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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

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 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.

smaili 10y ago
> 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. Why not? Couldn't we use machines to automate this and analyze the results?
- JimmyM 10y ago
  I think it might take a while. http://coolconversion.com/math/factorial/What-is-the-number-of-zeros-on-the-end-of_175_factorial http://coolconversion.com/math/factorial/What-is-the-number-...
- sixQuarks 10y ago
  When you're talking about 175 different genes, there are far more combinations of genes than there are atoms in the universe. Perhaps a quantum computer can tackle this kind of problem, but nothing we have today can brute-force the solution.
- alister 10y ago
  They got it down to 473 genes, but let's say that minimal life is some 20 of those genes. A brute force approach would require trying 10^34 combinations[1]. And that's already with the simplifying assumption that 20 genes is the minimal set rather than 19 or 106 or some other subset. [1] http://www.wolframalpha.com/input/?i=473+choose+20 http://www.wolframalpha.com/input/?i=473+choose+20
gtycomb 10y ago
I am thinking of George Boole (boolean algebra and logic) who wrote in the 18th centuary -- that a symbol (an individual gene in this case) in itself is not meaningful but that its meaning depends on how it combines with with other symbols. Quote- "..the validity of the processes of analysis does not depend upon the interpretation of the symbols which are employed, but solely on their laws of combination. Every system of interpretation which does not affect the truth of the relations supposed, is equally admissible, and it is true that the same process may,under one scheme of interpretation, represent the solution of a question on the properties of numbers, under another, that of a geometrical problem, and under a third, that of a problem of dynamics or optics." (Boole 1847)
SilasX 10y ago
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 https://en.wikipedia.org/wiki/Gene#Functional_definitions
- grandalf 10y ago
  This is an excellent point. It also illustrates how a useful abstraction at one level can hinder reasoning at another.
- thaumasiotes 10y ago
  > the term historically existed (AIUI) to denote regions that the researcher found to have phenotypic relevance That's Mendelian genetics. Geneticists focused on DNA as a physical molecule rather than a conceptual unit of inheritance use the same word to refer to a region of DNA that produces a protein. They're both important concepts, but they're not the same concept.
  - dragonwriter 10y ago
    Arguably, the production of a protein is nearly the smallest element of the observable characteristic of an organism produced by the interaction of its genotype with the environment, and thus sort of the fundamental unit of phenotype, so, from that perspective, they are exactly the same thing.
    - thaumasiotes 10y ago
      They are not the same thing from any useful perspective. You can remove a (protein-coding) gene, or replace it, without altering the phenotype at all. You can make changes outside protein-coding regions and get large phenotypic changes.
  - SilasX 10y ago

smaili 10y ago

> 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. Why not? Couldn't we use machines to automate this and analyze the results?

JimmyM 10y ago
I think it might take a while. http://coolconversion.com/math/factorial/What-is-the-number-of-zeros-on-the-end-of_175_factorial http://coolconversion.com/math/factorial/What-is-the-number-...
sixQuarks 10y ago
When you're talking about 175 different genes, there are far more combinations of genes than there are atoms in the universe. Perhaps a quantum computer can tackle this kind of problem, but nothing we have today can brute-force the solution.
alister 10y ago
They got it down to 473 genes, but let's say that minimal life is some 20 of those genes. A brute force approach would require trying 10^34 combinations[1]. And that's already with the simplifying assumption that 20 genes is the minimal set rather than 19 or 106 or some other subset. [1] http://www.wolframalpha.com/input/?i=473+choose+20 http://www.wolframalpha.com/input/?i=473+choose+20

gtycomb 10y ago

I am thinking of George Boole (boolean algebra and logic) who wrote in the 18th centuary -- that a symbol (an individual gene in this case) in itself is not meaningful but that its meaning depends on how it combines with with other symbols. Quote- "..the validity of the processes of analysis does not depend upon the interpretation of the symbols which are employed, but solely on their laws of combination. Every system of interpretation which does not affect the truth of the relations supposed, is equally admissible, and it is true that the same process may,under one scheme of interpretation, represent the solution of a question on the properties of numbers, under another, that of a geometrical problem, and under a third, that of a problem of dynamics or optics." (Boole 1847)

SilasX 10y ago

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 https://en.wikipedia.org/wiki/Gene#Functional_definitions

grandalf 10y ago
This is an excellent point. It also illustrates how a useful abstraction at one level can hinder reasoning at another.
thaumasiotes 10y ago
> the term historically existed (AIUI) to denote regions that the researcher found to have phenotypic relevance That's Mendelian genetics. Geneticists focused on DNA as a physical molecule rather than a conceptual unit of inheritance use the same word to refer to a region of DNA that produces a protein. They're both important concepts, but they're not the same concept.
- dragonwriter 10y ago
  Arguably, the production of a protein is nearly the smallest element of the observable characteristic of an organism produced by the interaction of its genotype with the environment, and thus sort of the fundamental unit of phenotype, so, from that perspective, they are exactly the same thing.
  - thaumasiotes 10y ago
    They are not the same thing from any useful perspective. You can remove a (protein-coding) gene, or replace it, without altering the phenotype at all. You can make changes outside protein-coding regions and get large phenotypic changes.
- SilasX 10y ago