About That Genetic Code

A Smoke Screen

We recently looked at the enormous problems that the DNA, or genetic, code pose for evolutionary theory. Here is a paper that seems to have come to the same conclusion. The authors argue that the underlying patterns of the genetic code are not likely to be due to “chance coupled with presumable evolutionary pathways,” (P-value < 10^-13), and conclude that they are “essentially irreducible to any natural origin.”

A common response from evolutionists, when presented with evidence such as this, is that we still don’t understand biology very well. This argument from ignorance goes all the way back to Darwin. He used it in Chapter 6 of Origins to discard the problem of evolving the electric organs in fish, such as the electric eel (which isn’t actually an eel). The Sage from Kent agreed that it is “impossible to conceive by what steps these wondrous organs” evolved, but that was OK, because “we do not even know of what use they are.”

Setting aside the fact that Darwin’s argument from ignorance was a non-scientific fallacy, it also was a set up for failure. For now, a century and half later, we do know “what use they are.” And it has just gotten worse for evolution.

Darwin’s argument has been demolished, once again demonstrating that arguments from ignorance, aside from being terrible arguments, are not good science.

The truth is, when evolutionists today claim that the many problems with their chance theory are due to a lack of knowledge, they are throwing up a smoke screen.

Religion drives science, and it matters.

Here is Why Steven Novella is Wrong About That Harvard Experiment

Going Nowhere Fast

Steven Novella, neurologist at Yale University School of Medicine, has commented on a recent Harvard University experiment for visualizing bacterial adaptation to antibiotics. The Harvard researchers constructed a giant petri dish with spatially-varying antibiotics to watch how bacteria adapt over time and space (the researchers came up with a great name for the experiment: The microbial evolution and growth arena [MEGA]–plate). And adapt they did. Those adaptations, however, were instantly claimed as an example of evolution in action. The researchers wrote that the “MEGA-plate provides a versatile platform for studying microbial adaption and directly visualizing evolutionary dynamics.” And the press release informed the public that the experiment provided “A powerful, unvarnished visualization of bacterial movement, death, and survival; evolution at work, visible to the naked eye.” Likewise, Novella called it “a nice demonstration of evolution at work in a limited context.” There’s only one problem: The experiment did not demonstrate evolution, it falsified evolution.

First off, Novella deserves some credit for acknowledging at least some limitations in the experiment’s results:

Of course, this one piece of evidence does not “prove” something as complex and far ranging as the evolution of life on Earth.

Novella also deserves credit for acknowledging that evolutionary change that requires a few mutations, rather than merely one, is a big problem. Novella has solutions which he believes resolve this problem (as we shall see below), but at least he acknowledges what too often is conveniently ignored.

What Novella does not acknowledge, however, is that bacteria adaptation research, over several decades now, has clearly shown non evolutionary change. For instance, bacterial adaptation has often been found to be rapid, and sensitive to the environmental challenge. In other words, when we look at the details, we do not find the evolutionary model of random variation slowly bringing about change, but rather environmentally directed or influenced variation.

That is not evolution.

And indeed, the Harvard experiment demonstrated, again, very rapid adaptation. In just 10 days the bacteria adapted to high doses of lethal antibiotic. As one of the researchers commented, “This is a stunning demonstration of how quickly microbes evolve.”

True, it is “stunning,” but “evolve” is not the correct term.

The microbes adapted.

The ability of organisms to adapt rapidly falls under the category of epigenetics, a term that encompasses a range of sophisticated mechanisms which promote adaptation which is sensitive to the environment. Given our knowledge of bacterial epigenetics, and how fast the bacteria responded in the Harvard experiment, it certainly is reasonable to think that epigenetics, of some sort, may have been at work.

Such epigenetic change is not a new facet of evolution, it contradicts evolution. Not only would such complex adaptation mechanisms be difficult to evolve via random mutations, they wouldn’t provide fitness improvement, and so would not be selected for, even if they did somehow arise from mutations.

Epigenetic mechanisms respond to future, unforeseen conditions. Their very existence contradicts evolution. So the Harvard experiment, rather than demonstrating evolution in action, is probably yet another example of epigenetic-based adaptation. If so, it would contradict evolution.

Another problem, that Michael Behe has pointed out, is that it appears that most of the mutations that occurred in the experiment served to shutdown genes. In other words, the mutations broke things, they did not build things. This is another way to see that this does not fit the evolutionary model. It’s devolution, not evolution. Novella begs to differ, and says Behe has made a big mistake:

Behe is wrong because there is no such thing as “devolution.” Evolution is simply heritable change, any change, and that change can create more complexity or more simplicity. Further, altering a protein does not “degrade” it – that notion is based on the false premise that there is a “correct” sequence of amino acids in any particular protein. Evolution just makes proteins different. Proteins perform “better” or “worse” only in so much that they contribute to the survival and reproduction of the individual. If it is better for the survival of the organism for an enzyme to be slower, then the slower enzyme is better for that organism.

First, Novella ignores the fact that many of the mutations introduced stop codons, and so did not merely slow an enzyme but rather shut it down altogether.

Secondly, it is not Behe here who is making the mistake, it is Novella. He says “Evolution is simply heritable change …”

But this is an equivocation.

On the one hand, evolutionists want to say that shutting down or slowing a gene is “evolution,” but on the other hand, evolutionists say that a fish turning into a giraffe is “evolution.”

Unfortunately evolutionists routinely make this equivocation. This is because they don’t think of it as an equivocation. In their adherence and promotion of the theory, the distinction is lost on them. All change just smears together in one big long process called evolution. You can see other examples of this here and here.

So the comments, press releases, and articles send a misleading message. Readers are told that the researchers have seen “evolution in action.” The message is clear: This is evolution, the evolution. But it isn’t. There is nothing in these findings that show us how a fish turns into a giraffe.

Multiple mutations

As mentioned above, Novella also believes that evolution coming up with designs requiring multiple mutations is not a problem. Novella’s reasoning is that while this would be a problem if most mutations are harmful, they aren’t. Most mutations are neutral, so evolutionary drift can introduce the many needed mutations, and once the set of required mutations are in place, then you have the new design.

This is a profound misunderstanding of the problem evolution faces. You can’t evolve a protein, for example, with drift. That most mutations are neutral does not suddenly resolve the curse of dimensionality and resolve this astronomical search problem. There just is no free lunch.

Similarly, Novella makes yet another profound mistake involving what he calls “the lottery fallacy.”

The first is basically the lottery fallacy – considering the odds of John Smith winning the lottery by chance alone and concluding it could not have happened by chance. Rather, you should consider the odds that anyone would win the lottery. This is actually pretty good. Behe looks at life on Earth and asks – what are the odds that this specific pathway or protein or whatever evolved by chance alone. He is failing to consider that there may have been billions of possible solutions or pathways down which that creature’s ancestors could have evolved. Species that failed to adapt either migrated to an environment in which they could survive, or they went extinct. In other words, Behe should not be asking what the odds are that this bit of complexity evolved, but rather what are the odds that any complexity evolved. It is difficult to know the number of potential complexities that never evolved – that number may dwarf the odds of any one bit evolving. Right there Behe’s entire premise is demolished …

This is a terribly flawed argument for several reasons. First, life needs proteins. All life that we know of needs proteins.

Thousands of proteins.

Yet proteins are far beyond evolution’s reach. It is true, per Novella’s point, that there are a whole lot of ways to make a given protein. There are many, many different amino acid sequences that give you a globin. But “many, many” is like a grain of sand compared to the astronomical amino acid sequence search space.

There just is no free lunch.

But Novella goes further than this, and this brings us to the second flaw. Novella is not merely arguing there are many different ways to construct life as we know it. He is pointing out that there are, or at least there could be, a whole bunch of different ways to make life, in the first place.

If you take them all together, you could have a pretty big set of possibilities. Perhaps it is astronomical. So what we got in this world—the life forms we observe, are not point designs in an otherwise lifeless design space. Rather, the design space could be chocked full of life forms. And hence, the evolution of life becomes likely, and “Right there Behe’s entire premise is demolished.”

What Novella is arguing for here is unobservable. He is going far beyond science, into an imaginary philosophical world of maybe’s.

Not only is Novella clearly appealing to the unobservable, but even that doesn’t work. At least for any common sense approach. There is no question that the design space is full of useless blobs of chemicals that do nothing. A speculative claim? No, that is what this thing called science has made abundantly clear to us. Even the simple case of a single protein reveals this. Only a relatively few mutations to most proteins rob them of their function. Protein function is known to dramatically reduce as different amino acids are swapped in.

Of course this is all obvious to anyone who understands how things work. Sure, Novella may be right that there are other, unknown, solutions to life. But that isn’t suddenly going to resolve evolution’s astronomical search problem. That problem was never contingent on the life we observe being the only possible life forms possible

Novella calls himself a skeptic. In fact, he is exactly the opposite.

How the Peppered Moth Backfired

The Poster Child Became the Rebuttal

It has been called one of the best examples of evolution observed in the wild—light colored peppered moths (Biston betularia) became dark colored in response to 19th century industrial pollution darkening the birch trees in their environment. Evolving a darker color helped camouflage the moths, and keep them hidden from predatory birds. And more recently, air pollution reductions lightened the environment and with it, the moths also began to revert to their lighter color. Proof of evolution, case closed, right? From popular presentations and museum exhibits, to textbooks and scientific papers, evolutionists have relentlessly pounded home the peppered moth as an undeniable confirmation of Darwin’s theory in action. There’s only one problem: All of this ignores the science.

There are two main problems with peppered moths story. First, changing colors is hardly a pathway leading to the kinds of massive biological change evolution requires. It is not as though a change in the peppered moth coloration is any kind of evidence for how the moths evolved, or how any other species, for that matter, could have evolved.

In fact changing the color of a moth not only fails to show how species could evolve, it also fails to show how any biological design could evolve. The peppered moth case doesn’t show how metabolism, the central nervous system, bones, red blood cells, or any other biological wonder could have arisen by evolution’s random mutations coupled with natural selection.

The moths were already there. Their wings were already there. Different colors were already there. The changing of color in moth populations, while certainly a good thing for the moths, is hardly an example of evolution.

Second, research strongly suggests that the cause of the darkening, at the molecular level, is an enormous genetic insertion. In other words, rather than a nucleotide, in a gene, mutating to one of the other three nucleotides, as you learned in your high school biology class, instead what has been found is an insertion of a stretch of more than 20,000 nucleotides. That long inserted segment consists of a shorter segment (about 9,000 nucleotides) repeated about two and one-third times.

Also, the insertion point is not in a DNA coding sequence, but in an intervening region (intron), which have been considered to be “junk DNA” in the past.

This observed mutation (the insertion of a long sequence of DNA into an intron), is much more complicated than a single point mutation. First, there is no change in the gene’s protein product. The mutating of the protein sequence was the whole idea behind evolution: DNA mutations which lead to changes in a protein can lead to a phenotype change with fitness improvement, and there would be subject to natural selection.

That is not what we are seeing in the much celebrated peppered moth example. The DNA mutation is much more complicated (~20,000 nucleotides inserted), and the fact it was inserted into an intron suggests that additional molecular and cellular mechanisms are required for the coloration change to occur.

None of this fits evolutionary theory.

For example, evolutionary theory requires that the needed random DNA mutational change is reasonably likely to occur. Given the moth’s effective population size, the moth’s generation time period, and the complexity of the mutation, the needed mutation is not likely to occur. Evolution would have to be inserting segments of DNA with (i) different sequences, at (ii) different locations, within the moth genome. This is an enormous space of mutational possibilities to search through.

It doesn’t add up. Evolution does not have the resources in terms of time and effective population size to come anywhere close to searching this astronomical mutational space. It’s not going to happen.

A much more likely explanation, and one that has been found to be true in so many other cases of adaptation (in spite of evolutionary pushback), is that the peppered moth coloration change was directed. The environmental change and challenge somehow caused the peppered moth to modify its color. This suggests there are preprogrammed, directed adaptation mechanisms, already in place that are ready to respond to future, potential, environmental changes, which might never occur.

Far from an evidence for evolution, this is evidence against evolution.

So there are at least two major problems with what is celebrated as a key evidence for evolution in action. First, it comes nowhere close to the type of change evolution needs, and the details of the change demonstrate that it is not evolutionary to begin with.

Fake News From PBS on the DNA Code

Heighten Public (Mis)Understanding

Evolution, according to the highly produced PBS Evolution Project, “determines who lives, who dies, and who passes traits on to the next generation. The process plays a critical role in our daily lives, yet it is one of the most overlooked -- and misunderstood -- concepts ever described. … The Evolution series' goals are to heighten public understanding of evolution and how it works, to dispel common misunderstandings about the process, and to illuminate why it is relevant to all of us.” In other words, the PBS Evolution Project would clear away the ignorance and bring the real news of evolution. And with a long list of evolution luminaries advising the project (including Rodger Bybee, Gerald Carr, John Endler, Paul Ewald, Larry Flammer, Douglas Futuyma, Anne Houde, Les Kaufman, Joseph Levine, David Maddison, Anne Magurran, Justin Marshall, Kenneth Miller, Martin Nickels, Kevin Padian, Diane Paul, David Reznick, Helen Rodd, Chris Schneider, Judy Scotchmoor, Daniel Simberloff, Neil Shubin, Meredith Small, David Wake, and Peter Ward), we would expect nothing less. Here is what they had to say about the DNA code:

Biologically and chemically, there is no reason why this particular genetic code, rather than any of millions or billions of others, should exist, scientists assert. Yet every species on Earth carries a genetic code that is, for all intents and purposes, identical and universal. The only scientific explanation for this situation is that the genetic code was the result of a single historic accident. That is, this code was the one carried by the single ancestor of life and all of its descendants, including us.

There was only one problem: that was fake news. The DNA, or genetic, code was and is, in fact, very special. This was known at the time of the PBS Evolution Project, and since then it has only gotten worse for the evolutionists.

It is the exact opposite of how the evolutionists informed their viewers. They could not have misrepresented the science any more than they did. Because when evolutionists seek to “heighten public understanding,” and “dispel common misunderstandings,” it doesn’t mean teaching science. It means promoting evolution, in spite of the science.

Religion drives science, and it matters.

The DNA Code and Evolution

My Dear Watson

The DNA code is used in cells to translate a sequence of nucleotides into a sequence of amino acids, which then make up a protein. In the past fifty years we have learned four important things about the code:

1. The DNA code is universal. There are minor variations scattered about, but the same canonical code is found across the species.

2. The DNA code is special. The DNA is not just some random, off the shelf, code. It has unique properties, for example that make the translation process more robust to mutations. The code has been called “one in a million,” but it probably is even more special than that. For instance, one study found that the code optimizes “a combination of several different functions simultaneously.”

3. Some of the special properties of the DNA code only rarely confer benefit. Many of the code’s special properties deal with rare mutation events. If such properties could arise via random mutation in an individual organism, their benefit would not be common.

4. The DNA code’s fitness landscape has dependencies on the DNA coding sequences and so favors stasis. Changes in the DNA code may well wreak havoc as the DNA coding sequences are suddenly not interpreted correctly. So the fitness landscape, at any given location in the code design space, is not only rugged but often is a local minimum, thus freezing evolution at that code.

Observation #1 above, according to evolutionary theory, means that the code is the ultimate homology and must have been present in the last universal common ancestor (LUCA). There was essentially zero evolution of the code allowed over the course of billions of years.

This code stasis can be understood, from an evolutionary perspective, using Observation #4. Given the many dependencies on the DNA coding sequences, the code can be understood to be at a local minimum and so impossible to evolve.

Hence Francis Crick’s characterization, and subsequent promotion by later evolutionists, of the code as a “frozen accident.” Somehow the code arose, but was then strongly maintained and unevolvable.

But then there is Observation #2.

The code has been found not to be mundane, but special. This falsified the “frozen accident” characterization, as the code is clearly not an accident. It also caused a monumental problem. While evolutionists could understand Observation #1, the universality of the code, as a consequence of the code being at a fitness local minimum, Observation #2 tells us that the code would not have just luckily been constructed at its present design.

If evolution somehow created a code to begin with, it would be at some random starting point. Evolution would have no a priori knowledge of the fitness landscape. There is a large number of possible codes, so it would be incredibly lucky for evolution’s starting point to be anywhere near the special, canonical code we observe today. There would be an enormous evolutionary distance to travel between an initial random starting point, and the code we observe.

And yet there is not even so much as a trace of such a monumental evolutionary process. This would be an incredible convergence. In biology, when we see convergence, we usually also see variety. The mammalian and cephalopod eyes are considered to be convergent, but they also have fundamental differences. And in other species, there are all kinds of different vision systems. The idea that the universal DNA code is the result of convergence would be very suspect. Why are there no other canonical codes found? Why are there not more variants of the code? To have that much evolutionary distance covered, and converge with that level of precision would very strange.

And of course, in addition to this strange absence of any evidence of such a monumental evolutionary process, there is the problem described above with evolving the code to begin with. The code’s fitness landscape is rugged and loaded with many local minima. Making much progress at all in evolving the code would be difficult.

But then there is Observation #3.

Not only do we not see traces of the required monumental process of evolving the code across a great distance, and not only would this process be almost immediately halted by the many local minima in the fitness landscape, but what fitness improvements could actually be realized would not likely be selected for because said improvements rarely actually confer there benefit.

While these problems obviously are daunting, we have so far taken yet another tremendous problem for granted: the creation of the initial code, as a starting point.

We have discussed above the many problems with evolving today’s canonical code from some starting point, all the while allowing for such a starting point simply to magically appear. But that, alone, is a big problem for evolution. The evolution of any code, even a simple code, from no code, is a tremendous problem.

Finally, a possible explanation for these several and significant problems to the evolution of the DNA code is the hypothesis that the code did not actually evolve so much as construct. Just as the right sequence of amino acids will inevitably fold into a functional protein, so too perhaps the DNA code simply is the consequence of biochemical interactions and reactions. In this sense the code would not evolve from random mutations, but rather would be inevitable. In that case, there would be no lengthy evolutionary pathway to traverse.

Now I don’t want to give the impression that this hypothesis is mature or fleshed out. It is extremely speculative.

But there is another, more significant, problem with this hypothesis: It is not evolution.

If true this hypothesis would confirm design. In other words, a chemically determined pathway, which as such is written into the very fabric of matter and nature’s laws, would not only be profound but teleological. The DNA code would be built into biochemistry.

And given Observation #2, it is a very special, unique, detailed, code that would be built into biochemistry. It would not merely be a mundane code that happened to be enabled or determined by biochemistry, but essentially an optimized code.

Long live Aristotle.

The problem is there simply is no free lunch. Evolutionists can try to avoid the science, but there it is.

Michael Skinner on Epigenetics: Stage Three Alert

Over the Top Lies

Readers here will know that Darwin’s God has covered the topic of epigenetics extensively for many years now, and so we were interested to read Michael Skinner’s Aeon article on this subject, which appeared last week. Skinner’s piece reminds us of the old maxim that truth passes through three stages. First, it is ridiculed. Second, it is violently opposed. Third, it is accepted as being self-evident. If we can slightly modify these three stages as follows, then we have the history of how evolution has struggled and opposed the scientific findings we now refer to as epigenetics:

1. Reject and persecute
2. Delegitimize and minimize
3. Rename and incorporate

Skinner’s position represents the move, which has been taking place in recent years, into Stage 3 (for example, see here).

Skinner’s Aeon article provides an excellent rundown of findings, both old and new, that confirm and elucidate what evolutionists have aggressively and violently opposed for a century: that epigenetics is not only real, but significant in causing long-term biological change. Natural selection plays no role in this process.

From 18th century observations of plants adapting to hotter temperatures, to Conrad Waddington fruit fly experiments in the 1950s (for more tidbits see here), to more recent observations of a range of species, Skinner provides an accessible summary and makes the inescapable conclusion:

Much as Lamarck suggested, changes in the environment literally alter our biology. And even in the absence of continued exposure, the altered biology, expressed as traits or in the form of disease, is transmitted from one generation to the next.

Much as Lamarck suggested? That is an astonishing admission given how evolutionists have, in the past century, vilified Lamarck and anyone who would dare associate with his ideas. And to this day such resistance continues, but it is waning. Hence evolutionists such as Skinner can broach the truth.

Skinner also comes clean on the problem that evolution’s basic source of biological variation, DNA mutations, is insufficient:

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

Mutations are too slow for evolution? Again, this is an astonishing admission. The last time mathematicians reported this inconvenient truth they were told by evolutionists that it didn’t matter because, after all, we all know that evolution is true. Nothing like contradicting the science. Skinner admits that a paradigm shift is needed.

Unfortunately for Skinner and his readers that is where the light ends and smoke begins. Qua evolutionist, Skinner must present this contradictory biology as, somehow, consistent with evolution. The first sign that Skinner will firmly plant himself in the Stage Three lie (Rename and incorporate) is the opening sentence:

The unifying theme for much of modern biology is based on Charles Darwin’s theory of evolution, the process of natural selection by which nature selects the fittest, best-adapted organisms to reproduce, multiply and survive.

Evolution is the unifying theme for much of modern biology? This not so secret handshake is such an over-the-top misrepresentation that it hardly seems worthwhile to dignify it with a rebuttal. Given how evolutionists are consistently surprised by biology, one would hope they at least could stop with this lie. But there it is.

Unfortunately it doesn’t stop there. Skinner’s next Big Lie, and the thesis of his article, is that the long rejected epigenetics will now fit conveniently into evolutionary theory. It was all a big misunderstanding and rather than rejecting epigenetics, we should see it as merely another component in the ever increasingly complex theory called evolution.

This is Stage Three: Rename, recast, retool, reimagine, and incorporate the new idol into our modern-day Epicureanism.

With enough massaging and story-telling evolutionists will forget the contradictions and convince themselves, and their fawning audiences, that the fit is perfect and epigenetics is, in fact, yet more proof of evolution.

There’s only one problem. This is all absurd.

What Skinner and the evolutionists won’t tell you is that all of this makes no sense on their theory. With epigenetics the biological variation evolution needs is not natural. It is not the mere consequence of biophysics—radiation, toxins or other mishaps causing DNA mutations. Rather, it is a biological control system.

It is not simple mistakes, but complex mechanisms.

It is not random, but directed.

It is not slow, but rapid.

It is not a single mutation that is selected, but simultaneous changes across the population.

This is not evolution.

And as Skinner inconveniently realizes, such epigenetics are found across a wide range of species. They are widely conserved and, for evolution, this is yet more bad news. It means the incredible epigenetics mechanisms must have, somehow, arisen very early in the history of evolution.

What the evolutionists will never admit is that epigenetics contradicts evolutionary theory. Not only must such incredibly complex mechanisms have evolved early on, and not only must they have arisen from chance mutation events, and so not only must evolution have created evolution, but they would have persisted in spite of any fitness advantage.

The whole idea behind the evolution mythology is that natural selection saves the day by directing the blind, chance mutations. Setting aside the silliness of this idea which we have discussed many times, the problem with epigenetics is that if they were to arise from chance mutations (and “oh what a big if”), they would not increase the organism’s fitness.

Epigenetics mechanisms are helpful at some future, unknown, time when the environmental challenge finally presents itself. They are useless when they initially arise, and so would not be preserved by evolution’s mythical natural selection.

Of course evolutionists will contrive yet more complex, silly, just-so stories about how epigenetics mechanisms arose from pre existing parts used for other purposes (the ridiculous co-adaptation argument), and about how they just happened to provide some other functions so as to improve fitness.

Skinner’s presentation of how to integrate epigenetics with evolution is entirely gratuitous. He has empirical evidence for the former, and religious dogma for the latter. There is no scientific need for the addition of evolution—it is a multiplied entity and is gratuitous. But Skinner needs it.

These are all the usual lies, which will be trotted out as yet more “facts.” Evolutionists must tell these lies. Otherwise they would have to move beyond Stage Three, and admit the science contradicts the theory.

And that is not going to happen. Old scientists don’t change their minds, they just die.

Religion drives science, and it matters.

Tim Ingold’s Question For Andy Gardner Says It All

A Not So Hidden Agenda

Anthropologist Tim Ingold’s question for Andy Gardner at last week’s “New trends in evolutionary biology” Scientific meeting at The Royal Society should disabuse those who still don’t get it. Gardner had finished his talk, “Anthropomorphism in evolutionary biology,” in which he acknowledged the design in biology. But if Gardner's organisms are actually designed, an agitated Ingold demanded, then how would Gardner’s explanation for their origin be any different from William Paley’s natural theology which invoked design?

Anyone who has interacted with evolutionists knows this moment all too well. The metaphysics and religion are always there for evolutionists, crouching at the door and ready to strike at any moment. Whether in lecture, seminar, or writings, the agenda is painfully obvious. As Eva Jablonka put it, “Not God—we’re excluding God.”

Evolution isn’t about the science—it never was. It doesn’t matter what the science shows, evolution must be true. Religion drives science, and it matters.

Here’s That Study That Found Pseudo-Pseudogenes

Evolution is Getting Demolished

It is one of the strongest arguments for evolution: dysteleology, the apparent lack of design in the biological world. And the most obvious and compelling examples of such dysteleology are in the genome. And the most celebrated examples of dysteleology in the genome are the pseudogenes—genes which are broken. They are the long since abandoned junk of the genome. And the most obvious example of such brokenness is a stop codon that has accidentally arisen somewhere in the middle of the gene. These so-called premature termination codons (PTCs) halt the production of proteins in mid-stream. And the most abundant source of pseudogenes is the olfactory receptor families—genes involved in detecting odors. All those pseudogenes are a sure sign that no designer worth his salt would have constructed such a world. Evolution must be true, as evolutionists from Charles Darwin to Jerry Coyne have proclaimed. There’s only one problem—such examples of junk always turn out to be false.

At evolution’s foundation is the claim of lack of function, and that is a terrible argument. First of all, it is metaphysical rather than scientific. It is not a positivist argument—evolutionists have no idea how genes, or anything else for that matter—actually evolved. The argument is that such nonfunctional structures would never have been designed or created. That conclusion does not come from science, and cannot be tested by science. It is a religious argument.

But in addition to the metaphysics, showing that a structure has no function makes no sense to begin with. For one would have to watch the structure, in the organism, for the entire life of the organism. And one would have to be able to measure function—all possible functions. Needless to say, no evolutionist has ever done that.

But it gets worse.

Not only is the dysteleology argument religious and nonsensical, it is also false. At least in the cases that have been investigated. Over and over, the long lists evolutionists make of nonfunctional structures just get shorter and shorter.

That brings us to pseudogenes.

For sometime it has been known that not all pseudogenes are pseudogenes. That is, not all pseudogenes are junk. Some pseudogenes have been found to be performing useful functions. But typically these are onesies, twosies.

Now, a new study has found something more interesting—a PTC in an olfactory receptor pseudogene that, in certain contexts, is not actually a termination codon after all. The gene has a stop codon, and yet the gene is successfully used to create a protein. The translation process somehow can read-through what normally would be a stop codon. The paper suggests this is accomplished with a near-cognate tRNA, which inserts an amino acid rather than causing a halt:

We suggest that read-through is due to PTC recognition by a near-cognate tRNA that allows insertion of an amino acid instead of translation termination.

What appeared to be a pseudogenes is actually functional. It is a pseudo pseudogene.

Furthermore, and importantly, this is not an isolated case. They found other examples, and conclude this could be a “widespread phenomenon.”

Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes. … We identify functional PTC-containing loci within different olfactory receptor repertoires and species, suggesting that such “pseudo-pseudogenes” could represent a widespread phenomenon.

Widespread phenomenon? This adds yet more support to the Project Encode suggestion, which evolutionists immediately pushed back on, that most of the genome is functional rather than junk as evolutionists had insisted (for example, see here, here, and here).

Pseudogenes comprise only a small fraction of the genome, but they have served as the poster child of junk DNA, and proof of evolution.

Instead, once again history appears to be reliable guide as pseudogenes appear to be going down the same path as those other supposedly “nonfunctional” structures. Instead of nonfunctional, pseudogenes are beginning to look like they may have a rather sophisticated function that was not apparent to evolutionists.

Of course function is often not apparent to evolutionists because they view biology as an accident. Organisms are built on a vast number of chance events so of course they will be found to be full of mistakes.

But in its inexorable march of progress, science always seems to find function. Evolution seeks lack of function, which makes no sense, and science just keeps on finding more function. Evolution and science, it seems, are in an eternal conflict.

Don’t expect contriteness anytime soon though. For evolutionists, the finding of function was never a problem. It simply is an example of evolution finding function for what was nonfunctional. The junk was repaired and took on some new function. In fact, it remains powerful evidence for evolution because it is obviously so quirky. When the supposedly “backward” retina of the mammalian eye was found to be incredibly sophisticated, evolutionists didn’t miss a beat. After all, it was still a kludge of a design. As Richard Dawkins put it, “it is the principle of the thing that would offend any tidy-minded engineer!”

So it really doesn’t matter how much function is found, and how optimal a design is. For man has found nature to be wanting, and so it must have formed by chance. This, in a nutshell, is Epicureanism.

Religion drives science, and it matters.

BioLogos: A New Book By Dennis Venema

Who Was Adam?

In Dennis Venema’s new book, Adam and the Genome, coauthored with Scot McKnight and available in January, readers will be told that evolution is a well-supported, scientific theory. The publisher explains that the authors “address up-to-date genomics data with expert commentary.” But unless Venema has dramatically changed his views, what readers will find is a series of misrepresentations, turning the evidence upside down in order to prove evolution. See, for example, my reviews of several of Venema’s flawed articles (here and here).

The BBC on Evolution: Chris Stringer Puts the Hammer Down

Right There in the Mirror

British anthropologist Chris Stringer of the Natural History Museum in London, a leading proponent of the “Out of Africa” hypothesis, is by any measure a leading light amongst evolutionists. And so not surprisingly religion drives his thinking. He made that clear in Chris Baraniuk’s article for the BBC about why evolution is a fact. As Baraniuk writes:

By comparing how many genes organisms share, we can figure out how they are related. For instance, humans share more genes with apes like chimps and gorillas than other animals, as much as 96%. That suggests they are our closest relatives.

"Try to explain that in any other way than the fact that those relationships are based on a sequence of changes through time," says Chris Stringer of the Natural History Museum in London. "We have a common ancestor with chimpanzees, and we and they have diverged since then from that common ancestor."

In other words, according to Stringer, genetic similarities between humans and apes cannot be explained in any way other than evolution. This sentiment, which runs all through evolutionary thought, is not scientific, it is metaphysical.

Stringer and the evolutionists insist that there is no explanation, other than evolution, for similarities we observe between species, such as the high genetic similarity between humans and chimpanzees.

And since there is no explanation, other than evolution, then we must conclude that “We have a common ancestor with chimpanzees.”

That must be the conclusion.

But this claim makes reference to the set of all possible explanations. You’ve got evolution, and then you’ve got all the others.

This means that Stringer and the evolutionists must have knowledge of all those explanations. All possible theories of origin are known to them.

Creationism comes to mind, but of course there could be different versions of creationism. And of course there could be other theories still.

A scientist, qua scientist, cannot have such knowledge. This is why Mr. Nelson was so careful to teach you in seventh grade science class that “The Scientist” works from observation to hypothesis to prediction to experiment. Scientists deal with hypotheses and theories, which they deduce and test.

They don’t make all-encompassing truth claims. The claim that Theory A explains Observation B is scientific. The claim that no theory except Theory A explains Observation B is metaphysical. A slight change in the language makes an enormous difference in the claim.

One is scientific, one is religious.

But it gets worse.

Because, as stated above, Stringer and the evolutionists are making claims about creationism. Stringer’s point is that God would not create genomes with so much similarity. This claim traces back to the Principle of Plenitude. That is the label that historian Arthur Lovejoy gave to a long running religious tradition in the history of thought about, simply put, how God would design the world.

The Principle of Plenitude is very much with us today, as much as it was with Plato, Anselm, Bruno, and Leibniz.

Evolutionists aren’t merely making some vague claims about colored marbles in an urn. They are making very specific claims about what God would and would not do.

That’s religious.

But it gets worse.

Not only are Stringer and the evolutionists driven by religious sentiment, but it forces them into a completely untenable position. If you genuinely want to test theories against the evidence, it is evolution that fails. In this case we’re talking about the comparisons between the species. How are they similar, and how are they different?

And these data demolish evolutionary theory.

The data do not fit the evolutionary model, not even close. One way to measure this is with the so-called consistency index, which consistently shows, pun intended, no consistency. The observables are closer to the random “null hypothesis” model than to the evolution model.

So while evolutionists criticize the skeptics for being religiously-driven, anti-science, smuggling metaphysics into science, and insisting on terrible theories, all those criticisms are, actually, right there in the mirror.

Religion drives science, and it matters.

The Big Day Has Finally Arrived

What Will The Decision Be?

After years of battling and debating, we have finally reached the big day with its big decisions. Tensions are running high as the old-guard status quo battles the radical new ideas—it is the “New Trends in Evolutionary Biology” meeting at the Royal Society where evolutionists are finally reckoning with the science which makes no sense on the theory. The problem is that species adapt not according to the random mutations coupled with natural selection, but according to mechanisms that respond directly to the environment. The Big Day Has Finally Arrived.

Ross Pomeroy Reminds us of P-Value Problems

But it is Much Worse

Ross Pomeroy’s article in yesterday’s Real Clear Science was a much needed reminder about the dangers of statistical hypothesis testing. But while Pomeroy rightly points out important problems, particularly with the so-called P-value, out here on the ground, the problem is much worse.

One of Pomeroy’s several legitimate concerns is the use of what is essentially a default value of 0.05 for P. Too often scientists don’t realize that, as David Colquhoun has pointed out, this will lead to false conclusions at least 30 percent of the time. Pomeroy also points out the common fallacy of interpreting the P value as the probability that the null hypothesis is true.

The result of such mishandling of hypothesis testing is that, “Quite simply, a large amount of published research is false.”

Would that it would end there. Unfortunately, when it comes to evolutionary studies, fixing these problems is like rearranging the deck chairs on the Titanic. These concerns about selecting a good alpha value and understanding the nuances of what P actually means, while important, pale in comparison to a much larger infraction: using the P-value to mask what is, in fact, a strawman argument.

One of the key, underlying, assumptions in using the P-value is that there are only two alternatives, the null and alternative hypotheses. These two hypotheses must be complementary—they must be distinct, mutually exclusive, and exhaustive. In other words, one of them must be true, and the other must be false. They cannot both be true, or both be false. They cannot overlap, and there can be no other possibilities.

And while such a perfect pair of hypotheses is possible in simple academic problems such as colored marbles in an urn, real world problems often are more complicated. Take something as seemingly simple as the question of whether or not it will rain today. Is it not binary? Either it will rain, or it will not rain. Right?

Well no. The weather has a multitude of complexities. It is spatially and temporally varying, with an infinite degree of variation. What if it sprinkles? What if the rain evaporates before it reaches the ground? How do you define the time and location? What if it rains in one location but not another?

What the P-value, and its null hypothesis, allows is for trivial null hypotheses to be erected and easily knocked down like strawmen, thus “proving” ones favored explanation.

The BBC on Evolution: It Just Gets Worse

“The Convictions of a Monkey’s Mind”

The previous post reviewed Chris Baraniuk’s article for the BBC about why evolution is such a great theory (“one of the greatest theories in all of science”), a fact, and so forth. The post showed how terrible the evidence is for evolution. In a sense, evolutionists themselves provide the most powerful critique of their theory. Just listen to their own explanations of why it is a fact. But there is more to the story. It gets worse because, well, that previous post didn’t cover Baraniuk’s complete article. That previous post only looked at part of Baraniuk’s article. It only looked at those parts of Baraniuk’s article that at least made some sense.

After discussing Richard Lenski’s long term experiment (LTEE), Baraniuk steps back to discuss the role of genes in evolution. Here is what he has to say:

Over the last century scientists have catalogued the genes from different species. It turns out that all living things store information in their DNA in the same way: they all use the same "genetic code".

What's more, organisms also share many genes. Thousands of genes found in human DNA may also be found in the DNA of other creatures, including plants and even bacteria.

These two facts imply that all modern life has descended from a single common ancestor, the "last universal ancestor", which lived billions of years ago.

So, to paraphrase, we have two premises and a conclusion. The premises are:

P1: All living things store information in their DNA in the same way.
P2: Organisms also share many genes.

And the conclusion is:

C1: All modern life has descended from a single common ancestor.

It would be wrong to say this is a false claim. When we say that someone has made a false claim, the implication is that, while wrong, there was at least some logical reasoning present, some logical thread to follow. A false claim is a claim that starts with some evidence and in the process of getting to the conclusion, fouls up in some sort of an observable way. There was a stumble in an otherwise, at least somewhat, logical train of thought. We can at least see what the fellow was getting at. We can sympathize a bit, and reconstruct his attempt, and fix if for him, at least as best as we can. It may still be a hopeless argument, but at least we can see where he was going.

For the evolutionist there is no train of thought—no logical reasoning present. It is closer to, ironically, what Darwin described as “the convictions of a monkey's mind.”

It is complete gibberish.

To say that the conclusion C1 above does not follow from the premises P1 and P2 would be like saying your pet dog failed to beat you at chess when all he did was barf all over the board. Your dog not only failed to beat you, he didn’t even play the game.

It is not that evolutionists make a few mistakes here and there in an otherwise well thought out attempt. It is that they completely fail to provide anything remotely resembling a scientific argument for their Epicurean conviction that the entire biological world (and everything else for that matter), arose by itself.

Religion drives science, and it matters.

The BBC on Why Evolution is Fact

A Series of Mistakes That Build Up

Last year science writer Chris Baraniuk wrote an article for the BBC that began with this: “Evolution is one of the greatest theories in all of science.” Baraniuk quoted liberally from several leading evolutionists, such as Steve Jones, Nancy Moran, Richard Lenski, and Chris Stringer, and he discussed the work of several others. The purpose of the article was to explain how we know evolution is a fact, as evolutionists claim. And by “fact,” evolutionists are not trying to apply a nuanced or artful spin to their claim. Quite the opposite, by “fact” evolutionists intend that their idea is beyond all reasonable doubt. Baraniuk well explains the claim:

For scientists, evolution is a fact. We know that life evolved with the same certainty that we know the Earth is roughly spherical, that gravity keeps us on it, and that wasps at a picnic are annoying.

Baraniuk appropriately reflects the certainty of evolutionists.

Baraniuk also makes several other good points. For instance, he doesn’t shy away from the heroic levels of Darwin’s idea. Baraniuk explains that under evolution humans must be descended from worms—an ancestor with more biblical allusions than Wilberforce’s “mushrooms.” Either way, such examples quickly reveal the sheer magnitude of the claim. It is, as Wilberforce winsomely put it, a “most unsuspected cousinship.”

Natural selection as creator

It is all the more unsuspected today given that it is supposed to have occurred by strictly random mutations. Natural selection, in contradistinction to how it often is presented, does nothing to induce these mutations. Selection doesn’t guide the evolutionary process like a Plastik Nature, it merely kills off the lesser designs. Death, in evolutionary theory, becomes the engine of progress and here Baraniuk correctly understands that selection “weeds out” those lesser organisms, but Baraniuk unfortunately also slips in the requisite teleological cover, stating that much of evolution is “driven by natural selection”:

Descent with modification, which is caused by random mutations in genes, ultimately leads to gradual changes and the formation of new species – much of it driven by natural selection, which weeds out those organisms that are less suited to their environments.

But evolution is not “driven by natural selection,” it is driven by random mutations. Their metaphysics require a random creation narrative, but for public consumption—and their own sanity—evolutionists quickly replace chance with natural selection.

Everyone knows that the Epicureans’ randomly swerving atoms—or randomly mutating nucleotides, as evolutionists would have it two thousand years later—do not a world create. Chance doesn’t work. Random mutations do not create millions of species, let alone a single protein. And so not too surprisingly evolutionists fall back on Aristotle’s teleological, goal-oriented, narrative. Natural selection is said to “drive” the evolutionary process. (You can see examples here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here, here,)

Darwin’s genius, if such banality can be described as genius, was in his formulation of natural selection as a concept that would simultaneously allow for the needed chance while providing the needed direction.

Natural selection was the director. Endless just-so stories have been told since 1859 about how natural selection drives the evolutionary process and its resulting biological wonders, producing X for the purpose of Y. But like the Emperor’s new clothes, it was all a fiction. Natural selection does not “drive” anything. A more accurate image is that of a weed out mechanism. Natural selection, stripped of its teleological gloss, merely kills off the failed or less prolific designs, leaving the more prolific designs as the evolutionary winners.

But stripping natural selection of the smuggled in Aristotelianism leaves the evolutionary process with nothing but those random mutations to create the species. Every organism, every structure, and every metabolic pathway, must have been constructed by an unimaginably long series of strictly random events occurring in an unimaginably high-dimensional design space. The curse of dimensionality, and the rugged, flat, fitness landscape both conspire to make clear what was obvious to the Stoics—this is absurd.

Baraniuk doesn’t understand this and his evolution informers have left him none the wiser. Baraniuk rightly explains that natural selection “weeds out those organisms that are less suited to their environments,” but he then applies the same old teleological gloss when he informs his readers that much of the evolutionary process is “driven by natural selection.”

The creature discovers the creator

An interesting consequence of evolutionary theory is that not only did it create the species, but it created a species which, in turn, discovered evolution. That is, evolution created a biological world including humans who eventually repaid the favor by discovering their chance creator. Baraniuk explains:

Given enough time, these changes mount up and lead to the appearance of new species and new types of organism, one small change at a time. Step by step, worms became fish, fish came onto land and developed four legs, those four-legged animals grew hair and – eventually – some of them started walking around on two legs, called themselves "humans" and discovered evolution.

But this doesn’t make sense. For if humans are the creation of a randomized world of matter and motion, then the result is no better. We are simply the result of a big long chemical experiment where the products have a lower free energy than the reactants. Our minds—which evolutionists will explain as nothing more than an emergent property which deceives us into thinking that our consciousness is something real and distinct from the moving molecules encased in our skulls—would have no knowledge of truth. In fact they would have no knowledge, period. It would be remarkable bit of luck if those moving molecules happened to formulate thoughts corresponding to reality. As Darwin stated in a letter:

But then with me the horrid doubt always arises whether the convictions of man's mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey's mind, if there are any convictions in such a mind?

This is one of the greatest own-goals of all time. Darwin’s point was that we should not trust the conclusion that chance is an insufficient creator. But the Sage of Kent was apparently oblivious that his argument was simultaneously circular and devastating to his own theory. If we are created rather than evolved from the lower animals, then Darwin’s “horrid doubt” is erased and poses no problem for creation. Yet if we are not created but rather evolved, then Darwin’s argument demolishes his own theory. As usual, the evolutionist’s criticism points right back at himself.

The evidence

It’s downhill from there as Baraniuk presents the scientific evidence for this new brand of Epicureanism. For example, Baraniuk’s survey of the fossil evidence, aided and abetted by Steve Jones, is a case study in fallacies. There is the equivocation that “the fossil record makes it clear that life has changed over time,” and the false history, from Steve Jones, that Darwin “knew that [the fossil record] was an irrefutable case that evolution had taken place.” (Darwin mostly apologized for the fossils which clearly showed abrupt appearance). And while Baraniuk correctly explains that the fossil record is characterized by the wrong pattern and so must be viewed as full of gaps:

The fossil record is only so much help here, because it is incomplete. "If you look at most fossil records, what you actually see is one form that lasts quite a long time and then the next bunch of fossils that you've got is quite different from what you had before," says Jones.

Baraniuk nonetheless claims that transitional fossils have more or less filled the gaps (they haven’t).

Baraniuk next presents the mandatory poster-child example of Darwin’s Finches, dramatically misrepresenting the evidence, which shows rapid, directed response to environmental challenges—the opposite of what evolution expects.

Baraniuk then moves on to Richard Lenski’s long-term evolution experiment (LTEE) at Michigan State University, an experiment which for several decades has revealed how little change comes about in laboratory bacteria, E. coli. The biggest observed change was the utilization of citrate in aerobic conditions (normally E. coli utilizes citrate only in anaerobic conditions). That adaptation has been represented as an important example of evolutionary change observed in the laboratory. Unfortunately Baraniuk swallowed it and the result is more pseudoscience.

Baraniuk informs the reader that E. coli cannot digest citrate (false, it cannot digest citrate under certain conditions), and that the observed change represented “a huge leap forward” and “radically new abilities.”

These are ridiculous pseudo science lies.

Evolutionists want so badly for evolution to be true they will pervert science to make their case. Baraniuk also explained that “This would be like humans suddenly developing the ability to eat tree bark.” That is an absurd analogy. E. coli expanding its citrate utilization to include aerobic conditions is nowhere close to humans developing the ability to eat tree bark. Statements such as these reveal an agenda rather than a search for truth.

In fact it is worth mentioning that this same, minor, adaptation has been observed to occur in a matter of weeks (this was not fully appreciated until after Baraniuk’s article). Lenski has tried to dismiss those findings as inconsequential because three weeks were required rather than merely a day or two:

While that’s a lot faster than 15 years, it’s still much longer than typical “direct selections” used by microbiologists where a readily accessible mutation might confer, for example, resistance to an antibiotic after a day or two.

This is an astonishing statement. Lenski did not elaborate on why three weeks versus two days is an important distinction because, well, it isn’t. What these short term experiments suggest is that E. coli can expand its citrate utilization using mechanisms other than evolution’s random mutations. Instead, it looks to be yet another example of directed adaptation—exactly the opposite of what evolution expects. The fact that E. coli can develop aerobic citrate utilization in a matter of weeks rather than years renders Lenski’s LTEE finding a big fat “So what?”

Lenski attempted to cast this LTEE finding as a significant evidence of evolution in action. This is not true simply because the magnitude of the change is tiny (an existing capability was now enabled when it ordinarily would be disabled). Beyond this, the fact that the change can occur in weeks further negates the claim of evolutionary significance. What Lenski and evolutionists should be asking themselves is not “How can we ignore this finding?”, but rather, “How did organisms, such as E. coli in this case, get the ability to respond directly to environmental challenges?” This makes no sense under evolution.

It also confirms another lesson.

Whenever adaptation is observed in a living organism, it should not simply be assumed it is due to the evolutionary concept of random mutations and natural selection. This view has failed repeatedly as so many adaptations have been found to be not due to the action of chance events, but directed mechanisms responding to the environment. This is yet another example of how evolutionary expectations have failed, and failed badly. It is inappropriate to interpret adaptations in living organisms as signs of evolution in action, yet evolutionists continue to do this.

Lost function

One example of change is apparent lost function. These are terrible evidences for evolution because evolution requires new functions to be created. The losing of existing functions does nothing to resolve the basic conundrum that evolutionists struggle with: How could biology’s wonders have evolved? Yet evolutionists, in a sign of how weak the evidence is, consistently resort to these examples of lost function, such as cave animals losing their vision, as one of their key evidences. Not surprisingly, but unfortunately, Baraniuk follows along, aided by Nancy Moran:

"It really shows the process of evolution," says Moran. "It's not all just adaptation and things getting better, there's also this big potential for things to get worse."

This is pathetic. Evolution has failed to show how the species and their many designs could have evolved, yet they claim the loss of such complex functions is evidence for evolution.

Baraniuk’s article is yet another good example of how ludicrous evolution is. Evolution is nothing more than our modern-day Epicureanism, and it is pathetic. Perhaps the best explanation for evolution comes straight from the evolutionist himself:

"That's what evolution is," says Steve Jones of University College London in the UK. "It's a series of mistakes that build up."

Of course what Jones means here is that the evolutionary process is the accumulation of a series of mistakes. That alone reveals the scientific absurdity. And so, a more accurate interpretation of Jones’ statement is the it is not the process of evolution, but the theory of evolution, that is a “series of mistakes that build up.”

So true.