Firstly what constitutes "minimal" depends on what you feed the organism. There's a set of bacteria called phytoplasma which are plant parasites that are missing genes to make nucleotides (even mycoplasmas have those) and they've adapted by sucking nucleotides from their hosts.
Some insider information: Most of the mystery essential genes are vague cell wall proteins. Probably what is going on is that if you knock out too many of these genes, you lose cell wall turgidity and the cell becomes nonviable. So what is important is not so much which of these genes you have, but how many of them you have.
Second insider information, for fun: The "hypothetical minimal genome" (syn2.0 is referred to as HMG in the paper) was actually a backronym because we called it the "hail mary genome" but decided that was inappropriate for publication.
One in-house ORM I worked with was called TFP, because it was entirely written on a plane ride to Houston, and they named it TFP because the authors liked to say they wouldn't touch it again with a ten foot pole. Their company later thought about trying to sell it, with the name "Technique for Persistence."
Sounds like dependency hell. Gene A only works in the presence of Gene B which only works when there's Gene C which needs Gene A. Knock any one of them out and everything breaks.
Random mutations are like that. It's almost like no-one was planning out how these things should work, and whatever did work stuck.
Weird, huh?
So maybe the environment needs to be changed to support an organism with a smaller genome. The world today is certainly different than when life began. It's probably difficult to evolve the environment, so they'd need to understand what goes wrong with gene deletions and figure out how a different environment could help.
I'm not exactly sure what went wrong, but I think you're really misunderstanding something dnautics said.
M. mycoides certainly does not survive on that. Mycoplasmas need cholesterol and lipids because they lack the HMGCoA reductase pathway and FAS, so all the media you grow them on are enriched for that (started as FBS, but we found horse serum worked great and was cheaper). In general, I think you need a few more things than just that for most basic life (nitrogen, phosphorus, metals)... Is using glucose cheating? Because you could use light for energy and CO2 for carbon, but that adds a ton ton ton of genes...
So this becomes a nitpicky definitional conundrum.
There are no bacteria with smaller genomes today, that was the point of making this one. I was not talking about the global environment either, but the number of options for what substances and concentrations may need to be present in the environment around a cell is certainly very large - making trial and error difficult.
That hints that you could just duplicate the same cell wall protein gene instead, right?
It is definitely a function vs identity. Many mutations of a single gene can perform the same function -- there is a lot of redundancy in genetic code.
>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.
This is very interesting. I expect also, that if they proceeded with their knockout in a different order or different sets at one time they would end up with a different set of genes. Maybe they have some massively parallel way to knockout genes, but I doubt they have explored the entire set of knockouts from the original functioning natural organism. They very likely could be at a local minima of genes required (eg no single gene can be knocked out, but no where near the absolute minimum).
There is a lot of redundancy in biology, which allows for biological systems to be pretty robust, adaptable and fault tolerant. Of course this also means it's really hard to fix that biological process when things go horribly wrong, such as in many forms of cancer.
Paper: “Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.” By Koon-Kiu Yan, Gang Fang, Nitin Bhardwaj, Roger Alexander, Mark Gerstein. Proceedings of the National Academy of Sciences, Vol. 107 No. 18, May 4, 2010.
Perhaps a good moment to refer to this one:
Cancer tumors as Metazoa 1.0: tapping genes of ancient ancestors http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148211/
Such environment should also be 'minimal' - i.e. having lowest number of resources required to construct it and lowest amounts of those resouces.
I think this is a pop-science misunderstanding of what the authors were trying to say. They couldn't find a single unique "minimal set" of genes- but there are genes that we know all organisms share, like the rRNA genes and homologous core ribosomal proteins. All organisms will also require some kind tRNAs and their genes from some source, even if the tRNA genes themselves are not highly homologously conserved.
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 through divergent evolution? It seems like the former option would greatly increase the fl component in the Drake Equation meaning alien life is even more likely than previously thought.
Not really. For one thing there's too much commonality across life in terms of things like the genetic code, i.e. what a sequence of genetic letters "means". The genetic code is arbitrary but essentially universal with minor variants.
For another thing, the organisms now present can be separated from each other by as much as 8 billion years of evolution (4 billion on each branch) meaning there's no particular reason to expect some shared gene to be present everywhere. New genes arise as mutations from old ones, old genes become obsolete and get removed, etc.
It's vaguely like how, if you fork a coding project, and the two projects are allowed to continue indefinitely, eventually there might be no code in common, even without a complete rewrite ever happening.
If that's the case, it isn't that unlikely that every evolutionary branch managed to improve (or discard) every part of the original machinery in some way.
[1] https://www.amazon.com/Creation-Life-Make-Steve-Grand/dp/067...
They do. What you're responding to says there's no one gene shared by all organisms. The genetic intersection of any two organisms is large; the genetic intersection over all organisms is empty.
Many groups of organisms do. All organisms is a tall order, if you think about it.
Maybe all is hidden behind getting blurry because of Heisebergs uncertainty principle.
Yes, isn't there a universal gene that encodes the RNA polymerase enzyme? I.e., the machinery that transcribes DNA into RNA?
RNA Pol is very diverse across clades.
The point isn't the minimal genome, it's to identify the genes important for a minimal genome.
Genetics is all about filtering the signal from the noise. Now we know that these 175 genes are important, we can start focusing efforts on them.
The problem isn't that we don't know how to figure out what a gene does, it's that there are so many goddamn genes we don't know where to start.
It should seem obvious in retrospect. Turing machines have many incarnations as different instruction sets in modern CPUs. I don't see why cells wouldn't have analogous multiple expressions, unless your deep belief was that there was only one way for protein chains to replicate.
Is there any way at all at simulating the tests? I'd like to apply metaheuristics to search for which combinatorics work
[1] https://en.wikipedia.org/wiki/RNA_world [2] https://en.wikipedia.org/wiki/Panspermia
The definition of life itself is not really obvious to me either, some sources count viruses as life other don't.
As to life without DNA. The methodology is somewhat in question for this but here is a more in depth link: http://science.sciencemag.org/content/332/6034/1163.full Now, this is really 1:1 with DNA just using slightly different chemistry, but it's hard to call something DNA when you swap out one of the building blocks.
Other examples are hard to locate in large part because you can't direct detect this stuff.
Anyway, my point was while a virus is 'stuck' using DNA as it needs to infect things that use DNA. However, they can use RNA internally.
PS: For a really out there example, prions seem really close to life.
Yes, it really wants phosphorus. But, a strong preference does not create phosphorus when there is none to be found.
Not that single cells really want or try etc, but you get the idea.
this seems to support the idea that instead of evolving from a single ancestral life form, all beings were created with care
edit: or at least would seem to support the weaker assertion that singl life form ancestry evolutionary theory is inaccurate.
if this is logically incorrect please feel free to tell my why. downvotes are not for disagreement!
At face value the statement "if not all living things share a common ancestor, that makes them appear more like they were intentionally created" (although that line of reasoning, i.e. the watchmaker argument, has been debunked time and time again) seems reasonable.
However the statement seems far more grandiose than it actually is.
If two very "primitive" organisms (i.e. operating at a much lower complexity with much smaller and fewer moving parts than even, say, an earthworm) don't share their sets of DNA that may be unexpected (because whatever step there was from "not having DNA" to "having DNA" had to happen twice, separately, successfully).
If we found out that, say, all higher lifeforms shared no common DNA with other lifeforms outside their group and those groups closely aligned to the Christian "kinds" (which don't really map to biologically distinct groups in meaningful or consistent ways) THAT would be astounding.
But even that extreme case wouldn't make the "creation hypothesis" (if you even want to call it that) more plausible because it presumes the existence of an unexplained organism that is far more complex than anything it supposedly created. It doesn't explain anything -- it just shuts up questions about the "origin" by giving an answer that is impossible to analyse further.
There may have been a creator. But it's impossible to make a consistent logical argument for it. And it's entirely impossible to make an argument that that creator would in any way resemble something modern mainstream religions are worshipping.
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.