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How Can Chemistry Become Biology?
45 Answers
How did life start?
Here's what I know roughly;
~ Big Bang: energy condensed to form nuclei, which formed atoms of Hydrogen;
~ Stellar furnaces: clouds of Hydrogen collapsed under gravity to form the first stars;
~ Super Nova: stars fuse Hydrogen into Helium and dying stars create heavier elements and propel them through space in a massive explosion;
~ Solar System: the Sun ignites and the planets form from 2nd/3rd generation stellar matter;
~ Asteroids: bring water and basic amino acids to early Earth (fundamental molecules for life)
~ Enviroment: volcanic erruptions, ferocious tides, intense lightning and acidic waters...
So I get the story before genesis, atoms and molecules forming from the cosmic soup post Big Bang... And I get after genesis, Darwins evolution of organisms to survive, thrive and multiply... What about genesis itself?
What happened to change chain's of molecules into a living creature that conforms to biology's standard requirements for live: movement, respiration, sensitivity, growth, reproduction, excretion and nutrition.
I presume an Amoeba follows instinct to guide it through life but how did atoms, chained into molecules, "learn" to form DNA for example, or become aware of it's surroundings?
What is science's best guess? Can you refer me to literature/media that could help me understand?
IHI
Here's what I know roughly;
~ Big Bang: energy condensed to form nuclei, which formed atoms of Hydrogen;
~ Stellar furnaces: clouds of Hydrogen collapsed under gravity to form the first stars;
~ Super Nova: stars fuse Hydrogen into Helium and dying stars create heavier elements and propel them through space in a massive explosion;
~ Solar System: the Sun ignites and the planets form from 2nd/3rd generation stellar matter;
~ Asteroids: bring water and basic amino acids to early Earth (fundamental molecules for life)
~ Enviroment: volcanic erruptions, ferocious tides, intense lightning and acidic waters...
So I get the story before genesis, atoms and molecules forming from the cosmic soup post Big Bang... And I get after genesis, Darwins evolution of organisms to survive, thrive and multiply... What about genesis itself?
What happened to change chain's of molecules into a living creature that conforms to biology's standard requirements for live: movement, respiration, sensitivity, growth, reproduction, excretion and nutrition.
I presume an Amoeba follows instinct to guide it through life but how did atoms, chained into molecules, "learn" to form DNA for example, or become aware of it's surroundings?
What is science's best guess? Can you refer me to literature/media that could help me understand?
IHI
Answers
OK '
08:56 Thu 21st Feb 2013
Life in its most basic form is about replication.
Replication started long before life in mineral crystals. Once carbon got involved in the mineral mix the possibilities expanded enormously.
The leading contender for abiogenesis is in the "white smokers" on the bottom of the ocean. Here alkaline hot water vents in olivine strata produce the mineral serpentine in bubble structures very similar in size to a primitive cell.
More importantly the chemical process involved is exactly the same as the most fundamental energy reaction that occurs in all living things, without exception.
One a fatty membrane had evolved the primitive organisms that formed in the mineral bubbles would have been able to leave the structure and float free in the ocean.
Replication started long before life in mineral crystals. Once carbon got involved in the mineral mix the possibilities expanded enormously.
The leading contender for abiogenesis is in the "white smokers" on the bottom of the ocean. Here alkaline hot water vents in olivine strata produce the mineral serpentine in bubble structures very similar in size to a primitive cell.
More importantly the chemical process involved is exactly the same as the most fundamental energy reaction that occurs in all living things, without exception.
One a fatty membrane had evolved the primitive organisms that formed in the mineral bubbles would have been able to leave the structure and float free in the ocean.
OK 'abiogenesis' is the biggie in Chemistry and Biology - not my exact field but here's some pointers.
A lot of interest was first sparked (excuse the pun) by the Miller-Urey experiment back in the 50s which took a lot of the chemicals about in the early earth, heated them and passed a spark through for several days and found traces of most of the amino acids necessary for life
We're not going to be looking for DNA - that's way to complex and a RNA basis may even be too complex althougth the 'RNA world' hypothesis suggests this others suggest a 'Thioester world' where sulphur chemistry is the key role
http://
Amino acids are the building blocks of proteins which in turn are the building blocks of life.
But that's not the same as a self replicating chemical - by a long shot.
The cell membrane is another important early requirement as you need a structure to keep everything together and an energy capture mecanism to run it all.
We'll probably never know exactly what happened on Earth - the evidence has been wiped out, but we may be able to work out how it could have happened
http://
One final thought - basic life appeared realy really fast on Earth (almost as soon as the early bombardment phase stops) which makes it look as if life probably starts quite easilly. It was another 3 billion years before complex life appears. That required the capture of one life form (mitochondria) by another.
This was an unbelieveably important event and catapulted life from being not much more than slime.
It may have been an amazingly improbable event - we don't know - there's only one example to look at.
The Universe is probably full of life - if that life is more than lichen - I'm not yet decided
A lot of interest was first sparked (excuse the pun) by the Miller-Urey experiment back in the 50s which took a lot of the chemicals about in the early earth, heated them and passed a spark through for several days and found traces of most of the amino acids necessary for life
We're not going to be looking for DNA - that's way to complex and a RNA basis may even be too complex althougth the 'RNA world' hypothesis suggests this others suggest a 'Thioester world' where sulphur chemistry is the key role
http://
Amino acids are the building blocks of proteins which in turn are the building blocks of life.
But that's not the same as a self replicating chemical - by a long shot.
The cell membrane is another important early requirement as you need a structure to keep everything together and an energy capture mecanism to run it all.
We'll probably never know exactly what happened on Earth - the evidence has been wiped out, but we may be able to work out how it could have happened
http://
One final thought - basic life appeared realy really fast on Earth (almost as soon as the early bombardment phase stops) which makes it look as if life probably starts quite easilly. It was another 3 billion years before complex life appears. That required the capture of one life form (mitochondria) by another.
This was an unbelieveably important event and catapulted life from being not much more than slime.
It may have been an amazingly improbable event - we don't know - there's only one example to look at.
The Universe is probably full of life - if that life is more than lichen - I'm not yet decided
Excellent article in the link provided, summarising many of the different theories of how life started.
Most are speculative hypotheses, for obvious reasons. Makes for interesting reading.
The key steps are self-replication, then the transition from the simple chain molecules to something resembling RNA and then onto DNA, and as Jake has already mentioned, the merging of mitochondria and the formation of membranes, which allowed for cells and hence complex life forms.
http://
Most are speculative hypotheses, for obvious reasons. Makes for interesting reading.
The key steps are self-replication, then the transition from the simple chain molecules to something resembling RNA and then onto DNA, and as Jake has already mentioned, the merging of mitochondria and the formation of membranes, which allowed for cells and hence complex life forms.
http://
Superb answers guys, exactly the depth of info I wanted to help me rationalise it all...
@jake - I'd heard of the Miller-Urey experiment, replicating condition on early earth, the mix of gases in the atmosphere, the hot chemical soup of the oceans, factoring in it's acidity and the use of a spark inside the 'atmosphere' flask to represent the violent lighting storms that ravaged early Earth. And It's quite amazing to see under laboratory conditions, with only the ingredients, heat and electricity, one can create amino acids. I get that.
I also get the replication thing, but in its more familiar form of cell mitosis (
@jake - I'd heard of the Miller-Urey experiment, replicating condition on early earth, the mix of gases in the atmosphere, the hot chemical soup of the oceans, factoring in it's acidity and the use of a spark inside the 'atmosphere' flask to represent the violent lighting storms that ravaged early Earth. And It's quite amazing to see under laboratory conditions, with only the ingredients, heat and electricity, one can create amino acids. I get that.
I also get the replication thing, but in its more familiar form of cell mitosis (
Energy, and simple chemical synthesis.If you want to get really fundamental about it, much of chemistry comes down to Redox reactions - reduction / oxidation. An amino acid is a relatively simple organic compound.
Whats imakes amino acids so significant, so useful in biochemical tersm is down to its 2 functional groups, an amine and a carboxylic acid group, and it is these active regions which allow for further synthesis and complexity, giving rise to things like proteins.
So,a selection of inorganic elements + power result in simple organic compounds.
What is fascinating to me is that, of all those amino acids, just 23 have become important for life - and all life uses the same 23 amino acids. Further, all of these 23 are L--stereoisomers. Sugars, on the other hand, are all D- stereoisomers.
This homochirality is a source of debate. Was it just a random choice, or does it offer weight to arguments around life being transported here aboard comets etc.?
Whats imakes amino acids so significant, so useful in biochemical tersm is down to its 2 functional groups, an amine and a carboxylic acid group, and it is these active regions which allow for further synthesis and complexity, giving rise to things like proteins.
So,a selection of inorganic elements + power result in simple organic compounds.
What is fascinating to me is that, of all those amino acids, just 23 have become important for life - and all life uses the same 23 amino acids. Further, all of these 23 are L--stereoisomers. Sugars, on the other hand, are all D- stereoisomers.
This homochirality is a source of debate. Was it just a random choice, or does it offer weight to arguments around life being transported here aboard comets etc.?
You might find this artilce informative especially page 3 on
http://
Don't think DNA think RNA which is a simpler single helix fwhich simpler organisms like bacteria depend on (although it's also found playing a role in complex cells too).
The other angle is the sulphur chemistry of Thioesters ( page 5 onwards). These happen to play a role in the ATP cycle which is the cycle that generates energy in the cell and so Thioester chemistry obviosly goes back a long way in evolutionary terms.
http://
Don't think DNA think RNA which is a simpler single helix fwhich simpler organisms like bacteria depend on (although it's also found playing a role in complex cells too).
The other angle is the sulphur chemistry of Thioesters ( page 5 onwards). These happen to play a role in the ATP cycle which is the cycle that generates energy in the cell and so Thioester chemistry obviosly goes back a long way in evolutionary terms.
Beso's comment above about deep sea water vents is very topical and this gives the latest info by British scientists:
http://
http://
@Lazygun
//"Energy, and simple chemical synthesis." - are you then saying that the physical laws of this Universe that govern the interaction of atoms with each other to form chains, when in a high energy liquid, necessarily start a process of combining and scaffolding itself to form more variations of form and increased complexity that inevitably tracks the path of evolution, "snowballing" the resulting chemical combinations (with their seemingly endless differing properties/reactive qualities) into the world we see today? All of this MUST happen if you combine, Sulphur, Nitrogen, Carbon Dioxide, water, heat and lightning?!? (may not be the full list)
So in essence, as all these ingredients are born of the "natural" processes of the Universe since it's creation, conforming to the known physical laws, mustn't it logically be Biology's only conclusion that life wasn't a curious fluke, but it must have and always was destined? I've not heard this said before... Do you know if modern science agrees with my 'guestemated' hypothesis?
@Old Geezer
I am your inner child :)
Please keep your answers coming, I'm truly gripped... Much to disinterest of my friends!! I couldn't have hoped for better minds to throw fact back at the mind of curiosity!
IHI
//"Energy, and simple chemical synthesis." - are you then saying that the physical laws of this Universe that govern the interaction of atoms with each other to form chains, when in a high energy liquid, necessarily start a process of combining and scaffolding itself to form more variations of form and increased complexity that inevitably tracks the path of evolution, "snowballing" the resulting chemical combinations (with their seemingly endless differing properties/reactive qualities) into the world we see today? All of this MUST happen if you combine, Sulphur, Nitrogen, Carbon Dioxide, water, heat and lightning?!? (may not be the full list)
So in essence, as all these ingredients are born of the "natural" processes of the Universe since it's creation, conforming to the known physical laws, mustn't it logically be Biology's only conclusion that life wasn't a curious fluke, but it must have and always was destined? I've not heard this said before... Do you know if modern science agrees with my 'guestemated' hypothesis?
@Old Geezer
I am your inner child :)
Please keep your answers coming, I'm truly gripped... Much to disinterest of my friends!! I couldn't have hoped for better minds to throw fact back at the mind of curiosity!
IHI
It's probably dangerous to say that life *had* to happen, though in the long run I think it's likely that this is what biophysics will be able to demonstrate. What IS true is that as a general law Physical systems try to minimise what is called "Free Energy". So, perhaps, if you can show that the molecules necessary to create life, i.e. Amino Acids and proteins, are both (a) fairily stable and (b) at or near a minimum of free energy, then life didn't so much have to happen, but it was just easier.
At least that's how I think it presumably is. At this point I don't think anyone's proved that -- the systems we're talking about are probably both too complicated and not really known anyway -- what WAS the Earth like when Life began? That famous experiment alluded to earlier showed that amino acids could be made, but little progress in that direction has been made since. I think the general view is that conditions at least in the atmosphere weren't quite as favourable as they were in that test-tube Miller-Urey used.
This is anyway outside my area of expertise and study, so this post could easily be complete and utter rubbish. But my gut feeling is that life emerging will turn out to have been in some sense more efficient than life not emerging.
At least that's how I think it presumably is. At this point I don't think anyone's proved that -- the systems we're talking about are probably both too complicated and not really known anyway -- what WAS the Earth like when Life began? That famous experiment alluded to earlier showed that amino acids could be made, but little progress in that direction has been made since. I think the general view is that conditions at least in the atmosphere weren't quite as favourable as they were in that test-tube Miller-Urey used.
This is anyway outside my area of expertise and study, so this post could easily be complete and utter rubbish. But my gut feeling is that life emerging will turn out to have been in some sense more efficient than life not emerging.
@Jim360 - No, I think your post sums it up pretty well.
We cannot conclude that the physics governing our universe that underpin the chemistry and hence biology will inexorably lead to life; We only have 1 planets worth of data out of a universe with 100s of billions of stars and 100s of billions of planets with which to judge :)
The Earths atmosphere 3.5 billion years ago is an unknown; Some hypothesize that it was not nearly so nitrogen rich as the Miller-Urey experiments were based upon.
The step from inorganic to organic; from long chain polymerisation to cellular life; the step from cellular life to multicellular - these are all steps where our knowledge is hypothetical and speculative.
So, I do not think we have sufficient evidence or even a well supported hypothesis to reasonably conclude that the physics of the universe will inexorably lead to complex life like our own.
The Earth, with its diversity of life sharing common biochemical principles, the development of complex life like our own could be an extremely improbable event.... You might argue that, had the universal constants and their relationships been different, that might have led to a more favourable environment for the development of complex lifeforms.....
We cannot conclude that the physics governing our universe that underpin the chemistry and hence biology will inexorably lead to life; We only have 1 planets worth of data out of a universe with 100s of billions of stars and 100s of billions of planets with which to judge :)
The Earths atmosphere 3.5 billion years ago is an unknown; Some hypothesize that it was not nearly so nitrogen rich as the Miller-Urey experiments were based upon.
The step from inorganic to organic; from long chain polymerisation to cellular life; the step from cellular life to multicellular - these are all steps where our knowledge is hypothetical and speculative.
So, I do not think we have sufficient evidence or even a well supported hypothesis to reasonably conclude that the physics of the universe will inexorably lead to complex life like our own.
The Earth, with its diversity of life sharing common biochemical principles, the development of complex life like our own could be an extremely improbable event.... You might argue that, had the universal constants and their relationships been different, that might have led to a more favourable environment for the development of complex lifeforms.....
Isn't the weight of evidence we have for nature playing the driving role in (if not formation) the evolution of life sufficient enough to propose a strong argument that there was no 'miricale intervension' needed to create life on habitable planets/moons?
We can never assume and I share science's belief that data analysis is the only way to form a conclusion, however might I myself personally me, disregard the emergence of life as divine intervention and concentrate solely on the difficult topic "Why does our Universe seem to have such finely tuned values for the forces, that when fractionally altered create sterile Universes?"
Multi-verse or Creator? What do you think?
IHI
We can never assume and I share science's belief that data analysis is the only way to form a conclusion, however might I myself personally me, disregard the emergence of life as divine intervention and concentrate solely on the difficult topic "Why does our Universe seem to have such finely tuned values for the forces, that when fractionally altered create sterile Universes?"
Multi-verse or Creator? What do you think?
IHI
Hmm... A fallacy of the fine tune argument remains its anthrocentric viewpoint.
Whilst changing some of the constants might be result in a universe inimical to human life, that does not necessarily invalidate some other sort of life. Nor does the argument ever properly consider the proposition that the relationships between the constants might also change if you changed some of the constants.
So I do not accept the fine-tuned universe as an argument, except in the trivial case that the conditions in our universe were ok for the formation of humanity. A couple of researchers have suggested that actually those constants that currently exist within our universe are actually at the marginal end of what might be considered "fine-tuned" :)
Remember also that the only evidence we have of life is the evidence collected from this planet - At the moment, all the science tells us about life in the universe is that just one planet, ours, Earth,, out of the thousands of billions of planets in the universe actually has life on it. Hardly a ringing endorsement of the finely-tuned universe proposition is it?
I certainly think that there is no real argument in favour of a creator. All the observation, all the evidence points to a natural process rather than divine intervention. So, I think you can consign the idea of a creator deity to the margins - extremely improbable.
And, to be honest with you, I do not know enough about the maths and the physics to comment on the idea of a multiverse. I am not sure that it has a robust mathematical basis,it does not have any observational evidence to support it, that I am aware of, so I would consider a multiverse to be something plausible but improbable :)
Whilst changing some of the constants might be result in a universe inimical to human life, that does not necessarily invalidate some other sort of life. Nor does the argument ever properly consider the proposition that the relationships between the constants might also change if you changed some of the constants.
So I do not accept the fine-tuned universe as an argument, except in the trivial case that the conditions in our universe were ok for the formation of humanity. A couple of researchers have suggested that actually those constants that currently exist within our universe are actually at the marginal end of what might be considered "fine-tuned" :)
Remember also that the only evidence we have of life is the evidence collected from this planet - At the moment, all the science tells us about life in the universe is that just one planet, ours, Earth,, out of the thousands of billions of planets in the universe actually has life on it. Hardly a ringing endorsement of the finely-tuned universe proposition is it?
I certainly think that there is no real argument in favour of a creator. All the observation, all the evidence points to a natural process rather than divine intervention. So, I think you can consign the idea of a creator deity to the margins - extremely improbable.
And, to be honest with you, I do not know enough about the maths and the physics to comment on the idea of a multiverse. I am not sure that it has a robust mathematical basis,it does not have any observational evidence to support it, that I am aware of, so I would consider a multiverse to be something plausible but improbable :)
So... Isn't God a creation of Human experience with is highly intelligent brain questioning how everything came to be? And so isn't the defining feature of life's miracle when the being is more than just the sum of it's parts? As most other animals on Earth survive on instinct and chemical triggers that precede changes in behaviour, isn't the ability of a Universe to have the value of it's constants set in such a way that high intelligence can evolve the over riding factor?
Thus mustn't the anthrocentric viewpoint of the fine tune argument be the very reason for it's importance in modern science and the understanding of why the cosmological constants are set as they are and why we are here to even ask the question "Why?"...?
IHI
Thus mustn't the anthrocentric viewpoint of the fine tune argument be the very reason for it's importance in modern science and the understanding of why the cosmological constants are set as they are and why we are here to even ask the question "Why?"...?
IHI
IHI - Sorry, my brain is not working well enough to decode your last post :) You may need to expand or clarify some of the points a bit.
"So... Isn't God a creation of Human experience with is highly intelligent brain questioning how everything came to be?"
I would say so, yes.
"And so isn't the defining feature of life's miracle when the being is more than just the sum of it's parts? As most other animals on Earth survive on instinct and chemical triggers that precede changes in behaviour......."
Not sure exactly what you mean by this. Firstly,much of human activity and behaviour is governed by instinct and chemical triggers, far more than many people realise. Consciousness, the sense of self, rationalisations and all of that are an emergent property overlaid upon the primal instinct and behavioural triggers.
So when you talk about "lifes miracle" - are you talking about consciousness, or life itself? I dislike the term miracle, because it is freighted with meaning - usually some sort of divine intervention. But again, based purely upon what we currently know about life ( life on earth), conscious life with a sense of self, with the ability for abstract thought and rationalisation is certainly extremely rare and remarkable.
"sn't the ability of a Universe to have the value of it's constants set in such a way that high intelligence can evolve the over riding factor"
How does this follow the previous statement? Consciousness/ abstract thought is an extremely rare commodity, as far as we know. On the one planet where we have been able to study lifeforms, consciousness as expressed in humans is extremely rare. As far as we know, we are the only examplars of such thinking in the Universe. so how can we then go on to claim that the universe is fine-tuned for such life?
"Thus mustn't the anthrocentric viewpoint of the fine tune argument be the very reason for it's importance in modern science and the understanding of why the cosmological constants are set as they are and why we are here to even ask the question "Why?"...?"
Sorry, IHI - I cannot parse what you are trying to say with this paragraph... I do not think I am complex enough :)... Could you clarify?
I will make this observation -When talking about the universal constants being "set" that implies several things that I am uncomfortable with. Firstly, it implies that they could adjusted, which in turn leads to the question - adjusted by what? It also fails to recognise that if you were able to change one or more of these fundamental constants, as they have been described, that may very well change the relationship between itself and some of the other constants.
By focusing on such fundamental constants, it ignores some other factors that were equally important in the history of the development of humanity - things like the extinction event that did for the dinosaurs, and thus cleared the way for the expansion of mammals.
That the anthropic principle exists is uncontroversial, and, to be honest, not all that remarkable ; To put the cart before the horse and state that because humans have evolved this means that the Universal conditions were set to allow our existence is to take the principle too far....
"So... Isn't God a creation of Human experience with is highly intelligent brain questioning how everything came to be?"
I would say so, yes.
"And so isn't the defining feature of life's miracle when the being is more than just the sum of it's parts? As most other animals on Earth survive on instinct and chemical triggers that precede changes in behaviour......."
Not sure exactly what you mean by this. Firstly,much of human activity and behaviour is governed by instinct and chemical triggers, far more than many people realise. Consciousness, the sense of self, rationalisations and all of that are an emergent property overlaid upon the primal instinct and behavioural triggers.
So when you talk about "lifes miracle" - are you talking about consciousness, or life itself? I dislike the term miracle, because it is freighted with meaning - usually some sort of divine intervention. But again, based purely upon what we currently know about life ( life on earth), conscious life with a sense of self, with the ability for abstract thought and rationalisation is certainly extremely rare and remarkable.
"sn't the ability of a Universe to have the value of it's constants set in such a way that high intelligence can evolve the over riding factor"
How does this follow the previous statement? Consciousness/ abstract thought is an extremely rare commodity, as far as we know. On the one planet where we have been able to study lifeforms, consciousness as expressed in humans is extremely rare. As far as we know, we are the only examplars of such thinking in the Universe. so how can we then go on to claim that the universe is fine-tuned for such life?
"Thus mustn't the anthrocentric viewpoint of the fine tune argument be the very reason for it's importance in modern science and the understanding of why the cosmological constants are set as they are and why we are here to even ask the question "Why?"...?"
Sorry, IHI - I cannot parse what you are trying to say with this paragraph... I do not think I am complex enough :)... Could you clarify?
I will make this observation -When talking about the universal constants being "set" that implies several things that I am uncomfortable with. Firstly, it implies that they could adjusted, which in turn leads to the question - adjusted by what? It also fails to recognise that if you were able to change one or more of these fundamental constants, as they have been described, that may very well change the relationship between itself and some of the other constants.
By focusing on such fundamental constants, it ignores some other factors that were equally important in the history of the development of humanity - things like the extinction event that did for the dinosaurs, and thus cleared the way for the expansion of mammals.
That the anthropic principle exists is uncontroversial, and, to be honest, not all that remarkable ; To put the cart before the horse and state that because humans have evolved this means that the Universal conditions were set to allow our existence is to take the principle too far....
LazyGun, I've written and rewritten my reply to your last to try to understand the question I'm asking myself, in vain... You're brain I assure you is as complex, if not more, as mine however you have clearer thought...
.. It's a complicated soup of facts, figures, theology, cosmology, philosophy, reason, doubt and madness, sloshing around the cavity where my used to occupy before these thoughts destroyed my cognitive ability.
Might I take some more time to allow these thought to settle so I might pick out the issues I'm struggling with? (I think it's pen and paper time to jot down some notes so it's not all in my head!!)
I hope that when I can cohearently attach meaning to the points I'm making with the subject we're dealing with, I wont have lost your interest! I shall try not to take long, I hate an infinite wait :)
IHI
.. It's a complicated soup of facts, figures, theology, cosmology, philosophy, reason, doubt and madness, sloshing around the cavity where my used to occupy before these thoughts destroyed my cognitive ability.
Might I take some more time to allow these thought to settle so I might pick out the issues I'm struggling with? (I think it's pen and paper time to jot down some notes so it's not all in my head!!)
I hope that when I can cohearently attach meaning to the points I'm making with the subject we're dealing with, I wont have lost your interest! I shall try not to take long, I hate an infinite wait :)
IHI
