Plant's Epigenome as Varied as Their Environments

A Big Challenge

You probably remember that an organism’s DNA is collectively referred to as the genome and that it contains genes that code for proteins. What you may not know is that the genome is tagged here and there with small molecules helping to determine which genes to express. These small molecules are collectively referred to as the epigenome and one recent study found a tremendous variation between the epigenomes in the same species of plant collected from different locations around the world. As one researcher explained:

We looked at plants collected from around the world and found that their epigenomes are surprisingly different. This additional diversity may create a way for plants to rapidly adapt to diverse environments without any genetic change in their DNA, which takes a very long time.

In other words, different specimens of a given species of plant, all with the same genome, had significantly different epigenomes.

Epigenetics is another example of how the species do not appear to have evolved. Evolution may be true or false, but the scientific evidence presents a great many challenges to the idea. Recall that under evolution the idea is that random biological changes that naturally occur and are inheritable, such as mutations in the germline, might luckily sometimes be an improvement to the organism’s fitness. In those cases the organisms with the change would likely be successful and procreate, thereby passing on the change to future generations.

But epigenetics challenges all this. First, the tagging of DNA does not naturally occur as mutations do. In order for an epigenetic change to occur and have any effect, there must be a small army of coordinated molecular machines that are working according to the same code. Some machines attach the tags according to external, environmental signals. Other machines remove or move the tags, again according to other signals. And yet other machines interpret the tags, thus influencing which proteins are expressed.

This is far more involved than a random mutation occurring that just happens to improve slightly how the organism works. In fact epigenetics would involve literally hundreds (and that is conservative) of changes required before any benefit would be realized.

The tagging machines not only need to be built, or adapted from other machines, but they need to know where in all the genome to place the tags. Likewise for the machines that remove and move the tags. In other words, it is not good enough merely to evolve the machines. They somehow much know where to place the tags given a spectrum of environmental signals.

And then the machines that interpret the tags would have to do so correctly. They would have to know what the tag means. So again, not only must these machines have evolved or adapted, but they must know what they are doing.

That is astronomically unlikely to occur according to our knowledge of science.

But that is not all. For even given such a miracle, such epigenetic tags would not be inheritable. And yet they are. So there are even more machines that must have arisen by chance to preserve the tags when the cell divides.

This brings us to yet another set of problems with epigenetics: the machinery described above is not inheritable unless is evolves in the germline. But in the germline it doesn’t do anybody any good. Only when it is a passed on to the progeny can it help.

But even then the epigenetics capability likely won’t help because this capability gives the organism the ability to respond to a wide range of environmental conditions—conditions that probably won’t even occur in the organism’s lifetime.

In other words, we must believe that an astronomically unlikely capability arose by chance and though most of it wasn’t helpful, it was preserved anyway. Then, in future generations, when a particular environmental shift occurred, the epigenetics came to the rescue.

These problems are highlighted by the new research discussed above, showing how the epigenetic tagging can be so different in the same species of plant, in different locations around the world. Those environments are very different, so the tagging is very different.

But the origin of the epigenetics machinery would have had to anticipate all these different environments, long in advance.

Simply put, this just doesn’t make much sense under evolution. Epigenetics goes against the evolutionary model. Not surprisingly, evolutionists resisted the early epigenetic findings. And when the findings became undeniable evolutionists downplayed their significance.

But these findings are an obvious and dramatic falsification of evolutionary expectations. And this problem comes after several other, equally vexing, problems, many of which were at least somewhat understood in Darwin’s time.

Epigenetics is an example of how the science does not bode well for evolutionary theory. But in evolution the science does not carry the day. The science represents a research problem to be worked out. Otherwise evolution is protected from such show-stoppers because evolution is known to be a fact from non scientific considerations. We may not know how epigenetics and a dozen other contradictions could have evolved, but we know they must have evolved.

For what about all the designs that make no sense, and all the designs that are harmful? No creator would have intended or created such a world. It must have evolved. That was Darwin’s argument and that remains the conviction today. As Stephen Jay Gould once explained:

Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.

You see evolution is, quite literally, a religious theory. Sometimes people say evolution is a religious theory because it is so unlikely and therefore requires faith to believe it. Others say evolution is a religious theory because it is driven by atheism.

No, evolution is a religious theory because it entails religious claims about God. Claims that, to a great many people, seem to be a given. These claims, as in Gould’s quote above, are taken to be so obvious that they are in no need of explaining or defending. In fact, they aren’t even religious. They simply are.

And so evolutionists do not understand the objection. They do not understand why their theory would be considered to be religious. Are they not simply reasoning according to evidence and science?

Meanwhile, the science shows evolution to be astronomically unlikely.

Religion drives science, and it matters.

Sharks Have an Incredible Voltage Sensor

Can Detect a Millionth of a Volt

Imagine if you had two really good wires that were 500 miles long, and you attached them to each end of a AA battery, and put the other ends of the wires in the Atlantic ocean off the coast of New York and Florida, respectively. You wouldn’t expect the tiny AA battery to have much if any effect on the ocean and its life. But in fact sharks can detect signals that incredibly small, and it uses those signals to find its prey. This is one of a great many examples of electrical organs in fish that give them astonishing capabilities to sense the environment around them.

A Question From a Reader

Need a Different Perspective

Recently an evolutionist asked me for scientific evidence for the Bible:

Cornelius, can you provide any scientific evidence that shows that everything in the bible is inerrant, and is the 'word of God'? Can you even show, scientifically, that either one is "probable"?

This blog is about evolution, but it is worth exploring this question. It is a tricky question because not only is the Bible a long book, but it covers a wide range of topics. There is prophecy, poetry, drama, wisdom literature, history, laws, and creation, to name a few. And a great deal of this material is not something that we would think one subjects to scientific scrutiny.

For example, if your friend told you “I think she loves me,” would you ask for scientific evidence? The Bible is a revelation of God to man. It tells us that God loves us. No matter what you think or have been told, God loves you. He loves you so much that Jesus endured a terrible fate and died a gruesome death in order to save you. He is your savior. So the Bible is a story of love and forgiveness. It is a story of how God saves sinners.

Unfortunately there are those who never will accept this message.

William Bialek: More Perfect Than We Imagined

Roll Over Voltaire

Three hundred years ago Gottfried Leibniz said we live in the best of all possible worlds but today Princeton’s world reknown theorist William Bialek explains that it is more perfect than we imagined. This video is long and it sometimes dwells on Bialek rather than the slide he is talking to, but those drawbacks are minor compared to what you will learn. If you want to hear an intelligent, thoughtful scientist scratch the surface of creation’s wonders and reflect on what it all means, then this video is for you.

Bialek, for instance, discusses compound eyes of insects such as the fly. These compound eyes have a large number of small lenses packed into an array. A large number of small lenses gives high resolution, just as does a digital camera with a large number of pixels.

But when the lens becomes too small its optics become distorted due to diffraction. So in determining the best lens size there is a tradeoff between resolution and diffraction. In the optimum solution the lens size is roughly proportional to the square root of the radius of the head. An indeed, Bialek shows an old paper surveying the compound eye designs in more than two dozen different insects. That paper shows that for the different size insects, the lens size is proportional, as predicted, to the square root of the head size.

This is one of Bialek’s half a dozen or so examples showing the optimization of biological designs and, as Bialek assures the audience, there are many, many more. Here is how one science writer explained it:

Yet for all these apparent flaws, the basic building blocks of human eyesight turn out to be practically perfect. Scientists have learned that the fundamental units of vision, the photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped.

“Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” …

Photoreceptors exemplify the principle of optimization, an idea, gaining ever wider traction among researchers, that certain key features of the natural world have been honed by evolution to the highest possible peaks of performance, the legal limits of what Newton, Maxwell, Pauli, Planck et Albert will allow. Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them the superb efficiency with which bacterial cells will close in on a food source; the precision response in a fruit fly embryo to contouring molecules that help distinguish tail from head; and the way a shark can find its prey by measuring micro-fluxes of electricity in the water a tremulous millionth of a volt strong — which, as Douglas Fields observed in Scientific American, is like detecting an electrical field generated by a standard AA battery “with one pole dipped in the Long Island Sound and the other pole in waters of Jacksonville, Fla.” In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants.

But there is much more to Bialek’s talk than examples of nature’s optimal designs. In a thoughtful segment Bialek discusses his philosophy of science. At the [16:30] mark he asks “That was fun, but what does it mean?” The answer, he begins, is that nature’s many examples of optimization help to highlight the difference between two ways of doing and thinking about science.

Bialek describes a cartoon in which a family is driving the car over a bridge with a posted weight limit. The son asks the father how they know what is the weight limit. The father responds that they wait until a sufficiently heavy truck destroys the bridge, they then weigh the remains of the truck, rebuild the bridge exactly as it was, and post the sign.

Bialek uses this funny cartoon as a metaphor for evolutionary theory’s reliance on contingency. This trial-and-error approach to understanding and invention is, Bialek explains, a very common view. The species are the way they are because that is the way they happened to evolve.

In fact, Bialek cogently points out, evolution’s promotion of contingency and trial-and-error is not so much out of scientific necessity. In the bridge example, we could actually model and compute the load limit, based on the design of the bridge and the types of materials used.

But given the “political context” in which many of these discussion occur, it is understandable why evolution is presented as a process of tinkering and not design. [19:30] In fact, the Yale biophysicist notes, these arguments are opposed to the idea of a “interventionist designer,” rather than the question of whether there are design principles in biology.

Bialek contrasts this approach with another view—the view that guides so many physicists—which he represents with Galileo’s famous quote that “The book of Nature is written in the language of mathematics.” Physics, Bialek points out, has been remarkably successful using this formula. It is, he notes, an “astonishing achievement” of the human mind over these four hundred past years. Bialek laments the evolutionary view that Galileo would never have said such a thing if he had known about biology.

Bialek’s point that evolution opposes the idea of a interventionist designer is crucial. For far from reflecting atheism, as so many have charged, and far from being a scientific finding as today’s positivist sentiment wants to believe, this foundation of evolutionary thought is religious.

That is not to say evolution is right or wrong, or true or false. It simply is religious. And until we understand the religion we are immersed in, we will not comprehend its influence on our thinking.

Without this religion, which is ubiquitous, evolution could certainly continue as a theory of mechanical origins. But evolutionary thought would be stripped of its core theoretic and its metaphysical certainty. The theory of evolution would then, rather than be mandated to be a fact, lie exposed to the light of science which shows it to be so improbable.

But it is precisely this distinction, this parsing of the religion from the science, that is so difficult to achieve. When I first began to study the evolutionary literature I was constantly fooled by its intertwining of metaphysics with the empirical science. The evolution literature is rife with religious claims in hiding.

But when properly distinguished and separated, one immediately can see that the conviction of evolution’s truth lies in the non scientific claims whereas the empirical evidence, alone, gives us no such confidence.

Religion drives science, and it matters.

The Evolution of an Explanation of a Small-Headed Sea Snake

Evolution’s “Tremendous Explanatory Power”

I once debated an evolution professor who explained that evolution has tremendous explanatory power. But what exactly does this mean, and is it a good thing? Everyone knows that evolution explains that the species evolved gradually, but for new forms appearing abruptly in the fossil record evolution explains that the species evolved rapidly. Likewise, evolution explains that similarities in species derive from a common ancestor, but for species that are too distant evolution explains that the similarities in the species arose independently. Or again, evolution explains that biological variation is random and not intelligent, but for variation that responds to environmental challenges evolution explains that it created a fantastic adaptive machine that creates such variation. It seems that evolution can explain a great variety of outcomes, even opposing outcomes.

Evolution has a remarkable ability to generate all kinds of explanations. Consider a new study that found “spectacular morphological diversity” among sea snakes that “appear to have diverged very recently and rapidly.” Of particular interest were two species of the snakes with almost indistinguishable genomes, but one is longer with a large head and feeds on crevice-dwelling eels while the other is shorter with a small head and feeds on eels in burrows. How could such a rapid evolutionary change occur? An evolutionist explained it this way:

One way this could have happened is if the ancestral species was large-headed, and a population rapidly evolved small heads to probe eel burrows -- and subsequently stopped interbreeding with the large-headed forms.

Once again evolution produced an explanation. The small-headed snakes rapidly evolved “to probe eel burrows.” But aside from the borrowed Aristotelian teleology (in evolution snakes do not evolve in order to probe burrows, or anything else for that matter), if there were no small-headed snakes then the evolutionists could have just as easily produced an explanation for why no such evolution occurred.

In other words, evolution produces explanations for what is observed. No matter how surprising the science is, evolution can always adjust and produce a new explanation to replace the old one. But the ability to produce explanations is not the same as tremendous explanatory power.

The Evolution of Circular RNA: A Marshall McLuhan Moment

“You know nothing of my work”

[Update: William Jeck has kindly responded and provided an explanation for how circular RNAs may have arisen.]

In the movie Annie Hall Woody Allen is trapped in a long theater line right in front of a rather loud-mouthed fellow. What’s worse, the fellow is pompously expounding on the work of Marshall McLuhan even though he’s all wrong. Allen finally runs out of patience but the fellow won’t back down. So amazingly Allen produces Mr. McLuhan himself, right then and there, who authoritatively informs the fellow of his ignorance (click to view the video). That funny scene sometimes plays out in evolution discussions for there are a great many evolution experts who, like Mr. McLuhan, may drop in at any moment and smash the critic. But the denouement is not always quite as Allen scripted it.

Occasionally evolution researchers such as university professors and graduate students visit this blog to set the skeptics straight. This happened last week in response to our post on circular RNA. That post pointed out the challenge for evolution posed by circular RNA, but an evolution researcher decided he had heard enough. Like Marshall McLuhan he would authoritatively inform us of our ignorance. Here is what he wrote:

I am one of the scientists working on circular RNAs (See Jeck et. al. 2012 in RNA), and probably ought to know better than to respond here, but the willful ignorance is just baffling. In fact my article points to a possible mechanism of circular RNA formation and evolution (through transposable elements, in particular the ALU repeat element). Science is complicated, and before you say that something CANNOT be explained, perhaps you should read up about it to see if, in fact, it already has been.

Wow. That is a big-time slam. The evolutionist explains that he is one of the few scientists working on this very topic of circular RNAs and that, in no uncertain terms, we don’t know what we’re talking about.

Can you imagine what bypassers must have thought. While average readers fill the room with noise, here a real evolutionary scientist rises above the din and easily disposes of the entire post as meaningless.

There was only one problem. What the evolutionist said so authoritatively is, well, not even wrong.

It is difficult to criticize this evolutionist and his paper because it is not that his explanation for how circular RNAs evolved is weak, fallacious or even absurd; it is that his explanation for how circular RNAs evolved is nonexistent.

That’s right. After all the bluster about our “willful ignorance” and how his paper has already explained the evolution of said circular RNAs, the fact is the paper provides no such explanation. So here is our response:

Thank you for pointing us to your 2012 paper on circular RNA that explains how it evolved:

http://www.ncbi.nlm.nih.gov/pubmed/23249747

Just to be clear, we did not say that the evolution of circular RNAs “CANNOT be explained.” We did point out that (i) the fact that exons code for circular RNAs constitutes yet another genetic information layer, making protein evolution even more challenging, and that (ii) evolutionists have no scientific explanation for how circular RNAs could have evolved.

Now that you have pointed us to your paper we can retract that latter statement. One question for you though: Why do you think your 2012 paper provides such a scientific explanation of circular RNA evolution?

Your paper said nothing about how exons could have evolved to include the circular RNA information layer. That would be on top of all the other information exons code for, such as for the protein and its multiple functions, instructions for transport and other interactions, for mRNA stability, mRNA editing, DNA copy error correction, the speed of translation, avoiding an amyloid state, for any other genes that overlap with the gene, and for controlling tRNA selection which can help to respond to different environmental conditions.

You did cite another study that found circular RNA in Archaea so you concluded that “the production of RNA circles is evolutionarily ancient.” But that just aggravates the problem, since that means that the circular RNA signals must have evolved early, long before there were multicellular organisms, for instance.

You also found circular RNA similarities between humans and mice, including the ALUs in the flanking introns. But aside from stating that these similarities reveal an evolutionary relationship, you again said nothing about how the circular RNA could have evolved. You seem to be saying that the observation of similarity implicitly constitutes a scientific explanation for how circular RNAs evolved.

In fact you mention evolution only four times, and in each instance you simply are making the assumption that circular RNA similarities reveals an evolutionary relationship.

So we’re happy to retract our statement, but need a little guidance first. Thanks again.

Not surprisingly, there has been no response.

Unfortunately this is a typical example of how these discussions go. The confidence is exceeded only by the lack of evidence. I’d like nothing more than to acknowledge the strong evidences for evolution. I can go with evolution being true, false, or anywhere in between. But I can’t go against science.

Here is Why the DNA Code is a Problem

A Good Case Study

The genetic code was discovered about fifty years ago and it has been a challenge for evolution ever since. As we saw last time it provides an example of evolution’s metaphysical reasoning. As Wikipedia puts it, “the genetic code used by all known forms of life is nearly universal with few minor variations. This suggests that a single evolutionary history underlies the origin of the genetic code.” That, of course, is false—at least from a scientific perspective. In science we may say hypothesis H predicts observation O, but not the reverse. O does not imply H. It doesn’t even suggest H. It merely doesn’t falsify H. To say anything more requires additional premises and, in this case, that is where the metaphysics comes into play. As evolutionist Mark Ridley put it in his evolution textbook, if the species were created they wouldn’t share the same code. That doesn’t come from science. Now there is nothing wrong with metaphysics, per se. The problem here is that evolution claims to be free of any such metaphysics. Like the drunk who doesn’t know he is drunk, those who are most influenced by metaphysics are the most oblivious to it. The evolutionist’s utter reliance on metaphysics reveals an internal contradiction in evolutionary thought.

But metaphysics is not the only problem that the DNA code reveals. For instance, the code is both conserved and unique. It is found throughout the species, apparently with only a few minor variations, and so if evolution is true this means the code must be difficult to evolve. It somehow arose very early in evolutionary history, and then remained constant thereafter for billions of years.

But the code is also unique and special. It has several profound properties that are very helpful. For instance its arrangement is such that the effects of copying errors are minimized. This means that if evolution is true, the code must have evolved by a long, drawn out process that “found” these special properties. That is, the code must have been repeatedly altered so that the design space was explored and selection must have guided this process to the extant code.

But if the code evolved in this sort of process, that means it is not particularly difficult to evolve. But we just pointed out above that if evolution is true the code must be difficult to evolve. So we have another contradiction.

Beyond all this, the fact that the code is unique and special also presents the problem that the code would be difficult to evolve. In fact a recent paper computed that the probability that the DNA code could have arisen via evolution is 0.0000000000001. Of course there are evolutionary assumptions built-in to this calculation, but even so the result is that the probability of the DNA code evolving is extremely small.

And yet given all the problems that the DNA code presents to evolution, evolutionists nonetheless claim the code as a powerful proof text for their theory. Religion drives science, and it matters.

A Common Code: Surely That Means They’re All Related—Doesn’t It?

A Teachable Moment, Almost

One of the most common metaphysical premises in evolutionary theory is the claim that similarity implies common descent. If two species share similar genes then they must share a common ancestor, from which those genes originated. Evolutionists don’t think twice about this metaphysical claim. Among friends it is taken for granted and any challenges from creationists don’t matter to begin with. Why is this claim metaphysical? Because it doesn’t come from science. There is no scientific experiment or observation that tells us that biological similarity implies common descent. And yet, in a sure sign of metaphysics at work, evolutionists are certain of this premise. Similarity must arise as a consequence of common descent. This conclusion can be trumped only by the finding of even more similarity elsewhere. And such conflicts are common. Evolutionists often need to retract earlier conclusions of relatedness, and the evolutionary tree is filled with conflicting similarities and differences.

All of this became evident, if only for an ephemeral moment, in The Great Debate – What is Life? Go to the [8:40] mark in the above video to hear the context. Craig Venter provides a brief sampling of the problems with evolution’s tree of life model to which Paul Davies incredulously asks if Venter actually doubts the tree of life (even though evolutionists have been doubting the troubled model for years).

The light at the end of the tunnel becomes brighter, however at the [11:20] mark where Richard Dawkins resumes the questioning where Davies left off. “I’m intrigued by Craig saying the tree of life is a fiction,” the evolution apologist begins. “I, I, mean the DNA code of all creatures that have ever been looked at is all but identical, and, um, surely that means that they’re all related. (pause) doesn’t it?”

Venter was smart enough to steer clear of the mud and his silent, wry smile left Dawkins’ dogma hanging in the air like liturgical incense. It was the longest second in evolutionary history as Dawkins, perhaps having a brief moment of doubt, appeared to realize that his metaphysical pronouncement was just that.

Any danger of an epiphany, however, was averted as Dawkins quickly returned to form in the next moment, condemning those stubborn creationists to which the relieved audience broke into spontaneous applause. When in doubt hit the Warfare Thesis button.

[8:40] LK: Craig, do you know from your work—do we yet know what the minimal configuration is to make life?

CV: You mean the minimum gene set.

LK: The minimum gene set.

CV: We’re whittling down on it, but there won’t be “a minimum gene set.” There will be multiple ones because—I’m not so sanguine as some of my colleagues here that there is only one life form on this planet. We have a lot of different types of metabolism, different organisms. I wouldn’t call you the same life form as the one we have that lives in pH 12 base, that would dissolve your skin if we dropped you in it.

PD: I’ve got the same genetic code, therefore a common ancestor.

CV: Well you don’t have the same genetic code. In fact the mycoplasma use a different genetic code that would not work in your cells. So there are a lot of variations on a theme.

PD: But you’re not saying it belongs to a different tree of life than me, are you?

CV: Well I think the tree of life is an artifact of some early scientific studies that aren’t really holding up. So the tree, you know, there may be a bush of life. … So there is not a tree of life. In fact from our deep sequencing of organisms in the ocean, out of, now we have about 60 million different unique gene sets, we found 12 that look like a very, very deep branching—perhaps fourth domain of life. That obviously is extremely rare, that only shows up in those few sequences. But it’s still DNA-based, but the diversity we have in the DNA world—I’m not so sanguine and ready to throw out the DNA world, I think we’re gonna, like Richard was saying, we’re gonna find the same molecules and the same base systems wherever we look.

[…]

[11:20] RD: I’m intrigued by Craig saying the tree of life is a fiction. I, I, mean the DNA code of all creatures that have ever been looked at is all but identical, and, um, surely that means that they’re all related. (pregnant silence) doesn’t it?

CV: A wry smile.

h/t: The man

Suppose They Gave a Theory and Nobody Argued?

Consider the Flowers

Why argue about evolution when we agree on so much? Everyone agrees on the scientific evidence. We agree on how the data were measured, the measurement error, and how to interpret the measurements. We also agree on the theory of evolution. Everyone agrees on what the theory states, what it predicts, and where those predictions have gone wrong. But anyone who attempts to test evolution against the empirical evidence soon finds out there is disagreement. Evolutionists believe their theory is a fact and beyond all reasonable doubt. And so with each problematic measurement and each falsified prediction, evolutionists adjust their theory to accommodate the new quandary. Now evolutionists have powerful reasons to believe in their theory. But are those reasons more powerful than so many empirical obstacles? Can we not take off the training wheels and allow the theory to stand or fall on its own? Or can we not at least acknowledge the falsifications and keep a tally? Evolutionists argue that any such move is merely an anti scientific ruse intended to smuggle in religious beliefs. Besides, just because evolution is a fact doesn’t mean it has all the answers and doesn’t need some refining. And so it goes, when new findings appear evolutionists automatically adjust the theory to fit, while skeptics see a theory that lacks explanatory power.

Consider, for example, new research out of Brazil showing that many flowers don’t fall into the expected common descent pattern. And as is often the case, what is more interesting than the uncooperative findings are the theoretical adjustments made to accommodate. In this case the research found that the different traits, both molecular and morphological, of the flowers do not fall into an evolutionary tree pattern. If two species of flowers are similar in one trait, for instance, they may be very different in another trait.

The response was simple and predictable. Some traits, it was concluded, simply are not appropriate for measuring evolutionary relatedness. Perhaps, for instance, those stubborn traits were subject to “episodic” (aka, rapid) evolution. As the evolutionists explained in one report:

Despite their striking differences in flower shape, Luetzelburgia, Sweetia, Vatairea, and Vataireopsis turned out to be close relatives. Moreover, the two genera with papilionate flowers were not each other’s closest relatives. According to Cardoso, “We showed that similarity in floral morphology does not predict phylogenetic relatedness. Indeed, genera with very different flower shapes are often very closely related (Luetzelburgia and Vatairea), and genera with highly similar flowers share such similarity via convergent evolution (Vatairea and Vataireopsis).” For these plants, other morphological characteristics may indicate relationships more reliably. “Floral traits are apparently more prone to rapid evolutionary changes in response to local ecological conditions,” Cardoso said, “whereas vegetative and fruiting traits are more conserved and not readily shaped by local conditions.”

These evidential problems and theoretical adjustments are not rare skirmishes. They are not the occasional tweak of an otherwise reliable hypothesis. Instead, evolutionists are constantly surprised by their next encounter with the data and evolution is constantly in combat with these hostile threats.

The problem for evolution here is not so much that there is no way out. In fact it always seems that some adjustment is possible. The problem is that the theory rapidly loses credibility. Not only is its track record full of failed expectations, but the very fact that it is so easy to fix and malleable is alarming. Its predictions, it turns out, never really were predictions. At least not the hard kind of predictions that philosophers like to see theories make. Instead those predictions were, upon failure, simply reversed with little more than the wave of a hand. “Oh, we didn’t mean that, we meant this,” seems to be the consistent message.

Maybe evolution is true, maybe it is false, or maybe it is somewhere in between. In any case, we need to remove our preconceptions and allow the empirical scientific data to speak for itself. It will only be then that we can agree.

Non-Coding RNA-Activators Regulate Genes Via a “Mediator”

Another Refutation

Remember when it was discovered that most of our DNA does not code for proteins and evolutionists said it was probably junk? And remember when it was discovered that most of that non coding DNA is nonetheless transcribed and evolutionists said it was probably erroneous transcription? Well it turns out that this non coding DNA continues to surprise, as not only is it transcribed, but it reveals all kinds of function. For instance, as one recent report explained, thousands of long segments of non coding DNA have, err, “a crucial role in turning genes on and off.”

The transcripts, known as non-coding RNA-activators (ncRNA-a), interact with a protein machine known as Mediator, and DNA sequences known as enhancers, to control the expression of genes that may be quite distant in the genome. There are a great many moving parts here and new research shows that a few mutations can disrupt the whole process, resulting in serious health problems.

And no, there is no scientific evidence that all this could have originated spontaneously, via any sort of gradual process. That means that there is no scientific evidence that all this could have evolved. And that means evolution is not supported by the evidence. This is not conjecture, it is a scientific fact. Evolutionists can make all the religious arguments they like, and that is their right, but that doesn’t change the science.

Discovery Institute Summer Seminars

Intelligent Design and Science and Society

The Center for Science and Culture at Discovery Institute announces two intensive 9-day seminars for college students to be held July 12-20, 2013.

The CSC Seminar on Intelligent Design in the Natural Sciences will prepare students to make research contributions advancing the growing science of intelligent design (ID). The seminar will explore cutting-edge ID work in fields such as molecular biology, biochemistry, embryology, developmental biology, paleontology, computational biology, ID-theoretic mathematics, cosmology, physics, and the history and philosophy of science. This seminar is open to students who intend to pursue graduate studies in the natural sciences or the philosophy of science. Applicants must be college juniors or seniors or already in graduate school.

The C.S. Lewis Fellows Program on Science and Society will explore the growing impact of science on politics, economics, social policy, bioethics, theology, and the arts. The program is named after celebrated British writer C.S. Lewis, a perceptive critic of both scientism and technocracy in books such as The Abolition of Man and That Hideous Strength. This seminar is open to college/university students who intend careers in the social sciences, humanities, law, or theology.

Students selected for these seminars will be provided with course materials, lodging and most meals. Travel assistance will also be provided up to a specified amount. Go here to learn more about the Discovery Institute summer seminars.

English Professor Completely Destroys Three Evolution Professors

And That Was Before He Saw Their Arguments

Because the only thing worse than having all your points refuted, is having all your points refuted before you even make them. In this telling exchange English professor Terry Scambray first shows Chemistry professor George Kauffman the door (“It’s disappointing to read George Kauffman assert … that everyone should accept Darwin’s “creation” story because a … congressman had a House Resolution passed saying that we should! Professor Kauffman … must know that House Resolutions are decorative statements, done to enhance politicians’ résumés. I hope that we could all agree that if members of Congress had to pay the cost to produce such trivia, none would exist.”) and then proceeds to anticipate and demolish the sophomoric, non scientific rebuttals that would come from Biology professors Paul Crosbie and Fred Schreiber. Scambray has just shown us that behind all the sound and fury of evolutionary bravado is nothing more than the same old themes. And so, without further ado, presenting, the man whom evolutionists should never debate.

Scambray first ensures that everyone understands the basics. And the basics are that the evidence does not support evolutionary theory very well. In fact there are major problems. Evolutionary theory certainly does not explain the data very well. But no sooner can Scambray warn that “No knowledgeable individual denies this” then the evolutionists, well, deny it:

TS: Animals and plants appear in the fossil record fully formed and remain unchanged through millions of years. No knowledgeable individual denies this.

PC/FS: Natural selection remains the mechanism that best explains the data we gather

Next Scambray forestalls the usual equivocation on evolution. The English professor is careful to ensure we understand what is meant by the word so we are not fooled when the inevitable equivocation was to come, and come it did, Scambray’s warnings notwithstanding:

TS: Such changes as occurred with these finches are sometimes referred to as "evolution in action." But these infinitesimal changes are not "evolution" in the way that Darwin meant the word. For he meant to explain how nature by itself could make something new, how one animal or plant over long periods of time could transform itself into something quite different, like a trout changing into a tiger, or a bacterium into a whale.

PC/FS: there unfortunately remain widespread misconceptions regarding not only whether evolution occurs, but about the meaning of the word theory. … Evolution is the change of organisms over time, observed most fundamentally in alterations of genes. This is a fact, directly observed in any organism that is investigated, and supported by thousands of research studies.

Scambray also explained that DNA similarities are not the profound confirmation that evolutionists claim they are, but of course the evolutionists could not resist, fulfilling yet again Scambray’s prophecy. Amazing, humans share more genetic similarities with dogs than with yeast. Will evolutionists ever learn?

TS: DNA studies have confirmed the traditional relationships and "genetic distances" between different plants and animals which have always existed as observed by humans over thousands of years.

PC/FS: Most recently, molecular biologists have found that DNA contains a record of the changes in organisms as they evolved. For example, closely related species such as humans, dogs and other mammals share about 90% of the same genes, whereas more distantly related organisms, such as the yeast cell, share about 50% of their genes with humans.

And of course there are the finches, flies, insects and bacteria that are supposed to prove evolution. Scambray wisely explains the problems and the fallacies and, yes, the evolutionists rush in.

TS: Over millions of generations of laboratory testing, fruit flies, as one example, when subjected to genetic changes have not changed into anything but mutated, crippled fruit flies. So also much the same thing happened with the famous "Galapagos finches" whose average beak size became bigger when the conditions there made it harder to find food due to bad weather. Then when food became more plentiful, the beak size of those finches that survived returned to normal. Thus the finches changed a little, adapted, while remaining fundamentally unchanged. In this way, nature moves back and forth, in cycles, rather than in a permanent upward climb or downward slide. … Resistance to pesticides and antibiotics does not mean that the insects and bacteria who survive these threats have "evolved." Quite the contrary. Those organisms "resist" the antibiotic or pesticide poisoning merely because of some feature of their cellular structure that does not bind with the poison.

PC/FS: Natural selection makes sense of much of modern medicine. Just as we explain the origin of antibiotic resistance in bacteria, we can explain why antiviral drugs work over the short term but become ineffective over the long term. Our knowledge of how viruses evolve is the basis for great concern about the H5N1 strain of the influenza virus that shifts from pigs to birds to humans.

Finally there is, of course, the underlying motivation for evolution, that creation must be false. And as usual Scambray does the explaining and the evolutionists do the shtick.

TS: Subsequently the tactic was to attack individuals who doubted Darwin by calling them "creationists" -- meaning "crackpots." As one historian writes, the Darwinists' attacks "have been in almost direct proportion to the shortcomings of the theory." Does this explain why congressional resolutions need to be relied on now to prop up Darwin?

PC/FS: Alternative ideas have been tested over the past two centuries, including special creation and versions of "intelligent design." Biologists rejected these alternatives decades ago. They have no explanatory power, no credible evidence, and have long been regarded as non-science, as they invoke supernatural causation, which is not considered by scientists.

No explanatory power, no credible evidence, and aren’t science anyway? I guess that covers it. He’s not my dog, he didn’t bite you, and besides you hit the dog first anyway. Evolutionary thought is so trite and so predictable that Scambray not only destroyed the evolutionist’s pablum, he did so before they even regurgitated it.

And in case there was any doubt about the standing of evolutionary thought, the evolutionists finish with their favorite motto, the non scientific, metaphysical claim from Theodosius Dobzhansky that “Nothing in Biology Makes Sense Except in the Light of Evolution.”

Religion drives science and it matters.

Circular RNAs: A Hidden, Parallel Universe

When Are These Surprises Going to Stop?

Remember when microRNA burst onto the scene a few years back and revolutionized our knowledge of cellular regulatory processes? Evolutionists had to scramble because, after all, when you say your theory explains something and it turns out you don’t really understand that something, well it looks like you don’t know what you’re talking about. It wasn’t much of a scramble though, because evolutionists can pretty much say anything they want, at any time, about their theory. So when microRNA burst onto the scene, evolutionists said “oh, evolution did that.” Well now it is happening all over again, but this time with long RNA which often interacts with microRNA, and this week it was with long RNA that is circular.

Evolutionists once dismissed these long, circular RNA macromolecules—which can be thousands of nucleotides long—as rare genetic accidents or experimental artefacts. Now circular RNA appears to be, err, an abundant and crucial part of genetic regulation. There are thousands of them, probably fulfilling a multitude of functional roles in what one evolutionist admitted is “a hidden, parallel universe” in the molecular world.

And amazingly the genes encoding these RNA macromolecules often overlap with protein-coding genes. Recall that protein-coding genes, in addition to coding for an incredible protein machine, may also contain several more layers of information encoding signals for the transcript (mRNA) stability, mRNA editing, DNA copy error correction, the speed of translation, the protein’s three-dimensional protein structure, the stability of that structure, the multiple functions of the protein, interactions of the protein with other proteins, instructions for transport, avoiding an amyloid state, any other genes that overlap with the gene, and controlling tRNA selection which can help to respond to different environmental conditions.

That is a tall order and now we have yet another layer of information for which genes much encode: circular RNA macromolecules which just happen to interact with microRNA and which just happen to be expressed at the right time, because if they are expressed at the wrong time you don’t have a normal brain. And amazingly, in protein-coding genes, circular RNA macromolecules may be encoded both in the antisense strand and in the sense strand. In fact numerous circular RNAs form by head-to-tail splicing of exons.

Not surprisingly, beyond “oh, evolution did that,” evolutionists have no scientific explanation for how circular RNAs could have evolved. As one evolutionist admitted, “You just wonder when these surprises are going to stop.”