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.

Wednesday, March 6, 2019

Kirk MacGregor: Evolution Proves Molinism

And Molinism Proves Evolution

“Evolution provides a theological solution to a theological problem, and the science is sandwiched somewhere in between. But the theological premises are denied so the theological result is seen as coming from science, and science inappropriately attains the status of truth giver.” I made that observation in Darwin’s God, and unfortunately it remains just as true today. The latest example of this phenomenon comes in the brand new volume, Calvinism and Middle Knowledge where, in Chapter 2, Kirk MacGregor strongly argues that evolution proves Molinism. Molinism was one of the dozen or more religious motivations and mandates for evolutionary thought, and now in the twenty-first century, evolution is used as a proof text for Molinism. See the sequence? Religion drives the science, and the resulting theory is then used to confirm the religion. This can only work where (i) there is a loss of historical continuity, where evolution is seen as an objective, tabula rasa, empirical finding, and (ii) there is a breakdown in the science. Below I summarize MacGregor’s argument, and explain why it fails scientifically, and is incoherent.

MacGregor’s argument

MacGregor explains that he accepts evolution for reasons that anyone familiar with the origins debate will recognize. He cites molecular and morphological evidences and arguments for how evolution could have occurred via a long sequence of mutations, and that evolution has far greater explanatory power than special creation. Just because evolution can occur, however, does not mean it is likely to have occurred. MacGregor accepts the evidences and arguments that evolution is astronomically unlikely to have occurred. It may seem that MacGregor has a dilemma: evolution occurred yet could not occur. But for MacGregor all of this demonstrates the truth of Molinism:

Far from constituting a threat to theism, the macroevolutionary account of life’s origins and development actually demonstrates the existence of God and the supremacy of God’s knowledge.  Due to the astronomically low probabilities of countless trans-group and simultaneous unrelated mutations, which I believe the scientific evidence demonstrates to have occurred, the God who created the universe must be endowed with middle knowledge.  Such knowledge of what would happen in every possible biological scenario, especially those which are causally unconstrained, is the only means whereby God could choose to create a world where this dizzying and interdependent array of biological improbabilities would naturally materialize to generate life in all its complexity.  In other words, the evolutionary schema, with its extraordinarily lengthy chain of remote probabilities, could only unfold in time-space if the God who exists knew what would contingently happen in every possible set of circumstances and then proceeded to create an initial quantum phenomenon which naturally issued in precisely those innumerable contingencies necessary for the evolution of intelligent life.  

In other words, what may appear to be a chance naturalistic process, was actually foreseen by God, and arranged by God by selecting an initial, quantum, state of the universe. MacGregor does not explore, and perhaps has not substantially considered, a key difference between his approach and Molinism; namely (and very simply put), with Molinism God foresees but does not determine the future decisions of His morally free creatures. This will lead to an incoherence in MacGregor approach (more below on this).

Scientific failure

MacGregor provides reasons and evidences for accepting evolution which are typical of the evolutionary literature. He is unaware that these reasons and evidences have been dealt with extensively and have long since failed badly on the science. To begin with, it is an exercise in confirmation testing. For each evidence, complicating factors are simply omitted. And the vast array of contradictory evidences not considered at all. One example of each will suffice.

One of MacGregor’s evidences are “suboptimal improvisations” and the so-called vestigial structures. For example, MacGregor writes that God’s special creation of whales with useless leg bones appears inexplicable, for whales would no longer descend from land-living ancestors with legs. No one could validly argue that such structures resulted from sin, as they emerged on anyone’s reckoning before the Fall.

This classic evolutionary argument from disutility has failed over and over, and it is no different this time. In this case, it has long since been considered that these “useless” whale bones are likely used in reproduction and this was eventually confirmed. As one evolutionist admitted:

Our research really changes the way we think about the evolution of whale pelvic bones in particular, but more generally about structures we call “vestigial.”

Another example of how MacGregor’s evidences do not serve his purposes is the so-called nested hierarchy pattern of biological forms which MacGregor claims is accounted for through the successive branching pattern of evolutionary transformation. Again, this icon of evolution has failed badly. It is simply false that the evolutionary tree pattern is explained by a successive branching pattern. As I have documented many times here, the problem is not that there are a few outliers. We’re not talking about a third-decimal point error. Empirical contradictions to the expected nested hierarchy are everywhere, and at all taxonomic levels. They are pervasive and consistent, and it is fair to say that the so-called nested hierarchy pattern is imposed onto the data rather than read out of the data. Homoplasy is rampant in biology, and there simply is no justification for the “nested hierarchy” pattern, such as it is, as an evidence for evolution. Indeed, by modus tollens what the evidence is telling us is that evolution is false, by any reasonable interpretation of the evidence. If an evidence would be powerful evidence for a theory, then the failure of that evidence must be evidence against the theory.

Incoherence

Finally, MacGregor’s position is incoherent for several reasons. First, as noted above MacGregor claims the so-called “suboptimal improvisations” found in biology are strong evidence for evolution. Evolution explains these, whereas with special creation such evidence is inexplicable, and is ruled out. This centuries-old argument is powerful, but it is theory-laden. This can be seen in MacGregor’s terminology: “improvisations.” On the evolutionary view, such suboptimal designs are “improvisations,” but on the special creation view they are not. Likewise, the term “vestigial structures” is also theory-laden. There is nothing inherently “vestigial” about those whale bones, our appendix, or the many other examples evolutionists cite. There is no measure of “vestigial-ness.” The very language MacGregor uses is steeped in evolutionary assumptions.

In fact, the evolutionist’s claim that such evidence is inexplicable and therefore rules out special creation hinges on the theological doctrine that divine intention is to optimize function and fitness. God must create according to the evolutionary concept that designs are driven by fitness (which, in turn, is defined as a reproductive advantage). We might say MacGregor’s theology is based on evolutionary theory but, of course, this goes back long before evolution. It would probably be more accurate to say MacGregor is a utilitarian, which was an important influence and mandate for evolution.

So the first problem is that MacGregor’s position is theory-laden, and circular. The evidence that MacGregor finds to be a powerful confirmation of evolution entails evolutionary assumptions. The next problem follows on the heels of the first; namely, that MacGregor’s position is unbiblical (the Bible does not present a utilitarian Creator, and at times flatly reveals the opposite). Normally this would not be a problem—anyone can hold and advocate any belief he wants to. But MacGregor’s entire argument is intended to be biblical. So he has a significant internal contradiction, in addition to being theory-laden, and circular.

Another problem is that MacGregor believes the divine creation acts are confined to the beginning. This sort of idea is sometimes labelled as “front-loading.” Rather than divine intervention occurring over time, the Creator sets up the initial conditions just right for the desired result (including the evolution of humanity) to unfold. MacGregor here follows the Greater-God theology which, again, traces back several centuries and was important in mandating an evolutionary origins narrative. The classic case study is Leibniz’s rejection and horror at Newton’s proposal that God tweaks the solar system every so often to maintain its stability. Leibniz slammed the notion as blasphemous. The greater god causes the causes of effects, rather than merely causes the effects themselves, as Darwin’s grandfather Erasmus put it. MacGregor follows this belief, and the resulting front-loading will be instrumental in his confirmation of Molinism.

But this confirmation of Molinism is arrived at not by an objective analysis of the empirical evidence, as MacGregor suggests. MacGregor did not have to incorporate front-loading. Following Robert Russel, MacGregor could have envisioned divine action as occurring, at the quantum level, over time. But that would have violated his greater god theology and, crucially, it would have obviated the confirmation of Molinism. So the thesis of the paper—that Molinism is confirmed by science (evolution in particular)—is false. In addition to the utilitarianism we saw above, the conclusion for Molinism also hinges on the greater god theology. On top of all this, as with utilitarianism, greater god theology also is not biblical. Again, this is a problem for MacGregor because his argument is intended to be biblical.

Finally, MacGregor’s utilitarianism and front-loading are contradictory. MacGregor simultaneously holds that (i) God would not create those suboptimal improvisations (hence evolution must be true), and (ii) God knows all possible futures, and how they are brought about, and He selected an initial state which created the world. This means that God created those suboptimal improvisations, which He would never create.

Unfortunately, religion has infected science and the result is bad religion and bad science.

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.