Abiogenesis

[iNow]

Speaking of evolution...

 

 

 

http://www.newscientist.com/article/dn16382-artificial-molecule-evolves-in-the-lab.html?DCMP=OTC-rss&nsref=online-news

Artificial molecule evolves in the lab

 

A new molecule that performs the essential function of life – self-replication – could shed light on the origin of all living things.

 

If that wasn't enough, the laboratory-born ribonucleic acid (RNA) strand evolves in a test tube to double itself ever more swiftly.

 

"Obviously what we're trying to do is make a biology," says Gerald Joyce, a biochemist at the Scripps Research Institute in La Jolla, California. He hopes to imbue his team's molecule with all the fundamental properties of life: self-replication, evolution, and function.

<more at link>

 

While the biologists played a large role in what the molecules did, it's just another fantastic piece of evidence which is testable and adds to the richness and vastness of the existing theories (in the scientific sense).

[padren]

I find the trouble people seem to have with the 'probability' of abiogenesis is in understanding the mechanisms involved and how they reduce the unlikeliness.

 

For example, if you were to consider the moon, inside a block of three dimensional space just large enough to contain it (a cube) and assumed say, the random chance of each cubic foot of space within that volume other "either containing rock or not containing rock" to create such a spherical form - the statistical odds of it being a sphere seem ridiculously nil.

 

It would be like taking the pieces of a watch and tossing it in a bucket, shaking it around, and ending up with a working watch.

 

However, we know enough about the nature of about the materials that make up the moon, how they become malleable when hot, and the effects of gravity - especially over time, to see how a very simple natural process could lead to this outcome far far far more easily.

 

 

While we haven't uncovered all the the natural processes involved in abiogenesis, research has shown a number of them (previously cited youtube videos for instance) remarkably ease the odds.

[npts2020]

I always wondered how you come up with the odds of any process occurring without fairly fully understanding that process to begin with.

[Mr Skeptic]

I always wondered how you come up with the odds of any process occurring without fairly fully understanding that process to begin with.

 

It is called an argument from ignorance. And as you say, an argument from ignorance is only convincing when we are very knowledgeable about the subject.

[Sione]

This is nice movie explaining it the way I come to understand it. The Origin of Life - Abiogenesis -http://nz.youtube.com/watch?v=U6QYDdgP9eg

 

The key words are: chance, lipids, fatty acids...

 

 

It seems you are all talking around the real question. Where did the first cell come from . This story about phospho-lipids spontaneously forming cell membranes is beside the point.

 

A cell is more specifically complex than anything man can dream of making so whether the story you tell is correct or not is irrelevant, finding a clay pit does not mean somewhere a brick wall has built itself.

 

On the other hand is this also kind of true, in a way that we can't really grasp, or we find it hard to believe, the sheer complexity this simple mechanism apparently leads to. Thought, this person seem to suggest God of Bible did it while I think it is still in the scope of chance, time and natural selection, this Goddess I call - "Princess Chance".

Edited January 16, 2009 by Sione

[scrappy]

This is nice movie explaining it the way I come to understand it. The Origin of Life - Abiogenesis -http://nz.youtube.com/watch?v=U6QYDdgP9eg

This video claims to explain the origin of the genetic code. Please take a closer look at it and tell me where it actually explains the code's origin.

[Mr Skeptic]

This video claims to explain the origin of the genetic code. Please take a closer look at it and tell me where it actually explains the code's origin.

 

This website claims to explain the origin of the genetic code. Please take a closer look at it and tell me where it actually explains the code's origin.

http://www.answersingenesis.org/

[scrappy]

This website claims to explain the origin of the genetic code. Please take a closer look at it and tell me where it actually explains the code's origin.

http://www.answersingenesis.org/

Unless this is span I really don't understand your rely.

[Mr Skeptic]

Unless this is span I really don't understand your rely.

 

That the "god did it" explanation has nothing in support of it either -- at least attempts to explain abiogenesis tries to give a real explanation. Look at it this way "chance did it" and "god did it" are similar explanations, and equally useless. However, abiogenesis theories try to figure out how chance could have done it, but religious people never try to figure out how god might have done it. Yet religious people think "chance did it" is an unacceptable explanation because it doesn't explain how, but are perfectly happy with "god did it" despite that it doesn't explain how either.

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Merged post follows:

Consecutive posts merged

Oh, and if anyone tells you they know how life started, that is a bunch of bull. There are many theories and no one has demonstrated which is true. Currently, all anyone who is honest can offer is how life may have started.

[mooeypoo]

I think you (all, actually) should read Richard Dawkin's book "The Selfish Gene".

It explains how Abiogenesis is possible and not with so much chance, as with just variations of molecules. Molecules are assembled and dissemble, etc, and it's only a matter of time in such a huge number-game for 1 type of molecule to have the "property" of, just, quite simple, multiplying itself.

 

When that happens, the molecule replicates, and replicates, etc etc, but mistakes always happen in replication - which is where a very VERY basic version of evolution is the process.

 

It's a very good read.

[Sione]

This video claims to explain the origin of the genetic code. Please take a closer look at it and tell me where it actually explains the code's origin.

 

Are you asserting something is wrong with proposed theory, or you just missed to notice that part? Anyway, here how it goes:

 

1.) lipid vesicles that can grow and divide.

(this is enough to explain Abiogenesis, as spontaneous formation of self-replicating molecule aka. LIFE.)

 

2.) genetic code = nucleotide polymers that can self-replicate.

(this is also enough to explain Abiogenesis, as spontaneous formation of self-replicating molecule aka. LIFE.)

 

 

Origin of genetic code: "The pre-biotic environment contained many different types of nucleotides beside DNA and RNA. Recent experiments have shown that some of these are capable of spontaneous polymerization, such as Phosphoramidate DNA."

 

 

Fatty acid vesicles are permeable to nucleotide monomers, but not polymers and once we have 2nd inside the 1st and if it can divide and split genetic material, then we can call it a CELL. I thought everyone else was referring to similar kind of theories, is this is something new?

 

 

I think you (all' date=' actually) should read Richard Dawkin's book "The Selfish Gene".

It explains how Abiogenesis is possible and not with so much chance, as with just variations of molecules. Molecules are assembled and dissemble, etc, and it's only a matter of time in such a huge number-game for 1 type of molecule to have the "property" of, just, quite simple, multiplying itself.

[/quote']

 

I agree with you, but there are two ways to think about chance.

 

 

Ultimately, all these complex structures will be simply an effect of even simpler mechanism - interaction of electromagnetic fields - that leads to bonding and more importantly the GEOMETRY of these molecules. In that sense, you could say it was no matter of chance at all, you could even say the life mechanics is directly built into electron-proton interaction and as such only a matter of time. I agree with that, with this kind of atomic affinity towards aggregation of molecules and with INFINITE space and time.... well, as you said, it was only a matter of time really.

 

However, what I refer to as chance is more in the terms of position of the Earth in the Solar system to be able to provide such very dynamic, yet not too destructive environment where all those changes and trial-and-error could happen. Temperature is the most important factor, not only the heat per se, but dynamics of any kind. Without the CHAOS and HELL, there would be no harmony or life. Similarly to fractals and strange attractors, life emerges as some side effect of the geometry of underlying subatomic physics.

Edited January 20, 2009 by Sione

[scrappy]

Are you asserting something is wrong with proposed theory, or you just missed to notice that part? Anyway, here how it goes:

 

1.) lipid vesicles that can grow and divide.

(this is enough to explain Abiogenesis, as spontaneous formation of self-replicating molecule aka. LIFE.)

 

2.) genetic code = nucleotide polymers that can self-replicate.

(this is also enough to explain Abiogenesis, as spontaneous formation of self-replicating molecule aka. LIFE.)

 

 

Origin of genetic code: "The pre-biotic environment contained many different types of nucleotides beside DNA and RNA. Recent experiments have shown that some of these are capable of spontaneous polymerization, such as Phosphoramidate DNA."

 

Fatty acid vesicles are permeable to nucleotide monomers, but not polymers and once we have 2nd inside the 1st and if it can divide and split genetic material, then we can call it a CELL. I thought everyone else was referring to similar kind of theories, is this is something new?

But, again, how does any of this explain the origin of genetic code? Lipid vesicle formation is not an answer. Nucleotide polymerization is not an answer. What's needed is an explanation of how chemical analogs managed to evolve a digitally coded language. Where is THAT explained?

[Sione]

But, again, how does any of this explain the origin of genetic code? Lipid vesicle formation is not an answer. Nucleotide polymerization is not an answer. What's needed is an explanation of how chemical analogs managed to evolve a digitally coded language. Where is THAT explained?

 

"digitally coded language" - what is this now? There is no such thing, what are you referring to?

 

 

Pay attention and be specific, otherwise you will confuse yourself like this again. You asked about ORIGIN of genetic code and answer was given. Nucleotide polymerization IS answer to your original question - it happens SPONTANEOUSLY given the conditions we have on Earth - that is explanation of the ORIGIN and what you originally asked.

 

 

Now, you have another question: "How could it have EVOLVED into what we see today?" Your new question is about EVOLUTION and answer to that is NATURAL SELECTION, about which I already made a comment in my 1st post. What part do you not understand? Do you not believe? What is the problem you have with all this and what is it you suggest?

Edited January 20, 2009 by Sione

[scrappy]

"digitally coded language" - what is this now? There is no such thing, what are you referring to?

I assumed, perhaps falsely, that you understood the digital nature of genetic information. I assumed you knew that genetic code has a digital alphabet. We might dicker on the "language" part, depending on how that is defined, but there is no question that:

 

"Genes are pure information—information that can be encoded, recorded and decoded, without any degradation or change of meaning. Pure information can be copied and, since it is digital informaion, the fidelity of the copying can be immense." (R. Dawkins, River Out Of Eden (1995, p. 19)

 

Pay attention and be specific, otherwise you will confuse yourself like this again.

No need to be condescending, especially when you don't seem to understand what a gene is.

 

You asked about ORIGIN of genetic code and answer was given. Nucleotide polymerization IS answer to your original question - it happens SPONTANEOUSLY given the conditions we have on Earth - that is explanation of the ORIGIN and what you originally asked.

SPONTANEOUSLY? Is that my answer? A SPONTANEOUS genetic code? Are you serious?

 

Now, you have another question: "How could it have EVOLVED into what we see today?"

Where did I ask that question. Please don't quote me if I have not stated what's in the quote.

 

Your new question is about EVOLUTION and answer to that is NATURAL SELECTION, about which I already made a comment in my 1st post. What part do you not understand?

Get off your high horse.

 

Do you not believe?

Believe in what? Evolution?

 

What is the problem you have with all this and what is it you suggest?

I suggest you are quite confused about neo-Darwinian evolution.

[Sione]

I assumed, perhaps falsely, tha

You reply is not an answer to my objection. There is no such thing as "DIGITALLY CODED LANGUAGE". By using the word "language" you're making silly assertions and showing inability to differentiate the concept of "pure information" and the concept of "language". Do not confuse those two or you will again make yourself look silly like that.

 

 

Now' date=' you have another question: "How could it have EVOLVED into what we see today?"

[/quote']

Where did I ask that question. Please don't quote me if I have not stated what's in the quote.

Stop making me repeat myself, pay attention!

 

YOU SAID: "What's needed is an explanation of how chemical analogs managed to evolve a digitally coded language." "EVOLUTION" is not equal to "ORIGIN", Can you grasp? You confused yourself by asking two different questions.

 

Of course, you still need to explain what you meant by "language".

 

SPONTANEOUSLY? Is that my answer? A SPONTANEOUS genetic code? Are you serious?

Yes' date=' of course.

 

Now, do you think you can actually articulate your confusion about it?

 

[b']"...some of these are capable of SPONTANEOUS polymerization, such as Phosphoramidate DNA."[/b]

 

What part do you not understand? What part of "SPONTANEOUS" do you not understand? Do you not believe experiments? Do you not know what is "polymerization"? Articulate your confusion, explain what confused you - don't just repeat how much confused you are, its obvious.

 

Get off your high horse.

What part do you not understand?

 

Believe in what? Evolution?

Yes evolution.

 

Are you planning to "answer" every question with even more confused questions? Can you please concentrate a bit and try to answer some questions with answers, not confusion.

 

I suggest you are quite confused about neo-Darwinian evolution.

What part of the presented theory you disagree with, again?

Edited January 21, 2009 by Sione

[Sayonara]

Short tempers make for short threads.

[scrappy]

Sione, you said in an earlier post that:

 

This is nice movie explaining it the way I come to understand it. The Origin of Life - Abiogenesis -http://nz.youtube.com/watch?v=U6QYDdgP9eg

I replied by saying that your nice video did not explain the origin of the genetic code, which is clearly does not. All the cartoon video (and you!) claims is that nucleotide polymerization is “spontaneous.” Are you saying that genetic code just showed up spontaneosly? Maybe you would prefer to call this the “magnificent spontaneous theory”?

 

Now I think I know why you “believe in evolution.”

 

YOU SAID: "What's needed is an explanation of how chemical analogs managed to evolve a digitally coded language." "EVOLUTION" is not equal to "ORIGIN", Can you grasp? You confused yourself by asking two different questions.

No, I can’t grasp it. I need more than a belief in “spontaneous origin” to feed my hungry mind. If you can get by on such religious fluff then eat your heart out.

 

Of course, you still need to explain what you meant by "language".

Well, we have a genetic alphabet, which comprises a genetic language. It’s not a syntactical language in the way Chomsky would define one. But it’s a non-syntactical language nevertheless, requiring translation and transcription by specialized RNA molecules.

 

Are you planning to "answer" every question with even more confused questions? Can you please concentrate a bit and try to answer some questions with answers, not confusion.

But I entered this thread with a question for you, which you have not yet answered. So, I'll ask it again: Where does your cartoon video explain the real crux of abiogenesis: the origin of the geneic code?

[CharonY]

2.) genetic code = nucleotide polymers that can self-replicate.

 

This is not the definition of the genetic code. The code are essentially triplets coding for an amino acid. And the code is not inherent to the DNA per se, but depending on tRNA. If the tRNA gets changed (either in its anticodon region or by loading with a different AA) the code becomes changed.

[scrappy]

This is not the definition of the genetic code. The code are essentially triplets coding for an amino acid. And the code is not inherent to the DNA per se, but depending on tRNA. If the tRNA gets changed (either in its anticodon region or by loading with a different AA) the code becomes changed.

What fascinates me most about the genetic code and the codons that carry the structural information is the fact that genes are, for the most part, non-stereochemical, meaning that the bonding sites of a codon on DNA do not usually match up with the bonding sites of the amino acid it's coded for. So, instead of a tinker-toy schema (purely sterochemical) for building proteins out of AAs from coded instructions (genes), there is a language or sorts that needs to be translated. I could see nature building a sterochemical code and keeping things simple that way, but it strikes me as a curious mystery that the code should evolve non-stereochemically. (The fact that it evolved at all is of course a bigger mystery.)

[Mr Skeptic]

What fascinates me most about the genetic code and the codons that carry the structural information is the fact that genes are, for the most part, non-stereochemical, meaning that the bonding sites of a codon on DNA do not usually match up with the bonding sites of the amino acid it's coded for.

 

Um, what bonding sites of a codon on DNA? Never heard of such thing, and furthermore, codons usually match the anti-codon except sometimes the third amino acid does not match.

 

So, instead of a tinker-toy schema (purely sterochemical) for building proteins out of AAs from coded instructions (genes), there is a language or sorts that needs to be translated. I could see nature building a sterochemical code and keeping things simple that way, but it strikes me as a curious mystery that the code should evolve non-stereochemically. (The fact that it evolved at all is of course a bigger mystery.)

 

If you are wondering about the reason that the third amino acid in a codon doesn't always need to match, there are two reasons for doing so. It makes the organism more resistant to mutation, an obvious requirement for proper evolution. Also, and this might be speculation, the different anti-codons that result in the same amino acid may be translated at different rates, making them a control for the rate of production of a protein.

[scrappy]

Um, what bonding sites of a codon on DNA? Never heard of such thing, and furthermore, codons usually match the anti-codon except sometimes the third amino acid does not match. If you are wondering about the reason that the third amino acid in a codon doesn't always need to match, there are two reasons for doing so. It makes the organism more resistant to mutation, an obvious requirement for proper evolution. Also, and this might be speculation, the different anti-codons that result in the same amino acid may be translated at different rates, making them a control for the rate of production of a protein.

If protein synthesis was purely sterochemical with the codons on DNA there would be no need for transcription and translation by RNA molecules. In such a case, which does not occur in nature, the DNA itself would produce proteins straight off its coded template of nucleotides. As such, there would be no the central dogma.

 

My curiosity asks: Why not a straight shot from code to polypeptide formation? Why the need for intermediary steps of code translation? So far, the best answer I’ve come up with is that without the central dogma there could be direct feedback from the polypeptide to DNA—a corruptive informational feedback that would make havoc out of biological evolution and probably prevent it.

[Mr Skeptic]

My curiosity asks: Why not a straight shot from code to polypeptide formation? Why the need for intermediary steps of code translation? So far, the best answer I’ve come up with is that without the central dogma there could be direct feedback from the polypeptide to DNA—a corruptive informational feedback that would make havoc out of biological evolution and probably prevent it.

 

That would be completely unfeasible. DNA is very carefully managed to protect it from mutations. DNA is where almost all the regulation occurs, which likely wouldn't work well if it was being copied. Without mRNA, there would be no way to rapidly commence production of proteins, since each mRNA can make several proteins. Without mRNA, protein production would be limited to the nucleus and more specifically to the specific gene being copied. Without RNA, there would be no way for the cell to remove introns, a process that seems to be part of the cell regulation, and which allows several proteins to be made from the same gene. I'm sure there are other reasons as well.

[CharonY]

Well, but the majority of arguments are only true for eukaryotes, no?

 

DNA is where almost all the regulation occurs, which likely wouldn't work well if it was being copied.

Well transcriptional regulation inhibits/enhances the formation of mRNA. So that would not matter. What is true is that the large amount of other regulatory mechanisms that work on the mRNA level would not work anymore.

 

Without mRNA, there would be no way to rapidly commence production of proteins, since each mRNA can make several proteins.

Well in theory it could commence the same way as it would with mRNA: multiple translations starts.

[Sione]

No' date=' I can’t grasp it. I need more than a belief in “spontaneous origin” to feed my hungry mind. If you can get by on such religious fluff then eat your heart out.

[/quote']

 

Obviously not.

 

"religious fluff", is perhaps a description of the substance with which you are trying to comprehend this unsuccessfully. We all noticed that you're unable to grasp it, but you need to point out the part that confuses you, saying stuff like "fluff" and "eat heart", goes only to show your adolescence and confusion, it is not a way to learn or discuss, but to stay ignorant and embarrass yourself, yet again.

 

 

It is ridiculous your attribute word "religious" to it. It can be either SPONTANEOUS or GOD DID IT, there is no third option my silly friend. So, if you refuse the "spontaneous" explanation, then God bless you altar boy.

 

 

 

But I entered this thread with a question for you' date=' which you have not yet answered. So, I'll ask it again: Where does your cartoon video explain the real crux of abiogenesis: the origin of the geneic code?

[/quote']

 

Stop insulting yourself, I gave you the answer. It is you who is failing to explain your confusion about it, you are failing to make an objection with arguments. Making angry statements and calling it a "fluff" is not an argument. You just keep repeating your questions, which is amusing, thanks for that. Anyway, smart people only need be told once, but for you, here is the answer again:

 

THE ORIGIN OF THE GENETIC CODE:

- "The pre-biotic environment contained many different types of nucleotides beside DNA and RNA. Recent experiments have shown that some of these are capable of spontaneous polymerization, such as Phosphoramidate DNA."

 

Can you explain what part do you not understand or you just going to keep repeating your question and perhaps call it names, eh fluffy?

 

 

 

- Do you think chemical molecules (like H2O and all the rest) form spontaneously, or how else?

 

a.) H2O molecules form spontaneously

c.) H2O molecules are created by God

d.) Something else - explain.

 

 

Fluffy, WHAT SAY YOU?

 

 

 

2.) genetic code = nucleotide polymers that can self-replicate.

 

This is not the definition of the genetic code. The code are essentially triplets coding for an amino acid. And the code is not inherent to the DNA per se' date=' but depending on tRNA. If the tRNA gets changed (either in its anticodon region or by loading with a different AA) the code becomes changed.

[/quote']

 

Abiogenesis is not the theory of EVOLUTION, but ORIGIN.

 

 

People, we are talking about ABIOGENESIS, this thread is about ORIGINS, the first ones, not about what is it today. Ok?

 

Humans evolved out of some single-cell organism, right?

 

That single-cell organism happened somehow, right?

 

We do not expect this FIRST form of life to be as we see it today, right?

 

The definition given is not what current genetic code is, but what it might have been in its origin, before it EVOLVED, ok?

 

 

Now, all I'm saying that these polymers form spontaneously as experiments prove. You are free to believe otherwise, but let us know what is your theory then. Anyway, can you explain why "nucleotide polymers that can self-replicate" is not a definition of 'genetic code'?

Edited January 21, 2009 by Sione

[CharonY]

Dude, explain why a polymer is a code if it codes for nothing? Where is the connection between code and replication? It looks like you use it synonymously.