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What is the origin of life according to ToE?

painted wolf

Grey Muzzle
Shall I just change my mind because three people tell me that I'm wrong without addressing my arguments or the arguments of my peer reviewed references? No, thank you.
Sorry, I was addressing the OP can you re-post the references you mentioned?

I do evolutionary biology research for a living. My passion for the subject is what is making me bother to pursue this here. Let me try another tack to address what I think you might have problems with.
Nice, it's good to have another evo bio person here... what organism are you studying?
I've done a little work in lab studying behavior and evolutionary relationships in subpopulations of Limulus polyphemus. :D

In the context of being a biologist who thinks about the practical benefits of evolutionary science every day, I guess I can say that we think about biological systems as physical and chemical systems. We don't assign any special status to living things. There is nothing particularly different about something that's alive. It's matter and energy applicable to laws of chemistry and physics. In this, the modern researchers paradigm, there is no reason at all to limit evolutionary theory to that which is alive. Especially given that we can't properly define life. Aspects of inorganic chemistry are subject to evolution by natural selection.
Wait... so you ignore decent with modification?
How do you get biological evolution in a system without it?
Or am I mis-reading you here? :shrug:

wa:do

ps... thanks for the links, I look forward to checking them out and getting back to you with my thoughts. :D
 
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ScottySatan

Well-Known Member
hi Painted Wolf. References reposted!

I've studied the evolutionary history of tobacco, the moss Phiscomytrella patens, budding yeast, and now comparative evolution between humans and all of the major model organisms, specifically with the aim of data-mining from genome sequence data in mind.

I don't understand your last question.
 

painted wolf

Grey Muzzle
hi Painted Wolf. References reposted!
Thanks a lot! :D

I've studied the evolutionary history of tobacco, the moss Phiscomytrella patens, budding yeast, and now comparative evolution between humans and all of the major model organisms, specifically with the aim of data-mining from genome sequence data in mind.
Very cool! Anyone that has to do that much work with BLAST has my sincere kudos! :bow:

I'm more an anatomist and ecologist than a geneticist.

I don't understand your last question.
I was curious about your stance that there isn't anything particularly different between living and nonliving systems... surely the process of genetic variation makes living systems significant?
Even from a basic molecular standpoint, the fact that RNA/DNA carries heritable traits that can vary from one copy to another is rather profound.

Ultimately this is the key to evolution.... heritability and variation.

The first biomolecules (exemplified by the self replicating RNA work of Joyce and Lincoln http://www.sciencemag.org/content/323/5918/1229) would not have been evolving per say...

wa:do

ps, I completely agree about the problems defining life. I think that this may be the actual issue in this discussion. For my purpose I'm willing to stretch the definition to things that reproduce and show heritable change.
 
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camanintx

Well-Known Member
Go find the definition of the theory of evolution that you learned.
Isn't biological evolution simply "any change in the frequency of alleles within a gene pool from one generation to the next." - Helena Curtis and N. Sue Barnes, Biology, 5th ed. 1989 Worth Publishers, p.974
 

jarofthoughts

Empirical Curmudgeon
Shall I just change my mind because three people tell me that I'm wrong without addressing my arguments or the arguments of my peer reviewed references? No, thank you.

Absolutely not, but I thought the explanations and counterpoints they brought up would seem sufficient.
I see however, that you appear to disagree.

In the context of being a biologist who thinks about the practical benefits of evolutionary science every day, I guess I can say that we think about biological systems as physical and chemical systems.

That is true, at least in some contexts.
I would argue, however, that in the multifaceted field of study we call Biology, that is not always the case, at least not solely.

We don't assign any special status to living things. There is nothing particularly different about something that's alive. It's matter and energy applicable to laws of chemistry and physics. In this, the modern researchers paradigm, there is no reason at all to limit evolutionary theory to that which is alive. Especially given that we can't properly define life. Aspects of inorganic chemistry are subject to evolution by natural selection.

That is also true as far as it goes, but living things also have descent with modification, something that I fail to see non-living things have.
It is true that the word 'evolution' can be applied to a number of processes, many of them non-living, but when we talk about the Theory of Evolution, we're talking about a specific scientific theory aimed at explaining specific processes, in this case the descent with modification that gives rise to the multitude of organisms that live on our planet.
Lumping the various theories and fields of study together and calling them one and the same can only result in muddying the waters and making things that are already complicated even more unclear.
 

jarofthoughts

Empirical Curmudgeon
Isn't biological evolution simply "any change in the frequency of alleles within a gene pool from one generation to the next." - Helena Curtis and N. Sue Barnes, Biology, 5th ed. 1989 Worth Publishers, p.974

That is what people are reffering to when they say that evolution is both a Theory and a fact. And the above is an undeniable observable fact, reproduced by first year biology students all over the world.
It should be noted though that the THEORY of Evolution contains somewhat more than that. :)
 

ScottySatan

Well-Known Member
Absolutely not, but I thought the explanations and counterpoints they brought up would seem sufficient.
I see however, that you appear to disagree.

No, Mr. Krok made it crystal clear he didn't understand what I was saying. He got more and more out of touch with every post.


Not sure what you meant later on in this post. mutations did occur in these prebiotic polymers. They were susceptible to potentially code-changing UV damage and reactive oxygen species like DNA is. Only more so because it was not as stable a molecule as DNA, lacked the repair mechanisms we enjoy today, and would not have had the protection of a cell. These things mutated like crazy. They did have something special about them. They weren't like any old molecule. A tablespoon of sugar won't evolve into life, for example. We do have some direc evidence for their existense, as there are many known vestigial remnants today; molecules that do most of the things that these prebiotic polymers should have.
 

ScottySatan

Well-Known Member
Isn't biological evolution simply "any change in the frequency of alleles within a gene pool from one generation to the next." - Helena Curtis and N. Sue Barnes, Biology, 5th ed. 1989 Worth Publishers, p.974

That is a common textbook definition of evolution that actually defines natural selection. Interestingly this one doesn't say that a nucleotide genome is required, or exclude the type of biological system I'm talking about. Don't know if that's on purpose or on accident.

As a definition of evolution, this isn't enough. natural selection kills things. It does not create diversity on its own. That plural use of the word alleles is a key part. you have to have a source of genetic change. Obviously natural selection can't work if everythig ni the population is identical. You need a source of variation first. you get random mutations and non-random large scale genetic changes. Then you need natural selection to change the frequency of those alleles in the population. neither genetic change nor natural selection on its own is sufficient for evolution.
 

ScottySatan

Well-Known Member
The first biomolecules (exemplified by the self replicating RNA work of Joyce and Lincoln Self-Sustained Replication of an RNA Enzyme) would not have been evolving per say...

Actually the authors of this paper say that the system underwent evolution. First sentence 4th paragraph.

"The catalytic properties of the cross-replicating RNA enzymes were improved by the use of in vitro evolution, optimizing the two component reactions in parallel and seeking solutions that would apply to both reactions when conducted in the cross-catalytic format "

The follow up studies, the ones that cite this paper, use the word evolution much more liberally.

That is a very cool paper. They're funded by NASA!

these prebiotic polymers DID have modifiable heritable traits. It's believed that the first autocatalytic repicating biomolecules were similar to RNA. They would have been mutating faster than RNA does today because they had no nucleotide repair pathways.
 

painted wolf

Grey Muzzle
Yes, they do evolve (not exactly "Darwinian" but they do evolve).... and if I had been paying attention and not rushing my posts I may well have stopped myself from looking like a silly boob. :banghead3:

Now that the lightbulb had light up fully let me try to restate my position and hopefully not make a further doofus of myself.

The process that brought the first biomolecules across the threshold to life was indeed evolutionary in nature.

But, the process that first allowed those biomolecules to form was not... that was abiogenesis/ basic chemistry. The assembly of amino acids into the first RNAs (or whatever they were) isn't evolution.
Evolution didn't create the first self-replicators, it only worked once the replicators got going (genetic drift) and started to have selective pressures applied to them.

Hopefully that makes more sense. :p

wa:do
 

Amill

Apikoros
Ok all, I'm not going to ask you to just take my word for it. Let's try something else.

Go find the definition of the theory of evolution that you learned. Go find out all the things that evolution is, and what it isn't. Show me where in that text it says that nonliving things are specifically excluded. Show me where it says that evolution didn't exist until the first cell was made. You will find definitions where it says the theory is about organisms, but you will not find in that text or any reference that can say why nonliving things should be excluded. Ask yourself why not.

I've already provided references to show my point, read it. Give a rebuttal of my references, provide your own references, or you've got nothing.
If we're including abiogenesis as a part of Evolution, couldn't we also go a few steps further back in time and count the creation of the various elements as part of Evolution then as well? Where would you draw the line and why?
 
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ScottySatan

Well-Known Member
But, the process that first allowed those biomolecules to form was not... that was abiogenesis/ basic chemistry.

But Painted Wolf, the old process that allows non-new biomolecules to form in an advanced cell inside an animal is also just basic chemistry.

If some people want to make an arbitrary cutoff and say that evolution began with the appearance of the first living thing, that's fine by me. However I will remind them that this cutoff is completely arbitrary, not necessary, and entirely by their own choice. Then I might want to ask them what the first living thing was, and where it came from. I would argue that that first living thing came from evolution by natural selection on non-living things, since the physical and chemical mechanism of that change is identical. Since the magnitude of physical difference between the last pre-living thing and the first living thing is going to be comparable to a single nucleotide polymorphism.
 
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ScottySatan

Well-Known Member
If we're including abiogenesis as a part of Evolution, couldn't we also go a few steps further back in time and count the creation of the various elements as part of Evolution then as well? Where would you draw the line and why?

I don't know about your specific case. I think you can extend it to entirely inorganic phenomena, but it becomes less and less useful/productive to do so, the further away you get from a system of competition and/or heredity.

It's exactly the same as how it's possibly to describe the behaviour of any piece of matter with quantum mechanics, like uncertainty of position. The idea originiated with subatomic particles, but still provides useful insights into moderately sized molecules. The larger the subject becomes, the less useful or productive it is to so. We can say there is some uncertainty as to the position of the water molecule, but not much uncertainty as to the position of that Chevy Nova.
 
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Astrid000

Member
Actually the authors of this paper say that the system underwent evolution. First sentence 4th paragraph.

"The catalytic properties of the cross-replicating RNA enzymes were improved by the use of in vitro evolution, optimizing the two component reactions in parallel and seeking solutions that would apply to both reactions when conducted in the cross-catalytic format "

The follow up studies, the ones that cite this paper, use the word evolution much more liberally.

That is a very cool paper. They're funded by NASA!

these prebiotic polymers DID have modifiable heritable traits. It's believed that the first autocatalytic repicating biomolecules were similar to RNA. They would have been mutating faster than RNA does today because they had no nucleotide repair pathways.


Hey there

I understand that how life first came to be is still being worked out. I see the topic of abiogenesis as comparable to the creation, really. That is the start of life that cannot be explained with confidence.

What I do not understand is the principle of minimum viable population size as it applies to the first living cells.

This link talks about a minimum viable population size of 4169 individuals.
ScienceDirect - Biological Conservation : Minimum viable population size: A meta-analysis of 30 years of published estimates

So when the first cells originated were they stuck to a rock or floating around in the sea or some pond.

We see that with research into Horizontal Gene transfer, now found in prokaryotes, that LUCA is no more a certainty. It appears that the new models speak to multiple arisings of primitive cells that transfered genes.

This leads me to a conclusion that all life that arose by some natural means was very similar. So similar in genetic makeup were these cells that they were able to negotiate gene transfer.

How does this minimum viable population fit in here? How did primtive cells stuck to a rock manage to transfer genes? How did cells floating around in the ocean or in a pond manage to do so?

Were there hundreds of thousands of these primitive cells all having come into existence with the same genetic structure or just a few that managed to find each other or is common thinking suggesting still just one cell, coming to life one time?

What is also interesting is that if earth or the universe are strewen with the precursors for life one would expect life would have arisen on more than one occasion with a very different genetic makeup. This does not appear to be the case.

I understand the initial RNA world, but RNA still has alleles don't they? I expect that RNA in all life must also be the same. However this does not appear to be the case. There are many deletions. If primitive cells had RNA, did RNA arise after reproduction was enabled or before. It appears reproduction cannot exist without a genetic mechanism already assembled to support it.
Structurally different alleles of the ath-MIR824 microRNA precursor are maintained at high frequency in Arabidopsis thaliana

"The modes of HGT are transformation. This actually appears to require other genetic material around at the time to uptake. Transduction requires a virus to be around for HGT to occur this way, Bacterial conjucation requires contact of the cells, Gene transfer agents also appear to need virus around. How did the fist living cells ever manage to negotiate gene transfer, particularly in the oceans re thermal vent abiogenesis? There was just bacteria, no virus yet evolved and no other genetic material was around at the time. The planet was lifeless apart from these primitive cells.
Nor is abiogenesis (the origin of the first life) due purely to chance. Atoms and molecules arrange themselves not purely randomly, but according to their chemical properties. In the case of carbon atoms especially, this means complex molecules are sure to form spontaneously, and these complex molecules can influence each other to create even more complex molecules. Once a molecule forms that is approximately self-replicating, natural selection will guide the formation of ever more efficient replicators. The first self-replicating object didn't need to be as complex as a modern cell or even a strand of DNA. Some self-replicating molecules are not really all that complex (as organic molecules go). " from the 5 misconceptions re evolution thread.

This info appears to be saying that all life that arises is going to be the same as it is not random but will arise according to their chemical properties. This article also suggests that scientists are uncertain how many cells were initially formed, yet they were numerous enough to negotiate HGT.


If only a few hundred cells arose initially, how come they did not die out according to this minimum viable population theory? Does it apply to asexually reproductive organisms?
 
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camanintx

Well-Known Member
I don't know about your specific case. I think you can extend it to entirely inorganic phenomena, but it becomes less and less useful/productive to do so, the further away you get from a system of competition and/or heredity.
So why not draw the line at systems that compete and/or inherit traits, in other words living organisms? Why include abiogensis when there is no evidence of either?
 

painted wolf

Grey Muzzle
Hey there

I understand that how life first came to be is still being worked out. I see the topic of abiogenesis as comparable to the creation, really. That is the start of life that cannot be explained with confidence.
Except that abiogenesis proposes a mechanism that can be tested, while creationism remains an unprovable "just so" story.

What I do not understand is the principle of minimum viable population size as it applies to the first living cells.
This is only an issue with multicellular life forms that reproduce via sexual reproduction alone.
Single celled life forms are much more "loose" with their genomes and are able to produce high amounts of diversity in short spans of time.

You can produce a viable population of E.coli from a single progenitor cell.

Yup... this paper is talking about mulitcellular sexually reproducing species like us... not single celled organisms.

So when the first cells originated were they stuck to a rock or floating around in the sea or some pond.
Not really. Single celled organisms can live anywhere.

We see that with research into Horizontal Gene transfer, now found in prokaryotes, that LUCA is no more a certainty. It appears that the new models speak to multiple arisings of primitive cells that transfered genes.
Depends on the LUCA... multicellular Eukaryotes have a LUCA. Not as universal as it could be, but nothing is perfect. :cool:

This leads me to a conclusion that all life that arose by some natural means was very similar. So similar in genetic makeup were these cells that they were able to negotiate gene transfer.
The ones that gave rise to living life were... but not all life needed to use the same molecules of inheritance. If they incomparable then no transfer would have happened.

How does this minimum viable population fit in here? How did primtive cells stuck to a rock manage to transfer genes? How did cells floating around in the ocean or in a pond manage to do so?
The same way they do now.

Were there hundreds of thousands of these primitive cells all having come into existence with the same genetic structure or just a few that managed to find each other or is common thinking suggesting still just one cell, coming to life one time?
Genetic structure predated cells.

What is also interesting is that if earth or the universe are strewen with the precursors for life one would expect life would have arisen on more than one occasion with a very different genetic makeup. This does not appear to be the case.
Actually, that is very likely the case. It's just that one was able to out compete the rest.

I understand the initial RNA world, but RNA still has alleles don't they? I expect that RNA in all life must also be the same. However this does not appear to be the case. There are many deletions. If primitive cells had RNA, did RNA arise after reproduction was enabled or before. It appears reproduction cannot exist without a genetic mechanism already assembled to support it.
Structurally different alleles of the ath-MIR824 microRNA precursor are maintained at high frequency in Arabidopsis thaliana
Before.

"The modes of HGT are transformation. This actually appears to require other genetic material around at the time to uptake. Transduction requires a virus to be around for HGT to occur this way, Bacterial conjucation requires contact of the cells, Gene transfer agents also appear to need virus around. How did the fist living cells ever manage to negotiate gene transfer, particularly in the oceans re thermal vent abiogenesis?
The same way they do today.
What is really cool, is that the first replicators were likely parasitic, stealing genetic material from others to build copies of themselves.

There was just bacteria, no virus yet evolved and no other genetic material was around at the time. The planet was lifeless apart from these primitive cells.
Actually it wasn't even bacteria yet... bacteria is pretty highly evolved. Viruses may be the secondarily simplified descendants of the first proto-cells

Nor is abiogenesis (the origin of the first life) due purely to chance. Atoms and molecules arrange themselves not purely randomly, but according to their chemical properties. In the case of carbon atoms especially, this means complex molecules are sure to form spontaneously, and these complex molecules can influence each other to create even more complex molecules. Once a molecule forms that is approximately self-replicating, natural selection will guide the formation of ever more efficient replicators. The first self-replicating object didn't need to be as complex as a modern cell or even a strand of DNA. Some self-replicating molecules are not really all that complex (as organic molecules go). " from the 5 misconceptions re evolution thread.

This info appears to be saying that all life that arises is going to be the same as it is not random but will arise according to their chemical properties. This article also suggests that scientists are uncertain how many cells were initially formed, yet they were numerous enough to negotiate HGT.
You only need 2 cells for HGT.. it isn't that complex. The real trick was stopping someone else from stealing your genes or forcing theirs on you.


If only a few hundred cells arose initially, how come they did not die out according to this minimum viable population theory? Does it apply to asexually reproductive organisms?
They didn't have any competition. Like mold growing on bread they will spread as long and as far as they have space and resources.
They also are pretty poor at copying their genomes with high fidelity... so there is a lot of genetic drift producing a fast burst of genetic variation. Modern Bacteria are not as good at copying their genomes as Eukaryotes are and can switch from slow reproduction with higher fidelity to fast reproduction with very low fidelity depending on their circumstances.

Also fun... modern bacteria can produce millions of descendants in 24 hours under the right conditions.

wa:do
 
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freethinker44

Well-Known Member
Oh yeah, well how does evolution explain the way the oceans tides work. IT CAN'T! Nothing can, we don't know. Evolution = fail, Jesus = win.


Just kidding. I was going to to get involved in this but at least 5 people said exactly the same thingsI was going to say.
 

painted wolf

Grey Muzzle
But Painted Wolf, the old process that allows non-new biomolecules to form in an advanced cell inside an animal is also just basic chemistry.
Very much so, and this is an important point showing that no supernatural intervention was needed. Abiogenesis IMHO is more a hypothesis of organic chemistry than evolution.

If some people want to make an arbitrary cutoff and say that evolution began with the appearance of the first living thing, that's fine by me. However I will remind them that this cutoff is completely arbitrary, not necessary, and entirely by their own choice.
Then I might want to ask them what the first living thing was, and where it came from.
This get's into the philosophical definition of life.

I would argue that that first living thing came from evolution by natural selection on non-living things, since the physical and chemical mechanism of that change is identical. Since the magnitude of physical difference between the last pre-living thing and the first living thing is going to be comparable to a single nucleotide polymorphism.
It's a tricky question, what was the first living thing?
Could the difference between life and non-life be such a simple thing as a single nucleotide change?
Or would it need to be more complex, say the keeping of RNA within a membrane?

Would a virus be alive? What do you think of macroviruses like Mimivirus?

wa:do
 
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