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In Newly Created Life-Form, a Major Mystery

quantamagazine.org

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

#101

Earlier quoted context omitted.

My understanding is that all known organisms share at least the ribosome RNA genes. Unless you're counting viruses, which is not exactly fair since they hijack the host's ribosomes.

but there is RPL1 up to RPL41, and same for RPS and then MRPL and MRPS , so despite the similarities, one can argue different organisms may have different rRNA genes.

RPL1 and such are genes for ribosomal proteins. I'm talking about the genes that encode the ribosomal RNA subunits. These genes are used to infer the evolutionary relationships of the tree of life, so presumably they are shared across all known organisms, or else it would not be possible to infer a phylogenetic tree.

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

#102

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…

Also see, Could a neuroscientist understand a microprocessor? http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.f...

They use various neuroscience techniques to see how far they can get reverse engineering an Atari.

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

#103
post #54

Earlier quoted context omitted.

In this analogy, they're not looking for the code to "work". They simply want it to compile.

That is wrong analogy. Compiling the code doesn't mean it will run.

Maybe life is written in Haskell

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

#104
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…

> 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.

Is there any way at all at simulating the tests? I'd like to apply metaheuristics to search for which combinatorics work

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

#105
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…

> That's the most interesting point to me, I deeply believed that organisms share the same basic set of genes.

Yes, isn't there a universal gene that encodes the RNA polymerase enzyme? I.e., the machinery that transcribes DNA into RNA?

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

#106
post #44
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…

Depends on what kind of life you consider. It's true for mammals. It's true for animals. It's probably even true further up our ancestry. But apparently it doesn't mean that "all things that have genes" share a subset of genes from the same common ancestor. As I understand it that's because they share a common ancestor that didn't have genes (but at that point I'm not sure whether "ancestor" is even the right word).

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

#107

Forgive my complete ignorance, but how do they even count genes? Given a very long string of base pairs, how is it possible to know where one gene ends and the next one begins? Do genes overlap?

I think this is a great question. I was vague on this as well but I found this site after a quick search [1]

A gene is a code for making a specific protein. Each gene is a sequence of three-letter "words" called "codons". There are special "start" and "stop" codons which mark the beginning and end of a gene.

[1] http://genetics.thetech.org/about-genetics/how-do-genes-work

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

#109

Earlier quoted context omitted.

the cellular genome size of RGD3.0, the organism with a 473 genome, is 531kbp according to the paper. this means that the genome encompasses ~531,000 nucleotides (base-pairs). for reference, the human genome encompasses approximately 3.3-billion base-pairs. you can download the human genome from here http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.... (it is recommended to use ftp, see: http://hgdownload.…

Thanks! By the way, when you say "you can download the human genome", presumably this is the genome of a specific individual whose DNA was sequenced? What person is that?

You can download Craig Venter's genome here:

http://hgdownload.soe.ucsc.edu/goldenPath/venter1/bigZips/

However, the human "reference" genome (the updated main product of the Human Genome Project) is a patchwork of about 20 donors' genomes. Many(most?) of the donors are anonymous volunteers from Buffalo, NY, USA.

http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/

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

#110
post #76
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…

>That's the most interesting point to me, I deeply believed that organisms share the same basic set of genes. 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…

It's obviously incorrect. It's not even really a logic error, it's a category error.

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.

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