Sunday, January 17, 2016

How Evolutionists Stole the Histones

A Textbook Example

The recent finding that the DNA packaging technology and structure, known as chromatin, is not limited to eukaryotes but is also present in archaea, and so from an evolutionary perspective must have “evolved before archaea and eukaryotes split apart—more than 2 billion years ago,” is merely the latest in a string of misadventures evolutionists have incurred ever since they stole the histones.

Histones are the hub-like proteins which (usually) serve as the hubs about which DNA is wrapped in the chromatin structure. Like a thread wrapped around a spool this design packs DNA away for storage with an incredible packing factor. Interestingly, the histone proteins are highly similar across vastly different species. Again, from an evolutionary perspective, this means they must have evolved early in evolutionary history to a very specific design. As one textbook explains:

The amino acid sequences of four histones (H2A, H2B, H3, and H4) are remarkably similar among distantly related species. For example, the sequences of histone H3 from sea urchin tissue and of H3 from calf thymus are identical except for a single amino acid, and only four amino acids are different in H3 from the garden pea and that from calf thymus. … The similarity in sequence among histones from all eukaryotes indicates that they fold into very similar three-dimensional conformations, which were optimized for histone function early in evolution in a common ancestor of all modern eukaryotes. [1]

But the new finding pushes back this evolutionary “optimization” far earlier in time. Once again, evolution’s heroics are moved to the distant past where no one can see. Early life was not simple.

And of course DNA needs to be accessed so this histone packaging is quite dynamic. It can roll or it can be removed and moved. The histones themselves have tails that stick out and are tagged with small chemical groups that influence whether the packaging is tight or unrolled. Again, early life was not simple.

But the fact that histones are so similar across a wide range of species leads to an entirely different dilemma for evolution. For from an evolutionary perspective, it means that the histones must not tolerate change very well. Here is how a leading 1994 textbook described it:

When the number of amino acid differences in a particular protein is plotted for several pairs of species against the time since the species diverged, the result is a reasonably straight line. That is, the longer the period since divergence, the larger the number of differences. … When various proteins are compared, each shows a different but characteristic rate of evolution. Since all DNA base pairs are thought to be subject to roughly the same rate of random mutation, these different rates must reflect differences in the probability that an organism with a random mutation over the given protein will survive and propagate. Changes in amino acid sequence are evidently much more harmful for some proteins than for others. From Table 6-2 we can estimate that about 6 of every 7 random amino acid changes are harmful over the long term in hemoglobin, about 29 of every 30 amino acid changes are harmful in cytochrome c, and virtually all amino acid changes are harmful in histone H4. We assume that individuals who carried such harmful mutations have been eliminated from the population by natural selection. [2]

So the reason the histone proteins are so similar, again from an evolutionary perspective, is because mutations changing those proteins could not be tolerated. This is the evolutionary prediction and here is how the next edition of that same textbook, eight years later in the year 2002, added to the discussion of the high similarity of the histone proteins:

As might be expected from their fundamental role in DNA packaging, the histones are among the most highly conserved eucaryotic proteins. For example, the amino acid sequence of histone H4 from a pea and a cow differ at only at 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids, so that a change in any position is deleterious to the cell. This suggestion has been tested directly in yeast cells, in which it is possible to mutate a given histone gene in vitro and introduce it into the yeast genome in place of the normal gene. As might be expected, most changes in histone sequences are lethal; the few that are not lethal cause changes in the normal pattern of gene expression, as well as other abnormalities.

There was only one problem. That is false. In fact, even at the time studies had already shown that histone H4 could well tolerate many changes. It was not merely an example of evolution pointing in the wrong direction and producing yet another failed prediction. It was an all too frequent example of evolution abusing science, force-fitting results into its framework. And of course all of this became doctrine for wider consumption. As a 2001 PBS documentary stated:

Histones interact with DNA in the chromosomes, providing structural support and regulating DNA activities such as replication and RNA synthesis. Their ability to bind to DNA depends upon a particular structure and shape. Virtually all mutations impair histone's function, so almost none get through the filter of natural selection. The 103 amino acids in this protein are identical for nearly all plants and animals.

But it is not, and was not, true that “virtually all mutations impair histone’s function.” That was not science, it was dogma disguised as science. And since then the dogma has become even more obvious. As one recent paper summarized:

Furthermore, recent systematic mutagenesis studies demonstrate that, despite the extremely well conserved nature of histone residues throughout different organisms, only a few mutations on the individual residues (including nonmodiļ¬able sites) bring about prominent phenotypic defects.

Similarly another paper bemoaned the confusing results:

It is remarkable how many residues in these highly conserved proteins can be mutated and retain basic nucleosomal function. … The high level of sequence conservation of histone proteins across phyla suggests a fitness advantage of these particular amino acid sequences during evolution. Yet comprehensive analysis indicates that many histone mutations have no recognized phenotype.

In fact, even more surprising for evolutionists, many mutations actually raised the fitness level:

Surprisingly, a subset of 27 histone mutants show a higher intensity after growth (log2 ratio >+1.5) suggesting they are collectively fitter and maintain a selective advantage under glucose limitation.

It was yet another falsified evolutionary prediction, and yet another example of evolution abusing science.

Now evolutionists propose a redundancy hypothesis. Those histone mutations are well tolerated because evolution constructed a backup mechanism. Both mechanisms would have to mutate and fail before any lethal effects could be felt.

As usual, contradictory results are accommodated by patching the theory with yet more epicycles. The epicycles make the theory far more complex, and far more unlikely, if that were so possible. In this case, evolution not only struck on incredible complexity, and did so early in history (before there were eukaryotes and nucleus’s in which to pack the DNA), but the whole design now must have incorporated layers of redundancy which we haven’t even been able to figure out yet.

And all of this, evolutionists insist, must be a fact. Anyone who would so much as doubt this truth must be blackballed.

It has been one misstep after another ever since the evolutionists stole the histones. Evolution is truly a profound theory, not for what it reveals about nature, but for what it reveals about people. Religion drives science, and it matters.

1. H Lodish, A Berk, SL Zipursky, et al., Molecular Cell Biology, 4th ed. (New York: W. H. Freeman, 2000).

2. B Alberts, D Bray, J Lewis, M Raff, K Roberts, J Watson, Molecular Biology of the Cell, 3rd ed. (New York: Garland Science, 1994), 243.

3. B Alberts, A Johnson, J Lewis, et. al., Molecular Biology of the Cell, 4th ed. (New York: Garland Science, 1994), 243.

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Monday, December 21, 2015

Get Rid of Evolution With This One Weird Trick

A Limited Time Offer

People have been begging me to tell them about this one weird trick to get rid of evolution. But up until now I have been hesitant. It’s almost too easy. Plus, getting rid of evolution would mean not having evolutionists around anymore, and what fun would that be? But now, for a limited time, you too can get rid of evolution with this one weird trick.

Sunday, December 20, 2015

Jason Rosenhouse: “I Think You Get the Idea”

The New Priesthood

I once heard an evolution professor insist that all of the biological evidences support and confirm the theory of evolution. Since then I found that this view occupies the consensus position. All of the findings in the life sciences are exactly what we would expect from an evolutionary perspective. You can see it everywhere from textbooks to evolutionary journal papers. A good recent example of this thinking comes from professor Jason Rosenhouse.

The idea that all of the biological evidences are exactly what evolution would expect is a misrepresentation of the science. The misrepresentation is striking given the extent to which the evidence contradicts evolutionary theory. You can see examples of these contradictions here.

It is important to understand that evolutionists are not merely saying their theory is an interesting idea that merits investigation. They are not merely saying their theory deserves to be considered or has some degree of merit. Such circumspect sentiment is not, and never has been, what evolutionary thought is about. Evolutionary thought is about high truth claims, with complete certainty, which contradict what we know about the world.

This cognitive dissonance is maintained by evolutionists using two moves. First, because evolution is taken to be true from the start (for non scientific reasons), the evidences naturally undergo interpretation and filtering.

The body of evidence, as understood by evolutionists, is what philosophers refer to as theory laden. For instance, contradictory evidences are often set aside. They may be viewed as incomplete, erroneous, not normative, or anomalous. One way or another they are not ready for prime time.

For example, evolutionists compare homologous genetic sequences between species to evaluate their evolutionary relationship. But the very act of comparing homologous sequences ignores, and filters out, the many sequences for which there is no homology.

The second move is to discount and delegitimize scientific objection as insignificant or nefarious. If you point out the many scientific problems with the Epicurean belief that chance events, coupled with natural laws, explain the origin of the world, then ironically the tables will be turned and you will be blamed for having the religious agenda.

Rosenhouse expresses these points, in typical fashion:

every scrap of evidence discovered by scientists points strongly in that direction [naturalism and evolution]. If evolution is false, for example, then it should have been trivially easy to disprove. And yet every scrap of data we have is consistent with what evolution tells us to expect.

Every scrap of evidence points strongly in the direction of naturalism and evolution? Even though I have seen such claims many times now, I still wince. They are, as they say, not even wrong. This is one of those rare times where superlatives really are appropriate. This is not just absurd, it is very absurd. Not just a misrepresentation but a perversion. Not just a lie, but a damn lie.

From the age-old evidence of breeding and twentieth century fly experiments to the more modern protein evolution studies and the violations of the common descent pattern across the species (a mere four of many examples), the “scraps” of evidence we actually have unequivocally do not point in the direction of naturalism and evolution.

This is simply a bald faced lie.

Rosenhouse then proceeds to discount the actual science as insignificant and merely the product of those religiously-driven creationists trying to prove their creator. What would evolutionists do without the Creationists?

Of course there is a reason for all the machinations. Evolutionists do not insist their modern-day Epicureanism is a fact, in spite of everything around us, without reason. Not surprisingly, that reason is really no different than that of the Epicureans. Modern thinkers have substantially elaborated on the theological details, but it boils down to religious beliefs about how a Creator would and should interact with the world.

First, if a creator were specifically design and create a world, it certainly would not look like this one. Beyond that, a truly great god would not use miracles anyway, and even if he would, the lowly things of this world are beneath his dignity to begin with. Furthermore science becomes impossible with an interventionist god.

The arguments go on and on, and they mandate a naturalistic origins. So not surprisingly, Rosenhouse explains that whatever concerns one might have with evolution, the real problem lies with the alternative:

For example, those biomolecular systems we were talking about never look quite so impressive after you study them in detail. … However superficially implausible they [the problems with evolution] seem, the only alternative on offer is much harder to believe.

After all, we just can’t really understand God:

Whatever mysteries you think you have found in the naturalistic view of life pale in comparison to what happens when you try to comprehend an entity with the attributes God is said to have.

For instance, how can God cause physical actions if he has no physical existence?

God is said to be mind without brain. For all the experience we have with actual minds and actual brains, that just looks like a contradiction in terms. God has no physical existence, yet acts of His will can cause whole universes with finely-tuned fundamental constants to appear where there was nothing before. How does He do that?

And what is the connection between His will and the creation of matter? Did you ever think of that?

What’s the connection between His will and the creation of matter? God knows what everyone is thinking at every moment of every day. How is that possible? How can he process and store all of that information? He exists “necessarily,” whatever that means, in contrast to the more mundane sort of existence we see all around us each day. I could go on multiplying the implausibilities, but I think you get the idea.

Yes, we certainly do get the idea. Evolutionists are driven by religious dogma in spite of the obvious evidence staring right at them. As even Rosenhouse must admit:

Personally, I find it incredible that the four fundamental forces of physics, operating from the moment after the Big Bang, could rearrange matter into everything that we see today. That unintelligent causes can ultimately lead to the creation of intelligent creatures, who can then rearrange matter and energy in clever ways, is, I entirely agree, hard to believe. And Darwinian evolution strains credulity as well. I am very sympathetic to the view that natural forces do not construct delicate, biomolecular machines.

But of course none of that matters because, after all, don’t forget the creationists. We must not allow God to interact with the world.

Young children are content with magical, supernatural explanations for things. But as we grow up most of us come to realize that invocations of God never really explain much of anything. They just create big mysteries where only small ones existed before.

Of course they are evolutionists, their religion requires it. Religion drives science, and it matters.

Saturday, December 19, 2015

Evolution is a Scientific Fact: A Proposition

Evolutionists disagree amongst themselves about the theory of evolution but they agree about the fact of evolution. If there is one point of agreement within evolution-dom, it is that evolution is a scientific fact. A few years after Darwin died Joseph Le Conte explained that evolution is a law, not a theory, and it is a law to which every department of natural studies must adhere. It is not merely as certain as gravity, "Nay, it is far more certain." Similarly, Teilhard de Chardin maintained that "evolution is a light which illuminates all facts, a trajectory which all lines of thought must follow—this is what evolution is."

In 1951 George G. Simpson wrote that there really is no point nowadays in continuing to collect and to study fossils simply to determine whether or not evolution is a fact. The question, concluded Simpson, has been decisively answered in the affirmative. Scientist and social critic Ashley Montagu elevated evolution beyond all other theories. It was, according to Montagu, "the most thoroughly authenticated fact in the whole history of science."

In his biology textbook Neil Campbell informed the student that “The term theory is no longer appropriate except when referring to the various models that attempt to explain how life evolves … it is important to understand that the current questions about how life evolves in no way implies any disagreement over the fact of evolution.”

For Douglas Futuyma evolution “is a fact, as fully as the fact of the earth’s revolution about the sun,” and Richard Lewontin says it is time “to state clearly that evolution is a fact.” Niles Eldredge claims that “Evolution is a fact as much as the idea that the earth is shaped like a ball.”

The National Academy of Sciences explains that in science the word “fact” can be used “to mean something that has been tested or observed so many times that there is no longer a compelling reason to keep testing or looking for examples. The occurrence of evolution in this sense is a fact. Scientists no longer question whether descent with modification occurred because the evidence supporting the idea is so strong.”

And Harvard's Ernst Mayr explained that the fact of evolution is so overwhelmingly established that it would be irrational to call it a theory.

That evolution is a scientific fact is an important claim. Let’s look at exactly what evolutionists are saying:

Evolution: For evolutionists this word refers to the idea that all the species arose via natural laws. God did not use miracles to create the biological world, instead everything arose by the play of the natural processes and laws we observe. Moths changing color or bacteria gain resistance to antibiotics do not constitute evolution. They are at best tiny examples of evolution. Such examples of adaptation do not prove evolution any more than a flat parking lot proves the flat earth theory. Evolution is a big theory.

Is: This evolutionary claim is not tentative. Evolutionists are not merely saying that some evidence supports their theory. They are not saying parts of evolution are true, or that evolution might be a fact. There is no wiggle room here. Evolution is a scientific fact.

Scientific: What type of fact is evolution? It is a scientific fact? This means that this conclusion is arrived at via logic. Scientific reasoning is, if anything, logical. Fallacies are rooted out and eliminated. And the evidence used in the reasoning is public. There is no private knowledge required to understand evolution and its status as a fact. Also, the premises of scientific reasoning are objective. There are no subjective axioms. One need not adhere to Buddhism or Baptism to understand and agree with scientific reasoning.

Fact: This word can mean different things to different people, but in this context evolutionists are quite clear about their usage. A favorite comparison, as demonstrated by Le Conte above, is with gravity. Evolution is a fact every bit as much as is gravity (or more so according to Le Conte). There’s not much nuance here. Sure evolution may not be true, but only in the sense that gravity might not be true. This existence could be a big dream, with none of what we experience being real. But aside from such Berkeleyan quandaries, we can count on the veracity of evolution.

Now that we understand just what evolutionists are claiming, what can we say about it? There is indeed much to say, but the most important observation that is immediately obvious from the evolution genre is that while evolutionists consistently make this claim, it is nowhere demonstrated.

To be sure evolution is often proved to be a fact, but in every case metaphysical premises are involved. If god wouldn’t have created the mosquito then yes, evolution in one form or another must be a fact. But such theological musings (yes, evolutionists really do assert this very premise) fall far outside of the objectivity criterion.

And while the evolution literature is often scientific, in those cases the theory is never shown to be a fact. This problem is not slight. It is not the case that evolution is quite convincing but just shy of fact-hood. Darwin’s theory, in whatever form it is presented, comes nowhere close to being a fact when we restrict the premises to the realm of empirical science. In fact—if we want to speak of facts—the fact is evolution is highly problematic.

For many years I have searched the evolution genre. I have scanned the journals and reviewed the texts. From Darwin and Le Conte to Carroll and Coyne, I have pored over the literature. I have nowhere found an exposition of this most important fact. I have seen evolution proven to be a fact, and I have seen evolution presented as science, but I have never seen evolution shown to be a scientific fact.

And so I have a proposition for evolutionists. Show me your fact and I will promote it. Explain why evolution is a scientific fact and I will retract my criticisms as unfounded. Back up your claim and I will be an evolutionist.

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Sunday, December 13, 2015

Biologos and Science: The Case of the OOL

Evolution is at a Tipping Point

Evolutionists claim their theory is a fact and one way they support this claim is by construing the relationship between religion and science according to what is known as the Warfare Thesis, a mythological retelling of history where scientific skepticism is marginalized as anti intellectual. But the Warfare Thesis is more than merely a perversion of history. When Biologos appeals to the Galileo Affair, for example, to support its evolutionary beliefs it is propagating a false history, but the misrepresentations do not stop there. The Warfare Thesis also relies on a false witness of science.

The Galileo Affair is the posterchild of the Warfare Thesis myth. As the story goes, poor old Galileo was a great scientist just doing his job when, after inventing the telescope, discovered the Earth goes around the Sun and this led to a firestorm of religious opposition from biblical literalists who naively and dogmatically referred to those passages of Scripture that say the Sun revolves around the Earth, and all this led to merciless persecution, torture and imprisonment of Galileo.

Furthermore, just as the literalists opposed poor old Galileo in the seventeenth century, so too they are opposing the innocent evolutionists today. If you admit that Galileo was right about heliocentrism back then, then you must agree that evolutionists today are right about mutations creating the species. It is just good solid science at work.

But this is a false argument on every count. First, this retelling of the Galileo Affair that we hear so often today is all wrong. Galileo did not invent the telescope, he did not discover, or otherwise prove, heliocentrism, he was not just a humble scientist, the serious opposition and legal problems he faced did not stem from biblical literalists, the Scripture does not say the Sun revolves around the Earth, and Galileo was not tortured and did not go to jail.

Yes, there were those who viewed heliocentrism as violating scripture, but generally they were easily dissuaded. There was much more serious resistance that Galileo would face. For example, his ideas unquestionably violated Aristotelian physics and ideology which not only was still active but at times had been elevated practically to the status of official church doctrine. Furthermore (i) Galileo’s caustic personality, and his penchant for humiliating people and making enemies (including his one-time friend, the Pope), (ii) the fact that leading astronomers of the day by no means were in agreement on this cosmological question and often held to opposing views, and (iii) the turbulent politics of the day, all conspired to make the going tough for Galileo.

It is misleading and a misrepresentation of history to hold up the Galileo Affair as an example of biblical literalism opposing scientific progress. Yet there it is.

But false history is not the only fruit of the Warfare Thesis, it also leads to false science. Just as historians prevaricate on the history, scientists prevaricate on the science. Consider, for example, the origin of life (OOL) problem.

The spontaneous generation of life was once accepted, but Darwin contemporary Louis Pasteur demonstrated it does not happen. His Law of Biogenesis stated Omne vivum ex vivo (all life from life), and the burden of proof fell to the evolutionists to prove that over time evolution gets lucky, or that there was something different about the early Earth that changes the rules. Well the early Earth was indeed different, but not in ways that help evolution. And deep time doesn’t help either. Evolutionists have been trying to demonstrate the plausibility of life arising spontaneously, over millions of years, from non living chemicals for almost a century now with no luck. And luck is exactly what is needed, an astronomical amount of luck.

Evolutionists have explored every conceivable mechanism, and then some, to tackle the OOL problem. Perhaps life evolved in a warm little pond, or in bubbles, or in crystals, or at deep sea vents, or in clay, or by hypercycles, or from comets. Some have even said it must have been planted here by extra terrestrials because otherwise the OOL problem requires a miracle to solve.

Not only have evolutionists failed but we now have an enormous body of work confirming what common sense (and Pasteur) indicated all along—the most complicated thing in the universe probably didn’t arise spontaneously by chance events.

But none of this changed the evolutionist’s high claims that their idea is a fact, beyond all reasonable doubt. Scientific evidence didn’t seem to matter. In fact for many years evolutionists were not shy about claiming victory, in spite of the obvious failures. Mainstream evolutionists, organizations, and textbooks insisted the OOL problem was essentially solved, with only the details to be ironed out.

That, of course, was an enormous misrepresentation of science. More recently evolutionists have fortunately been more forthcoming about the empirical findings. They have agreed that the problem has not been solved, and that solutionists are not right around the corner.

For evolutionists that was quite a concession, but it did not change their overall truth claims. Evolution is still an undeniable fact and the misrepresentation is now at more of a philosophical level. This is obvious, for example, at the BioLogos presentation on the evidences for evolution. which makes this argument:

The fact that there is no answer today does not mean there will be no answer tomorrow. Though an explanation for the origin of life is currently elusive, this does not mean divine intervention is the only possible explanation.

The religious agenda is obvious. God must not be an intervening God—special divine action must not be allowed. The state of the art must not be reported as indicating any serious problem for OOL; rather, the problem merely has not yet been solved. This opens the door to scientific misrepresentations which come next:

Although we do not know the path that led to these early bacterial forms, it seems likely DNA had emerged as the information molecule by this time. Microbiologist and physicist Carl R. Woese suggests there was a considerable amount of lateral gene transfer among the first forms of bacteria called archaebacteria. Lateral gene transfer, which is the movement of genes from one bacterium to another, would have enabled the exchange of genetic material, and it would therefore expedite the process of diversification of biological function acted upon by natural selection.

Most in the BioLogos audience won’t recognize the falsehoods in these technical claims. It is easy to fudge the facts when no knows any better but these are, nonetheless, serious misrepresentations. No, it is not “likely” that “DNA had emerged as the information molecule by [a 100 million years of the Earth cooling].” That would be a tremendous breakthrough in OOL research if that were true.

But it isn’t true.

There is no experiment or even calculation show that this is likely. In fact it is the exact opposite. Such a scenario is not likely by today’s science, and that is one of the many problems for OOL.

Next, to say that Carl Woese called for “a considerable amount of lateral gene transfer” is another misrepresentation. Woese called for an entirely different scheme which might be called lateral gene transfer on steroids. This is important because Woese’s idea has no analog in reality. Nothing of the sort has ever been observed in the field or synthesized in the laboratory. What Woese needed was a fanciful world of communities of unicellular organisms which somehow spontaneously arose and then engaged in a highly organized, complex process of sharing genetic material which, if not carefully controlled, would have wreaked havoc even if it somehow could have arisen spontaneously (for which Woese presented no evidence).

The article concludes with more philosophical and fallacious misrepresentations:

Life on this Earth appeared approximately 3.85 billion years ago, yet serious scientific study of its origins began just 60 years ago. A convincing scientific explanation may still emerge in the next 50 years.

Question: What do 3.85 billion, 60, and 50 have to do with each other? Or more to the point, why would an older event require more time to figure out? Would the OOL problem be easier if it was supposed to have occurred 1 billion years ago? And why is 110 years required to solve the problem rather than 60?

The answer, of course, is that this is simply more machinations to avoid the clear and obvious fact that the scientific state of the art does not support evolution. Another machination is the use of false dichotomies:

it is dangerously presumptuous to conclude the origin of life is beyond discovery in the scientific realm simply because we do not currently have a convincing scientific explanation. Although the origin of life is certainly a genuine scientific mystery, this is not the place for thoughtful people to wager their faith.

Wager their faith? Beyond discovery? Dangerously presumptuous? These warnings speak volumes for here we have a window into evolutionary thought. We must be evolutionists for otherwise we would be lost in a world of fideism where one’s very faith is staked to scientific failure. No wonder evolutionists are committed naturalists—their religion depends on it.

Finally, there is the ultimate argument which firewalls OOL off from evolution.

Finally, as a purely technical matter, the theory of evolution does not propose an explanation to the question of the origin of life at all. The theory of evolution becomes relevant only after life has already begun

As if sensing a problem, and just in case we were beginning to have doubts, we are told to forget about the whole thing. Forget about all those journals, conferences, textbook claims about the origin of life, popular books and newspaper articles, speeches and blogs. It all has nothing to do with evolution after all.

Evolutionists believe that the species, life, the Earth and planets, the Sun, the galaxies, yes the entire universe arose by chance events. There is no limit to what evolution can create, but when problems arise, the topic is simply dismissed as extraneous to the theory.

The fact, which evolutionists are at pains to avoid, is that OOL research has not merely failed to find a solution. It has positively succeeded in scientifically demonstrating that such a solution is unlikely. That is, according to today’s state of the art. Could that all change with future findings? Of course. Are philosophical end-arounds available such as redefining “evolution,” or invoking the anthropic principle and multiverse? Again, of course. But none of this changes the scientific facts.

Evolution is at a tipping point. In recent years evolutionists have increasingly had to admit that OOL research has not succeeded. The problem has not been solved save for a few minor details. Nor is there an obvious solution just around the corner.

But what evolutionists have not admitted to is what this implies about the fact of evolution. Evolution never was a fact and evolutionist’s insistence that it is has always been metaphysical. But the OOL problem is a good case study to make this crystal clear. It is abundantly obvious, to any objective observer, that evolution is not a fact. But evolutionists will not go there. At least not yet.

Religion drives science, and it matters.

BioLogos: Ex YEC Tells All

From the Frying Pan to the Fire

Movements need converts and evolutionists are now revealing yet another ex young Earth creationist who has seen the light. Growing up he was an enthusiastic apologist for creationism. As a teenager he spread the word on the radio and made trips to Kentucky to work with Ken Ham’s young-earth creationism (YEC) organization. He believed YEC was the only acceptable interpretation of the Bible. Without it he would lose his faith.

When he went to college for his biology degree his parents thought the teaching might sway him to evolution. But instead, he became even more convinced. His conversion to evolution would come later, when he went to seminary.

It was then that he realized the scriptures presented a far grander story and that evolution revealed a greater god. It was invigorating think of science as exploring the unknown and God became all the more wondrous. Science provided the mechanism by which life develops, and religion provided the agency behind the mechanism. It all fit so well. Science and religion were not in opposition, but rather complemented each other.

He also realized that it is a dangerous fallacy to demand that evolution provide answers to every possible question. Just because evolution cannot explain every detail does not mean it is false. And in fact evolution does provide good answers based on solid scientific research.

That, in a nutshell is the evolution story. It is the story of one man’s journey to Epicureanism, but it is also the story of countless others, including Charles Darwin. The road goes through religion, not science. It was the seminary rather than the biology degree that convinced the young man that the world arose spontaneously. It is not science, but religion that drives men to absurdity. And once there, it seems so right. After all, it makes for a more wondrous theology and it frees up our scientific inquiry. Epicureanism is needed for both God and man.

Religion drives science, and it matters.

Monday, November 23, 2015

The Dark Proteome and Dark Evolution

Evolution Did It

A new PNAS paper published last week on the dark proteome has some interesting implications for the theory of evolution. The paper presents a survey of protein sequences, focusing on the many sequences for which the corresponding three dimensional protein structure is not known, and cannot be inferred from any remotely similar sequence. Why is this so-called “dark proteome” so large? The survey finds that the various hypotheses to explain this—that the dark proteins are intrinsically disordered, or their sequences are compositionally biased, or they are transmembrane proteins, all reasons that can confound structure determination—don’t work very well. The paper concludes that “a surprisingly large fraction of dark proteins … cannot be easily accounted for by these conventional explanations.” And not surprisingly, these dark proteins are less common across the species. So where did all these dark protein sequences come from? Well evolution did it. As the paper explains, “dark proteins may be newly evolved proteins or rare proteins adapted to specific functional niches.”

We might call this dark evolution. Once again, the pattern is not one of common descent, but of unique structures.

The results also have implications for the so-called orphans, open reading frames found only in a particular species. Such genetic sequences contradict evolution and when they were first discovered evolutionists predicted they would be found in other species as more genomes were decoded. Instead the number of orphans just continued to grow.

Evolutionists next predicted that orphan sequences were probably not part of a mature protein coding gene and did not form functional proteins. That has not been found to be true, and this new survey provides further evidence for this. As the authors conclude, “Thus, our results suggest that many of the uncharacterized orphan sequences … are indeed real proteins.”

Protein science, however, is clear that blind mutations cannot form real proteins this fast from scratch (or at all for that matter). Hence we must believe that built-in cellular processes must have created these proteins—processes that are complex and require, among other things, proteins.

Real ones.

Tuesday, September 29, 2015

Metaphysics From John Ray to Nima Arkani-Hamed

An Ad Hoc, Capricious Creation

When John Ray refused to conform to the 1662 Act of Uniformity—aimed mainly at the Puritans—and so was forced to leave his position at Cambridge University, he roamed Europe for three years doing what he loved: observing nature. Ray and his companions were in for a surprise: unfathomable diversity. They found thousands of different kinds of insects, animals and plants. Every place had a different flora and fauna, and with different interactions. Life did not seem to follow the kind of compact formulas Isaac Newton was discovering for the new physics. With the overthrow of Aristotelianism, physics was becoming more parsimonious in line with Occam’s Razor. But biology was headed in the opposite direction. Were all these organic life forms and their detailed life histories really necessary? Ralph Cudworth had warned that the immense details of the world, while refuting Descartes’ rejection of final causes, were surely beneath the sovereign Creator’s dignity, and Ray’s three-year tour upped the ante. The Infra Dignitatem argument for a less hands-on creation story was born. There must have been something between the majestic Creator and this ad hoc, capricious, gritty creation. Like the Gnostics, the Aristotle of England, who would also become the father of natural theology, called for a separation between the Creator and the world.

The ancient Greeks described the cosmos as a set of concentric spheres that rotated and rubbed against each other producing harmonious tones. We have always wanted a simple, beautiful world. Certainly that is what God would have wanted too. But nature has not lived up to our expectations.

In fact ever since Newton, physics has been backsliding and becoming increasingly complex. All this was well explained in a Quanta magazine article from last week about leading physicist Nima Arkani-Hamed:

in recent years one question about the universe has come to preoccupy him, along with the field as a whole. Particle physicists seek to know whether the properties of the universe are inevitable, predictable, “natural,” as they say, locking together into a sensible pattern, or whether the universe is extremely unnatural, a peculiar permutation among countless other, more mundane possibilities, observed for no other reason than that its special conditions allow life to arise. A natural universe is, in principle, a knowable one. But if the universe is unnatural and fine-tuned for life, the lucky outcome of a cosmic roulette wheel, then it stands to reason that a vast and diverse “multiverse” of universes must exist beyond our reach — the lifeless products of less serendipitous spins. This multiverse renders our universe impossible to fully understand on its own terms. As things stand, the known elementary particles, codified in a 40-year-old set of equations called the “Standard Model,” lack a sensible pattern and seem astonishingly fine-tuned for life. Arkani-Hamed and other particle physicists, guided by their belief in naturalness, have spent decades devising clever ways to fit the Standard Model into a larger, natural pattern. But time and again, ever-more-powerful particle colliders have failed to turn up proof of their proposals in the form of new particles and phenomena, increasingly pointing toward the bleak and radical prospect that naturalness is dead.

Like Ray’s seventeenth century findings about biology, today’s physicists are finding what seems to be a capricious creation. There is no natural explanation as the world seems to consist of a long list of ad hoc, randomly selected designs. One thing they know for sure: no creator would have done this. It must have arisen by chance.

Religion drives science, and it matters.

Saturday, September 26, 2015

Evolution’s Junk Science at the University of Maine

It’s Not About Science

Thinking about taking CHY 431—Structure and Mechanism in Biological Chemistry next semester at the University of Maine? If so you likely will be fed junk evolutionary science like this page:


The page compares the amino acid sequences from the protein cytochrome c across 38 different species. A few of the residues are conserved across all 38 species. For example, position 10 consistently has the amino acid phenylalanine. And what’s the conclusion?  That “Clearly, evolution selects against any change at these positions.”

Clearly?

Actually this evolutionary reasoning has long since been demonstrated to be false with another, even more highly conserved protein—histone IV. If this was about science then students would at least learn what the observations, rather than the dogma, have to say.

Furthermore, the idea that the cytochrome c proteins from all of these species (from cows and ducks to yeast, fungus and bacteria) are related via common descent means that evolution must have created cytochrome c very early in evolutionary history. Certainly earlier than the advent of the electron transport chain (ETC) for which cytochrome c plays an important role. In other words, random mutations somehow created cytochrome c (a feat which itself has no scientific explanation), and then eons later the protein just happened to fit in with one of the most fantastic inventions in all of biology.

The serendipity is astonishing.

Later the page discusses the cytochrome c sequence positions that are highly variable. Here the student is told that “evolutionary drift randomizes these residues.” This is unfortunately yet more evolutionary dogma. In fact there is no scientific evidence that these residues have been “randomized.” That notion comes from the belief that evolution is true, in spite of the science. It may be true that those positions are neutral with respect to function and so can be “randomized,” but that is hardly obvious. Evolution has a long history of claiming structures are random and useless junk, only later to be corrected by scientific findings of function.

Finally the page compares the evolutionary tree based on the cytochrome c protein sequences with the traditional evolutionary tree and makes the ridiculously false claim that “Such trees tend to agree closely with those constructed by evolutionary biologists using morphological data, and provide independent evidence of common descent.”

In fact such trees often do not agree closely with trees based on morphological data. The differences are so significant that they cannot be explained merely as evolutionary “noise.” Therefore by modus tollens, according to the page’s own logic, the science falsifies common descent. No sense in telling the students about that though.

Religion drives science, and it matters.

Friday, September 25, 2015

Yockey and a Calculator Versus Evolutionists

Zero Probability is Not a Problem

In a 1977 paper published in the Journal of Theoretical Biology, Hubert Yockey used information theory to evaluate the likelihood of the evolution of a relatively simple protein. Yockey’s model system was cytochrome c, a protein consisting of about one hundred amino acids. Cytochrome c plays an important role in the mitochondria’s electron transport chain (ETC) which helps to convert the chemical energy in carbon-carbon and carbon-hydrogen bonds, in the food we eat, to an electrochemical potential energy in the form of hydrogen ions (or protons) stored within the mitochondria’s inner membrane. Like water pressing against a dam and turning its turbines to generate electricity, the high-concentration hydrogen ions drive the ATP synthase “turbine” to create the high-energy ATP molecule. Like the electrical outlets in your house, the ATP molecule provides a standardized form of energy that is used for a wide range of applications in your body, such as muscle contraction and nerve signals. There is no scientific explanation for how the ETC evolved. There also is no scientific explanation for how a single protein, such as cytochrome c, evolved. Yockey explained this in 1977, and since then the problem has only gotten worse.

Given 20 different amino acids to choose from, then for a protein with a sequence of 101 amino acids, such as cytochrome c, there are 20 raised to the power of 101, or 20^101, different possible amino acid sequences. That represents an astronomically (and impossible) number of sequences for evolution to search through to find a functional cytochrome c protein.

The problem is more complicated than this, however, since the different amino acids are not equally likely and there are many different sequences that will form a functional cytochrome c protein.

Yockey accounts for these factors to determine the effective number of sequences evolution would have to search through to find cytochrome c. For instance, Yockey uses the known cytochrome c proteins at the time, from many different species, to get an idea of the different amino acids that are possible at each position, within the sequence of 101 residues. Some residues allow for quite a few different amino acids while others seem to be more stringent.

This approach is reasonable, but by no means the only way of estimating the number of different amino acid sequences that could work. One way or another, the bottom line is this: while the number of different sequences that could form a successful type of protein, such as cytochrome c, is a pretty big number, it doesn’t solve the problem.

Yockey found that the probability of evolution finding the cytochrome c protein sequence is about one in 10^64. That is a one followed by 64 zeros—an astronomically large number. He concluded in the peer-reviewed paper that the belief that proteins appeared spontaneously “is based on faith.”

Indeed, Yockey’s early findings are in line with, though a bit more conservative than, later findings. A 1990 study of a small, simple protein found that 10^63 attempts would be required for evolution to find the protein.

A 2004 study found that 10^64 to 10^77 attempts are required, and a 2006 study concluded that 10^70 attempts would be required.

These requirements dwarf the resources evolution has at its disposal. Even evolutionists have had to admit that evolution could only have a maximum of 10^43 such experiments. It is important to understand how tiny this number is compared to 10^70. 10^43 is not more than half of 10^70. It is not even close to half. 10^43 is an astronomically tiny sliver of 10^70.

Furthermore, the estimate of 10^43 is, itself, entirely unrealistic. For instance, it assumes the entire history of the Earth is available, rather than the limited time window that evolution actually would have had. And it assumes the pre existence of bacteria and, yes, proteins. In fact, the evolutionists assumed the earth was covered with bacteria, and each bacteria was full of proteins. That of course is not an appropriate assumption for the question of how proteins could have evolved in the first place. In fact, it is circular.

Of course the evolution of a single protein is only one of many problems for evolution. Consider, for example, the cellular apparatus that constructs proteins—the protein synthesis machinery. One paper used a back-of-the-envelope, simple and conservative calculation to show that the probability of such an apparatus evolving by chance is one in 10^1018. That’s a one followed by 1,018 zeros. Normally in science this would be considered far beyond impossible, so therefore evolutionists are considering an infinite universe, or multiverse, to solve the problem. In such a universe, it does not matter how improbable any event is, it will eventually occur:

Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe … In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.

There you have it. Probabilities don’t matter. You can point out how unlikely evolution is, and evolution remains a fact. Science is done by people, and people seek certain answers, regardless of the data.

Religion drives science, and it matters.

Thursday, September 24, 2015

Evolutionists: We Now Have Empirical Evidence For the Evolution of Kin Recognition

Here We Go Again

In a new study out of the University of Liverpool evolutionists now say they have found empirical evidence that a genetic complex, involving dozens of protein-coding genes related to altruism, can evolve. Such a finding would be truly ground-breaking given that, at least up until now, the evolution of even a single protein has been found to be scientifically unlikely. It would be astonishing if now evolutionists have overturned a substantial body of work establishing molecular evolution to be effectively impossible. But of course evolutionists have done no such thing. There was no finding of molecular evolution, no new proteins or genes, no empirical evidence, nothing. Just another ridiculous claim made by evolutionists. It’s the same old pattern—evolutionists look at profoundly complicated biological structures, assume they evolved, and then claim they have found evidence of evolution.

Altruistic behavior creates many problems for evolution. You can see my explanation of some of them here. One problem I did not explain was the starting point: kin recognition. As I explain, evolutionists unsuccessfully tried to explain altruism using the concept of kin selection, and while that creates many scientific problems, you can’t even get to kin selection without kin recognition. How do animal siblings or cousins recognize each other.

The new study out of the University of Liverpool has found a genetic basis for kin recognition. It is a genetic complex of a couple dozen protein-coding genes and the problems with this are several.

First, it means that kin selection hinges on several proteins working together. Evolving a single protein is, from a scientific perspective, so unlikely as to be effectively impossible. But here evolution needs several proteins. Evolve just one protein and you still don’t have kin recognition. You would have to evolve several others, so the problem is even more difficult.

Second, the genetic cluster is species-specific. Apparently there is no common kin recognition mechanism across the vertebrates as evolutionists had assumed. Of course evolutionists had assumed this, for to have different mechanisms, particular to species or groups of species, would make their theory even more absurdly improbable. Kin recognition would have to re-evolve, in various ways, over and over. Well that is exactly what this new finding is suggesting. As usual, biology shows specific, particular, solutions that are unique to one or a few species, rather than falling into the expected common descent pattern.

Once again, common descent fails to serve as a useful guide. And once again evolutionists, in spite of the science, claim more proof for their theory.

Saturday, August 29, 2015

Seth Shostak: Just Add Water

Not Even Wrong

In a recent KCBS radio interview about his work for the search for extraterrestrial life, the Center for SETI research Director Seth Shostak repeatedly made claims about the simplicity of life. “Life is just chemistry,” Shostak informed interviewer Jeff Bell. Shostak elaborated that life is merely a collection of big molecules and that “You’re nothing more than that.” This just-add-water view of life is one of the many consequences of evolutionary theory and is so far from science that there is no point in even issuing a rebuttal. It is another example of metaphysics posing as science and making absurd statements with a straight face.

Religion drives science, and it matters.

Tuesday, August 18, 2015

BioLogos: Fundamentalists Were Wrong About Galileo, So They’re Also Wrong About Darwin

A Flawed History



It is one thing to point out particular conflicts between religion and science, it is quite another to characterize broadly the relationship between religion and science as one of conflict. The former is simply recognizing realities, the latter is the failed view known as the Conflict or Warfare Thesis. Certainly there are some genuine conflicts that arise from certain religious sects or traditions, but historically the relationship between religion and science is far more complicated than simply an on-going conflict. The BioLogos organization is very much concerned with this conflict, but they point out that they are careful to avoid the Warfare Thesis. Unfortunately this claim depends on a carefully crafted definition of the Warfare Thesis.

What is the Warfare Thesis?

The Warfare Thesis is bad history, but ironically too often the Warfare Thesis itself is the victim of bad history. Proponents of the Warfare Thesis are not necessarily atheists as they are sometimes portrayed. Nor do proponents of the Warfare Thesis necessarily see religion and science as mortal enemies, locked in an inevitable and necessary conflict. Like any broad movement the Warfare Thesis occupies a spectrum of views. From Voltaire and Edward Gibbon, to Hume, Kant, Washington Irving, Antoine-Jean Letronne, Thomas H. Huxley, John William Draper, Andrew Dickson White, and the many twentieth century proponents, the Warfare Thesis has had a wide variety of inputs and influences. Within its ranks one can find theists, agnostics and atheists. A common thread, however, is not the identification of conflict between religion and science so much as between fundamentalist religion and science. The problem lies with those scriptural literalists who can’t, or won’t, understand poetry or nuance in God’s word. Religion, once loosened from the fundamentalist grip, can take on its proper role. One of the Warfare Thesis strongest exponents, Andrew Dickson White, made this quite clear:

My belief is that in the field left to them—their proper field—the clergy will more and more, as they cease to struggle against scientific methods and conclusions, do work even nobler and more beautiful than anything they have heretofore done. And this is saying much. My conviction is that Science, though it has evidently conquered Dogmatic Theology based on biblical texts and ancient modes of thought, will go hand in hand with Religion; and that, although theological control will continue to diminish, Religion, as seen in the recognition of “a Power in the universe, not ourselves, which makes for righteousness,” and in the love of God and of our neighbor, will steadily grow stronger and stronger, not only in the American institutions of learning but in the world at large.

This religious sentiment was nowhere better illustrated than in the final scene of Inherit the Wind (click video above) which has the fictional character Henry Drummond (based on Clarence Darrow and played by actor Spencer Tracy) paying respects to his now deceased courtroom opponent, Matthew Harrison Brady (based on William Jennings Bryan and played by actor Fredric March).

Such sentimentalism does not sit well with atheist journalist E. K. Hornbeck (based on H. L. Mencken and played by actor Gene Kelly). Drummond quotes Scripture from memory and laments that “A giant once lived in that body, but Matt Brady got lost because he looked for God too high up and too far away.”

Hornbeck cries foul: “You hypocrite. You fraud. The atheist who believes in God,” but he is easily vanquished by the wiser Drummond who excoriates Hornbeck and his shallow skepticism. Hornbeck retreats from the courtroom while Drummond thoughtfully weighs his law book in one hand and the Bible in the other hand. He places the Good Book on top and victoriously walks out the other door to the rising crescendo of the Battle Hymn of the Republic.

Inherit the Wind is a classic staging of the Warfare Thesis. The ultimate target of Jerome Lawrence’s and Robert Lee’s script was McCarthyism and its witch hunts, but it was its weapon of choice—the Warfare Thesis—that made the play, and its many stagings and screenings, so popular.

And just as the Warfare Thesis is constructed from a false history, so too is Inherit the Wind based on a fictional retelling of the famous 1925 Monkey Trial. The historical furniture is rearranged to convey a false message of conflict, and yet the script is routinely held up as a cogent and accurate message for today. Such is the power of the enduring Warfare Thesis mythology.

So the Warfare Thesis is not an atheistic mission. Nor is it an attack on all things religious. Rather it is a religious view that seeks a harmonization which avoids the pitfalls of literalism and recognizes the advances of science. That may sound good, but in its attack on fundamentalism it fails to appreciate the complex relationship between religion and science. Religion, for example, can provide useful ideas to science and it can guiding restraints. The influence may or may not be cooperative, but it often is subtle and complicated.

What is BioLogos?

BioLogos is many things, but regarding the religion and science, BioLogos is concerned about conflicts. And not just any conflicts. President Deborah Haarsma recently reiterated BioLogos’ long-standing concern with Christians who do not accept the fact of evolution. Meanwhile Senior Editor Jim Stump expresses concern that design advocates are misleading people in areas such as climate change and vaccines.

These are all classic Warfare Thesis topics. They are politically, economically and metaphysically laden areas where the science is easily influenced by non scientific factors. Consider vaccines, for example, a topic that comes right out of Andrew Dickson White’s work. The facts are that vaccines provide varying levels of immunity at the very remote risk of injury. The details vary with the vaccine but, in general, patients are faced with a risk-reward tradeoff for which there is no scientific formula. Unfortunately the whole area has become politically charged and accurate statistics can be difficult to obtain. Even the mention of risk, which is a scientific fact, is too often met with disdain. It is the height of scientism—a spin-off of the Warfare Thesis—to argue that science dictates the answer. This is a human decision.

One of BioLogos’ arguments for its position is that it is following in the tradition of Copernicus and Galileo who advocated heliocentrism against scriptural opposition. Is it not obvious that Christians were right to alter their interpretation of biblical verses suggesting geocentrism, such as Psalm 104:5, Joshua 10:12-13 and Ecclesiastes 1:5.

The answer, of course, is “yes.” And for most such a modification was not difficult since it was doctrinally inconsequential. Indeed, most of Galileo’s opposition had little or no problem with such modifications and the scriptural questions were not high on his list of disputes he had to deal with.

Furthermore, when the perspective of those verses is understood (or as we say in science, the “reference frame”), there is no contradiction with heliocentrism. Galileo had plenty of political opposition, and he created much of it with his overbearing personality, but in his favor he had empirical evidences that were fairly suggestive of heliocentrism.

This is not analogous to today’s Warfare Thesis situation. The science does not at all suggest that the species arose spontaneously. We can argue over how unlikely this is, but BioLogos argues it is a fact. And as with all evolutionists, their confidence comes from the metaphysics, not the science. There are many proofs of evolution, but there is no scientific argument that supports the evolutionist’s claim that evolution is a fact. That is not my opinion, that is a fact of the literature.

Likewise, to compare the politically-charged man-made global warming theory with Galileo and heliocentrism is an insult to the great scientist and the theory he championed. Thoughtful commentators such as Matt Ridley have explained the non scientific influences on AGW, but the myth of certainty persists. This is not to say AGW is not true, perhaps it is. But we are far from knowing what its proponents proclaim as undeniable truth, and that is the point. The truth claims reveal that it isn’t about the science.

I tried to explain these issues at the BioLogos website. The website’s rule is the comments are closed after four days of inactivity. In this case, however, the evolutionists suddenly changed the rule and closed the discussion after a criticism of my points.

BioLogos is certainly on target to argue that scientific findings need to be acknowledged and recognized. And BioLogos obviously rejects the over-the-top atheistic versions of the Warfare Thesis. But that doesn’t change the fact that BioLogos’ support for non scientific mandates falls right into the Warfare Thesis tradition.

Monday, August 17, 2015

Evolutionists Have a Brand New Theory

The Philosopher is Dead, Long Live the Philosopher

For a theory that is supposed to be scientific, and therefore not teleological, evolution certainly does have its share of Aristotelian commitments. In fact, the Philosopher seems to be present at every turn in evolutionary thought. Consider the latest thinking from evolutionists—a brand new theory formulated to replace the last brand new theory which, not surprisingly, failed just as badly as the previous theories. The new one is called the extended evolutionary synthesis. First there was evolution. Then there was the evolutionary synthesis. Now there is the extended evolutionary synthesis. Well at least this one affords evolutionists a three-letter acronym. Here is how evolutionists describe it (as usual, watch for the infinitive form):

the EES regards the genome as a sub-system of the cell designed by evolution to sense and respond to the signals that impinge on it. Organisms are not built from genetic ‘instructions’ alone, but rather self-assemble using a broad variety of inter-dependent resources. Even where there is a history of selection for plasticity, the constructive development perspective entails that prior selection underdetermines the phenotypic response to the environment.

Designed by evolution? To sense and respond? Organisms self-assemble? This isn’t science, this is absurdity.