte wrote this:

Evolution is certainly a legitimate induction from the facts of biology. But we are prepared to go much further. We are confident that evolution is absolutely certain. Not, indeed, evolution as a special theory—Larmarckian, Darwinian, Spencerian—for these are all more or less successful modes of explaining evolution … but evolution as a law of derivation of forms from previous forms; evolution as a law of continuity, as a universal law of becoming. In this sense it is not only certain, it is axiomatic. …

So also, the origins of new organic forms may be obscure or even inexplicable, but we ought not on that account to doubt that they had a natural cause, and came by a natural process; for so to doubt is also to doubt the validity of reason, and the rational constitution of organic Nature. The law of evolution is naught else than the scientific or, indeed, the rational mode of thinking about the origin of things in every department of Nature. … the law of evolution is as certain as the law of gravitation. Nay, it is far more certain …

More recently, evolutionist R. C. Lewontin wrote this in a scientific journal:

It is a fact that all living forms come from previous living forms. Therefore, all present forms of life arose from ancestral forms that were different. Birds arose from nonbirds and humans from nonhumans. No person who pretends to any understanding of the natural world can deny these facts any more than she or he can deny that the earth is round, rotates on its axis, and revolves around the sun.

Evolutionist Neil Campbell wrote this in his biology textbook:

The term theory is no longer appropriate except when referring to the various models that attempt to explain how life evolves … it is important to understand that the current questions about how life evolves in no way implies any disagreement over the fact of evolution.

Here’s another example textbook example from Douglas Futuyma:

A few words need to be said about the "theory of evolution," which most people take to mean the proposition that organisms have evolved from common ancestors. In everyday speech, "theory" often means a hypothesis or even a mere speculation. But in science, "theory" means "a statement of what are held to be the general laws, principles, or causes of something known or observed." as the Oxford English Dictionary defines it. The theory of evolution is a body of interconnected statements about natural selection and the other processes that are thought to cause evolution, just as the atomic theory of chemistry and the Newtonian theory of mechanics are bodies of statements that describe causes of chemical and physical phenomena. In contrast, the statement that organisms have descended with modifications from common ancestors--the historical reality of evolution--is not a theory. It is a fact, as fully as the fact of the earth's revolution about the sun. Like the heliocentric solar system, evolution began as a hypothesis, and achieved "facthood" as the evidence in its favor became so strong that no knowledgeable and unbiased person could deny its reality. No biologist today would think of submitting a paper entitled "New evidence for evolution;" it simply has not been an issue for a century.

Even the National Academy of Sciences states that evolution is a fact. They explain that in science the word “fact” can be used “to mean something that has been tested or observed so many times that there is no longer a compelling reason to keep testing or looking for examples. The occurrence of evolution in this sense is a fact. Scientists no longer question whether descent with modification occurred because the evidence supporting the idea is so strong.”

In his book What Evolution Is evolutionist Ernst Mayr wrote:

However, throughout the nineteenth century whenever people talked about evolution, they referred to it as a theory. To be sure, at first, the thought that life on Earth could have evolved was merely a speculation. Yet, beginning with Darwin in 1859, more and more facts were discovered that were compatible only with the concept of evolution. Eventually it was widely appreciated that the occurrence of evolution was supported by such an overwhelming amount of evidence that it could no longer be called a theory. Indeed, since it was as well supported by facts as was heliocentricity, evolution also had to be considered a fact, like heliocentricity. …

Evolution is a historical process that cannot be proven by the same arguments and methods by which purely physical or functional phenomena can be documented. Evolution as a whole, and the explanation of particularly evolutionary events, must be inferred from observations. Such inferences subsequently must be tested again and again against new observations, and the original inference is either falsified or considered strengthened when confirmed by all of those tests. However, most inferences made by evolutionists have by now been tested successfully so often that they are accepted as certainties.

Mayr also concludes:

It is very questionable whether the term “evolutionary theory” should be used any longer. That evolution has occurred and takes place all the time is a fact so overwhelmingly established that is has become irrational to call it a theory. …

Evolution is not merely an idea, a theory, or a concept, but is the name of a process in nature, the occurrence of which can be documented by mountains of evidence that nobody has been able to refute. Some of this evidence was summarized in Chapters 1-3. It is now actually misleading to refer to evolution as a theory, considering the massive evidence that has been discovered over the last 140 years documenting its existence. Evolution is no longer a theory, it is simply a fact.

And in his book Why Evolution is True, evolutionist Jerry Coyne writes:

Now, when we say that “evolution is true,” what we mean is that the major tenets of Darwinism have been verified. Organisms evolved, they did so gradually, lineages split into different species from common ancestors, and natural selection is the major engine of adaptation. No serious biologist doubts these propositions.

These are representative quotes of the evolutionist’s consensus position. It would be difficult to find more obvious examples of misrepresentations of science.

Another Key Evidence For Evolution is Getting Squashed

A new paper out of Germany on the evolution of animal embryos reveals yet again the typical trajectory of evolution’s treatment of the science. Evidence that is barely understood is declared to confirm powerfully evolution. Then, years later, when science looks under the hood and uncovers the incredible details, the mismatch between the data and the theory becomes more clear. At that point the evidence, rather than confirming the theory, is interpreted according to the theory. Rather than the evidence explaining the theory, it is the theory that is explaining the evidence, no matter how awkward. In the end the evidence is contorted every which way in order to serve the theory of evolution. All of this must be presented with great care to avoid any sign of trouble:

There is a remarkable similarity in the appearance of groups of animal species during periods of their embryonic development. This classic observation has long been viewed as an emphatic realization of the principle of common descent.

In other words, before discussing evolution in the light of new scientific evidence, which inevitably makes evolution look bad, one first must give the secret handshake—a proclamation indicating that evolution is unquestionably true and good, and that all the evidential contradictions you are about to discuss will be force-fit into the evolutionary doctrine.

Despite the importance of embryonic conservation as a unifying concept, models seeking to predict and explain different patterns of conservation have remained in contention. 

Now you are free to openly discuss the evidence which, in fact, never did support evolution as much as evolutionists claimed. In fact,

Here, we focus on early embryonic development and discuss several lines of evidence, from recent molecular data, through developmental networks to life-history strategies, that indicate that early animal embryos are not highly conserved. 

with the inexorable march of scientific progress, the contradictions always monotonically increase with time.

Bringing this evidence together, we argue that the nature of early development often reflects adaptation to diverse ecological niches. Finally, we synthesize old and new ideas to propose a model that accounts for the evolutionary process by which embryos have come to be conserved.

And so new evolutionary just-so stories are badly needed to replace the old ones that fared so poorly.

von Baer’s observations, and in particular his third law, provided foundational evidence supporting Darwin’s theory of common descent.

See, it wasn’t just an English idea. The Germans also want some credit for the idea that took over the world, even if that idea requires an endless supply of just-so stories to fend off the evidential onslaught.

In fact evolutionists now must believe that those random mutations regularly produce embryological do-overs, without altering the adult form. This, to explain the evidence which is that sister species are often found to have very different development patterns.

As the figure shows, evolutionists have had to construct ever more elaborate just-so stories to explain the supposed evolution of embryonic development.

Confusion abounds and the evolutionists conclude, contra the traditional evolution view, that given the early embryo of an animal species, it would be possible to infer “comparatively little about its evolutionary trajectory.” That once powerful evidence that Darwin and the evolutionists proclaimed is now in the crowded dustbin of evolutionary proofs.

Evolution Just Took Another Hit—Right Where it Counts

Evolution is all about reproduction—those that reproduce the most are the winners. And if you were paying attention in biology class you will remember that nature has many different types of reproduction designs. These reproduction subsystems, according to evolution, should align with the other biological subsystems to form a consistent evolutionary tree. This consistency is, evolutionists say, a powerful confirmation of their idea. Except when it isn’t. Now a tiny lizard from Africa has been found to have a reproduction subsystem that is unique and remarkably similar to that of humans.

In the viviparous lizard Trachylepis ivensi (Scincidae) of central Africa, reproducing females ovulate tiny ∼1 mm eggs and supply the nutrients for development by placental means. Histological study shows that this species has evolved an extraordinary placental pattern long thought to be confined to mammals, in which fetal tissues invade the uterine lining to contact maternal blood vessels. The vestigial shell membrane disappears very early in development, allowing the egg to absorb uterine secretions. The yolk is enveloped precocially by the trilaminar yolk sac and no isolated yolk mass or yolk cleft develops. Early placentas are formed from the chorion and choriovitelline membranes during the neurula through pharyngula stages. During implantation, cells of the chorionic ectoderm penetrate between uterine epithelial cells. The penetrating tissue undergoes hypertrophy and hyperplasia, giving rise to sheets of epithelial tissue that invade beneath the uterine epithelium, stripping it away. As a result, fetal epithelium entirely replaces the uterine epithelium, and lies in direct contact with maternal capillaries and connective tissue. Placentation is endotheliochorial and fundamentally different from that of all other viviparous reptiles known. Further, the pattern of fetal membrane development (with successive loss and re-establishment of an extensive choriovitelline membrane) is unique among vertebrates. T. ivensi represents a new extreme in placental specializations of reptiles, and is the most striking case of convergence on the developmental features of viviparous mammals known.

Or in plain English:

In central Africa, an unassuming little lizard has evolved a spectacular and oddly human feature of gestation: a complex placenta. It is the first time that scientists have observed such an advanced version of this organ connecting the fetus to the womb in nonmammals.

Biologist Alexander Flemming made the anatomical find, announced late last year, while sorting through specimens at the Port Elizabeth natural history museum in South Africa. Flemming and his collaborator, Daniel Blackburn, knew that about 20 percent of lizards give birth to live young, but finding the placenta came as a shock.

Whereas virtually all cold-blooded reptiles supply embryos with nutrients from a large egg yolk, five-inch-long Trachylepis ivensi females ovulate small, yolk-poor eggs that implant in the uterus. As the fetus develops, its tissues become intimately entangled with the blood vessels of its mother, providing ready access to nutrients and oxygen in the mother’s blood. Sound familiar? “The fetal tissues actually invade the uterine ones, much like in humans,” Blackburn says. “It’s totally unexpected.”

A lizard with a human-like reproduction system? It is yet another example in the long list of evolutionary expectations gone wrong. We must believe that random mutations just happened to replicate a complex, mammalian-like placental pattern in a lizard, though it had a perfectly good reproductive system to begin with.

Nothing in biology makes sense in the light of evolution.

Here’s the Rundown on the Latest Evolution Blackball Operation

University of Texas El Paso mathematics professor Granville Sewell wrote a paper on how the second law of thermodynamics bears on the theory of evolution. The paper was peer-reviewed and accepted for publication. But after a blogger complained the journal, Applied Mathematics Letters (AML), pulled the article, in violation of its own professional standards. That evolutionary blackball operation ended up costing the journal $10,000 in attorney’s fees.

The evolutionist’s next move was not only to continue to reject the letter, but to publish criticism of the peer-reviewed, accepted, unpublished, rejected paper in the journal Mathematical Intelligencer (MI). And their final move was to reject Sewell’s response to the criticism, again in violation of their own standards.

It is yet another episode of the Banality of Evilution which has evolutionists falling over themselves to blackball those who disagree.

Here is That Secret Gnosis Evolutionists Have

In the previous post we learned that evolutionists have a secret gnosis. They say science must be limited to naturalistic explanations (the so-called methodological naturalism), yet their science knows no limits (the so-called property of completeness) and is presented as a reasonably accurate model of reality (the so-called property of realism). Now there’s nothing wrong with constraining science to methodological naturalism, but what if there is a phenomenon that is not natural? Then the methodological naturalism constraint could not provide an accurate explanation. We would either have to avoid such phenomena (incompleteness), or we would have to settle for inaccurate explanations (anti realism). But evolutionists do not settle for such limitations. How can they mandate method (specifically methodological naturalism) and yet enjoy completeness and realism? The answer lies in their secret gnosis, of which we give an example here.

SIDEBAR: Does evolutionary science really entail completeness?

One evolution professor wrote to me that evolutionary science does not claim completeness. Evolutionists readily agree that phenomena may lie outside the realm of strict naturalism. Is that true?

One sure sign of incompleteness at work is a scientist, when grappling with a difficult problem, allowing for even just the possibility that the problem may not be strictly naturalistic. One would expect these scientists to be found, at least on rare occasions, discussing the boundary between naturalism and non naturalism, even if they are not sure where it lies or even if there are any non naturalistic phenomena. But such conversations are hard to find amongst evolutionists.

And it is not as though they don’t have their share of hard to crack problems. After all, there is no scientific evidence that something (in this case everything) comes from nothing, as they believe. Nor does science support their rather heroic contention that life and all the millions of species arose spontaneously. There certainly are no easy answers for consciousness but again, evolutionists rush in, where wise men fear to tread, with their unlikely explanations.

Evolutionists don’t even hesitate when it comes to the origin of the universe itself. And when problems arise they even call upon a multitude of universes—the so-called multiverse. From multiverses to the origin of life and emergence of complexity, evolutionists evidence little awareness or concerns about potential incompleteness limitations.

So how did this evolution professor defend his claim that evolutionary science does not claim completeness? Believe it or not, his source was that fount of knowledge, the famous Judge John Jones, as though the judge was now an authority on the subject. Yes, this is the same judge who, regarding his preparation for the Dover trial, explained that  “I understood the general theme. I’d seen Inherit the Wind.”

One of the many examples of the evolutionist’s secret gnosis comes from an essay written by Theodosius Dobzhansky entitled “Nothing in biology makes sense except in the light of evolution.” It is a fitting example because that title has become a popular phrase in the evolutionary literature, including the popular literature and peer-reviewed research papers.

In that essay Dobzhansky rehearses the typical theological naturalism (i.e., theological arguments mandating a strictly naturalistic creation narrative) which is endemic to the evolution literature. For instance, Dobzhansky explained that the fossil record reveals many extinctions, and while this would be understandable under evolution, it would make no sense for God to do this:

but what a senseless operation it would have been, on God's part, to fabricate a multitude of species ex nihilo and then let most of them die out!

Or again, can we really believe that all existing species were generated by supernatural fiat a few thousand years ago, pretty much as we find them today? For “what is the sense of having as many as 2 or 3 million species living on earth?”

The beauty of natural selection is that it does not work according to a foreordained plan. But it would make no sense for a Creator to intentionally create the species we find. As Dobzhansky explains:

Was the Creator in a jocular mood when he made Psilopa petrolei for California oil fields and species of Drosophila to live exclusively on some body-parts of certain land crabs on only certain islands in the Caribbean?

Echoing Kant from centuries ago, who theorized of creation by natural means to avoid a capricious Creator, Dobzhansky explains:

The organic diversity becomes, however, reasonable and understandable if the Creator has created the living world not by caprice but by evolution propelled by natural selection.

And what about the fundamental biochemistry built into the species? Again, evolution is mandated for intentional design and creation of such a pattern is offensive to us, as Dobzhansky explains:

But what if there was no evolution and every one of the millions of species were created by separate fiat? However offensive the notion may be to religious feeling and to reason, the anti-evolutionists must again accuse the Creator of cheating. They must insist that He deliberately arranged things exactly as if his method of creation was evolution, intentionally to mislead sincere seekers of truth.

These are the types of powerful religious arguments that motivate and justify the evolutionary thought. It is all about metaphysics. Evolution must be a fact and so, of course, evolutionists enjoy completeness and realism along with their methodological naturalism. This is their secret gnosis.

What Evolutionists Don’t Understand About Methodological Naturalism

[Ed: An oldie-but-goodie from July 5, 2011]

OK let’s try this again. One more time, this time with pictures. In their celebrated volume  Blueprints, evolutionists Maitland Edey and Donald Johanson argued that “What God did is a matter for faith and not for scientific inquiry. The two fields are separate. If our scientific inquiry should lead eventually to God … that will be the time to stop science.” Similarly for evolutionist Niles Eldredge, the key responsibility of science—to predict—becomes impossible when a capricious Creator is entertained:

But the Creator obviously could have fashioned each species in any way imaginable. There is no basis for us to make predictions about what we should find when we study animals and plants if we accept the basic creationist position. … the creator could have fashioned each organ system or physiological process (such as digestion) in whatever fashion the Creator pleased. [The Monkey Business, p. 39, Washington Square Press, 1982.]

Or again, evolutionist Paul Moody explains that:

Most modern biologists do not find this explanation [that God created the species] satisfying. For one thing, it is really not an explanation at all; it amounts to saying, “Things are this way because they are this way.” Furthermore, it removes the subject from scientific inquiry. One can do no more than speculate as to why the Creator chose to follow one pattern in creating diverse animals rather than to use differing patterns. [Introduction to Evolution, p. 26, Harper and Row, 1970.]

Likewise Tim Berra warns that we must not be led astray by the apparent design in biological systems, for it “is not the sudden brainstorm of a creator, but an expression of the operation of impersonal natural laws, of water seeking its level. An appeal to a supernatural explanation is unscientific and unnecessary—and certain to stifle intellectual curiosity and leave important questions unasked and unanswered.” In fact, “Creationism has no explanatory powers, no application for future investigation, no way to advance knowledge, no way to lead to new discoveries. As far as science is concerned, creationism is a sterile concept.” [Evolution and the Myth of Creationism, pp. 66, 142, Stanford University Press, 1990.]

In his undergraduate evolution text Mark Ridley informs the student that “Supernatural explanations for natural phenomena are scientifically useless,” [Evolution, p. 323, Blackwell, 1993] and commenting on the Dover legal decision Eugenie Scott of the National Center for Science Education explains that supernatural explanations:

would be truly a science stopper, because once we allow ourselves to say, “Gee, this problem is so hard; I can’t figure out how it works—God did it,” then we stop looking for a natural explanation; and if there is a natural explanation, we’re not going to find it if we stop looking.

Over and over evolutionists today agree that science must strictly be limited to naturalistic explanations. One finds this throughout the evolutionary literature and it is a consistent refrain in discussions and debates about evolution.

But this sentiment by no means arose with today’s evolutionists. In 1891 UC Berkeley professor Joseph LeConte argued strenuously for this philosophical mandate:

The origins of new phenomena are often obscure, even inexplicable, but we never think to doubt that they have a natural cause; for so to doubt is to doubt the validity of reason, and the rational constitution of Nature. So also, the origins of new organic forms may be obscure or even inexplicable, but we ought not on that account to doubt that they had a natural cause, and came by a natural process; for so to doubt is also to doubt the validity of reason, and the rational constitution of organic Nature.

Likewise Darwin argued that whether one “believes in the views given by Lamarck, by Geoffroy St. Hilaire, by the author of the ‘Vestiges,’ by Mr. Wallace or by myself, signifies extremely little in comparison with the admission that species have descended from other species, and have not been created immutable: for he who admits this as a great truth has a wide field open to him for further inquiry.”

Explanations needed to be naturalistic for scientific inquiry. And as usual the foundations for this evolutionary mandate long predate 1859. Miracles were increasingly eschewed by leading thinkers and a century before philosopher David Hume had made persuasive arguments against miracles. Much of Hume’s material came from theological debates earlier in the century. On the continent leading Lutherans had already discarded the supernatural.

Method, completeness and realism in pictures

So when an evolutionist today insists that science must be naturalistic he is standing on a deep foundation of ideas. But setting aside this history for a moment, what about this argument? Remember that these same evolutionists claim their idea is also a fact. Is there not something curious about these tandem claims? I was once in a debate where the evolutionists claimed that we know evolution is a fact, and that it also is necessary in order to do science. How did they know that? Let’s have a look.

First, imagine the set of all possible explanations, as represented by the blue area below:

Because the blue area contains all possible explanations, it includes false as well as true explanations, lousy as well as good explanations, aesthetic and clumsy ones, and natural and non natural ones. It is every possible explanation in one set.

Now consider the set of all solutions that are according to a particular method, such as naturalism, as illustrated in the orange area below. All explanations that are strictly naturalistic are in the yellow area, and all other explanations are outside the orange area. Because the blue area contains all possible explanations, the orange area is a subset—it is wholly within the blue area.

Next consider the set of all true explanations as represented by the green circle below. These true explanations provide realistic models of nature. Again, this set of explanations must be wholly within the blue area, but otherwise we don’t know just where this green circle is. It could be in the orange area, it could be outside the orange area, or it could overlap. We don’t know what the true solutions all are, which is why we do science.

I have drawn the green circle above as partly inside and partly outside the orange area merely to illustrate the possibilities. But we don’t know where it is, and therefore whenever we mandate, a priori, a method such as naturalism, we automatically exclude a set of explanations that might be true.

In the early days of modern science philosophers were keen to this issue. Francis Bacon, for instance, wanted science only to pursue true explanations. But Bacon also wanted science to restrict itself to naturalistic explanations. Bacon realized that the restriction to naturalism would exclude any realistic, true, explanations that were not strictly naturalistic.

Bacon said that such non naturalistic phenomena should not be pursued by science. So Bacon insisted on naturalism and realism, but forfeited completeness. Science would not investigate all things. The thick black line below illustrates how this position limits itself to explanations that are both realistic and naturalistic, while potentially forfeiting some true explanations (depending on where exactly the green circle really is).

Like Bacon, another early philosopher, Rene Descartes, also insisted on naturalism. But he didn’t like the idea of forfeiting completeness. Descartes wanted science to be able to investigate all phenomena. But what if some realistic, true, explanations fall outside of naturalism? So what.

Descartes solution was to forfeit realism. Science, according to Descartes, would occasionally produce untrue explanations that otherwise could very well be useful. This approach is illustrated by the thick line below that encompasses all the naturalistic explanations, but misses some of the true explanations. Science might produce useful fictions along the way. Descartes mandated method and completeness, but in doing so had to forfeit realism.

After Descartes several scientists did not like this idea of forfeiting realism, as Descartes did, or forfeiting completeness, as Bacon did. These empiricists were interested in true solutions for all phenomena. This approach is illustrated below with the thick line encompassing the true solutions. But in order to maintain such realism and completeness, this approach cannot guarantee what method would be necessary. They might require non naturalistic explanations, for instance. So this approach provides realism and completeness, but forfeits any guarantee of method, such as naturalism.

Bacon, Descartes and the empiricists represent three different approaches to doing science. All are logically consistent. And who knows, the different methods might yield different insights—let a thousand flowers bloom.

But of course all three approaches have a limitation. Like the Heisenberg Uncertainty Principle, you cannot have realism, completeness and method all in one. You cannot have your cake and eat it too.

This brings us back to the evolutionists. Unlike Bacon, Descartes and the empiricists, evolutionists do have their cake and eat it too. They claim evolution is a fact, they mandate naturalism, and their science knows no limits. They have realism, method, and completeness all together. How can this be?

The answer is simple. One cannot have realism, method, and completeness simultaneously without some extra, non scientific, knowledge. Evolution’s gnosis is, of course, that true solutions are, indeed, naturalistic. This is illustrated below by the thick line that encompasses all true explanations, but it is also wholly naturalistic. How so? The trick is that the green circle has been moved. It is completely within the orange area. Knowing the location of the green circle, even before doing the science, is evolution’s gnosis—their secret knowledge.

It is this secret knowledge the evolutionists possess that allows them to have their cake and eat it too, and this brings us back to the history of the idea. There is no great mystery here, for evolutionists have for centuries made strong theological arguments that the world must have arisen naturalistically. The true explanations are all naturalistic. Therefore it is little wonder that, while not knowing how the world could have evolved, evolutionists are sure it did evolve. Evolution, one way or another, is a fact.

It is here that many fail to appreciate evolution’s conundrum. They often criticize evolution’s method mandate. Have not evolutionists been wrong to insist on methodological naturalism? No, such a method is perfectly fine.

The problem with evolution is not its insistence on method, but on its underlying theology. By insisting on method and realism and completeness, evolutionists are literally not equipped to consider other legitimate possibilities. They have already made a metaphysical commitment, without knowing whether or not it is true. They have confined themselves to a box. For when problems are encountered there is no way to tell whether the correct naturalistic solution has simply not yet been found, or whether the phenomenon itself is non natural. Of course evolutionists must always opt for the former, no matter how absurd the science becomes.

So the problem with evolution is not that the naturalistic approach might occasionally be inadequate. The problem is that evolutionists would never know any better. The evolutionists truth claims, and the underlying theology, have immense consequences. Religion drives science, and it matters.

Here is the Language of Evolution

A common claim of evolutionists is that “Nothing in biology makes sense except in light of evolution.” It shows up everywhere from the popular literature to the peer-reviewed research papers. This claim is equivalent to “Certain things in biology makes sense only in light of evolution,” which in turn is equivalent to “Only evolution can explain certain things in biology.” Or, in the language of scientific hypothesis testing, this is equivalent to: “Evolution and only evolution predicts certain things in biology.”

But this is hardly a scientific hypothesis. In science hypotheses and theories are constructed and predictions are made based on the hypothesis. If the prediction is successful then the hypothesis escapes falsification. If not, then the hypothesis fails. It must be modified or perhaps even discarded.

This reasoning process is sometimes denoted as IF P, THEN Q. And if NOT Q, THEN NOT P.

In other words, if hypothesis P is true, then prediction Q will also be true. And if Q is found to be false, then P is false.

This is the language of science. Of course there are other ways of doing science as well, but the evolutionary claim that “Evolution and only evolution predicts certain things in biology” is, on the other hand, very different. It is not the language of science but rather the language of metaphysics. For science cannot know that a hypothesis, and only that one particular hypothesis, can explain something we observe.

This reasoning process is denoted as IF AND ONLY IF P, THEN Q.

In other words, if hypothesis P is true, and only if hypothesis P is true, then Q will also be true.

In this case Q is not a prediction, but rather something that has already been observed. Q is already known to be true. And P is the theory of evolution. The claim is that there are no possible explanations for these aspects of biology, except for evolution.

Straightaway one can see this claim entails knowledge of all possible explanations. Science has no such knowledge.

What this claim reveals is evolution’s underlying religion foundation that derives from the Enlightenment and remains as crucial as ever today. This claim, in its many different versions, pervades the evolutionary literature. It is the language of evolution.

[Ed: Several modifications were made to the logical statements to make them more robust]

This New Research Reveals One More Awesome Aspect of Pigeon Navigation

Evolution may be unguided but its creations certainly are not. From ants and bees to fish and birds, nature’s creatures have remarkable built-in guidance and navigation capabilities. Birds, for instance, can fly thousands of miles and return to the same location. How organisms are able to  perform these feats, let alone how evolution could have created such capabilities, has puzzled scientists for years. Such capabilities can be divided into several functions such as sensing information from the environment, storing the sensed information, comparing the stored information with reference information, deciding how to act given the comparisons, and so forth. New research is now helping to explain a bit more about the storing function in pigeons.

The new research suggests that there must be, as yet undiscovered, magnetic field sensors in the bird’s inner ear which report compass readings to the brainstem. The story is further complicated, however, by activity in other regions of the brain as well. The researchers were able to detect signals in specific neurons, and how different neurons were sensitive to particular compass readings.

The researchers suspect that the reference information is stored in the hippocampus. As one writer explains:

In some birds that hide seeds and return later to their caches with astonishing accuracy, the hippocampus grows and shrinks seasonally, presumably as they map their hiding spots.

It has been an on-going and difficult area of research and this latest study is being called “stunning.” But it is only a small part of the story and there is much more to learn.

What is being slowly revealed is an astonishingly complex guidance and navigation system. As its profound complexity is increasingly understood the belief that it arose by chance biological variation becomes increasingly exposed for what it is: a non scientific and outdated view of origins. In this case, we would have to believe that sensors arose by chance, with multiple neurons that by chance reported their data to parts of the brain that by chance stored the information, and that other parts of the brain by chance evolved capabilities to store reference information, and that other parts of the brain evolved capabilities to compare the sensed information with the reference information and to make decisions. All of this had to be constructed in the embryonic stages and operate robustly in the mature bird. And all of this is so complex our best scientists still can’t figure it out how it works, let alone how it could have evolved. And yet evolutionists are certain that it did evolve. That is a conviction, not a scientific conclusion.

This Non Scientific Claim Regularly Appears in Evolutionary Peer Reviewed Papers

Early in the twentieth century scientists studied blood immunity and how immune reaction could be used to compare species. The blood studies tended to produce results that parallel the more obvious indicators such as body plan. That is, humans are more closely related to apes than to fish or rabbits. These findings were soon proclaimed to be powerful confirmations of evolution. In 1923 evolution professor H. H. Lane cited this evidence as supporting “the fact of evolution.” This evidence would become another icon of evolution, lasting well through the twentieth century. In their 1976 text Evolution: Process and Product Edward Dodson and Peter Dodson argued that only evolution can explain the blood immunity data (which by the way is a non scientific claim to begin with, but that’s another story). Likewise Tim Berra argued from the blood immunity data in his 1990 Evolution and the Myth of Creationism. But the congruence that evolutionists celebrated was fleeting. Under the hood biology was not so cooperative.

Even by mid century contradictions to evolutionary expectations were becoming obvious in serological tests. As J.B.S.Haldane explained in 1949:

Now every species of mammal and bird so far investigated has shown quite a surprising biochemical diversity by serological tests. The antigens concerned seem to be proteins to which polysaccharides are attached. We do not know their functions in the organism, though some of them seem to be part of the structure of the cell membrane. I wish to suggest that they may play a part in disease resistance, a particular race of bacteria or virus being adapted to individuals of a certain range of biochemical constitutions, while those of other constitutions are relatively resistant.

Indeed these polysaccharides, or glycans, would become rather uncooperative with evolution. As one recent paper explained, glycans show “remarkably discontinuous distribution across evolutionary lineages,” for they “occur in a discontinuous and puzzling distribution across evolutionary lineages.” This dizzying array of glycans can be (i) specific to a particular lineage, (i) similar in very distant lineages, (iii) and conspicuously absent from very restricted taxa only. In other words, the evidence is not what evolution expected.

Here is how another paper described early glycan findings:

There is also no clear explanation for the extreme complexity and diversity of glycans that can be found on a given glycoconjugate or cell type. Based on the limited information available about the scope and distribution of this diversity among taxonomic groups, it is difficult to see clear trends or patterns consistent with different evolutionary lineages. It appears that closely related species may not necessarily share close similarities in their glycan diversity, and that more derived species may have simpler as well as more complex structures. Intraspecies diversity can also be quite extensive, often without obvious functional relevance.

So is the evidence a problem for evolution? No, of course not. For as the paper explains:

Here we discuss the significance of this remarkable diversity, mindful of the oft-repeated adage of Dobzhansky's that “nothing in biology makes sense, except in the light of evolution.”

And so we are back to that “another story” again. This non scientific claim is, for evolutionists, the gift that just keeps on giving. It seems any evidential problem is easily disposed of with this handy truism. It is like a chant for evolutionists. Say it enough times and evolution is, as they say, a fact, in spite of the evidence. Here is how another, slightly more self-conscious, paper put it:

While we would certainly agree with the statement that “nothing in glycobiology makes sense, except in the light of evolution”, we must also realize that evolution only occurred once and that evolution does not follow well-defined rules. This situation is somewhat alleviated by the fact that after lineages diverge, more often than not they remain separated for good and, thus provide researchers with large numbers of iterations (“pseudo samples”) for which evolutionary processes have occurred independently. The study of these divergent lineages provides a good opportunity to elucidate evolutionary mechanisms.

Even in the worst of circumstances this favorite tenet of evolutionary thought is serviceable. It can always do the heavy lifting when necessary.

Religion drives science and it matters.

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Evolution is Crumbling and Now Even Issuing its Own Disclaimers

The cell is not only profoundly complex in the inside, its outer surface is also incredible with its wide array of molecular machines and entities. One important type of molecule on the cell’s surface is the glycans—long carbohydrate molecules that come in phenomenal variety. In fact, this variety is not only tremendous, the trade secret is that it violates every rule of evolution. For instance, though the term “lineage-specific biology,” which is the exact opposite of evolutionary expectations, has been popular in recent years, it could have been used half a century ago for glycans when J.B.S.Haldane observed that “every species of mammal and bird so far investigated has shown quite a surprising biochemical diversity by serological tests. The antigens concerned seem to be proteins to which polysaccharides are attached.” In fact, as one recent paper explains, glycans show “remarkably discontinuous distribution across evolutionary lineages,” for they “occur in a discontinuous and puzzling distribution across evolutionary lineages.” This dizzying array of glycans can be (i) specific to a particular lineage, (i) similar in very distant lineages, (iii) and conspicuously absent from very restricted taxa only. The contradictions are so common even evolutionists are now issuing their own disclaimers.

In a section entitled, “Disclaimer about limitations of evolutionary research,” the trade secret is explained:

While we would certainly agree with the statement that “nothing in glycobiology makes sense, except in the light of evolution”, we must also realize that evolution only occurred once and that evolution does not follow well-defined rules. 

There you have it. The obligatory, utterly non scientific, secret handshake (“nothing makes sense except evolution … blah, blah, blah”) is always needed before any disclosure of the embarrassing, contradictory facts.

Evolution doesn’t make sense, therefore it simply “does not follow well-defined rules.” In other words, anything goes. Evolution must be true, no evolutionist can deny the prime directive. But they haven’t the slightest idea, beyond endless tautologies and speculation, how that could be.

Evolutionists live in their own world where what they are always right and you are always wrong, regardless of the scientific evidence. Religion drives science, and it matters.