In Newly Created Life-Form, a Major Mystery • Hacker News Board

Re: In Newly Created Life-Form, a Major Mystery

#61

Post by Retric » Wed, Jun 22, 2016, 5:12 PM UTC

kens wrote: post #32

Retric wrote: post #29

Earlier quoted context omitted.

The definition of life is a tricky question. The most obvious example is red blood cells dump their DNA. So they can't replicate, and virus can't target them. However, insect drones also can't reproduce and are considered alive so it's a little more open to debate than you might think. As to life without DNA. The methodology is somewhat in question for this but here is a more in depth link: http://science.sciencemag.…

The paper you cite about the bacterium that uses arsenic instead of phosphorus in its DNA was conclusively discredited. http://www.nature.com/news/arsenic-life-bacterium-prefers-ph...

This does not mean that arsenate does not get into the bacteria, he points out. “It just shows that this bacterium has evolved to extract phosphate under almost all circumstances.”

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.

Re: In Newly Created Life-Form, a Major Mystery

#62

Post by gort » Wed, Jun 22, 2016, 5:23 PM UTC

slg wrote: post #44

davnn wrote: post #10

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…

"Isn't the current theory that all life on Earth has a common ancestor? Wouldn't this point put that into question"

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.

Re: In Newly Created Life-Form, a Major Mystery

#63

Post by roadnottaken » Wed, Jun 22, 2016, 5:30 PM UTC

no_flags wrote: post #42

Interesting work, but it reminds me of the famous "Could a biologist fix a radio?" paper [1]. The paper imagines biologists trying to determine what parts of a radio are essential using a similar trial and error technique. As you can imagine, this technique would lead to many erroneous conclusions, especially when paired with the "publish or perish" and "gold rush" mentalities so prevalent in academia. It makes you w…

> It makes you wonder if we are trying to understand biological systems with a fundamentally wrong approach.

Got a better idea?

Re: In Newly Created Life-Form, a Major Mystery

#64

Post by stcredzero » Wed, Jun 22, 2016, 5:30 PM UTC

dnautics wrote: post #35

davnn wrote: post #10

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…

I worked in the synthetic biology lab (on a different project) while the early stages of the Syn3.0 was being done, and also have paid several visits to chat with them in the meantime. [Proof: first author on http://dx.doi.org/10.3390/ijms16012020 ] I was a fly on the wall for most of the group meetings and even contributed some unpublished results (there were transposons that were causing problems by shuffling the t…

The "hypothetical minimal genome"...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."

Re: In Newly Created Life-Form, a Major Mystery

#65

Post by majkinetor » Wed, Jun 22, 2016, 5:34 PM UTC

djsumdog wrote: post #46

daveguy wrote: post #17

Earlier quoted context omitted.

> They found that not a single gene is shared across all of life. 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…

Years ago I read an interesting paper comparing the types of subsystems found in the Linux kernel with subsystems found in biology (or what we understand of them currently). 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 ma…

Thanks for that last paper, epic!

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/

Re: In Newly Created Life-Form, a Major Mystery

#66

Post by otto_ortega » Wed, Jun 22, 2016, 5:35 PM UTC

"The function of 79 genes is a complete mystery.'We don't know what they provide or why they are essential for life — maybe they are doing something more subtle, something obviously not appreciated yet in biology' "

It is the activation key God puts on each living being... Ain't gonna work without it. =P

Re: In Newly Created Life-Form, a Major Mystery

#67

Post by jameshart » Wed, Jun 22, 2016, 5:38 PM UTC

gort wrote: post #62

slg wrote: post #44

Earlier quoted context omitted.

>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…

"Isn't the current theory that all life on Earth has a common ancestor? Wouldn't this point put that into question" 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 ea…

Deep down, somewhere in the genetic code, it still says "Mozilla (compatible)"

Re: In Newly Created Life-Form, a Major Mystery

#68

Post by stcredzero » Wed, Jun 22, 2016, 5:39 PM UTC

davnn wrote: post #10

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…

Is there a single set of instructions needed for Turing Completeness? It's possible to have Turing Completeness in a random access machine with just one instruction. I should think you really need to satisfy certain capabilities, and there would be many ways to satisfy those.

Re: In Newly Created Life-Form, a Major Mystery

#69

Post by majkinetor » Wed, Jun 22, 2016, 5:41 PM UTC

daveguy wrote: post #17

davnn wrote: post #10

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…

> They found that not a single gene is shared across all of life. 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…

This means that we need first to decide on common environment that minimal synthetics will live on. Then, with this environment fixed, we could try to isolate minimal set of genes for multiple different organisms that are originally viable in this environment.

Such environment should also be 'minimal' - i.e. having lowest number of resources required to construct it and lowest amounts of those resouces.

Re: In Newly Created Life-Form, a Major Mystery

#70

Post by thaumasiotes » Wed, Jun 22, 2016, 5:43 PM UTC

davnn wrote: post #10

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…

> I deeply believed that organisms share the same basic set of genes

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.