How NOT To Think About Cells

[MarkE]

"A few years ago Veritasium posted a video portraying 'molecular machines'. But is that really the right way to think about the inner workings of our cells? Are we all just running on molecular clockwork?"

https://youtu.be/jPhvic-eqbc?si=_AaJLOYY5FPiZ8aK

I thought this was worth sharing (the presenter assumes evolution; not a creationist video). He challenges the machine metaphor for cells and the electronic circuit for enzyme function.

I guess evolution will claim this as the messy and jerry-built product of trial and error, and ID will claim it as adaptable multifunctional design beyond human conception.

Either way, enjoy, and consider that our understanding of the cell may be far less that we realise.

[Ernest Major]

Hadn't you noticed that the Intelligent Design movement is very keen on
machine model of a cell? Claiming a design beyond human conception is
not an effective route to convincing people, so they find it to be
rhetorically advantageous to play up similarities to mechanical devices.

--
alias Ernest Major

[Öö Tiib]

Current biotechnology understands about half of what is going on actually. That
understanding is not detailed enough for to design totally new synthetic life, but is
plentiful for to do things with positive economic impact. Global genetic engineering
market size is in billions dollars and growing rapidly. Those visualisation might help
people who are studying to be specialists of that market to gain knowledge. There
are enough similarities between nano and macro world for these animations to be
useful for illustrating that.

Otherwise yes, things that work on that nano level act somewhat differently than
clocks and bicycles. Similarly microprocessors work somewhat differently than big
electrical circuits. It is not beyond human comprehension, just that there are
differences. But for the creationist/materialist dispute the animation is probably
useless; anyone can see something that conforms with their views; also anyone
can say that whatever in it is illusion caused by it being just a "model" and/or
"abstraction".

[MarkE]

Both evolution and ID predict "a design beyond human conception" - hence the inherent conflict.

As much as I appreciate the reframe of the video, the flagellum, for example, *is* a machine! Along with kinesin, ribosome, spliceosome, etc, etc... If it walks like machine and quacks like a machine, it probably is a mechanical duck :)

And the cell in total? The "factory" or "city" metaphor seems like a reasonable starting point - apparent chaos resulting in order and output.

[MarkE]

I've wondered - is there a logical/mathematical limit to how much we can ever understand ourselves? Intuitively, the complexity of an observer must be much greater than the complexity of an object for "full" understanding?

[Öö Tiib]

In my experience there are no limits as there are no need for anyone of us to
understand anything fully. We are not doomed to work alone, so there are no
point. For example Google Chrome web browser contains about 35 millions of
lines of program code. If a hypothetical very bright programmer could read and
understand it at speed of 35 lines per minute then it would still take about 9
years to go through all of it for him. No one does that and so everybody working
on the code base have full understanding of only some parts of it.

[broger...@gmail.com]

You can certainly define "machine" in such a way that the flagellum or the ribosome "*is* a machine!" That tells you nothing new about flagella or ribosomes, only about how you've decided to use words.

[MarkE]

Sure, it's definitions and semantics. But would you agree that the following object might qualify as a "machine" by some definitions?

"The prokaryotic flagellum spins, driven by a rotary motor at speeds of over 100,000 rpm in at least one species. The torque generated by the motor is converted to thrust by the corkscrew-shaped filament or propeller."

"Bacterial Flagellum: Visualizing the Complete Machine In Situ"
https://www.sciencedirect.com/science/article/pii/S096098220602286X

[MarkE]

You raise an interesting point. The accumulated collective human knowledge on say humans vastly exceeds an individual's capacity to even read it, let alone "understand" it. Is it still possible to claim "full" collective human understanding if by definition this knowledge can never be integrated and assessed holistically?

Moreover, regardless, is the number of human minds applied to understanding the human mind irrelevant, i.e. is there a circularity here that logically prevents this?

[MarkE]

That is, '...qualify as a "machine" by some widely accepted definitions?'

[Öö Tiib]

One does not need deep understanding of something for to use and integrate
it. Kid needs to know Pythagorean theorem for to use it to solve some
geometrical problem. Full knowledge why it is so and how to prove the
theorem is not needed. More details can be learned when needed.

> Moreover, regardless, is the number of human minds applied to understanding the human mind irrelevant, i.e. is there a circularity here that logically prevents this?
>

Seems there are no problems. We are already in process of making and
improving artificial minds as collective without anyone having full
understanding how minds work. Individual specialist may have good
knowledge of some detail like analyzing time series or pattern matching or
such, but no one has individual full knowledge of everything.

Or how that synthetic genome was composed by 2016 in Craig Venter
laboratory without anyone knowing function of 149 genes from total 473.
It is possible to use things not only without fully understanding those but
without understanding those at all. They knew function of 324 genes so rest
will be also perhaps figured out with time.

[broger...@gmail.com]

Sure, why not? Just so long as you are careful not to attribute characteristics to the bacterial flagellum inherited from other definitions of "machine" which include characteristics like "artificial" or "man-made" and imply a designer.

[Mark Isaak]

I'm reminded of a comment near the beginning of _The Extended Mind_
(which I am very much enjoying; thanks to whomever mentioned it here
earlier): When computers were first invented, they were compared to
brains. Later, the metaphor switched, and brains came to be compared to
computers. Before that, they were compared with switchboards; before
that, no doubt to something else. Metaphors shift according to
available technology.

Cells are not machines. They are cells.

--
Mark Isaak
"Wisdom begins when you discover the difference between 'That
doesn't make sense' and 'I don't understand.'" - Mary Doria Russell

[Glenn]

You really think you are on the side of science, don't you.

[Glenn]

Mark, you may be interested in Michael Levin's work. Look him up on youtube.

[MarkE]

Thanks - I have seen him talk about bioelectricity.

[MarkE]

On Wednesday, October 4, 2023 at 1:25:57 AM UTC+11, Mark Isaak wrote:
> On 10/1/23 10:32 PM, MarkE wrote:
> > "A few years ago Veritasium posted a video portraying 'molecular machines'. But is that really the right way to think about the inner workings of our cells? Are we all just running on molecular clockwork?"
> >
> > https://youtu.be/jPhvic-eqbc?si=_AaJLOYY5FPiZ8aK
> >
> > I thought this was worth sharing (the presenter assumes evolution; not a creationist video). He challenges the machine metaphor for cells and the electronic circuit for enzyme function.
> >
> > I guess evolution will claim this as the messy and jerry-built product of trial and error, and ID will claim it as adaptable multifunctional design beyond human conception.
> >
> > Either way, enjoy, and consider that our understanding of the cell may be far less that we realise.
> I'm reminded of a comment near the beginning of _The Extended Mind_
> (which I am very much enjoying; thanks to whomever mentioned it here
> earlier): When computers were first invented, they were compared to
> brains. Later, the metaphor switched, and brains came to be compared to
> computers. Before that, they were compared with switchboards; before
> that, no doubt to something else. Metaphors shift according to
> available technology.
>
> Cells are not machines. They are cells.
>

Don't be afraid of metaphors:

"In science, metaphors have proved to be very useful because they facilitate analogical reasoning, the process whereby scientists transfer what they understand about one subject or phenomenon to another seemingly disparate and less familiar one. This sometimes leads to the discovery or expansion of a more general pattern, phenomenon, mechanism or law. Metaphors and analogies might therefore be called the engines of scientific advancement."

How about "factory" as a metaphor for the cell?

"Examples like ‘the cell is a factory’ demonstrate that sometimes a metaphor can become literal not because it changes the way we use language, but because it changes the very nature of the thing being described metaphorically. The metaphorical description of the cell as a factory became literal when scientists genetically engineered bacteria to express the gene for human insulin (among others), turning these cells into literal factories for the production of valuable commodities. This was a hugely beneficial development for people with diabetes, but it illustrates another reason why metaphors must be used cautiously: they may end up changing not just the way we speak, but our environments, our societies and ourselves in very tangible ways. (Which version of the human genome will our descendants be running – H. sapiens 2.0?)"

https://www.rsb.org.uk/biologist-features/master-your-metaphors

[broger...@gmail.com]

Yes, metaphors or analogies can be very useful for generating ideas. They don't, by themselves, though, tell you anything at all. If you say "the bacterial flagellum is analogous to an outboard motor, it must have some kind of fuel," then you have to do a bunch of experiments to show how the energy released by hydrolysis of ATP is coupled to motion of the flagellum. Saying "there must be some kind of fuel but we are not going to investigate what the fuel is, how it works or where it is produced" won't cut it.

[jillery]

On Tue, 3 Oct 2023 18:07:35 -0700 (PDT), MarkE <me22...@gmail.com>
wrote:

Metaphors illustrate and describe. The danger to using metaphors is
to base conclusions which go beyond their scope. For example, the Sun
has been metaphorically thought of as a lump of coal, because it too
gives off light and heat, but we have known for a long time that its
source of energy is very different.

--
To know less than we don't know is the nature of most knowledge

[Glenn]

He's an interesting individual. His regard for evolution is unclear, though he has made statements that appear to be possibly ways to avoid the ire of evolutionists. The purpose of his research is claimed to be for practical engineering applications, and I have found nothing in his philosophy that would support an insistence of materialistic, unguided, random evolution. What he seems to have discovered so far though should be quite shocking to atheist evolutionists, and possibly as well as to some IDers. Hopefully he can keep the money flowing and not get booted for what he might find in the future.

[Glenn]

Saying random mutations all added up to produce such complicated systems is what won't cut it. Stick that in your metaphor and smoke it.