subject:"Re\: The origin of life has not been explained"

Re: The origin of life has not been explained

2019-07-27 Thread Philip Thrift


It's *consciousery* vs. *machinery.*

@philipthrift


On Saturday, July 27, 2019 at 4:31:27 AM UTC-5, Cosmin Visan wrote:
>
> You said a good thing maybe even without realizing it. The "machinary" is 
> not a "machinary" at all. Is a system of interacting conscious agents that 
> work together to implement mechanical functions.
>
> On Saturday, 27 July 2019 03:34:20 UTC+3, smitra wrote:
>>
>>
>> That's like trying to build a self-driving car by trying to figure out 
>> how to burn gasoline. Just because metabolism is of crucial importance 
>> to life doesn't mean one can get to life just by getting some of the 
>> important metabolic reactions started in some setting. Most of the 
>> complexity of life is in the molecular machinery. A microbe considered 
>> as a machine is more similar to the set of all factories, companies, 
>> managers and politicians of a country than to a single machine. 
>>
>> Saibal 
>>
>

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Re: The origin of life has not been explained

2019-07-27 Thread 'Cosmin Visan' via Everything List

You said a good thing maybe even without realizing it. The "machinary" is 
not a "machinary" at all. Is a system of interacting conscious agents that 
work together to implement mechanical functions.

On Saturday, 27 July 2019 03:34:20 UTC+3, smitra wrote:
>
>
> That's like trying to build a self-driving car by trying to figure out 
> how to burn gasoline. Just because metabolism is of crucial importance 
> to life doesn't mean one can get to life just by getting some of the 
> important metabolic reactions started in some setting. Most of the 
> complexity of life is in the molecular machinery. A microbe considered 
> as a machine is more similar to the set of all factories, companies, 
> managers and politicians of a country than to a single machine. 
>
> Saibal 
>

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Re: The origin of life has not been explained

2019-07-26 Thread smitra


On 27-07-2019 01:29, 'Brent Meeker' via Everything List wrote:

On 7/26/2019 4:13 PM, smitra wrote:

On 27-07-2019 00:39, 'Brent Meeker' via Everything List wrote:

On 7/26/2019 3:07 PM, smitra wrote:

On 23-07-2019 21:26, 'Brent Meeker' via Everything List wrote:

On 7/23/2019 12:07 PM, smitra wrote:

On 23-07-2019 04:10, 'Brent Meeker' via Everything List wrote:

On 7/22/2019 3:55 PM, smitra wrote:
This doesn't address the fundamental problems. People like 
Leslie Orgel have explained why metabolism first is a 
non-starter.


And you think Nick Lane hasn't read Orgel?


Orgel's original arguments can be generalized into a no-go 
argument that precludes all existing biochemical models for 
abiogenesis. This has been pointed out by Paul Davies. However, 
Davies then argues that this means that the problem lies with the 
fundamental laws of physics, but one can also circumvent the 
problems raised by sticking to ordinary physics and getting to the 
right structures within which the conventional models can work.




He has argued on the basis of the difficulties of getting to 
functional RNA, and more recently people like Paul Davies have 
pointed out the fundamental nature of this problem. My 
suggestion is not some new model, it simply makes conventional 
models such as e.g. the protocell work better by putting these 
in a micro-environment that itself has been forged in far from 
equilibrium conditions. The micro-environments break the 
symmetry that can steer the chemistry that takes place inside 
more coherently in one or the other direction compared to 
whatever chemistry can go on in a macroscopic environment.


Keep in mind that the simplest functional living organism is 
likely going to be similar to a microbe, involving hundreds of 
thousands of different enzymes that are then all necessary to 
make each other and maintain and copy the organism. There thus 
exists a massive gap from simple chemistry to the simplest 
self-reproducing lifeforms. The only plausible solution is then 
a scenario where simpler systems that would not function good 
enough to be able to reproduce with a multiplication factor of 
larger than one, can reproduce with a multiplication factor 
larger than 1 in a protected environment.


Which Lane and others postulate to alkaline "white smokers".


This is impossible, because you need to build  structures on the 
molecular scale without the enzymes that living organisms have 
available. Local thermal equilibrium won't allow chemical 
reactions to proceed differently a few atoms distance away at one 
site of a large molecule compared to another. So, one needs to 
consider processes in an environment where local thermal 
equilibrium will be violated on a molecular scale. This can happen 
in a cryogenic environment in space where UV radiation creates 
radical and ions and occasional cosmic ray interaction causes 
heating allowing nearby ions and radicals to form bonds. Such 
processes have been studied with the ail of getting to the 
fundamental building blocks of life, but that doesn't really work 
because of the random nature of the products.


But under those conditions one will also get extremely large 
clusters of organics, and they can serve as the housing within 
which one can have the right structures for conventional models to 
work. Confinement in a small volume is essential as there will be 
as small number of structures inside each such system. This means 
that the net effect of all the structures inside any particular 
system will differ due to statistical fluctuations. In a larger 
volume, the average effects of the structures would average out to 
some mean effect, also the effect the structures on the surface 
have on the chemistry taking place in the entire volume would be 
less the larger the volume becomes.


Which is why the huge surface area and fractal-like compartments of
white-smokers are needed for the origin of life:

http://hoffman.cm.utexas.edu/courses/hydrothermal_vents.pdf

I direct your attention to Box 3.

Brent



You can't get such structures down to the molecular scale there.


Catalyzing a reaction on a surface is at molecular scale.



Yes, but in a trivial sense as the surfaces are smooth on the 
molecular scale. You can, of course, get many interesting chemical 
reactions in such conditions, but there is no way you can build 
molecular machines that have specially crafted molecules as their 
parts this way that are then able to make their own parts or the parts 
of other machines. You're starting from a situation where the massive 
amount of information needed to specify how all the machines in the 
end product (a living organism) doesn't exist, and it won't therefore 
come into existence by virtue of having realized a number of 
biochemical processes.


You are ignoring the point of the abiogensis from the metabolism first
view.  The reactions are thermodynamically favored and don't require
specific proteins to catalyze them.


That's like

Re: The origin of life has not been explained

2019-07-26 Thread 'Brent Meeker' via Everything List





On 7/26/2019 4:13 PM, smitra wrote:

On 27-07-2019 00:39, 'Brent Meeker' via Everything List wrote:

On 7/26/2019 3:07 PM, smitra wrote:

On 23-07-2019 21:26, 'Brent Meeker' via Everything List wrote:

On 7/23/2019 12:07 PM, smitra wrote:

On 23-07-2019 04:10, 'Brent Meeker' via Everything List wrote:

On 7/22/2019 3:55 PM, smitra wrote:
This doesn't address the fundamental problems. People like 
Leslie Orgel have explained why metabolism first is a non-starter.


And you think Nick Lane hasn't read Orgel?


Orgel's original arguments can be generalized into a no-go 
argument that precludes all existing biochemical models for 
abiogenesis. This has been pointed out by Paul Davies. However, 
Davies then argues that this means that the problem lies with the 
fundamental laws of physics, but one can also circumvent the 
problems raised by sticking to ordinary physics and getting to the 
right structures within which the conventional models can work.




He has argued on the basis of the difficulties of getting to 
functional RNA, and more recently people like Paul Davies have 
pointed out the fundamental nature of this problem. My 
suggestion is not some new model, it simply makes conventional 
models such as e.g. the protocell work better by putting these 
in a micro-environment that itself has been forged in far from 
equilibrium conditions. The micro-environments break the 
symmetry that can steer the chemistry that takes place inside 
more coherently in one or the other direction compared to 
whatever chemistry can go on in a macroscopic environment.


Keep in mind that the simplest functional living organism is 
likely going to be similar to a microbe, involving hundreds of 
thousands of different enzymes that are then all necessary to 
make each other and maintain and copy the organism. There thus 
exists a massive gap from simple chemistry to the simplest 
self-reproducing lifeforms. The only plausible solution is then 
a scenario where simpler systems that would not function good 
enough to be able to reproduce with a multiplication factor of 
larger than one, can reproduce with a multiplication factor 
larger than 1 in a protected environment.


Which Lane and others postulate to alkaline "white smokers".


This is impossible, because you need to build  structures on the 
molecular scale without the enzymes that living organisms have 
available. Local thermal equilibrium won't allow chemical 
reactions to proceed differently a few atoms distance away at one 
site of a large molecule compared to another. So, one needs to 
consider processes in an environment where local thermal 
equilibrium will be violated on a molecular scale. This can happen 
in a cryogenic environment in space where UV radiation creates 
radical and ions and occasional cosmic ray interaction causes 
heating allowing nearby ions and radicals to form bonds. Such 
processes have been studied with the ail of getting to the 
fundamental building blocks of life, but that doesn't really work 
because of the random nature of the products.


But under those conditions one will also get extremely large 
clusters of organics, and they can serve as the housing within 
which one can have the right structures for conventional models to 
work. Confinement in a small volume is essential as there will be 
as small number of structures inside each such system. This means 
that the net effect of all the structures inside any particular 
system will differ due to statistical fluctuations. In a larger 
volume, the average effects of the structures would average out to 
some mean effect, also the effect the structures on the surface 
have on the chemistry taking place in the entire volume would be 
less the larger the volume becomes.


Which is why the huge surface area and fractal-like compartments of
white-smokers are needed for the origin of life:

http://hoffman.cm.utexas.edu/courses/hydrothermal_vents.pdf

I direct your attention to Box 3.

Brent



You can't get such structures down to the molecular scale there.


Catalyzing a reaction on a surface is at molecular scale.



Yes, but in a trivial sense as the surfaces are smooth on the 
molecular scale. You can, of course, get many interesting chemical 
reactions in such conditions, but there is no way you can build 
molecular machines that have specially crafted molecules as their 
parts this way that are then able to make their own parts or the parts 
of other machines. You're starting from a situation where the massive 
amount of information needed to specify how all the machines in the 
end product (a living organism) doesn't exist, and it won't therefore 
come into existence by virtue of having realized a number of 
biochemical processes.


You are ignoring the point of the abiogensis from the metabolism first 
view.  The reactions are thermodynamically favored and don't require 
specific proteins to catalyze them.


Brent



Saibal





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Re: The origin of life has not been explained

2019-07-26 Thread smitra


On 27-07-2019 00:39, 'Brent Meeker' via Everything List wrote:

On 7/26/2019 3:07 PM, smitra wrote:

On 23-07-2019 21:26, 'Brent Meeker' via Everything List wrote:

On 7/23/2019 12:07 PM, smitra wrote:

On 23-07-2019 04:10, 'Brent Meeker' via Everything List wrote:

On 7/22/2019 3:55 PM, smitra wrote:
This doesn't address the fundamental problems. People like Leslie 
Orgel have explained why metabolism first is a non-starter.


And you think Nick Lane hasn't read Orgel?


Orgel's original arguments can be generalized into a no-go argument 
that precludes all existing biochemical models for abiogenesis. This 
has been pointed out by Paul Davies. However, Davies then argues 
that this means that the problem lies with the fundamental laws of 
physics, but one can also circumvent the problems raised by sticking 
to ordinary physics and getting to the right structures within which 
the conventional models can work.




He has argued on the basis of the difficulties of getting to 
functional RNA, and more recently people like Paul Davies have 
pointed out the fundamental nature of this problem. My suggestion 
is not some new model, it simply makes conventional models such as 
e.g. the protocell work better by putting these in a 
micro-environment that itself has been forged in far from 
equilibrium conditions. The micro-environments break the symmetry 
that can steer the chemistry that takes place inside more 
coherently in one or the other direction compared to whatever 
chemistry can go on in a macroscopic environment.


Keep in mind that the simplest functional living organism is 
likely going to be similar to a microbe, involving hundreds of 
thousands of different enzymes that are then all necessary to make 
each other and maintain and copy the organism. There thus exists a 
massive gap from simple chemistry to the simplest self-reproducing 
lifeforms. The only plausible solution is then a scenario where 
simpler systems that would not function good enough to be able to 
reproduce with a multiplication factor of larger than one, can 
reproduce with a multiplication factor larger than 1 in a 
protected environment.


Which Lane and others postulate to alkaline "white smokers".


This is impossible, because you need to build  structures on the 
molecular scale without the enzymes that living organisms have 
available. Local thermal equilibrium won't allow chemical reactions 
to proceed differently a few atoms distance away at one site of a 
large molecule compared to another. So, one needs to consider 
processes in an environment where local thermal equilibrium will be 
violated on a molecular scale. This can happen in a cryogenic 
environment in space where UV radiation creates radical and ions and 
occasional cosmic ray interaction causes heating allowing nearby 
ions and radicals to form bonds. Such processes have been studied 
with the ail of getting to the fundamental building blocks of life, 
but that doesn't really work because of the random nature of the 
products.


But under those conditions one will also get extremely large 
clusters of organics, and they can serve as the housing within which 
one can have the right structures for conventional models to work. 
Confinement in a small volume is essential as there will be as small 
number of structures inside each such system. This means that the 
net effect of all the structures inside any particular system will 
differ due to statistical fluctuations. In a larger volume, the 
average effects of the structures would average out to some mean 
effect, also the effect the structures on the surface have on the 
chemistry taking place in the entire volume would be less the larger 
the volume becomes.


Which is why the huge surface area and fractal-like compartments of
white-smokers are needed for the origin of life:

http://hoffman.cm.utexas.edu/courses/hydrothermal_vents.pdf

I direct your attention to Box 3.

Brent



You can't get such structures down to the molecular scale there.


Catalyzing a reaction on a surface is at molecular scale.



Yes, but in a trivial sense as the surfaces are smooth on the molecular 
scale. You can, of course, get many interesting chemical reactions in 
such conditions, but there is no way you can build molecular machines 
that have specially crafted molecules as their parts this way that are 
then able to make their own parts or the parts of other machines. You're 
starting from a situation where the massive amount of information needed 
to specify how all the machines in the end product (a living organism) 
doesn't exist, and it won't therefore come into existence by virtue of 
having realized a number of biochemical processes.


Saibal


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Re: The origin of life has not been explained

2019-07-26 Thread 'Brent Meeker' via Everything List

On 7/26/2019 3:07 PM, smitra wrote:

On 23-07-2019 21:26, 'Brent Meeker' via Everything List wrote:

On 7/23/2019 12:07 PM, smitra wrote:

On 23-07-2019 04:10, 'Brent Meeker' via Everything List wrote:

On 7/22/2019 3:55 PM, smitra wrote:
This doesn't address the fundamental problems. People like Leslie
Orgel have explained why metabolism first is a non-starter.

And you think Nick Lane hasn't read Orgel?

Orgel's original arguments can be generalized into a no-go argument
that precludes all existing biochemical models for abiogenesis. This
has been pointed out by Paul Davies. However, Davies then argues
that this means that the problem lies with the fundamental laws of
physics, but one can also circumvent the problems raised by sticking
to ordinary physics and getting to the right structures within which
the conventional models can work.

He has argued on the basis of the difficulties of getting to
functional RNA, and more recently people like Paul Davies have
pointed out the fundamental nature of this problem. My suggestion
is not some new model, it simply makes conventional models such as
e.g. the protocell work better by putting these in a
micro-environment that itself has been forged in far from
equilibrium conditions. The micro-environments break the symmetry
that can steer the chemistry that takes place inside more
coherently in one or the other direction compared to whatever
chemistry can go on in a macroscopic environment.

Which Lane and others postulate to alkaline "white smokers".

This is impossible, because you need to build structures on the
molecular scale without the enzymes that living organisms have
available. Local thermal equilibrium won't allow chemical reactions
to proceed differently a few atoms distance away at one site of a
large molecule compared to another. So, one needs to consider
processes in an environment where local thermal equilibrium will be
violated on a molecular scale. This can happen in a cryogenic
environment in space where UV radiation creates radical and ions and
occasional cosmic ray interaction causes heating allowing nearby
ions and radicals to form bonds. Such processes have been studied
with the ail of getting to the fundamental building blocks of life,
but that doesn't really work because of the random nature of the
products.

But under those conditions one will also get extremely large
clusters of organics, and they can serve as the housing within which
one can have the right structures for conventional models to work.
Confinement in a small volume is essential as there will be as small
number of structures inside each such system. This means that the
net effect of all the structures inside any particular system will
differ due to statistical fluctuations. In a larger volume, the
average effects of the structures would average out to some mean
effect, also the effect the structures on the surface have on the
chemistry taking place in the entire volume would be less the larger
the volume becomes.

Which is why the huge surface area and fractal-like compartments of
white-smokers are needed for the origin of life:

http://hoffman.cm.utexas.edu/courses/hydrothermal_vents.pdf

I direct your attention to Box 3.

Brent

You can't get such structures down to the molecular scale there.

Catalyzing a reaction on a surface is at molecular scale.

Brent

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Re: The origin of life has not been explained

2019-07-26 Thread smitra

On 23-07-2019 21:26, 'Brent Meeker' via Everything List wrote:

On 7/23/2019 12:07 PM, smitra wrote:

On 23-07-2019 04:10, 'Brent Meeker' via Everything List wrote:

On 7/22/2019 3:55 PM, smitra wrote:
This doesn't address the fundamental problems. People like Leslie
Orgel have explained why metabolism first is a non-starter.

And you think Nick Lane hasn't read Orgel?

Orgel's original arguments can be generalized into a no-go argument
that precludes all existing biochemical models for abiogenesis. This
has been pointed out by Paul Davies. However, Davies then argues that
this means that the problem lies with the fundamental laws of physics,
but one can also circumvent the problems raised by sticking to
ordinary physics and getting to the right structures within which the
conventional models can work.

He has argued on the basis of the difficulties of getting to
functional RNA, and more recently people like Paul Davies have
pointed out the fundamental nature of this problem. My suggestion is
not some new model, it simply makes conventional models such as e.g.
the protocell work better by putting these in a micro-environment
that itself has been forged in far from equilibrium conditions. The
micro-environments break the symmetry that can steer the chemistry
that takes place inside more coherently in one or the other
direction compared to whatever chemistry can go on in a macroscopic
environment.

Which Lane and others postulate to alkaline "white smokers".

This is impossible, because you need to build structures on the
molecular scale without the enzymes that living organisms have
available. Local thermal equilibrium won't allow chemical reactions to
proceed differently a few atoms distance away at one site of a large
molecule compared to another. So, one needs to consider processes in
an environment where local thermal equilibrium will be violated on a
molecular scale. This can happen in a cryogenic environment in space
where UV radiation creates radical and ions and occasional cosmic ray
interaction causes heating allowing nearby ions and radicals to form
bonds. Such processes have been studied with the ail of getting to the
fundamental building blocks of life, but that doesn't really work
because of the random nature of the products.

But under those conditions one will also get extremely large clusters
of organics, and they can serve as the housing within which one can
have the right structures for conventional models to work. Confinement
in a small volume is essential as there will be as small number of
structures inside each such system. This means that the net effect of
all the structures inside any particular system will differ due to
statistical fluctuations. In a larger volume, the average effects of
the structures would average out to some mean effect, also the effect
the structures on the surface have on the chemistry taking place in
the entire volume would be less the larger the volume becomes.

Which is why the huge surface area and fractal-like compartments of
white-smokers are needed for the origin of life:

http://hoffman.cm.utexas.edu/courses/hydrothermal_vents.pdf

I direct your attention to Box 3.

Brent

You can't get such structures down to the molecular scale there.

Saibal

Re: The origin of life has not been explained

2019-07-24 Thread Bruno Marchal


> On 23 Jul 2019, at 20:26, Philip Thrift  wrote:
> 
> 
> 
> On Tuesday, July 23, 2019 at 9:23:45 AM UTC-5, telmo wrote:
> 
> 
> On Tue, Jul 23, 2019, at 14:15, Philip Thrift wrote:
>> 
>> 
>> On Tuesday, July 23, 2019 at 8:56:07 AM UTC-5, telmo wrote:
>> 
>> 
>> On Tue, Jul 23, 2019, at 13:45, Philip Thrift wrote:
>>> 
>>> Keep in mind there is no consciousness without matter.
>> 
>> Is there matter without consciousness?
>> 
>> Telmo.
>> 
>> 
>> According to panpsychists, no. :) 
>> 
>> https://www.iep.utm.edu/panpsych/ 
> 
> I know :)
> But panpsychists are still materialists. Which leads me to the tougher 
> question: does matter exist outside of first-person conscious experience? If 
> your answer is "yes", my follow-up question is quite predictable: how do you 
> know?
> 
> Telmo.
> 
> 
> 
> 
> There us no reason to know (and one cannot claim to know) anything whatsoever 
> outside of knowing one's selfhood.
> 
> Anything else is just best-effort-guessing.

Right.
What we can do is expressed those guess in the form of theories, and try to 
refute them, either by showing internal contradictions, or discrepancy with 
repeatable facts in nature.

Bruno



> 
> 
> @philipthrift 
> 
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>  
> .

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Re: The origin of life has not been explained

2019-07-24 Thread Philip Thrift

On Wednesday, July 24, 2019 at 3:05:16 AM UTC-5, Cosmin Visan wrote:
>
> Keep in mind that "matter" is just an idea in consciousness.
>
> On Tuesday, 23 July 2019 16:45:29 UTC+3, Philip Thrift wrote:
>>
>>
>> Keep in mind there is no consciousness without matter.
>>
>

But even given that the only thing one knows exists is one's selfhood
(consciousness), our experience includes reading about and finding out
about all the weird stuff matter does (via materials science).

If there was only selfhoods, there would only be imaginings of matter. But
what matter actually presents to us *goes beyond* what mere imaginings of
what it is and does.

@philipthrift

*Students learn at Materials Camp*
https://www.columbiadailyherald.com/news/20190723/students-learn-at-materials-camp

By Special to The Oak Ridger
Posted Jul 23, 2019 at 5:30 PM

To understand how and why things work, sometimes you have to take a close
look. A really close look. Avery, a Roane County High School senior, did
just that at this summer’s *Materials Camp*, sponsored in part by the Y-12
National Security Complex.

She and 14 other East Tennessee high school students studied nickel, iron,
aluminum, copper, and other metals not by opening a textbook but by
heating, hammering, grinding, bending, rolling, and polishing the materials.

“We learned how these materials behave under certain conditions and
stresses,” Avery stated in a Y-12 news release. “Then we examined their
microstructures, the different grain structures, using a scanning electron
microscope and other analytical equipment.”

One of the campers’ favorite activities was pounding a hot iron bar with a
forging hammer during the blacksmithing demonstration.

“That was really fun and cool,” said Avery, who wanted to make sure
everyone, including her camp instructors, got in a few whacks at the bar.

“Avery wasn’t going to let us leave until I had a chance to take out some
aggression on that metal bar,” said Claudia Rawn, one of the camp
coordinators and associate professor in the University of Tennessee’s
Materials Science and Engineering department and director of UT’s Center
for Materials Processing.

Having fun while learning is all part of the camp formula. Through hands-on
activities and an escape-room scenario, camp instructors introduced
students to materials science, which involves the properties of materials
and their application in everything from high-performance electronics and
airplanes to stents, heart valves, and other biotechnologies to renewable
energy.

“I think all of the students now have a different view that everything is
made of a variety of materials and there are opportunities to have a
fascinating education and career with materials,” said Camp Coordinator Bob
Bridges, a Y-12 metallurgist.

Before the weeklong camp, many of the students had never heard of materials
science.

“Most high school students thinking about majoring in an engineering
discipline don’t know about materials science and engineering,” Rawn said.
“A lot of STEM-oriented students know they want to major in engineering,
and knowing about materials science and engineering helps them to make a
more informed choice.”

The camp not only serves as a recruiting tool for area colleges but also
feeds the workforce pipeline. Y-12 sponsors the camp as part of its
educational outreach efforts to develop the science, technology,
engineering, and math skills the site will need in the future.

“Because of this camp, I’m thinking about pursuing an education in
materials science,” Avery said. “It got me thinking about different avenues
for college and a career.”

In addition to UT and Consolidated Nuclear Security, which manages and
operates Y-12 for the National Nuclear Security Administration, camp
sponsors included the ASM Materials Education Foundation and Pellissippi
State Community College.

Electron Optics Instruments and IXRF Systems, Shimadzu Scientific
Instruments, Mager Scientific, and Carl Zeiss Microscopy provided almost
$400,000 worth of equipment for students to use as well as staff to train
campers on how to use it.

“This camp would not be possible without the huge number of volunteers who
work with the students behind the scenes and donate equipment and provide
expertise,” said Teri Brahams, executive director for Economic and
Workforce Development at Pellissippi State Community College.

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Re: The origin of life has not been explained

2019-07-24 Thread 'Cosmin Visan' via Everything List

You talk of life as if is some kind of mechanism, which is not. Life is a 
product of consciousness. So your entire analysis is beyond meaninglessness.

On Tuesday, 23 July 2019 22:07:05 UTC+3, smitra wrote:
>
> On 23-07-2019 04:10, 'Brent Meeker' via Everything List wrote: 
> > On 7/22/2019 3:55 PM, smitra wrote: 
> >> This doesn't address the fundamental problems. People like Leslie 
> >> Orgel have explained why metabolism first is a non-starter. 
> > 
> > And you think Nick Lane hasn't read Orgel? 
>
> Orgel's original arguments can be generalized into a no-go argument that 
> precludes all existing biochemical models for abiogenesis. This has been 
> pointed out by Paul Davies. However, Davies then argues that this means 
> that the problem lies with the fundamental laws of physics, but one can 
> also circumvent the problems raised by sticking to ordinary physics and 
> getting to the right structures within which the conventional models can 
> work. 
>
> > 
> >> He has argued on the basis of the difficulties of getting to 
> >> functional RNA, and more recently people like Paul Davies have pointed 
> >> out the fundamental nature of this problem. My suggestion is not some 
> >> new model, it simply makes conventional models such as e.g. the 
> >> protocell work better by putting these in a micro-environment that 
> >> itself has been forged in far from equilibrium conditions. The 
> >> micro-environments break the symmetry that can steer the chemistry 
> >> that takes place inside more coherently in one or the other direction 
> >> compared to whatever chemistry can go on in a macroscopic environment. 
> >> 
> >> Keep in mind that the simplest functional living organism is likely 
> >> going to be similar to a microbe, involving hundreds of thousands of 
> >> different enzymes that are then all necessary to make each other and 
> >> maintain and copy the organism. There thus exists a massive gap from 
> >> simple chemistry to the simplest self-reproducing lifeforms. The only 
> >> plausible solution is then a scenario where simpler systems that would 
> >> not function good enough to be able to reproduce with a multiplication 
> >> factor of larger than one, can reproduce with a multiplication factor 
> >> larger than 1 in a protected environment. 
> > 
> > Which Lane and others postulate to alkaline "white smokers". 
>
> This is impossible, because you need to build  structures on the 
> molecular scale without the enzymes that living organisms have 
> available. Local thermal equilibrium won't allow chemical reactions to 
> proceed differently a few atoms distance away at one site of a large 
> molecule compared to another. So, one needs to consider processes in an 
> environment where local thermal equilibrium will be violated on a 
> molecular scale. This can happen in a cryogenic environment in space 
> where UV radiation creates radical and ions and occasional cosmic ray 
> interaction causes heating allowing nearby ions and radicals to form 
> bonds. Such processes have been studied with the ail of getting to the 
> fundamental building blocks of life, but that doesn't really work 
> because of the random nature of the products. 
>
> But under those conditions one will also get extremely large clusters of 
> organics, and they can serve as the housing within which one can have 
> the right structures for conventional models to work. Confinement in a 
> small volume is essential as there will be as small number of structures 
> inside each such system. This means that the net effect of all the 
> structures inside any particular system will differ due to statistical 
> fluctuations. In a larger volume, the average effects of the structures 
> would average out to some mean effect, also the effect the structures on 
> the surface have on the chemistry taking place in the entire volume 
> would be less the larger the volume becomes. 
>
> Saibal 
>
>
> > 
> > Brent 
> > 
> >> But that environment must then have features that would have to play 
> >> the role of the more sophisticated molecular machinery that makes the 
> >> more advanced life forms work. Fixed features on the inner surface 
> >> area of a micro-environment can then work. The effect such features 
> >> have over the entire volume can be non-negligible in a small system. 
> >> 
> >> Saibal 
> >> 
> >> 
> >> On 07-07-2019 08:32, 'Brent Meeker' via Everything List wrote: 
> >>> I think Nick Lane's metabolism-first theory, which he discusses in 
> >>> his 
> >>> book "The Vital Question", is more plausible.  There's good online 
> >>> talk by Lane https://www.youtube.com/watch?v=PhPrirmk8F4. 
> >>> 
> >>> Brent 
> >>> 
> >>> On 7/6/2019 8:32 AM, smitra wrote: 
>  https://arxiv.org/abs/1711.01945 
>  
>  
>  A followup article which focuses more on the mathematical issues is 
>  under construction, the key points are: 
>  
>  1) In interstellar space, simple organic compounds captured in small 
>  ice

Re: The origin of life has not been explained

2019-07-24 Thread 'Cosmin Visan' via Everything List

Keep in mind that "matter" is just an idea in consciousness. 

On Tuesday, 23 July 2019 16:45:29 UTC+3, Philip Thrift wrote:
>
>
> Keep in mind there is no consciousness without matter.
>

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Re: The origin of life has not been explained

2019-07-24 Thread Telmo Menezes



On Tue, Jul 23, 2019, at 18:26, Philip Thrift wrote:
> 
> 
> On Tuesday, July 23, 2019 at 9:23:45 AM UTC-5, telmo wrote:
>> 
>> 
>> On Tue, Jul 23, 2019, at 14:15, Philip Thrift wrote:
>>> 
>>> 
>>> On Tuesday, July 23, 2019 at 8:56:07 AM UTC-5, telmo wrote:
 
 
 On Tue, Jul 23, 2019, at 13:45, Philip Thrift wrote:
> 
> Keep in mind there is no consciousness without matter.
 
 Is there matter without consciousness?
 
 Telmo.
>>> 
>>> 
>>> According to panpsychists, *no*. :) 
>>> 
>>> https://www.iep.utm.edu/panpsych/
>> 
>> I know :)
>> But panpsychists are still materialists. Which leads me to the tougher 
>> question: does matter exist outside of first-person conscious experience? If 
>> your answer is "yes", my follow-up question is quite predictable: how do you 
>> know?
>> 
>> Telmo.
>> 
> 
> 
> 
> There us no reason to know (and one cannot claim to know) *anything 
> whatsoever* outside of knowing one's *selfhood*.
> 
> Anything else is just best-effort-guessing.

I agree.

Telmo.

> 
> 
> @philipthrift 
> 

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>  
> .

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Re: The origin of life has not been explained

2019-07-23 Thread 'Brent Meeker' via Everything List





On 7/23/2019 12:07 PM, smitra wrote:

On 23-07-2019 04:10, 'Brent Meeker' via Everything List wrote:

On 7/22/2019 3:55 PM, smitra wrote:
This doesn't address the fundamental problems. People like Leslie 
Orgel have explained why metabolism first is a non-starter.


And you think Nick Lane hasn't read Orgel?


Orgel's original arguments can be generalized into a no-go argument 
that precludes all existing biochemical models for abiogenesis. This 
has been pointed out by Paul Davies. However, Davies then argues that 
this means that the problem lies with the fundamental laws of physics, 
but one can also circumvent the problems raised by sticking to 
ordinary physics and getting to the right structures within which the 
conventional models can work.




He has argued on the basis of the difficulties of getting to 
functional RNA, and more recently people like Paul Davies have 
pointed out the fundamental nature of this problem. My suggestion is 
not some new model, it simply makes conventional models such as e.g. 
the protocell work better by putting these in a micro-environment 
that itself has been forged in far from equilibrium conditions. The 
micro-environments break the symmetry that can steer the chemistry 
that takes place inside more coherently in one or the other 
direction compared to whatever chemistry can go on in a macroscopic 
environment.


Keep in mind that the simplest functional living organism is likely 
going to be similar to a microbe, involving hundreds of thousands of 
different enzymes that are then all necessary to make each other and 
maintain and copy the organism. There thus exists a massive gap from 
simple chemistry to the simplest self-reproducing lifeforms. The 
only plausible solution is then a scenario where simpler systems 
that would not function good enough to be able to reproduce with a 
multiplication factor of larger than one, can reproduce with a 
multiplication factor larger than 1 in a protected environment.


Which Lane and others postulate to alkaline "white smokers".


This is impossible, because you need to build  structures on the 
molecular scale without the enzymes that living organisms have 
available. Local thermal equilibrium won't allow chemical reactions to 
proceed differently a few atoms distance away at one site of a large 
molecule compared to another. So, one needs to consider processes in 
an environment where local thermal equilibrium will be violated on a 
molecular scale. This can happen in a cryogenic environment in space 
where UV radiation creates radical and ions and occasional cosmic ray 
interaction causes heating allowing nearby ions and radicals to form 
bonds. Such processes have been studied with the ail of getting to the 
fundamental building blocks of life, but that doesn't really work 
because of the random nature of the products.


But under those conditions one will also get extremely large clusters 
of organics, and they can serve as the housing within which one can 
have the right structures for conventional models to work. Confinement 
in a small volume is essential as there will be as small number of 
structures inside each such system. This means that the net effect of 
all the structures inside any particular system will differ due to 
statistical fluctuations. In a larger volume, the average effects of 
the structures would average out to some mean effect, also the effect 
the structures on the surface have on the chemistry taking place in 
the entire volume would be less the larger the volume becomes.


Which is why the huge surface area and fractal-like compartments of 
white-smokers are needed for the origin of life:


http://hoffman.cm.utexas.edu/courses/hydrothermal_vents.pdf

I direct your attention to Box 3.

Brent



Saibal




Brent

But that environment must then have features that would have to play 
the role of the more sophisticated molecular machinery that makes 
the more advanced life forms work. Fixed features on the inner 
surface area of a micro-environment can then work. The effect such 
features have over the entire volume can be non-negligible in a 
small system.


Saibal


On 07-07-2019 08:32, 'Brent Meeker' via Everything List wrote:

I think Nick Lane's metabolism-first theory, which he discusses in his
book "The Vital Question", is more plausible.  There's good online
talk by Lane https://www.youtube.com/watch?v=PhPrirmk8F4.

Brent

On 7/6/2019 8:32 AM, smitra wrote:

https://arxiv.org/abs/1711.01945


A followup article which focuses more on the mathematical issues 
is under construction, the key points are:


1) In interstellar space, simple organic compounds captured in 
small ice grains were subject to UV radiation and occasional 
heating due to incident cosmic rays (CR). This induced a bond 
percolation process that led to large clusters of organic 
molecules on a time scale of $\gtrsim 10^6$ years.


2) On a proto-planet, such clusters can merge into loosely bound 
superclusters. The

Re: The origin of life has not been explained

2019-07-23 Thread smitra


On 23-07-2019 04:10, 'Brent Meeker' via Everything List wrote:

On 7/22/2019 3:55 PM, smitra wrote:
This doesn't address the fundamental problems. People like Leslie 
Orgel have explained why metabolism first is a non-starter.


And you think Nick Lane hasn't read Orgel?


Orgel's original arguments can be generalized into a no-go argument that 
precludes all existing biochemical models for abiogenesis. This has been 
pointed out by Paul Davies. However, Davies then argues that this means 
that the problem lies with the fundamental laws of physics, but one can 
also circumvent the problems raised by sticking to ordinary physics and 
getting to the right structures within which the conventional models can 
work.




He has argued on the basis of the difficulties of getting to 
functional RNA, and more recently people like Paul Davies have pointed 
out the fundamental nature of this problem. My suggestion is not some 
new model, it simply makes conventional models such as e.g. the 
protocell work better by putting these in a micro-environment that 
itself has been forged in far from equilibrium conditions. The 
micro-environments break the symmetry that can steer the chemistry 
that takes place inside more coherently in one or the other direction 
compared to whatever chemistry can go on in a macroscopic environment.


Keep in mind that the simplest functional living organism is likely 
going to be similar to a microbe, involving hundreds of thousands of 
different enzymes that are then all necessary to make each other and 
maintain and copy the organism. There thus exists a massive gap from 
simple chemistry to the simplest self-reproducing lifeforms. The only 
plausible solution is then a scenario where simpler systems that would 
not function good enough to be able to reproduce with a multiplication 
factor of larger than one, can reproduce with a multiplication factor 
larger than 1 in a protected environment.


Which Lane and others postulate to alkaline "white smokers".


This is impossible, because you need to build  structures on the 
molecular scale without the enzymes that living organisms have 
available. Local thermal equilibrium won't allow chemical reactions to 
proceed differently a few atoms distance away at one site of a large 
molecule compared to another. So, one needs to consider processes in an 
environment where local thermal equilibrium will be violated on a 
molecular scale. This can happen in a cryogenic environment in space 
where UV radiation creates radical and ions and occasional cosmic ray 
interaction causes heating allowing nearby ions and radicals to form 
bonds. Such processes have been studied with the ail of getting to the 
fundamental building blocks of life, but that doesn't really work 
because of the random nature of the products.


But under those conditions one will also get extremely large clusters of 
organics, and they can serve as the housing within which one can have 
the right structures for conventional models to work. Confinement in a 
small volume is essential as there will be as small number of structures 
inside each such system. This means that the net effect of all the 
structures inside any particular system will differ due to statistical 
fluctuations. In a larger volume, the average effects of the structures 
would average out to some mean effect, also the effect the structures on 
the surface have on the chemistry taking place in the entire volume 
would be less the larger the volume becomes.


Saibal




Brent

But that environment must then have features that would have to play 
the role of the more sophisticated molecular machinery that makes the 
more advanced life forms work. Fixed features on the inner surface 
area of a micro-environment can then work. The effect such features 
have over the entire volume can be non-negligible in a small system.


Saibal


On 07-07-2019 08:32, 'Brent Meeker' via Everything List wrote:
I think Nick Lane's metabolism-first theory, which he discusses in 
his

book "The Vital Question", is more plausible.  There's good online
talk by Lane https://www.youtube.com/watch?v=PhPrirmk8F4.

Brent

On 7/6/2019 8:32 AM, smitra wrote:

https://arxiv.org/abs/1711.01945


A followup article which focuses more on the mathematical issues is 
under construction, the key points are:


1) In interstellar space, simple organic compounds captured in small 
ice grains were subject to UV radiation and occasional heating due 
to incident cosmic rays (CR). This induced a bond percolation 
process that led to large clusters of organic molecules on a time 
scale of $\gtrsim 10^6$ years.


2) On a proto-planet, such clusters can merge into loosely bound 
superclusters. The deep interior of such superclusters can provide 
for chemical micro-environments in which conventional models of 
abiogenesis driven by cold-warm cycles can be considered.


3) Rapid fluctuations in the chemical potentials of certain chemical 
compounds that can

Re: The origin of life has not been explained

2019-07-23 Thread Philip Thrift



On Tuesday, July 23, 2019 at 9:23:45 AM UTC-5, telmo wrote:
>
>
>
> On Tue, Jul 23, 2019, at 14:15, Philip Thrift wrote:
>
>
>
> On Tuesday, July 23, 2019 at 8:56:07 AM UTC-5, telmo wrote:
>
>
>
> On Tue, Jul 23, 2019, at 13:45, Philip Thrift wrote:
>
>
> Keep in mind there is no consciousness without matter.
>
>
> Is there matter without consciousness?
>
> Telmo.
>
>
>
> According to panpsychists, *no*. :) 
>
> https://www.iep.utm.edu/panpsych/
>
>
> I know :)
> But panpsychists are still materialists. Which leads me to the tougher 
> question: does matter exist outside of first-person conscious experience? 
> If your answer is "yes", my follow-up question is quite predictable: how do 
> you know?
>
> Telmo.
>
>


There us no reason to know (and one cannot claim to know) *anything 
whatsoever* outside of knowing one's *selfhood*.

Anything else is just best-effort-guessing.


@philipthrift 

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Re: The origin of life has not been explained

2019-07-23 Thread Telmo Menezes



On Tue, Jul 23, 2019, at 14:15, Philip Thrift wrote:
> 
> 
> On Tuesday, July 23, 2019 at 8:56:07 AM UTC-5, telmo wrote:
>> 
>> 
>> On Tue, Jul 23, 2019, at 13:45, Philip Thrift wrote:
>>> 
>>> Keep in mind there is no consciousness without matter.
>> 
>> Is there matter without consciousness?
>> 
>> Telmo.
> 
> 
> According to panpsychists, *no*. :) 
> 
> https://www.iep.utm.edu/panpsych/

I know :)
But panpsychists are still materialists. Which leads me to the tougher 
question: does matter exist outside of first-person conscious experience? If 
your answer is "yes", my follow-up question is quite predictable: how do you 
know?

Telmo.

> 
> @philipthrift
> 

> --
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>  
> .

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Re: The origin of life has not been explained

2019-07-23 Thread Philip Thrift



On Tuesday, July 23, 2019 at 8:56:07 AM UTC-5, telmo wrote:
>
>
>
> On Tue, Jul 23, 2019, at 13:45, Philip Thrift wrote:
>
>
> Keep in mind there is no consciousness without matter.
>
>
> Is there matter without consciousness?
>
> Telmo.
>


According to panpsychists, *no*. :) 

https://www.iep.utm.edu/panpsych/

@philipthrift

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Re: The origin of life has not been explained

2019-07-23 Thread Telmo Menezes



On Tue, Jul 23, 2019, at 13:45, Philip Thrift wrote:
> 
> Keep in mind there is no consciousness without matter.

Is there matter without consciousness?

Telmo.

> 
> @philipthrift
> 
> 
> On Tuesday, July 23, 2019 at 7:30:20 AM UTC-5, Cosmin Visan wrote:
>> Keep in mind that life is linked to consciousness. There is no such thing as 
>> "material life". Whatever happened had to involve consciousness one way or 
>> another.
>> 
>> On Tuesday, 23 July 2019 01:55:58 UTC+3, smitra wrote:
>>> Keep in mind 
> 

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>  
> .

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Re: The origin of life has not been explained

2019-07-23 Thread Philip Thrift


Keep in mind there is no consciousness without matter.

@philipthrift


On Tuesday, July 23, 2019 at 7:30:20 AM UTC-5, Cosmin Visan wrote:
>
> Keep in mind that life is linked to consciousness. There is no such thing 
> as "material life". Whatever happened had to involve consciousness one way 
> or another.
>
> On Tuesday, 23 July 2019 01:55:58 UTC+3, smitra wrote:
>>
>> Keep in mind 
>>
>

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Re: The origin of life has not been explained

2019-07-23 Thread 'Cosmin Visan' via Everything List

Keep in mind that life is linked to consciousness. There is no such thing 
as "material life". Whatever happened had to involve consciousness one way 
or another.

On Tuesday, 23 July 2019 01:55:58 UTC+3, smitra wrote:
>
> Keep in mind 
>

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Re: The origin of life has not been explained

2019-07-22 Thread 'Brent Meeker' via Everything List

On 7/22/2019 3:55 PM, smitra wrote:
This doesn't address the fundamental problems. People like Leslie
Orgel have explained why metabolism first is a non-starter.

And you think Nick Lane hasn't read Orgel?

He has argued on the basis of the difficulties of getting to
functional RNA, and more recently people like Paul Davies have pointed
out the fundamental nature of this problem. My suggestion is not some
new model, it simply makes conventional models such as e.g. the
protocell work better by putting these in a micro-environment that
itself has been forged in far from equilibrium conditions. The
micro-environments break the symmetry that can steer the chemistry
that takes place inside more coherently in one or the other direction
compared to whatever chemistry can go on in a macroscopic environment.

Which Lane and others postulate to alkaline "white smokers".

Brent

But that environment must then have features that would have to play
the role of the more sophisticated molecular machinery that makes the
more advanced life forms work. Fixed features on the inner surface
area of a micro-environment can then work. The effect such features
have over the entire volume can be non-negligible in a small system.

Saibal

On 07-07-2019 08:32, 'Brent Meeker' via Everything List wrote:

I think Nick Lane's metabolism-first theory, which he discusses in his
book "The Vital Question", is more plausible. There's good online
talk by Lane https://www.youtube.com/watch?v=PhPrirmk8F4.

Brent

On 7/6/2019 8:32 AM, smitra wrote:

https://arxiv.org/abs/1711.01945

A followup article which focuses more on the mathematical issues is
under construction, the key points are:

1) In interstellar space, simple organic compounds captured in small
ice grains were subject to UV radiation and occasional heating due
to incident cosmic rays (CR). This induced a bond percolation
process that led to large clusters of organic molecules on a time
scale of $\gtrsim 10^6$ years.

2) On a proto-planet, such clusters can merge into loosely bound
superclusters. The deep interior of such superclusters can provide
for chemical micro-environments in which conventional models of
abiogenesis driven by cold-warm cycles can be considered.

3) Rapid fluctuations in the chemical potentials of certain chemical
compounds that can penetrate the supercluster, will be damped down.
Long term gradual and periodic changes then dominate, allowing any
biochemical systems inside the superclusters to more easily evolve
toward exploiting the conditions in their micro-environments,
compared to a similar system in the outside environment.

4) As the supercluster breaks up, the system experiences more of the
shorter term fluctuations that has more of a random character. The
system can then evolve to adapt to these fluctuations, when doing so
right from the start might not have worked.

5) On a small fraction of the superclusters these processes led to
microbes capable of surviving in the outside environment.

6) Microbes were transferred to Earth via a collision of a
microbe-containing proto-planet with the Moon. Fragments containing
microbes resulting from the giant impact rained down on the Earth.

Saibal

On 06-07-2019 10:48, 'Cosmin Visan' via Everything List wrote:

https://www.youtube.com/watch?v=r4sP1E1Jd_Y [1]

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[2].

Links:
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[1]
https://www.youtube.com/watch?v=r4sP1E1Jd_Yfbclid=IwAR03cRVkBTOeYnPldcuLzFGCNiWqCR0dE5FENXF9JJtRlk75sbq5Dh2wxcY
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Re: The origin of life has not been explained

2019-07-22 Thread smitra

This doesn't address the fundamental problems. People like Leslie Orgel
have explained why metabolism first is a non-starter. He has argued on
the basis of the difficulties of getting to functional RNA, and more
recently people like Paul Davies have pointed out the fundamental nature
of this problem. My suggestion is not some new model, it simply makes
conventional models such as e.g. the protocell work better by putting
these in a micro-environment that itself has been forged in far from
equilibrium conditions. The micro-environments break the symmetry that
can steer the chemistry that takes place inside more coherently in one
or the other direction compared to whatever chemistry can go on in a
macroscopic environment.

Keep in mind that the simplest functional living organism is likely
going to be similar to a microbe, involving hundreds of thousands of
different enzymes that are then all necessary to make each other and
maintain and copy the organism. There thus exists a massive gap from
simple chemistry to the simplest self-reproducing lifeforms. The only
plausible solution is then a scenario where simpler systems that would
not function good enough to be able to reproduce with a multiplication
factor of larger than one, can reproduce with a multiplication factor
larger than 1 in a protected environment. But that environment must then
have features that would have to play the role of the more sophisticated
molecular machinery that makes the more advanced life forms work. Fixed
features on the inner surface area of a micro-environment can then work.
The effect such features have over the entire volume can be
non-negligible in a small system.

Saibal

On 07-07-2019 08:32, 'Brent Meeker' via Everything List wrote:

I think Nick Lane's metabolism-first theory, which he discusses in his
book "The Vital Question", is more plausible. There's good online
talk by Lane https://www.youtube.com/watch?v=PhPrirmk8F4.

Brent

On 7/6/2019 8:32 AM, smitra wrote:

https://arxiv.org/abs/1711.01945

A followup article which focuses more on the mathematical issues is
under construction, the key points are:

1) In interstellar space, simple organic compounds captured in small
ice grains were subject to UV radiation and occasional heating due to
incident cosmic rays (CR). This induced a bond percolation process
that led to large clusters of organic molecules on a time scale of
$\gtrsim 10^6$ years.

2) On a proto-planet, such clusters can merge into loosely bound
superclusters. The deep interior of such superclusters can provide for
chemical micro-environments in which conventional models of
abiogenesis driven by cold-warm cycles can be considered.

3) Rapid fluctuations in the chemical potentials of certain chemical
compounds that can penetrate the supercluster, will be damped down.
Long term gradual and periodic changes then dominate, allowing any
biochemical systems inside the superclusters to more easily evolve
toward exploiting the conditions in their micro-environments, compared
to a similar system in the outside environment.

5) On a small fraction of the superclusters these processes led to
microbes capable of surviving in the outside environment.

6) Microbes were transferred to Earth via a collision of a
microbe-containing proto-planet with the Moon. Fragments containing
microbes resulting from the giant impact rained down on the Earth.

Saibal

On 06-07-2019 10:48, 'Cosmin Visan' via Everything List wrote:

https://www.youtube.com/watch?v=r4sP1E1Jd_Y [1]

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Re: The origin of life has not been explained

2019-07-07 Thread 'Brent Meeker' via Everything List

Read Nick Lane.  He makes a good argument for a metabolism first 
abiogenesis.  He observes that the ADP<->ATP energy cycle is the same in 
every organism and he shows how it could have originated in alkaline 
ocean vents.

Brent

On 7/6/2019 5:09 PM, John Clark wrote:
On Sat, Jul 6, 2019 at 6:34 PM Lawrence Crowell 
> wrote:

/> The idea of the RNA world runs into trouble with the ribosome,
which is a hugely complex system of RNA and proteins/

In the RNA world there would be nothing nearly as large and competent 
as modern ribosomes and there would be no proteins at all, there would 
just be short single strands of RNA floating in a sea of nucleotides. 
As far as I know nobody has yet found a RNA string that could catalyze 
the duplication of a string of nucleotides as large as itself, but 
they have found a RNA string called tC19Z that could reliably copy, 
without the help of proteins, RNA sequences 95 nucleotides long. And 
that is almost half as long as tC19Z itself. I find that encouraging.

Ribozyme-Catalyzed Transcription of an Active Ribozyme 

John K Clark

RNA sequences up to 95 letters
no be anything as big as a ribosome or any proteins at all, there 
would be short single strands of RNA floating in a sea of nucleotides

neucteatides

On Saturday, July 6, 2019 at 5:04:40 PM UTC-5, John Clark wrote:

On Sat, Jul 6, 2019 at 4:18 PM Lawrence Crowell
 wrote

> We have lots of hypotheses on this, but it is a point
where biological evolution loses explanatory power, just
as general relativity fails at the center of black hole
collapse. 

I think that's the key point, Darwinian Evolution can't take
over until you have a replicator of some sort, in fact I would
say the origin of heredity is the same thing as the origin of
life. That first replicator was certainly far simpler than
anything alive today and it almost certainly didn't have any
DNA in it. RNA is only single stranded not double as DNA is
and it is usually much shorter too, and RNA would help in
getting over the chicken or the egg problem. RNA can carry
information, not as well as DNA can but it can do it. And RNA
can act like an enzyme and catalyze chemical reactions, not as
well as proteins can but it can do it.So the first RNA life
would be very incompetent by modern standards but with Darwin
you don't have to be perfect you just have to be better than
the competition.

In 1986 Nobel Laureate Walter Gilbert said in the journal Nature:

"/One can contemplate an RNA world, containing only RNA
molecules that serve to catalyze the synthesis of themselves.
The first step of evolution proceeds then by RNA molecules
performing the catalytic activities necessary to assemble
themselves from a nucleotide soup/."

However some people, like Chemist Graham Cairns-Smith think
that even the RNA world, although far simpler than modern
life, was still too complicated to be the first replicator aka
the first life. Cairns-Smith proposed that the very first
replicators were not organic at all but were clays were
information was encoded in a pattern of defects in silicate
crystals. In 1985 he wrote a book about it that is now online:

Seven clues to the origin of life

The problem with figuring out how life started is that
chemicals usually don't have fossils, so even evolutionary
biologist and militant atheist Richard Dawkins admits that
although he likes the Cairns-Smith theory we may never be able
to say this is definitely how life started and it couldn't
have started any other way, the best we can do is find a
plausible way that life *could* have started.

 John K Clark

The complexity group at Santa Fe Institute has a 3 month course on
the origins of life. I thought about joining, but decided not
because my plate is already a bit full and frankly all we really
have to go with are hypotheses. The idea of the RNA world runs
into trouble with the ribosome, which is a hugely complex system
of RNA and proteins. How that got going is difficult to know.

I had this idea about RNA interactions with carbon nanofibers.
Could RNA coil up around these and these could serve as some
system for translation? Maybe in time this became more complex
with more RNA and proteins bound to the system. Eventually this
evolved into the ribosome. I looked this up and found of course
other had taken up this idea.

LC
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Re: The origin of life has not been explained

2019-07-07 Thread PGC

On Sunday, July 7, 2019 at 11:52:41 AM UTC+2, Philip Thrift wrote:
>
>
>
> He does have the correct *contemplative, far-away look* on his home page:
>
> http://nick-lane.net/
>

Heh! Yeah good try on the look. For yours truly it's gotta be the chest 
out, stoic, pointing out into the distance/horizon explorer look though.

Concerning origin of life there have to be more approaches than RNA  and 
protein. I tend to think the ribozyme research is amazing and that 
panspermia just displaces the problem and fuels unwarranted speculation and 
unknowns. 

But we need more attempts at good soup and the processes therein. For now, 
visiting Chinese parts of town or Hong Kong yields the most convincing 
results: if you catch the right chef and restaurant, I'm sure that some 
amazing wonton soup would support the creation of all life. Greens, 
veggies, noodles, proteins AND RNA intelligently seasoned and *folded just 
the right way*: it supports all of it! 

PGC's wonton theory: IF panspermia then the Chinatown equivalent of the 
multiverse laced all meteorites with primordial wonton. Age and cycles of 
the multiverse can be derived from how sophisticated your local soup is: 
how many folds.  PGC

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Re: The origin of life has not been explained

2019-07-07 Thread Philip Thrift

He does have the correct *contemplative, far-away look* on his home page:

http://nick-lane.net/

*Acetyl phosphate as a primordial energy currency at the origin of life*
Alexandra Whicher, Eloi Camprubi, Silvana Pinna, Barry Herschy and Nick Lane
Orig Life Evol Biosph (2018)
https://doi.org/10.1007/s11084-018-9555-8

*Abstract*
Metabolism is primed through the formation of thioesters via acetyl CoA and 
the phosphorylation of substrates by ATP. Prebiotic equivalents such as 
methyl thioacetate and acetyl phosphate have been proposed to catalyse 
analogous reactions at the origin of life, but their propensity to 
hydrolyse challenges this view. Here we show that acetyl phosphate (AcP) 
can be synthesised in water within minutes from thioacetate (but not methyl 
thioacetate) under ambient conditions. AcP is stable over hours, depending 
on temperature, pH and cation content, giving it an ideal poise between 
stability and reactivity. We show that AcP can phosphorylate nucleotide 
precursors such as ribose to ribose-5-phosphate and adenosine to adenosine 
monophosphate, at modest (~2%) yield in water, and at a range of pH. AcP 
can also phosphorylate ADP to ATP in water over several hours at 50 °C. But 
AcP did not promote polymerization of either glycine or AMP. The amino 
group of glycine was preferentially acetylated by AcP, especially at 
alkaline pH, hindering the formation of polypeptides. AMP formed small 
stacks of up to 7 monomers, but these did not polymerise in the presence of 
AcP in aqueous solution. We conclude that AcP can phosphorylate 
biologically meaningful substrates in a manner analogous to ATP, promoting 
the origins of metabolism, but is unlikely to have driven polymerization of 
macromolecules such as polypeptides or RNA in free solution. This is 
consistent with the idea that a period of monomer (cofactor) catalysis 
preceded the emergence of polymeric enzymes or ribozymes at the origin of 
life.

http://nick-lane.net/publications/

@philipthrift

On Sunday, July 7, 2019 at 1:33:05 AM UTC-5, Brent wrote:
>
> I think Nick Lane's metabolism-first theory, which he discusses in his 
> book "The Vital Question", is more plausible.  There's good online talk 
> by Lane https://www.youtube.com/watch?v=PhPrirmk8F4. 
>
> Brent 
>
> On 7/6/2019 8:32 AM, smitra wrote: 
> > https://arxiv.org/abs/1711.01945 
> > 
> > 
> > A followup article which focuses more on the mathematical issues is 
> > under construction, the key points are: 
> > 
> > 1) In interstellar space, simple organic compounds captured in small 
> > ice grains were subject to UV radiation and occasional heating due to 
> > incident cosmic rays (CR). This induced a bond percolation process 
> > that led to large clusters of organic molecules on a time scale of 
> > $\gtrsim 10^6$ years. 
> > 
> > 2) On a proto-planet, such clusters can merge into loosely bound 
> > superclusters. The deep interior of such superclusters can provide for 
> > chemical micro-environments in which conventional models of 
> > abiogenesis driven by cold-warm cycles can be considered. 
> > 
> > 3) Rapid fluctuations in the chemical potentials of certain chemical 
> > compounds that can penetrate the supercluster, will be damped down. 
> > Long term gradual and periodic changes then dominate, allowing any 
> > biochemical systems inside the superclusters to more easily evolve 
> > toward exploiting the conditions in their micro-environments, compared 
> > to a similar system in the outside environment. 
> > 
> > 4) As the supercluster breaks up, the system experiences more of the 
> > shorter term fluctuations that has more of a random character. The 
> > system can then evolve to adapt to these fluctuations, when doing so 
> > right from the start might not have worked. 
> > 
> > 5) On a small fraction of the superclusters these processes led to 
> > microbes capable of surviving in the outside environment. 
> > 
> > 6) Microbes were transferred to Earth via a collision of a 
> > microbe-containing proto-planet with the Moon. Fragments containing 
> > microbes resulting from the giant impact rained down on the Earth. 
> > 
> > 
> > Saibal 
> > 
> > On 06-07-2019 10:48, 'Cosmin Visan' via Everything List wrote: 
> >> https://www.youtube.com/watch?v=r4sP1E1Jd_Y [1] 
> >> 
> >>  -- 
> >>  You received this message because you are subscribed to the Google 
> >> Groups "Everything List" group. 
> >>  To unsubscribe from this group and stop receiving emails from it, 
> >> send an email to everyth...@googlegroups.com . 
> >>  To view this discussion on the web visit 
> >> 
> https://groups.google.com/d/msgid/everything-list/a43531f9-d34c-4806-97f0-7665befc7e95%40googlegroups.com
>  
> >> 
> >> [2]. 
> >> 
> >> 
> >> Links: 
> >> -- 
> >> [1] 
> >> 
> https://www.youtube.com/watch?v=r4sP1E1Jd_Yfbclid=IwAR03cRVkBTOeYnPldcuLzFGCNiWqCR0dE5FENXF9JJtRlk75sbq5Dh2wxcY
>  
> >> 
> >> [2] 
> >> 
>

Re: The origin of life has not been explained

2019-07-07 Thread 'Brent Meeker' via Everything List

I think Nick Lane's metabolism-first theory, which he discusses in his
book "The Vital Question", is more plausible. There's good online talk
by Lane https://www.youtube.com/watch?v=PhPrirmk8F4.

Brent

On 7/6/2019 8:32 AM, smitra wrote:

https://arxiv.org/abs/1711.01945

A followup article which focuses more on the mathematical issues is
under construction, the key points are:

1) In interstellar space, simple organic compounds captured in small
ice grains were subject to UV radiation and occasional heating due to
incident cosmic rays (CR). This induced a bond percolation process
that led to large clusters of organic molecules on a time scale of
$\gtrsim 10^6$ years.

2) On a proto-planet, such clusters can merge into loosely bound
superclusters. The deep interior of such superclusters can provide for
chemical micro-environments in which conventional models of
abiogenesis driven by cold-warm cycles can be considered.

3) Rapid fluctuations in the chemical potentials of certain chemical
compounds that can penetrate the supercluster, will be damped down.
Long term gradual and periodic changes then dominate, allowing any
biochemical systems inside the superclusters to more easily evolve
toward exploiting the conditions in their micro-environments, compared
to a similar system in the outside environment.

5) On a small fraction of the superclusters these processes led to
microbes capable of surviving in the outside environment.

6) Microbes were transferred to Earth via a collision of a
microbe-containing proto-planet with the Moon. Fragments containing
microbes resulting from the giant impact rained down on the Earth.

Saibal

On 06-07-2019 10:48, 'Cosmin Visan' via Everything List wrote:

https://www.youtube.com/watch?v=r4sP1E1Jd_Y [1]

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[2].

Links:
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[1]
https://www.youtube.com/watch?v=r4sP1E1Jd_Yfbclid=IwAR03cRVkBTOeYnPldcuLzFGCNiWqCR0dE5FENXF9JJtRlk75sbq5Dh2wxcY

[2]
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Re: The origin of life has not been explained

2019-07-06 Thread spudboy100 via Everything List

Very well. If it's math, them, it;s at least quasi-Platonic and that is 
well-above my pay grade intellectually. How math principles become cells is an 
intense topic. It's a pity we cannot yet produce this today. Set up an 
experiment and evolve basic elements into something that quacks. Noteworthy, if 
possible? 


-Original Message-
From: smitra 
To: everything-list 
Sent: Sat, Jul 6, 2019 6:43 pm
Subject: Re: The origin of life has not been explained

Although there is an element of panspermia in this proposal, as I 
explain in the conclusion, the panspermia element is a side issue as I 
need to explain how something cooked up in space ends up on Earth. The 
main problem to be solved is how to get from building blocks to 
machines. The problem has actually little to do with biochemistry, it's 
a mathematical problem because you would always stumble on that problem 
in any model of artificial chemistry. The solution is percolation in 3 
dimensions to get from building blocks to a large number of 
micro-environments with features in the interior that can act as 
catalysts. Each micro-environment breaks symmetries in different ways, 
some are are better than others for harboring an RNA world than others.




On 06-07-2019 20:11, spudboy100 via Everything List wrote:
> Panspermia for sure. Did it work that way in the universe? Maybe. I am
> guessing we'd require a close-by stellar activity place where life all
> started, and thus, floomed it's way to a hungry earth? My suspicion
> would be if we'd see life on the other planets in our solar system,
> your reasoning would be spot-on! Since life appears sketchy around
> these parts, I am no enthusiast of panspermia. It made for a great
> tale in Stephen Baxter's Evolution (2002), and one of Larry Niven's
> short tales however. (The Green Marauder).
> 
> -Original Message-
>  From: smitra 
>  To: everything-list 
>  Sent: Sat, Jul 6, 2019 11:32 am
>  Subject: Re: The origin of life has not been explained
> 
> https://arxiv.org/abs/1711.01945 [1]
> 
> A followup article which focuses more on the mathematical issues is
> under construction, the key points are:
> 
> 1) In interstellar space, simple organic compounds captured in small
> ice
> grains were subject to UV radiation and occasional heating due to
> incident cosmic rays (CR). This induced a bond percolation process
> that
> led to large clusters of organic molecules on a time scale of $gtrsim
> 10^6$ years.
> 
> 2) On a proto-planet, such clusters can merge into loosely bound
> superclusters. The deep interior of such superclusters can provide for
> 
> chemical micro-environments in which conventional models of
> abiogenesis
> driven by cold-warm cycles can be considered.
> 
> 3) Rapid fluctuations in the chemical potentials of certain chemical
> compounds that can penetrate the supercluster, will be damped down.
> Long
> term gradual and periodic changes then dominate, allowing any
> biochemical systems inside the superclusters to more easily evolve
> toward exploiting the conditions in their micro-environments, compared
> 
> to a similar system in the outside environment.
> 
> 4) As the supercluster breaks up, the system experiences more of the
> shorter term fluctuations that has more of a random character. The
> system can then evolve to adapt to these fluctuations, when doing so
> right from the start might not have worked.
> 
> 5) On a small fraction of the superclusters these processes led to
> microbes capable of surviving in the outside environment.
> 
> 6) Microbes were transferred to Earth via a collision of a
> microbe-containing proto-planet with the Moon. Fragments containing
> microbes resulting from the giant impact rained down on the Earth.
> 
> Saibal
> 
> On 06-07-2019 10:48, 'Cosmin Visan' via Everything List wrote:
>> https://www.youtube.com/watch?v=r4sP1E1Jd_Y [2][1]
>> 
>> --
>> You received this message because you are subscribed to the Google
>> Groups "Everything List" group.
>> To unsubscribe from this group and stop receiving emails from it,
>> send an email to everything-list+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> 
> https://groups.google.com/d/msgid/everything-list/a43531f9-d34c-4806-97f0-7665befc7e95%40googlegroups.com
> [3]
>> [2].
>> 
>> 
>> Links:
>> --
>> [1]
>> 
> https://www.youtube.com/watch?v=r4sP1E1Jd_Y=IwAR03cRVkBTOeYnPldcuLzFGCNiWqCR0dE5FENXF9JJtRlk75sbq5Dh2wxcY
> [4]
>> [2]
>> 
> https://groups.google.com/d/msgid/everything-list/a43531f9-d34c-4806-97f0-7665befc7e95%40googlegroups.com?utm_medium=email_source=footer
> [5]
> 
> --
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> 
>

Re: The origin of life has not been explained

2019-07-06 Thread John Clark

On Sat, Jul 6, 2019 at 6:34 PM Lawrence Crowell <
goldenfieldquaterni...@gmail.com> wrote:

*> The idea of the RNA world runs into trouble with the ribosome, which is
> a hugely complex system of RNA and proteins*


In the RNA world there would be nothing nearly as large and competent as
modern ribosomes and there would be no proteins at all, there would just be
short single strands of RNA floating in a sea of nucleotides. As far as I
know nobody has yet found a RNA string that could catalyze the duplication
of a string of nucleotides as large as itself, but they have found a RNA
string called tC19Z that could reliably copy, without the help of proteins,
RNA sequences 95 nucleotides long. And that is almost half as long as tC19Z
itself. I find that encouraging.

Ribozyme-Catalyzed Transcription of an Active Ribozyme


John K Clark






RNA sequences up to 95 letters
no be anything as big as a ribosome or any proteins at all, there would be
short single strands of RNA floating in a sea of nucleotides
neucteatides




On Saturday, July 6, 2019 at 5:04:40 PM UTC-5, John Clark wrote:
>>
>> On Sat, Jul 6, 2019 at 4:18 PM Lawrence Crowell 
>> wrote
>>
>>> > We have lots of hypotheses on this, but it is a point where
>>> biological evolution loses explanatory power, just as general relativity
>>> fails at the center of black hole collapse.
>>
>>
>> I think that's the key point, Darwinian Evolution can't take over until
>> you have a replicator of some sort, in fact I would say the origin of 
>> heredity
>> is the same thing as the origin of life. That first replicator was
>> certainly far simpler than anything alive today and it almost certainly
>> didn't have any DNA in it. RNA is only single stranded not double as DNA is
>> and it is usually much shorter too, and RNA would help in getting over the
>> chicken or the egg problem. RNA can carry information, not as well as DNA
>> can but it can do it. And RNA can act like an enzyme and catalyze
>> chemical reactions, not as well as proteins can but it can do it. So the
>> first RNA life would be very incompetent by modern standards but with
>> Darwin you don't have to be perfect you just have to be better than the
>> competition.
>>
>> In 1986 Nobel Laureate Walter Gilbert said in the journal Nature:
>>
>> "*One can contemplate an RNA world, containing only RNA molecules that
>> serve to catalyze the synthesis of themselves. The first step of evolution
>> proceeds then by RNA molecules performing the catalytic activities
>> necessary to assemble themselves from a nucleotide soup*."
>>
>> However some people, like Chemist Graham Cairns-Smith think that even the
>> RNA world, although far simpler than modern life, was still too complicated
>> to be the first replicator aka the first life. Cairns-Smith proposed that
>> the very first replicators were not organic at all but were clays were
>> information was encoded in a pattern of defects in silicate crystals. In
>> 1985 he wrote a book about it that is now online:
>>
>> Seven clues to the origin of life
>> 
>>
>> The problem with figuring out how life started is that chemicals usually
>> don't have fossils, so even evolutionary biologist and militant atheist
>> Richard Dawkins admits that although he likes the Cairns-Smith theory we
>> may never be able to say this is definitely how life started and it
>> couldn't have started any other way, the best we can do is find a plausible
>> way that life *could* have started.
>>
>>  John K Clark
>>
>
> The complexity group at Santa Fe Institute has a 3 month course on the
> origins of life. I thought about joining, but decided not because my plate
> is already a bit full and frankly all we really have to go with are
> hypotheses. The idea of the RNA world runs into trouble with the ribosome,
> which is a hugely complex system of RNA and proteins. How that got going is
> difficult to know.
>
> I had this idea about RNA interactions with carbon nanofibers. Could RNA
> coil up around these and these could serve as some system for translation?
> Maybe in time this became more complex with more RNA and proteins bound to
> the system. Eventually this evolved into the ribosome. I looked this up and
> found of course other had taken up this idea.
>
> LC
>
> --
> You received this message because you are subscribed to the Google Groups
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> 
> .
>

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Re: The origin of life has not been explained

2019-07-06 Thread Lawrence Crowell

Panspermia just kicks the can down the road. It does not explain the 
origins of life, but rather how life got here and flourished. If the 
universe were eternal and stationary, what Fred Hoyle thought, then it 
would just be a part of this eternal recurrence of things. The big bang 
puts a past time limit on things. So some where life got going.

LC

On Saturday, July 6, 2019 at 5:43:17 PM UTC-5, smitra wrote:
>
> Although there is an element of panspermia in this proposal, as I 
> explain in the conclusion, the panspermia element is a side issue as I 
> need to explain how something cooked up in space ends up on Earth. The 
> main problem to be solved is how to get from building blocks to 
> machines. The problem has actually little to do with biochemistry, it's 
> a mathematical problem because you would always stumble on that problem 
> in any model of artificial chemistry. The solution is percolation in 3 
> dimensions to get from building blocks to a large number of 
> micro-environments with features in the interior that can act as 
> catalysts. Each micro-environment breaks symmetries in different ways, 
> some are are better than others for harboring an RNA world than others. 
>
>
>
>
> On 06-07-2019 20:11, spudboy100 via Everything List wrote: 
> > Panspermia for sure. Did it work that way in the universe? Maybe. I am 
> > guessing we'd require a close-by stellar activity place where life all 
> > started, and thus, floomed it's way to a hungry earth? My suspicion 
> > would be if we'd see life on the other planets in our solar system, 
> > your reasoning would be spot-on! Since life appears sketchy around 
> > these parts, I am no enthusiast of panspermia. It made for a great 
> > tale in Stephen Baxter's Evolution (2002), and one of Larry Niven's 
> > short tales however. (The Green Marauder). 
> > 
> > -Original Message- 
> >  From: smitra > 
> >  To: everything-list > 
> >  Sent: Sat, Jul 6, 2019 11:32 am 
> >  Subject: Re: The origin of life has not been explained 
> > 
> > https://arxiv.org/abs/1711.01945 [1] 
> > 
> > A followup article which focuses more on the mathematical issues is 
> > under construction, the key points are: 
> > 
> > 1) In interstellar space, simple organic compounds captured in small 
> > ice 
> > grains were subject to UV radiation and occasional heating due to 
> > incident cosmic rays (CR). This induced a bond percolation process 
> > that 
> > led to large clusters of organic molecules on a time scale of $gtrsim 
> > 10^6$ years. 
> > 
> > 2) On a proto-planet, such clusters can merge into loosely bound 
> > superclusters. The deep interior of such superclusters can provide for 
> > 
> > chemical micro-environments in which conventional models of 
> > abiogenesis 
> > driven by cold-warm cycles can be considered. 
> > 
> > 3) Rapid fluctuations in the chemical potentials of certain chemical 
> > compounds that can penetrate the supercluster, will be damped down. 
> > Long 
> > term gradual and periodic changes then dominate, allowing any 
> > biochemical systems inside the superclusters to more easily evolve 
> > toward exploiting the conditions in their micro-environments, compared 
> > 
> > to a similar system in the outside environment. 
> > 
> > 4) As the supercluster breaks up, the system experiences more of the 
> > shorter term fluctuations that has more of a random character. The 
> > system can then evolve to adapt to these fluctuations, when doing so 
> > right from the start might not have worked. 
> > 
> > 5) On a small fraction of the superclusters these processes led to 
> > microbes capable of surviving in the outside environment. 
> > 
> > 6) Microbes were transferred to Earth via a collision of a 
> > microbe-containing proto-planet with the Moon. Fragments containing 
> > microbes resulting from the giant impact rained down on the Earth. 
> > 
> > Saibal 
> > 
> > On 06-07-2019 10:48, 'Cosmin Visan' via Everything List wrote: 
> >> https://www.youtube.com/watch?v=r4sP1E1Jd_Y [2][1] 
> >> 
> >> -- 
> >> You received this message because you are subscribed to the Google 
> >> Groups "Everything List" group. 
> >> To unsubscribe from this group and stop receiving emails from it, 
> >> send an email to everyth...@googlegroups.com . 
> >> To view this discussion on the web visit 
> >> 
> > 
> https://groups.google.com/d/msgid/everything-list/a43531f9-d34c-4806-97f0-7665befc7e95%40googlegroups.com
>  
> > [3] 
> >> [2]. 
> >> 
> >> 
> >> Links: 
> >> -- 
> >> [1] 
> >> 
> > 
> https://www.youtube.com/watch?v=r4sP1E1Jd_Y=IwAR03cRVkBTOeYnPldcuLzFGCNiWqCR0dE5FENXF9JJtRlk75sbq5Dh2wxcY
>  
> > [4] 
> >> [2] 
> >> 
> > 
> https://groups.google.com/d/msgid/everything-list/a43531f9-d34c-4806-97f0-7665befc7e95%40googlegroups.com?utm_medium=email_source=footer
>  
> > [5] 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> > Groups "Everything List" group. 
> > To unsubscribe from this group and stop receiving

Re: The origin of life has not been explained

2019-07-06 Thread Philip Thrift



On Saturday, July 6, 2019 at 10:32:54 AM UTC-5, smitra wrote:
>
> https://arxiv.org/abs/1711.01945 
>
>
> A followup article which focuses more on the mathematical issues is 
> under construction, the key points are: 
>
> 1) In interstellar space, simple organic compounds captured in small ice 
> grains were subject to UV radiation and occasional heating due to 
> incident cosmic rays (CR). This induced a bond percolation process that 
> led to large clusters of organic molecules on a time scale of $\gtrsim 
> 10^6$ years. 
>
> 2) On a proto-planet, such clusters can merge into loosely bound 
> superclusters. The deep interior of such superclusters can provide for 
> chemical micro-environments in which conventional models of abiogenesis 
> driven by cold-warm cycles can be considered. 
>
> 3) Rapid fluctuations in the chemical potentials of certain chemical 
> compounds that can penetrate the supercluster, will be damped down. Long 
> term gradual and periodic changes then dominate, allowing any 
> biochemical systems inside the superclusters to more easily evolve 
> toward exploiting the conditions in their micro-environments, compared 
> to a similar system in the outside environment. 
>
> 4) As the supercluster breaks up, the system experiences more of the 
> shorter term fluctuations that has more of a random character. The 
> system can then evolve to adapt to these fluctuations, when doing so 
> right from the start might not have worked. 
>
> 5) On a small fraction of the superclusters these processes led to 
> microbes capable of surviving in the outside environment. 
>
> 6) Microbes were transferred to Earth via a collision of a 
> microbe-containing proto-planet with the Moon. Fragments containing 
> microbes resulting from the giant impact rained down on the Earth. 
>
>
> Saibal 
>
>
>
Interesting.

@philipthrift 

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Re: The origin of life has not been explained

2019-07-06 Thread smitra

Although there is an element of panspermia in this proposal, as I
explain in the conclusion, the panspermia element is a side issue as I
need to explain how something cooked up in space ends up on Earth. The
main problem to be solved is how to get from building blocks to
machines. The problem has actually little to do with biochemistry, it's
a mathematical problem because you would always stumble on that problem
in any model of artificial chemistry. The solution is percolation in 3
dimensions to get from building blocks to a large number of
micro-environments with features in the interior that can act as
catalysts. Each micro-environment breaks symmetries in different ways,
some are are better than others for harboring an RNA world than others.

On 06-07-2019 20:11, spudboy100 via Everything List wrote:

Panspermia for sure. Did it work that way in the universe? Maybe. I am
guessing we'd require a close-by stellar activity place where life all
started, and thus, floomed it's way to a hungry earth? My suspicion
would be if we'd see life on the other planets in our solar system,
your reasoning would be spot-on! Since life appears sketchy around
these parts, I am no enthusiast of panspermia. It made for a great
tale in Stephen Baxter's Evolution (2002), and one of Larry Niven's
short tales however. (The Green Marauder).

-Original Message-
From: smitra
To: everything-list
Sent: Sat, Jul 6, 2019 11:32 am
Subject: Re: The origin of life has not been explained

https://arxiv.org/abs/1711.01945 [1]

A followup article which focuses more on the mathematical issues is
under construction, the key points are:

1) In interstellar space, simple organic compounds captured in small
ice
grains were subject to UV radiation and occasional heating due to
incident cosmic rays (CR). This induced a bond percolation process
that
led to large clusters of organic molecules on a time scale of $gtrsim
10^6$ years.

2) On a proto-planet, such clusters can merge into loosely bound
superclusters. The deep interior of such superclusters can provide for

chemical micro-environments in which conventional models of
abiogenesis
driven by cold-warm cycles can be considered.

3) Rapid fluctuations in the chemical potentials of certain chemical
compounds that can penetrate the supercluster, will be damped down.
Long
term gradual and periodic changes then dominate, allowing any
biochemical systems inside the superclusters to more easily evolve
toward exploiting the conditions in their micro-environments, compared

to a similar system in the outside environment.

5) On a small fraction of the superclusters these processes led to
microbes capable of surviving in the outside environment.

6) Microbes were transferred to Earth via a collision of a
microbe-containing proto-planet with the Moon. Fragments containing
microbes resulting from the giant impact rained down on the Earth.

Saibal

On 06-07-2019 10:48, 'Cosmin Visan' via Everything List wrote:

https://www.youtube.com/watch?v=r4sP1E1Jd_Y [2][1]

https://groups.google.com/d/msgid/everything-list/a43531f9-d34c-4806-97f0-7665befc7e95%40googlegroups.com
[3]

[2].

Links:
--
[1]

https://www.youtube.com/watch?v=r4sP1E1Jd_Y=IwAR03cRVkBTOeYnPldcuLzFGCNiWqCR0dE5FENXF9JJtRlk75sbq5Dh2wxcY
[4]

[2]

https://groups.google.com/d/msgid/everything-list/a43531f9-d34c-4806-97f0-7665befc7e95%40googlegroups.com?utm_medium=email_source=footer
[5]

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[6].

Links:
--
[1] https://arxiv.org/abs/1711.01945
[2] https://www.youtube.com/watch?v=r4sP1E1Jd_Y
[3]
https://groups.google.com/d/msgid/everything-list/a43531f9-d34c-4806-97f0-7665befc7e95%40googlegroups.com
[4]

Re: The origin of life has not been explained

2019-07-06 Thread Lawrence Crowell

On Saturday, July 6, 2019 at 5:04:40 PM UTC-5, John Clark wrote:
>
> On Sat, Jul 6, 2019 at 4:18 PM Lawrence Crowell  > wrote
>
>> > We have lots of hypotheses on this, but it is a point where biological 
>> evolution loses explanatory power, just as general relativity fails at the 
>> center of black hole collapse. 
>
>
> I think that's the key point, Darwinian Evolution can't take over until 
> you have a replicator of some sort, in fact I would say the origin of 
> heredity 
> is the same thing as the origin of life. That first replicator was 
> certainly far simpler than anything alive today and it almost certainly 
> didn't have any DNA in it. RNA is only single stranded not double as DNA is 
> and it is usually much shorter too, and RNA would help in getting over the 
> chicken or the egg problem. RNA can carry information, not as well as DNA 
> can but it can do it. And RNA can act like an enzyme and catalyze 
> chemical reactions, not as well as proteins can but it can do it. So the 
> first RNA life would be very incompetent by modern standards but with 
> Darwin you don't have to be perfect you just have to be better than the 
> competition.  
>
> In 1986 Nobel Laureate Walter Gilbert said in the journal Nature: 
>
> "*One can contemplate an RNA world, containing only RNA molecules that 
> serve to catalyze the synthesis of themselves. The first step of evolution 
> proceeds then by RNA molecules performing the catalytic activities 
> necessary to assemble themselves from a nucleotide soup*."
>
> However some people, like Chemist Graham Cairns-Smith think that even the 
> RNA world, although far simpler than modern life, was still too complicated 
> to be the first replicator aka the first life. Cairns-Smith proposed that 
> the very first replicators were not organic at all but were clays were 
> information was encoded in a pattern of defects in silicate crystals. In 
> 1985 he wrote a book about it that is now online:
>
> Seven clues to the origin of life 
> 
>
> The problem with figuring out how life started is that chemicals usually 
> don't have fossils, so even evolutionary biologist and militant atheist 
> Richard Dawkins admits that although he likes the Cairns-Smith theory we 
> may never be able to say this is definitely how life started and it 
> couldn't have started any other way, the best we can do is find a plausible 
> way that life *could* have started.   
>
>  John K Clark
>

The complexity group at Santa Fe Institute has a 3 month course on the 
origins of life. I thought about joining, but decided not because my plate 
is already a bit full and frankly all we really have to go with are 
hypotheses. The idea of the RNA world runs into trouble with the ribosome, 
which is a hugely complex system of RNA and proteins. How that got going is 
difficult to know. 

I had this idea about RNA interactions with carbon nanofibers. Could RNA 
coil up around these and these could serve as some system for translation? 
Maybe in time this became more complex with more RNA and proteins bound to 
the system. Eventually this evolved into the ribosome. I looked this up and 
found of course other had taken up this idea.

LC 

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Re: The origin of life has not been explained

2019-07-06 Thread John Clark

On Sat, Jul 6, 2019 at 4:18 PM Lawrence Crowell <
goldenfieldquaterni...@gmail.com> wrote

> > We have lots of hypotheses on this, but it is a point where biological
> evolution loses explanatory power, just as general relativity fails at the
> center of black hole collapse.

I think that's the key point, Darwinian Evolution can't take over until you
have a replicator of some sort, in fact I would say the origin of heredity
is the same thing as the origin of life. That first replicator was
certainly far simpler than anything alive today and it almost certainly
didn't have any DNA in it. RNA is only single stranded not double as DNA is
and it is usually much shorter too, and RNA would help in getting over the
chicken or the egg problem. RNA can carry information, not as well as DNA
can but it can do it. And RNA can act like an enzyme and catalyze chemical
reactions, not as well as proteins can but it can do it. So the first RNA
life would be very incompetent by modern standards but with Darwin you
don't have to be perfect you just have to be better than the competition.

In 1986 Nobel Laureate Walter Gilbert said in the journal Nature:

"*One can contemplate an RNA world, containing only RNA molecules that
serve to catalyze the synthesis of themselves. The first step of evolution
proceeds then by RNA molecules performing the catalytic activities
necessary to assemble themselves from a nucleotide soup*."

However some people, like Chemist Graham Cairns-Smith think that even the
RNA world, although far simpler than modern life, was still too complicated
to be the first replicator aka the first life. Cairns-Smith proposed that
the very first replicators were not organic at all but were clays were
information was encoded in a pattern of defects in silicate crystals. In
1985 he wrote a book about it that is now online:

Seven clues to the origin of life

The problem with figuring out how life started is that chemicals usually
don't have fossils, so even evolutionary biologist and militant atheist
Richard Dawkins admits that although he likes the Cairns-Smith theory we
may never be able to say this is definitely how life started and it
couldn't have started any other way, the best we can do is find a plausible
way that life *could* have started.

John K Clark

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Re: The origin of life has not been explained

2019-07-06 Thread Lawrence Crowell

On Saturday, July 6, 2019 at 5:53:28 AM UTC-5, Philip Thrift wrote:
>
>
>
> On Saturday, July 6, 2019 at 3:48:12 AM UTC-5, Cosmin Visan wrote:
>>
>> https://www.youtube.com/watch?v=r4sP1E1Jd_Y 
>> 
>>
>
>
>
> You know that this YouTube channel - *T**he Discovery Science News 
> Channel is the official Youtube channel of Discovery Institute's Center for 
> Science & Culture* - is via a conservative evangelical Christian 
> organization.
>
> https://en.wikipedia.org/wiki/Discovery_Institute
>
> *The Discovery Institute (DI) is a politically conservative non-profit 
> think tank based in Seattle, Washington, that advocates the 
> pseudoscientific concept of intelligent design (ID). Its "Teach the 
> Controversy" campaign aims to permit the teaching of anti-evolution, 
> intelligent-design beliefs in United States public high school science 
> courses in place of accepted scientific theories, positing that a 
> scientific controversy exists over these subjects.*
>
> *Center for Science and Culture (CSC) promotes "a rigorously God-centered 
> view of creation, including a new 'science' based solidly on theism.*
>
> @philipthrift
>

The speaker James Tour also signed the *Scientific Dissent from Darwinism*, 
which is a bit like the list of 100 physicists who disagreed with Einstein. 
Einstein quipped back, why do you need 100, when only 1 with a correct 
argument would suffice? Tour is a fundy, and while he may have done 
reasonable research, he appears religiously biased here. I also can tell in 
the way he talks that he can pound people down with words pretty well.

Tour is right in that we do not know the origins of life. We have lots of 
hypotheses on this, but it is a point where biological evolution loses 
explanatory power, just as general relativity fails at the center of black 
hole collapse. Tour though makes the implicit statement that this will 
never be answered, or that it is a scientific impossibility to know. The 
real problem is that we have no data; we have a complete paucity of data on 
the chemistry that lead to the development of life. We might find such data 
on other planets, and maybe Mars is a start. Maybe prebiotic chemistry has 
degraded and been lost there, so maybe Enceladus or ... ? We may even in 
fact never find such data and be left dangling with only hypotheticals. We 
are in a better position to understand the origins of the universe than the 
origins of life, and this question may be with us for a while. 

The problem I have with people such as Tour is the same I would have with 
similar of argumenta by similar people in the 17th century who might say we 
humans can never know the principles of planetary motion. They would argue 
this is the province of God and His heavenly hosts and that we will never 
find physical principles when this is all a matter of divine providence and 
supernatural power. The net effect of such an argument is to stop inquiry.

LC

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Re: The origin of life has not been explained

2019-07-06 Thread spudboy100 via Everything List

Panspermia for sure. Did it work that way in the universe? Maybe. I am guessing 
we'd require a close-by stellar activity place where life all started, and 
thus, floomed it's way to a hungry earth? My suspicion would be if we'd see 
life on the other planets in our solar system, your reasoning would be spot-on! 
Since life appears sketchy around these parts, I am no enthusiast of 
panspermia. It made for a great tale in Stephen Baxter's Evolution (2002), and 
one of Larry Niven's short tales however. (The Green Marauder).

-Original Message-
From: smitra 
To: everything-list 
Sent: Sat, Jul 6, 2019 11:32 am
Subject: Re: The origin of life has not been explained

https://arxiv.org/abs/1711.01945

A followup article which focuses more on the mathematical issues is 
under construction, the key points are:

1) In interstellar space, simple organic compounds captured in small ice 
grains were subject to UV radiation and occasional heating due to 
incident cosmic rays (CR). This induced a bond percolation process that 
led to large clusters of organic molecules on a time scale of $\gtrsim 
10^6$ years.

2) On a proto-planet, such clusters can merge into loosely bound 
superclusters. The deep interior of such superclusters can provide for 
chemical micro-environments in which conventional models of abiogenesis 
driven by cold-warm cycles can be considered.

3) Rapid fluctuations in the chemical potentials of certain chemical 
compounds that can penetrate the supercluster, will be damped down. Long 
term gradual and periodic changes then dominate, allowing any 
biochemical systems inside the superclusters to more easily evolve 
toward exploiting the conditions in their micro-environments, compared 
to a similar system in the outside environment.

4) As the supercluster breaks up, the system experiences more of the 
shorter term fluctuations that has more of a random character. The 
system can then evolve to adapt to these fluctuations, when doing so 
right from the start might not have worked.

5) On a small fraction of the superclusters these processes led to 
microbes capable of surviving in the outside environment.

6) Microbes were transferred to Earth via a collision of a 
microbe-containing proto-planet with the Moon. Fragments containing 
microbes resulting from the giant impact rained down on the Earth.

Saibal

On 06-07-2019 10:48, 'Cosmin Visan' via Everything List wrote:
> https://www.youtube.com/watch?v=r4sP1E1Jd_Y [1]
> 
>  --
>  You received this message because you are subscribed to the Google
> Groups "Everything List" group.
>  To unsubscribe from this group and stop receiving emails from it,
> send an email to everything-list+unsubscr...@googlegroups.com.
>  To view this discussion on the web visit
> https://groups.google.com/d/msgid/everything-list/a43531f9-d34c-4806-97f0-7665befc7e95%40googlegroups.com
> [2].
> 
> 
> Links:
> --
> [1]
> https://www.youtube.com/watch?v=r4sP1E1Jd_Y=IwAR03cRVkBTOeYnPldcuLzFGCNiWqCR0dE5FENXF9JJtRlk75sbq5Dh2wxcY
> [2]
> https://groups.google.com/d/msgid/everything-list/a43531f9-d34c-4806-97f0-7665befc7e95%40googlegroups.com?utm_medium=email_source=footer

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Re: The origin of life has not been explained

2019-07-06 Thread spudboy100 via Everything List

Scientifically, nobody has yet, pursued a chain, where people can create life 
out of base elements* (Ulam-Miller?), where is a telling point for me.  So in 
our inability we must either not be looking, or it may be impossible, or how to 
get life started is being misunderstood.
*Carbon Hydrogen Oxygen Nitrogen and maybe potassium, sodium, etc...  
Biologists need to get their act together, otherwise, they are peddling an 
incomplete understanding. Beyond this, I care more about Life Scientists 
ability to cure disease, than I am about creating life. Ever, the pragmatist, 
I. 


-Original Message-
From: Philip Thrift 
To: Everything List 
Sent: Sat, Jul 6, 2019 8:01 am
Subject: Re: The origin of life has not been explained



What does "social status" have to do with a program shown on a far-right 
channel?
I care about the truth of identifying the source of information.
Do you care about that truth at all?
@philipthrift


On Saturday, July 6, 2019 at 6:39:19 AM UTC-5, Cosmin Visan wrote:
So you care more about social status than truth ? Quite irrational, don't you 
think ?

On Saturday, 6 July 2019 14:37:30 UTC+3, Philip Thrift wrote:
Who cares?


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Re: The origin of life has not been explained

2019-07-06 Thread John Clark

On Sat, Jul 6, 2019 at 4:48 AM 'Cosmin Visan' via Everything List <
everything-list@googlegroups.com> wrote:

Science has a good explanation how to go from the simplest bacteria to
human beings. Science has also made a good start at explaining how to go
from simple chemicals to simple bacteria, but in that it still has a way to
go. Meanwhile the God theory has managed to explain precisely NOTHING, all
it does is kick the problem upstairs. It is the very nature of an
explanation to show how a simple thing can produce a complex thing, the God
theory does the reverse. If an explanation is more complicated than the
thing it's trying to explain then it is of no use to anyone.

John K Clark



John K Clark

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Re: The origin of life has not been explained

2019-07-06 Thread Philip Thrift



What does "social status" have to do with a program shown on *a far-right 
channel*?

I care about the truth of identifying *the source* of information.

Do you care about that truth at all?

@philipthrift


On Saturday, July 6, 2019 at 6:39:19 AM UTC-5, Cosmin Visan wrote:
>
> So you care more about social status than truth ? Quite irrational, don't 
> you think ?
>
> On Saturday, 6 July 2019 14:37:30 UTC+3, Philip Thrift wrote:
>>
>> Who cares?
>>
>>

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Re: The origin of life has not been explained

2019-07-06 Thread 'Cosmin Visan' via Everything List

So you care more about social status than truth ? Quite irrational, don't 
you think ?

On Saturday, 6 July 2019 14:37:30 UTC+3, Philip Thrift wrote:
>
> Who cares?
>
>

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Re: The origin of life has not been explained

2019-07-06 Thread Philip Thrift



On Saturday, July 6, 2019 at 6:18:38 AM UTC-5, Cosmin Visan wrote:
>
> What does this has to do with what that guy is saying ?
>
> On Saturday, 6 July 2019 13:53:28 UTC+3, Philip Thrift wrote:
>>
>>
>>
>> You know that this YouTube channel
>>
>>
Who cares?

But you should identify the source of what you post.

One can say something I can agree with, but if they say it on a far-right 
venue (for example), I will identify the "channel" they are speaking on.

It's called "full disclosure".

@philipthrift

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Re: The origin of life has not been explained

2019-07-06 Thread 'Cosmin Visan' via Everything List

What does this has to do with what that guy is saying ?

On Saturday, 6 July 2019 13:53:28 UTC+3, Philip Thrift wrote:
>
>
>
> You know that this YouTube channel
>
>

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Re: The origin of life has not been explained

2019-07-06 Thread Philip Thrift

On Saturday, July 6, 2019 at 3:48:12 AM UTC-5, Cosmin Visan wrote:
>
> https://www.youtube.com/watch?v=r4sP1E1Jd_Y 
> 
>

You know that this YouTube channel - *T**he Discovery Science News Channel 
is the official Youtube channel of Discovery Institute's Center for Science 
& Culture* - is via a conservative evangelical Christian organization.

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

*The Discovery Institute (DI) is a politically conservative non-profit 
think tank based in Seattle, Washington, that advocates the 
pseudoscientific concept of intelligent design (ID). Its "Teach the 
Controversy" campaign aims to permit the teaching of anti-evolution, 
intelligent-design beliefs in United States public high school science 
courses in place of accepted scientific theories, positing that a 
scientific controversy exists over these subjects.*

*Center for Science and Culture (CSC) promotes "a rigorously God-centered 
view of creation, including a new 'science' based solidly on theism.*

@philipthrift

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Re: The origin of life has not been explained

2019-07-06 Thread Samiya Illias

Thank you for this interesting share! 
This might be of interest: 
https://signsandscience.blogspot.com/2018/08/the-creation-emergence-of-species.html
 

> On 06-Jul-2019, at 1:48 PM, 'Cosmin Visan' via Everything List 
>  wrote:
> 
> https://www.youtube.com/watch?v=r4sP1E1Jd_Y
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