Creation Moment 11/29/2025 - The Miraculous Moonseed and the “Molecular Archaeology” Myth

Although they claimed to be wise, they became fools.... 

Romans 1:22 NIV

"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.

Q: 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.

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.

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.”

Q: 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.

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.

So 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."

CEH