Moonseed Evolution or Another Looney Tune?
The evolutionary paradigm
requires a seamless story, so
the story must supply the seam
The Miraculous Moonseed and the “Molecular Archaeology” Myth
by John D. Wise, PhD
I have been writing for CEH for only six months, a brief moment compared with the twenty-five years our editor David Coppedge has invested in this work. Even so, with a lifetime in philosophy and a much more than passing knowledge of scientific literature behind me, I did not think I could still be surprised by evolutionary storytelling. I read evolutionary papers every day. I know the usual routines, the narrative sleights of hand, the confident metaphysics humming beneath the surface.
Still, this one caught me off guard.
“Tracing the stepwise Darwinian evolution of a plant halogenase,” Science Advances, 13 August, 2025.
The chemistry was dense, the jargon layered like geological strata, and I initially assumed my own ignorance was the problem. But as I pulled at the loose threads, with ChatGPT helping unravel the scientific machinery, I discovered something I had not fully appreciated before. It was not just a flaw in a single argument. It was a template, a workflow, a standard operating procedure for evolutionary narratives.
Once I saw it, I could not unsee it.
The Moonseed Enzyme
Canadian moonseed is one of the very few plants on Earth that can attach a chlorine atom to one of its defensive molecules. Chlorine chemistry in plants is vanishingly rare, with less than five examples in all the plant kingdom. When researchers found the enzyme responsible by sequencing the full genome, they naturally asked where it came from. Evolution, after all, must explain novelty through continuity.
In other words, when stuff happens – in this case a plant-based halogenization – we must be able to explain its evolutionary lineage.
From what did this unique enzyme (DAH) derive?
The Ancestral Guesswork Begins
They picked flavonol synthase (FLS), an enzyme common across plants that performs a completely different reaction. FLS does not halogenate anything. It has none of the specialized architecture needed for chlorine chemistry. But it shares some sequence similarity with the moonseed enzyme, so into the ancestry slot it goes.
“Close enough.”
Reasonable. But this is where a little Socratic humility would have helped. Something like, “We could be wrong,” or “There are other possibilities,” or “Maybe this gene has nothing to do with it.” Instead, FLS gets drafted into the story simply for being in the vicinity, like the guy at the crime scene who vaguely resembles the suspect.
And the narrative closes around it with an audible “snap.”
To test this evolutionary proposal, the authors reconstructed a hypothetical “ancestral” FLS enzyme using computational inference. Then they synthesized it in the lab and tested whether it could perform even a faint version of the moonseed reaction.
It did.
A Two Percent Ancestry?
“Decoding the ‘impossible’ chemistry of moonseed to rewrite the understanding of plant evolution,” Phys.org, August 18, 2025. Jing-Ke Weng, professor of chemistry, chemical biology and chemical engineering at Northeastern, whose Weng Lab led this project said:
“We managed to recover around 1% to 2% of the halogenase activity by starting from the ancestral state. That means evolution really has taken a really narrow path to come to this newly optimized activity. There’s a lot of serendipity in the path and it took many turns, but it eventually found a way to achieve this reactivity in this newly evolved enzyme.”
Wait.
The reconstructed enzyme managed one to two percent of the modern enzyme’s (DAH) activity? In biochemical terms, this is indistinguishable from no function at all. Natural selection does not refine noise. A reaction operating at two percent of the necessary rate produces no meaningful effect inside a living cell. There is no selectable advantage. There is no evolutionary traction.
Yet the researchers embrace this flicker of activity as the starting point of a long evolutionary journey.
As some of my favorite old infomercials used to say, “but wait … THERE’S MORE!”
Enter “Molecular Archaeology”
This brings us to one of the most remarkable statements in the Phys.org reporting:
“To understand what has happened in the past that leads to the current state of things in terms of cultures, countries and many other things, we rely on archaeology,” Weng says. “The work we took here is essentially molecular archaeology.”
I read that line three times to make sure it was not satire.
I’m a serious fan of archaeology. Archaeology digs up potsherds, inscriptions, bones, metalwork, clay tablets, walls and foundations of ruined cities. You brush away sand and find an object someone held in his hand three thousand years ago. You photograph it. You weigh it. You catalog it.
It exists.
Watch the hilarious Short Reel about this article! Click to view it now.
This “molecular archaeology” is nothing like that. You don’t find anything in the dirt, or even in the genome or the fossil record. You generate a speculative sequence with a computer, build it in the lab, and then congratulate yourself for discovering a past that left no trace. This is not unearthing history. It is creating an imagined ancestor and treating the imagination as evidence.
If a real archaeologist did this — drew a picture of a hypothetical pot, buried it in the backyard, dug it up the next morning, and then announced a breakthrough in Bronze Age pottery — we would call it performance art, not science.
Who’s kidding who here?
And Then Comes the Certainty Game
The popular article continues:
“They tracked DAH back to a gene found in other plants, flavonol synthase (FLS), giving them their first indication that DAH started as a much more common enzyme. They were then able to see how, over the course of hundreds of millions of years, moonseed underwent a gradual series of gene duplications, losses and mutations to reach the point where a once-regular enzyme could swap oxygen for chlorine.”
Did you catch that? “They were then able to see how”?
As if they watched it happen?
As if the intermediate proteins were fossilized neatly in the strata and you could track the unfolding history?
In reality, they saw nothing. A computation aligned with an expectation, and an intelligently designed, laboratory-constructed enzyme managed to add a chlorine atom 1-2% of the time.
What these researchers “saw” was a narrative supplied by their paradigm, not by the data.
That’s not vision. It’s projection.
If the authors had written “we assume” or “we propose,” the rhetoric would match the evidence. Instead, the language of certainty quietly converts speculation into something that sounds like observation.
A Final Thought
The moonseed enzyme study is fascinating in its chemistry but even more revealing in its rhetoric. The one to two percent activity of the supposed ancestral enzyme is not a pathway. It is a cliff. The evolutionary continuity exists only in their imagination and certainly not in the data. The authors know this, but the evolutionary framework they inhabit requires a story of gradualism, so the language of discovery stands in for the work of demonstration.
At some point my shock became clarity. There is a pattern here, and once you recognize it, you see it everywhere.
Here is the workflow we just uncovered, stripped of its jargon:
- Find a modern enzyme doing something impressive.
- Assume it evolved from something simpler.
- Pick the nearest similar-looking gene as the “ancestor,” whether or not it performs anything like the required chemistry.
- Infer a hypothetical ancestor with a computer algorithm.
- Synthesize the imaginary ancestor in the lab.
- Test it, discover it barely works, and call the chemical static a “proto-function.”
- Fill in the rest with a narrative of slow, steady improvement over “hundreds of millions of years.”
- Use the language of observation (“we saw how it evolved”) to give the story the force of evidence.
That’s the procedure in a nutshell.[1]
But here is what knocked the wind out of me: this is not a one-off accident. This is standard operating procedure in evolutionary molecular biology. This is how countless enzyme-origin stories are written. Smart, sophisticated, technically brilliant scientists do this every day, confident that their reconstructions reflect real history and never allowing themselves to see that they are manufacturing the past they believe they are uncovering.
The problem is not intelligence. It is what we have called the Hegelian Compulsion to Closure at work.
The paradigm requires a seamless story, so the story must supply the seam.
So, CEH readers, the next time an evolutionary paper announces that scientists have “reconstructed” a pathway or “seen” an ancient process unfold, you can smile, shake your head, and remember the moonseed enzyme.
If hypothetical sequences created on a computer now qualify as archaeological artifacts, then we’ve given up on observing the past.
Instead – for evolutionary biology in any case – we are inventing it.
Footnote
[1] And notice that every step is intentional and intelligently designed. The laboratory procedure of synthesizing a unique protein enzyme is technologically advanced. The discovery, testing, statistics and procedures are saturated with intelligent design, yet this is the one thing that evolutionary biology will not allow to its subject. Stunning.
John Wise received his PhD in philosophy from the University of CA, Irvine in 2004. His dissertation was titled Sartre’s Phenomenological Ontology and the German Idealist Tradition. His area of specialization is 19th to early 20th century continental philosophy.
He tells the story of his 25-year odyssey from atheism to Christianity in the book, Through the Looking Glass: The Imploding of an Atheist Professor’s Worldview (available on Amazon). Since his return to Christ, his research interests include developing a Christian (YEC) philosophy of science and the integration of all human knowledge with God’s word.
He has taught philosophy for the University of CA, Irvine, East Stroudsburg University of PA, Grand Canyon University, American Intercontinental University, and Ashford University. He currently teaches online for the University of Arizona, Global Campus, and is a member of the Heterodox Academy. He and his wife Jenny are known online as The Christian Atheist with a podcast of that name, in addition to a YouTube channel: John and Jenny Wise.