Origins of the First Living Cell and Evolution

Discussions on topics related to biochemistry and molecular biology, functional genomics, etc.

Re: Origins of the First Living Cell and Evolution

Postby Forest_Dump on April 11th, 2017, 10:12 am 

Braininvat wrote:If God can sit in a laboratory and stitch together proteins and protein-synthesizing nanomachines and then plant them in ponds on the young Earth, then you have definitely postulated a metaphysical theory that God is, itself, a physical being that interacts with other physical matter. And using such a postulate to fill explanatory gaps in the process of abiogenesis would seem outside the realm of biochemistry. So, either we get back to probabilistic analysis of spontaneous protein synthesis and replication, based on actual science, or we move the thread.


That was my insertion, of course, which as simply intended to close off a minor point from near the beginning of this. In these kinds of critiques, personally I'm not sure how often it is really possible to seal off science, etc., from exterior belief systems be they religious, economic, political, etc. As we see here, neither "science" nor the broader public live or act in a vacuum.
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on April 13th, 2017, 8:43 am 

Eclogite » March 31st, 2017, 2:44 pm
Most and probably all of the subsequent points you make in your OP are predicated on the truth of your statement: there is no credible theory of the origin of the first living cell. We need, therefore, to deal with that statement first. What is it that you find incredible out these hypotheses?

Stuart Kauffman's Autocatalytic Sets

Christian de Duve's pathway from thiosesters to RNA to protocells

Cairn-Smith's Clay Templates


Eclogite
I realise that I haven’t responded to your suggested sources – apologies.

In brief I have now checked them out and discovered that Kauuffman and de Duve have only made credible proposals about how the first single-celled organisms developed into multi-cell organisms. Those proposals are interesting but are unproven, and do not address my core point – the origin of the first cell.

I have already mentioned that the outline idea of Cairn-Smith about crystals on the edges of muddy pools have not been shown to work with amino acids or even the nucleotide components of RNA. They do not even begin to address the questions of assembling proteins or the sequence of codes inherent in the only reproductive mechanism that we have.
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on April 13th, 2017, 9:16 am 

vivian maxine » April 10th, 2017, 8:32 pm
Forest is right. Oxygen (safe oxygen) was a late-comer.

"Oxygen Revolution, 1800Myr. Although animals need oxygen to survive, primitive life began in the absence of free oxygen, and when oxygen built up in the sea-water, it was deadly poison for organisms unequipped to deal with it."


Hi Vivian
The point which Forest seemed to be making was that the only reason why amino acids and nucleotides haven't been shown to be active with any of the suggested mechanisms is because of the presence of free oxygen in our current environment. By implication he was saying that if free oxygen could be removed then such things would be possible - and that hasn't been demonstrated in the lab to my knowledge.

We know that different rocks which appear in the earth's crust are believed to come from two planetary bodies that collided some 4.5 billion years ago. As the water is here, it is likely that one of those bodies held most of the water/oxygen when the other had virtually none. This, I thought, was one of the basic arguments for the different types of rock and the environments that they were formed in.

It is entirely possible that free oxygen could be present somewhere in the planet even in the earliest days - possibly even in large quantities - but that doesn't mean it was everywhere. Tectonic activity could easily melt rocks and mix them with organic material later.

Having said that, I agree that life probably did originally form in an environment without free oxygen, even if this was murky fluids devoid of free oxygen - but that doesn't detract from the core point. None of the proposed environments seem to support the generation/manipulation of either amino acids or nucleotides.

Indeed, I believe that the only way in which nucleotides can be produced in the lab is through re-cyling or the use of ribosomes. There is no known manufacturing process outside the living cell.
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Re: Origins of the First Living Cell and Evolution

Postby Eclogite on April 13th, 2017, 9:43 am 

scientificphilosophe » Thu Apr 13, 2017 1:16 pm wrote:We know that different rocks which appear in the earth's crust are believed to come from two planetary bodies that collided some 4.5 billion years ago. As the water is here, it is likely that one of those bodies held most of the water/oxygen when the other had virtually none. This, I thought, was one of the basic arguments for the different types of rock and the environments that they were formed in.
It is, perhaps, off-topic, but I am not sure where you got these ideas from. They are incorrect, or at best a badly mangled interpretation of the currently understood situation.

The rocks present in the Earth's crust do not come from either Theia (the Mars sized protoplanet collider) or the proto-Earth. The energy of the collision insured the Earth was molten and without a crust. Perhaps you meant that the material now present in the Earth's crust came from the two protoplanets. That is correct, but is quite different in its implications from what you actually said.

Thinking on the nature of the collisions and the character of the two bodies continues to evolve, but as to the best of my understanding there has been no serious suggestion that the water was concentrated in one or other. Indeed, the consensus view at present appears to be that both Theia and the proto-Earth formed in roughly the same portion of the proto-planetary disc and consequently have similar compositions, including water.

The variety of rocks to be found in the crust are a consequence of post-collision developments, including development of the crust, formation of oceans and atmosphere, inception of plate tectonics, etc. It has nothing to do with differences or similarities of the two protoplanets.

I don't think, either way, this impacts on your thesis or questions, but I felt it was a serious enough misunderstanding to merit correction.
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Re: Origins of the First Living Cell and Evolution

Postby SciameriKen on April 13th, 2017, 9:50 am 

scientificphilosophe » Thu Mar 30, 2017 2:47 pm wrote:If the process of evolution cannot explain the origin of the first cell then you are back into the realms of God so it is an important consideration for everyone - whether you have religious leanings or not. It is not my problem per se.


Greetings SP - I am not sure if this is your position or if you are merely representing the lay person - but why is there a need to invoke the "realms of god" if evolution cannot explain the origins? Sure to do so answers the question where did life come from - but that is it - where do we go from there? If we search for life on other planets will we look for signs that God was there? :D
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on April 13th, 2017, 10:00 am 

Eclogite » April 13th, 2017, 2:43 pm

The rocks present in the Earth's crust do not come from either Theia (the Mars sized protoplanet collider) or the proto-Earth. The energy of the collision insured the Earth was molten and without a crust. Perhaps you meant that the material now present in the Earth's crust came from the two protoplanets. That is correct, but is quite different in its implications from what you actually said.


Hi Eclogite
I am happy for the point to be clarified in terms of the way in which my words are read, but I believe I was making the correct point.

We have only theorised about the different planetary bodies because of the presence of two different types of rock in the crust. That they are different means that they haven't mixed.
I don't disagree that the surface was molten - but they didn't mix so they were true to their sources - if the theory is correct.

As oxygen was thought to become 'free' after the solidification of the rocks, the different types of source rock, (some of which I believe could be formed in an environment with oxygen), does seem to point to one planet being without oxygen/water, and the other having it.
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Re: Origins of the First Living Cell and Evolution

Postby Forest_Dump on April 13th, 2017, 10:22 am 

scientificphilosophe wrote:We have only theorised about the different planetary bodies because of the presence of two different types of rock in the crust. That they are different means that they haven't mixed.


I am curious about what the two different types are. Do you mean felsic vs. mafic? Or those that formed in an oxygen free environment vs. those that formed in an atmosphere with free oxygen? If the latter dichotomy, then we would have to take into account time of when the rocks formed as both kinds are forming today. Rocks forming at the surface, for example, are forming in an atmosphere with free oxygen while rocks forming deep down from overall cooling of the earth are still forming in an oxygen free environment but can then be exposed from various causes.
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on April 13th, 2017, 10:30 am 

SciameriKen » April 13th, 2017, 2:50 pm

Greetings SP - I am not sure if this is your position or if you are merely representing the lay person - but why is there a need to invoke the "realms of god" if evolution cannot explain the origins? Sure to do so answers the question where did life come from - but that is it - where do we go from there? If we search for life on other planets will we look for signs that God was there? :D


Greetings to you too SciameriKen.
Good ID name bye-the way - assuming it reflects your real first name!

I briefly raised the point about God in response to the personalisation of a previous post which sought to make the issue 'my problem'. It isn't.

Having said that, as I made clear in a later response, we can all be challenged by people with religious beliefs and it is useful to know how to answer such points.

There are many grades of religious belief, and also many religions.
I am not concerned with that. I am interested in what can be reasonably demonstrated.

Science can determine facts, but these still have to be interpreted. We have to explain all facts because they never change - only our interpretations change. Equally, science has to work with philosophy because it is the disciplines of philosophy which help to structure our speculations about the unknown.... but the theorising always has to match the facts.

It is a fact that the Theory of Evolution doesn't demonstrably work before the first cell.
That will ultimately lead us to questions about spontaneity, randomness and the abilities of existence to set a direction, or even to design outcomes. Whether we talk about hidden properties of matter at the deeper levels of existence; other types of stuff; or indeed, God - there are certain logical steps/factors that have to be overcome and these generally point to certain capabilities. Whether you attribute them to God or something else is a personal choice... but the necessary capabilities seem to be required.

In my opinion the search for other life is not bound to the questions posed by the dilemmas of origin, but the issues of the 'origin of life' may help to reveal more about ourselves and the nature of the Universe we occupy.

The emergence of Life is a second point of apparently fundamental change. If so, that seems to require a spontaneous, random, or external influence.

If living things demonstrate a level of control, spontaneity, consciousness etc that cannot be explained by physical matter alone then something else may be involved. If it is something like another 'force' then we might use it. I suspect that we may have less success in trying to 'bottle God'. ):
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Re: Origins of the First Living Cell and Evolution

Postby Eclogite on April 13th, 2017, 10:42 am 

scientificphilosophe » Thu Apr 13, 2017 2:00 pm wrote:Hi Eclogite
I am happy for the point to be clarified in terms of the way in which my words are read, but I believe I was making the correct point.

Unfortunately you have a fundamental misunderstanding, but I am happy to work with you to resolve it.

scientificphilosophe » Thu Apr 13, 2017 2:00 pm wrote:We have only theorised about the different planetary bodies because of the presence of two different types of rock in the crust. That they are different means that they haven't mixed.
This is completely incorrect. Can you tell me where you picked up this notion. And, to repeat Forest's question, what two types are you referring to?

There is no evidence - and I cannot state this too strongly - of two different types of rocks thought to have originated on different protoplanets. This is absolute. If you believe you have evidence to the contrary please post it.

The closest I can get to your perception is that by looking at isotope ratios in meteorites, moon rocks and the Earth, we can make certain deductions as to the original composition of Theia and the proto-Earth. This is totally different (much more subtle and elegant and complex and difficult) than there being two remnant rock types of the Earth.

scientificphilosophe » Thu Apr 13, 2017 2:00 pm wrote:I don't disagree that the surface was molten - but they didn't mix so they were true to their sources - if the theory is correct.
I take the risk of being repetitive. There is no such theory. I would be delighted to be proven wrong, for it would open up worlds of possibilities. I expect to be disappointed.


scientificphilosophe » Thu Apr 13, 2017 2:00 pm wrote:As oxygen was thought to become 'free' after the solidification of the rocks, the different types of source rock, (some of which I believe could be formed in an environment with oxygen), does seem to point to one planet being without oxygen/water, and the other having it.
This makes no sense to me at all. You are aware, are you not, that oxygen is the most abundant element in most rocks?
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Re: Origins of the First Living Cell and Evolution

Postby vivian maxine on April 13th, 2017, 11:33 am 

Having reached the bottom of this thread, I now forget who mentioned rocks that form at the surface and rocks that form deep underground. Are talking about volcanic rocks and sedimentary rocks?
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on April 20th, 2017, 6:46 pm 

Eclogite » April 13th, 2017, 3:42 pm

There is no evidence - and I cannot state this too strongly - of two different types of rocks thought to have originated on different protoplanets. This is absolute. If you believe you have evidence to the contrary please post it.



Hi Eclogite

Thanks for taking the trouble to write this, and I am happy to learn if people seek to argue their case.

In truth this was a foolish venture of mine into an area that isn't my main strength, but I did it to make a point to Forest, which still stands. I will return to this later.

There have been many hypotheses that postulated about different forms of rocks here on earth - admittedly largely based on different oxygen isotopes - but from one apparently incorrect article I saw, this extended to fundamentally different chemical compositions.

In 2014 a German research team claimed in support of this 'two rock type' hypothesis, that chemical analysis of moon rock has shown that it had a fundamentally different isotope profile. However a newer article I have just discovered makes reference to this and now disputes those findings.

http://newsroom.ucla.edu/releases/moon- ... planetMoon was produced by a head-on collision between Earth and a forming planet

If you look it up it claims that the rocks on Earth and the Moon basically have identical isotope proportions... more specifically it says that the UCLA team could find no differences.

While I have no preference on who to believe it does show you that other theories do exist, and that it is conceivable that material/rock might form without oxygen.


The underlying point I was trying to make is that you can't make assumptions about the earliest conditions on Earth or the potential for regularly generating amino acids and nucleotides in the same conditions.
This has never been demonstrated in the lab let alone in the real world.
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Re: Origins of the First Living Cell and Evolution

Postby Forest_Dump on April 20th, 2017, 8:16 pm 

Whichever ever of the two contrasting papers is correct, it is moot for this discussion. Regardless of whether there were two isotope signatures or one or twn, there is no question that there was oxygen present but it was not free oxygen in the atmosphere as O2 - ot was bound up with other atoms such as carbon dioxide.
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Re: Origins of the First Living Cell and Evolution

Postby vivian maxine on April 21st, 2017, 11:37 am 

scientificphilosophe, I don't know how much this will contribute. Just thought I'd mention it. New Scientist Collections, volume three, issue 5, has an article about how life came to be on Earth. "What If We Came From Space?". #7 on page 22.

The point is made that life appeared on Earth far too fast to have simply slowly developed here. It has to have come from elsewhere. It goes on to contend that "the galaxy is teeming with life, and our biosphere is just part of a vast, interconnected cosmic ecosystem". From there it introduces something called "Panspermia", making four points: sky-high bugs (evidence on a balloon experiment in 2012), alien fossils, lifelike light from space and red rain. Red rain? Is anyone thinking "Pern"?

So, make of it what you will/can. I never heard of Panspermia. And I am not sure there is any value in these ideas. Just a contribution to your original question of where life started.
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on May 7th, 2017, 10:38 pm 

Hi Vivian

Seeding from space has been a very long established way to try to overcome the mathematical odds of life happening, but there is no evidence for it.

The most we have ever encountered are some amino acids in the tails of comets - but we can easily create those here. What we struggle to do is to create all of the necessary amino acid types, and then assemble them in a reproducible way to create proteins.

Again - I believe there is no known way to synthesise nucleotides in order to generate DNA and RNA, and we can only 'manufacture' such things using living cells... that's even before we consider the code aspects of this mechanism.

To my knowledge no cell has ever been found in material from space - not even dead ones.

Many will argue that extending the potential 'source' area to our galaxy still isn't sufficient to make the odds credible. To then extend the generation ground to the entire visible universe then runs into problems with the amount of time such cells would have to survive to cross the enormity of space.... which would be bad enough even within the Milky Way.

In short the seeding from space hypothesis is not credible.

I personally feel that we have to search for mechanisms/processes that could operate here - in conditions which are suitable for sustaining life. However, as with other aspects of physical origin when you look at what has to occur it seems virtually impossible with the mechanisms as we know them. This is why people consider the possibility of other capabilities... which may or may not include God - but certainly going beyond what we are officially aware of today.
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Re: Origins of the First Living Cell and Evolution

Postby vivian maxine on May 8th, 2017, 7:38 am 

As good reasoning as any other I have heard, scientificphilosophe.
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Re: Origins of the First Living Cell and Evolution

Postby bangstrom on May 9th, 2017, 11:17 am 

scientificphilosophe » May 7th, 2017, 9:38 pm wrote:
To my knowledge no cell has ever been found in material from space - not even dead ones.

Dead cells from Mars may have been found. I suspect we will know in a few years if the speculation is correct.

https://www2.jpl.nasa.gov/snc/nasa1.html
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on June 24th, 2017, 4:19 pm 

scientificphilosophe » 07 May 2017 09:38 pm wrote:However, as with other aspects of physical origin when you look at what has to occur it seems virtually impossible with the mechanisms as we know them.


Care to walk me through establishing that statement, which you seem to be using as fact? It's not the argument from self incredulity again, is it? I don't think the impossibility of abiogensis on Earth, virtual or otherwise, has ever been established.

If anything, quite a bit of evidence points to the ability of organic matter - matter which has been shown to spontaneously form under Earthly conditions - to self assemble under certain (yes you guessed it) Earthly conditions. And more evidence demonstrates how such matter can evolve complexity over time. So... How exactly did you establish this impossibility?
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on June 24th, 2017, 6:20 pm 

Hi BioWizard

I said that it was virtually impossible with the mechanisms as we know them.
It is obviously a possibility that there are other capabilities which we do not yet know... but a lot of people have been trying to resolve the issues for a long time and they are not even close.

To answer your direct question...
We are not talking here about organic matter as that appears to be entirely based on the living cell. We are talking about inorganic matter prior to the first cell.
I have also mentioned that there is no known way to manufacture/synthesise nucleotides. We can only recycle ones that exist or manufacture more through... living cells.
Earlier posts have touched on the near impossible odds of a single protein occurring - which would seem to preclude any of the necessary re-occurrence for these short-lived organic molecules. We haven't touched on the 200 others all coming together at the same time, or the chain of 4 codes that underpin the whole process.
Codes.... not direct chemistry.

You should try to read books like 'Our Existence' which present the facts, the implications of those facts, as well as the full range of philosophies that might explain them
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on June 24th, 2017, 7:25 pm 

Hi scientificphilosophe. Before we get into the mystery at hand, let's try to warm up our detective muscles for a second.

Let's say you tell me a crime occurred in an apartment on the 10th floor of a building on a street in Chicago. If you provide me with evidence that a given Person X was within 5 blocks from the building 30 mins prior to the time of the crime, I will conclude that it is possible for Person X to be the person who committed the crime. If you provide me with proof that Person X was in New York 30 mins before the crime occurred, I will conclude that Person X is not likely to be the criminal, but that it's still possible. If you provide me with evidence that Person X was in China 30 mins before the time of the crime, I will conclude that it's almost impossible for Person X to be the actual criminal. However, I will submit that there is a possibility, however slim, that he (or she) is still the direct criminal (think remote controlled drones killing people at the other side of the planet).

Now of course, if I am to prove without doubt that Person X IS the actual criminal, it would take quite a bit of incriminating evidence. But so would proving the utter impossibility that Person X was the criminal. Especially nowadays, and especially if no other criminal is found. Why? Because nowadays, conditions would allow that to be possible - from incredibly sophisticated robotics to satellite links to lightening fast internet speeds. In other words, you can't say something is impossible just because you fail to imagine how it might be possible - especially so when conditions exist that may make it more likely, and more so when you have some information that could increase the likelihood of such conditions being relevant (for example, Person X is a robotics buff and has been building killbots all their life). I mean, that would at least raise a flag about the mere possibility, wouldn't it?

So why is this relevant to what we are discussing? Well, it's because we have multiple threads of evidence which show that organic molecules (*see more below on organic molecules) can form spontaneously on Earth, that they can self assemble into complex structures, that they can harness enthalpy (from the sun, volcanic vents, etc) to overcome entropy, and that their complexity could increase through selection. Granted, this is all far from enough to say without a scrape of doubt that Abiogenesis is exactly how life appeared on Earth. But it is at least enough to say that it is by no means an impossibility. The fact that humans haven't been able to replicate, in a couple decades of trying with technology that is remotely adequate, a process that has occurred over billions of years, is not really all that convincing as proof of the impossibility of the process now, is it?

scientificphilosophe » 24 Jun 2017 05:20 pm wrote:Hi BioWizard

I said that it was virtually impossible with the mechanisms as we know them.


Yep, you did say that. The issue is that I still haven't seen you (or anyone) actually demonstrate it.

It is obviously a possibility that there are other capabilities which we do not yet know...


What exactly is meant by "capabilities" here?

but a lot of people have been trying to resolve the issues for a long time and they are not even close.


How exactly are you quantifying that? Please be precise so I can understand where you're coming from.

To answer your direct question...
We are not talking here about organic matter as that appears to be entirely based on the living cell. We are talking about inorganic matter prior to the first cell.


My chemistry bias is showing. While most people use the word organic chemistry to mean the chemistry of life, chemists tend to use it to mean the chemistry of carbon. So when I said organic compounds, I was indeed including compounds that were precursors to life, not just products of it. Sorry for any confusion I may have caused there.

I have also mentioned that there is no known way to manufacture/synthesise nucleotides. We can only recycle ones that exist or manufacture more through... living cells.


Who is we? You and I? Because if that's what you meant, then yes that may very well be true. But if you mean people in general, then your statement is false. Nucleotides can be (and are) synthesized and isolated in the lab.

Earlier posts have touched on the near impossible odds of a single protein occurring - which would seem to preclude any of the necessary re-occurrence for these short-lived organic molecules.


Where was it demonstrated that proteins were a necessary requirement for the simplest of life forms to have emerged? Earlier life forms need not have had proteins like the ones we encounter in extant biology. Also remember that proteins and RNA are short lived today because of the presence of destructive conditions that may not have existed back then. For example the biggest destructive force for RNA is contamination by RNase that gets shed by all the living organisms walking around the Earth today. RNases are proteins, so back before proteins RNA may have enjoyed much longer stability.

We haven't touched on the 200 others all coming together at the same time, or the chain of 4 codes that underpin the whole process.
Codes.... not direct chemistry.


Where was it demonstrated that all these things would have had to come together at the same time for life to have emerged and evolved into its current form?

You should try to read books like 'Our Existence' which present the facts, the implications of those facts, as well as the full range of philosophies that might explain them


Yes! I should always try to read more - I agree. Would you, however, count it to my credit that I have over 20 years of research experience in biochemistry, and have probably read enough peer reviewed research papers to compile a 100 books or so? Other than it being a job requirement, I like to formulate my own opinions. So I go straight to the research and synthesize my thoughts based on the available evidence. Don't get me wrong, I would probably enjoy such a book as you describe quite a bit (assuming I had the time to read one). I just wouldn't mistake it for anything other than what it is - someone's opinion, not "fact".
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on June 25th, 2017, 3:11 pm 

Hi BioQWizard

I wasn't aware that we could synthesise nucleotides. Can you point me towards some literature on this?
All the information I have available is for re-cycling or the use of living cells to manufacture them.

We all know that carbon can form sterile molecules when combined with other elements, but that doesn't even remotely equate to life.

While it is true that the absence of proof is not proof of absence, the scientific community (in broad terms), will go by the real evidence of what is available today as the most likely indicator of requirements. In much the same way that most physicists will deny that 'other types of stuff' than matter/energy may underpin physical reality, (despite indicators to the contrary), the absence of any form of life that is not based on the living cell (incl.the associated proteins), doesn't promote your case that they may once have existed.

The fact that any alternative evolutionary path must generate working codes that are applied by the different types of RNA/DNA while at the same time generating exact templates for each protein, also suggests that the viable proteins for life must have existed for a large part of the pre-cell period.

Until there is a theory that can even vaguely suggest an alternative evolutionary process then you have no basis on which to suggest that life could emerge through a process other than chance. You are also speculating that in the formative period proteins could survive almost indefinitely (hundreds of thousands of years) to allow sufficient time for workable mechanisms between different molecules to emerge without a sense of direction equivalent to 'survival of the fittest'.

You seem to have only presented a higher level of speculation than I was attempting... but I am really interested by our discussion if you wish to pursue it..
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 1st, 2017, 1:15 pm 

scientificphilosophe » 25 Jun 2017 02:11 pm wrote:Hi BioQWizard

I wasn't aware that we could synthesise nucleotides. Can you point me towards some literature on this?
All the information I have available is for re-cycling or the use of living cells to manufacture them.


Synthesis of adenine for highschool students:
https://www.ncbi.nlm.nih.gov/pmc/articl ... 0525/#ref7

Synthesis of purine, adenine, cytosine, and 4(3H)-pyrimidinone:
https://www.ncbi.nlm.nih.gov/pubmed/11377183

Chemical synthesis route to make adenosine nucleoside:
http://ieeexplore.ieee.org/document/576 ... eload=true

Nucleosides phosphoramidites, which can be used to synthesize DNA entirely artificially without any isolation from cells, can be produced chemically (and have been since the 1980s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC340760/

From there, entire genes can be artificially synthesized using solid-phase chemical synthesis: https://www.ncbi.nlm.nih.gov/pubmed/23775808

As can proteins:
https://www.ncbi.nlm.nih.gov/pubmed/23584057

You see, we use bacteria to produce nucleotides because they are cheap and easy to grow, and they readily produce high yield, NOT because it is technically impossible to synthesize them chemically. Kind of like why most of the protein in our diet comes from animals and plant sources - it's a lot easier and cheaper to grow animals and plants and harvest their protein. It doesn't mean that we can't synthesize proteins ab initio.

These are just a few examples of course, and I can flood you with instances of synthetic biology. But that would be missing the point. All you need is one example of something occuring to refute the claim that it isn't possible.

In 2010, Craig Venter's team created a completely synthetic genome of a bacterium called M. mycoides. Then they transplanted the fully synthetic genome into a host cell from which the genome was removed, which turned the host cell into M. mycoides:
http://science.sciencemag.org/content/329/5987/52

Fortunately, they didn't stop there. In 2016, they reported creating their own custom genome that resembles nothing out there in nature. In other words, they designed the blueprint of an entirely new cell from scratch. They again fully synthesized their designed genome, and put it in a host, and the new cell took off.

Converting ADP to ATP can be done outside living cells. In fact, the first attempt to synthesize ATP outside of living cells was described back in 1975. It used an artificially imposed proton gradient and sub-mitochondrial particles: https://www.ncbi.nlm.nih.gov/pubmed/237916

In 2005, two scientists at UCLA took it even further and created an artificial organelle with only two proteins and a membrane, and used it to produce ATP: https://www.ncbi.nlm.nih.gov/pubmed/16351211

Though it can also be done chemically:
http://www.sciencedirect.com/science/ar ... 8773900154

You get the idea - there doesn't seem to be any unearthly magic involved.

Vitalism has been dying since the 1828 (should be well dead by now), since Wohler synthesized the first biological molecule from nonbiological building blocks:
https://www.ncbi.nlm.nih.gov/pubmed/10213830

And you're going to have a very hard time reviving vitalism here, especially given how fast synthetic biology is developing now: http://www.nature.com/news/minimal-cell ... .19633#/b2

In summary, the claim that nucleotides can only be produced inside living cells is demonstrably FALSE.
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 1st, 2017, 3:35 pm 

scientificphilosophe » 25 Jun 2017 02:11 pm wrote:You seem to have only presented a higher level of speculation than I was attempting...


I don't believe I have.

Please do not conflate (1) proving definitively that life originated on Earth with demonstrating that (2) it is at least possible for life to have originated on Earth. I have made it very clear that I am not trying to prove anything even remotely close to the former. And let's not lose track of the fact that you are the one who made the extraordinary claim here. The burden of proof is on you to show that this is indeed impossible. The biochemical data I've shared so far doesn't necessarily hint for extraterrestrial origins, and in fact may lend support to the possibility of Earthly origin. So what evidence do you have to demonstrate your extreme position?

scientificphilosophe, I appreciate you acknowledging that absence of proof isn't proof of absence. This encourages me to want to continue the discussion with you. For now, however, I'm going to give you a chance to wrap your head around my post above, then we can continue to your other points. I want to handle your claims one by one so that nothing gets missed. Let me know when you're ready and I'll move on to your claims about pre-protein life.

p.s.: Would you please point me to the source where you learned that nucleotides can only be created by living cells? Also, if you can reference your statements in the future, the way I'm referencing mine, that would be very helpful. It makes a big difference whether you are being intentionally misinformed by someone, are selectively cherry picking evidence, or simply can't find the information you're seeking for whatever reason. Knowing which is the case will be important moving forward. Thanks.
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on July 2nd, 2017, 5:52 am 

Hi BioWizard

Your posts on synthesising nucleotides are truly very useful to me, (although I haven't read them yet).

I will need some time to absorb the content, but I am disappointed that you feel that I am trying to manipulate the debate by deliberately introducing falsehoods or avoiding certain facts. I have spent my whole life doing the exact opposite - being honest about all facts and keeping an open mind. To this extent I will not necessarily accept any view that has serious gaps. We should only accept the potential that the different viewpoints offer - until such time as they can prove their case.

I have been very open about the information that I have available.
None of us can do anything other than operate on the information we have. Nobody can claim to have full knowledge either, and my posts have all been aimed at exploring what is known - but honestly acknowledging the gaps.

It is not up to me to exclusively prove my premise just because I am making a point. I am also responding to an equally extreme pronouncement that evolution can explain everything - when scientifically it can't do so with the only mechanism that is offered. Just because a bunch of scientists have only promoted one single hope for a solution to the issues, doesn't make it true - even if it has become the common starting point for debate. There are other valid viewpoints within the science available.

We don't have an answer.

Just because you seem to assume there is an alternative inevitable evolutionary chemical process based on the known principles of matter/energy, doesn't mean that this assumption is correct. There may be other types of stuff that exist in the Universe and the religious lobbies may point to God as a third possibility. We don't know, but the materialist stance which you seem to be advocating cannot be deemed the only option when it can't complete major steps in its own logic.

You have steadfastly ignored my points about codes within the reproductive process of cells, and these are normally perceived as intellectual matters not ones based on pure chemicals. You even mention that scientists have introduced new protein sequences which a cell can replicate - but this merely plays to the religious lobby which says that design must be a factor.

To my knowledge, new genetic sequences still utilise genes already found in nature. I have not heard that any new 'artificial' sequence of amino acids to create an new protein has resulted in anything useful for life.
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 2nd, 2017, 11:32 am 

scientificphilosophe wrote:I am disappointed that you feel that I am trying to manipulate the debate by deliberately introducing falsehoods or avoiding certain facts.


Don't be disappointed yet, because I made no such claim. I have merely asked you whether or not that is the case. There's no harm in asking, is there?

scientificphilosophe wrote: Nobody can claim to have full knowledge either, and my posts have all been aimed at exploring what is known - but honestly acknowledging the gaps.


I commend you for this, and would love to join you on this journey if you'd allow me the honor. Let's acknowledge gaps and try to fill them together. However, I have two very simple requests, which given what you've said about wanting to keep the process honest, I have a feeling that you will readily agree with them:

1- we can only hope to handle falsifiable claims/hypotheses
2- we can not use absence of proof as proof of absence, and certainly not as proof of the alternate hypotheses (especially when there is no evidence to even suggest the alternate hypotheses)

Do these two conditions seem reasonable to you? If not, then this discussion probably does not belong in the science forum, and I will kindly request that you take it to the philosophy section.

Speaking of which, I will ask you at some point in the future to explain to me what you meant when you said that evolution claims to explain "everything". But please, don't worry about it for now.

scientificphilosophe wrote:You have steadfastly ignored my points about codes within the reproductive process of cells, and these are normally perceived as intellectual matters not ones based on pure chemicals. You even mention that scientists have introduced new protein sequences which a cell can replicate - but this merely plays to the religious lobby which says that design must be a factor.


Absolutely not. I promised you that I will get to all of that, did I not? I do not want to overwhelm you with all the material that I have in store for you, however. I will deal with each and every point you've made, so long as it is a scientific question and can be answered using the scientific method (because otherwise we shouldn't be discussing it in the science section). At the moment, I am specifically addressing this claim:

scientificphilosophe wrote:Again - I believe there is no known way to synthesise nucleotides in order to generate DNA and RNA, and we can only 'manufacture' such things using living cells... that's even before we consider the code aspects of this mechanism.


I will move to your other points once I'm done with this one.

scientificphilosophe wrote:I will need some time to absorb the content


Take your time.
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 2nd, 2017, 6:22 pm 

scientificphilosophe, while you're doing your research on nucleotides, could you kindly answer my question about where you obtained your information on this?

BioWizard wrote:p.s.: Would you please point me to the source where you learned that nucleotides can only be created by living cells?


Thanks.
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on July 3rd, 2017, 6:17 pm 

Hi BioWizard


1- we can only hope to handle falsifiable claims/hypotheses
2- we can not use absence of proof as proof of absence, and certainly not as proof of the alternate hypotheses (especially when there is no evidence to even suggest the alternate hypotheses)




While I think I agree with the general sentiment, I'm not sure I agree with the exact words.
To be honest I don't know what "handle falsifiable claims/hypotheses" means but it is not the only thing we can do. For a start it seems to assume that something is false, rather than to demonstrate it. We can also look for core indicators and positives as well as trying to deem something false.

If there are gaps in a theory they can be small or large. Large ones will have the impact of reducing credibility more than small ones. We can also judge the relative merits of one speculative idea compared to another - especially when neither has a mechanism to support it.

Two hypotheses which have no mechanism could potentially be regarded as having an equal chance, for instance rather than one seeming to dominate just because it is flavour of the month.
I will keep an open mind because I don't have an axe to grind.

As I have said many times before, I am a firm believer in Evolution as a source of increasing complexity once the mechanism is in place. But prior to the first living cell no scientific mechanism has been offered. That's a big gap. Within this there are approx. 4 - 6 major issues within the scientific assumption of an alternative evolutionary process, which collectively build an overall impression.

I really want to close those gaps and one of them is the creation of nucleotides.
I have to say this wasn't the most critical one in my opinion because it doesn't challenge the core capabilities of Matter/Energy, whereas codes do.

But let's see where we go.
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Re: Origins of the First Living Cell and Evolution

Postby hyksos on July 3rd, 2017, 9:51 pm 

The idea that a membrane-bound organism would appear on earth "by chance" is so unlikely that it is absurd to hypothesize that at all. I think we can all agree on that. But this new creationist talking point, wherein a protein chain could, "never form in the right order because there was not enough time" I'm not entirely convinced of this and I have never read it anywhere outside of creationist blogs and chat rooms. The op's constant hammering away at that particular point seems to be getting tired after two pages.

Luckily I believe I can turn this ship in a more fruitful direction.

(1.)
There is an enormous amount of phosphorous tied up in DNA. (it appears in the so-called "backbone" of the DNA molecular chain). That is a lot of phosphorous, and science has no idea how that much phosphorous made its way to the surface of the earth. This is an unsolved problem in science.

(2.)
DNA is replicated by a complex machine called a reverse transcripterase enzyme. RTEs are required to replicate DNA, but RTEs are encoded by DNA. (howcouldDNAhavecodedtheenzymethatreplicatesitwhenitencodesth--! ) Hmmm.... Biochemistry offers little towards this problem and the solution to this chicken-and-egg conundrum stands unresolved.

(3.)
What is "life"? What does something being "alive" mean? Give your answer in terms of physics. Many brilliant scientists have tried to define life in terms of physics. All have failed. Freeman Dyson wrote a book where he really seriously tried to answer "What is life?" In the final chapter he admits failure and relents. A particular quote from that book struck me and sticks with me until today :

Life by its very nature is resistant to simplification , whether on the level of single cells or ecological systems or human societies.


(by the word "membrane" I didn't mean to include bubbles in clay formed by accident. Nor the happenstance of hydrophobic lipids that line up in water to form a pocket.)
Last edited by BioWizard on July 6th, 2017, 2:50 pm, edited 1 time in total.
Reason: Edited to combine addendum note with post
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 3rd, 2017, 9:59 pm 

hyksos » 03 Jul 2017 08:51 pm wrote:The idea that a membrane-bound organism would appear on earth "by chance" is so unlikely that it is absurd to hypothesize that at all. I think we can all agree on that.


Who's "we all"? Because it doesn't include me.

Actually, please don't answer.

I would like to keep this discussion focused on the nucleotides point for now - as I had mentioned - before moving on to the next one, if that is OK with you.
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 3rd, 2017, 10:04 pm 

scientificphilosophe, as the moderator running this thread now, I request that you hold off on responding to hyksos's post and stay focused on the nucleotides point.
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 3rd, 2017, 10:15 pm 

Also, scientificphilosophe, I'm still waiting for you to provide me with the reference/link to the source where you got the nucleotides claim. If you could provide me with that while you're doing your research (so that I can do mine), that'd be great.
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