Genome complexity: what genes do and don't do (Introduction)

by dhw, Wednesday, February 13, 2019, 14:24 (1898 days ago) @ David Turell

DAVID: Again, I don't believe the large steps required in rearranging a species into a new one is simply cell adaptation. [...]

dhw: I have never said speciation was “simply cell adaptation”. But it is sometimes difficult to draw a borderline between adaptation and innovation, as in legs becoming flippers. And I have repeated ad nauseam that we do not know if cell communities can innovate (= take the necessary large steps), which is why my hypothesis is an unproven hypothesis, as is your own.

DAVID: The problem for you is you accept the necessity for design but not the designer.

That is why I am an agnostic and do not confine my hypotheses to a single, top-down designer. But we are discussing the process of evolution, not my agnosticism.

DAVID: My point is living organisms run on information stored in the genome, much of which had to be pre-programmed for life to have formed at all. Inorganic matter does not have functional information, which means as life started from the inorganic, information had to be GIVEN from someone.

dhw: Once again you scurry back to the origin of life, whereas my point is that living organisms do NOT run on information stored in the genome but – in your own words – they run on their “own operating system” for interpreting that information and acting on it. Information without the means to interpret and act on it would be no use to any organism. But having told us that organisms must have their own operating system, you still insist that they don’t – all their actions are apparently the result of your God’s dabbles or their automatic, non-interpreting, non-decision-making obedience to instructions passed down by the first living cells through 3.8 billion years’ worth of innovations, lifestyles and natural wonders.

DAVID: Just like Darwin (as usual) you avoid the origin of life, the worst problem for naturalism, which exists in a continuum with further evolution and most always be part of the discussion.

Why “must” it be? In our discussions I have accepted the possibility that your God designed the first living organisms. (So, by the way, did the agnostic Darwin.) Our disagreement concerns Chapter 2: if your God exists, and if – as we both believe – evolution took place, then what were his purposes and methods?

Dhw (re bacterial resistance): Maybe the mechanism is not “spontaneous”, and maybe resistance/non-resistance depends on what you would call each bacterium’s “own operating system” for interpreting information and acting on it, i.e. “single cells change their metabolic pathways"… and “learn” and “create instructions on the hoof”, as proposed in the article you initially agreed with. The expansion of resistant bacteria would then take time because those bacteria which work out the solution to the new problems would have to pass on the new information.

DAVID: The one percent who have resistance multiply every 20 minutes. Not much time to take. Lenski's E.coli show this.

Time is not the main point here, as we are discussing the mechanisms that enable resistance: your 3.8-billion year old library of information and instructions, or an autonomously intelligent “own operating system” in which bacteria create their own instructions. I mentioned time because it can take a while before antibiotics become ineffective.
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Under “new axons may make local decisions”:

DAVID: A new study strongly suggests that newly developing axons have some degree of self-control […] (dhw’s bold)

If distant parts of the system have a degree of self-control, doesn't this suggest to you that the central part of the system itself also has self-control or, in your own words, its "own operating system".

https://medicalxpress.com/news/2019-02-nerve-cells-foot-soldier-axon.html

QUOTES (dhw’s bold):
"We are not the first to think that there has to be some autonomy…"

"This finding [...] proposes a more intricate web of decision-making and the existence of semi-independent units far from central command."

"What our results suggest is that growth cones are capable of taking in information from the outside world, making signaling decisions locally, and functioning semi-autonomously without the cell body," he said.

Macklis proposes that the cell body may be like a server connected to smart PCs that have the capability to interface with the world.

[NB: we should not forget that PC’s are a form of artificial intelligence. The PC is therefore used as an image for natural intelligence.]

DAVID: The findings open up part of the black box of how complex regions of the human brain can develop into five cooperative layers in the frontal cortex. My thought is the nucleus of the neuron tells the axon what to look for in a set of connections and the axon finds them on its own, as the article suggests, growing toward what it senses, far away from the body of the neuron. This was evolved when the first complex set of neurons made an early form of the brain, by design.

Thank you once more for your integrity in presenting yet more evidence that cells and cell communities are run by independent, decision-making intelligence, as bolded. In this context, I take “semi-autonomous” to mean that some decisions are taken independently of the main control system (the nucleus and cell body).