February 7, 2023 | David F. Coppedge

Nitrogen Fixation: No Evolution Here

It’s “one of the most energetically challenging biochemical reactions
in nature,” and it just appeared and never changed.

 

Here’s the scoop: a complex reaction essential to life on earth has never been replicated by engineers, but it “emerged” in bacteria somehow, and has not evolved since. Does that sound like Darwinian evolution?

Nitrogenase is a true wonder of nature. This enzyme, found in certain bacteria, is able to break the tough triple bonds in atmospheric nitrogen (N2), allowing plants to utilize the essential element found in every protein. Human engineers, eager to fix nitrogen for fertilizers, have to use a very energy-intensive process at high temperatures and pressures to break those bonds (the Haber-Bosch Process), but the bacteria do it easily at room temperature. How did this near-miraculous feat “emerge” in the world’s so-called simplest organisms, and why hasn’t it evolved? Therein lies a tale. It’s told in a preprint that appeared this month.

Nitrogenase resurrection and the evolution of a singular enzymatic mechanism (bioRxiv, 5 Feb 2023). Researchers at the University of Wisconsin and Utah State decided to look into the evolution of nitrogenase enzymes. When did they first appear? Is there an evolutionary sequence from a common ancestor? Here’s what they found, contradicting their assumptions about evolutionary “emergence.”

The planetary biosphere is powered by a suite of key metabolic innovations that emerged early in the history of life. However, it is unknown whether life has always followed the same set of strategies for performing these critical tasks. Today, microbes access atmospheric sources of bioessential nitrogen through the activities of just one family of enzymes, nitrogenases. Here, we show that the only dinitrogen reduction mechanism known to date is an ancient feature conserved [i.e., unevolved] from nitrogenase ancestors.

For their experiments, they used engineering (a form of intelligent design). They engineered what they consider an “ancestral” form of the enzyme and inserted it into a living bacterium. If evolution were true, there should have been so many changes over billions of years that it would seem unlikely to work at all.

We designed a paleomolecular engineering approach wherein ancestral nitrogenase genes were phylogenetically reconstructed and inserted into the genome of the diazotrophic bacterial model, Azotobacter vinelandii, enabling an integrated assessment of both in vivo functionality and purified nitrogenase biochemistry. Nitrogenase ancestors are active and robust to variable incorporation of one or more ancestral protein subunits. Further, we find that all ancestors exhibit the reversible enzymatic mechanism for dinitrogen reduction, specifically evidenced by hydrogen inhibition, that is also exhibited by extant A. vinelandii nitrogenase isozymes.

The “ancestors” they speak of are other forms of bacteria that the authors believe evolved over time. Where was the evolution? Even accepting their premise of ancestry, none of their explanation bears on how nitrogenase first appeared.

Our results suggest that life may have been constrained in its sampling of protein sequence space to catalyze one of the most energetically challenging biochemical reactions in nature. The experimental framework established here is essential for probing how nitrogenase functionality has been shaped within a dynamic, cellular context to sustain a globally consequential metabolism.

They’re saying that however it “emerged,” nitrogenase was “constrained” from evolving because it had too important a job to do. It couldn’t let the Stuff Happens Law take over. So after some unexplained “emergence” (a virtual miracle without plan or foresight), it did not evolve further. And thank goodness it didn’t, because its value has global consequences for the metabolism of every other living thing.

Sequence Space

But what is this “protein sequence space” they speak of? It’s like a game of chance. Think of the philosopher’s analogy of an urn with colored marbles. Natural selection, with no foresight, purpose or goal, periodically takes a marble out and puts it back, not remembering what it had already drawn. Say that most of the marbles are white, but rare ones are red. If evolution’s “emergence” task depends on finding a red one, how long would it take for something useful to be selected? Read on….

Introducing creative destruction as a mechanism in protein evolution (PNAS, 2 Feb 2023). In a commentary paper, Margaux Aubel and Erich Bornberg-Bauer try out a new theory about protein evolution. They begin with the sequence space problem:

To be innovative, molecular evolution needs to screen a gigantic search space, e.g., for a protein of “typcial” [sic] length with 300 amino acids, 20300 (equal to a number with 391 zeroes) combinations are possible. It has been a long-standing riddle how evolution has managed to find the presumably small patches in this sheer endless space, which host functional and structured proteins.

They severely understated the problem faced by materialist evolutionists. Let us elaborate with the marble analogy. The number of red marbles in our urn is staggeringly small, unthinkably, impossibly small. Considering that our whole universe only has about 5×1078 atoms, it would take multiple multiverses of stars with earthlike planets to hold the number of urns full of white marbles to draw from to get a fair representation of the challenge facing the Stuff Happens Law. Out of all these “sheer endless” multiverses, a few red marbles are scattered at random.* These represent “useful” proteins of a typical length that fold and can perform some function.

*For one estimate, Doug Axe estimated that one in 10164 sequences of length 150 amino acids would be useful; for a protein 300 amino acids long, the probability would be lower by many, many orders of magnitude. See the video below from Illustra Media illustrating the problem.

The Darwinist sends a blind man out into one of the gazillion universes to search urns on quintillions of exoplanets to pick out marbles at random. What are the chances it will be a red one? Don’t even hope. The odds are beyond silly. Even if the blind man lucks out within the age of the universe, it does no good unless it is found on our Earth, where the goddess of Evolution needs it. The next lucky red marble will be even more difficult to obtain, because it has to match the first one. And so on.

So what do these authors do? They try a “modular” approach. Maybe the search space can be reduced if lucky sequences are shorter than 300 amino acids.

A common theme in many areas of evolution is modularity, which helps to reuse existing parts efficiently and puts them together such that novel traits can be explored with less danger to go astray.

Following the modularity concept, the recombination of small independent units swiftly leads to novelty. By combining or rearranging those modular units, large and more complex ones can be generated enabling the exploration of new functions, without the need to go through the vast sequence space.

Sounds simple. Does it work? They give examples of modular proteins in living cells, but that begs the question that they originated by chance. Given words, sentences can join together in random ways that might make some sense. But here, again, is a combinatorial problem: out of all the possible word combinations, how many will make sense, and how many of those will be found at the same time and place to create meaning? Going back to the marble analogy, how many sets of 10 or 20 marbles will turn up all red, when red marbles are extremely rare? It’s the old conundrum of hoping for a dictionary to emerge from an explosion in a print shop.

Art by J. Beverly Greene for CEH. All rights reserved.

That’s only the beginning of headaches for materialists. Remember that evolution has no way to store the marbles in sets. Amino acid chains (polypeptides) are subject to destruction immediately upon formation. They are not going to stick around long enough for other modules to show up and work together. This is a ridiculously false hope.

Dr James Coppedge, in his book (online here), tried random combinations of letters and after tens of thousands of tries, only got useless words that mean nothing together. Out of 30,000 draws of letters, he got 3 sequences of 6 letters that had possible meanings (agmcap, weeted, and ruinpa), and only one with 7 letters (see ch. 6). But if those sequences were to disassemble within minutes of formation (as happens with amino acids in a primordial soup), nothing would ever be gained.

Look at the cartoon by Brett Miller above. Let’s play with the authors’ idea of modularity. After millions of years of trial and error, we land upon the word “oops” by chance. That’s our first module. Suppose, by chance, a copy reverses it and the word spoo emerges. Then the two modules merge, and become oopsspoo. Some of the letters interchange, and maybe the next stage of evolution produces oopspsoo. More modules are added, and some letters drop off, and we get opspsoopoopoo, and so forth. Does anybody really believe this is a way to derive meaning and function by chance?

The rest of the PNAS commentary makes no sense. The two authors try to support a notion called “creative destruction,” wherein lucky sequences improve when parts get lopped off. Here’s an analogy they give to explain this.

Your honor, I wish to show Exhibit A to the jury.

This scenario is reminiscent of the cassette player being modeled into an mp3 player, where the bulky cassette is destroyed to make way for the much smaller mp3 player…. This [creative destruction in protein folds] would be analogous to the bulky cassette player speakers being remodeled into mp3 headphones.

No further questions, your honor.

Do evolutionists realize how silly they look? Let’s use another example of “creative destruction.” An urban legend has it that Michelangelo was asked how to make a statue of David. He answered, you start with a block of limestone and simply cut away all the parts that don’t look like David.

Now, imagine the Stuff Happens Law doing this. A block of limestone falls from a cliff and lands in a sand dune. Nobody is around to watch or care about what happens next. Over millions of Darwin Years, sand grains pummel the limestone, and eventually, a statue of David “emerges.” The sand, you see, just happened to erode all the parts that didn’t look like David. To make it happen faster, sand grains recombined into modules. Those are known as rocks. Since it would take too long for sand to carve the statue, rocks pummeled the limestone and accomplished the job in less time.

Don’t be intimidated by their jargon and degrees. These otherwise smart people are spouting utter nonsense. They believe in miracles. Creationists can accept intelligently-designed miracles by an almighty God who has the power and wisdom to do mighty works for a purpose; that makes sense. But we don’t have enough faith to believe in the ridiculous miracles of chance required by evolutionary theory.

Now watch this video from Illustra Media and gain the confidence to laugh at nonsense.

 

 

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