Friday, January 27, 2017

About Those Placental Regulatory Genes

Evolution Recruits and Deploys Genes

Last time we noted the teleological ideas and language used to describe the hypothetical evolution of several genes that are expressed for a mere few hours, in the early development stages of many placental mammals. And by early we mean when we consist of only 8-16 cells. The teleology is not a mere slip-up. As we have documented many times, it is a common thread running throughout the genre of evolutionary literature. It is needed to make sense of the data, because evolution doesn’t.

That teleological language appeared in an article about the research. Not too surprisingly, teleological language also appears in the research journal paper as well. To wit:

A small number of lineage-specific tandem gene duplications have occurred, and these raise questions concerning how evolutionarily young homeobox genes are recruited to new regulatory roles. For example, divergent tandem duplicates of the Hox3 gene have been recruited for extra-embryonic membrane specification and patterning in dipteran and lepidopteran insects, a large expansion of the Rhox homeobox gene family is deployed in reproductive tissues of mouse, and duplicates of TALE class genes are expressed in early development of molluscs.

Two of the evolutionists’ favorite words are “recruited” and “deployed.” They sound so active. What better way to obviate the rather awkward problem that, if evolution is true, all biological variation must be random with respect to fitness (a claim which, by the way, has been falsified so many times we stopped counting). Evolutionists nonetheless continue to spread this fake news.

And no teleological idea would be complete with the mandatory infinitive form (“for … specification and patterning”). Religion drives science and it matters.

Regulatory Genes Are Expressed For But a Few Hours

“Grabbed by Evolution”

How would you explain the evolution of a small set of genes that are expressed for but a few brief hours—when we consist of only 8-16 cells—in a finely-tuned choreography unique to placental mammals? The answer, of course, is to use teleological language because the evolutionary explanation is so transparently unrealistic. To wit, Ignacio Maeso explains:

It was really shocking to find these genes are only read for a pulse of a few hours in our entire lifetime. … They are found on chromosome 19, known to be an unstable part of our genome. Think of it as a bubbling cauldron of DNA, with individual bits of DNA being added and taken away, occasionally forming whole new genes. At the dawn of placental mammals, 70 million years ago, these genes emerged and were grabbed by evolution to perform a new task, acting to control what cells do in the earliest stages of development.

As usual, the infinitive form tells the tale.

Religion drives science, and it matters.

Wednesday, January 25, 2017

How Big is the Closet?

A Report From Academia

When a theory repeatedly fails its fundamental predictions, and is unable to explain even the basic facts, well there is bound to be doubt. No evolutionist who has ever peered into a microscope can look in the mirror and maintain self-respect. So I wasn’t too surprised when a friend told me that all across the country, life science professors “have told me in private they have questions about evolution,” and he keeps their identities secret. One wonders: How big is the closet?

Tuesday, January 24, 2017

The Sea Anemone: A Proverbial Precambrian Rabbit

A Contradiction of Another “Widely Held Belief”

When asked what evidence would disprove evolution, the famous 20th century evolutionist J.B.S. Haldane is famously said to have responded “a fossil rabbit in the preCambrian.” In other words, a fossil rabbit would have to be found in strata dating to long before rabbits, or mammals for that matter, are normally found. And by “long,” we’re talking about somewhere between roughly one-half a billion years to several billion years. It was an exercise in what philosophers refer to as theory protectionism—erecting insurmountable protective barriers around a theory. The fossil record was sufficiently understood in Haldane’s day to know that such as finding was highly unlikely. And it was also known that much less astounding, and more feasible, fossil findings would (or at least should) pose serious problems for evolutionary theory. In fact there are many such contradictions in the rocks, but if a rabbit in the preCambrian is the evidential standard, then evolution is comfortably safe. Haldane’s preCambrian rabbit response was also an exercise in na├»ve falsificationism—the thinking that a single finding is going to take down a theory so deeply imbedded in our thinking, and so confidently held to be true. In fact evolutionary theory has survived myriad contradictory evidences of at least as much severity as a preCambrian rabbit without so much as skipping a beat. Consider, for example, the genome of the starlet sea anemone, Nematostella vectensis. Here is how one report summarized it:

The genome of the sea anemone, one of the oldest living animal species on Earth, shares a surprising degree of similarity with the genome of vertebrates, researchers report in this week's Science. The study also found that these similarities were absent from fruit fly and nematode genomes, contradicting the widely held belief that organisms become more complex through evolution. The findings suggest that the ancestral animal genome was quite complex, and fly and worm genomes lost some of that intricacy as they evolved.

In other words, it was the genomic equivalent of Haldane’s preCambrian rabbit—a preCambrian genome had, err, all the complexity of species to come hundreds of millions of years later. In other cases it has more complexity than species such as worms and flies which, according to evolution, must have lost enormous amounts of genetic complexity.

The lead author of the sea anemone study explained that “We have this basic toolkit now for the whole animal kingdom.” Of course the idea of foresight is contradictory to evolutionary theory. As one evolutionist admitted, it is surprising to find such a “high level of genomic complexity in a supposedly primitive animal such as the sea anemone.” It implies that the ancestral animal “was already extremely highly complex, at least in terms of its genomic organization and regulatory and signal transduction circuits, if not necessarily morphologically.”

Or as another evolutionist put it:

It is commonly believed that complex organisms arose from simple ones. Yet analyses of genomes and of their transcribed genes in various organisms reveal that, as far as protein-coding genes are concerned, the repertoire of a sea anemone — a rather simple, evolutionarily basal animal — is almost as complex as that of a human.

None of this makes any sense on evolutionary theory. Of course it is “commonly believed” by evolutionists “that complex organisms arose from simple ones.” That would be rather fundamental to the theory. And yet we repeatedly find early complexity. This is another example of how resistant evolution is to testing and falsification.

The science contradicts the theory.

Saturday, January 21, 2017

Repetitive Elements: Evolution Has a Toolkit, And Several Other Findings

Tightly Coupled Molecular Machines Make Evolution Work

I’m not an expert carpenter, but if I know what needs to be built I’ll eventually get there. It may not be beautiful, but given a blueprint I can build a structure. What if I didn’t have that blueprint? What if I had no idea what needed to be built—no notion of where the task was headed? Furthermore, what if I had no knowledge of structures in general. Just randomly cutting wood and pounding nails probably would not end well. This is the elephant in the room for evolution, for according to evolutionary theory, random actions are precisely what built the world. It is what the Epicureans claimed two thousand years ago, and this random-creation hypothesis fares no better today than it did then. In fact, with the findings of modern science we now know far more about the details than did the Epicureans, and it has just gotten worse for their hypothesis. This is why evolutionists, as we have repeatedly documented, consistently appeal to teleological language. Regulatory genes “were reused to produce different functions,” Dinosaurs “were experimenting” with flight, and the genome was “designed by evolution to sense and respond.” Such Aristotelianism, which casts evolution as an intelligent process working toward a goal, makes the story more palatable; after all, evolution had a blueprint in mind. All of this makes for a glaring internal contradiction: on the one hand evolution has goals; yet on the other hand evolution is a mindless, mechanical process driven by random, chance events. As Jernej Ule explained last week:

We’re all here because of mutations. Random changes in genes are what creates variety in a species, and this is what allows it to adapt to new environments and eventually evolve into completely new species.

This makes evolution, rather inconveniently, dependent on random events (no, natural selection doesn’t change this—it cannot coax the right mutations to occur) which, by definition, do not work towards a goal—they do not build anything:

This ambiguity creates a great challenge. On the one hand, mutations are needed for biological innovation, and on the other hand they cause diseases.

Indeed. This is not looking good. As one Michael Skinner recently explained:

the rate of random DNA sequence mutation turns out to be too slow to explain many of the changes observed. Scientists, well-aware of the issue, have proposed a variety of genetic mechanisms to compensate: genetic drift, in which small groups of individuals undergo dramatic genetic change; or epistasis, in which one set of genes suppress another, to name just two. Yet even with such mechanisms in play, genetic mutation rates for complex organisms such as humans are dramatically lower than the frequency of change [between species if evolution is true] for a host of traits, from adjustments in metabolism to resistance to disease.

Whereas Skinner appealed to epigenetics to save the theory, Ule appeals to repetitive elements. Evidence has shown that far from being “junk DNA,” repetitive elements plays a genetic regulatory role. As a result evolutionists such as Ule have concluded repetitive elements “are an important toolkit for evolution.”

Like any good carpenter, evolution has a toolkit.

Ule and his co-workers are now elaborating on the details of how repetitive element toolkit might work. It goes like this: (i) Random mutations gradually modify repetitive elements, (ii) these repetitive elements are sometimes incorporated as part of the blueprint instructions for making a protein, (iii) there are several complicated molecular machines that either repress or allow such incorporation of these repetitive elements in the blueprint.

According to Ule, this complicated process, including these two opposing machines which are “tightly coupled,” allows evolution to experiment and successfully evolve more complicated species, such as humans:

We’ve known for decades that evolution needs to tinker with genetic elements so they can accumulate mutations while minimising disruption to the fitness of a species. … This [process we have discovered] allows the Alu elements to remain in a harmless state in our DNA over long evolutionary periods, during which they accumulate a lot of change via mutations. As a result, they become less harmful and gradually start escaping the repressive force. Eventually, some of them take on an important function and became indispensable pieces of human genes. To put it another way, the balanced forces buy the time needed for mutations to make beneficial changes, rather than disruptive ones, to a species. And this is why evolution proceeds in such small steps – it only works if the two forces remain balanced by complementary mutations, which takes time. Eventually, important new molecular functions can emerge from randomness.

These suggestions from Skinner and Ule are the latest in a long, long line of ideas evolutionists have come up with, in an attempt to make sense of their random creation hypothesis. In modern evolutionary thought, the first such idea was natural selection.

The reason there is a long, long line of ideas is none of them work. They are becoming ever more complicated, ever more unlikely, and equally useless in solving the basic problem of random events constructing the world.

But Ule’s latest attempt highlights yet another problem: serendipity. All of the solutions, from natural selection on up to epigenetics and repetitive elements rely on serendipity, and this reliance is increasing. Ule’s solution is serendipity on steroids, for the idea holds that evolution just happened to create (i) repetitive elements, and (ii) the complicated, finely-tuned, opposing molecular machines that repress or allow those repetitive elements into the protein instructions.

This isn’t going to work, but the point here is that even if it did somehow work, it amounts to evolution creating evolution. In order for evolution to have created so many of the species, it first must have lucked into creating these incredible mechanisms, which then in turn allowed evolution to occur. And all of this must have occurred with no foresight.

This is just silly. This violates the very basics of science. Imagine a car factory that uses highly complex machines, such as drill presses and lathes, to build the cars. Now imagine the factory first creating those machines by random chance, so then the cars could be built, by yet more random chance events.

Religion drives science, and it matters.

Sunday, January 15, 2017

About That Oparin Prediction …

Very, Very Soon

Although we have chronicled all manner of new and rehashed ideas for how life is supposed to have evolved—including the latest doozy that life arose “almost instantaneously”—Alexander Oparin’s 1924 prediction that origin of life research would be solved “very, very soon” may not only have been premature but, in fact, out and out false. For as evolutionist Kepa Ruiz-Mirazo now admits, most likely we will, err, “never manage to find the answer to how life began.” Fortunately evolution is a fact, otherwise people might begin to doubt.

Saturday, January 14, 2017

Evolutionists Now Have a Simple Proposal For The Origin of Life

Reductio Ad Absurdum 

The latest example in the recent stream of findings of “rapid evolution,” which seem to be coming at an ever increasing pace, is that with the finding of graphite in a 4.1 billion year zircon, life on Earth may have started, err, “almost instantaneously.” Someone tell the angels that Oparin can now rest in peace, for his 1924 prediction that origin of life research would be solved “very, very soon” has finally come to pass. Life arose “almost instantaneously”—though we suspect Oparin was hoping for a bit more detail.

The problem is that with its inexorable march of progress, science just continues to narrow those evolutionary time windows. Darwin insisted evolution required hundreds of millions of years, but the Cambrian Explosion, and all the other so-called Big Bangs of the historical record—which tell us that the appearance of everything from flowers to horses was punctuated rather than gradual—must have occurred in no more than a few million years.

It means the evolutionary tree is the exact opposite of what evolutionists expected. Rather than the slow, gradual, buildup of diversity over the eons of time, instead bursts of radically new species appeared out of nowhere, over and over, only to be winnowed out by extinction.

And it all started with the first life. Except that where a few tens of millions of years once seemed to be available, which itself was inadequate, that speck of graphite now leaves us with nothing but an evolutionary nanosecond.

Merrilee Salmon Propagates the Warfare Thesis

The Will to Believe

Merrilee Salmon’s review of Richard Williams and Daniel Robinson 2015 volume, Scientism: The New Orthodoxy, starts out well enough, explaining that scientism is “a philosophical view about the power and scope of the techniques of the natural sciences. It is generally understood to hold that all genuine knowledge about the world around us, including about human behavior, is obtainable only through the particular scientific methods that have proved so successful in physics, chemistry, and the other natural sciences. In other words, knowledge gained through use of the scientific method has a unique claim to truth, and, some would say, constitutes the only path to real knowledge.” But the professor emerita from one of the leading HPS programs in the country (University of Pittsburgh) unfortunately ends up devolving into the same old Warfare Thesis myth which contributed and underwrote today’s scientism in the first place. To wit, Salmon erroneously identifies, yes Galileo and Darwin, (oh no, not this again), as examples where science triumphed over religion:

Simply recognizing that both science and theology are cultural institutions, however, does not solve the problem of what to believe when the two collide. The historic cases of Galileo Galilei and Charles Darwin remind us that science has the superior record when it comes to producing evidence for claims that have been challenged by theologians.

Arg. Has history taught us nothing?

Do we need to recount yet again how theology underwrote evolution, and that rebuttals were about the science? Do we need to, one more time, retell the facts of the Galileo Affair? That questions about Joshua 10 and Ecclesiastes 1 paled in comparison to the political, social, Aristotelian, and most importantly, scientific problems with heliocentrism?

Unfortunately, over and over, we see that the mythological Warfare Thesis is not the product of the ignorant but the elite. From the playwrights to the professors, the Warfare Thesis is a powerful and enduring myth for the same reasons any myth is powerful and enduring—we want to believe it.

Religion drives science, and it matter.

Monday, January 9, 2017

Graur and Martin Explain Monumental Failure in Molecular Clock Uncertainty Estimate

Mirages Contain No Water

The scientific evidence contradicts evolutionary theory. Consider, for example, the problem of tracing out the mammalian evolutionary tree. According to evolution similar species should be neighbors on the evolutionary tree. For example, the flying squirrel and sugar glide certainly are similar—they both sport distinctive “wings” stretching from arm to leg. Shouldn’t they be neighboring species? The problem is that, while they have incredible similarities, they also have big differences. Most notably, the flying squirrel is a placental and the sugar glider is a marsupial. So they must be placed far apart in the mammalian evolutionary tree. The problem in this example is that different characters, across the two species, are not congruent. Here is how evolutionists rationalize the contradiction:

Flying squirrels and sugar gliders are only distantly related. So why do they look so similar then? Their gliding "wings" and big eyes are analogous structures. Natural selection independently adapted both lineages for similar lifestyles: leaping from treetops (hence, the gliding "wings") and foraging at night (hence, the big eyes).

This is a good example of how contradictory evidence drives evolutionists to use irrational just-so stories. Natural selection cannot “adapt” anything. Natural selection kills off the bad designs. It cannot influence the random mutations which must, somehow, come up with such amazing designs. This is the hard reality, but in order to rationalize the evidence, evolutionists must resort to this sort of teleological language, personifying and endowing natural selection with impossible powers. As usual, the infinitive form (“for similar lifestyles”) is a dead giveaway. Natural selection becomes a designer.

This example is by no means exceptional. In fact, this sort of incongruence is rampant in biology. Evolutionists have attempted to deny it in the past, but it is undeniable. It is the rule rather than the exception. As one recent paper, entitled “Mammal madness: is the mammal tree of life not yet resolved?” admitted:

Despite the keen interest in mammals, the evolutionary history of this clade has been and remains at the center of heated scientific debates. In part, these controversies stem from the widespread occurrence of convergent morphological characters in mammals.

In addition to the morphological characters, evolutionists make extensive use of molecular sequence data using the so-called molecular clock method. The molecular clock method, however, has a long history of problems. You can see here and here how the molecular clock method has failed, but an entirely different problem is the non-scientific, misuse, of this approach. Consider how evolutionists have misused it in the mammalian evolutionary tree problem:

Two articles in this issue address one such node, the root of the tree of living placental mammals, and come to different conclusions. The timing of the splitting event—approximately 100 Ma based on molecular clocks—is not in debate, at least among molecular evolutionists. Rather the question is the branching order of the three major lineages: afrotherians (e.g., elephants, manatees, hyraxes, elephant shrews, aardvarks, and tenrecs), xenarthrans (sloths, anteaters, and armadillos), and boreoeutherians (all other placentals; fig. 1).

Such overly optimistic interpretation of the molecular clock results unfortunately has a long history. Dan Graur and William Martin have showed how such over confidence became common in evolutionary studies. They write:

We will relate a dating saga of ballooning inapplicability and snowballing error through which molecular equivalents of the 23rd October 4004 BC date have been mass-produced in the most prestigious biology journals.

Graur and Martin chronicle how a massive uncertainty was converted to, err, zero, via a sequence of machinations, including the arbitrary filtering out of data simply because they do not fit the theory:

A solution to the single-calibration conundrum would be to use multiple primary calibrations because such practices yield better results than those obtained by relying on a single point. Indeed, it was stated that “the use of multiple calibration points from the fossil record would be desirable if they were all close to the actual time of divergence.” However, because no calibrations other than the 310 +/- 0 MYA value were ever used in this saga, the authors must have concluded that none exists. This is not true. Moreover, deciding whether a certain fossil is “close to the actual time of divergence” presupposes a prior knowledge of the time of divergence, which in turn will make the fossil superfluous for dating purposes.

Not only are uncooperative data discarded, but tests are altogether dropped if they don’t produce the right answer:

The results indicated that 25% of the homologous protein sets in birds and mammals failed the first part of the consistency test, that is, in one out of four cases the data yielded divergence times between rodents and primates that were older than those obtained for the divergence between synapsids and diapsids. One protein yielded the absurd estimate of 2333 MYA for the human–chicken divergence event, and as an extreme outlier was discarded. For the remaining proteins, the mean bird–mammalian divergence estimate was 393 MYA with a 95% confidence interval of 471-315 MYA. In other words, the 310 MYA landmark was not recovered. Because neither condition of the consistency test was met, it was concluded that the use of the secondary calibration is unjustified.

In one example, a monumental dating uncertainty, roughly equal to the age of the universe, is magically reduced by a factor of 40:

Were calibration and derivation uncertainties taken into proper consideration, the 95% confidence interval would have turned out to be at least 40 times larger (~14.2 billion years).

Now of course there is little question that evolutionists will resolve their evolutionary tree problems. A combination of filtering the data, selecting the right method, and, of course, deciding there is nothing at all improbable about natural selection “adapting” designs in all manner of ways, can solve any problem. But at what cost? As the paper concludes, “Unfortunately, no matter how great our thirst for glimpses of the past might be, mirages contain no water.”

Saturday, January 7, 2017

Tasneem Zehra Husain, The Multiverse, and Plenitude

How Physicists Learned to Love the Multiverse

Tasneem Zehra Husain has an excellent article on the multiverse in this month’s Nautilus. In this age of the expert whom we must trust to give us the truth, Husain’s transparent and clear explanation of some of the underlying philosophical concerns regarding the multiverse is refreshing. I only wish that her writing was more aware of the historical plenitude traditions. Many of the philosophical concerns regarding the multiverse interact heavily with, or even are mandated by, plenitude thinking. Husain makes this quite clear, and locating this thinking in the historical matrix of plenitude traditions would further enrich and elucidate her explanation of the multiverse hypothesis.

Plenitude thinking holds that everything that can exist will exist. As Lovejoy observed, it had an obvious influence on a range of thinkers since antiquity, including Bruno’s infinity of worlds (read extra-terrestrials) and Leibniz’ view that the species are “closely united,” and “men are linked with the animals.”

Though I don’t suspect plenitude thinking had a direct influence on the initial development of the multiverse hypothesis, it doesn’t take a physicist to see a fairly obvious connection. If everything that can exist will exist, then why should there be only one universe?

But a more interesting interaction comes in how physicists evaluate and justify the multiverse hypothesis which, after all, isn’t very satisfying. With the multiverse, difficult scientific questions are answered not with clever, enlightening, solutions but with a sledgehammer. Things are the way they are because things are every possible way they could be. We are merely living in one particular universe, with one set of circumstances, so that is what we observe. But every possible set of circumstances exists out there in the multiverse. There is no profound explanation for our incredible world. No matter how complicated, no matter how unlikely, no matter how uncanny, our world is just another ho-hum universe. All outcomes exist, and all are equally likely. Nothing special here, move along.

As Princeton cosmologist Paul Steinhardt puts it, the multiverse is the “Theory of Anything,” because it allows everything but explains nothing. Given this rather unsatisfying aspect of the multiverse, how can it be defended?

Enter plenitude thinking. An important theme in plenitude thinking is that there should be no arbitrary designs in nature. If everything that can exist will exist, then no particular designs will exist where others are also possible.

This has become a powerful element in evolutionary philosophies of science. As Leibniz explained, the entire, continuous, range of designs should be manifest in nature, rather than a particular, arbitrary design. That would be capricious.

This rule holds unless there is sufficient reason for it not to (Leibniz’ PSR). If only one design can arise in the first place, due to some reason or technicality, then all is good—the design is no longer viewed as arbitrary. The problem is, we can find no such reason or technicality for our universe. It seems any old universe could just as easily arise.

Plenitude thinking mandates that the designs we find in nature should fill the space of feasible designs. We should not find particular designs where others are possible. But this seems to be precisely what we find in our universe. It is a particular design where others are possible. Theoreticians have been unable to find any reason for why this design should have occurred.

If we say the universe was designed, then it is a design that is arbitrary, and that violates the Principle of Plenitude. The solution to this conundrum is the multiverse.

This is how physicists can learn to love the multiverse. Yes it is a sledgehammer approach, but it satisfies plenitude thinking. Our universe is no longer arbitrary. Instead, the full range of universes exists out here. Husain beautifully explains this, and here is the money passage:

For decades, scientists have looked for a physical reason why the [universe’s] fundamental constants should take on the values they do, but none has thus far been found. … But to invoke design isn’t very popular either, because it entails an agency that supersedes natural law. That agency must exercise choice and judgment, which—in the absence of a rigid, perfectly balanced, and tightly constrained structure, like that of general relativity—is necessarily arbitrary. There is something distinctly unsatisfying about the idea of there being several logically possible universes, of which only one is realized. If that were the case, as cosmologist Dennis Sciama said, you would have to think “there’s [someone] who looks at this list and says ‘well we’re not going to have that one, and we won’t have that one. We’ll have that one, only that one.’ ”

Personally speaking, that scenario, with all its connotations of what could have been, makes me sad. Floating in my mind is a faint collage of images: forlorn children in an orphanage in some forgotten movie when one from the group is adopted; the faces of people who feverishly chased a dream, but didn’t make it; thoughts of first-trimester miscarriages. All these things that almost came to life, but didn’t, rankle. Unless there’s a theoretical constraint ruling out all possibilities but one, the choice seems harsh and unfair.

Clearly such an arbitrary design of the universe is unacceptable. (By the way, Husain also adds the problem of evil as an associated problem: If the universe was designed, then “how are we to explain needless suffering?”)

The multiverse solves all this. Yes, the multiverse is an unsatisfactory, sledgehammer approach. But it saves plenitude, and that is the more important consideration.

Husain’s article is a thoughtful, measured explanation of how physicists today are reckoning with the multiverse hypothesis. But make no mistake, religion does the heavy lifting. The centuries old plenitude thinking is a major theme, running all through the discourse. That, along with a sprinkling of the problem of evil, make for decisive arguments.

The multiverse is another good example of how religion drives science in ways that are far more complex than is typically understood.

Friday, January 6, 2017

“When Facts Fail”: Oh The Irony

Fossils and DNA

Because when an evolutionist, such as Michael Shermer in this case, warns readers that people don’t change their minds even when presented with the facts, the irony should be savored:

Have you ever noticed that when you present people with facts that are contrary to their deepest held beliefs they always change their minds? Me neither. In fact, people seem to double down on their beliefs in the teeth of overwhelming evidence against them. The reason is related to the worldview perceived to be under threat by the conflicting data.

Yes, there certainly are conflicting data.

It gets worse:

Creationists, for example, dispute the evidence for evolution in fossils and DNA because they are concerned about secular forces encroaching on religious faith.

Evidence for evolution in DNA? What exactly would that be? Ultra conserved elements, orphans, replication, duplication, the universal DNA code, protein synthesis, protein coding genes, genetic regulation, recurrent evolution, convergence, cascades of convergence, and … well you get the idea. The evolutionist is demonstrating some of those “facts that fail” and the attendant doubling down, right before our eyes.

And what about those fossils? More “evidence for evolution”? How about those fossils that appear “as though they were planted there” as Richard Dawkins once admitted. One of those “planted” classes, the humble trilobites, had eyes that were perhaps the most complex ever produced by nature. [1] One expert called them “an all-time feat of function optimization.”

And even Shermer’s go-to source, Wikipedia, admits ancestral forms, err, “do not seem to exist”:

Early trilobites show all the features of the trilobite group as a whole; transitional or ancestral forms showing or combining the features of trilobites with other groups (e.g. early arthropods) do not seem to exist.

Likewise, even the evolutionist Niles Eldredge admitted [2] they didn’t make sense on standard evolutionary theory:

If this theory were correct, then I should have found evidence of this smooth progression in the vast numbers of Bolivian fossil trilobites I studied. I should have found species gradually changing through time, with smoothly intermediate forms connecting descendant species to their ancestors.

Instead I found most of the various kinds, including some unique and advanced ones, present in the earliest known fossil beds. Species persisted for long periods of time without change. When they were replaced by similar, related (presumably descendant) species, I saw no gradual change in the older species that would have allowed me to predict the anatomical features of its younger relative.

And it just gets worse:

The story of anatomical change through time that I read in the Devonian trilobites of Gondwana is similar to the picture emerging elsewhere in the fossil record: long periods of little or no change, followed by the appearance of anatomically modified descendants, usually with no smoothly intergradational forms in evidence.

Any more facts Mike?

1. Lisa J. Shawver, “Trilobite Eyes: An Impressive Feat of Early Evolution,” Science News, p. 72, Vol. 105, February 2, 1974.

2. Niles Eldridge, “An Extravagance of Species,” Natural History, p. 50, Vol. 89, No. 7, The American Museum of Natural History, 1980.

Thursday, January 5, 2017

Evolutionist: Evolution Is Happening Faster Than We Thought


The fact that we can travel at speeds of hundreds and even thousands of miles per hour does not mean we can go faster than light. We can fly to the Moon in a matter of days, but the propulsion technology that allows us to do that is not scalable to travelling faster than 186,000 miles per second. A fundamentally different technology is required. The creators of Star Trek understood that, and so they created the concept of warp drive, a faster-than-light propulsion technology, fundamentally different from today’s technology. One would have to be very ignorant to confuse the two, but this is precisely what evolutionists do when they cast biological adaptation as confirmatory evidence of evolution. Adaptation and evolution are two very different things.

Biological adaptation relies on the preexistence of populations, organisms, genetics, DNA, genes, alleles, proteins, massive molecular machines, inheritance, cellular and molecular mechanisms such as horizontal gene transfer and epigenetics, directed mutations, and so forth.

Evolution, on the other hand, is a theory that attempts to explain the origin of all those things.

Observations of the former are not evidence of the latter. That is backwards. It also would also introduce enormous serendipity. For it would mean that evolution created the very structures and mechanisms required for, drumroll, evolution.

Evolution, in other words, created itself.

And even if we were to go along with this ridiculous idea, the resulting biological adaptation is not capable of generating evolutionary change. Adaptation does small things, evolution requires big things.

Even evolutionists, in their honest moments, have understood this. Macroevolution is more than repeated rounds of microevolution. As one evolutionist admitted, “the rate of random DNA sequence mutation turns out to be too slow to explain many of the changes observed.” His point, which is not new and has been known for a long time, is not that adaptation cannot occur, but that the idea of mutations (which can fuel adaptation) adding up to result in novel, large-scale evolutionary change doesn’t work.

Adaptation and evolution are fundamentally different “technologies.”

You can’t travel faster than the speed of light by combining liquid hydrogen and liquid oxygen, and you can’t create novel, complex, biological structures via adaptation mechanisms.

This is why evolutionary biologist Menno Schilthuizen’s article from last year in the Sunday Review is of concern. The article is entitled: “Evolution Is Happening Faster Than We Thought,” and it is all about various adaptations observed in city-dwelling species. Unfortunately, Schilthuizen presents those examples of adaptation as examples of evolution, and proof that, amazingly enough, evolution happens orders of magnitude faster than we once thought:

For a long time, biologists thought evolution was a very, very slow process, too tardy to be observed in a human lifetime. But recently, we have come to understand that evolution can happen very quickly

Evolution’s deep time requirement was particularly evident when William Thomson (later Lord Kelvin), only a few years after Darwin had published his book on evolution, argued that the earth could be no older than 100 million years. Thomson later revised that figure downward to as little as 20-40 million years.

This short time window was an enormous problem for evolution. As Darwin wrote, “Thomson’s views of the recent age of the world, have been for some time one of my sorest troubles.” As Darwin’s friend Thomas Huxley explained, “Biology takes its time from Geology.”

Lord Kelvin’s estimate was eventually dropped, but this example illustrates how important deep time was, both to nineteenth and twentieth century evolutionists. And therefore, the rapid evolution that is now commonly celebrated by evolutionists such as Schilthuizen represents an enormous falsification of a major, fundamental, prediction of evolutionary theory.

It also represents terribly flawed thinking. Adaptation is not evolution.

Wednesday, January 4, 2017

Desert Mice Fur Changes Color to Match the Terrain

An Example of Evolution in Every Detail?

About fifteen years ago researchers discovered genetic differences that probably explain the different fur coloring in desert mice populations in New Mexico and Arizona (see papers here and here). Mice populations living on light colored terrain tend to have light colored fur, and those on dark colored terrain tend to have dark colored fur. Blending in with the terrain helps to camouflage the mice, protecting them from predators. And that is, apparently, exactly what the mice did about a thousand years ago when desert lava flows produced the darkened terrain. But that is where the science is overtaken by the dogma. Evolutionists have misappropriated this research work, casting it as a textbook example of evolution, and creating a highly produced video (see above) used to indoctrinate students.

The first problem in casting the dark colored mice as an example of evolution is that their genetic differences are not known to be the result of random mutations. For evolutionists there simply is no question that the genetic differences that are thought to cause the dark fur color arose from random mutations.

Now that may be correct. But it may not be. We simply do not know.

This is not merely a technical objection—in spite of evolutionary theory which called for random mutations to be the source of change, in recent decades directed mutations have been found to be at work in an ever increasing number of cases. For many years evolutionists have ignored and even resisted these findings. Too often I have debated evolutionists who, when I point to this evidence, simply deny it.

So while the genetic differences in those dark mice may well be the result of random mutations, evolutionists do not even give this a second thought. They simply assume from the start, and inform their audience in no uncertain terms, that random mutations are the cause.

This is an example of what philosophers refer to as a “theory-laden observation.” Science can get into trouble when the measurements and observations themselves, rather than being theory-neutral and independent of the theories which explain them, are in fact intertwined with those theories.

This can become circular very quickly, and this desert mouse case is a good example of that. Evolutionists assume the genetic differences arose from random mutations, and then claim the evidence as a powerful confirmation of evolution.

The second problem in casting the dark colored mice as an example of evolution is that the dark coloration may be the result of multiple genetic changes. In one case, four mutations are identified, all of which perhaps are required to bring about the coloration change.

It very well could be that only a lone, single mutation is required. But that is not known.

And if multiple genetic changes are required, then this quickly transitions from an example of what random mutations can do to an example of what random mutations cannot do. If four mutations are required, then we’ve just found yet another hard failure of evolution. But again, the evolutionists give no hint of this interesting question. If everyone had their “burning curiosity,” (as Clarence Darrow put it) then science would have long since come to an end.

The third problem in casting the dark colored mice as an example of evolution is that the coloration is too precise. The dark colored fur appears on the top of the mice, but not their underbelly. This makes sense since the topside is mainly what is exposed to predators. But in the evolution narrative, there is no fitness advantage to such precision. Darkening the entire mouse would, apparently, work just as well.

Small scale adaptation

Everything we’ve talked about so far is an unknown. Evolutionists are proclaiming a slam dunk, case closed, example when in fact there are many unknowns. Some of them could demolish the evolution narrative altogether.

But there is one big known we haven’t yet mentioned. It is that none of this amounts to evolution in the first place. It would be a deceptive equivocation to label fur coloration change via a few mutations as “evolution” when, in fact, this is nothing more than small scale adaptation.

In their “honest moments,” as Stephen J. Gould once put it, even evolutionists admit that random mutation isn’t enough, and that adaptation mechanisms are not enough, to explain the kind of large scale change evolution requires.

Mice changing fur color does not demonstrate how metabolism, the central nervous system, bones, red blood cells, or any other biological wonder could have arisen by evolution’s random mutations coupled with natural selection.

This is an old myth evolutionists have exploited ever since Darwin. Demonstrate biological change, any biological change no matter how trivial, and claim victory. Evolutionist Steve Jones once claimed that the changes observed in viruses contain Darwin’s “entire argument.” That is a gross equivocation and misrepresentation of the science, designed to mislead audiences.

It is a pathetic canard which evolutionists continue to rely on. In the above video, Sean Carroll states that thanks to these mice, “science has an example of evolution, crystal clear, in every detail.” [6:42-48]

It would be difficult to imagine a more absurd misrepresentation. Mice changing color is not a crystal clear “example of evolution … in every detail.” Not even close. Carroll should be ashamed of himself.

Religion drives science, and it matters.

Monday, January 2, 2017

Orangutan Does What No Chimp Has Ever Done

Dynamic, Interactive Vocal Fold Control

In a study published last year an adolescent male orangutan achieved a milestone in vocal control never before performed by any great ape, including chimpanzees. As the study reported:

These results confirm the capacity of orang-utans to learn and acquire new calls into their individual repertoires, both in the form of voiceless consonant-like calls and voiced vowel-like calls.

This has “never been demonstrated directly in a non-human primate.” That includes chimpanzees.

Perhaps a chimp will someday exhibit the same skill, but that has yet to be seen. We suspect there is a reason why this finding involved an orangutan. It is another example of their relatively advanced abilities.

Sunday, January 1, 2017

A Salamander Two-fer: Non Homologous Development and an ORFan

A Faulty Foundation

Salamanders have their own way of doing things. For most animals, if an important body part, such as a limb, is lost, it is gone for good. But for salamanders, they just grow a new one. Also, salamanders use different embryonic development patterns. For example, their digits (fingers and toes for us humans) form in the wrong order—going, essentially, in the wrong direction. You can see this in the figure below (taken from this paper from Neil Shubin’s group, but note the labeling error, VI rather than IV). In the figure, the numbers across the top show the order in which the digits appear. Salamanders go against the common pattern. This “reverse polarity” in what otherwise is a highly conserved development pattern in the tetrapods is a quandary for evolution.

Early evolutionists who first seriously reckoned with this “striking deviance from an otherwise conserved pattern in tetrapods,” as the Shubin paper puts it, as well as other distinctive features of salamander limb development, concluded that the salamanders probably arose independently of the other tetrapods. In other words, these development inconsistencies were so profound they required an independent origins—there were two different origins of tetrapods.

The problem, however, is the set of similarities between the salamanders and their cousin tetrapods is so massive, that any such independent origins would be absurd from an evolutionary perspective.

So evolutionists were left needing an explanation for the profound divergence. Perhaps salamanders got their start with a loss of digits. If the first salamanders had only two digits, and then re-evolved the other digits (catching up to their ancestral forms), the development order could have been rearranged.

Unfortunately such a hypothetical evolutionary history, where the salamanders begin by losing digits, does not fit the data (both molecular and fossil) very well, even within the context of evolutionary theory.

Perhaps the salamander digit development deviance arose as a larval adaptation. Or perhaps the salamander development pattern is not a “deviance” at all, but rather is the nominal, ancient pattern, but is retained only in salamanders among living tetrapods.

But these hypotheses have problems as well. In fact the salamander character data are full of contradictions:

The evolution and phylogeny of crown group salamanders is plagued by homoplasy. In fact, a large a number of highly derived anatomical characters, including body elongation, tail autonomy, and life history pathways, have been demonstrated or are debated to have evolved multiple times.

[Note that these anatomical characters have not “been demonstrated” to have evolved multiple times. That is a misrepresentation of the science. They only have “been demonstrated” to have evolved multiple times if one assumes evolution at the outset.]

Yet another problem plaguing these evolutionary hypotheses is the finding of genes unique to the salamander that are crucial for its limb regeneration ability and unique embryonic development patterns. You can read more about these here and here, and this brings us to the second half of our two-fer.

Whether they are called unique genes, novel genes, orphans, ORFans, taxonomically-restricted genes (TRGs), lineage-specific genes (LSGs), or whatever, they are a problem for evolution. First, they counter the above hypotheses attempting to explain the salamander’s unique development. As one paper explains:

the notion of an ancient limb regeneration programme has been challenged by reports of salamander lineage-specific genes (LSGs) upregulated during regeneration. One salamander LSG in particular, the Prod1 gene, was shown to be required for proximodistal patterning during limb regeneration and for ulna, radius and digit formation during forelimb development. The existence of urodele LSGs expressed and involved in regeneration has lent support to the hypothesis that limb regeneration is a derived urodele feature.

In other words, the salamander gets it done using genes unique to its lineage, and that contradicts the hypothesis that the salamander’s unique capabilities were there all along.

It also contradicts the evolutionist’s long-standing, but rapidly fading, hope that ORFans would go away. As we have explained, evolutionists hoped that such lineage-specific genes would be found in other species as more genomes were decoded. But instead the number of ORFans just continued to grow.

Evolutionists next predicted that similar ORFan sequences would be found in the so-called non-coding DNA. Although that is sometimes the case, it is not generally, and the Prod1 gene is another example of this.

Evolutionists next predicted that ORFan sequences were probably not part of a mature protein coding gene and did not form functional proteins. That also is wrong, and Prod1 is yet another example of an ORFan that is indeed a real protein.

The findings of unique (non homologous) development patterns, and lineage-specific genes make no sense on evolution. And attempts to explain these findings according to evolution with clever, detailed hypotheses just cause more problems.

If you try to build a house on a faulty foundation, it will just get worse. Evolution is a flawed theory, and the more we learn about biology, the more evident that becomes.

Evolution may be true, it may be false. That is debatable. What is not debatable, however, is that the empirical evidence contradicts the theory.

Field Studies Pay Off: “I was flabbergasted” (By The Lungless Frog)

Adaptive Development

Why do biologists travel the world over? They go to the bottom of the ocean and to the tops of mountains, to deserts and jungles. The reason is they are rewarded for their efforts. The one rule in biology is there are no rules. Everything is different, and everywhere is different. When John Ray toured Europe for three years, from 1663 to 1666, studying the flora and fauna, he found the organisms and their interactions were different everywhere he went. Biology is full of diversity, and it consistently makes no sense on evolution.

Consider Barbourula kalimantanensis, the frog that has no lungs. These small, elusive, lungless amphibians live in cold, fast rivers, deep in the rainforests of Borneo. Ten years ago David Bickford and his patient international team of biologists worked hard and long to find some specimens for their study.

Bickford and his colleagues had an idea of what they were looking for, but they had no idea, and no reason to suspect, that the two inch frog would be lungless. As Bickford recounted:

At first I did not believe that the frogs had no lungs, but then, we just kept on seeing the evidence pile up. I was flabbergasted.

It was all a lesson, once again, in biology’s only rule, and that exploration seems to always payoff:

The thing that struck me most then and now is that there are still major firsts — for example, first lungless frog! — to be found out in the field. All you have to do is go a little ways beyond what people have done before, and — voila! … There are so many difficulties in field work, and yet it remains my biggest joy. Having the undeniable privilege of going out to these remote sites, seeing some of the last and greatest treasures that exist in the wild, and then getting to study them — well, every day I feel lucky.

It was also a lesson once again that biology makes no sense on evolution. It turns out that some species can forego their lungs altogether in their embryonic development, given the right environmental conditions. This is another example of rapid, directed adaptation, in response to the environment.

If such a sophisticated development plasticity could have evolved—“and oh! what a big if!” *—it would provide no immediate fitness improvement, and so would not be selected for. It would be subject to harmful mutations, and be long forgotten in the annals of evolutionary history.

This is intelligent adaptation which makes no sense on evolution.

Religion drives science, and it matters.