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cameron marical

Surely, evidence of everything alive (especially humans) supports Darwin's theory?

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not entirly machines. I can decide to destory myself, or where i want to go or eat. A microbe machine works strictly on chemistry. A microbe seems to me that it works much more like a computer program and if statements. Using magnetic pulls and chemistry to cause its actions to take place. Its hard to explain. The best way i can explain what i am seeing to another person is by using computer programs as examples.

 

You're not different. Your choices are just a lot harder to predict, because the physical processes in your brain determining them are much more complicated.


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We're not really all that complicated compared to other living things. We're smarter though.

 

I wouldn't say we're the most complex life form over all (though we might be, I just don't know), but surely we can at least say we're a lot more complicated than one-celled organisms?

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We're not really all that complicated compared to other living things. We're smarter though.

 

Well, that remains to be seen. After all... This thread has people still to this day challenging the idea of evolution. :doh:

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not entirly machines. I can decide to destory myself, or where i want to go or eat. A microbe machine works strictly on chemistry. A microbe seems to me that it works much more like a computer program and if statements. Using magnetic pulls and chemistry to cause its actions to take place. Its hard to explain. The best way i can explain what i am seeing to another person is by using computer programs as examples.

 

Cells can decide to destroy themselves as well. This is called apoptosis. Cells decide what to eat and where to go. You too work strictly on chemistry. Feel free to point out what process you have that isn't a chemical process.


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I wouldn't say we're the most complex life form over all (though we might be, I just don't know), but surely we can at least say we're a lot more complicated than one-celled organisms?

 

I'm not sure. By a measure of DNA or of number of different proteins, we get beaten all the time by other multicellular life. I don't know about single-celled organisms though, but I imagine the colonial ones could be about as complex.


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Well, that remains to be seen. After all... This thread has people still to this day challenging the idea of evolution. :doh:

 

I don't think acceptance of evolution is a particularly good measure of intelligence.

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I don't think acceptance of evolution is a particularly good measure of intelligence.

Okay, but a lack of acceptance sure is.

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Okay, but a lack of acceptance sure is.

 

Absolutely brilliant! I must remember that. However, has not the point been proven over and over again in different fields, that evolution (as we understand it today) is in fact supported by all life on earth. I suppose this has become more of a thread for adding to the mass of information, which while a tad excessive, is very interesting. I think that were it not for discretion of the religious community, a lot of these posts ought to be fused into a sticky titled- Evolution is true; get on with your life. (either that, or go to baskin robbins, both are excellent options!)

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Okay, but a lack of acceptance sure is.

 

I agree. Intelligent people don't tend to accept something just because someone told them so, they like to see the evidence and judge for themselves. An intelligent person who does not have enough biology background to see the evidence for evolution is unlikely to accept it simply because its the scientific consensus.

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I think that being intelligent is more of a choice than a set in stone inherit.

 

Yes, some people do naturally have a high level of intelligence due to heredity, but many others who are born with that level of intelligence never even try to go up to it. I cant name of one person in my school that is as curious as they can be, wich, may not be the only measurement of intelligence, but i beleive it is a great necessity to have a high curiosity level in order to establish a high intelligence level.

 

a lack of acceptance is to me a sign of not being interested or wanting to beleive something else.

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But I struggle to understand why only chemical analogues are important to “prebiotic evolution.” Life—biological life, anyway—is more than just little cells full of vigorous chemicals…much more!

 

Actually, no. Single celled organisms are alive and are "just little cells full" of chemicals such that the cell can do the 4 activities that, together, constitute life.

 

I can’t so lightly pass over the obvious requirement of genes to make living things biologically alive.

 

That's not a requirement. Look at the characteristics the define something as biologically alive. Those characteristics do not require genes to get the characteristics. What you've done is make a strawman requirement based on modern life.

 

Still, I’ll respect your POV, made all the more credible by a recent article coauthored by Harold Morowitz.

 

Whenever I see Harold Morowitz attach his name to something I pay attention; he of course is a major player in p-chem and biochem.

 

You do realize this is the Argument from Authority, don't you? I think you are thinking of an article in the June 2007 issue of SciAm, by Robert Shapiro.

 

Here are a few of my observations of this article:

 

1. The formation of protocells in the early stages of abiogenesis may not have been necessary, because the pore spaces in rocks could have provided the needed enclosure to facilitate certain aspects of prebiotic chemistry.

 

Remember my claim. I never claimed that protocells were actually how life started. I claimed that they are one way to get life from non-life. However, the ease with which protocells form and the resemblance of fossilized early cells to artificially fossilized protocells makes it likely that protocells from proteinoids was, at least, one of the ways early cells came into existence.

 

2. Morowitz and his crew prefer the “Metabolism First” hypothesis to the “Genetic First/RNA World” hypothesis, mainly because they see life as system of chemical analogues, with its perfunctory genetics coming along naturally and as needed in the course of abiogenesis (but just how that happened, they do not elaborate).

 

And the protocells provide part of the "how". 1. The protocells will make DNA/RNA. Otherwise, there is no abiogenetic chemistry that will do this. 2. Because

 

5. The authors are predisposed to see abiogenesis as a chemical necessity rather than a matter of pure chance.

 

I agree. The chemistry to first make proteins from amino acids and then have them make cells is just too simple not to happen.

 

At some critical point in the process of abiogenesis—the point where biological life qualified as being truly alive—there had to be “invented” a genetic language capable of recording a cell’s building instructions in digital code. And not only that, but also a system had to be “invented” for transcribing and translating that digital code into a cell’s infrastructure.

 

Nope. You don't need that. The chemical interactions among the proteins and between proteins and water will build the cell. Reproduction also doesn't need a genetic language. Genetics (really what you are describing is "directed protein synthesis") evolves later and provides a selective advantage by reducing variation among offspring.

 

Do you know of any principle of nature—the kind of principle that scientists should be looking for—that accounts for the reduction of chemical analogues into a digital code? Not even Morowitz can persuade me to accept that such an incredible feat should be regarded as perfunctory in the process of abiogenesis.

 

Yes. It involves how proteins and the bases of RNA/DNA interact. The principle is hydrogen bonding. As noted, proteins with a lot of lycine will associate with DNA/RNA with regions of poly U and poly C. Proteins with a lot of arginine, OTOH, associate with DNA/RNA with regions of poly A and poly G.

 

In terms of transfer RNA (the RNA in the cytosol that carries specific amino acids to the mRNA in ribosomes), work has been done associating conformation with specific amino acids bound to the tRNA and the hydrogen bonding to the mRNA codon: 4. Margaret E. Saks, Jeffrey R. Sampson, John Abelson Evolution of a transfer RNA gene through a point mutation in the anticodon. Science, 279, Number 5357 Issue of 13 March 1998, pp. 1665 - 1670

 

The protocells are not "chemical analogues", but real cells. Remember, the metabolic processes in cells -- such as the Krebs cycle -- are catalyzed by proteins (enzymes). As it happens, in the internal ordering of proteins as the form from amino acids, it is inevitable that you are going to get proteins that catalyze the chemical reactions in the Krebs cycle. The catalytic rate may not be great, but all you need is some catalytic activity. Better catalytic activity can be generated later by natural selection.


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Okay, but a lack of acceptance sure is.

 

Not necessarily. It can merely indicate an emotional need or bias overwhelming the intellect. I think we can all agree that Albert Einstein was one of the most intelligent people ever. Yet he too rejected a well-supported theory: quantum mechanics (even tho his Nobel Prize was for a paper laying the foundations of QM!). The indeterminism in QM conflicted with his emotional desire that the universe be determined: "God does not play dice."


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At least you're getting two POVs: genes first v. metabolism first. It will take a lot more knowledge to see who's right.

 

It does not have to be an "either-or" proposition. The RNA World could have been happening alongside the protocells. That is, RNA molecules could have been making 1) more RNA and 2) proteins. (Remember, all you need is the RNA in ribosomes to make a protein. It will not be directed by mRNA, but the ribosome will make protein without the mRNA.) The protocells could then have absorbed the proto-ribosome and had it making proteins inside the cell.

 

BTW, if you want a step-by-step summary of how you get a "digital code" by Darwinian evolution and directed protein synthesis, read this article:

1. AM Poole, DC Jeffares, D Penney, The path from the RNA world. J. Molecular Evolution 46: 1-17, 1998.

 

You'll probably have to go to a university library. I have a photocopy of the article but not a digital copy.

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Actually, no. Single celled organisms are alive and are "just little cells full" of chemicals such that the cell can do the 4 activities that, together, constitute life.

If you say so. But I'm talking about biological life, the kind that with hereditary tools. Your kind of life could include crystals and sea form. I'm more interested in the kind of life that carries digital information forward from generation to generation.

 

That's not a requirement. Look at the characteristics the define something as biologically alive. Those characteristics do not require genes to get the characteristics. What you've done is make a strawman requirement based on modern life.

Please show me a form of biological life that doesn't require genetics. Even viruses require genetics, and they are not regarded as living organisms.

 

Still, I’ll respect your POV, made all the more credible by a recent article coauthored by Harold Morowitz.You do realize this is the Argument from Authority, don't you? I think you are thinking of an article in the June 2007 issue of SciAm, by Robert Shapiro.

No. Here it is in the June 2009 issue of American Scientist. It's your cup of tea. Interesting that the authors stay clear of any mention of how chemical analogues get transformed into digital information.

 

Remember my claim. I never claimed that protocells were actually how life started. I claimed that they are one way to get life from non-life. However, the ease with which protocells form and the resemblance of fossilized early cells to artificially fossilized protocells makes it likely that protocells from proteinoids was, at least, one of the ways early cells came into existence.

This is fine...for the chemical analogues. How about the digital information?

 

And the protocells provide part of the "how". 1. The protocells will make DNA/RNA. Otherwise, there is no abiogenetic chemistry that will do this. 2. Because

Just because? You confidence in those protocells exceeds mine by a nautical mile. It is a "Poof!" theory—Poof! And there you are with a digital genetic alphabet. From my POV, it badly needs to to be explained beyond the simple Poof!

 

I agree. The chemistry to first make proteins from amino acids and then have them make cells is just too simple not to happen.

I'm fine with that.

 

The chemical interactions among the proteins and between proteins and water will build the cell. Reproduction also doesn't need a genetic language. Genetics (really what you are describing is "directed protein synthesis") evolves later and provides a selective advantage by reducing variation among offspring.

"Evolves later"? But how?

 

The principle is hydrogen bonding.

That might explain how a nucleic acid is formed, but it doesn't explain how a genetic alphabet is formed.

 

As noted, proteins with a lot of lycine will associate with DNA/RNA with regions of poly U and poly C. Proteins with a lot of arginine, OTOH, associate with DNA/RNA with regions of poly A and poly G.

Yes, but that doesn't get you very far toward a genetic alphabet.

 

In terms of transfer RNA (the RNA in the cytosol that carries specific amino acids to the mRNA in ribosomes), work has been done associating conformation with specific amino acids bound to the tRNA and the hydrogen bonding to the mRNA codon: 4. Margaret E. Saks, Jeffrey R. Sampson, John Abelson Evolution of a transfer RNA gene through a point mutation in the anticodon. Science, 279, Number 5357 Issue of 13 March 1998, pp. 1665 - 1670

Once again, I have no quibble over how chemical analogues are formed. It's the digital language that moves across generational lines that interests me.

 

BTW, if you want a step-by-step summary of how you get a "digital code" by Darwinian evolution and directed protein synthesis, read this article:

1. AM Poole, DC Jeffares, D Penney, The path from the RNA world. J. Molecular Evolution 46: 1-17, 1998.

 

You'll probably have to go to a university library. I have a photocopy of the article but not a digital copy.

I'll try to get a copy of it and check it out. I managed to get a copy of Fran Crick's 1968 paper "The Origin of the Genetic Code" (J. Mol. Biol. 1968, 38, pp. 367-379). It will be interesting to see how Poole et al. differ in their explanation.

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Your kind of life could include crystals and sea form.

What do you mean by "sea form"? I don't recall hearing this term before.

 

/strokes the chin of intrigue.

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Please show me a form of biological life that doesn't require genetics. Even viruses require genetics, and they are not regarded as living organisms.

 

Just because it's not around today doesn't mean it's not possible. If we judge solely by what exists today, we'd say no terrestrial animal can weigh more than an African elephant. Given than molecules don't fossilize well, we're left trying to judge the past by a paltry selection of species that happen to be currently around, which is never a good idea.

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What do you mean by "sea form"? I don't recall hearing this term before.

 

/strokes the chin of intrigue.

I meant "sea foam," of course.


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Just because it's not around today doesn't mean it's not possible. If we judge solely by what exists today, we'd say no terrestrial animal can weigh more than an African elephant. Given than molecules don't fossilize well, we're left trying to judge the past by a paltry selection of species that happen to be currently around, which is never a good idea.

I like this theory. So, Mokele, should we just believe in those highly improbable phantoms of the past? Because they just had to be there?

 

There are two schools of thought regarding abiogenesis: 1) the school of inevitable emergence, and 2) the school of the one-off event. I happen to be persuaded by the second school, but this is OT on this thread.

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So, Mokele, should we just believe in those highly improbable phantoms of the past? Because they just had to be there?

 

No, but we cannot rule them out on the basis of lack of current taxa. That doesn't mean they existed. It doesn't even mean that if they did exist, they were anything but a dead end. But it also means we cannot simply assume they did not.

 

By analogy, we have no fossils of definitively arboreal dinosaurs (at least outside of birds), but we cannot rule out the possibility that they existed and have either not been found or not been preserved. An entire sub-field of paleontology relies on this, specifically the claim for 'trees-down' evolution of flight in birds.

 

There are two schools of thought regarding abiogenesis: 1) the school of inevitable emergence, and 2) the school of the one-off event. I happen to be persuaded by the second school, but this is OT on this thread.

 

False dichotomy. Something can happen more than once and not be 'inevitable'.

 

Consider powered flight: it's happened 4 times (5 if you count our use of technology), but it's hardly an inevitability (I strongly doubt we'll ever see flying turtles).

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False dichotomy. Something can happen more than once and not be 'inevitable'.

 

Consider powered flight: it's happened 4 times (5 if you count our use of technology), but it's hardly an inevitability (I strongly doubt we'll ever see flying turtles).

Wait, wait! My grandson has one: http://www.growingtreetoys.com/product/flying-turtle

 

More to the point: How would you know if abiogenesis was an inevitable emergence or a one-off event? (If this is too OT I'd be willing to start a new thread for it. The old one on abiogenesis got scotched by a nervous mod.)

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Well, once we accomplish it in the lab, repeat the experiment with various parameters, both slight variations of the sucessful one and more dramatic variations based on the geochemistry of planets we know of (hopefully by this point we'll have better information about the exoplanets we've found so far). This could give a good estimate of how likely it is.

 

More directly, in the far future once we're out in the void playing Star Trek, we can count up the planets with life versus those without, then discount any planets which gained life from elsewhere, either via panspermia or actual colonization by other spacefaring races.

 

Of course, this means we can't know *now*, but the same thing can be said for a lot of issues in science, and there's still plenty of interesting work to be done on the subject until then.

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Well, once we accomplish it in the lab, repeat the experiment with various parameters, both slight variations of the sucessful one and more dramatic variations based on the geochemistry of planets we know of (hopefully by this point we'll have better information about the exoplanets we've found so far). This could give a good estimate of how likely it is.

About as likely as Jesus coming again to stomp out the Easter Bunny. Mokele, I think you have an unwarranted faith in The Church of Miller-Urey. What you expect to accomplish in your lab is the discovery of the magical ingredients of your so-called prebiotic soup. I don't believe that will ever happen, because I think abiogenesis was a one-off event.

 

More directly, in the far future once we're out in the void playing Star Trek, we can count up the planets with life versus those without, then discount any planets which gained life from elsewhere, either via panspermia or actual colonization by other spacefaring races.

 

Of course, this means we can't know *now*, but the same thing can be said for a lot of issues in science, and there's still plenty of interesting work to be done on the subject until then.

Yes, until then, which assumes of course that Homo sapiens will survive the next mass-extinction. And the likelihood of our extinction would seem to be much greater than the likelihood of a real Star Trek adventure.

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About as likely as Jesus coming again to stomp out the Easter Bunny. Mokele, I think you have an unwarranted faith in The Church of Miller-Urey. What you expect to accomplish in your lab is the discovery of the magical ingredients of your so-called prebiotic soup. I don't believe that will ever happen, because I think abiogenesis was a one-off event.

 

And?

 

How do you prove your claim? And how do I prove mine? The only way is to keep trying. Maybe I'm right, and that effort will lead to success. Maybe you're right, and that effort will come to naught.

 

But right now, there's not sufficient evidence for either of us to be considered right, so all we can do is keep trying.

 

Well, I say 'we', but I really mean 'people other than me, who don't fall asleep the moment a lecture drops below the whole-organism level'.

 

Yes, until then, which assumes of course that Homo sapiens will survive the next mass-extinction. And the likelihood of our extinction would seem to be much greater than the likelihood of a real Star Trek adventure.

 

I dunno, we're persistent little bastards, like mammalian cockroaches.

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In terms of transfer RNA (the RNA in the cytosol that carries specific amino acids to the mRNA in ribosomes), work has been done associating conformation with specific amino acids bound to the tRNA and the hydrogen bonding to the mRNA codon: 4. Margaret E. Saks, Jeffrey R. Sampson, John Abelson Evolution of a transfer RNA gene through a point mutation in the anticodon. Science, 279, Number 5357 Issue of 13 March 1998, pp. 1665 - 1670

BTW, if you want a step-by-step summary of how you get a "digital code" by Darwinian evolution and directed protein synthesis, read this article:

AM Poole, DC Jeffares, D Penney, The path from the RNA world. J. Molecular Evolution 46: 1-17, 1998.

luscapa, one of our posters, GDG, was kind enough to seed me a PDF of the Poole et al. article. I’m still reading it over, slowly, because I am not as good a biochemist or p-chemist as either you or those authors. Their main idea here is that they were able to identify a hypothetical route of stereochemistry that could have possibly led to the adoption of a genetic code and the first “ribo-organism RNA genome.” Their consideration even includes a route from prebiotic conditions (late RNA-world phase) to eukaryotic organisms before degenerating (my term) into prokaryotes (I’ve never thought of that).

 

I think their work is good and necessary. It’s hypothetical thinking in the right direction. If they are right then they would agree with Stuart Kauffman (1995, At Home in the Universe, p. 45):

 

There are compelling reasons to believe that whenever a collection of chemicals contains enough different kinds of molecules, a metabolism will crystallize from the broth. If this argument is correct, metabolic networks need not be built one component at a time; they can spring up full-grown from a primordial soup. Order for free, I call it. If I am right, the motto of life is not We the improbable, but We the expected.

 

I am not so easily led down that hopeful path to the garden where “metabolic networks…spring up full-grown from a primordial soup.” Yes, I know how much you, Morowitz, and a whole lot of other good chemists believe in your chemicals. I wouldn’t expect anything else. If you all are right then science is on the threshold of discovering a new natural law: Chemical analogues, totally on their own and given the right conditions, can indeed reduce themselves to purely digital coded information.

 

I’d say “Golly, gee whitacers, Mr. Science!” to that. I’d also say “Now, what about cold fusion?”

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If you say so. But I'm talking about biological life, the kind that with hereditary tools. Your kind of life could include crystals and sea form.

 

No, the definition of life does NOT include crystals and sea foam. Remember, all four characteristics have to be present. Crystals grow, but they don't respond to stimuli or have metabolism. Sea foam reproduces and responds to stimuli, but doesn't have metabolism. Fire grows, reproduces, responds to stimuli, and has catabolism. But it doesn't have metabolism. Only biological life, so far, has all four.

 

What you have done is attach an unnecessary characteristic to "life" -- hereditary tools. In particular, you demand that life " carries digital information forward from generation to generation." That isn't necessary to be alive. The protocells have heredity and carry information from generation to generation. You have never countered the arguments and data concerning this.

 

Please show me a form of biological life that doesn't require genetics.

 

LOL! You are still hung up on what I said you were: modern life. Thanks for proving my point. Also showing that you aren't really listening to what people are saying. All modern life has directed protein synthesis. But that doesn't mean that all life must. And I just did show you a form of life that doesn't require genetics! The protocells.

 

 

American Scientist is a completely different publication than Scientific American! No wonder I couldn't find it looking at Scientific American, you got the magazine wrong.

 

It's your cup of tea. Interesting that the authors stay clear of any mention of how chemical analogues get transformed into digital information.

 

What are "chemical analogues" to you? But actually, the article did mention it:

"Shelley Copley at the University of Colorado at Boulder has been sorting out the intermediate chemistry leading to the current nucleic acid–protein system of genetic coding, with an eye toward resolving the chicken-and-egg problem. These experiments represent a major paradigm shift from the top-down control envisioned in RNA World scenarios. Rather than supposing that a few large RNA molecules control the adaptation of a passive small-molecule reaction network, Copley supposes that whole networks of intermediate molecules support each other on the path toward complexity. In this experimental setting, networks of small and randomly synthesized amino acids and single RNA units aid each others’ formation, assembly into strings and evolution of catalytic capacity. Both types of molecules grow long together. Complexity, adaptation and control are distributed in such networks, rather than concentrated in one molecular species or reaction type. Distributed control is likely to be a central paradigm in the development of Metabolism First as a viable theory. We eagerly anticipate more experimental efforts like these to explore the many facets of small-molecule system organization."

 

Notice the bold. What you call "digital information" is directed protein synthesis. Instead of having this "poof" into existence, Copley is looking at proteins and RNA formed by chemical reactions. The formation of proteins is exactly what the protocells is all about. Proteins are formed from single amino acids by heating. You don't get "small proteins", but large ones. The proteins then make RNA. The RNA in turn then helps to make proteins.

 

This is fine...for the chemical analogues. How about the digital information?

 

The protocells are living cells, not "chemical analogues". For one thing, the protocells are composed of chemicals, not "analogues".

 

 

It is a "Poof!" theory—Poof! And there you are with a digital genetic alphabet.

 

No, far from "poof". First you have the protocells making RNA. Now you have the RNA for the RNA World Hypothesis. Second, you have the observation that proteins with preponderance of particular amino acids associate with RNA/DNA with a preponderance of particular bases. That's the start of the type of association you need for directed protein synthesis. Then you have the observation that ribosomes with just RNA can make proteins. From that you move to particular RNAs covalently binding particular amino acids. That's transfer RNA. NOW you have a "digital genetic alphabet". Many, many steps in between.

 

luscapa, one of our posters, GDG, was kind enough to seed me a PDF of the Poole et al. article.

 

I wish he'd sent me one. But I found it on my own.

 

Their consideration even includes a route from prebiotic conditions (late RNA-world phase) to eukaryotic organisms before degenerating (my term) into prokaryotes (I’ve never thought of that).

 

Other people have. There is an extensive literature proposing the eukaryotes came first and that prokaryotes were derived from them as the introns were excised.

 

I am not so easily led down that hopeful path to the garden where “metabolic networks…spring up full-grown from a primordial soup.”

 

That's exactly what happens with the protocells. Because each protocell is formed from quintillions of proteins, each has at least some proteins with all the catalytic properties of a metabolic network. Or several metabolic networks. Those networks would not be efficient as those in modern cells (product of 3.8 billion years of evolution), but the evidence is that the metabolic networks necessary for life do exist within the protocells. After all, there is the metabolic network to make proteins and another to make nucleic acids.

 

This is just one of the cool things about the protocells: they provide, ready-made in just two steps, the metabolism and metabolic networks of life.

 

What you really mean by "digital information" is that a particular RNA molecule with a particular anti-codon (3 bases), always binds to a particular amino acid. This RNA molecule with the amino acid attached (tRNA) then binds to the 3 complementary bases on a messenger RNA molecule. Let's discuss the Poole et. al. article because it gives a pathway for this to happen.

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I wish he'd sent me one. But I found it on my own.

 

Sorry, thought you already had one. :embarass:

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No, the definition of life does NOT include crystals and sea foam. Remember, all four characteristics have to be present. Crystals grow, but they don't respond to stimuli or have metabolism. Sea foam reproduces and responds to stimuli, but doesn't have metabolism. Fire grows, reproduces, responds to stimuli, and has catabolism. But it doesn't have metabolism. Only biological life, so far, has all four.

I think your point is that, along the course of abiogenesis, life existed before the first living organism emerged. I don't have a big problem with that, because it wasn’t biological life. When we talk about biological life we usually talk about living organisms. Yet we don't stick to the rules, because we often refer to living or dead viruses, which don't qualify as living organisms. So, what's the precise meaning of your definition of life? Even if your chemicals scored on all four points, the fun didn't start until the first organism showed up.

 

What you have done is attach an unnecessary characteristic to "life" -- hereditary tools. In particular, you demand that life " carries digital information forward from generation to generation." That isn't necessary to be alive. The protocells have heredity and carry information from generation to generation. You have never countered the arguments and data concerning this.....And I just did show you a form of life that doesn't require genetics! The protocells.

So what? Chemical information is propagated and expressed by the growth of crystals. And it could have metabolism, too, if you wanted to play around with words. None of this however explains how the first living organism popped out of one of your "living" protocells.

 

American Scientist is a completely different publication than Scientific American! No wonder I couldn't find it looking at Scientific American, you got the magazine wrong.

Who, other than you, said anything about Scientific American? Go back and take a look.

 

What are "chemical analogues" to you? ...

 

The protocells are living cells, not "chemical analogues". For one thing, the protocells are composed of chemicals, not "analogues".

All chemicals are analogues. In the case of ribonucleic acids the DNA or RNA molecules are analogues, while the information they carry is digital. Remember, genes are "pure digital information" (Dawkins); the chemical analogues make up the physical infrastructure that holds the digital information. You could have two DNA molecules, identical down to every chemical analogue, including the hydrogen bonds, and each carry a different cache of digitally coded instructions, because the order of nucleotides (digital bits) would be different.

 

No, far from "poof". First you have the protocells making RNA. Now you have the RNA for the RNA World Hypothesis. Second, you have the observation that proteins with preponderance of particular amino acids associate with RNA/DNA with a preponderance of particular bases. That's the start of the type of association you need for directed protein synthesis. Then you have the observation that ribosomes with just RNA can make proteins. From that you move to particular RNAs covalently binding particular amino acids. That's transfer RNA. NOW you have a "digital genetic alphabet". Many, many steps in between.

Oops! There’s that “poof” again: “…NOW you have a "digital genetic alphabet". I’m not convinced.

 

There is an extensive literature proposing the eukaryotes came first and that prokaryotes were derived from them as the introns were excised.

I’d like to learn more about that. Before that happened, though, the information carried by the chemical analogues had to be reduced to digital code using a 4^3 digital alphabet.

 

That's exactly what happens with the protocells. Because each protocell is formed from quintillions of proteins, each has at least some proteins with all the catalytic properties of a metabolic network. Or several metabolic networks. Those networks would not be efficient as those in modern cells (product of 3.8 billion years of evolution), but the evidence is that the metabolic networks necessary for life do exist within the protocells. After all, there is the metabolic network to make proteins and another to make nucleic acids.

 

This is just one of the cool things about the protocells: they provide, ready-made in just two steps, the metabolism and metabolic networks of life.

 

What you really mean by "digital information" is that a particular RNA molecule with a particular anti-codon (3 bases), always binds to a particular amino acid. This RNA molecule with the amino acid attached (tRNA) then binds to the 3 complementary bases on a messenger RNA molecule. Let's discuss the Poole et. al. article because it gives a pathway for this to happen.

Yes, and I think it is an important hypothesis. There had to a pathway of some kind that led from soup to nuts; I don’t deny that. I don’t think there was a “poof.” Poole et al. is a worthy effort, but it’s also a testament to how little we know about abiogenesis. What's going on in the lab? I’m still waiting for that biological version of the Miller–Urey experiment. Come on, you chemists, make it happen with your chemical analogues! They're all just a bunch of electrons flowing down hill, anyway. What’s taking you so long?

Edited by scrappy

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