Review - Creating Life in the Lab

It really doesn't matter what method you want to hypothesize, the fact is that it appears that there would be insufficient time. In fact, Biophysicist Hubert Yockey estimated that given the maximum time available for the code to originate, natural selection would have to evaluate 10^55 codes per second to find the code. What known algorithm or process is there that could have done that inside the first life-form, at that rate, and in that period of time? Why is that reasonable given the physics, chemistry, and complexity of the actual situation?

1 vote

#2 - Tue Feb 15, 2011 5:43 PM EST

XNihil0Zer0

It really doesn't matter what method you want to hypothesize

It does if you are proposing design. Evolution(through replication, variation, and selection) is a prerequisite of design. If you'll indulge me in this thought experiment, I'll demonstrate it.

You're in a room with a circle on the floor some distance in front of you. You are given a rubber band. Your goal is to figure out how to stretch the rubber band in order to shoot it, such that it consistently lands in the circle. How do you accomplish this?

3 votes

#2.1 - Tue Feb 15, 2011 6:03 PM EST

Yockey's lame musings have been debunked many times. Firstly he doesn't even stop at simple self-replicator molecules (which do form by chance quickly, even in lab experiments). His math fails to take many factors into account.

In fact, his magnum-opus is to simply calculate the odds of cytochrome-c forming. All that is needed for the proto-bionts is for any of certain proteins to form, and his math explicitly ignores that because it positively refutes his ideology.

See links and items in www.infidels.org/library/modern/richard_carrier/addendaB.html#Yockey

2 votes

#2.2 - Wed Feb 16, 2011 1:43 AM EST

http://arxiv.org/PS_cache/arxiv/pdf/1010/1010.5178v1.pdf

Are you misunderstanding? This is about the genetic code, not the information being encoded. Once a code is established, there are extreme selective pressures to not allow significant changes, since that would corrupt any previously encoded information. The point here is that this code appears to be highly optimized, but yet had insufficient processes or time to have been selected or modified to get to this optimized state. The available phase space of possible codes is large, so why the universal one and not another?

I'll repeat: What known algorithm or process is there that could have done that inside the first life-form, at that rate, and in that period of time? Why is that reasonable given the physics, chemistry, and complexity of the actual situation?

Based on your understanding, how much time would you allow for this to have occurred -- before the first lifeforms started using it?

1 vote

#2.3 - Wed Feb 16, 2011 12:21 PM EST

Alway

^A mathematical proof that there was, indeed, plenty of time.

Life forms don't require some silly 'master code.' Life is so versatile because it can use all sorts of combinations and fare hardly any different than other combinations.

there are extreme selective pressures to not allow significant changes

This is entirely false, DNA is quite flexible. The common occurrences of stop codons means any single codon change can't affect more than a gene or two. As our large quantities of junk DNA shows, our DNA is neither in some sort of fully optimized state, nor is it intolerant of random mutation.

Take prions, for instance. They are an example of one of the most basic life forms, to the point where they are just on the boundary of living/nonliving. They replicate themselves with no requirement for DNA or other genetic material; they are simple proteins capable of self-replication. This, at its core, is all life really needs: the ability to self replicate.

Now, you were asking about a combinatorial optimization algorithm?
http://en.wikipedia.org/wiki/Evolutionary_computation
As it happens, evolutionary computation, a field in computer science derived from evolution, does just that.

In computer science, evolutionary computation is a subfield of artificial intelligence (more particularly computational intelligence) that involves combinatorial optimization problems.

Some applications of evolutionary computation are even used to generate computer programs.

4 votes

#2.4 - Fri Feb 18, 2011 7:00 PM EST

Alway, you are correct -- cept about prions (sort of).

The 'science' of the material presented in the book(s) represents either a most tenuous grasp of the material or an intentional attempt to deceive (well, or a combination thereof).

The code is actually absurdly inefficient. How many codons represent the same stuff.

Like, CGA represents Arg... but so does CGU, CGG, and CGC.

Then we have CUA, CUG, CUC and CUU representing Lau.

But we have UUU and UUC representing Phe AND then have UUG and UUA representing Lau. Oh wait, but we already have CUA, CUG, CUC and CUU representing Lau.

Wait, did CGA, CGU, CGC, and CGG represent Arg? But so does AGA and AGG.

So much for efficiency. We have 64 codon combinations, and 20 amino-acids being represented, and a stop and a trp and that's it. Looks both wasteful AND it introduces an increased risk of errors.

4 votes

#2.5 - Fri Feb 18, 2011 7:39 PM EST

cept about prions (sort of).

If I may expand upon this, what Chirmly probably means is that prions cannot technically reproduce themselves from scratch - they transfer a misfolded protein state to other properly folded proteins. The properly folded proteins required a living cell, DNA, RNA, ribosomes and a host of other proteins to produce them.

But, this is still very important, because it demonstrates that "inheritability" doesn't require nucleic acids, and there are likely a plethora of other more simple chemical examples that can produce this phenomenon as well. And where you have that, you can have selection. And where you have selection, you have evolution. The very first "organism" (so to speak) may have been nothing more than a self-perpetuating chemical reaction that utilized neither amino or nucleic acids.

So the complexity of bacteria is a horrible argument for Intelligent Design. If it was shown that simpler structures than bacteria were not subject to selection, then it would be a fantastic argument. But unfortunately for the ID advocates, the exact opposite is true.

4 votes

#2.6 - Fri Feb 18, 2011 8:10 PM EST

This is about 380 genes, somewhere on the order of 600,000 sequenced base-pairs, that together specify the minimal instruction set required for a living organism.

I assume the book was referring to the hilariously named Mycoplasma laboratorium, which itself is based upon Mycoplasma genitalium - which has 500 or so genes, and which is (and this is vital!) the smallest known genome of any organism that can be grown in free culture. This is a critical distinction, because 380 of those genes are essential for a free living bacterium, and saying that this is the minimum gene count necessary for "life" is flat out incorrect. Heck, the endosymbiont Carsonella ruddii has less than 200 genes.

Depending on various definitions of the word "life", viruses either fall within that definition or they do not. As a biologist, I accept that viruses are in fact alive, because to adopt a definition in which they are not would be to likewise accept that prions are alive, and that is an illogical distinction. And viruses do, in fact, have far fewer genes than bacteria. The smallest known viral genome for an animal virus is the hepatitis delta virus, which produces two proteins.

Additionally, the smallest known viroid is only 220 nucleobases in length.

So, yes, there are "organisms" in the natural world that are far less complex than Mycoplasma. Heck, we also know that ribonucleic acid can catalyze its' own reproduction with no assistance from anything else.

So, as a biologist, I've got to say that any argument advocating intelligent design based solely upon bacteria is extremely short sighted and borderline irresponsible for a scientist to propose. But at least the individuals that wrote this book don't appear to actually be objecting to evolutionary theory - just abiogenesis. That's a little better...I guess. I actually don't have a problem with that, if it turns out to be falsifiable. That would be a wonderful discovery. But it is completely contradictory with the concept of an omnipotent or omniscient God. So I reject it not only from a scientific standpoint but also from a theological one until substantial evidence demonstrates otherwise.

7 votes

#3 - Tue Feb 15, 2011 7:36 PM EST

http://www.informatics.sussex.ac.uk/users/ctf20/dphil_2005/CSNs/Minimal%20Genome/itaya.pdf

Well, you can take your argument up with Craig Venter, since clearly you need to set him straight about biology. Based on their research, this is the minimal gene set that they determined and use as their benchmark. Since clearly this is an estimate, no one is claiming that this is a hard and fast number. Note: M. genitalium is a parasite, and hence is not capable of independent existence for extended periods of time without having certain compounds provided that it can't manufacture independently. Also, the context of this kind of research is to reverse engineer the simplest organism possible and then to create something novel that can be considered alive. Most researchers don't consider viruses to be alive.

This research article shows results consistent with Venter's group:

After you've read the book, I'd love to hear your thoughts. If you actually find an inaccuracy in the book, let me know.

1 vote

#3.1 - Wed Feb 16, 2011 12:11 PM EST

Well, you can take your argument up with Craig Venter, since clearly you need to set him straight about biology.

Venter is a genius and I respect him greatly. But you apparently don't fully understand the limitations of the conclusions that can be drawn from his research.

Based on their research, this is the minimal gene set that they determined and use as their benchmark.

Right, for a bacterium. No biologist in their right mind would claim that the very first form of "life" on this planet was a fully formed, functional bacterial cell that utilized DNA as the genetic material. That's ridiculous. And it is not what abiogenesis proposes or ever has proposed, so any argument in favor of Intelligent Design based on that demonstrates a lack of understanding or confirmational bias.

Note: M. genitalium is a parasite, and hence is not capable of independent existence for extended periods of time without having certain compounds provided that it can't manufacture independently

lol, I know - but guess what? It's still referred to as free-living. I agree though, this is a misleading term and I wish someone would change it. We biologists are notorious for naming things in a manner that is not particularly descriptive or accurate. Which brings me to the next point:

Most researchers don't consider viruses to be alive.

Most? No, far from it. Some do not, which I already mentioned and explained my reason for disagreeing with them. This is an arbitrary distinction because there is no unequivocal definition for "life". All we can do as biologists is describe it. A critical distinction that some people make is that things which are alive have the capability to reproduce themselves without help. This is likewise arbitrary, and illogical, because it would mean that viruses are not alive while self-replicating RNA molecules are, for example.

Viruses straddle the fence on the definition of life. Do they possess genetic material? Yes. Can they reproduce? Yes, but indirectly. Are they self-organizing? Yes. Do they function on negative entropy? Yes. Can they "die"? Yes. But here's a big clincher that I think is more important than all of that: are they subject to natural selection and evolution? YES.

So the distinction is one that is made to make us feel good that we can define life. In reality, life is not easy to define and in reality, life probably cannot be defined. That is a profound realization.

3 votes

#3.2 - Wed Feb 16, 2011 1:03 PM EST

Actually, only 270 genes are necessary, in that organism, for life. Through a painstaking and apparently mind-numbingly meticulous process of knocking-out each and every individual gene in the 380 original gene sequence, the researchers discovered that only 270 were apparently needed.

However, it might be considerably fewer, since it's possible that they could have knocked out 2 or more at a time, because knocking out (for example) gene A might depend on gene B (which relied on gene A or C)... Basically the individual knock-out selection phase experiment was a methodology known and accepted to have it's weaknesses with regard to determining the absolute lowest number of genes in that organism.

However, 270 genes is pretty low for an advanced creature (4 billion years old).

1 vote

#3.3 - Wed Feb 16, 2011 5:18 PM EST

Actually, only 270 genes are necessary, in that organism, for life. Through a painstaking and apparently mind-numbingly meticulous process of knocking-out each and every individual gene in the 380 original gene sequence, the researchers discovered that only 270 were apparently needed.

Hey Chirmly do you by chance have a link to that? Last I checked it was still 380, so I'd be really interested in reading about the additional genes that they knocked out. That's totally awesome.

1 vote

#3.4 - Wed Feb 16, 2011 6:50 PM EST

Eric, indeed... one link is in :

protist.biology.washington.edu/biol355-wtr08/papers/PAPER%202%20Cell%20evolution.pdf

or a more technical source :

Glass, J. I. et al. Essential genes of a minimal bacterium. Proc. Natl Acad. Sci. USA 103, 425-430 (2006)

avail kind of at www.ncbi.nlm.nih.gov/pmc/articles/PMC1324956/ (seems like the entire paper is there)...

1 vote

#3.5 - Wed Feb 16, 2011 7:20 PM EST

Thanks Chirmly you rock I'll read it in a few hours.

1 vote

#3.6 - Wed Feb 16, 2011 7:41 PM EST

The book can basically be summed as argument from incredulity and appeal to ignorance with liberal sprinklings of strawman and heaps of Texas-Sharpshooter fallacy. Other than that, I'm sure it's wonderful.

2 votes

#4 - Wed Feb 16, 2011 1:45 AM EST

Clearly you are speaking from ignorance about the book and the author. Why not actually consider what they have to say before trying to smear them?

1 vote

#4.1 - Wed Feb 16, 2011 12:14 PM EST

Ok, does he not use the 10^70th figure, the alleged homochirality 'problem' and the cellular-membrane arguments? Those were debunked about 15 years ago.

His argument, as in his other books, is basically 'we don't see how this could have happened" right?

3 votes

#4.2 - Wed Feb 16, 2011 12:27 PM EST

Randi is a girl

Crab People, Crab People; look like crabs, talk like people.

2 votes

#5 - Wed Feb 16, 2011 12:06 PM EST

ruthlessmoose

it is very unlikely that life could have formed from undirected, naturalistic processes. Dr. Rana makes a solid case that instead of providing support for an evolutionary explanation to the Origin of Life problem, we now have solid empirical evidence from the process of developing and studying life in the lab that shows that the creation of life requires intelligent input and rational design.

At least they understand what this study would actually evidence.

1 vote

#6 - Thu Feb 17, 2011 1:47 PM EST

UNA_Lion

Personally, I've no issue with genetic manipulation, though don't think we'll ever be able to "create" life from scratch.

#7 - Thu Feb 17, 2011 5:39 PM EST

We've created DNA from scratch -- sort of.

We copied a known DNA sequence, molecule by molecule. We took a sequence, and assembled it from the raw components (ie., we didn't take DNA and break it down to put it together).

We put the DNA back into a cell (of a different organism) and it replicated and survived.

It's a first step, but, considering we have only had the technology to do this for about 5-10 years, it's a great first step.

We could synthesize each portion of each organelle too, but the DNA is the hardest.

2 votes

#7.1 - Thu Feb 17, 2011 7:28 PM EST

UNA_Lion

That is impressive. What I don't think we will achieve is to put all those components together and make it actually live as an organism.

Meh, for that matter I don't think we'll ever leave our solar system either (with manned craft), but that's another story.

#7.2 - Thu Feb 17, 2011 7:35 PM EST

UNA, we put the DNA into the cell and it lived. Is there a portion that's harder to make than the DNA?

2 votes

#7.3 - Thu Feb 17, 2011 8:16 PM EST