Monday, October 14, 2019

The Functional Advantages of Protein Oligomerization

Evolution Creates Evolution

As I have discussed many times, a single, run-of-the-mill, protein is beyond evolutionary explanation. The fitness landscape in protein sequence space is typically rugged, with occasional spikes representing protein designs. The resources required to evolve even a relatively simple protein exceed what evolution has available by at least 27 orders of magnitude. And that is generous as it comes from studies done by evolutionists. But proteins cause many more problems for evolution beyond their initial origin. For instance, something like a third of proteins form oligomers—protein machines consisting multiple subunits that bind together. Hemoglobin, for example, consists of four units, two alpha chains and two beta chains. Each chain is roughly 140 amino acids long. Michael Behe showed in his book The Edge of Evolution that the origin of simply the oligomeric interfaces is beyond evolutionary explanation. But again, the problems do not stop there. Even if evolution could somehow oligomerize proteins, what would happen then?

Oligomers may be homogeneous, consisting of repeats of the same subunit, or they may be heterogeneous, consisting of different subunits. Either way, it is unlikely that if evolution were somehow get lucky and not only construct proteins, but oligomerize them, that some great new function would arise. If so, it would represent a great amount of serendipity, for the new function would have been a lucky result. Imagine combining a few shovels to get a windmill.

But if there was no new function, then what would be the value of the new oligomer? The problem is not that evolutionists have no idea, but rather that they have too many ideas, none of which make sense. Here are six potential functional advantages that oligomerization may confer, as summarized in a review paper:

(1) More complex scaffolds may better support function, for example, by the introduction of a new active site at the interface between subunits. It has been estimated that roughly one sixth of oligomeric enzymes has an active site located at the inter-subunit interface.
(2) Oligomeric proteins can be allosterically regulated, introducing an additional level of control.
(3) There is a greater likelihood of an error-free transcript in a shorter protein sequence. A large protein composed of multiple, short, subunits, is more likely to be synthesized without errors than a single chain protein of comparable size.
(4) Where the monomer and oligomer differ in activity, additional regulatory flexibility may be achieved by regulating the conditions of oligomerization.
(5) Oligomeric proteins may be subjected to amplified evolutionary pressures, as deleterious mutations may be more pronounced and thus removed sooner from the gene pool. Conversely, the advantages of beneficial mutations may also be made evident sooner.
(6) Larger proteins are more resistant to degradation and denaturation. Indeed, an increase in oligomerization state is one of the protein stabilization strategies observed in thermophilic organisms.

Evolutionists are deeply wedded to teleological thinking. They have also constructed a theory full of serendipity. This summary is an example of both these trends, which often go together.

These six functional advantages imagined by evolutionists do not represent immediate improvements. For example, the second entry states that “oligomeric proteins can be allosterically regulated, introducing an additional level of control.” But immediately upon oligomerization, there would be no such regulation.

In fact, that is a generous understatement. For the evolution of allosteric regulation is far beyond evolution’s resources. The point here is that these imagined functional advantages of oligomerization call for an enormous helping of serendipity. Evolution creates X, which then enables some later evolutionary step to be taken. In this case, oligomerization is supposed to have assisted in the evolution of allosteric regulation.

Or again, the fifth entry states that “oligomeric proteins may be subjected to amplified evolutionary pressures.” Forget about the possible instabilities this could introduce, it apparently makes for a superior evolutionary process. So again, we have evolution constructing X, which then makes for better evolution. In short, evolution creates evolution.

Religion drives science, and it matters.

Sunday, October 13, 2019

Nathan Lents in USA Today: Evolution is Certain

Darwin’s Dangerous Idea

In a recent USA Today opinion piece evolutionist Nathan Lents states that the human race has “evolved through a long line of ancestry that connects with all other living things going back nearly 4 billion years.” And if there was any doubt, Lents later clarifies that it is “the undeniable scientific truth that the human population evolved from ancestor ape species and shares common descent with all living things.” Simply put, Lents is stating that evolution is an undeniable scientific truth.

This claim of high certainty is nothing new. From the Epicureans in antiquity, to their modern descendants, mandates of a strictly naturalistic origins have consistently been foisted with no less confidence. Lents’ certainty is the rule, not only for today’s evolutionists, but in the long history of Epicurean thought.

One immediate sign of trouble is that such claims of certainty are inevitably in conflict. For example, proponents of monergistic and synergistic theories of the origin of the Solar System (where the Sun and planets formed simultaneously or in sequence, respectively), were both certain their theories were correct. But they cannot both be right. As Dire Straits put it, “Two men say they’re Jesus, one of them must be wrong.”

Lack of detail is another sign of trouble. How can we be certain of theories which gloss over a host of details, and really are little more than just-so stories?

But it gets worse. For inevitably, such claims of certainty are made about theories that make little scientific sense. Daniel Bernoulli was certain the solar system resulted from the solar atmosphere forcing the planets into the ecliptic. Bernoulli was a brilliant scientist, but in this case, not so much. The irony is that he chose to express absolute confidence in what was undoubtedly the biggest blunder of his career.

It is no different with evolutionists today. They are absolutely certain, but their certainty is exceeded only by their inability to defend their theory. Evolution has left a trail of failed predictions. And with each failure the theory becomes more contorted, complex, and mysterious. There is no explanation, beyond mere hand-waving, of how the entire biological world is supposed to have arisen by itself—spontaneously. The idea is a scientific failure.

All of this leads to the inevitable question of why. Why do Lents and the epicureans make such claims? Surely they must know better.

Indeed they do know better, or at least should know better. There simply is no question that Lents and his fellow evolutionists are aware of the science. In a very real sense they are without excuse. They massively misrepresent the science, and it is tempting to brand them as liars and be done with it. And indeed, in a sense they are liars—they make ridiculously false claims and they know it. Given their training and experience, there simply is no way they could be innocently na├»ve of the basic scientific facts they so consistently contradict with complete assurance.

But to stop there would superficial. Anyone who knows evolutionists knows they do not easily fit into the liar category. To begin with, evolutionists really do believe what they say. A liar makes statements he knows are false.

So how can evolutionists understand the science and yet believe evolution is true? The answer is a long story but, suffice it to say, it is a story about religion. What we are dealing with here is much more complicated than a simple lie. And much more dangerous.

Religion drives science, and it matters.

Sunday, April 28, 2019

Satellite DNA is Essential and Species-Specific in Drosophila melanogaster

Seems Incompatible

This week’s “we thought it was junk but it turned out to be crucial” study comes with the added bonus that the so-called “junk” is also species-specific / taxonomically restricted. The general topic is tandemly repeated satellite DNA in the much studied fruit fly, Drosophila melanogaster. These satellite DNA regions comprise 15-20% of D. melanogaster’s genome, and one of the regions, AAGAG(n), is transcribed across many of D. melanogaster’s cell types.

While evolutionists have hoped and argued that transcription (not to mention mere presence) does not imply function (after all biology is one big hack-job, so RNA polymerase doesn’t always know what it is doing), D. melanogaster is once again not cooperating. Not only is the satellite DNA ubiquitous and widely transcribed, the AAGAG RNA was found to be important for male fertility. Kind of important.

But it gets worse. Much worse.

Not only is D. melanogaster’s satellite DNA ubiquitous, widely transcribed across many cell types, and of crucial importance, it is species-specific. The levels of AAGAG satellite DNA is orders of magnitude lower in D. simulans and D. sechellia, and nearly absent in other species within the Drosophila genus.

This makes no sense on evolution. Now we must say that not only does a massive quantity of AAGAG satellite DNA abruptly appear in a particular fly species, but it immediately takes on an absolutely crucial role. A role which, of course, was somehow already fulfilled in the putative evolutionary ancestor.

In other words, the function in question (male fertility) was rumbling along just fine, and then with a new species, and not in many of its sister species, the crucial function was somehow rewired and reassigned to a relatively new, massive, DNA satellite sequence.

This is absurd.

Even the paper admits that, “Finally, it is worth noting that the expression of simple satellites for essential functions seems incompatible with the fast evolution of satellite DNAs, reflected in dramatic changes in both sequence types and copy numbers across species.”

Ya think?

The next step will be for evolutionists to convert this spectacular failure into compelling evidence that evolution can produce DNA that is both (i) species-specific, and (ii) functionally essential.

And why is that true?

Because, after all, the satellite DNA evolved, of course. And since it is species-specific and essential, we now have evidence evolution can produce such an unexpected outcome.

That’s just good, solid, scientific research.

Religion drives science, and it matters.

Saturday, February 23, 2019

The “All Outcomes Are Equiprobable” Argument

I Had to Write “Evolution Is True” 500 Times

I’ve been busy lately with a big landscaping job for the neighborhood evolutionist. He wanted a massive set of stones to be carefully arranged in his backyard. He wanted stones of different colors, and the careful arrangement would spell out “Evolution Is True.”

Unfortunately, the day I finished this big job there was an earthquake in the neighborhood which jumbled the stones I had carefully arranged. I had to go back to the evolutionist’s property and put the stones back in order.

To makes matters worse, the evolutionist wouldn’t pay me for the job. When I sued him he told the judge that I was lying. He said I didn’t do the job, but instead the arrangement of the stones was due to the recent earthquake.

I explained to the judge that such an event would be unlikely, but the evolutionist retorted that landscapers don’t understand probability. The evolutionist explained to the judge that all outcomes are equally probable. Every outcome, whether it spells out “Evolution Is True” or nothing at all, have a probability of one divided by the total number of possible arrangements. He said that I was committing a mistake that is common with nonscientific and uneducated people. He explained that if you toss a coin 500 times the sequence of heads and tails will be astronomically unlikely. But it happened. All such sequences, even if they spell out a message in Morse code, are equiprobable.

The judge agreed. He fined me for bringing a frivolous lawsuit against the evolutionist and made me write “Evolution Is True” 500 times.

Saturday, February 16, 2019

Finally, the Details of How Proteins Evolve

A Step-By-Step Description

How did proteins evolve? It is a difficult question because, setting aside many other problems, the very starting point—the protein-coding gene—is highly complex. A large number of random mutations would seem to be required before you have a functional protein that helps the organism. Too often such problems are solved with vague accounts of “adaptations” and “selection pressure” doing the job. But this week researchers at the University of Illinois announced ground-breaking research that provides a step-by-step, detailed, description of the evolution of a new protein-coding gene and associated regulatory DNA sequences. The protein in question is a so-called “antifreeze” protein that keeps the blood of Arctic codfish from freezing, and the new research provides the specific sequence of mutations, leading to the new gene. It would be difficult to underestimate the importance of this research. It finally provides scientific details answering the age-old question of how nature’s massive complexity could have arisen. As the paper triumphantly declares, “Here, we report clear evidence and a detailed molecular mechanism for the de novo formation of the northern gadid (codfish) antifreeze glycoprotein (AFGP) gene from a minimal noncoding sequence.” Or as lead researcher, professor Christina Cheng, explained, “This paper explains how the antifreeze protein in the northern codfish evolved.” This is a monumental finding. Having the scientific details, down to the level of specific mutations, of how a new protein-coding gene evolved—not from a related gene but from non-coding DNA—is something evolutionists could only dream of only a few short years ago. There’s only one problem: it is all junk science.

The first problem is that this new “research” is, in actuality, a just-so story:

In science and philosophy, a just-so story is an unverifiable narrative explanation for a cultural practice, a biological trait, or behavior of humans or other animals. The pejorative nature of the expression is an implicit criticism that reminds the hearer of the essentially fictional and unprovable nature of such an explanation. Such tales are common in folklore and mythology.

For example, the antifreeze protein is of relatively low complexity chiefly consisting a repeating sequence of three amino acids (threonine-alanine-alanine), and the evolutionists claim that these repeating sequences “strongly suggest” that the protein-coding gene “evolved from repeated duplications of an ancestral 9-nucleotide threonine-alanine-alanine-coding element.”

Why is that true?

Why does a repeating genetic sequence “strongly suggest” that it “evolved from repeated duplications?” What experiment revealed this truth? What evidence gives us this profound principle? The answer, of course, is that there is none. Nowhere do the evolutionists justify this claim because there is no empirical justification.

There is no scientific evidence for it. Zero.

The paper continues with yet more non-empirical claims. Those nine nucleotides “likely originated within a pair of conserved 27-nucleotide” segments that flank each side of the repetitive region. And these four 27-nucleotide segments are similar to each other, “indicating they resulted from the duplication of an initial copy.” As the paper concludes, “chance duplications” of an ancestral 27-nucleotide segment “produced four tandem copies.”

But why are those claims true? Why do such similarities imply an origin via evolutionary mechanisms? The problem is, they don’t. There is no empirical evidence for any of this. This is completely evidence-free.

The evolutionists next explain that the 9-nucleotide segment duplicated a large number of times because it worked well:

We hypothesize that, upon the onset of selective pressure from cold polar marine conditions, duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred.

The above quote is an example of the non-empirical, teleology that pervades evolutionary thought. It was upon the onset of cold conditions that the needed genetic duplications occurred. This is not empirical; this is story-telling.

The paper continues with a series of one-time, contingent events crucial to their story and non-empirical claims. The genetic sequence “was appropriately delimited by an existing in-frame termination codon.”

Appropriately delimited?

The presence of a region in two of the species “indicates that it existed in the gadid ancestor before the emergence of the AFGP.” The absence of a thymine nucleotide at a location in some of the species “very likely resulted from a deletion event,” causing a fortuitous frameshift which supplied the crucial signal peptide segment, telling cellular machinery that the protein should be secreted to the bloodstream. As the paper concludes, “the emerging AFGP gene was thus endowed with the necessary secretory signal.”

Endowed with the necessary signal?

There is no empirical evidence for any of this.

Another problem with this just-so account, is the substantial level of serendipity required. The new antifreeze protein did not arise from some random DNA sequence, but rather from crucial, preexisting segments of DNA that just happened to be lying around. In other words, the fish were facing a colder environment, they needed some antifreeze in their blood, and the pieces needed for such an antifreeze gene were fortuitously available.

The authors hint at this serendipity when they conclude that their story of how this protein evolved is an example of “evolutionary ingenuity.”

Evolutionary ingenuity?

The press release is even more revealing. Cheng admits that the evolution of this gene “occurred as a result of a series of seemingly improbable, serendipitous events.” For “not just any random DNA sequence can produce a viable protein.” Furthermore, in addition to the gene itself, “several other serendipitous events occurred.”

The DNA was “edited in just the right way,” and “somehow, the gene also obtained the proper control sequence that would allow the new gene to be transcribed into RNA.”

Even the evolutionists admit to the rampant serendipity. Nonetheless they are triumphant, for “the findings offer fresh insights into how a cell can invent ‘a new, functional gene from scratch.’”

Fresh insights?

In actuality the findings arose from a series of non-empirical claims.

Religion drives science, and it matters.