A Non Genetic Protein Translation Mechanism Adds More Complexity to Cellular Adaptation

Biology's sophisticated adaptation machine has now been discovered to be even more sophisticated. In recent years the types of adaptation often claimed to be examples of evolution in action have been found to be driven by complex mechanisms that respond to environmental pressures. It was yet another falsification of evolutionary expectations. Organisms responded far more quickly than neo Darwinism predicted, and this was because the responses were not the result of evolution's blind variation, but rather of directed mechanisms. Gene regulation and even gene modification mechanisms have been discovered which not only implement helpful adaptations, but they implement adaptations that are heritable.

Now we can add another chapter to the adaptation story. New research has found that proteins are modified as they are being constructed to help them fend off a virus, bacteria or toxic chemical. Proteins are constructed by glueing amino acids together in a string. The type of amino acid to use at each position is specified by a gene, as interpreted according to the DNA code.

The new research found that during this construction stage proteins may be modified if the cell is under stress. Specifically, the amino acid methionine is used at certain points in the sequence of amino acids even though it is not called for. Methionine can help provide protective armor due to the sulfur atom it carries in its side chain. It seems that some mechanism is intentionally inserting methionine in spite of what the genetic blueprint for the protein says. As was reported this week:

These "regulated errors" comprise a novel non-genetic mechanism by which cells can rapidly make important proteins more resistant to attack when stressed.

It is yet another finding that not only was not expected by evolution, but is difficult for evolution to explain with anything more than just-so stories.

De Novo Genes: What are the Chances?

We have been discussing the de novo gene T-urf13 found in the mitochondrial genome of certain varieties of corn. Readers have asked about the evolutionary claim that the gene arose via blind evolution, and in particular about the role of mutations. Let's have a look.

First, the time frame over which T-urf13 arose is too short for mutations to play a significant role. The evolutionary explanation is that existing, non proteins coding, DNA sequences in the corn mitochondrial genome provided the raw material for the new protein-coding gene, T-urf13.

Under evolution non protein coding DNA sequences are not supposed to carry a pre-planned protein coding information layer. Such information layers are common. For instance, in a communication system it is possible to transmit multiple messages simultaneously. Several telephone conversations or Internet users could, for example, share a single wire. In other words, there can be multiple messages superimposed on a signal.

And just as multiple messages can be transmitted in a wire, so too there can be multiple messages, or layers of information, in a DNA sequence. Of course evolution expected no such level of cleverness. Hence the surprise when overlapping genes were discovered in DNA. In recent years DNA has been found to contain several layers of information.

Could it be that there is another such layer of information that the cell uses to create new genes? Apparently so, for we now find de novo genes such as T-urf13. But because evolution dogmatically rejects any possibility of design, it does not allow non protein coding DNA sequences to carry a preplanned protein coding information layer.

Instead, such protein coding information must exist only by random chance. And when chance rearrangements occur, and a complete protein sequence just happens to form, then de novo genes can appear. A sophisticated protein such as URF13 may appear to be designed, but such an appearance must be deceptive. Such events must occur by chance, not by design.

And what are the chances of this occurring? The corn mitochondrial genome is about half a million base pairs in length. That is enough room to contain about 2,000 T-urf13 sized genes. This number can be increased by accounting for DNA's six different reading frames, and decreased by accounting for the fact that only part of the corn mitochondrial genome is available. It can also be increased by allowing for some overlap in the hidden genes.

Let's be conservative and say there is room for 100,000 such genes in the corn mitochondrial genome. Nonetheless this is seven orders of magnitude shy of the million million sequences needed for any hope of obtaining a functioning gene, as found in one experiment. And even that estimate was conservative because only the minor function of ATP binding was required.

In contrast, the URF13 protein is a far more complex, cleverly designed machine. It is designed such that several copies fit together to form a protein machine. And that machine fits into the inner mitochondria membrane, a very complex environment. And the machine provides a channel that allows only certain types of chemicals to pass through the membrane. And did I mention the channel is gated, with a molecular switch to open the gate?

The URF13 protein design dwarfs the experimentally screened function of ATP binding. And yet, even in that simple case, and with conservative assumptions, we find the probabilities of the T-urf13 de novo gene arising via blind evolution to be one in ten million (that is, 1 in 10,000,000). The real number undoubtedly has many more zeroes.

This is the story of evolutionary probabilities. Over and over we come up with so many zeros. In design after design, and species after species, evolution repeatedly draws upon unlikely events to create its marvels. Evolutionists now contemplate a multiverse--a super universe containing an untold number of unseen universes toiling away through the ages--in order to beat the odds. Sure these designs would never appear if there was just one universe, but what if there was a near infinity of universes? Surely one of them would get lucky.

Evolutionists do not worry that their story is unlikely. They insist de novo genes must, one way or another, be simply the result of blind processes. This is a good example of the absurdity of evolution. Like a robot that hits a wall but just keeps on trying, evolution cannot adjust to the scientific data. This is because evolution is not, at bottom, a scientific theory. It is driven by the metaphysical mandate that matter and motion must explain everything, regardless of the evidence. This mandate has arisen from a long history of thought in science, philosophy and theology. Religion drives science and it matters.

Evolution and Medicine: Return of the Witch Doctor

Ever wonder what it would have been like to see a doctor in centuries past? How about the village witch doctor? From blood letting to rituals, it is sickening--no pun intended--to think of how ignorance and religious dogma have led to so much needless suffering. Now evolutionists want to bring their religious dogma into modern medicine. Today's doctor, they say, must be fully indoctrinated in their Darwinian ways. As one new "peer-reviewed" (sic) paper in a government funded journal explains:

Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease.

If you have ever wondered why history is important, wonder no more. Evolution has led the life sciences down so many false trails it is difficult even to keep track. Evolution is constantly wrong and evolutionists are always surprised by nature. And now they incredibly want to force modern medicine to go back in time and embrace absurd nineteenth century naivete. The last thing we want our doctors to be spending time and effort on is religiously motivated pseudo science.

If you don't understand why the controversy over evolution is important, then consider this: Evolutionists are not, and never were, content to be free to pursue their silly religious ideas. Like so many religious movements, they want you to be subject to their beliefs. They insist evolution is a fact to which every student must accede, every scientist must pay homage, and every medical doctor must be indoctrinated. And they will use your tax dollars to do so. Blood letting anyone?

Special Creation False: Your Tax Dollars at Work

Over at the National Science Foundation, where your tax dollars go to promoting Darwin's religious theory, evolutionist Jim Secord asks the question "Where did Charles Darwin become convinced of the truth of evolution?" That's a good way of putting it because Darwin and evolutionists ever since have indeed been convinced that evolution is true. It is, as they like to say, a fact every bit as much as gravity is a fact. That's quite a claim. You would think they might say it is a fact as much as are Alexander the Great's conquests or some other historical record. That would still be a misrepresentation of the scientific evidence, but it would not be as blatant. The comparison with gravity is downright ludicrous, and precisely for this reason it is a tipoff that evolution is not the product of empirical science. Experimental measurements and hypothesis testing do not produce metaphysical certainty.

As Secord explains, Darwin's observations led not to scientific conclusions but religious concerns:

The different varieties of tortoises and mockingbirds provided powerful evidence of the relations between the Galapagos fauna and that of nearby South America. In geographical space, as in geologic time, closely allied species emerged successively and in order, just as they did in the fossil record. These relations, which impressed Darwin throughout the voyage, suggested that species were not specially created.

Let's see now, where's that verse in Genesis about birds on islands being completely different than those on the nearest mainland? Oh well, in any case Darwin argued powerfully that special creation must be false. The evidence for evolution was weak at best, but it had to be true. Religion drives science and it matters.

De Novo Genes and Normal Science

Science can be wrong about some things and still make great discoveries and inventions. One can believe the earth is flat or that electrons are nothing more than tiny billiard balls and still make progress. The history of science is a fascinating story of erroneous theories and beliefs intertwined with remarkable progress. And even today’s life science research journals are full of asinine statements, arising from a belief in evolution, mingled with perfectly good scientific research. Most scientists can distinguish between the hard data gathered in the laboratory and the obligatory evolutionary framework into which the data are forced and presented. You focus on the former in order to make progress and tolerate the latter in order to get funded. Such are the practical realities of working in science.

But the origins debate is different. Here the evolution paradigm itself is questioned. That evolutionary framework and filter through which all data and hypotheses must fit is up for debate. Perhaps evolution, or at least core parts of the framework, are not true.

One may scorn at such folly and remain within the paradigm. Or one may argue against such folly. But one may not do both. It makes no sense to interpret the evidence from within the paradigm, and then argue that such interpretations prove the paradigm. In order to defend evolution as true, one must examine the evidence from a theory-neutral perspective.

Here is a simple example: A new horse fossil is discovered and evolutionists decide where it fits best amongst the already known fossils. It may not fit perfectly, and the evolutionists may be unsure about which twig in the evolutionary bush is right for this new fossil (or if perhaps a new twig should be hypothesized). But they believe evolution is true and so the fossil must fit somewhere. They announce to the world that horse evolution is now better understood and apologists then use the finding as an example of powerful evidence for evolution. After all, the evolution of the horse has been revealed.

But of course the fossil revealed no such evolutionary step—it was interpreted as an evolutionary step. Unfortunately this sophistry is common. All the time I see evolutionists making just this sort of argument. Arthur Hunt, for instance, uses de novo genes in just such an argument. Genes that are found in only one or a few allied species are sometimes thought to be newly evolved. Hunt realizes the evolution of such genes might seem “difficult to some” as there are “judicious” events that must have occurred.

Now from within the evolution paradigm, there is the question of whether such genes really are de novo. Could they not have evolved via some other mechanisms, such as lateral gene transfer. Evolutionists investigate such options, and sometimes can find none that work. In these instances they conclude a gene must be newly evolved. Hunt explains these issues and then erroneously argues that since the other evolutionary options have been eliminated for these genes, therefore they must be de novo genes, and therefore de novo genes do not pose a problem for evolution. He writes:

I would encourage readers to read the paper … This is the best way to appreciate that this one pillar of [design] thought, that new protein-coding genes cannot arise by “natural” means, is an illusion.

Design can occur by natural means but that is another story. What is even more problematic than this caricature of design is Hunt’s argument for evolution according to its own assumptions.

The paper, of course, provides no compelling explanation for the blind evolution of de novo genes. As usual the paper presupposes that such blind evolution must have occurred. Therefore the paper’s conclusions must be carefully weighed rather than simply employed as evidence for blind evolution. This logical fallacy is, unfortunately, pervasive in the origins discussion.

De Novo Genes: The Evolutionary Explanation

Cells have remarkable adaptation capabilities. They can precisely adjust which segments of the genome are copied for use in the cell. They can edit and regulate those DNA copies according to their needs. And they can even modify the DNA itself, such as with adaptive mutations, to accommodate environmental pressures. And in addition to these examples, cells can create completely new, de novo, genes in an evolutionary instant. It is yet another biological capability that reveals the scientific weakness of evolutionary theory.

One apparent de novo gene is T-urf13 which was found in certain varieties of corn. T-urf13 is not in the main genome in the cell’s nucleus, but rather in the smaller genome in the mitochondria. The mitochondria is the cell’s power plant which produces adenosine triphosphate (ATP) molecules—the standard unit of chemical energy.

Like a dam that is full of water, mitochondria are filled with protons. And just as water flowing through the dam turns a turbine to produce electricity, protons flowing through a mitochondrial membrane turn a molecular turbine to produce chemical energy in the form of ATP. This molecular turbine, known at ATP synthase, is one of many types of transmembrane proteins—proteins that are imbedded in and span a membrane wall.

The T-urf13 gene produces another transmembrane protein—URF13. Multiple copies of URF13 group together to provide a channel opening in the membrane for water-loving molecules to cross. The URF13 channel is normally closed and opens only when certain molecules bind to the exterior side of the channel. (Yes, this is a complicated design.) The binding molecule serves to alter the URF13 structure so as to open the channel in just the right way. Unfortunately toxins from certain fungal pathogens also bind and open the URF13 channel. This wreaks havoc because it is like poking a hole in a dam.

This problem arose about forty years ago and since then we have learned much about the T-urf13 gene. It is found in only one corn line and appears to have arisen rapidly. A small part of the gene (about 15%) is highly similar to a small part of a different gene in the same mitochondrial genome. That other gene codes not for a protein, but rather for a ribosomal RNA. Most of the remainder of the T-urf13 gene is quite similar to a flanking sequence, just outside of that same ribosomal RNA gene. Finally, there is a small segment of the T-urf13 gene that has no matches elsewhere in the mitochondrial genome.

It appears that T-urf13 is a de novo gene, having been constructed mostly from two segments in or around a ribosomal RNA gene. It is intriguing that segments associated with an RNA gene would combine to form a protein-coding gene. It is another sign of the fascinating re-use and mixing and matching capabilities that seem to be built into the cell’s design.

Evolutionists, who see biology as a big fluke, don’t see it that way. They amazingly conclude that the T-urf13 gene, which produces such an incredibly complex protein, arose by random chance.

Their idea is that spontaneous genomic rearrangements blindly produce new segments of protein-coding DNA on a regular basis. And once in awhile even a blind process finds a marvel like T-urf13. Does this not suggest that the vast genome is a source of de novo genes? Evolution created genomes consisting of billions of nucleotides, and those DNA segments then become sources of future genes, so their thinking goes.

There’s only one problem: the idea makes little scientific sense. Even a random DNA sequence the length of the entire corn genome does not contain a single gene that likely would code for a functioning gene. One study, for instance, found that more than a million million random sequences were needed to find a single functioning protein. In that study, not only was the protein shorter than URF13 (URF13 is 50% longer and the chances likely degrade rapidly with length), but what qualified as “function” was quite modest (mild ATP binding was defined as function which, compared to the URF13 channel, is like a tricycle compared to a jetliner).

We may not be able to compute precisely the probability of evolution’s explanation for de novo genes such as T-urf13, but we do know the chances are not very good. And that is being kind. Religion drives science and it matters.

De Novo Genes: What We Know and Don’t Know

I once debated an evolutionist who listed a dozen or so major areas of evidence he said proved evolution. The problem was each of the areas of evidence was problematic for evolution. True, one could find within those areas, as he did, supportive evidences. But the story was not so simple. In fact the areas of scientific evidence, when carefully examined from a theory-neutral perspective, reveal all kinds of problems for evolution. Is evolution false? Is it true? The answer is there are no easy answers. There certainly are substantial scientific problems with Darwin’s idea—that much we do know. If evolution is true then there is much we have to learn about science. But the scientific evidence can tell us something else, and with far more certainty. It tells us that we should not turn to evolutionists for a serious evaluation of the scientific evidence.

It is both shocking and disappointing how grossly evolutionists misrepresent science. This becomes painfully obvious when they, as with the evolutionist I debated, claim problematic areas of evidence as powerful proofs. Consider, for example, the findings of de novo genes.

One of the facts of biology that evolutionists claim as powerful supporting evidence is the many similarities in genes between the different species. There are many such similar genes, and they certainly do fall in the list of supporting evidence. But if such genomic similarities are powerful evidence for evolution, then what about the genomic differences?

There are, in fact, substantial genomic differences even between otherwise allied species. And it stands to reason that these evolutionary surprises would fall in the list of contradictory evidence, right?

Wrong. With evolutionists, all evidences support evolution, one way or another. Evolutionist Arthur Hunt, for instance claims that the findings of de novo genes refutes the notion that evolution alone can’t do the job “in no uncertain terms.” The idea that proteins can’t arise from scratch, explains Hunt, “is an illusion.”

And just how did evolution perform this feat? According to Hunt and the evolutionists, at some point in evolutionary history a segment of DNA recruited the machinery needed to begin coding for a protein. Fortunately that DNA segment contained the proper message so the resulting peptide was indeed a functioning protein. And of course subsequent mutations may have enhanced or modified the newly minted molecular machine.

There you have it. No details regarding how likely (or should I say unlikely) a non coding segment of DNA just happens to code for a functioning protein. No details on how often this would have to occur in order to evolution to get lucky.

Now don’t get me wrong—I’m not saying this evolutionary interpretation is impossible. I wasn’t there and, frankly, I don’t know enough to calculate the probabilities. (I don’t think any else does either which would explain why evolutionists haven’t provided them).

We do have some relevant experimental data. A functioning protein arising from a random DNA sequence of about 400 base pairs is extremely unlikely. Even shorter sequences need millions upon millions of tries to get anything even slightly functional.

But of course mere function isn’t good enough in the evolutionary world. Becoming fixed in the population requires useful function, or luck, or some combination of the two. And then there is the recruitment of the machinery to make the sequence code for a protein. How many times would that have to occur, and what are the probabilities?

Impossible? Certainly not, but we’re a long way from certainty. Unfortunately, certainty is precisely what Hunt and the evolutionists have. We can argue about what the scientific evidence implies, but it does not give us certainty about questions of origin. We are simply nowhere close to the evolutionist’s claim that their theory is a fact just as much as is gravity.

The claims of evolutionists are both shocking and disappointing. We scientists have the serious responsibility of public trust. Others depend on us for a fair and honest assessment of what the scientific evidence reveals—and what it doesn’t reveal. We do them, and science, an injustice by providing anything less.

Podcast: The Religious Foundations of Darwinism and the Failure of Naturalism

Go here and click on the green podcast symbol to listen to the rest of the discussion about the origins debate and Darwin's predictions.

Podcast: Darwin's Predictions With Cornelius Hunter

Go here and click on the green podcast symbol to listen to a discussion about the origins debate and Darwin's predictions.

RNA Repair Better Than New

One of the many examples of incredible complexity in biology is the DNA repair system. It is also an example of incredible complexity that appeared incredibly early in the history of life. If complexity evolves from simplicity, then it does so at an astonishing pace. As amazing as this story is, it is only the beginning. We now know that DNA's transcript--its sister molecule RNA--has its own repair system which also must have arisen early.

Not surprisingly the RNA repair system is immensely complex. But an interesting twist is that after the RNA molecule has been repaired it is sealed with a methyl group, making it stronger than it was in the first place.

It is just the sort of thing we would never expect with evolution. A complex and esoteric design appearing very early in the history of life. With evolution we must imagine that such an intricate and precise sealing capability just happened to arise for no reason in some of the earliest cells. The blind dart thrower just happened to hit the bull's eye.

And of course if that's true, then the walls must be covered with all the darts that didn't hit the mark--the only way a blind dart thrower could luckily hit the mark is with a great many tries. Evolution must have produced bizarre and useless designs at an unheard of pace.

It is an aspect of evolution that evolutionists don't often discuss: if precise designs arose by chance, then how many tries were required? Such awkward questions are often covered over with Lamarckian language. It is said that environmental pressures brought about the designs. This may sound good, but there is one problem. With evolution environmental pressures do no such thing. The jaw-dropping designs must arise for no reason. It's amazing how well evolution works.

Transposable Elements in the Rice Genome: New Data for an Old Theory

Evolution has many false predictions to its credit, but for every false prediction there is an adjustment. Evolution's expectations are constantly being upended, but each time the unabashed evolutionists simply add another patch to their theory. They never stop to consider that there could be a problem--after all, evolution is a fact.

Consider, for example, the evolutionary expectation that biological adaptation is, like water eroding rock, a long slow process requiring eons of time. Only by the magic of natural selection acting on blind mutations are species able to adapt to environmental pressures. Only rarely does a mutation serendipitously cause a helpful change, and even then it might not spread through the population. It's amazing that species have survived at all.

But biology reveals that species adapt rapidly, enacting adaptations that help deal with the environmental pressures. In many cases selection has nothing to do with it, and it doesn't require eons of time. You can read more about this false prediction of evolution here.

Research continues to fill in our understanding of this intelligent adaptation capability. For instance, new findings are now revealing more about how rice can rapidly adapt. In this case the smart adaptations were caused by transposable elements which are small segments of DNA that evolutionists thought inconveniently plopped themselves down in the genome whereever they happened to land. The transposable elements would help only rarely when a lucky insertion occurred.

But instead, the research demonstrated a transposable element that not only does not act randomly, but provides rapid resistance to environmental pressures (low water and high salt environments were tested). As the lead researcher explained:

What we discovered was brand new and really stunning.

What is equally stunning is how conservative and resistant to change are evolutionists. Evidence like this makes no difference for religion, not science, drives evolutionary thinking.

Complexity: A Prediction of Evolution

How can evolutionists explain biology's complexities such as the sonar tracking capabilities that outperform our best military equipment? One argument is that we must never doubt evolution, for such doubt is a science stopper. Another argument is that we mustn't think of God as a designer, for that is to anthropomorphize God. Aside from such philosophical and theological arguments, evolutionists also turn this apparent difficulty into a success story. That's right, evolutionists claim complexity as a fulfilled prediction. As Jerry Coyne writes in his book Why Evolution is True, "The deepest (and oldest) layers of rock would contain the fossils of more primitive species, and some fossils should become more complex as the layers of rock become younger." [17]

But this is not a prediction of evolution. Believe me, evolution would not skip a beat if we found primitive life forms on a distant planet that had not changed for billions of years. Evolution makes no prediction that complexity should emerge.

Perhaps what Coyne and the evolutionists mean is that given that complex life exists today, then we should see it emerge from primitive forms. In other words, evolution predicts simple, not complex, beginnings.

But in that case, the prediction has not been a fruitful one. From the trilobite eye to the DNA code, early life does not show signs of simplicity. In fact, evolutionary reconstructions of what the ancient common ancestor to all life would have looked like come up with more complexity than simplicity. As evolutionist Nick Lane recently wrote:

There is no doubt that the common ancestor possessed DNA, RNA and proteins, a universal genetic code, ribosomes (the protein-building factories), ATP and a proton-powered enzyme for making ATP. The detailed mechanisms for reading off DNA and converting genes into proteins were also in place. In short, then, the last common ancestor of all life looks pretty much like a modern cell.

Similarly the cell's proteins, often referred to as the building blocks of life, do not reveal simple beginnings if evolution is true. As one evolutionist admitted last year:

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

You can read more about the failure of this evolutionary expectation here. Dogma doesn't help science.