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If I were a biology/biochem/genetics/etc type of student today this is exactly what I would love to work on. Perhaps someday we will actually understand how life works. That's both exciting and incredibly scary.
Earlier quoted context omitted.
> I deeply believed that organisms share the same basic set of genes. Many groups of organisms do. All organisms is a tall order, if you think about it.
The more I think about that the more makes me believe that the Genome is not the smallest order which defines "life". Maybe all is hidden behind getting blurry because of Heisebergs uncertainty principle.
I'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…
That's like forking someone's program, but not understanding two thirds of the code. (What's the big deal? It happens!) If you take someone's 4000-5000 line program and whittle it down to 473 lines which are still somehow useful, "newly created" doesn't apply in full honesty, let alone if you don't know what a third of those lines do.
TL;DR: Venter and his collaborators originally set out to design a stripped-down genome based on what scientists knew about biology. ... 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," ... So the team took a different and more labor-intensive tack, replacing the design approach with trial and e…
>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. Isn't the current theory that all life on Earth has a common ancestor? Wouldn't this point put that into question and introduce the possibility that life has developed multiple times independently of each other or would this lack of shared genes eventually appear…
I'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…
Also, isn't there an issue of "gene" being something of an unnatural category? Nature doesn't provide a clean labeling of what part of the sequence is "a" gene, and the term historically existed (AIUI) to denote regions that the researcher found to have phenotypic relevance. So I'm not sure it's helpful to phrase a minimum in terms of "n genes". See: https://en.wikipedia.org/wiki/Gene#Functional_definitions
I 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.
"Second layer of information in DNA confirmed"
My take-away: Work like this is somewhat akin to attempting to determine the specification of Intercal through reverse engineering given a working program and a compiler.
After a while that got old.
I 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…
with a handful of exceptions (for example TER units, and DnaA, which seems to need to be close to the replication origin), for most microbes, placement and arrangement don't matter. I believe they wanted to modularize the bacteria by placing cassettes of common functionality (e.g. all the tRNAs together) in parts of the genome. I don't know if they are still are working on that, or how it went. In yeasts, the tRNAs h…