Creating life from matter

[Wowbagger]

That's not how I see it. My reasoning is as follows:

Hey, I understand what you are saying.

But, in your original form, your wording wouldn't cut it.

I could say anything, "ionization is proved by the very existence of life" or "bagels are proven by the very existence of life". Without further explanation, any such statements are meaningless. You have show why the idea would have merit, outside the 'very existence' of something else.

 

[Skeptic Ginger]

The replicating molecules seem to me unfortunate introduction of a false premise we have previously discussed.
As I have been previously pointed out, self-replicating molecules seem to me a false assumption; they are theoretically impossible, undemonstrated in the test-tube and not needed for either evolution or abiogenesis.

I see no suggestion in your post that you have a better viable hypothesis.

Wiki on Abiogenesis^WP has a summary of the current research models. Is there a model there you favor?

I think the RNA models have the most research behind them.
Mechanism for prebiotic RNA synthesis

Self-Sustained Replication of an RNA Enzyme

Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment

The stability of the RNA bases: Implications for the origin of life

 

[Zeuzzz]

Why is abiogenesis any more magical than the Big Bang or the unobserved but theorized Earth's core?

Very nicely said

 

[Reality Check]

I would not regard him as a troll, more a person who's way too skeptical of anything that is considered "unorthodox".

I am only skeptical of anything that has little evidence presented to support it. When I do not understand the evidence, I ask questions.
Thus when John Hewitt asserted that that self replicating molecules did not exist because of theoretical objections that he had, I asked him to state them.
He stated that self replicating molecules violate Carnot's theorem.
I asked him to explain how he knew that they violate Carnot's theorem.
He gave a bogus explanation about thermal gradients and his belief that they were too big. But Carnot's theorem is not about thermal gradients, it is about the maximum efficiency of a heat engine.
So I asked him for his actual Carnot's theorem calculation.
He has not answered yet so I remind him whenever he makes the same assertion.

And then I found out that self replicating molecules actually exist!

Probably would be a good idea to reply to them, if you have the time, just don't expect him to chance his mind even if you rebut his points.

I have no points to rebut. I have 4 simple questions. If John Hewitt can provide the answers then I will change my mind about his assertion having no evidence.

 

[Reality Check]

Please note that I have tried to engage with him previously, at some length, and the only thing that ever came back was the kind of cut-and-paste job you see in his last post.

Yes you have tried ato engage with me to some extent and I thank you for that.
The problem is that when I asked you relevant questrions you did not answer (except that Carnot's theorem one that you got wrong). So I asked you again.


N.B. If you cannot answer the questions then just say so, e.g.

• You have no evidence that self replicating molecules are theoretically impossible.
• Self replicating molecules actually exist.
• There is no evidence that "chemical oscillations" replicate and so they cannot evolve.

I have previously looked for threads to which he has posted without this kind of trolling but I can't find one. I have also asked him to identify such a thread but he didn't reply. If anyone on this forum knows of a thread in which "Reality Check" is not simply repeating himself, please point it out.

Sure:
The Big Bang - Woo or not?
"NASA Pseudo-skeptic Receives Rebuttal from Electric Universe Theorist"
Anthony Peratt's Plasma Model of Galaxy Formation
Fine Structure Constant not so constant ...
Question: Inflation and Homogeneity
Arp objects, QSOs, Statistics
Chemical Vs Electrodynamic Propulsion
Magnetic reconnection and physical processes
ClimateGate: Who will get prosecuted? Not the scientists who hid the data.
etc.

I do not "repeat myself" - I remind posters about the questions that they are ignoring. I especially remind them when they repeat the baseless assertions that evoked the questions in the first place.

 

[Perpetual Student]

Hey, I understand what you are saying.

But, in your original form, your wording wouldn't cut it.

I could say anything, "ionization is proved by the very existence of life" or "bagels are proven by the very existence of life". Without further explanation, any such statements are meaningless. You have show why the idea would have merit, outside the 'very existence' of something else.

I do not agree. All we know of and can scientifically verify are natural processes. That includes the galaxy, the sun, the solar system, the earth, life's existence, diversity and beginnings. Any claims to the contrary require evidence. There is no evidence for non-natural stuff, including deities and tooth fairies. Hence: abiogenesis!
I challenge any creationist or other believer in any other variety of paranormal, non-natural, gods, fairies and witches to provide scientific evidence to the contrary.

 

[Perpetual Student]

I do not agree. All we know of and can scientifically verify are natural processes. That includes the galaxy, the sun, the solar system, the earth, life's existence, diversity and beginnings. Any claims to the contrary require evidence. There is no evidence for non-natural stuff, including deities and tooth fairies. Hence: abiogenesis!
I challenge any creationist or other believer in any other variety of paranormal, non-natural, gods, fairies and witches to provide scientific evidence to the contrary.

Furthermore, I believe that it is in this arena that we have allowed creationists and other bogeyman believers to put science based explanations on the defensive when we should be playing offense. It is the deists that should provide evidence for their claims. It has been said, "extraordinary claims require extraordinary evidence." If any but natural explanations are given for any phenomenon, then the evidence for that non-natural cause should be demanded. Let's not allow them to debate nuances of the fossil record when their own theory is so lacking in evidence and so utterly intellectually bankrupt.

 

[John Hewitt]

I see no suggestion in your post that you have a better viable hypothesis.

Wiki on Abiogenesis^WP has a summary of the current research models. Is there a model there you favor?

I think the RNA models have the most research behind them.
Mechanism for prebiotic RNA synthesis

Self-Sustained Replication of an RNA Enzyme

Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment

The stability of the RNA bases: Implications for the origin of life

Sure, those theories have been expounded at great length, and nobody ever seems to dump them, even though their silliness is repeatedly pointed out. I'm not going to go through those arguments yet again here.

Crick was one of the early proposers of the RNA world theory, along with Gilbert, but could find absolutely no way to make it work. Instead he ended up suggesting directed panspermia - one might say he moved from the unworkable to the ridiculous. (I think Crick's book on this is "Life Itself." It's worth a read, if only to make you more skeptical about what great scientists say.) In any case, then he abandoned the field altogether and started working on consciousness.

A much better review of origin of life theories is Shapiro's classic "Origins - A skeptics guide to the creation of life on earth." It's 25 years old now, and everything it says is still true and still unanswered. He destroys the RNA world theory. Later, he explicitly argued that a replicator was not involved in and not needed for the origin of life. I agree with him on all counts.

The only replication my hypothesis needs is that involved in the daily or yearly cycles of the sun on the earth. Do I need a link or a reference to justify that?

 

[Reality Check]

The only replication my hypothesis needs is that involved in the daily or yearly cycles of the sun on the earth. Do I need a link or a reference to justify that?

Yes you do need to justify this - there is no replication in the daily or yearly cycles of the sun on the earth. A cycle is not replication. Days do not replicate. Years do not replicate. They repeat.

A rotation of the Earth is not followed by many rotations of the Earth the next day (replication).

The temperature difference between night/day or summer/winter might be a driver for chemical reactions such as chemical oscillation (chemical clocks). Chemical oscillation does not replicate - it cycles. But if you have scientific evidence otherwise you can present it.

 

[steenkh]

I get that part. But it sounded like you were claiming, if it was proved that nol abiogenesis theory options occurred it would have no impact on evolution theory. And that's what I don't agree with. Because if you claim that no abiogenesis occurred, then you have irreducible complexity and that is not consistent with evolution theory.

Why would it be a problem for evolution if no abiogenesis event occurred? Many Christians (including me when I was very young) think that God created life (which I gather is not regarded as abiogenesis), and from that moment evolution kicked in.

Irreducible complexity was proposed as an argument against evolution - or more specifically common descent. Evolution as a mechanism would start at any point where life exists, no matter if it was billions of years ago, or yesterday. The evidence that it has actually taken billions of years has led to the formulation of common descent using evolution as its vehicle.

If one day it was ascertained that there exists life that is unrelated to other life on Earth, common descent would have to be modified, but evolution would be unaltered, and in effect for the new kind of life, provided that this life is based on replication, and that replication errors can happen.

 

[wogoga]

"Self-replicating molecules"

The replicating molecules seem to me unfortunate introduction of a false premise we have previously discussed.
As I have been previously pointed out, self-replicating molecules seem to me a false assumption; they are theoretically impossible, undemonstrated in the test-tube and not needed for either evolution or abiogenesis.

If we assume self-replicating molecules capable of evolving further into the first living cell(s), then the abiogenesis-evolution dichotomy becomes even more questionable.

Yet I still agree with what I wrote in a post of 1999:

We cannot reproduce the behaviour of enzymes of the early earth because their behaviour depends on psychons which have further evolved. So amino acid sequences which would have folded millions or billions of years ago, today do not fold any more. In the same way, sequences which fold today did not fold on the early earth.​

Self-Sustained Replication of an RNA Enzyme

As far as I can see we are dealing with self-ligating ligases. The procedure to create such "self-replicating" RNA-ligases is rather simple:

• Analyze the sequences of RNA-enzymes naturally ligating RNA chains and search for a ligase pair
  • Ligase 1 must contain a sequence similar to the one naturally put together by Ligase 2
  • Ligase 2 must contain a sequence similar to the one naturally put together by Ligase 1
• By spitting Ligase-1 at the center of the corresponding sequence we get two RNA chains, from which a complete Ligase-1 chain can be created by Ligase-2
• By spitting Ligase-2 at the center of the corresponding sequence we get two RNA chains, from which a complete Ligase-2 chain can be created by Ligase-1
• Produce for each of the two ligases the corresponding two RNA-chains
• Put a huge number of these four RNA chains in a test tube
• Add Ligase 1 and Ligase 2, and "replication" can start

In the already above referenced post I also took a stand on the "Lee peptide" a "self-replicating protein":

What is a self-replicating protein?

One capable of reproducing itself from spare amino acids.

I agree. But the Lee peptide is not capable of reproducing itself from spare amino acids! To call a simple peptide ligase a 'self-replicating protein', even if it is able to ligate two halves of its own amino acid sequence, is not only misleading but maybe even dishonest! see: http://www.scripps.edu/pub/ghadiri/

The Lee peptide is made of 32 building blocks. There are 20 different building blocks, and it is normal to attribute the probability 20^-32 to the special sequence of the Lee protein.

20^-32 = 2.33 * 10^-42 = 0.000'000'000'000'000'000'000'...

The self-ligating Lee protein is made of 2 building blocks and there are only 2 building blocks. So instead of

20^-32 = 2.33 * 10^-41

we have a probability of only

2^-2 = 0.25 !!!​

Cheers, Wolfgang

Relevant extracts from my posts of March 1999

 

[John Hewitt]

If we assume self-replicating molecules capable of evolving further into the first living cell(s), then the abiogenesis-evolution dichotomy becomes even more questionable.

Yet I still agree with what I wrote in a post of 1999:

We cannot reproduce the behaviour of enzymes of the early earth because their behaviour depends on psychons which have further evolved. So amino acid sequences which would have folded millions or billions of years ago, today do not fold any more. In the same way, sequences which fold today did not fold on the early earth.​

Wolfgang.
I am afraid I don't understand your posting. I googled the word psychon and it seems to be a concept associated with the ideas of "pandualism," a system of ideas whose concepts I also do not understand.

Myself, I trained in chemistry, physical chemistry, molecular biology and biochemistry - that kind of stuff - and I like concepts I can understand in those terms.

Consequently, I just don't get the kind of stuff your terminology is pointing at and, beyond expressing some empathy with your off-centre stance, I don't think I can reply to you.

 

[Skeptic Ginger]

Sure, those theories have been expounded at great length, and nobody ever seems to dump them, even though their silliness is repeatedly pointed out. I'm not going to go through those arguments yet again here.

Probably a good idea on your part since I don't find your opinion very credible in this matter.

...A much better review of origin of life theories is Shapiro's classic "Origins - A skeptics guide to the creation of life on earth." It's 25 years old now, and everything it says is still true and still unanswered. He destroys the RNA world theory. Later, he explicitly argued that a replicator was not involved in and not needed for the origin of life. I agree with him on all counts.

Harvard News: NYU chemist Robert Shapiro decries RNA-first possibility

Shapiro said. “The odds against [RNA forming on its own] are astronomical.”

We know how well that argument is against evolution theory.

I wouldn't rule out any hypothesis at this time. But big deal, you find the metabolism first more promising and I find the RNA first more probable. So what?

The only replication my hypothesis needs is that involved in the daily or yearly cycles of the sun on the earth. Do I need a link or a reference to justify that?

Tide goes in, tide goes out, clearly proof of your favored hypothesis.

 

[Skeptic Ginger]

Why would it be a problem for evolution if no abiogenesis event occurred? Many Christians (including me when I was very young) think that God created life (which I gather is not regarded as abiogenesis), and from that moment evolution kicked in.

Irreducible complexity was proposed as an argument against evolution - or more specifically common descent. Evolution as a mechanism would start at any point where life exists, no matter if it was billions of years ago, or yesterday. The evidence that it has actually taken billions of years has led to the formulation of common descent using evolution as its vehicle.

If one day it was ascertained that there exists life that is unrelated to other life on Earth, common descent would have to be modified, but evolution would be unaltered, and in effect for the new kind of life, provided that this life is based on replication, and that replication errors can happen.

You are welcome to your gap god hypothesis.

The problem I have with that hypothesis is it is entirely based on the fictional creation of an explanation. It is not following the scientific process to make up the conclusion first then seek to confirm it. In science one develops hypotheses based on evidence, not based on wishful or magical thinking.

So, if you had any evidence whatsoever that there is a real point of irreducible complexity, feel free to pursue that line of inquiry. For myself, I don't find magical explanations belong in the mix.

 

[steenkh]

The problem I have with that hypothesis is it is entirely based on the fictional creation of an explanation. It is not following the scientific process to make up the conclusion first then seek to confirm it. In science one develops hypotheses based on evidence, not based on wishful or magical thinking.

We agree completely.

So, if you had any evidence whatsoever that there is a real point of irreducible complexity, feel free to pursue that line of inquiry. For myself, I don't find magical explanations belong in the mix.

Neither do I.

But I pointed out that a magical creation of life would not actually be against evolution - for the simple fact that evolution does not cover how replication started.

 

[Skeptic Ginger]

.....
But I pointed out that a magical creation of life would not actually be against evolution - for the simple fact that evolution does not cover how replication started.

Round and round the mulberry bush
the debate it did wander
but low and behold when we came to page 4
we found ourselves back where we started.



Where is the place you claim evolution begins and what defines that place? Unless this question has a satisfactory answer, all you have is hand waving: "Evolution starts at this point because I say so."

My position is there is no such magical place and if one follows that common ancestor back to the beginning, you have to follow it all the way back to non-life.

 

[steenkh]

Round and round the mulberry bush
the debate it did wander
but low and behold when we came to page 4
we found ourselves back where we started.

Yes, I am sorry, I was not around in this thread when this discussion started. I read the lot, and I was not satisfied with the replies given then.

Where is the place you claim evolution begins and what defines that place? Unless this question has a satisfactory answer, all you have is hand waving: "Evolution starts at this point because I say so."

I would say that the place is defined by the scope of evolution. The theory of evolution that I am acquainted with, describes change through mutation and selection. Now, selection can be said to be active everywhere, mutation can only happen when there is replication. Before life, there is no replication, and I have yet to see somebody explain why selection and mutation should be driving forces for molecules that do not replicate.

That is why I say that evolution should be valid for everything within scope. Is this an unreasonable position?

My position is there is no such magical place and if one follows that common ancestor back to the beginning, you have to follow it all the way back to non-life.

Please describe how non-life is governed by mutation and selection. Then I could perhaps understand it.

In a previous post I also asked where you would start evolution, and why? What is non-life? As I said, you could go all the way back to the Big Bang when you do not set the limit at replication.

 

[wogoga]

I am afraid I don't understand your posting.

I can hardly imagine that you are unable to understand. (Yet I would be really astonished if you agreed with my pandualism.)

• You argue against self-replicators (e.g. in this highly recommendable post)
• Others have claimed that you are refuted by the very existence of self-replicating molecules
• I argue that such molecules do not more than uniting two pre-fabricated halves of their own nucleotide or amino-acid chains, and that one should not call them "self-replicators".

Let us assume that one correctly chained RNA-sequence consisting of only 10 nucleotides results in a self-replicating enzyme. Let us even take for granted that this ribozyme is able to produce correctly chained RNA-pieces of each 10 nucleotides.

There are 4^10 = 1 million different possibilities for a 10-nucleotide chain. Where does our RNA-enzyme get the information from, with which peptide to start, and which one to add at each of the nine remaining positions?

The only half-way reasonable possibility within reductionist materialism is base-pairing:

• An RNA-enzyme unfolds
• For each nucleotide of the enzyme a complementary nucleotide is attached
• The original and the complementary chain separate
• Both chains fold into a corresponding enzyme

In the biological world, such life cycles with different states and complementary entities (female/male) are quite normal. In physics and chemistry however, normally only one direction is favored, namely the one towards less usable energy (higher entropy).
So either the folding or the unfolding of the chain should be the favored downhill-process.

And if the attachment of complementary nucleotides to a chain is favored by energy balance, then why should the separation of the two complementary chains also be favored by energy balance?

Cheers, Wolfgang

 

[Skeptic Ginger]

Yes, I am sorry, I was not around in this thread when this discussion started. I read the lot, and I was not satisfied with the replies given then.

No worries. I was actually referring to the whole discussion, not just your post. If someone answered my question about where one starts evolution theory if one segregates abiogenesis from the theory, I missed the answer. And the answer to that question is key to the discussion.

I would say that the place is defined by the scope of evolution. The theory of evolution that I am acquainted with, describes change through mutation and selection. Now, selection can be said to be active everywhere, mutation can only happen when there is replication. Before life, there is no replication, and I have yet to see somebody explain why selection and mutation should be driving forces for molecules that do not replicate.

Think about your premise.

If true, you are suggesting those replicating molecules occurred completely by chance and not because the non-replicating molecule precursors were selected by the conditions they collected in.

RNA is a self replicating molecule. It forms more easily than DNA and replicates more easily outside a more complex 'lifeform'. But the first RNA molecule, regardless if you prefer John's favored hypothesis or not, at some point RNA molecules had to form. And conditions that allowed that RNA molecule essentially selected the molecule. But selection of replicating molecule precursors is not my point.

That is why I say that evolution should be valid for everything within scope. Is this an unreasonable position?

Please describe how non-life is governed by mutation and selection. Then I could perhaps understand it.

In a previous post I also asked where you would start evolution, and why? What is non-life? As I said, you could go all the way back to the Big Bang when you do not set the limit at replication.

I don't disagree that one should start evolution theory at the first self replicating molecule. And I don't disagree one can describe the pre-replicating molecule precursors as conditions conducive to, rather than conditions 'selecting' the RNA. It's analogous in my concept of evolution theory to conception. The ovum and sperm are different from the fetus.

But at the same time, you don't define the ovum and sperm as, 'not part of fetal development'. My gripe is specifically with the claim one can dismiss abiogenesis when discussing evolution theory. The sperm and the ovum had to exist before the fetus began developing. Fertilization had to occur before the fetus began developing. I can decide to only discuss fetal development, but it is a given that the sperm and ovum and fertilization preceded that fetal development.

Abiogenesis is typically brought up as a challenge to evolution theory, or as some supposed evidence for Intelligent Design. That challenge to evolution theory isn't any more valid than the claim that gaps in the fossil record challenges evolution theory. So why do people feel the need to say, we can set the abiogenesis question aside, we don't need to talk about it? Why is everyone not saying loudly and clearly, "The unanswered abiogenesis question not a challenge to evolution theory. There's enough evidence supporting evolution theory to assume abiogenesis occurred and there are several promising avenues to figure out how it occurred. Do you have any evidence it did not?"

Instead of saying to deniers, "it's not a problem," many in the scientific community say, "we don't need to answer that, it isn't part of evolution theory." It's like saying, we don't have to admit there had to have been an ovum, sperm, and fertilization, the fetus is a fact. Evolution is a fact and unless life began in the Big Bang or the gods dit it, then abiogenesis occurred.

 

[steenkh]

Think about your premise.

If true, you are suggesting those replicating molecules occurred completely by chance and not because the non-replicating molecule precursors were selected by the conditions they collected in.

Actually, I did not suggest anything about how those replicating molecules occurred. It could be a freak chance, it could be inevitable, given the circumstances of the young Earth, it could be seeded by aliens, or created by God.

I don't disagree that one should start evolution theory at the first self replicating molecule. And I don't disagree one can describe the pre-replicating molecule precursors as conditions conducive to, rather than conditions 'selecting' the RNA. It's analogous in my concept of evolution theory to conception. The ovum and sperm are different from the fetus.

Of course I agree that abiogenesis is a fascinating and necessary theory, but I do not see why it should be part of the theory of evolution, just like I do not think that a book about bicycle development needs to start in the mines.

But at the same time, you don't define the ovum and sperm as, 'not part of fetal development'.

They are governed by the same genes, whereas abiogenesis and evolution is not governed by the same rules.

My gripe is specifically with the claim one can dismiss abiogenesis when discussing evolution theory.

And that is exactly what I cannot understand: though one is a precursor to the other, but apart from that, they have nothing in common. The formation of the Solar system is also a necessary precursor for life on Earth, but surely we would not include that in a discussion of evolution?

Abiogenesis is typically brought up as a challenge to evolution theory, or as some supposed evidence for Intelligent Design. That challenge to evolution theory isn't any more valid than the claim that gaps in the fossil record challenges evolution theory.

When abiogenesis is brought up as a challenge to evolution, it it from a misunderstanding of what evolution is. Those creationists who are making this challenge have it all in one theory, but there lots and lots of religious believers who believe in a god who has created life, and still think that the theory of evolution has got it right. These people think that their god kick-started life, but evolution took over. They are not wrong about this: evolution really works exactly according to specification in this scenario.

So why do people feel the need to say, we can set the abiogenesis question aside, we don't need to talk about it? Why is everyone not saying loudly and clearly, "The unanswered abiogenesis question not a challenge to evolution theory. There's enough evidence supporting evolution theory to assume abiogenesis occurred and there are several promising avenues to figure out how it occurred. Do you have any evidence it did not?"

When they mix up abiogenesis and evolution, I point out that they cannot blame a theory for something it does not cover, but that I am willing to discuss abiogenesis. It is important to distinguish because if we do not, we will be forced to deal with silliness such as "rocks mutating into life", along with the usual "cats mutating into horses".

Although I do not mind talking about it, I do think that we are overstating the case when we claim that we have evidence for abiogenesis. We cannot see any obstacles to abiogenesis, and we can see several possible pathways, but we certainly do not have positive evidence that it happened. This is quite contrary to evolution where w have positive evidence for it happening ranging from a distant past right up to now. Even if we could produce an abiogenesis event in a lab, we still would not have proof that we had reproduced the correct abiogenesis event.