"A radical new theory rewrites the story of how life on Earth began"

You are using the term IC (irreducible complexity) rather loosely, Mark.
There is plenty of unsurmounted complexity, but the "irreducible" part is
not mentioned. It seems that you are thinking of "a lot of help" as one great
irreducible mass: couldn't do without the help of at least some of it.

Anyway, welcome back. I'm glad I caught you so soon. The last time you
were here, you got burnout from an intensive back-and-forth with
Bill Rogers, over ten posts in the space of two weekend days -- exactly
when I couldn't call Bill out on the way he was channeling the debate
in the directions he wanted it to go.

No wonder you think a thread won't last a month in talk.origins: you lose
interest in the repetitiousness of what the usual responses to you are,
and for a good reason. You exhaust their repertoire of aspects of
abiogenesis that they want to talk about.

I added my own take on the foolishness of Sutherland et. al. before
I looked at yours. Perhaps you will enjoy reading my criticism of Sutherland
before the hordes of "Mother Earth did it easily" folks here try to
blunt yours.

That depends on a very broad definition of "life", utterly unlike
life as we know it. Even the simplest viruses are far more
sophisticated than what one reads about below.

Post by MarkE
It turns out that all the key molecules of life can form from the same simple carbon-based chemistry. What’s more, they easily combine to make startlingly lifelike ‘protocells’.”

This author is purposely vague about "all the key molecules". This has
absolutely no analogue in the parts of a car. Instead, it is a bit like saying
that we have all the key ingredients to build a hydrogen bomb, but
only a few people have the wherewithal to put it all together or the
knowledge of how to do it. In this case, everyone is in the same boat
as all but that tiny few were wrt the H-bomb.

"startlingly lifelike" is gee-whiz type foolishness, reminiscent of
the foolishness that greeted Fox's "microspheres" which were made
of proteinoids instead of proteins and were an evolutionary dead end.

Post by MarkE
The first challenge is finding a plausible natural scenario for the simultaneous production of building blocks for membranes, genetic polymers, and proteins.

Yup, that's your stages 1 and 2, but the really big hurdles come in stage 3 and 4.

Post by MarkE
“By combining a similar organic compound called cyanamide with other simple chemicals, John Sutherland at the MRC Laboratory of Molecular Biology in Cambridge, UK, has created nucleotides, the building blocks of RNA.

Vintage stage 1.

Post by MarkE
The reaction requires “ Life’s key molecules can form together thanks to ‘Goldilocks’ chemistry” ultraviolet light, heating and drying, and wetting with water.

So how come Urey and Miller didn't already do it 60 years ago? I suppose
they didn't mix exactly the right starting chemcals, eh?

Funny, I see no mention of WHAT the right starting chemicals are below.

Post by MarkE
Sutherland’s team found that the same starting chemicals can also make the precursors of amino acids and lipids. “All the cellular subsystems could have arisen simultaneously through common chemistry,” he concluded.

"subsystems" is pretending that these rudimentary collections of
molecules bear some resemblance to the actual subsystems that
are involved. I bet their cell membranes have nothing like the
pores that make our cell membranes so versatile.

Post by MarkE
The key is what Sutherland calls “Goldilocks chemistry”: a mixture with enough variety for complex reactions to occur, but not so much that it becomes a jumbled mess.”
The second challenge is their assembly. The author makes this statement: “What’s more, they easily combine to make startlingly lifelike ‘protocells’.”
I’m interested in two aspects of this assertion: “easily combine” and “startlingly lifelike ‘protocells’”.
It is demonstrable that spherical membranes (vesicles) can form spontaneously: “If these lipids were subsequently added to salt water and shaken, they formed spherical blobs with two outer layers of lipids, just like cells.”
Membranes, therefore, can be said to “easily combine”. What about genetic polymers and proteins?
The author has already answered this question with respect to RNA: “However, biochemists have spent decades struggling to get RNA to self-assemble or copy itself in the lab, and now concede that it needs a lot of help to do either.” The appeal to the “everything-first” hypothesis is based on the claim that naked RNA self-assembly and copying doesn’t work. But suddenly we’ve jumped to “easily combining” a lipid membrane around some RNA, self-assembled and even copying itself.
“Szostak’s group has even persuaded RNA to copy itself within protocells.”
Szostak’s work with RNA template copying in protocells requires magnesium ions for nucleotide assembly on the existing RNA, and uses a citrate molecule to clamp on to a magnesium ion preventing it from reacting with a fatty acid but still allowing it to interact with the RNA [3].
It's important to read the fine print: “Despite lacking any of the complex cellular machinery, they can reproduce by dividing to form daughter protocells. “What’s missing is a replicating genetic material,” Szostak says.” So we have “simple “protocells”, essentially bubbles of fatty acids”, expanding by the addition of further lipids and “pearling” and/or transforming into branched filaments, and to produce more bubbles. No RNA involved in this process though.
And metabolism?
“The one system still missing from these protocells is metabolism. This is particularly challenging because it means creating entire sequences of chemical reactions. In modern organisms, these are controlled by battalions of protein enzymes, which can’t have existed when life began. However, other researchers have begun finding ways to get metabolic chemical reactions going without proteins.”
“startlingly lifelike ‘protocells’”?
- a lipid vesicle
- RNA whose origin is not discussed
- RNA strand templating with chemistry to prevent degradation of the membrane (speed and fidelity unknown)
- a plausible supply of nucleotides, especially through the membrane
- RNA duplication
- a mechanism for vesicle division with RNA division
- metabolism
What we have is essentially an inert bag of Lego bricks, with no information, no energy supply, and highly doubtful material supply. I’ll rephrase the claim of “startlingly lifelike ‘protocells’” as “superficially lifelike to someone who does not grasp the essential nature of living cells.”
It would be easy enough to dismiss all of this as the optimistic musings of a writer aiming to sell a science magazine. But Szostak himself demonstrates the same overreach: “He says there is still some way to go before the system works well enough to sustain living organisms. For example, Szostak wants the copying to be faster and more accurate.”
Similar optimism from Joyce and Szostak eslewhere [4]: “The experiments described above bring the field tantalizingly close to a replicating and evolving protocell.”
Prediction: The Miller–Urey experiment was originally hailed as “life in a test tube” (or tantalizingly close to it), but nearly 70 years later has proven to be little more than tar in test tube; decades from now when the irreducible complexity, intricacy and functionality of the simplest life is properly acknowledged, so will it be for these protocell experiments.
----------
[1] Michael Marshall: “freelance science journalist”; MSc Science Communication, MPhil Experimental Psychology, BA Natural Sciences.

Talk about having a boy do a man's job!

But then, that's the caliber of all but one or two talk.origins regulars
where abiogenesis is concerned, and Bill Rogers, who is probably one of them,
acts like a boy instead of the man he could act like.

Post by MarkE
[2] New Scientist, 5 August 2020
https://www.newscientist.com/article/mg24732940-800-a-radical-new-theory-rewrites-the-story-of-how-life-on-earth-began/#ixzz6XS0GHV5a
You can purchase the whole article for USD 1.99 here, as I did: https://www.sciencedirect.com/science/article/abs/pii/S0262407920313774
[3] https://www.newscientist.com/article/dn24669-synthetic-primordial-cell-copies-rna-for-the-first-time/#ixzz6XSHBE3F4
[4] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120706/

Well done, Mark. I am terribly busy with online teaching and evaluation,
and with a number of other threads, so I can only contribute maybe an
average of one post a day on weekdays to your threads. [I only post on
weekends for the most extraordinary reasons, and am averaging less
than once a year on that.]

But I will try to make my contributions have maximum impact.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos

Glenn

2020-09-08 20:30:31 UTC

A "lot of help" in the *lab* to synthesize short bits of RNA, Peter.

But the whole quote does "invoke" IC, in my opinion.

"It is, some researchers are starting to realise, like trying to build a car by making a chassis and hoping wheels and an engine will spontaneously appear.”

This seems an evolutionist's only solution, an irreducibly complex system that is "too complex to have formed all at once".

Post by Peter Nyikos
Anyway, welcome back. I'm glad I caught you so soon. The last time you
were here, you got burnout from an intensive back-and-forth with
Bill Rogers, over ten posts in the space of two weekend days -- exactly
when I couldn't call Bill out on the way he was channeling the debate
in the directions he wanted it to go.
No wonder you think a thread won't last a month in talk.origins: you lose
interest in the repetitiousness of what the usual responses to you are,
and for a good reason. You exhaust their repertoire of aspects of
abiogenesis that they want to talk about.
I added my own take on the foolishness of Sutherland et. al. before
I looked at yours. Perhaps you will enjoy reading my criticism of Sutherland
before the hordes of "Mother Earth did it easily" folks here try to
blunt yours.

That depends on a very broad definition of "life", utterly unlike
life as we know it. Even the simplest viruses are far more
sophisticated than what one reads about below.

This author is purposely vague about "all the key molecules". This has
absolutely no analogue in the parts of a car. Instead, it is a bit like saying
that we have all the key ingredients to build a hydrogen bomb, but
only a few people have the wherewithal to put it all together or the
knowledge of how to do it. In this case, everyone is in the same boat
as all but that tiny few were wrt the H-bomb.
"startlingly lifelike" is gee-whiz type foolishness, reminiscent of
the foolishness that greeted Fox's "microspheres" which were made
of proteinoids instead of proteins and were an evolutionary dead end.

Post by MarkE
The first challenge is finding a plausible natural scenario for the simultaneous production of building blocks for membranes, genetic polymers, and proteins.

Yup, that's your stages 1 and 2, but the really big hurdles come in stage 3 and 4.

Vintage stage 1.

Post by MarkE
The reaction requires “ Life’s key molecules can form together thanks to ‘Goldilocks’ chemistry” ultraviolet light, heating and drying, and wetting with water.

So how come Urey and Miller didn't already do it 60 years ago? I suppose
they didn't mix exactly the right starting chemcals, eh?
Funny, I see no mention of WHAT the right starting chemicals are below.

Talk about having a boy do a man's job!
But then, that's the caliber of all but one or two talk.origins regulars
where abiogenesis is concerned, and Bill Rogers, who is probably one of them,
acts like a boy instead of the man he could act like.

Well done, Mark. I am terribly busy with online teaching and evaluation,
and with a number of other threads, so I can only contribute maybe an
average of one post a day on weekdays to your threads. [I only post on
weekends for the most extraordinary reasons, and am averaging less
than once a year on that.]
But I will try to make my contributions have maximum impact.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos

jillery

2020-09-08 22:41:02 UTC

Post by Glenn

A "lot of help" in the *lab* to synthesize short bits of RNA, Peter.
But the whole quote does "invoke" IC, in my opinion.
"It is, some researchers are starting to realise, like trying to build a car by making a chassis and hoping wheels and an engine will spontaneously appear.”
This seems an evolutionist's only solution, an irreducibly complex system that is "too complex to have formed all at once".

Your quote doesn't invoke IC but instead 1) acknowledges the
researchers' current ignorance and 2) admits to a hope that
self-organization will help to fill in the blanks.

A more closely related meme to that quote would be Creationism. Are
you saying IC and Creationism are similar?

<snip remaining>

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

Peter Nyikos

2020-09-09 01:14:53 UTC

It isn't even a model, unless you think of a paper airplane to be a
model of the real thing.

I glossed over this the first time around, and this time I recognized
it as a straw man: "just one component" is unspecified, and later
on it turns out that he is talking about components as simple
as "precursors of amino acids" (! Sutherland surely wouldn't
write something that ridiculous) and single nucleotides.

Post by MarkE
When put into practice in the lab, however, these ideas don’t produce anything particularly lifelike. It is, some researchers are starting to realise, like trying to build a car by making a chassis and hoping wheels and an engine will spontaneously appear.”

Post by MarkE
And, “However, biochemists have spent decades struggling to get RNA to self-assemble or copy itself in the lab, and now concede that it needs a lot of help to do either.”

Yes, because they are trying to build precursors of real cars,
and not fiddling around with ways of producing three kinds of molecules
from a single batch of chemicals.

Post by MarkE
As an aside, note the invocation of irreducible complexity by a non-ID proponent.

A "lot of help" in the *lab* to synthesize short bits of RNA, Peter.

Yes, that much is pretty clear.

Post by MarkE
But the whole quote does "invoke" IC, in my opinion.

Agreed there too. Obviously, the under-qualified author is a foe of ID and of
creationism.

Post by MarkE
"It is, some researchers are starting to realise, like trying to build a car by making a chassis and hoping wheels and an engine will spontaneously appear.”
This seems an evolutionist's only solution, an irreducibly complex system that is "too complex to have formed all at once".

Instead of "evolutionist" I would say "a believer in un-directed abiogenesis."
Watch how this dude reveals how little progress Sutherland has actually made.

<snip for focus>

That is, the emergence of "life" so simple, that few here besides Mark Isaak
would consider it to be life.

<snip>

Post by MarkE
What’s more, they easily combine to make startlingly lifelike ‘protocells’.”

This author is purposely vague about "all the key molecules".

Also, he is forced to put "protocells" in scare quotes, because if
they were closely inspected, they would be seen to be little toys
with no tangible potential to evolve into life as we know it.

Here is one of the "subsystems" that Sutherland has brought together

Building blocks indeed! I wonder whether ANYONE has any idea how
many of these building blocks are required for a true replicator like
the protein that some viruses use to make copies of themselves.

I doubt that even Sutherland has any idea of the NUMBER, and it's
a sure bet he hasn't the foggiest idea what their nucleotide sequence
might look like. That's the "specified complexity" about which ID foes
sneer and jeer, but none can help Sutherland with.

[ID foe jillery didn't even sneer and jeer at that level. Maybe
she can get specific enough to do so later, but she'll probably
need the help of someone like Bill Rogers.]

Another "subsystem" is amino acids, produced by Urey and Miller almost
seven decades ago. And here is the third, the most "spectacular" of the

Post by MarkE
It is demonstrable that spherical membranes (vesicles) can form spontaneously: “If these lipids were subsequently added to salt water and shaken, they formed spherical blobs with two outer layers of lipids, just like cells.”

This "subsystem" has been talked about for decades. The author is turning
figurative carwheels over how all three "subsystems" emerged from a single carefully selected batch of chemicals.

Peter Nyikos
VIRTUAL FOUR LINE .SIG
This post has a good scientific component,
and is highly relevant for some of the topics for which talk.origins was set up.

PS I've left in MarkE's spot-on criticism below. It will be interesting
to see whether his nemesis, Bill Rogers, will try to salvage something
of the article's reckless optimism.

Post by MarkE
Membranes, therefore, can be said to “easily combine”. What about genetic polymers and proteins?
The author has already answered this question with respect to RNA: “However, biochemists have spent decades struggling to get RNA to self-assemble or copy itself in the lab, and now concede that it needs a lot of help to do either.” The appeal to the “everything-first” hypothesis is based on the claim that naked RNA self-assembly and copying doesn’t work. But suddenly we’ve jumped to “easily combining” a lipid membrane around some RNA, self-assembled and even copying itself.
“Szostak’s group has even persuaded RNA to copy itself within protocells.”
Szostak’s work with RNA template copying in protocells requires magnesium ions for nucleotide assembly on the existing RNA, and uses a citrate molecule to clamp on to a magnesium ion preventing it from reacting with a fatty acid but still allowing it to interact with the RNA [3].
It's important to read the fine print: “Despite lacking any of the complex cellular machinery, they can reproduce by dividing to form daughter protocells. “What’s missing is a replicating genetic material,” Szostak says.” So we have “simple “protocells”, essentially bubbles of fatty acids”, expanding by the addition of further lipids and “pearling” and/or transforming into branched filaments, and to produce more bubbles. No RNA involved in this process though.
And metabolism?
“The one system still missing from these protocells is metabolism. This is particularly challenging because it means creating entire sequences of chemical reactions. In modern organisms, these are controlled by battalions of protein enzymes, which can’t have existed when life began. However, other researchers have begun finding ways to get metabolic chemical reactions going without proteins.”
“startlingly lifelike ‘protocells’”?
- a lipid vesicle
- RNA whose origin is not discussed
- RNA strand templating with chemistry to prevent degradation of the membrane (speed and fidelity unknown)
- a plausible supply of nucleotides, especially through the membrane
- RNA duplication
- a mechanism for vesicle division with RNA division
- metabolism
What we have is essentially an inert bag of Lego bricks, with no information, no energy supply, and highly doubtful material supply. I’ll rephrase the claim of “startlingly lifelike ‘protocells’” as “superficially lifelike to someone who does not grasp the essential nature of living cells.”
It would be easy enough to dismiss all of this as the optimistic musings of a writer aiming to sell a science magazine. But Szostak himself demonstrates the same overreach: “He says there is still some way to go before the system works well enough to sustain living organisms. For example, Szostak wants the copying to be faster and more accurate.”
Similar optimism from Joyce and Szostak eslewhere [4]: “The experiments described above bring the field tantalizingly close to a replicating and evolving protocell.”
Prediction: The Miller–Urey experiment was originally hailed as “life in a test tube” (or tantalizingly close to it), but nearly 70 years later has proven to be little more than tar in test tube; decades from now when the irreducible complexity, intricacy and functionality of the simplest life is properly acknowledged, so will it be for these protocell experiments.
----------
[1] Michael Marshall: “freelance science journalist”; MSc Science Communication, MPhil Experimental Psychology, BA Natural Sciences.

Talk about having a boy do a man's job!
But then, that's the caliber of all but one or two talk.origins regulars
where abiogenesis is concerned, and Bill Rogers, who is probably one of them,
acts like a boy instead of the man he could act like.

Well done, Mark. I am terribly busy with online teaching and evaluation,
and with a number of other threads, so I can only contribute maybe an
average of one post a day on weekdays to your threads. [I only post on
weekends for the most extraordinary reasons, and am averaging less
than once a year on that.]
But I will try to make my contributions have maximum impact.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos

MarkE

2020-09-09 14:05:29 UTC

Post by Peter Nyikos
It isn't even a model, unless you think of a paper airplane to be a
model of the real thing.

Post by MarkE
And, “However, biochemists have spent decades struggling to get RNA to self-assemble or copy itself in the lab, and now concede that it needs a lot of help to do either.”

Yes, because they are trying to build precursors of real cars,
and not fiddling around with ways of producing three kinds of molecules
from a single batch of chemicals.

Post by MarkE
As an aside, note the invocation of irreducible complexity by a non-ID proponent.

A "lot of help" in the *lab* to synthesize short bits of RNA, Peter.

Yes, that much is pretty clear.

Post by MarkE
But the whole quote does "invoke" IC, in my opinion.

Agreed there too. Obviously, the under-qualified author is a foe of ID and of
creationism.

Instead of "evolutionist" I would say "a believer in un-directed abiogenesis."
Watch how this dude reveals how little progress Sutherland has actually made.
<snip for focus>

That is, the emergence of "life" so simple, that few here besides Mark Isaak
would consider it to be life.
<snip>

Post by MarkE
What’s more, they easily combine to make startlingly lifelike ‘protocells’.”

This author is purposely vague about "all the key molecules".

Also, he is forced to put "protocells" in scare quotes, because if
they were closely inspected, they would be seen to be little toys
with no tangible potential to evolve into life as we know it.
Here is one of the "subsystems" that Sutherland has brought together

Building blocks indeed! I wonder whether ANYONE has any idea how
many of these building blocks are required for a true replicator like
the protein that some viruses use to make copies of themselves.

I am regularly surprised by the lack of real concern for the scale of the problem of OOL by natural processes. Szostak's optimism is an example. People like James Tour rightly I think dismantle his assessment that laboratory-made self-replicating and evolving protocells are "tantalisingly close."

I was listening to this informative short video "Origins of Life: Early Life - Protocells".

At 9:40, the presenter disappointingly but all-too-familiarly repeats the same blithely optimistic just-so narrative:

"So when we think about the evolution of our protocells, essentially we start with some kind of prebiotic soup, and aggregation happens so that we form the self-assembled protocells that have some lifelike properties but are maybe not fully alive. Through some natural processes - some people might like to call it chemical evolution, we end up decreasing the molecular diversity of the prebiotic soup, but at the same time we increase our functional complexity by selection processes and by iterative rounds of replication of our protocells. This leads to first life, which is a much simpler form of life than what we expect to see in modern organisms, and that first life will then undergo true Darwinian evolution with information polymers..."

Some takeaways:
1. "some kind of prebiotic soup" - insert James Tour's critique
2. "aggregation happens" - virtually axiomatic, akin to "sh*t happens"
3. "chemical evolution" - as soon as the term "evolution" is invoked, no further explanation is required - all-powerful selection takes over and any and every possible outcome is fait accompli

Point 3 is the universal get-out-of-jail-free card. Once natural selection starts in any form, just stand back and watch the magic happen. Therein lies the power of challenging naturalism at the origin of life: it nullifies much of this sleight of hand by locating the debate pre-evolution (by definition). The contention remains with "chemical evolution", but that's less exempt from scrutiny at least.

Post by Peter Nyikos
I doubt that even Sutherland has any idea of the NUMBER, and it's
a sure bet he hasn't the foggiest idea what their nucleotide sequence
might look like. That's the "specified complexity" about which ID foes
sneer and jeer, but none can help Sutherland with.
[ID foe jillery didn't even sneer and jeer at that level. Maybe
she can get specific enough to do so later, but she'll probably
need the help of someone like Bill Rogers.]
Another "subsystem" is amino acids, produced by Urey and Miller almost
seven decades ago. And here is the third, the most "spectacular" of the

This "subsystem" has been talked about for decades. The author is turning
figurative carwheels over how all three "subsystems" emerged from a single carefully selected batch of chemicals.
Peter Nyikos
VIRTUAL FOUR LINE .SIG
This post has a good scientific component,
and is highly relevant for some of the topics for which talk.origins was set up.
PS I've left in MarkE's spot-on criticism below. It will be interesting
to see whether his nemesis, Bill Rogers, will try to salvage something
of the article's reckless optimism.

Talk about having a boy do a man's job!
But then, that's the caliber of all but one or two talk.origins regulars
where abiogenesis is concerned, and Bill Rogers, who is probably one of them,
acts like a boy instead of the man he could act like.

Well done, Mark. I am terribly busy with online teaching and evaluation,
and with a number of other threads, so I can only contribute maybe an
average of one post a day on weekdays to your threads. [I only post on
weekends for the most extraordinary reasons, and am averaging less
than once a year on that.]
But I will try to make my contributions have maximum impact.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos

MarkE

2020-09-09 13:13:03 UTC

If IC is defined as lack of viable sequential/independent development pathways for the essential components of a system, the car analogy seems to fit this: "...like trying to build a car by making a chassis and hoping wheels and an engine will spontaneously appear." The implication being that wheels and engines by themselves have no selectable function and are therefore not independently evolveable. But it may be a loose application - not a crucial point either way.

Thank you; I enjoy dropping in as time allows. Interested to hear your contributions here and in other topics. As our understanding of true complexity and precision of the simplest cells grows, so too do the inadequacies naturalistic OOL explanations.

That depends on a very broad definition of "life", utterly unlike
life as we know it. Even the simplest viruses are far more
sophisticated than what one reads about below.

This author is purposely vague about "all the key molecules". This has
absolutely no analogue in the parts of a car. Instead, it is a bit like saying
that we have all the key ingredients to build a hydrogen bomb, but
only a few people have the wherewithal to put it all together or the
knowledge of how to do it. In this case, everyone is in the same boat
as all but that tiny few were wrt the H-bomb.
"startlingly lifelike" is gee-whiz type foolishness, reminiscent of
the foolishness that greeted Fox's "microspheres" which were made
of proteinoids instead of proteins and were an evolutionary dead end.

Post by MarkE
The first challenge is finding a plausible natural scenario for the simultaneous production of building blocks for membranes, genetic polymers, and proteins.

Yup, that's your stages 1 and 2, but the really big hurdles come in stage 3 and 4.

Vintage stage 1.

Post by MarkE
The reaction requires “ Life’s key molecules can form together thanks to ‘Goldilocks’ chemistry” ultraviolet light, heating and drying, and wetting with water.

So how come Urey and Miller didn't already do it 60 years ago? I suppose
they didn't mix exactly the right starting chemcals, eh?
Funny, I see no mention of WHAT the right starting chemicals are below.

Talk about having a boy do a man's job!
But then, that's the caliber of all but one or two talk.origins regulars
where abiogenesis is concerned, and Bill Rogers, who is probably one of them,
acts like a boy instead of the man he could act like.

Well done, Mark. I am terribly busy with online teaching and evaluation,
and with a number of other threads, so I can only contribute maybe an
average of one post a day on weekdays to your threads. [I only post on
weekends for the most extraordinary reasons, and am averaging less
than once a year on that.]
But I will try to make my contributions have maximum impact.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos

Peter Nyikos

2020-09-15 17:47:10 UTC

I was hoping to do better than this as far as participation on this
thread goes, Mark, but now that Harshman has painted himself into
several corners in his cowardly, hypocritical attacks on me in
the thread on Phylogenetic Systematics, and his cronies can't really
make a case against me without Harshman, I might get to participate
a bit more this week on this thread than I could last week.

If IC is defined as lack of viable sequential/independent development pathways for the essential components of a system,

NO, you must be working from sources who misrepresent IC
in order to falsely claim that it has been refuted.

The definition is utterly different: a well-coordinated system of interacting
parts, producing a specified function, such that the loss of ANY of the
parts causes loss of function.

Post by MarkE
the car analogy seems to fit this: "...like trying to build a car by making a chassis and hoping wheels and an engine will spontaneously appear."

Nothing spontaneous, just a gradualist sequence of events that
eventually produce each and every part.

Post by MarkE
The implication being that wheels and engines by themselves have no selectable function and are therefore not independently evolveable.

All that has to do with the conclusions one tries to draw from the
IC nature of the system and nothing to do with defining IC.

And the conclusions have to be established on a case by case basis.
In the case of the clotting system, the 12 or so factors in the clotting
cascade did not evolve independently. They arose one by one thru gene
duplication. Each time, the system ceased being IC for a while, but
then as the duplicated piece evolved, the system reverted to being IC.

The issue is whether the system, as it occurs in humans and many mammals,
is IC in its present state. That has NEVER been refuted.

Yet the system DID evolve from just one or two factors, because of the
all-important quality of each factor being autocatalytic.

Only a few people here have fathomed the absolute importance of that
quality. Most of them parrot the claim that "gene duplication and
subsequent divergence is enough, and their minds are closed to the
fact that this alone is completely inadequate.

Post by MarkE
But it may be a loose application - not a crucial point either way.

It's absolutely crucial, because of the tremendous amount of
disinformation about IC that feeds into the Wikipedia-promoted,
Sandwalk-promoted, NAS-promoted canard that ID is a pseudoscience.

Yes. I underestimated how well you critiqued Szostak when I posted the
reply to your OP that I did. But I am puzzled by something.

<snip for focus>

What exactly is meant here by "RNA template copying"? What's the alleged
process, and how long are the RNA strings involved?

Touche.

Post by MarkE
And metabolism?
“The one system still missing from these protocells is metabolism. This is particularly challenging because it means creating entire sequences of chemical reactions. In modern organisms, these are controlled by battalions of protein enzymes, which can’t have existed when life began. However, other researchers have begun finding ways to get metabolic chemical reactions going without proteins.”
“startlingly lifelike ‘protocells’”?
- a lipid vesicle
- RNA whose origin is not discussed
- RNA strand templating with chemistry to prevent degradation of the membrane (speed and fidelity unknown)

I can't understand this use of the word "templating."

Post by MarkE
- a plausible supply of nucleotides, especially through the membrane
- RNA duplication
- a mechanism for vesicle division with RNA division
- metabolism
What we have is essentially an inert bag of Lego bricks, with no information, no energy supply, and highly doubtful material supply. I’ll rephrase the claim of “startlingly lifelike ‘protocells’” as “superficially lifelike to someone who does not grasp the essential nature of living cells.”
It would be easy enough to dismiss all of this as the optimistic musings of a writer aiming to sell a science magazine. But Szostak himself demonstrates the same overreach: “He says there is still some way to go before the system works well enough to sustain living organisms. For example, Szostak wants the copying to be faster and more accurate.”

"some way to go" is dishonestly self-serving, and is typical of insincere
people like Bill Rogers, Mark Isaak, Oxyagena, and others I could name.

"At least 99% of the way to go" is fully defensible, but you'd never guess
that from reading this kind of weasel-worded drivel.

Post by MarkE
Similar optimism from Joyce and Szostak eslewhere [4]: “The experiments described above bring the field tantalizingly close to a replicating and evolving protocell.”
Prediction: The Miller–Urey experiment was originally hailed as “life in a test tube” (or tantalizingly close to it), but nearly 70 years later has proven to be little more than tar in test tube; decades from now when the irreducible complexity,

Sorry -- you are still using a "definition" that is a straw man, built
for the express purpose of knocking it down.

Post by MarkE
intricacy and functionality of the simplest life is properly acknowledged, so will it be for these protocell experiments.

You are on solid ground here.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
U. of South Carolina at Columbia
http://people.math.sc.edu/nyikos

Post by MarkE
----------
[1] Michael Marshall: “freelance science journalist”; MSc Science Communication, MPhil Experimental Psychology, BA Natural Sciences.

Talk about having a boy do a man's job!
But then, that's the caliber of all but one or two talk.origins regulars
where abiogenesis is concerned, and Bill Rogers, who is probably one of them,
acts like a boy instead of the man he could act like.

Well done, Mark. I am terribly busy with online teaching and evaluation,
and with a number of other threads, so I can only contribute maybe an
average of one post a day on weekdays to your threads. [I only post on
weekends for the most extraordinary reasons, and am averaging less
than once a year on that.]
But I will try to make my contributions have maximum impact.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos

MarkE

2020-09-17 12:59:05 UTC

Post by Peter Nyikos
I was hoping to do better than this as far as participation on this
thread goes, Mark, but now that Harshman has painted himself into
several corners in his cowardly, hypocritical attacks on me in
the thread on Phylogenetic Systematics, and his cronies can't really
make a case against me without Harshman, I might get to participate
a bit more this week on this thread than I could last week.

Peter, I urge you to minimise exchanges of that kind, and press the substance of the argument.

If IC is defined as lack of viable sequential/independent development pathways for the essential components of a system,

NO, you must be working from sources who misrepresent IC
in order to falsely claim that it has been refuted.
The definition is utterly different: a well-coordinated system of interacting
parts, producing a specified function, such that the loss of ANY of the
parts causes loss of function.

Post by MarkE
the car analogy seems to fit this: "...like trying to build a car by making a chassis and hoping wheels and an engine will spontaneously appear."

Nothing spontaneous, just a gradualist sequence of events that
eventually produce each and every part.

Post by MarkE
The implication being that wheels and engines by themselves have no selectable function and are therefore not independently evolveable.

All that has to do with the conclusions one tries to draw from the
IC nature of the system and nothing to do with defining IC.
And the conclusions have to be established on a case by case basis.
In the case of the clotting system, the 12 or so factors in the clotting
cascade did not evolve independently. They arose one by one thru gene
duplication. Each time, the system ceased being IC for a while, but
then as the duplicated piece evolved, the system reverted to being IC.
The issue is whether the system, as it occurs in humans and many mammals,
is IC in its present state. That has NEVER been refuted.
Yet the system DID evolve from just one or two factors, because of the
all-important quality of each factor being autocatalytic.
Only a few people here have fathomed the absolute importance of that
quality. Most of them parrot the claim that "gene duplication and
subsequent divergence is enough, and their minds are closed to the
fact that this alone is completely inadequate.

Post by MarkE
But it may be a loose application - not a crucial point either way.

It's absolutely crucial, because of the tremendous amount of
disinformation about IC that feeds into the Wikipedia-promoted,
Sandwalk-promoted, NAS-promoted canard that ID is a pseudoscience.

How about Behe's definition?

“An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.” (A Response to Critics of Darwin’s Black Box, by Michael Behe, PCID, Volume 1.1, January February March, 2002; iscid.org/)

Yes. I underestimated how well you critiqued Szostak when I posted the
reply to your OP that I did. But I am puzzled by something.
<snip for focus>

What exactly is meant here by "RNA template copying"? What's the alleged
process, and how long are the RNA strings involved?

https://elifesciences.org/articles/17756

https://onlinelibrary.wiley.com/doi/full/10.1002/ange.202004934

Touche.

I can't understand this use of the word "templating."

"some way to go" is dishonestly self-serving, and is typical of insincere
people like Bill Rogers, Mark Isaak, Oxyagena, and others I could name.
"At least 99% of the way to go" is fully defensible, but you'd never guess
that from reading this kind of weasel-worded drivel.

James Tour would agree.

Sorry -- you are still using a "definition" that is a straw man, built
for the express purpose of knocking it down.

I can't find original reporting of the Miller–Urey experiment, but I find the following strong evidence that it was and still is in practice vastly overrated:

"Primordial Soup's On: Scientists Repeat Evolution's Most Famous Experiment"

https://www.scientificamerican.com/article/primordial-soup-urey-miller-evolution-experiment-repeated/

"So how did the biology textbooks respond to these discoveries showing that Stanley Miller’s experiment missed the mark? Many of them in 2000 persisted in using images of the Miller-Urey apparatus to convince students that scientists had demonstrated the first step in the origin of life. And many biology textbooks are still doing this. For example, Kenneth Mason, Jonathan Losos and Susan Singer’s 2014 edition of Raven and Johnson’s widely used Biology acknowledges that there is a controversy over the composition of the Earth’s early atmosphere, but it proceeds to tell the standard story anyway. It concludes that Stanley Miller demonstrated that “the key molecules of life could have formed in the reducing atmosphere of the early Earth.”

"Kenneth Miller and Joseph Levine’s 2014 Biology includes a drawing of the Miller-Urey apparatus with the following caption: “Miller and Urey produced amino acids, which are needed to make proteins, by passing sparks through a mixture of hydrogen, methane, ammonia, and water vapor. Evidence now suggests that the composition of Earth’s early atmosphere was different from their 1953 experiment. However, more recent experiments with different mixtures of gases have produced similar results.”

"This last statement is profoundly misleading, if not downright false. As we saw above, Stanley Miller himself showed that his experiment needed excess hydrogen to produce even the simplest amino acid, and methane was necessary to produce more complex amino acids. So the “different mixtures of gases” that Kenneth Miller and Joseph Levine claim “produced similar results” must have been very different from the probable atmosphere of the early Earth.

"According to the 2014 edition of Campbell Biology and the 2014 edition of Scott Freeman’s Biological Science (both of which feature drawings of Miller’s apparatus), Miller-Urey-type experiments using realistic mixtures of volcanic gases have produced organic molecules such as formaldehyde and hydrogen cyanide. Yes, but as we saw above, these chemicals are very toxic to living cells. Life could not have emerged spontaneously from a primordial soup containing significant amounts of them.

"The 2016 edition of Mader and Windelspecht’s Biology accompanies its drawing of the Miller-Urey apparatus with this: “In 2008, a group of scientists examined 11 vials of compounds produced from variations of the Miller-Urey experiment and found a greater variety of organic molecules than Miller reported, including all 22 amino acids.” True, but the additional amino acids all came from experiments that used a mixture of reducing gases, so the experiments suffered from the same flaw as the original one.

"The 2014 edition of Campbell Biology mentions the same 2008 study: “Perhaps the first organic compounds formed near volcanoes. In a 2008 test of this hypothesis, researchers used modern equipment to reanalyze molecules that Miller had saved from one of his experiments. The 2008 study found that numerous amino acids had formed under conditions that simulated a volcanic eruption.”

"That sounds pretty convincing, except that it’s dead wrong.

"In all fairness, the authors of Campbell Biology may have made an honest mistake in this case, misled by a 2008 article in Science titled “The Miller Volcanic Spark Discharge Experiment.” Jeffrey Bada (who completed his Ph.D. under Stanley Miller) and five other scientists examined samples saved from a 1955 experiment in which Miller modified his apparatus by using a narrow nozzle to inject steam from the boiling water into the circulating gases. Based on a 2000 report suggesting that small water droplets in volcanic eruptions can attract lightning, Bada and his colleagues claimed that this modification “possibly simulates the spark discharge synthesis by lightning in a steam-rich volcanic eruption,” and they called this “the volcanic experiment.

"But Miller himself did not call it “volcanic,” and for good reason. The only thing “volcanic” about it was that instead of passing the gases over boiling water, Miller injected steam into them. But the gases he used in 1955 were the same he had used in 1953: methane, ammonia, hydrogen, and water vapor. Calling the experiment “volcanic” gave the false impression that criticisms of the 1953 experiment had been overcome in the new experiment, but they had not. Nevertheless, Bada and his colleagues are continuing to promote the Miller-Urey experiment, including what they call its “volcanic” version. They have even posted online instructions on how to re-enact the experiment in a science classroom. So despite its irrelevance to the origin of life on Earth, the Miller-Urey experiment just keeps coming back. Why?"

https://world.wng.org/content/textbooks_of_the_living_dead

Post by MarkE
intricacy and functionality of the simplest life is properly acknowledged, so will it be for these protocell experiments.

You are on solid ground here.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
U. of South Carolina at Columbia
http://people.math.sc.edu/nyikos

Post by MarkE
----------
[1] Michael Marshall: “freelance science journalist”; MSc Science Communication, MPhil Experimental Psychology, BA Natural Sciences.

Talk about having a boy do a man's job!
But then, that's the caliber of all but one or two talk.origins regulars
where abiogenesis is concerned, and Bill Rogers, who is probably one of them,
acts like a boy instead of the man he could act like.

Well done, Mark. I am terribly busy with online teaching and evaluation,
and with a number of other threads, so I can only contribute maybe an
average of one post a day on weekdays to your threads. [I only post on
weekends for the most extraordinary reasons, and am averaging less
than once a year on that.]
But I will try to make my contributions have maximum impact.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos

jillery

2020-09-17 15:54:12 UTC