Neo-Darwinism Is Dead,. THETHEORY OF INTELLENCE DESIGN MUST BE ADDED TO COMPLETE EVOLOTION

• I want to thank Perry Marshall for hosting the conversation, and I want to thank Denis Noble for participating in it. It was a lot of fun, and I hope you enjoy it.
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• Neo-Darwinism Is Dead
• If you’re not familiar with Noble, he is not a supporter of intelligent design, but he is a vocal critic of neo-Darwinian evolution. Last year I wrote about the fact that he said quite plainly in an interview that “neo-Darwinism is dead.” Last year he also wrote an article in Nature titled “It’s time to admit that genes are not the blueprint for life,” where he said, “Classic views of evolution should also be questioned,” and urged scientists to consider new ideas about how life works:

• It’s time to stop pretending that, give or take a few bits and pieces, we know how life works. Instead, we must let our ideas develop as more discoveries are made in the coming decades. Sitting in uncertainty while working to make those discoveries will be biology’s monumental task for the twenty-first century.

• In a post covering his article, I noted that part of Noble’s vision for the future of biology is the role played by teleology or teleonomy:

• Noble also thinks there’s a place for “agency and purpose” in biology. He’s not talking about the intelligent design of life by an external agent, but he is acknowledging that much in biology is purposeful, noting that multiple experts now “argue that agency and purpose are definitive characteristics of life that have been overlooked in conventional, gene-centric views of biology.” Again, this isn’t the modern theory of intelligent design, but once we begin to allow agency and purpose into our understanding of how life works, we’re taking important steps towards being able to recognize design in biology.

• Technical Difficulties
• The conversation with Perry and Denis took place in November 2024 but was hit with technical difficulties from the start.
• For one, the conversation took place right after my wife and I went multiple days without power after a bomb cyclone hit Seattle. Perhaps this was a blessing in disguise, because with no Internet at home I could read (sometimes by flashlight) various books on “Third Way” evolution in preparation. These readings inspired me to create a rough Venn diagram comparing the similarities and differences between Neo-Darwinism, Third Way Evolution, and Intelligent Design, which Denis, Perry, and I discussed during the conversation.
• The second technical difficulty was that the video element did not record. The good news is that the audio came out fine, and so Perry has now posted an audio version of the conversation, with video overlain showing images of the speakers and the aforementioned Venn diagram for the viewer’s reference.
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• Programming in Biology
• One last note about the conversation: there was one point where I in artfully addressed whether cells contain “programming.” My exact words were that they don’t necessarily contain “programming,” but what I should have said is that they “don’t contain programming that’s exactly like human software.” Now context is key because in that section we were discussing whether DNA contains “conditional logic” like you find in computer programming. It’s true that you won’t find an explicit “if-then” programming statement in the DNA itself. That’s all I was saying. Yet DNA does unmistakably contain programming: it contains commands and instructions that are read, interpreted, and executed by cellular machines (e.g., the ribosome) much like the hardware of a computer reads, interprets, and executes the instructions in software. This shows that DNA contains properties very similar to computer programs.
• I’m not a professional computer programmer, but I do know a bit about programming, having, among other things, written over 30,000 lines of Python code during my PhD. Though you won’t find an explicit “if-then” statement in DNA, that doesn’t mean that there isn’t programming in DNA or conditional logic in biology. What is really going on in cells is that the programming in DNA encodes the parts to build cellular machinery, which produces protein and RNA molecules, and these molecular products of DNA’s programming then go out into the cell and perform chemistry-based logical operations that frequently amount to nothing less than conditional logic. Many examples could be discussed, but let’s consider a famous one: the lac operon.
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• An operon is a group of genes expressed together to produce a single RNA transcript with stop codons separating protein-coding regions. The lac operon regulates production of enzymes that help many bacteria species break down and use lactose as a food source. Here’s roughly how it works in E. coli:
• Glucose is E. coli’s preferred sugar. The bacterium thus only wants to turn on the lac operon when two logical conditions are met: (1) glucose is depleted; and (2) lactose is present.
• When glucose is present, E. coli doesn’t need to use lactose. But when glucose is depleted, this initiates a cascade that ultimately recruits the RNA polymerase to bind to the promoter sequence on the bacterial chromosome.
• And when lactose is absent, the bacterium doesn’t want to waste resources transcribing and translating the genes that produce the enzymes that metabolize lactose (lac, Placy, and lava). So when lactose is absent, a repressor molecule binds to the bacterial chromosome in just the right place to prevent the RNA polymerase from transcribing those genes. But when lactose is present, this allows the production of a derivative (allo lactose), which binds to the repressor, causing the repressor to release from the chromosome—clearing the way for transcription to occur.
• When both conditions are met—glucose is depleted and lactose is present—this allows the genes for metabolizing lactose to be transcribed and lactose to be used as a food source in the cell.
• This is conditional logic, and if we were to express it in pseudocode, it might look something like this:
• That essentially represents conditional-logic-based programming in biology. But if that wasn’t clear, here’s a rough homemade.
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