When would it be valid for scientists to claim that they have created life?

[Tim_T-Bonham.net]

@davidmich

Does the claim to have created life count as such if that life form was made from ‘scratch’ based on an existing bacterium?

Doesn’t this describe pretty much all of evolution, from the single-celled organisms floating in the primordial sea down to current species?

[chorpler]

@Chronos

Actually, I’ve seen studies that suggest fairly strongly that the current genetic encoding did evolve. The authors came up with an objective figure of merit for measuring a genetic code, and found that the one we actually have is better than 99.9% of all possible genetic codes. This suggests that many different genetic codes were in fact tried early in life’s history, and that the one that led to us outcompeted all of the others.

I’m extremely interested in reading this if you can tell me where to look.

[Chronos]

All I can remember of the source is that it was in Scientific American, probably some time post-1999. Of course, by that time, there was some absolute garbage making its way past the SciAm editors, so who knows how strong that result actually was.

[Lemur866]

@SamuelA

http://www.nature.com/nature/journal/v464/n7287/full/nature08817.html

Maybe. It’s only a possibility. The thing it shows is that this limitation is one that evolution cannot directly bypass, because in order to do so, it would have to, mutation by mutation, design the computational machinery to turn the codebase of an existing cell into one that uses the new system.

Its a good, solid, concrete example of the kind of barriers that evolution can’t beat as an algorithm (but intelligent design can)

Evolution cannot bypass this limitation it because the machinery would only need to be used once, is very complex, and would not provide any benefit until it is used.

You are correct that a cell that needs another amino acid would probably just repurpose a codon that has duplicate encodings.

If having more amino acids to expand the space of possible proteins were so advantageous, there’s plenty of room in the triplet codon regime to do so. There are 64 possible codes, but only 20 amino acids used, plus a stop. So there’s plenty of redundant codes that could be used to code for novel amino acids, you wouldn’t have to invent a whole new coding scheme to do so.

So your idea that with 4 times the amino acids an organism would have lots of ways to evolve novel proteins ignores that we could already have 3 times the amino acids without changing the encoding scheme, just changing the code.

But that’s doesn’t seem to happen. Mutations supstituting in novel amino acids could occur, but they don’t seem to give the organism any particular advantage, rather the reverse, since no known organisms make use of novel amino acids.

Alloprotein

[chorpler]

@Chronos

All I can remember of the source is that it was in Scientific American, probably some time post-1999. Of course, by that time, there was some absolute garbage making its way past the SciAm editors, so who knows how strong that result actually was.

OK thanks. If my search reveals anything I will report back.

[igor_frankensteen]

This is yet another question whose answer depends very much on why it’s being asked.

That isn’t an accusation or an attempt to perform some kind of “gotcha” trick, it’s a basic application of logic.

WHY you are asking, determines which definition of “create” and of “life” should be used in order to answer you.

[Peter_Morris]

@Chronos

In that 2010 case, did the scientists author the code from scratch, or merely craft it?

That is to say, at some point they must have needed, for instance, a transcriptase enzyme in their organism. Did they look up the sequence of some existing transcriptase enzyme and copy-and-paste that into the DNA, or did they come up with their own sequence from scratch for a novel transcriptase enzyme? I’m almost completely certain that it was the former. Which makes their work comparable to the student who re-types an essay from one they found in a book. Even if it was the student’s fingers striking the keys, one still wouldn’t say that they created the essay.

@LSLGuy

@Chronos: I’d say it’s more comparable to a student who cut and pasted bits of a dozen essays and wiki articles together, did some rewriting to make the voice more consistent, then sent that in as original work.
…
IOW: impressive, but as you say, not ab initio.

I’m a computer programmer. I might want to create a user interface with elements such as radio buttons and text boxes. I don’t need to create them from scratch. I’ve got libraries of routines I can call on. Putting a complex tool on the screen can be done with a single line of code.

The library routines themselves were programmed using other library routines. Drawing a square text box is quite complex. It needs four straight lines. Drawing a straight line on a computer screen is in itself a complex algorithm. The people who wrote the text box library used a “draw line” library. They didn’t re-create it from scratch. Filling the box with a particular colour, right to the edge and not a pixel beyond, that’s another complex task that requires a library routine.

So my computer program consists in large part of elements copied from other people, who themselves copied from other people.

Would it be fair to say that I haven’t created an original program?

[Chronos]

That depends. Are you claiming to have created a program, or programming?

[si_blakely]

The 2010 announcement showed that a synthesised strand of prokaryote DNA could be inserted into the cell and worked.

In that case, they basically copied the existing bacterial DNA and made a few simple changes (signatures in the junk DNA, proven DNA knock-outs/substitutions).

However, it meant that they could then start on determining what is necessary and sufficient for a working bacterium, by editing out sections of that base DNA strand with a very high degree of accuracy. They did not have CRISPR-Cas9 in 2010 - they relied on DNA knockouts that were far less reliable and accurate.

The aim was to build a library of DNA elements that could be used to develop entirely synthetic organisms with a minimum of DNA elements that could then be extended.

And it looks like they succeeded last year
‘Minimal’ cell raises stakes in race to harness synthetic life | Nature

But there are still 149 genes (of 473) that they do not understand that are required in the genome.

So - yes - Venter and team have created an entirely synthetic lifeform - they just don’t quite understand 1/3 of it.

[LSLGuy]

ETA: @Peter Morris and I see I’m late to the response party again. Sigh.

I too am a CS guy though I’ve not devved for a living in the last 5-ish years. As a practicing physicist Chronos has doubtless cobbled together a few executables for whatever reason. And may well be a giant in specialty software in his field for all I know.

You raise a very valid point. Which was brought out by several posters. Including me.

How original is original enough? More specifically, at what level of abstraction does “originality” reside or need to reside? What about this complaint:
Heck, they used plain old carbon and hydrogen to make their so-called “artificial life” har har; why didn’t they create their own chemical elements fer Crissakes!? Damn lazy copycats.That’s nonsense of course, but it points out that when you dig down deep enough into the abstraction layers nothing is novel; everything is boilerplate.

So which level is the one where originality matters? Darn good question you asked.

A point related to yours is igor’s post just above yours. Until the OP tells us what question he’s really asking, we can’t decide which level(s) of abstraction are the ones that matter to him for his purposes.

To be sure, even if Venter *et al *used only the very highest of high level “APIs” of bacterial biochemistry plus employed lots of partly-understood cut-and-paste coding, they still accomplished a heck of a feat, a biotech tour de force for the state of *our *art.

Which at the same time is merely a chimp sharpening a stick to poke into an anthill compared to biology’s own internal state of *it’s *art.

[SimonLeigh]

Nobody can create life unless life first goes extinct, and it hasn’t and won’t. New life forms, yes, but “life” means self-sustaining and replicating. Reacting chemicals don’t do that.

[Chronos]

Oh, and another point on the programming analogy: Maybe you didn’t write your own box-drawing routine, or line-drawing routine, but if push came to shove, you could have. Certainly, a whole team of programmers (including some who routinely work at low level) could. Or at least write a much simpler but still functional program that didn’t use boxes.

[LSLGuy]

It’s interesting to me how the decision / debate about the appropriate abstraction level has come up here and in the multiverse thread during the same afternoon.

Ref e.g. http://boards.straightdope.com/sdmb/showthread.php?p=20146643#post20146643

Which demonstrates simultaneously how generic and how very special is the notion of “life.”

[Peter_Morris]

But the scientists could have created their own transcriptase enzyme.

Using an existing one is like a computer program using a library. It doesn’t disqualify them as having “created life”

It really depends if they have put the parts together in a unique and original way or not.

[chorpler]

@Peter_Morris

But the scientists could have created their own transcriptase enzyme.

Could they? Wouldn’t we need a general solution to the protein folding problem to do that? Or a whole lot of trial and error, I guess…

[Peter_Morris]

I don’t know anything about biochemistry, so I can’t answer that.

My point is, copying an enzyme found in nature is analogous to using a pre-existing library routine. It doesn’t in itself mean they didn’t create new life.

[Darren_Garrison]

@watchwolf49

I think saying evolution can’t develop this four unit codon isn’t established, not without the specific reasons … at most we can say that the three unit codon is the best economy and this is the form that we find in nature today … and that a four unit codon is very very unlikely to evolve … but the probability is not zero, just very very close to zero …

I’ve seen speculation based on the pattern of codons that they were originally only 2 letters long. Look at a DNA codon chart and you’ll see that CTs, GTs, TCs, CCs, ACs, GCs, CGs, and GGs each all code for the same amino acid no matter what the third letter is. The speculation is that once all amino acids used were coded for with only 2 letters (and 16 possibilities) and that adding an additional letter allowed for more amino acids to be coded for.

[Hector_St_Clare]

@Chronos

I’m not at all convinced that such an arrangement would be superior. There’s already room in the genetic code for more amino acids, but it’s not used. I think the simplest explanation for that is that there just aren’t all that many amino acids, or at least, not all that many useful ones. And fitting those 20 amino acids into 256 different codings instead of 64 would mean that you’d have a lot more mutations which didn’t change protein sequences at all, which would probably mean slower evolution.

Meanwhile, you’re also costing the organism more overhead to support the longer genome, and for every new amino acid you add, you’re also adding overhead for the pathways to make and use those aminos. It’s hard to see that you’d get any benefits large enough to make up for the costs.

As a minor point, there are actually 22 amino acids that are used in proteins- the two extra ones are selenocysteine and pyrrolysine. Neither of them has a specific dedicated codon for it: rather both are encoded for by what are normally “stop” codons, and there are additional elements in the mRNA that tell the organism to insert a selenocysteine or pyrolysine there instead of ending transcription.

Selenocysteine is interesting because it uses an element (selenium, in place of sulfur) that isn’t all that common in living organisms. In some situations the selenocysteine version of an enzyme (glutathione peroxidase, for example) is apparently more effective than the sulfur-containing version, but of course it requires the specialized machinery to incorporate an unusual amino acid. Plants generally contain selenium-free GPx while animals use the selenium containing version.

[August_West]

@LSLGuy

ETA: @Peter Morris and I see I’m late to the response party again. Sigh.

I too am a CS guy though I’ve not devved for a living in the last 5-ish years. As a practicing physicist Chronos has doubtless cobbled together a few executables for whatever reason. And may well be a giant in specialty software in his field for all I know.

You raise a very valid point. Which was brought out by several posters. Including me.

How original is original enough? More specifically, at what level of abstraction does “originality” reside or need to reside? What about this complaint:
Heck, they used plain old carbon and hydrogen to make their so-called “artificial life” har har; why didn’t they create their own chemical elements fer Crissakes!? Damn lazy copycats.That’s nonsense of course, but it points out that when you dig down deep enough into the abstraction layers nothing is novel; everything is boilerplate.

So which level is the one where originality matters? Darn good question you asked.

A point related to yours is igor’s post just above yours. Until the OP tells us what question he’s really asking, we can’t decide which level(s) of abstraction are the ones that matter to him for his purposes.

To be sure, even if Venter *et al *used only the very highest of high level “APIs” of bacterial biochemistry plus employed lots of partly-understood cut-and-paste coding, they still accomplished a heck of a feat, a biotech tour de force for the state of *our *art.

Which at the same time is merely a chimp sharpening a stick to poke into an anthill compared to biology’s own internal state of *it’s *art.

‘If you wish to make an apple pie from scratch, you must first invent the universe.’ - Carl Sagan

[davidmich]

@davidmich

Hi
When would it be valid for scientists to claim that they have created life?In other words what ingredients in nature that constitute the elemental constituents of life would scientists not be permitted to depend on to make the claim that they have created life?
I look forward to your feedback.

Thank you all. Very helpful.