Scientists Discover a Self-Replicating Protein Structure, And It Could Have Built The First Life on

[scruffy]

Done what?

Who?

Yes but who are "they"?

You want a whole list of some 6,000 labs world wide?

 

[Sherlock Holmes]

You want a whole list of some 6,000 labs world wide?

No I don't want a list of labs, perhaps some papers or articles all about it would be nice.

 

[scruffy]

No I don't want a list of labs, perhaps some papers or articles all about it would be nice.

How about one example to start with?

If you'd like more, there's plenty more.

These people is San Diego study "minimal cells". They want to know, what is the smallest set of molecules that can sustain life.

A minimal cell is a cell that has a genome that only contains the genes that are essential for its survival. The idea behind minimal cells is that by studying the functions of all the genes and components in a minimal cell, scientists can learn the basics of cellular biology.

In 2016, J. Craig Venter and his team at the J. Craig Venter Institute (JCVI) created a minimal cell by synthesizing a genome that contained only the essential and quasi-essential genes from the bacterium Mycoplasma mycoides. This cell, called JCVI-syn3B, has a genome of 531,490 base pairs, 438 protein-coding genes, and 35 RNA-coding genes, making it the smallest genome of any organism that can be grown in a laboratory. The cell performs the same cellular functions as other organisms, but any mutation in its genes could be fatal, so it was unclear if it could evolve. However, in 2023, a team was able to grow the cell through 2,000 generations and showed that it can evolve and recover from some of the fitness costs of its streamlined genome.

The JCVI/SGI team has also been developing tools and semi-automated processes to speed up the process of building cells from the bottom up. For example, they use MOSAIC, a process that involves recombining a focal chromosome with synthetic DNA fragments containing known essential genes from that chromosome. The result is a library of cells with substantially reduced, or even minimal, focal chromosomes.

First Minimal Synthetic Bacterial Cell

Researchers from the J. Craig Venter Institute (JCVI) and Synthetic Genomics, Inc. (SGI) have accomplished the next feat in synthetic biology...

www.jcvi.org

 

[Sherlock Holmes]

How about one example to start with?

If you'd like more, there's plenty more.

These people is San Diego study "minimal cells". They want to know, what is the smallest set of molecules that can sustain life.

A minimal cell is a cell that has a genome that only contains the genes that are essential for its survival. The idea behind minimal cells is that by studying the functions of all the genes and components in a minimal cell, scientists can learn the basics of cellular biology.

In 2016, J. Craig Venter and his team at the J. Craig Venter Institute (JCVI) created a minimal cell by synthesizing a genome that contained only the essential and quasi-essential genes from the bacterium Mycoplasma mycoides. This cell, called JCVI-syn3B, has a genome of 531,490 base pairs, 438 protein-coding genes, and 35 RNA-coding genes, making it the smallest genome of any organism that can be grown in a laboratory. The cell performs the same cellular functions as other organisms, but any mutation in its genes could be fatal, so it was unclear if it could evolve. However, in 2023, a team was able to grow the cell through 2,000 generations and showed that it can evolve and recover from some of the fitness costs of its streamlined genome.

The JCVI/SGI team has also been developing tools and semi-automated processes to speed up the process of building cells from the bottom up. For example, they use MOSAIC, a process that involves recombining a focal chromosome with synthetic DNA fragments containing known essential genes from that chromosome. The result is a library of cells with substantially reduced, or even minimal, focal chromosomes.

First Minimal Synthetic Bacterial Cell

Researchers from the J. Craig Venter Institute (JCVI) and Synthetic Genomics, Inc. (SGI) have accomplished the next feat in synthetic biology...

www.jcvi.org

Right, yes I've heard of this I think.

Well you're in luck because James Tour discusses this in an interesting article he wrote in Inference in 2019, here's what he says about the Venter work, emphasis mine:

In 2010, a team led by Craig Venter made a copy of a known bacterial genome and transplanted it into another cell. In 2016, they did something better, removing all but 473 genes from a natural genome and transplanting it into another cell. Venter and his team were circumspect; the press was enthusiastic. More recently, Henrike Niederholtmeyer, Cynthia Chaggan, and Neal Devaraj have made what they term, “mimics of eukaryotic cells.” Science declared them “the most lifelike artificial cells yet.”

Microcapsules made of plastic and containing clay were prepared using microfluidic techniques. Clay has a high affinity for binding DNA. Thus, when DNA was added to the solution, it diffused through the semiporous plastic microcapsules and bound to the clay. The requisite RNA polymerases, together with the ribosomes, tRNA, amino acids, enzymatic cofactors, and energy sources were either purchased or extracted from living systems. The expected chemical reactions did result in protein synthesis.

Newly formed proteins diffused from their microcapsules of origin to other microcapsules. The nearer the neighboring microcapsule, the greater the exchange of reagents between them. Diffusion between microcapsules the authors dubbed quorum sensing. The chemistry would work no matter the container, whether a test tube or a large-scale industrial production tank. If the experimental design is clever, the synthesis is unremarkable. Phys.org reported these modest results in markedly flamboyant terms, referring to “gene expression and communication rivaling that of living cells.” There is no rivalry here. All of the active chemical components were extracted from living systems. If these are “the most lifelike artificial cells yet,” this serves only to underscore the point that no one has ever come close to the real thing.

So how does using already living systems to create something, demonstrates that living systems can arise from non-living systems in nature?

Well one way is to do as you do and that is to declare "everything is alive" hey presto - magic!

 

[scruffy]

Right, yes I've heard of this I think.

Well you're in luck because James Tour discusses this in an interesting article he wrote in Inference in 2019, here's what he says about the Venter work, emphasis mine:



So how does using already living systems to create something, demonstrates that living systems can arise from non-living systems in nature?

Well one way is to do as you do and that is to declare "everything is alive" hey presto - magic!

Getting from here to where you can design and program embryonic molecular gradients, is the point.

These scientists are "reducing scope" so they can answer a simple question. They're not looking at support structures like microtubules and actin. They want to know how to program the life cycle of a gap gene.

We already know a whole lot about molecular self assembly. Helical structures abound in biology, and complex shapes are built with them. The question is how these shapes play into cellular dynamics. The DNA is much like a computer program, it's a linear sequence of code that's been g-zipped. So now you have to build a bunch of little mini-apps that look for particular sequences and do something with them. It's a step beyond designing pharmaceuticals.

The key to life is the sequencing of expression. So, we start simple. We first figure out how you define what is the "first" gene that gets expressed, and how to turn it on and off. Then you move to parallel computing with multiple CPU's and shared busses.

You can't claim to understand something until you can do something useful with it, like build a circuit or something. In this case we want the circuit to do something simple, create a gradient and determine its time course. To do that, we need to define the "shape" of the gradient, starting with which end is up. All advanced organisms are cephalized, there's not a single one that isn't. And, we can trace that structure all the way back to bacteria, where we find that some are and some aren't - so we have to look THERE to find out how the basic mechanism works and what the requirements are.

When we do, we discover that orientation is defined at a molecular level, and it comes from the symmetry properties of self organizing molecules. Tubulin being the prime example.

So that means, before we can program a gradient, we have to know how to program tubulin and how to locate it so it defines an orientation inside the cell. This is topology, it's shapes and symmetries. Topology tells us how you get handedness and head-tail, they call it the "orientability" of a surface. The same surface that's orientable in 3 dimensions may not be orientable in 4, so the degrees of freedom in your surrounding tissues matters.

A tubulin monomer is a simple globular protein. It self-assembles in various ways depending on the local ionic conditions. You can get two of them to live at right angles to each other if you set up the environment correctly. Ionic concentrations also have "shapes" inside the cell. Therefore you need scaffolding that controls the concentrations of ion channels in the outer membrane.

All this, before you can program your first gradient.

Just like, you need a CPU and some memory before you can say let x=5.

 

[Sherlock Holmes]

Getting from here to where you can design and program embryonic molecular gradients, is the point.

These scientists are "reducing scope" so they can answer a simple question. They're not looking at support structures like microtubules and actin. They want to know how to program the life cycle of a gap gene.

We already know a whole lot about molecular self assembly. Helical structures abound in biology, and complex shapes are built with them. The question is how these shapes play into cellular dynamics. The DNA is much like a computer program, it's a linear sequence of code that's been g-zipped. So now you have to build a bunch of little mini-apps that look for particular sequences and do something with them. It's a step beyond designing pharmaceuticals.

The key to life is the sequencing of expression. So, we start simple. We first figure out how you define what is the "first" gene that gets expressed, and how to turn it on and off. Then you move to parallel computing with multiple CPU's and shared busses.

You can't claim to understand something until you can do something useful with it, like build a circuit or something. In this case we want the circuit to do something simple, create a gradient and determine its time course. To do that, we need to define the "shape" of the gradient, starting with which end is up. All advanced organisms are cephalized, there's not a single one that isn't. And, we can trace that structure all the way back to bacteria, where we find that some are and some aren't - so we have to look THERE to find out how the basic mechanism works and what the requirements are.

When we do, we discover that orientation is defined at a molecular level, and it comes from the symmetry properties of self organizing molecules. Tubulin being the prime example.

So that means, before we can program a gradient, we have to know how to program tubulin and how to locate it so it defines an orientation inside the cell. This is topology, it's shapes and symmetries. Topology tells us how you get handedness and head-tail, they call it the "orientability" of a surface. The same surface that's orientable in 3 dimensions may not be orientable in 4, so the degrees of freedom in your surrounding tissues matters.

A tubulin monomer is a simple globular protein. It self-assembles in various ways depending on the local ionic conditions. You can get two of them to live at right angles to each other if you set up the environment correctly. Ionic concentrations also have "shapes" inside the cell. Therefore you need scaffolding that controls the concentrations of ion channels in the outer membrane.

All this, before you can program your first gradient.

Just like, you need a CPU and some memory before you can say let x=5.

Well Tour's questions were never answered, so he's right to argue we are clueless, if we cannot answer the basic questions then we are clueless.

 

[scruffy]

Right, yes I've heard of this I think.

Well you're in luck because James Tour discusses this in an interesting article he wrote in Inference in 2019, here's what he says about the Venter work, emphasis mine:



So how does using already living systems to create something, demonstrates that living systems can arise from non-living systems in nature?

Well one way is to do as you do and that is to declare "everything is alive" hey presto - magic!

No one's asking what "alive" means. Like the Buddha said, "that is an irrelevant question".

The goal is useful behavior. We can worry about philosophy later.

The goal is to build the circuit. For that we dont have to understand how electrons move in wires, the observation that they do is sufficient.

Vacuum tubes come later. We're still at the level of resistors.

 

[scruffy]

Well Tour's questions were never answered, so he's right to argue we are clueless, if we cannot answer the basic questions then we are clueless.

First we had to build a resistor before we could figure out how it works.

That's what Venter's team did, they built a resistor.

Now they're playing with it, and in a couple of years they'll discover Ohm's law. And from there it's a short step to a useful circuit.

 

[Sherlock Holmes]

First we had to build a resistor before we could figure out how it works.

That's what Venter's team did, they built a resistor.

Now they're playing with it, and in a couple of years they'll discover Ohm's law. And from there it's a short step to a useful circuit.

Such faith, admirable.

 

[scruffy]

Such faith, admirable.

I have a long history of accomplishing the impossible for people who don't fully appreciate it.

 

[westwall]

Such faith, admirable.

What faith? That is merely digging in to the act of creating something.