The Design of the Simplest Self-Replicator
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27-07-2015, 05:36 PM
The Design of the Simplest Self-Replicator
The Design of the Simplest Self-Replicator

http://elshamah.heavenforum.org/t2125-th...replicator

Following article shows the minimal structure of a cell that is required for self-replication to occur. It takes a lot of faith to believe, the cell could arise due to random natural chemical reactions.


Goals, Assumptions and Requirements


Goals:


Develop insights into internal design of the cell
Evaluate complexity in creating an artificial cell


Assumptions:


There is an intake of materials from the outside of cell
There is an output of waste materials from inside to outside of the cell
We assume throughout that we design for building an artificial cell – that need not have a biological basis (not built with carbon-based chemistry) but is rather a ‘clunky’ one (made from metal, plastic, semiconductors, etc.)


Requirements


The cell has an Enclosure to separate it and protect it from its environment
The cell is capable to create an identical copy of itself


What would have to happen during the replication of our artifical cell ?


Input materials processed through material extraction into good materials for fabrication of parts or for energy generation
Energy is generated and made available throughout the cell
Fabrication function starts to fabricate parts, components and assemblies for:
Cloning (creating copies) of all cell internal elements
Creating scaffolding elements for the growing cell interior
Creating new elements that are added to the growing enclosure
When the cloning of all original cell internal parts completed, the cell division starts:
The original cell content is now at (for example) “north pole” of the cell enclosure
The cloned cell content (the “nascent daughter cell”) is now at the “south pole” of the cell enclosure
The SSR enclosure and its content now divides at the “equatorial” plane and the separate “mother” (at North) and daughter (at South) cell emerge.
It would not be possible by using a mechanical copy process – similar with that used to duplicate house keys. Using internal design information would be required in combination with computer controlled roboters.


Control of Input Flow, Functions of Material Identification and Material Extraction


Opens/closes the enclosure input gateways
Acts based on the nature of input material/part and commands from other functions
Identifies nature of input materials and parts
Tags input materials and parts, manufactured materials and fabricated parts with type Id (bar code like)
Uses specific processes to extract manufacturing materials from raw materials
Uses specific machinery and parts
Our cell needs to have gates which permit material to get in or out. Further it needs to be able to recognize and identify what the incoming materials in are made of. So the cell must be able to act like a roboter, programmed and automatically, by itself, to recognize the materials and permit or refuse their entrance.


Function of Energy Generation and internal transport highways and transport vessels


The cell needs to be able to generate energy from raw or processed materials. It needs to be able to transport and distribute materials, and managing energy requirements
( electricity ) It has to use special machinery: generators, transformers, converters.
An open question is, what material basis to provide energy: fuel, oil, coal, chemical, atomic etc.
Transport materials and parts/components
Uses containers, conduits, wires, carriers
Transports also energy and information


Ability of chain supply, recycling and function of output Flow control


Ensures steady supply of materials, energy and parts
Coordinating and scheduling capability
Re-introduce useful materials and parts in the fabrication cycle
Selects materials and parts as refuse; cleans spaces
Sends refuse materials and parts outside the cell
Controls output gateways of the enclosure


Storage of a catalog of all materials , Construction Plan , registration of construction status


Catalogs of all materials and all parts
For each element: its composition in sub-elements and materials
Catalog of construction plan and design of all parts, components, assemblies including the cell as a whole
Catalog of all processes
Catalog of all procedures
Uses replicas of construction plans to mark construction progress
Status updated by functions involved in fabrication and construction


Hability of Manipulation , Fabrication of all parts, and Fabrication quality Control


Ability to “grab”, “handle”, “manipulate” materials, parts, components
Implemented with robot arm – like machinery
Must be able to fabricate any and all cell parts and components
In particular able to fabricate all cell machinery
Follows the construction plans
Commands the fabrication function to manufacture next elements in the plan


Function of Communication and Notification, Growth Function through scaffolding and Enclosure Growth




Facilitates communication between the “control” centers and “execution” centers
Notifications from “executor” to “controller”
Controls construction and growth of cell scaffolding
Mostly on the “daughter” cell side
Controls the construction and growth of the enclosure
Addition of enclosure gateways; flexible geometry


Cloning Function, Hability of cell Division and Replication


Choreographs the cloning phase
Coordinates fabrication of the clone and growth of scaffolding and enclosure
Copies info catalogs and software into the cloned parts
Choreograph the cell division phase
“start the engines” of the “daughter” cell just before division completes
Highest level function:
Implements the designer commandments
- Grow and
- Multiply


What we learned about the artificial Cell?


The cell must be designed for growth and division: the enclosure must support changing surface, volume and shape
The cell must contain detailed, structured, cohesive descriptive information that must be accurately and integrally passed to next cell generation.


Required information:


-all used materials: identification, description, characteristics
-manufacturing materials: extraction procedures and processes
-bill of materials for all fabricated parts, components and assemblies
-procedures and processes for energy generation, storage (if needed) transportation and management
-construction plans for all fabricated parts, components and assemblies including the cell itself.
-all fabrication processes and procedures
-all assemblage procedures
-all recycling procedures and processes


The cell


must contain advanced materials and parts identification capabilities as well as material extraction capabilities
must contain sophisticated, fully automated and computer-controlled capabilities for energy generation, transportation, management and distribution
must contain very sophisticated fabrication and assemblage capabilities that must be information-driven for full automation and computer control.
must posses advanced computing (information processing) capabilities as well as good information communication capabilities.
must control its many parts and layered functions through very advanced software running on cell-computer(-like) machinery.
Above all: the cell must be based on a very sophisticated design that harmoniously, precisely and completely provides full automation and self-sufficiency for all machinery and processes that happens inside an cell during its growth, division and replication.
The design of a cell can be successful only if it is harmoniously integrated and precisely coordinated with the design and characteristics of its environment.


An artificial cell most probable must contain:


a material mining sub-unit
a metallurgic subunit
a chemical plant
a power plant
an electricity distribution network
a network of avenues, alleys and conduits for robotized transportation
a semiconductor manufacturing plant
a computer manufacturing plant
an extended communication network connecting by wire or rather wirelessly all plants and robots
a software manufacturing plant and software distribution and installation agents.
a materials and parts recycling and refuse management plant
an army of intelligent robots for transportation and manipulation
a highly sophisticated distributed, multi-layered software system that controls in a cohesive manner all plants, robots and communications.


Evaluating the Complexity of an artificial cell


The Cell: autonomous, computerized and automated


There is no comparable human engineering artifact in terms of:


Autonomy (materials, energy, fabrication closure, information closure, ‘intelligence’)
full manufacturing automation
spectrum of processes and fabrication types


No successful attempt so far on building a real autonomous artificial cell from scratch


Attempts so far:


software simulations
cellular automata
self-replicating software entities
RepRap – self replicating 3D printers
self-assembling Lego robots
Micro Electro Mechanical Systems (MEMS)
Craig Venter’s synthetic bacterial cell


Comparing a genuine artificial Cell with:


An advanced car manufacturing/assembly line:


many/most parts are fabricated elsewhere
not fully automated; many manual operations performed by humans
no material identification, material extraction capabilities
not so many process technologies involved
mostly an assembly operation


The Large Hadron Collider (HDC) in Switzerland


no fabrication
not comparable in terms of automation, process diversity


The Martian Rover


some good amount of autonomy
no fabrication


Our articial cell, and the Origin Of Life (OOL) Research


Any OOL credible explanation should provide answers to the following questions:
How the self describing information (of so many varieties) residing in the cell originated?
How the energy generation and transport function originated?
How the material identification function and the material extraction function originated?
How the fabrication function originated
How the transport and manipulation functions originated?
How the coordinated control of various functions originated?
How the whole sophisticated design of the cell originated?
Is it reasonable to believe/accept that the cell resulted through random/natural processes when the 21st century scientists are only beginning to understand only SOME OF THE INTERNALS of a cell?
Is it reasonable to believe/accept that the cell resulted through random/natural processes when the 21st century scientists and engineers are still not able to design and create an artificial cell?

The Metaphysics of It All

A reasonable scientific hypothesis is that the Master Designer designed wisely all life types for this successful cohabitation of Homo Sapiens
with all other types of life.
More so it is hypothesized (again scientifically) that the Earth, the Solar System, the Milky Way Galaxy and the Whole Universe was designed and finely adjusted by the Master Designer so that Homo Sapiens and all other life forms have a comfortable and enjoyable place to live.
More so, besides having a comfortable place to live Homo Sapiens have plenty of cell types to study and to marvel at the fabulous skills of the Master Designer revealed so blatantly in His cell designs.
More so, besides having amazing engineering feats to discover and admire, the Homo Sapiens has a rightful Master Designer to praise and worship all his life.
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27-07-2015, 10:44 PM
RE: The Design of the Simplest Self-Replicator
I think the first replicators were likely individual molecules with no cell wall. The cell wall may have been a significant advance that would have accelerated the pace of evolution but I'm dubious of any claim that the wall was required for evolution to begin. We may or may not figure this one out exactly but I think I'll reserve judgement on the creator hypothesis until we actually know something about the process.

Give me your argument in the form of a published paper, and then we can start to talk.
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28-07-2015, 05:39 AM
RE: The Design of the Simplest Self-Replicator
(27-07-2015 10:44 PM)Hafnof Wrote:  I think the first replicators were likely individual molecules with no cell wall. The cell wall may have been a significant advance that would have accelerated the pace of evolution but I'm dubious of any claim that the wall was required for evolution to begin. We may or may not figure this one out exactly but I think I'll reserve judgement on the creator hypothesis until we actually know something about the process.

Steven A. Benner, Ph.D. Chemistry, Harvard, prominent origin-of-life researcher and creator of the Foundation for Applied Molecular Evolution, was posted on Huffington Post on December 6, 2013. In it he said,

"We have failed in any continuous way to provide a recipe that gets from the simple molecules that we know were present on early Earth to RNA."

That lead Leslie Orgel to say :

It would take a miracle if a strand of RNA ever appeared on the primitive Earth.

(Dover, 1999, p. 218).

I would have thought it relevant to point out for biologists in general that not one self-replicating RNA has emerged to date from quadrillions (1024) of artificially synthesized, random RNA sequences

Three successive steps in the evolution of a self-replicating system of RNA molecules capable of directing protein synthesis.

How could the first living cells with DNA-based molecular biology have originated by spontaneous chemical processes on the prebiotic Earth? Primordial DNA synthesis would have required the presence of specific enzymes, but how could these enzymes be synthesized without the genetic information in DNA and without RNA for translating that information into the amino acid sequence of the protein enzymes? In other words, proteins are required for DNA synthesis and DNA is required for protein synthesis.

This classic "chicken-and-egg" problem made it immensely difficult to conceive of any plausible prebiotic chemical pathway to the molecular biological system. Certainly no such chemical pathway had been demonstrated
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28-07-2015, 05:49 AM
RE: The Design of the Simplest Self-Replicator
It talks about mitosis/meiosis as if this system would require a higher power to ignite that force because a power needs that to create a system.

But we've figured out how to manipulate and copy/replicate even without needing to do that process via cloning methods. I don't find these proclamations very valid and based on knowledge that is firm. It's far to hopeful and in that wiggly roam of always hyping the assumed impact an intelligence must make.

Beyond that it just so poorly visually designed of a post. Being of uncertainty or not knowing is far from a proclamation of faith though.

"Allow there to be a spectrum in all that you see" - Neil Degrasse Tyson
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28-07-2015, 05:53 AM
RE: The Design of the Simplest Self-Replicator
(27-07-2015 05:36 PM)Godexists Wrote:  It takes a lot of faith to believe, the cell could arise due to random natural chemical reactions.

Possibly -- but it doesn't need to cook up the idea that you're best buddies with the guy who created the entire fuckin' universe.....

So - same amount of belief -- just far less narcissism and egotistical bragging....

.......................................

The difference between prayer and masturbation - is when a guy is through masturbating - he has something to show for his efforts.
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28-07-2015, 06:00 AM
RE: The Design of the Simplest Self-Replicator
Oh look, it's ol' Existy-pants with another line of bullshit.

If God does exist, why does he appoint *you* to tell the world? Since you're so feckin' horrible at it? He could hire an ad agency but noooooooooooo...

We'll love you just the way you are
If you're perfect -- Alanis Morissette
(06-02-2014 03:47 PM)Momsurroundedbyboys Wrote:  And I'm giving myself a conclusion again from all the facepalming.
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28-07-2015, 10:18 AM
RE: The Design of the Simplest Self-Replicator
(28-07-2015 05:39 AM)Godexists Wrote:  
(27-07-2015 10:44 PM)Hafnof Wrote:  I think the first replicators were likely individual molecules with no cell wall. The cell wall may have been a significant advance that would have accelerated the pace of evolution but I'm dubious of any claim that the wall was required for evolution to begin. We may or may not figure this one out exactly but I think I'll reserve judgement on the creator hypothesis until we actually know something about the process.

Steven A. Benner, Ph.D. Chemistry, Harvard, prominent origin-of-life researcher and creator of the Foundation for Applied Molecular Evolution, was posted on Huffington Post on December 6, 2013. In it he said,

"We have failed in any continuous way to provide a recipe that gets from the simple molecules that we know were present on early Earth to RNA."

Yes we have. If you are going to come in here you really need to be up to date.
http://www.nature.com/nchem/journal/v7/n...m.2202.pdf

(28-07-2015 05:39 AM)Godexists Wrote:  That lead Leslie Orgel to say :

It would take a miracle if a strand of RNA ever appeared on the primitive Earth.

(Dover, 1999, p. 218).

I would have thought it relevant to point out for biologists in general that not one self-replicating RNA has emerged to date from quadrillions (1024) of artificially synthesized, random RNA sequences

Again, you need to be up to date. A D-RNAse has been found that makes a mirror image RNA (L-RNA). Hence, the L-RNAse is a catalyst that can synthesize the original D-RNA. So yes, we do have a mechanism by which self replication can take place.

http://www.nature.com/nature/journal/v51...13900.html

(28-07-2015 05:39 AM)Godexists Wrote:  Three successive steps in the evolution of a self-replicating system of RNA molecules capable of directing protein synthesis.

How could the first living cells with DNA-based molecular biology have originated by spontaneous chemical processes on the prebiotic Earth? Primordial DNA synthesis would have required the presence of specific enzymes, but how could these enzymes be synthesized without the genetic information in DNA and without RNA for translating that information into the amino acid sequence of the protein enzymes? In other words, proteins are required for DNA synthesis and DNA is required for protein synthesis.

This classic "chicken-and-egg" problem made it immensely difficult to conceive of any plausible prebiotic chemical pathway to the molecular biological system. Certainly no such chemical pathway had been demonstrated
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28-07-2015, 10:28 AM
RE: The Design of the Simplest Self-Replicator
Ohjesusfuck. That was such a pile of nothing.

Come on, just pick up a science book, for fuck's sake. Really. I'll wait. Drinking Beverage

Ok, I won't really wait to discuss but, DO read a science book... you are seriously lacking.

A new type of thinking is essential if mankind is to survive and move to higher levels. ~ Albert Einstein
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28-07-2015, 10:37 AM
RE: The Design of the Simplest Self-Replicator
(28-07-2015 06:00 AM)morondog Wrote:  Oh look, it's ol' Existy-pants with another line of bullshit.

If God does exist, why does he appoint *you* to tell the world? Since you're so feckin' horrible at it? He could hire an ad agency but noooooooooooo...

Why do we, as Thinking Atheists, resort to ad hominem attacks? It doesn't give our credibility a boost.

There should be plenty of documentation/studies/experiments out there that blow his arguments out of the water.

EDIT;
Like what Inigo did
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28-07-2015, 11:09 AM (This post was last modified: 28-07-2015 01:43 PM by Bucky Ball.)
RE: The Design of the Simplest Self-Replicator
(27-07-2015 05:36 PM)Godexists Wrote:  The Design of the Simplest Self-Replicator

http://spammyspamspamspamdaspamspam

"Following article ...."

Is complete horseshit.

Quote:A reasonable scientific hypothesis is that the Master Designer designed wisely all life types for this successful cohabitation of Homo Sapiens
with all other types of life.

Proof this fool knows nothing about how science works. It is hilarious though these religious nutcases get that science is what provides the most information to humans in 2015, thus they *need* to hitch their crazy-wagons up to it somehow, to attempt to have science lend some credence to their nonsense.

Quote:More so it is hypothesized (again scientifically) that the Earth, the Solar System, the Milky Way Galaxy and the Whole Universe was designed and finely adjusted by the Master Designer so that Homo Sapiens and all other life forms have a comfortable and enjoyable place to live.
More so, besides having a comfortable place to live Homo Sapiens have plenty of cell types to study and to marvel at the fabulous skills of the Master Designer revealed so blatantly in His cell designs.
More so, besides having amazing engineering feats to discover and admire, the Homo Sapiens has a rightful Master Designer to praise and worship all his life.

False.
Complete bullshit.
The universe is remarkably inhospitable to Homo sapiens, apart from a very very tiny range it lives within. The examples of poor design abound. This idiot is just so scientifically ignorant, he's unaware of them.

He's also a liar. He was about to get banned, and he said he was making his last post, last week. And look who's back. The Master Liar.

Insufferable know-it-all.Einstein God has a plan for us. Please stop screwing it up with your prayers.
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