Tuesday, January 29, 2013

What Really Matters

Just This One Thing

I believe there are big problems with evolution. But I could be wrong. Or perhaps I’m right but some form of evolution is nonetheless true. Evolutionists, on the other hand, are much more certain and there is a never-ending drum roll of high truth claims from their camp. These truth claims are unwarranted and it is them, rather than the theory itself, that are the problem. So I’m not so much concerned about the theory itself as I am about the certainty with which it is presented. All of this makes for an interesting, and I think important, debate. But the debate again and again, inevitably, engages religion. There are good reasons for this, and there is nothing wrong with bringing religion into the debate, per se. But I want to avoid one thing. If you are an evolutionist, please do not link your strong feelings and support for evolution with a rejection of the Bible and Jesus Christ.

If you are an evolutionist, please do not peg yourself to atheism, pantheism, Gnosticism, or any other belief that rejects the truth and saving grace of Jesus Christ, merely because you are an evolutionist. There are a great many Christians who are evolutionists. You can be an evolutionist and a Christ follower.

So do me one favor. Give Jesus a chance. You may think creationists are ignorant and evolution is compelling, but give Him a chance. Here’s a suggestion, read one of the gospels (Matthew, Mark, Luke and John). Read a page a day and it will require only a month or two. It will make you more knowledgeable of what is, after all, the most influential book ever written. Shouldn’t you have some knowledge of what that book actually says?

Don’t make more out of evolution than what it is. Jesus died for our sins and without Him we have no hope.

Monday, January 28, 2013

Evolution is Getting Slammed Again in This Transcription Factor Research

This is Getting Ridiculous

New research on how certain transcription factors work together is causing major problems for the theory of evolution. Transcription factors are proteins that attach to DNA and turn genes on or off. These regulatory proteins have recently been promoted to star status by evolutionists because their expectation that evolution proceeds by creating new proteins has fallen short. Instead of creating new proteins, our modern-day Epicureanism is now supposed to have reprogrammed how existing proteins are used in a mind boggling circuitry of molecular regulators, of which transcription factors play a major role. As one evolutionist explained:

Although the number of protein coding genes has remained fairly constant throughout metazoan evolution, the number of regulatory DNA elements has increased dramatically.

With this move evolutionary theory not only becomes far more complex, it also takes on yet more serendipity. For instance, can you imagine that evolution created all those proteins which just happened to have set the stage for the higher life forms?

Likewise those DNA regions, where transcription factors bind, had to have evolved while the transcription factors themselves had to have evolved. And these separate evolutionary pathways not only had to result in the right kind of binding at the right place in the billion-nucleotide long genome, but said binding had to sometimes produce something useful. Simply put, those DNA regions and the transcription factors have special properties that evolution must have somehow accidentally created. In fact, as one evolutionist explained, evolution must have created these DNA regions “which may allow evolutionary adaptation to novel conditions.” In other words, evolution created special DNA regions so that evolution could then occur.

And the new research makes all of this even more improbable, if that were so possible. The research elucidates how different transcription factors work together. Specifically, not only are DNA regions and transcription factors finely tuned to work together, but transcription factors are finely tuned to work together. In this case, when one transcription factor binds to a second transcription factor, that second transcription factor is then able to bind to DNA. This occurs via a rather dramatic structural change in the second transcription factor—a very difficult and unlikely stunt.

It is a great piece of research on a very interesting system, and the result is yet more absurdity for evolutionary theory. For evolution’s random mutations must have hit upon dozens of different mutations that just happened to result in this coordinated action between the two transcription factors and the right DNA region. It is astronomically unlikely.

Evolutionists once argued that deep time solved all their problems. Now they argue that on top of all those eons of time, there is a near infinity of universes in which evolutionary experiments are constantly on-going. Yes evolution is unlikely, but given all those universes, you’re bound to get lucky sometime.

And how many universes would that be? That’s easy: as many as are required. Infinity raises philosophical problems, but so what. With each new finding, evolutionists can simply ratchet up the universe count to whatever is needed.

Religion drives science, and it matters.

Sunday, January 27, 2013

RetroVirus Turned Hero: “We Once Thought it Was Junk”

A Complete Meltdown

You won’t believe this one. According to evolutionists, millions of years ago a retrovirus infected our ancestors’ genome causing disease, but then through the usual random events, which is to say the usual unknown events, it somehow turned hero and now appears to be highly active and playing a crucial role in stem cells. As one evolutionist admits:

The human genome is filled with retrovirus DNA thought to be no more than fossilized junk. Increasingly, there are indications that these sequences might not be junk. They might play a role in gene expression after all.

Amazing what those random mutations can do.

You Won’t Believe What Politicians Are up to Now

New Jersey Needs a Recall

Rep. Rush Holt (NJ), with the help of the atheists at the American Humanist Association, wants Congress officially to designate February 12, 2013 as Darwin Day. And you wondered why our government is a disaster. Holt believes that “Without Charles Darwin, our modern understandings of biology, ecology, genetics, and medicine would be utterly impossible.”

Utterly impossible? It would be difficult to imagine a more ludicrous claim. Gregor Mendel certainly wasn’t following Darwin’s religious pablum when he founded modern genetics. Nor did Darwin magically enable the twentieth century’s uncovering of the structure and function of the genome.

Indeed, it is precisely the other way round. Evolutionists have had to scramble and add epicycle after epicycle to their theory to account for the profound findings of science. Which is why the introduction of Holt’s resolution is so underhanded:

H.RES.41 -- Expressing support for designation of February 12, 2013, as Darwin Day and recognizing the importance of science in the betterment of humanity.

Darwin does not equate with science, unless you count the abuse of science. Of course it doesn’t stop there. Holt next believes that Darwin’s theory is “logical”:

Whereas Charles Darwin's theory of evolution by the mechanism of natural selection, together with the monumental amount of scientific evidence he compiled to support it, provides humanity with a logical and intellectually compelling explanation for the diversity of life on Earth

Sorry but it is not “logical,” in any sense of that word, that the world spontaneously arose. It is not “logical” that something comes from nothing. Perhaps it did somehow, but until we find supporting evidence, “logic” continues to tell us the something does not come from nothing and all of biology did not spontaneously arise via swerving atoms, mutations, or whatever random events Holt imagines did the job.

Of course evolution is built not on positive but negative arguments and so it is no surprise that Holt quickly pivots to cover his absurdity with irrelevant swipes at all the usual suspects:

Whereas the advancement of science must be protected from those unconcerned with the adverse impacts of global warming and climate change;

Whereas the teaching of creationism in some public schools compromises the scientific and academic integrity of the United States education systems;

But we’ve only just begun. Holt next wants to commit us to a “global celebration” of  “humanity”:

Whereas Charles Darwin is a worthy symbol of scientific advancement on which to focus and around which to build a global celebration of science and humanity intended to promote a common bond among all of Earth's peoples

If we ever needed an example of what’s wrong with our government, we now have it. Holt’s resolution is a bizarre, pathetic attempt at indoctrination. It is frightening that people like this are running our country. I wouldn’t want him as Sewer Commissioner.

Friday, January 25, 2013

Here is That New Paper on Synonymous Nucleotides

Evolutionists Are Bailing Out

One of the most common tests evolutionists use, when studying how genes are supposed to have evolved, is to compare the non-synonymous and synonymous genetic differences. That is, if a gene that codes for a particular protein is found in several species, then evolutionists interpret differences in the gene, across those species, as the result of mutations in the evolutionary process. And while most mutations cause a change in the resulting protein amino acid sequence, some mutations do not affect the amino acid that is coded for. These two kinds of mutations are referred to as non-synonymous and synonymous, respectively, and their relative proportions are important to evolutionists. They believe that the while the non-synonymous mutations are important, because they change the resulting protein, the synonymous mutations on the other hand are not important. Therefore, if the ratio of the non-synonymous to synonymous mutations is high, then evolutionists think most of the mutations are important and so the gene is undergoing strong selection which is driving significant evolutionary change. But if the ratio of the non-synonymous to synonymous mutations is low, then evolutionists think most of the mutations are not important and so the gene is undergoing purifying selection which rejects most changes because the lower fitness. In that case the synonymous mutations occur merely because they don’t change the protein. As you can see this entire approach is deeply wedded to evolutionary assumptions and its main result is an inference about how genes evolved. If evolution is true then that is useful information, but if not then the entire exercise is a waste. Well for several years evidence has been growing that this approach and its results do, in fact, have much less meaning than evolutionists believe and, as we discussed here, there is a much better way.

Very simply put, the problem with comparing non-synonymous to synonymous differences between genes is that synonymous differences are not unimportant as evolutionists have assumed. As we have discussed protein coding genes carry a multitude of signals and the resulting protein amino acid sequence is just one of many layers of information in the gene sequence. And for most of these signals, what are synonymous differences in the protein sequence are most definitely not synonymous in the message the signal sends.

All of this is highlighted in a new survey paper on messenger RNA, the copy of the DNA gene. As the paper explains:

There are several well-documented ways in which synonymous sites exert their impact on gene functions: effect on mRNA splicing, mRNA folding, stability and regulation of translation through utilization of preferred synonymous codons that translate more efficiently and accurately. Additional and sometimes opposing selective forces appear to affect codon frequency as well. Previous findings show roles for synonymous positions in RNA–RNA interactions, which influence the translation efficiency, and in RNA–RNA cross-talk, which is a key to biological regulation of expression and transcriptome complexity. Emerging evidence shows that “silent” substitutions carry a wealth of information, which is written over the encoded amino acid sequence, and that this information can be used to regulate translation speed, protein homeostasis, metabolic fate and even posttranslational modifications, which will be discussed in this review. Here we will focus on the RNA level of regulation and the role of synonymous sites and mRNA structure in generating biological complexity.

Once again evolutionary assumptions are being proven wrong by science. The facts of molecular biology make no sense on evolution, yet untold numbers of evolutionary studies, incorporating this test of the ratio of non-synonymous to synonymous mutations, are beholden to evolutionary assumptions.

Tuesday, January 22, 2013

Forty Years On, Concerns Linger

Safe, Legal and Rare Accessible

On this 40th anniversary of the Roe v. Wade Supreme Court decision, while many Americans are delighted that infanticide is legal, there remain lingering concerns. Probably most pressing is the fact that since most infanticides are paid for out of pocket, it is more difficult for poor people to murder their children than for rich people. And while, as the evolutionists at the Guttmacher Institute remind us, infanticide is now safer for all involved (except for the child of course), nonetheless some women must travel 50 miles or more to murder their baby. Clearly there remain many barriers to infanticide which must be overcome. For as the evolutionists conclude, keeping murder legal, safe and accessible “is and must always remain an urgent national priority.” Indeed, this certainly is an urgent national priority.

Monday, January 21, 2013

Genes Code For Many Layers of Information

They May Have Just Discovered Another

Your internet line carries multiple signals simultaneously and likewise a gene carries multiple biological signals. A gene does not merely code for a protein. As difficult as it would be to randomly find a protein-coding gene sequence, it would be much more difficult to find a real gene because they carry so many more signals. For instance, the gene’s DNA sequence determines the important stability of the DNA copy—the so-called mRNA strand, and the mRNA interactions with proteins such as editing machinery.

Also it has been discovered that gene sequences are cleverly arranged to complement the cell’s error correction mechanisms and so minimize copying errors. On top of that information, the gene also contains signals that help to control the speed at which the new protein is synthesized. These signals have been found to be quite sophisticated

The gene sequence also determines the protein’s three-dimensional protein structure, the stability of that structure, the function of the protein, interactions of the protein with other proteins, instructions for transport, and so forth.

One interaction that must be avoided is the propensity of proteins to stick to each other and form fibrils in what is known as an amyloid. As one researcher explained, “The amyloid state is more like the default state of a protein, and in the absence of specific protective mechanisms, many of our proteins could fall into it.”

Also, some genes are overlapping with other genes. In other words, the stretch of DNA where a gene resides may be shared with another gene entirely. So the genetic information is now doubled. And even if this is not the case, researchers are increasingly finding that genes perform multiple tasks. In what is known as gene sharing, the protein product of a gene may carry out several separate and distinct functions. As one researcher concluded, “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.”

A new signal?

The gene sequence specifies the amino acids to be used in making the new protein. But for many of the twenty amino acids there are several codes available. These “codes” are three-letter nucleotides in the gene sequence, called codons. The codons attract different amino acid carrying machines (called tRNAs) which have the corresponding amino acid attached on their other side.

It has long been known that the different tRNAs that carry a common particular amino acid are not all equal. They may have different abundances in the cell, and the gene sequences do not use them all equally. This may depend, for instance, on how often the gene is used.

But new research has now found yet another distinguishing factor between the different synonymous tRNAs: they don’t all work equally well under different environmental conditions. Specifically, when the supply of amino acids is low, some tRNAs continue to be loaded with its amino acid, but other tRNAs fail to be loaded.

This means the way a DNA gene sequence chooses between the different synonymous tRNAs may influence whether it successfully produces a protein, in different conditions. For instance, perhaps some proteins should have lower priority than other proteins, in certain conditions. That could be coded for in the way their respective gene sequences use the synonymous tRNAs.

It could be yet another layer of information coded for by gene sequences.

Euthanasia, Japanese Style

Ideas Have Consequences

It’s not even 2022 yet and evolutionist Taro Aso, who happens to be Japan’s Deputy Prime Minister, not to mention its Finance Minister, is already saying that the elderly should be allowed to “hurry up and die” instead of costing the government money for end-of-life medical care. After all, the second most powerful man in Japan added, “You cannot sleep well when you think it’s all paid by the government.” Not to worry, however, Aso later clarified his remarks, explaining that they merely were his own opinion. We wonder when Mr. Aso will take his turn.

Friday, January 18, 2013

A Marine Mollusk Grinds Down Rock

It May Lead to Better Engineering Machinery

Algae do not merely grow on rocks, they also grow in the cracks and crevices of rocks making the seaweed organisms a difficult meal for consumers such as Cryptochiton stelleri, otherwise known as gumboot chiton, a marine mollusk off the coast of California. This tenacious chiton solves the problem by grinding down rocks with an amazing set of teeth which contain the hardest known biomineral, magnetite. The outer shell of the chiton’s teeth, as professor David Kisailus explains in his latest paper, develop in four distinct stages:

(i) the formation of a crystalline α-chitin organic matrix that forms the structural framework of the non-mineralized teeth, (ii) the templated synthesis of ferrihydrite crystal aggregates along these organic fibers, (iii) subsequent solid state phase transformation from ferrihydrite to magnetite, and (iv) progressive magnetite crystal growth to form continuous parallel rods within the mature teeth.

What is remarkable is that the formation of this advanced,  super-hard material, occurs at standard temperature and pressure. This inspires Kisailus to use these same strategies to produce cost-effective, advanced nanomaterials.

That’s a great idea. An even better one would be to steal the chiton’s designs for using its teeth to grind down rock. As one report explains:

Over time, chitons have evolved to eat algae growing on and within rocks using a specialized rasping organ called a radula, a conveyer belt-like structure in the mouth that contains 70 to 80 parallel rows of teeth. During the feeding process, the first few rows of the teeth are used to grind rock to get to the algae. They become worn, but new teeth are continuously produced and enter the “wear zone” at the same rate as teeth are shed.

The report explains that all this evolved. In other words, random mutations just happened to construct the elaborate process of forming the chiton’s teeth and the complex structures, mechanisms and processes for using the teeth to grind down the rock, to obtain a modest meal of seaweed.

Every mutation, at every point along the way, must have been random. They could not have been induced by the need of the moment. Those are the rules. Otherwise teleology and final causes would be back in play, and that is not allowed in evolutionary theory.

You see evolutionary theory is not driven by empirical science. It is driven by metaphysics. In fact evolutionists have no idea how the amazing gumboot chiton evolved. But they are certain that it did evolve, because they are certain that everything evolved.

Religion drives science, and it matters.

Thursday, January 17, 2013

For Evolutionists, Crime Does Pay

Ruining Careers and Reputations to Get Their Way

Why is there no debate over evolution? Why does everyone believe in the Epicurean vision that the world arose spontaneously? Just ask David Coppedge, the IT guy at the Jet Propulsion Laboratory who dared question evolution. Coppedge was an excellent employee who enjoyed his job, but when he openly questioned Darwin’s theory all that changed. The evolutionists at JPL manipulated his reviews, creating a false paper trail which they would later use against him. Coppedge was demoted, eventually fired, and had his good name taken away. Now a judge, who no doubt like Judge Jones “understood the general theme,” has ruled in favor of the evolutionists. For evolutionists it is all about control because they cannot tolerate an open exchange of ideas. It is yet another disgraceful case of evolutionary blackballing, and that is why there is no debate over evolution.

If You Understand Nothing Else About Evolution Understand IFF

Christians (And Everyone Else) Should Know This

Should Christians reject evolution because it violates the Bible by leaving no room for Adam and Eve and the Fall, or should Christians accept evolution because it is the obvious scientific conclusion? That, according to one history professor, is how the debate will be framed at an upcoming conference. If so, it would be an unfortunate repeat of a centuries old false dichotomy and what would be missing would be any discussion of what evolution really is.

Evolution does not necessarily exclude Adam and Eve and the Fall, and evolution is not a scientific conclusion, obvious or otherwise. For Christians to reckon with evolution they must understand evolution. And to understand evolution, they must understand IFF. Understanding IFF does not force one’s position on evolution, but it does force one’s understanding of evolution.

What is IFF and why does it matter?

IFF is a logical connective and is shorthand for “If and only IF.” For example, if and only if it is Saturday, then I eat pizza. This not only means that I eat pizza on Saturdays. It also means I don’t eat pizza on any other day.

And while this is a perfectly good use of IFF, IFF has no place in scientific hypotheses. A scientist would never say “if and only if my hypothesis is true, then we will observe a certain observation.”

Scientists use hypotheses to make predictions, but they cannot know that a particular hypothesis is the only explanation for a observation. So scientists say “If hypothesis H, then observation O,” but they never say “if and only if H, then O.”

IFF is a religious truth claim, and not scientific statement, because it entails knowledge of all possible explanations. And science affords no such knowledge.

But while IFF is not scientific, it lies at the very heart of evolutionary thought. For example, the practically official motto of evolution is that “nothing in biology makes sense except in the light of evolution.” This phrase shows up repeatedly in evolutionary papers and every evolutionist believes it. Yet it is an IFF statement (you can see why here).

Pop quiz

Here is a typical example, from this week, of how evolutionary thinking entails IFF and how, for evolutionists, it proves evolution to be true. See if you can find the IFF statement in this quote (hint: I’m giving you some help):

Why am I as sure as I could be of any thing in science that humans and other primates have common ancestors? There are millions of complex mutations (transposable element insertions and other insertions or deletions as well as multiple point mutations in proximity) that are exactly reproduced at the corresponding (orthologous) locations in the human genome and in chimp and in many cases gorilla, orangutan and even gibbon and other monkey genomes. In the case of individual transposon insertions, the peculiarities of the particular event, e.g. the degree of truncation or the specific rearrangement of the element, the exact length of the short direct repeats that flank the insertion, are reproduced in the genomes of different species. The age of the insertion, as estimated by the sequence divergence of the transposable element sequence, matches the age determined by which species contain the insertion (the phylogenetic age) of the insertion. The same kind of observations on the inactivating mutations in unitary pseudogenes that are shared by multiple species confirm that these are records in multiple species of the same mutation events occurring millions of years ago during the branching descent of these species. If you look at really ancient transposon insertions, they tell the same story about mammals in general. There is no way to account for these millions of genomic observations in multiple species except common descent. That is what biologists are talking about when they say evolution is a fact. It is possible to argue from now on about mechanisms of evolution, but the starting point is common descent. These observations about genomes don’t depend at all on any theory of the mechanism of evolution, whether all the mutations are really “random,” or whether the elements involved have since acquired some function. The process of insertion of these elements has been very thoroughly studied for several decades and the results are clear.

There you have it. This is the essence of evolutionary thought, and it is not scientific. Here the evolutionist explains that there is “no way” to account for observations O, except for on his hypothesis, H. This is equivalent to claiming that if and only if H, then O.

Science simply cannot provide this sort of knowledge. And likewise, science cannot be used to refute such a claim. Evolutionary truth claims are not vulnerable to science, for they are not scientific to begin with.

Indeed from a purely scientific perspective the notion that the entire biological world (and by extension everything else for that matter, because evolutionary thought is by no means limited to the origin of species) arose spontaneously is silly.

But from a religious perspective it is true. That religious perspective, however, is not biblical. It may be challenging to fit the gospel message into evolution, but that doesn’t begin to address the real conflict between evolution and the Bible.

There will always be evolutionists and there will always be evolution skeptics. Let’s at least be clear about what evolution is.

Monday, January 14, 2013

Trending: Evolution’s Information Technology

What Next?

Art may not imitate life but evolution certainly does. Once the leading edge in biology was breeding and so evolution was cast as a natural breeder. Now the state of the art is genetic engineering and, so, evolution is cast as a natural genetic engineer. And of course the unquestionable trending topic of our time is Information Technology. Just check the employment pages. Do you know Networking, Epic, SAN Citrix, Notes, NextGen, BES, Android, VMware, TCPIP, UNIX, Windows, Active Directory, EMC, Peoplesoft, iPhone, iPad, LANWAN, blade, VoIP, CAT5 and Avaya? If so then you’re trending. And so is evolution. After all, as Matt Ridley explained, “it’s from information technology.” Or as Paul Davies writes this week, “Life's origins may only be explained through a study of its unique management of information.” And Emory University evolutionists are now telling us that chemical evolution includes the “capture, mutation, and propagation of molecular information.” And within Information Technology the trending term is “network,” and so it is with evolution as well:

Chemical evolution includes the capture, mutation, and propagation of molecular information and can be manifested as coordinated chemical networks that adapt to environmental change. The robustness of a chemical network depends on the diversity of its membership, which establishes the probability for the successful selection of superior chemical species and populations. A dynamic exchange of network component structures and assemblies, via both covalent and noncovalent associations, is fundamental for the network’s ability to learn, to capture and integrate information about an environment that ensures the network’s future response to similar conditions, as an inherent part of chemical evolution.

For as one evolutionist has explained, “Molecular cell biology has uncovered sophisticated networks in all organisms.”

If this doesn’t exactly strike you as the stuff of random mutations, consider the most recent evolutionary epicycle, molecular intelligence:

These diverse approaches to deconvolution and reintegration of the origins of the cell, projected in collaboration through the lens of chemical evolution, suggest a remarkable degree of intrinsic molecular intelligence that guide the bottom-up emergence of living matter. … A population of simple molecules, storing and copying information to ensure their own survival prebiotically, argues that intelligent behavior is not restricted to complex genomes but is an inherent property of matter. Darwin’s hypothesis further predicts the emergence of new intelligent materials, ones not limited to what can be deduced from biology’s “archeological” remnants but even more diverse and exotic realms of dynamic chemical systems that might never have been explored by extant biochemistry.

Molecular intelligence, networks, platforms for molecular information, management of information, information technology?

Does evolution also know VMware and TCPIP?

Why is it that evolution follows whatever is trending? Could it be that evolution, rather than uncovering new and remarkable truths about nature, is actually a cultural construct, meeting our needs and expectations for an origins narrative? Could it be that rather than creating life, evolution imitates life? Just Sayin’

Here is How Evolutionists Lie to the Public

A Classic Example

Hitler called it the Big Lie. To convince people your mythology is unquestionably true, small lies won’t do because the average person, who tells small lies himself, will not be fooled. But we believe outrageous, big lies, because we can’t believe anyone would have such audacity to promote them so forcefully. It must be true. And while we have always had myths, and shamans and priests to tell them to us, this time is different because the lie comes in the form of science, such as exemplified in this latest BBC video which we pick up at the 2:25 mark where evolutionist Matt Ridley, in response to the softball question of whether there is any debate in science about the fact of evolution, has these lies to tell:

No, it’s not. It’s quite clear now to scientists because the evidence has got stronger and stronger as the years go by. We now have genetic evidence, as well as the evidence from fossils and other things. We’ve sequenced the genome of Neandertal man, and we can clearly see how it is related to us, and related to the chimpanzee and so on, and we can see that we cross bred with it about 40,000 years ago”

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

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

Fifty years ago you could just about say “well, we still don’t know, what makes living matter different from non living matter. There might be something very special and incomprehensible about it.” That’s gone. We now know that it’s from information technology like any other, and it’s been evolving by sequential changes in DNA sequences.

That was such a dizzying flurry of big lies we, frankly, lost count. Those lies are so absurd, so unequivocally false, and spoken with such conviction, that the average person is sure to believe them.

Unfortunately such lies are the rule rather than the exception. This evolution propaganda segment was no mistake—it is unfortunately typical.

Of course one can make truthful arguments for evolution. And one can try to find scientific evidence to support it. It is not easy, but it can be done. But that is not what evolutionists do. They mandate evolution. They insist evolution is a fact in spite of the evidence. And that is a big lie.

Friday, January 11, 2013

Evolutionist, You Are the Man!

More Religious Hypocrisy

After David arranged for Uriah to be killed in battle so he could have Uriah’s beautiful wife, Nathan the prophet told David a parable of a rich man who stole a poor man’s cherished little lamb. David had no difficulty in identifying the wrong, but how shocked he was when, in the very next moment, he realized the story was about him. “You are the man!,” exclaimed Nathan. How easy it is for us to exercise our reason and judgment when we are removed from the picture. And so how surprised atheists will be when they realize that, while accusing others of mindless fideism, it is they who “are the man.” Atheists accuse others of holding to comforting but vacuous and misleading religious beliefs. But that is a perfect description of themselves and their religion.

In this week’s Sunday Review Susan Jacoby issued all the usual hypocrisies. Religious believers enjoy the “comfort of their faith” but atheists like her are not religious. And that frees Jacoby and religion-free thinkers like her of the “theodicy problem.”

That was after Jacoby explained that she chose atheism because God wouldn’t allow so much suffering. Here is the money paragraph:

Now when students ask how I came to believe what I believe, I tell them that I trace my atheism to my first encounter, at age 7, with the scourge of polio. In 1952, a 9-year-old friend was stricken by the disease and clinging to life in an iron lung. After visiting him in the hospital, I asked my mother, “Why would God do that to a little boy?” She sighed in a way that telegraphed her lack of conviction and said: “I don’t know. The priest would say God must have his reasons, but I don’t know what they could be.”

Eight years later that little boy died but by that time Jacoby no longer had to ask the questions, for she was a committed atheist:

I do not have to ask, as all people of faith must, why an all-powerful, all-good God allows such things to happen.

It is true that theists are left with this question of why an all-powerful, all-good God allows such things to happen. But atheists such as Jacoby are left with questions of why such things ought not to happen in the first place. Such questions, as Whitehead so well observed, “appear so obvious that people do not know what they are assuming.”

And one of those things atheists are assuming is that God wouldn’t do it that way. As P.Z. Myers exclaimed to world he is:

pretty certain that if there were an all-powerful being pulling the strings and shaping history for the benefit of human beings, the universe would look rather different than it does.

Pretty certain God wouldn’t have made this world? While Myers criticizes others for their religious beliefs, Myers’ notion of how the universe would and would not look if such an all-powerful being created it is, itself, a religious belief.

Perhaps Myers’ certainty is at the 99% level. How did he arrive at such a value? You see whether Myer’s certainty is 99%, 98%, 90%, or whatever, does not matter. For in any case, it is a religious claim. There is no scientific experiment or evidence to back up Myers’ belief. There is no logic or rationale to which Myers could appeal.

Myers concludes with atheism, but his very atheism undermines his religious claim. If atheism were true, then no religious claims could be known to be true. One could claim there is a 99% chance God would or would not do this or that, but such a claim would be worthless.

Now Jacoby repeats this illogical exercise yet again. She claims freedom from theodicy not realizing she is a captive. Jacoby did not obviate religion as she imagines, she swallowed it. Jacoby no longer asks such questions not because they are no longer relevant to her, but rather because she has committed to them.

She has decided that God wouldn’t do that to a little boy and so, she concludes, there is no God. Not only is her premise a religious belief, but her conclusion makes it vacuous.

At this point atheists dig themselves even deeper with their standard, F6, response that they are “just testing your belief.” If that were the case then there would be no basis for their conclusion. For all that they would have proved is that people who believe that (i) God created this world and (ii) God would not create this world, are wrong.

When Myers states that God probably would not create this world and Jacoby says God would not do that to a little boy, they are expressing their religious beliefs. For atheists, it’s all about God. You Are the Man.

Thursday, January 10, 2013

When I Pointed Out the Absurdity an Evolution Professor Gave Me Pushback

More Religion and More Denials

Perhaps the biggest myth in today’s origins debate is that evolution is the result of good, objective scientific research. And so anyone who would reject evolution’s mandate that the world arose spontaneously must be religious while those who, on the other side, insist on our modern-day Epicureanism are simply all about science. In order to prop up this myth we must tell ourselves that all those scientific arguments against evolution are nothing more than disingenuous ploys by those religious rascals, and that all those religious mandates for evolution also don’t matter because they are nothing more than helpful explanations offered up by the secular good guys. Both of these are false of course. The significant scientific problems with evolution are not contrived, they are real. And the religious mandates for evolution are not a sidebar, they underwrite evolutionary thought. Without them there would be no evolution. So maintaining this myth requires some effort. We must deny the obvious scientific problems while at the same time presenting evolution as good science. And we must deny any religious mandate while at the same time proclaiming our metaphysical certainties that require evolution. I repeat this sad state of affairs not only as a public service, but also because two convenient examples presented themselves yesterday. Let’s look at the first one.

First, an evolution professor told me I was all wrong about this. This professor had made the non scientific statement that “the gap in understanding of the molecular evolution of eye components is all but closed.” You can read about this here.

But when I pointed out that this was another example of religion driving science the professor pushed back. That was before he made his religious pronouncement for evolution. Here is what he wrote:

“Religion drives science and it matters,” Is completely false, and opposite to the truth. Throwing up our hands and saying “God did it” gets us no farther, gains us nothing. … “Godddidit” gets us nowhere. With that attitude, we’d all still be hunter-gatherers allowing our fates to be determined by superstitions.

That, in case you didn’t notice, is a religious argument. And it’s not just any religious argument. It is one of the dozen or so metaphysical pillars that motivated evolutionary thought and justify it to this day.

Evolution’s metaphysical arguments and mandates fall into two broad categories, one about God and one about man. I use the labels “Greater God” and “Intellectual Necessity” for these two categories and you can see my phylogeny here.

The professor’s argument, that appealing to special divine action is not allowed, is a classic religious claim squarely within the various Intellectual Necessity traditions such as the seventeenth century Protestant doctrine of cessationism, religious rationalism and deism, all of which eschewed miracles.

In the eighteenth century various versions of the argument were heavily promoted by Lutherans on the continent and Anglicans in England. By Darwin’s day any such “Godddidit” explanations were increasingly out of vogue and at Oxford Baden Powell gravely warned that they would “endanger all science.”

And so not surprisingly this Intellectual Necessity of evolutionary thinking was a recurring theme for Darwin in his formulation and justification of his new theory. Later in the nineteenth century Joseph Le Conte at Berkeley continued the theme:

the origins of new organic forms may be obscure or even inexplicable, but we ought not on that account to doubt that they had a natural cause, and came by a natural process; for so to doubt is also to doubt the validity of reason

The very validity of reason was at stake and in the twentieth century evolutionists continued to issue their metaphysical warnings for the Intellectual Necessity of their theory.

And so when the professor insists that “Godddidit” gets us nowhere and would lead to primitive superstitions, he is simply regurgitating the same old metaphysics that evolutionists have been proclaiming for centuries.

That, after assuring us that religion certainly does not drive science, and that any such thinking is “completely false, and opposite to the truth.”

Right. Completely false.

Of course the professor is an evolutionist. Of course he believes that the eye, and everything else for that matter, arose spontaneously. His religion requires it. Only religion could produce such absurdity.

That evolution is a scientific theory is the biggest myth in today’s origins debate.

Monday, January 7, 2013

New Research Elucidates Directed Mutation Mechanisms

No More RM+NS

It has been known for years that organisms and populations adapt to environmental challenges by mutating DNA nucleotides that are particularly exposed during transcription. In other words, when faced with an environmental challenge a cell identifies certain genes which can help meet the challenge. But the gene might require some modification. And so when the DNA double helix is unwound (in order to make a copy of the gene) the exposed single stranded DNA is subject to mutation. Therefore mutations don’t occur randomly in the genome, but rather in the genes where they can help to address the challenge. But there is more. The gene’s single stranded DNA has certain coils and loops which expose only some of the gene’s nucleotides to mutation. So not only are certain genes targeted for mutation, but certain nucleotides within those genes are targeted in what is referred to as directed mutations. As one paper explained:

The resulting mutants provide appropriate variants for selection by the stress involved, thus accelerating evolution with minimal random damage to the genome.

Note the word appropriate, for it is key. It means that the genetic variants that are created are not random with respect to the threat. Instead, they have a far greater probability of enhancing the organism’s ability to deal with the environmental challenge.

Now follow-on research indicates that these mutagenic mechanisms are essentially the same in all living cells. Therefore these mutagenic mechanisms, which target mutations in response to environmental challenges, must have arisen very early in evolutionary history. As the paper explains:

Unique metabolic reactions to a particular environmental stress apparently target specific genes for increased rates of transcription and mutation, resulting in higher mutation rates for those genes most likely to solve the problem.

These findings contradict evolution’s prediction that mutations are random with respect to need and sometimes just happen to occur in the right place at the right time. Instead, evolution created mechanisms which directly respond to future threats. These mechanisms would, themselves, bring about evolution. In other words, evolution creates evolution. That’s incredible.

Thursday, January 3, 2013

Here is That One and Only Leaping Cockroach

Another Example of Lineage-Specific Biology

Here is a video of Saltoblattella montistabularis, the only leaping cockroach of four thousand species of the unloved insect. The cockroach uses complex spring-loaded hind legs, with “grooved femora into which the tibiae engage fully in advance of a jump,” to accelerate at 23 g’s and out jump even grass hoppers. This tremendous leaping ability is quite useful in its native environment of tall sedge grass in South Africa. So naturally, that is why it evolved its leaping ability, as a researcher explained:

They’re in a vertically stratified environment. It’s awfully tough to get up and down [in sedge grass], so leaproaches evolved to do what grasshoppers do — jump between stems.

But that raises an interesting question. For as everyone knows, evolution has no foresight and there are no final causes. The researcher’s teleological language was merely figurative. The leaproach did not evolve “to do” anything. It was all just by chance.

What the evolutionist intended to convey is that the leaproach just happened to undergo a series of random mutations which together conferred its fantastic leaping design and ability which was then selected for because it was so advantageous.

But is this teleological language, which is rampant in the evolutionary literature and first noticed by Adam Sedgwick, merely for brevity? Is it nothing more than scientific shorthand?

We ask because every time it is said that evolution at one time evolved yet another peculiar and advanced design in one particular species which was then selected due to the one particular environment, it is therefore implied that evolution is at all times evolving most all designs in most all species in most all environments.

We just don’t know it because most of those designs were not selected because they were not advantageous at those times for those species in those environments.

In other words, evolution must be a hyperactive creator.

This must be true because otherwise we would have to say that evolution just happened to create only the advantageous designs at the right times, for the right species in the right environments.

And that would imply foresight, teleology and final causes, which we all know do not exist.

So the rampant use of teleological language might not be merely for brevity. It might not be nothing more than scientific shorthand. Perhaps the teleological language is rampant because, well, it sounds better.

Oh and one other thing. The leaproach’s fantastic design shows “remarkable convergence” with design of the grasshopper “with whom they share their habitat.” Just saying …

Wednesday, January 2, 2013

Horizontal Transfer Finally Reaches the Eukaryotes

It Was Inevitable

If falsifiability is essential in science then perhaps evolutionary theory belongs in a different box. Repeatedly evolution sustains contradictory evidence without missing a beat and the latest example is the next step in the long story of horizontal transfer of genomic material. Once evolutionary theory held that when the species were compared they would form an evolutionary tree, common descent, pattern. And when the genes of bacteria violated this pattern, it was said they had been horizontally transferred—a complicated mechanism that allows bacteria to trade genetic material with each other rather than merely inheriting it. Suddenly the framework of evolutionary theory was much more fluid as most any genetic pattern could be explained. The horizontal gene transfer explanation was used liberally and it was even recruited and greatly expanded in highly speculative narratives of how early evolution created its designs. But all of that was for bacteria. The higher eukaryote species, evolutionists argued, still very much confirmed the traditional evolutionary tree model. The theory was solid and falsifiable, the evolutionists assured their skeptics. That is, until now. For new research has brought horizontal transfer to the front and center for eukaryotes as well. To wit:

In higher organisms such as vertebrates, it is generally believed that lateral transfer of genetic information does not readily occur, with the exception of retroviral infection. However, horizontal transfer (HT) of protein coding repetitive elements is the simplest way to explain the patchy distribution of BovB, a long interspersed element (LINE) about 3.2 kb long, that has been found in ruminants, marsupials, squamates, monotremes, and African mammals.

The point here is not that any of this is impossible. The details of how such horizontal transfer of genetic material could occur and then propagate in the higher species are not well understood. But that doesn’t mean it cannot happen. In fact BovB has been found in a reptile tick. So BovB vectors do exist.

The point, rather, is that this is another example of how failed predictions are so easily sustained by evolutionary theory. And when you sustain failed predictions you crush the theory’s explanatory power. For when a theory explains everything, then it really is nothing more than a tautology.

This new research demonstrates yet again how evolutionary predictions about the species patterns don’t really matter. In particular, the evolutionary tree and common descent are not predictions that, when found to be false, falsify evolution. Instead, when found to be false those predictions, as with the many others, are simply forfeited. Therefore practically any pattern can be explained by evolutionary theory. And those that cannot are simply classified as research problems.

What cannot be forfeited is the theoretical core of evolutionary thought, which is that the world arose spontaneously, via chance events and according to natural laws and processes. This cannot be forfeited because we know it to be true.

The epistemological claims of evolution are entirely separate and distinct from the research claims of evolution.

Cellular Machinery Redesigns Genes For Cold Temperature Operation

Really Cool

The central nervous system is constantly sending electronic impulses called action potentials which are propagated along nerve cells via the finely-tuned actions of various proteins that are located in the nerve cell’s membrane. First, there is a membrane protein that simultaneously pumps potassium ions into the cell and sodium ions out of the cell. This sets up a chemical gradient across the membrane. There is more potassium inside the cell than outside, and there is more sodium outside than inside. Also, there are more negatively charged ions inside the cell so there is a voltage drop (50-100 millivolt) across the membrane. In addition to the sodium-potassium pump, there are also sodium channels and potassium channels. These membrane proteins allow sodium and potassium, respectively, to pass through the membrane. They are normally closed, but when the action potential travels along the nerve cell tail, it causes the voltage-controlled sodium channels to open quickly. Sodium ions outside the cell then come streaming into the cell down the electro-chemical gradient. As a result the voltage drop is reversed and the decaying electronic impulse, which caused the sodium channels to open, is boosted as it continues on its way along the nerve cell tail. When the voltage goes from negative to positive inside the cell, the sodium channels slowly close and the potassium channels open. Hence the sodium channels are open only momentarily, and now with the potassium channels open, the potassium ions concentrated inside the cell come streaming out down their electro-chemical gradient. As a result the original voltage drop is reestablished. This process repeats itself until the impulse finally reaches the end of the nerve cell tail.

Not surprisingly this process is sensitive to conditions. Its sensitivity to temperature is mainly in the falling phase, when the original voltage drop is reestablished. This suggests that the potassium channels are more sensitive to temperature and researchers indeed discovered that extreme cold temperatures slows the closing of the potassium channels causing the action potential’s voltage profile to broaden and slowing the nerve cell’s capacity to transmit action potentials.

So how do organisms in extreme cold temperatures compensate? One might think that the potassium channels genes would be adapted, with the proper nucleotide substitutions that would lead to the proper modifications in the potassium channel protein.

But new research, examining octopus species in warm and cold regions, shows that the genetic differences are minor. As the paper explains:

On the basis of conventional natural selection, we hypothesized that the channels’ genes would have evolved mutations to help tune them to their respective environments. Surprisingly, the primary sequences encoded by the two genes were virtually identical, differing at only four positions.

So how do these cold temperature organisms adjust their potassium channels? As the paper concludes, by editing the RNA transcript, the so-called mRNA, of the gene:

the transcribed messenger RNAs are extensively edited, creating functional diversity. One editing site, which recodes an isoleucine to a valine in the channel’s pore, greatly accelerates gating kinetics by destabilizing the open state. This site is extensively edited in both Antarctic and Arctic species, but mostly unedited in tropical species

I just rearranged a sentence in this post. Imagine if I created a computer program to edit the text rather than me editing it manually? That is what these octopus species have, editing machinery to adjust the potassium channels genes automatically, after they are copied from the DNA and before they are translated into proteins. Wow.