Tracing evolutionary relationships of flagellar parts

[RonO]

https://onlinelibrary.wiley.com/doi/10.1002/bies.202100004

You have to pay to read the paper, but a preprint is available as it
existed before peer review. I don't know how much the contents changed
from what is in the preprint.

https://www.biorxiv.org/content/10.1101/2021.01.01.425057v2

They are looking at the part of the flagellum related to the F0-ATPase
complex. My guess is that the F0-ATPase first evolved in the first
chemotrophic lifeforms. It is one of the ATPases that rotate as ATP is
produced or hydrolized. It is still found in chemotrophs found in
places like around deep sea vents. It probably got coopted by the
photosynthetic organisms to be used in photosynthesis. It is also the
ATPase used used by oxidative lifeforms in the oxidative phosphorylation
pathway. These researchers started looking at homologous genes used in
the flagellum.

They found something interesting. Multiple subunits that likely evolved
by gene duplication (They claim that they are homologous) are found in a
cistron (all the related genes are regulated as a single transcribed
unit that codes for multiple genes). It turns out that they have a
specific gene order that is the same in all these distantly related
systems. The genes of these systems are so distantly related that their
homology is inferred by the structure of the protein and not the
sequence. The amino acid sequences have changed a lot over the billions
of years that these systems have existed, but their structure and
function have been conserved.

They think that the conserved gene order of the cistron indicates that
it was the entire cistron that was coopted for use in the varied systems
including the flagellum. They claim it as additional evidence of the
homology of these genes. As wild as it may seem they think that this
gene cistron may have evolved in an ancestor that predates the last
common ancestor of extant lifeforms. This ancestor existed before the
lineage that became archaea, eubacteria and eukaryotes. Sort of strange
that this might be a window into figuring out lifeforms that may have
existed before the last common ancestor of extant lifeforms.

Ron Okimoto

[Glenn]

https://en.wikipedia.org/wiki/Nick_Matzke

Twilight Zone reruns are more interesting.

[RonO]

Willful ignorance is never going to change reality.

I didn't even notice that Matzke was one of the authors. Unlike Luskin
Matzke got a research position after he got his PhD and seems to be
publishing some real science. Shouldn't you compare that to what the
IDiots are doing?

It looks like he might have done better in the publication of his
research (in real peer reviewed science journals) than all the ID perps
combined for the last 5 years. Just think that Sternberg hasn't
published a peer reviewed science paper since he joined the ID perps in
2007. They have been employing him at the Biologic Institute for over
13 years and what has he produced?

https://pubmed.ncbi.nlm.nih.gov/?term=Matzke+NJ&cauthor_id=33998015

Ron Okimoto

[Glenn]

https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.950030109

Nick is an atheist activist, and as useless to science as tits on a boarhog. Twilight Zone reruns are more interesting.

[RonO]

Projection of IDiocies issues like this is stupidly dishonest. Lying to
yourself about reality isn't going to change anything. Matzke got a
degree and real research position, doing real science. ID Perps like
Sternberg and Dembski are just getting paid off for their past dubious
contributions to the ID scam. Who were the political activists that did
something bogus and dishonest, and are now getting paid to do just about
nothing. If you can't see the difference you are as insane as you
project yourself to be.

Ron Okimoto

[Glenn]

False narratives "R You.

[RonO]

Willful ignorance of the simple truth is sadly stupid and insane at this
point. Just think if IDiocy could produce some equivalent science? Why
is it that no ID science ever got done? If you think that simple
straightforward statement is wrong, just put up any ID science that ever
verified anything about IDiocy. The ID perps used to claim that they
could do the science, but what did they do instead? Did Behe ever do
any verification testing for IC? He claimed that it could be done, so
why hasn't he done any such testing?

One thing that I am curious about is why you put up the Wiley reference
to some essay from 1985. This predates the loss of scientific
creationism in the Supreme court case. If it is supposed to support
your IDiotic beliefs it obviously failed. Since I couldn't get access
to the aticle you have to state why you put it up, and give some idea of
what the essay is about. From the Abstract it looks like it has nothing
to do with what you are lying to yourself about in this thread.

Ron Okimoto

[jillery]

On a related note, the following is a link to a video that models the
molecular structure and activity of ATPase in mitochondria and
chloroplasts:

<https://www.youtube.com/watch?v=kXpzp4RDGJI>

and here's a link to a video that models the molecular structure and
activity of bacterial flagella:

<https://www.youtube.com/watch?v=B7PMf7bBczQ>

The two appear to have little in common. Both rotate, and both are
driven by proton transport across a membrane. But bacterial flagella
are much larger and more complex. And what of the Type Three Secretory
System aka T3SS Ken Miller famously made famous?

The following is a link to a video which answers these questions:

<https://www.youtube.com/watch?v=xHUQf7Rjy8g&t=0s>

Short version: The flagellar base originated as a simple pore
specialized to regulate the flow of specific molecules by duplicating
and mutating the same core protein (DEVOUTION!). Jammed into this
specialized pore is our friend ATPase. Add to this base a mechanism
to attach a hollow pilus to an external substrate, and Et Voilà! a
T3SS. Now bend the pilus and extend it to some arbitrary length, and
add an anchoring stator to the base, and Et Voilà! a bacterial
flagella.

If the above sounds trivializing, remember it's a SHORT VERSION. For
a deeper dive, cites are included in the video descriptions.

--
You're entitled to your own opinions.
You're not entitled to your own facts.

[RonO]

The paper claims that the type III secretory system has a similar ATPase
(homologous to the F type).

For energy production in chemotrophs, Ox Phos, and photosynthesis the
ATPase acts as a sort of proton pump across membranes. If protons go in
one way ATP can be generated, but if ATP is burned the protons can be
transported in the other direction. Related ATPases are used to
transport other things including proteins across the membranes. You'd
think that they would have had to enlarge the pore, but the parts are
the same. If you go to figure 1 of the paper they show where the genes
that they are talking about are in the motor. They are at the base of
the motor and you can see why the ATPases are supposed to be related.

Ron Okimoto

[Glenn]

And you have a PhD???

[Glenn]

Hopefully the long version includes a pinch of salt added.

[jillery]

Correction: Instead of ATPase, I should have written ATP synthase. My
bad.

ATPase hydrolyzes ATP into ADP, which removes a phosphate and provides
energy to transport ions against an out-of-equilibrium gradient across
a membrane. ATP synthase does the opposite, to use the energy of an
out-of-equilbrium gradient to add a phosphate to ADP to make ATP and
store energy.

Bacterial flagella and T3SS use both F1F0-ATP synthase and
V1V0-ATPase.

[jillery]

On Sun, 12 Sep 2021 19:01:26 -0700 (PDT), Glenn <GlennS...@msn.com>
wrote:

Reading the cited articles works so much better than salt.

[Glenn]

Where there's salt there's life. Just ask NASA.

[RonO]

And it doesn't matter does it. The ID perps with PhDs are scam artists
because you know that no one is going to get any ID science out of them.
The bait and switch will keep going down on rubes like you because you
want to be lied to. Luskin got a PhD so he could lie to the rubes more
effectively. Matzke got a PhD and is actually adding to our scientific
knowledge, and all you want to do is wallow in denial.

Demonstrate that this is not the case. Put up a single instance where
the ID perps delivered the ID science. What will happen to the next
group of IDiot rubes stupid enough to believe the ID scam stupidity?
There don't seem to be many IDiots that stupid left because they all
know what you know, and they should all know that no one is going to get
any ID science because it does not exist. No ID science was ever
produced. You have none to put up because there is none. All you ever
got were the untestable claims and god-of-the-gaps denial stupidity.
Luskin just put up the Top Six again and you are still running from
them. The best evidence for ID isn't anything that you want to understand.

Ron Okimoto

[RonO]

The two are the same. The F0 ATPase is used as an ATP synthase in
chemotrophs, photosynthesis and oxidative phosphorylation. The complex
will rotate if you burn ATP or make ATP.

>
> ATPase hydrolyzes ATP into ADP, which removes a phosphate and provides
> energy to transport ions against an out-of-equilibrium gradient across
> a membrane. ATP synthase does the opposite, to use the energy of an
> out-of-equilbrium gradient to add a phosphate to ADP to make ATP and
> store energy.
>
> Bacterial flagella and T3SS use both F1F0-ATP synthase and
> V1V0-ATPase.
>

Like I said the complex does both. You can rotate the flagellum by
burning ATP or you can generate a proton gradient between the inner or
outer membrane.

Ron Okimoto

[jillery]

The terms refer to two functions of a class of molecular complexes. I
acknowledge there are some forms which work as both ATP synthase to
make ADP into ATP, and ATP-ase to make ATP into ADP. However,
bacterial and mitochondrial ATP synthase forms have a subunit which
inhibits ATP hydrolysis and promotes ATP synthesis:

<https://elifesciences.org/articles/43128>

At the same time ATP synthase makes ATP, it also makes the interior
progressively more acidic, reducing the disequilibrium that drives ATP
synthase. Something must pump protons back out to maintain the
disequilibrium. But instead of reversing ATP synthase, mitochondria
use a separate electron transport chain:

<https://courses.lumenlearning.com/wm-biology1/chapter/reading-electron-transport-chain/>

<https://tinyurl.com/hnpr5vve>

The electron transport chain shuttles high-energy electrons through a
cascade of steps. Each step uses part of the electrons' energy to
pump protons out of the interior into the inter-membrane space,
ultimately dumping the spent elections onto molecular oxygen and
hydrogen to create water.

[RonO]

"inhibits" ATP hydrolysis is the key term. Why is it that the
mitochondrial ATPase is called an ATPase? Related ATPases are used to
transport ions and things like peptides and amino acids.

When I was working on mitochondria it was called an ATPase, and people
were expected to know that it had the two functions.

They call the entire complex that contains the ATPase the mitochondrial
ATP synthase because that is what the complex mostly does. This paper
under discussion in this thread is talking about the ATPase part of the
complex. It is the ATPase that is being discussed, not the synthase
complex. You can Google mitochondrial ATPase and get multiple
publications on the inhibitor in the complex.

Some don't make much of a distinction, but some do. Some call it both
because it has been called both.

https://academic.oup.com/hmg/article/8/11/1967/2526991

QUOTE:
We report a new type of fatal mitochondrial disorder caused by selective
deficiency of mitochondrial ATP synthase (ATPase).
END QUOTE:

Ron Okimoto

[jillery]

Ok, that suggests the labels are a matter of convention and
preference, as opposed to a meaningful distinction. Thanks for taking
the time to point this out.

>> <https://elifesciences.org/articles/43128>
>>
>> At the same time ATP synthase makes ATP, it also makes the interior
>> progressively more acidic, reducing the disequilibrium that drives ATP
>> synthase. Something must pump protons back out to maintain the
>> disequilibrium. But instead of reversing ATP synthase, mitochondria
>> use a separate electron transport chain:
>>
>> <https://courses.lumenlearning.com/wm-biology1/chapter/reading-electron-transport-chain/>
>>
>> <https://tinyurl.com/hnpr5vve>
>>
>> The electron transport chain shuttles high-energy electrons through a
>> cascade of steps. Each step uses part of the electrons' energy to
>> pump protons out of the interior into the inter-membrane space,
>> ultimately dumping the spent elections onto molecular oxygen and
>> hydrogen to create water.

[RonO]

You just have to live with the conventions. In maize genetics we used
to call a major gene expressed in maize endosperm (developing seed part)
sucrose synthase when we knew that it's major function was taking
sucrose made by photosynthesis and breaking it down into glucose and
fructose so that the monosaccharides could be used to make starch in the
developing kernal.

Ron Okimoto