In Newly Created Life-Form, a Major Mystery
quantamagazine.org
In Newly Created Life-Form, a Major Mystery
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Re: In Newly Created Life-Form, a Major Mystery
#2Article summary and Article http://www.cba.mit.edu/docs/papers/16.04.minimal.pdf
edit: appears to be the full article (scroll down past summary)
Re: In Newly Created Life-Form, a Major Mystery
#3I wonder how they removed the genes? I am not an expert in microbiology. I work with mainly eukaryotes, but I am guessing intergenic distances are not a huge factor here? What about spatial arrangement of the genes? Did they generally leave that alone?
Genes are not independent functional modules. Their placement and arrangement on the genome matters. Did they only mess with coding features (genes)? Or did they also mess with other genomic features? Or do such things just not matter with bacteria?
Re: In Newly Created Life-Form, a Major Mystery
#4I find it fascinating we still don't really know how life works. I have a hunch we are going to find the large scale 3D structure of the chromosome is a big deal, and these genes regulate it. There aren't many good tools to study chromosome structure and it's quite possible there's a whole layer of information we've missed so far.
Re: In Newly Created Life-Form, a Major Mystery
#5I find it fascinating we still don't really know how life works. I have a hunch we are going to find the large scale 3D structure of the chromosome is a big deal, and these genes regulate it. There aren't many good tools to study chromosome structure and it's quite possible there's a whole layer of information we've missed so far.
>it's quite possible there's a whole layer of information we've missed so far
Can you expand on this comment? What would such a layer look like? Have we missed layers before and then found them?
Re: In Newly Created Life-Form, a Major Mystery
#6I find it fascinating we still don't really know how life works. I have a hunch we are going to find the large scale 3D structure of the chromosome is a big deal, and these genes regulate it. There aren't many good tools to study chromosome structure and it's quite possible there's a whole layer of information we've missed so far.
This was my thought as well. Likely the remaining genes represent some kind of meta-process, effecting and/or controlling how the genes we understand are expressed.
Re: In Newly Created Life-Form, a Major Mystery
#7I'm afraid it's not the individual genes themselves that are important to life, but a specific combination of those genes. Further complicating the problem is that we have no idea how many genes comprise an "essential group". Is it a combination of 2 genes? 3, 5, 10?
When you're talking about 175 unknown genes, the combination of all of these is a huge number. It's like finding a needle in a haystack the size of the solar system.
I don't think this brute force approach is going to work, we need a different way to figure this out, but I'm confident that once figured out, it will seem simple looking back on it.
Re: In Newly Created Life-Form, a Major Mystery
#8I wonder how they removed the genes? I am not an expert in microbiology. I work with mainly eukaryotes, but I am guessing intergenic distances are not a huge factor here? What about spatial arrangement of the genes? Did they generally leave that alone? Genes are not independent functional modules. Their placement and arrangement on the genome matters. Did they only mess with coding features (genes)? Or did they also…
If I understand correctly, they built the technology to synthesize arbitrary genomes. So they remove genes by omitting them from the synthesis.
Re: In Newly Created Life-Form, a Major Mystery
#9I find it fascinating we still don't really know how life works. I have a hunch we are going to find the large scale 3D structure of the chromosome is a big deal, and these genes regulate it. There aren't many good tools to study chromosome structure and it's quite possible there's a whole layer of information we've missed so far.
>it's quite possible there's a whole layer of information we've missed so far Can you expand on this comment? What would such a layer look like? Have we missed layers before and then found them?
The whole story of molecular biology has been discovering layers of control and information: DNA, genes, gene regulation, RNA, RNA splicing, protein structure and regulation, protein interactions, micro-RNAs... and it's usually been limited by the tools that scientists could bring to bear. Possibly there's another control layer in charge of the long range structure of the chromosome. Being wet, squishy and fragile, it's hard to study.
Re: In Newly Created Life-Form, a Major Mystery
#10TL;DR: Venter and his collaborators originally set out to design a stripped-down genome based on what scientists knew about biology.
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With the right tools finally in hand, the researchers designed a set of genetic blueprints for their minimal cell and then tried to build them. Yet “not one design worked,"
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So the team took a different and more labor-intensive tack, replacing the design approach with trial and error. They disrupted M. mycoides’ genes, determining which were essential for the bacteria to survive.
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Venter is careful to avoid calling syn3.0 a universal minimal cell. If he had done the same set of experiments with a different microbe, he points out, he would have ended up with a different set of genes.
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In fact, there’s no single set of genes that all living things need in order to exist.
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They found that not a single gene is shared across all of life. “There are different ways to have a core set of instructions,”
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Venter’s minimal cell is a product not just of its environment, but of the entirety of the history of life on Earth.
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He and others are trying to make more basic life-forms that are representative of these earlier stages of evolution.
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Some scientists say that this type of bottom-up approach is necessary in order to truly understand life’s essence. “If we are ever to understand even the simplest living organism, we have to be able to design and synthesize one from scratch,”
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“We are still far from this goal.”
As @sixQuarks has already written, finding the minimal amount of genes when there are 175 unknown ones and you don't know anything about their dependencies and relationships seems to be pretty much impossible.
> In fact, there’s no single set of genes that all living things need in order to exist. ... They found that not a single gene is shared across all of life.
That's the most interesting point to me, I deeply believed that organisms share the same basic set of genes.