Stephen Jay Gould (Harvard), though an evolutionist, acknowledged: “The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology.” (Natural History, 1977).

Even secular scientists like Lynn Margulis rejected Darwinian mechanisms for macroevolution, saying: “Natural selection eliminates and maybe maintains, but it doesn’t create.” (Acquiring Genomes, 2002).

There is active debate among biologists, philosophers of science, and bioengineers. The following challenge core Darwinian assumptions:

Your Claim: “Nothing in biology or pharmacology works without evolution.”

This is factually false and often used as a slogan (from Dobzhansky’s famous statement). In reality: Pharmacology, genetics, molecular biology, and bioengineering operate with design principles, not evolutionary models.

Drug design depends on biochemical interactions, not the assumption that a structure evolved. Bacterial resistance, often cited as proof of evolution, usually involves degradation of function, not new structures.

Your Claim: “Mutations making stuff not function is evolution. Example: lactase persistence or antibiotic resistance.” Lactase persistence and antibiotic resistance are adaptations, not examples of new functional systems arising. Lactase persistence is a regulatory mutation that keeps a gene on longer than usual—not a new gene.

These are all modifications or losses within existing systems. They don’t explain the origin of the system.

Your Ad hominem: “Michael Behe is a fraud…”

This is a logical fallacy—ad hominem attack. It avoids addressing the data Behe presents, which includes: Published in peer-reviewed journals (e.g., Quarterly Review of Biology)

Provided detailed analysis of protein-protein binding sites: Identified the statistical improbability of random mutations producing such systems (see Darwin’s Black Box, 1996).

Disagreeing with someone doesn’t justify calling them a fraud. A legitimate argument must address evidence, not attack the person.

“Behe said ‘most’ mutations aren’t helpful, but not all, so he’s wrong.”

This is a straw man fallacy. Behe admits some beneficial mutations exist but shows they are: Degradative in nature (e.g., breaking genes to survive) Not constructive innovations.

Bacterial adaptation often involves disabling surface proteins to block viral infection—not a gain of function, but loss.

The burden of proof is not showing some beneficial mutations, but showing a continuous pathway from no information to complex systems via undirected mutations.

Your Claim: Dawkins’ statement is wrong. The quote from Dawkins is widely cited: “Most mutations are bad. A very few are good, and the rest are neutral.” (The Greatest Show on Earth, p. 113).

This is consistent with all known mutational data from: Lenski’s E. coli experiment (majority were non-beneficial or neutral) Human disease mutation databases.
Claim: “E. coli evolved the ability to digest citrate.”

This is a grossly misrepresented example: Lenski’s long-term evolution experiment (LTEE) did show citrate metabolism—but under aerobic conditions, which E. coli already can do anaerobically.

The mutation was a duplication of a pre-existing gene promoter, allowing its expression in a new context—not the invention of a novel function. It wasn’t new information; it was repurposing existing parts—the biological equivalent of rewiring, not inventing a machine.

Your Claim: “Transitional trilobite in the ‘Richiida order’.” There is no such recognized order as Richiida—perhaps the critic meant Redlichiida (a known Cambrian trilobite order). Even so, trilobites appear suddenly and fully formed in the fossil record, with:

You said: “You act like new body plans evolve in one generation.”

Straw man. The argument never claimed that evolution asserts body plans arise in a single generation. Rather: Evolution requires a plausible step-by-step pathway from existing structures to new ones, with each intermediate step being selectable and beneficial.

The Problem: There is no evidence of a mutational pathway from:

• No wings → full bird wings
• Scales → feathers
• Worms → trilobites

And there is no evidence that mutations alone can coordinate the massive epigenetic and developmental changes necessary.

You said: “Evolution is about birth defects providing advantages.”

Yes—and that’s the problem. Birth defects are loss-of-function mutations—rarely constructive or information-building.

A beneficial mutation like sickle cell is a degeneration that offers malaria resistance at the cost of overall health.

It’s a trade-off, not a creative advancement. This is not evidence that birth defects can build: Complex organs, Sensory systems, Irreducible mechanisms like the bacterial flagellum.

You said: “You used the Discovery Institute script.” Another ad hominem fallacy.

This avoids the evidence presented by labeling the argument as scripted. The Discovery Institute’s work, including peer-reviewed papers, addresses real scientific questions: Biocomplexity journal, Conferences with PhDs in chemistry, biology, paleontology.

Criticizing a source without refuting its specific claims is intellectually lazy.

You said: “You’re defending evolution by pointing to examples of degeneration, duplication, and regulatory shifts—none of which explain the origin of complex biological systems or new body plans.

The real issue is not whether mutations happen, but whether unguided mutations can create functional, specified information and integrated anatomy.

Antibiotic resistance, sickle cell anemia, and citrate metabolism are modifications of existing systems, not inventions. And attacking Behe or citing slogans doesn’t substitute for evidence.

The true scientific challenge remains: Where is the mechanism that builds the code and coordination required for life from randomness? That’s the heart of the debate.

Augustus Smith Did Not Reply