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

by David Turell , Friday, February 08, 2019, 15:31 (1905 days ago) @ dhw

DAVID: I theorize and so do you. What has a 50/50 chance is only that cells have some ability to intelligently respond to stimuli with simple adaptations. The rest of your statement is conflation.

dhw: The rest of my statement concerns your own hypothesis, so I don’t know what you think I’m conflating. Nobody knows how innovation takes place, although it is sometimes difficult to draw a borderline between invention and adaptation (e.g. legs becoming fins and vice versa), but at least we know that adaptation does happen, and you have not (yet) included instructions for that in your vast library.

The bold in your comment above is conflation. Changing leg to fin is full blown evolution of a new species, never to be compared to minor adaptation which is all bacteria do. They adapt but do not change into a new species. Lenski's E. coli are a clear example with some alterations in metabolic use of substrates. What most cells do in all organs is their job without variations.

dhw: And so you have a fixed belief in an extraordinarily convoluted hypothesis, as bolded, for which there is no evidence, but you reject a far more straightforward hypothesis because there is no evidence.

As Paul Davies notes, "we don't know how the hardware produces the software', to which
I answer, the genome has many functional layers we still do not understand. My theory lies in those areas as an expectation Davies answer will be found there. I'll change my view based on factual research. Convolution is in the eye of the beholder. Living biochemistry is extremely complicated which includes convolutions of many processes operating in concert and at times antagonistically in feedback loops.

DAVID: Conflation again. I'm talking about current scientists, not the older ones you quote.

dhw: Shapiro is not an “older one”, and it is absurd and probably libellous to dismiss the findings of current scientists as fake simply because they confirm the findings of older scientists with whom you disagree. You never complain about the grant system if an article seems to support your own fixed belief in "automaticity", and in any case you didn’t disagree with the article you quoted: you said it expressed your own thoughts.

You are off point. I'm discussing the very current overstatements of the research results as to proof. Again look at the series of theoretical origin of life for examples. The hyperbole
is a recent event in the past ten years or so. Faux articles are constantly being accepted by borderline journals. I still have the right to present and re-interpret the findings, in order to counter to the overblown conclusions. Findings are fixed fact. Interpretations are another breed of cat.

DAVID: Multicellular organisms are not bacteria. I don't think Shapiro's point carries over.

dhw: At least you now seem to be accepting Shapiro’s view that bacteria work out their own ways to cope with new threats. Do you honestly think that if single cells can do this, communities of cells can’t?

In multicellular organisms things are much more complex and cells in organs have very specific fixed jobs. Single cells must do everything and must be able to make simple altered responses to a variety of stimuli that present themselves, a wholly different set of circumstances that does not transfer over to the much more complex organisms. You are trying to compare cows to clams.

dhw:[…] what interests me here is the versatility of stem cells. When conditions change, cells/cell communities must also change if they are to survive (adaptation), but perhaps innovation takes place when certain cells are given totally new functions. It seems that stem cells can do precisely this.
DAVID: Yes.

DAVID: (under “stem cells”) I can't find my recent entry which indicated not much is known, but here is an entry about a coming conference:
https://www.the-scientist.com/sponsored-webinars/stem-cells--opportunities--hurdles--an...

"Since Sir. Martin Evans’ 1981 identification of embryonic stem cells in mice, stem cells have been at the center of the drive to revolutionize medicine and the drug discovery process. In 1998, human embryonic stem cells were grown in a lab, and the field was further boosted in 2006 with the pivotal discovery of induced pluripotent stem (iPS) cell techniques, which removed the need to destroy embryos. […] The Scientist is bringing together a panel of experts who will share their research, explore cellular reprogramming, and discuss the next steps.
"Topics to be covered:
Molecular mechanism of induced pluripotency
Roadblocks to iPSC reprogramming, and erasing transcriptional memory in cellular reprogramming"

DAVID: all that is known is from very recent work

dhw: Maybe the conference will yield more details, though the experts don't seem to be concerned with possible implications for how evolution works. What they call “pluripotency” (= my “versatility”) could be the key to the whole process. Many thanks for searching.

Speciation must be done through stem cells. We know of some processes that alter their eventual output, both chemical and mechanical.