Origins of the First Living Cell and Evolution

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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on July 4th, 2017, 10:24 am 

Hi BioWizard

The links which you gave me concerning the synthesising of nucleotides were just what I was hoping for – thank you - although I wasn’t able to download many of the full articles as quite a few of the sites required full membership, which I don’t have.

Based on the summaries therefore I am pleased to discover that there are now ways to synthesise nucleotides in modest quantities compared to the miniscule quantities before. When I first wrote a series of discussion papers quite a few years ago, nobody considered the ‘miniscule routes’ as credible processes of origin. Yet it seemed ridiculous to think that we couldn’t find a ‘major’ synthetic process, considering that we are dealing with chemicals that can be generated chemically by biological means. I’m glad that this part of the puzzle has been filled.

However in terms of abiogenesis, there are still a number of unresolved factors as far as I can see.

Firstly, I am not aware that nucleotides are generated in the natural environment outside a living cell, and as you acknowledged, re-cycling or the use of bio-mechanisms remains the primary means of production in the lab. If there was a successful high yield process before, why do we not see remnants of it now?

The initial articles that you mentioned placed a great emphasis on Hydrogen Cyanide (HCN), particularly when deployed with a series of more complex chemicals, and catalysts. HCN has also apparently been linked to the generation of some amino acids via different processes. But this is where we start hitting more problems.

As a practical way for generating the large number of nucleotides and amino acids necessary for the ‘random’ generation of useful proteins and RNA etc. the synthetic methods so far identified seem to need HCN to be present at the start but then to have been almost completely removed from the environment by the time that the first cells appear, (probably as bacteria). How did the removal occur? (To argue that it all happened in space and that the Earth was just seeded with the more complex chemicals such as diaminomaleonitrile (DAMN), and ammonium formate, is undermined by the fact that this doesn’t seem to be still happening).

Most guesses about the early proto-atmosphere, (particularly in relation to amino acids – along the lines of the Miller/Urey approach), do not include HCN. The catalysts which were used to enhance the outputs of certain experiments also do not seem to be abundant in the world, and not on a scale which the ‘natural experimentation of sterile chemicals would seem to require.

We can also say that some synthesis techniques apparently require freezing temperatures while others require very high temperatures, but the resulting, highly reactive chemicals have to survive and then migrate to different environments in order to enable the development of life by mixing with the many other chemical molecules which had to be generated in parallel, yet using a series of alternate chemical processes/environments.

On top of this, most theories of the early planetary environment suggest that regular asteroid collisions would have wiped-out all early forms of experimental life of several occasions – further reducing the period of time available for bio-experimentation.

In short, there are a lot of convoluted processes that all have to miraculously converge to produce the first cell within an ever reducing timescale. The only way to apparently overcome this is through a process which will probably need a sense of direction in order to see an evolutionary progression – one that will not be available through survival of the fittest or positive selection, (which is based in Thought).

It is this sense of ‘primordial direction’ by unthinking/unaware chemicals which takes us well out of the accepted capabilities of matter energy and forces us to consider other means by which those capabilities might arise. The deployment of codes plays even more heavily on this consideration.

In the world of physics, we see exactly the same questions being raised when people try to resolve the facts surrounding the ‘dual slit’ and ‘faster-than-light’ experiments... which could be easily resolved with other types of stuff for instance. Instead, the mainstream scientific community which is determined to avoid obvious possibilities, jumps through hoops backwards to try and resolve things within their view of reality, and end up promoting ideas that undermine the very things they are trying to protect... their concept of matter/energy.
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 4th, 2017, 11:01 am 

Hi scientificphilosophe,

Your initial statement on nucleotides did not mention anything about yield or types of starting material or synthetic routes:

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.


As such, all the qualifiers that you've now introduced have no bearing on whether the statement is true or false. That of course doesn't mean I don't want to get into all those new points that you've raised - I do and I look forward to it. However, before we proceed, would you please grant me the courtesy of explicitly acknowledging that the statement (quoted above), which you had originally assumed was true, is indeed false? I know you've already strongly implied that in your above post - but it would be honorable and credible of you if you make that explicit.
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 7th, 2017, 11:06 am 

Hi scientificphilosophe. Any luck with finding the source for the "nucleotides can't be synthesized" fallacy? I'm still interested in checking it out, if you'd be kind enough to share it with us.
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on July 10th, 2017, 8:14 am 

Hi Biowizard

I have found such a reference in an old Wikipedia download from 10 years ago. The article under that same banner headline now seems to have been re-written avoiding the point altogether.

In fairness, I wasn't aware of such a process, so to that extent it was true. I have acknowledged that there are now processes which can truly synthesise as opposed to the 'accidental' production which was assumed by earlier processes due to their incredibly low yields.

Can we move on?
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Re: Origins of the First Living Cell and Evolution

Postby hyksos on July 10th, 2017, 12:48 pm 

Am I allowed to start posting in this thread again?
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 10th, 2017, 12:53 pm 

scientificphilosophe » 10 Jul 2017 07:14 am wrote:Hi Biowizard

I have found such a reference in an old Wikipedia download from 10 years ago. The article under that same banner headline now seems to have been re-written avoiding the point altogether.

In fairness, I wasn't aware of such a process, so to that extent it was true. I have acknowledged that there are now processes which can truly synthesise as opposed to the 'accidental' production which was assumed by earlier processes due to their incredibly low yields.

Can we move on?


Yes, thanks.
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 10th, 2017, 12:56 pm 

hyksos » 10 Jul 2017 11:48 am wrote:Am I allowed to start posting in this thread again?


Yes, go ahead. I can start a new thread from here on for each of the points I want to discuss with scientificphilosophe in a focused way. Thanks for holding off.
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on July 12th, 2017, 5:39 am 

hyksos » July 4th, 2017, 2:51 am wrote: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.


I am not a creationist - I simply recognise a good point when I see it. It needs to be answered.

To clarify, as per the opening pages of comments, it is not that a useful protein chain couldn't form by accident, but that if it happened once it could never be expected to happen again by chance - and this is important when we consider that these are relatively short lived molecules.

In short, if it can't happen by chance then there needs to be a process, and so far we don't seem to be even close to identifying such a process that could operate before the first living cell.

It is also important to find a sense of direction for unthinking chemical to follow if there is to be an alternate evolutionary process, otherwise there is no way for one rare complex protein to be identified as 'useful' when used with another equally rare protein, amidst a myriad of random protein-like crap.

Those were the earlier points, but you have made some interesting comments too.

(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.


I hadn't been alerted to this, so very interested to investigate further.

(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.


Are these the enzymes that work with ribosomes and RNA to assemble the proteins reliably?
If so, I understand that the role of these enzymes is to help weaken the monomer bonds to enable the polymer bonds to form - even in an aqueous environment. Is that right?

(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.


Wikipedia talks of over 280 definitions, and it's a good point.
I would re-phrase the quote which you gave along the following lines...
For the 2nd Law of Thermodynamics to operate, something has to be assembled before it can be returned to a more chaotic state, and there are only two assembling forces - gravity and life.
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on July 12th, 2017, 5:42 am 

BioWizard » July 10th, 2017, 5:56 pm wrote:
I can start a new thread from here on for each of the points I want to discuss with scientificphilosophe in a focused way.


Do we have to start a new thread? Can't you just answer the other points here?
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on July 24th, 2017, 9:06 am 

Hi BioWizard
Are you going to address the other points I made?
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Re: Origins of the First Living Cell and Evolution

Postby BioWizard on July 24th, 2017, 9:50 am 

scientificphilosophe » 24 Jul 2017 08:06 am wrote:Hi BioWizard
Are you going to address the other points I made?


Hey. Do you mind wrapping up the other thread before we continue this one?

Other thread: viewtopic.php?f=18&t=33090&p=325532#p325528

If you're done there, you can just post do on there and I'll shift my attention back to this one. I'm way too busy at the moment to do multiple parallel threads. Thanks.
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Re: Origins of the First Living Cell and Evolution

Postby scientificphilosophe on August 10th, 2017, 5:15 am 

As a summary of the conversation so far, and as an invitation for others to contribute, the position we have reached is this:-

There still doesn’t seem to be an explanation for the origin of the first living cell, and there are valid reasons to consider that Matter/Energy may not be the only factor responsible for the emergence of Life.

Even if we can find mechanisms to produce basic nucleotides and amino acids that are consistent with the historical circumstances of our planet (and I don’t believe we have yet found those), then there are mathematical realities which make the emergence of the first living cell by ‘chance’ almost impossible –in terms of

• the available timeframes, (in the few million years between rocks solidifying on our early planet and the first fossils seemingly appearing), which are shortened even further by a presumed series of catastrophic early collisions with asteroids/meteorites etc.;
• the fact that ‘chance’ isn’t possible within the principle of cause & effect;
• the mechanisms of life are not just chemical, but based in a series of linked codes, which imply purpose and direction that should be outside the realms of unthinking chemicals;
• in establishing a method by which a consistent pattern of improvement/development may be generated in any alternate process of Evolution; and
• there is no perceived evolutionary path for the Ribosome.

The current process for Evolution is reliant on the Living Cell as the one mechanism available, and also generally requires a sense of direction to be established through survivability and even Thought, (eg. deploying ‘positive selection’ to accelerate the evolutionary process as concluded to be necessary by Richard Dawkins etc.). Survivability is marginally possible for a chemical presence even if it doesn’t establish a basis of continual improvement for sterile chemicals.

So we have a number of fundamental challenges before we can explain life in a determinist way based on Matter/Energy alone.

Recent posts have been dominated by the desire to show that we now have ways in which to synthesise potentially large quantities of nucleotides via a particular set of chemical reactions based on a starting position of Hydrogen Cyanide, (which is a good improvement on 30 years ago), but it remains inconsistent with our experience of life in that Hydrogen Cyanide would have to disappear completely so as to prevent it from killing off the living cells it was supposedly producing. If we suggest that Hydrogen Cyanide is still present as clouds of gas in the vicinity of our solar system, then this not only has to be demonstrated but it also has to be explained why we don’t continue to see the intermediate chemicals raining down on us from outer space in the world today.

It has also been admitted that in the modern world it remains easiest to generate nucleotides via living cells, or to re-cycle these chemicals, rather than generating them from scratch in the lab.

Some amino acids have been shown to arise quickly in some chemical mixtures, but this does not included all of the ones deemed necessary for life from the same starting conditions, and there is a lot of guesswork about what the chemical conditions were on our planet in the distant past. However that isn’t the real difficulty. Assembling them into useful chains/polymers is key.

Both protein polymers and DNA/RNA polymers are short lived chemicals outside their protective cellular environments so they need to be reliably reproduced if they are to have the time to ‘naturally' form workable combinations, rather than the suggestion that they all happened to miraculous appear on the right day in the right form with the right codes available at the fortuitous moment that a membrane encompassed them. The only way to reproduce them reliably is the living cell. We have no other process.

While the timeframes could be extended by saying that life developed elsewhere in the Universe, we have to then explain how it managed to get here. To suggest that Proteins, DNA, RNA and even living cells travelled across the extreme conditions of space for millions or even billions of years seems far fetched even using the vehicle of a comet. Of course there could be spaceships....

The point of all this is to be honest about the challenges we face in providing an explanation and potentially recognising that other factors than sterile chemicals might be involved.
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Re: Origins of the First Living Cell and Evolution

Postby SciameriKen on August 10th, 2017, 10:05 am 

scientificphilosophe » Thu Aug 10, 2017 9:15 am wrote:As a summary of the conversation so far, and as an invitation for others to contribute, the position we have reached is this:-

There still doesn’t seem to be an explanation for the origin of the first living cell, and there are valid reasons to consider that Matter/Energy may not be the only factor responsible for the emergence of Life.

Even if we can find mechanisms to produce basic nucleotides and amino acids that are consistent with the historical circumstances of our planet (and I don’t believe we have yet found those), then there are mathematical realities which make the emergence of the first living cell by ‘chance’ almost impossible –in terms of

• the available timeframes, (in the few million years between rocks solidifying on our early planet and the first fossils seemingly appearing), which are shortened even further by a presumed series of catastrophic early collisions with asteroids/meteorites etc.;
• the fact that ‘chance’ isn’t possible within the principle of cause & effect;
• the mechanisms of life are not just chemical, but based in a series of linked codes, which imply purpose and direction that should be outside the realms of unthinking chemicals;
• in establishing a method by which a consistent pattern of improvement/development may be generated in any alternate process of Evolution; and
• there is no perceived evolutionary path for the Ribosome.


Valid reasons to consider matter/energy may not be the only factor?? What do you mean by this? A supernatural force? I've read nothing in this thread that supports that view point if that's where you are going with that statement.

Here is a good article on the topic:
https://www.newscientist.com/article/mg ... eplicator/

Regarding your bulleted list:
• the available timeframes, (in the few million years between rocks solidifying on our early planet and the first fossils seemingly appearing), which are shortened even further by a presumed series of catastrophic early collisions with asteroids/meteorites etc.;

Millions of years may not be important in geologic terms, but quite substantial in biological terms - I do not see the short timeframe as an important factor for the Origins of life, give the proper catalyst for all we know the process could take minutes.

• the fact that ‘chance’ isn’t possible within the principle of cause & effect;
Chance is a human concept that roughly means the same thing as "we do not know what the true mechanism is"

• the mechanisms of life are not just chemical, but based in a series of linked codes, which imply purpose and direction that should be outside the realms of unthinking chemicals;
Something exist because of the mechanisms that allow for its existence, including "unthinking" chemicals bonded to one another in a manner that allows for replication of these patterns - of course the "mechanisms of life are not just chemical" is a very vague statement so I am not sure what you are truly getting at here.

• in establishing a method by which a consistent pattern of improvement/development may be generated in any alternate process of Evolution; and

I'm not sure if that's a sentence

• there is no perceived evolutionary path for the Ribosome.
Because you do not perceive it? Even if your statement is true does that mean the ribosome did not evolve? Hardly.

I'm not here to debate any of these points, particularly as it appears none of this summary is shaped by any of Bio's comments - but feel free to take my thoughts as you will.
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Re: Origins of the First Living Cell and Evolution

Postby Eclogite on August 11th, 2017, 10:54 am 

scientificphilosophe » Thu Aug 10, 2017 9:15 am wrote:There still doesn’t seem to be an explanation for the origin of the first living cell, and there are valid reasons to consider that Matter/Energy may not be the only factor responsible for the emergence of Life.

There are multiple hyptheses for the origin of the first living cell. several of these have been referenced earlier in the conversation. It has been noted, at least once, that the details have not yet been determined, nor the precise pathway to life identified. However, that is quite different from claiming that there is no explanation for the origin of the first living cell.

Given the multiple hypothesese available (and the interesting possibility that more than one of them may be true) there is no reason to propose something supernatural to explain the origin of life. That would only be the case if all hypotheses proved to be dead ends and subtantial evidence pointed towards the supernatural. Neither is the case.

scientificphilosophe » Thu Aug 10, 2017 9:15 am wrote:Even if we can find mechanisms to produce basic nucleotides and amino acids that are consistent with the historical circumstances of our planet (and I don’t believe we have yet found those),
I stand ready to be corrected on this next point. You appear to perceive the primeval environment as a singular one. Such was not the case. There was great diversity in terms of temperatures, pressures, composition, energy supplies, etc. If you accept - as you appear to have done earlier - that nucleotides and amino acids can be naturally synthesised then there is no difficulty in finding an appropriate environment for such synthesis. What is your reason for disputing this?
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Re: Origins of the First Living Cell and Evolution

Postby hyksos on August 11th, 2017, 5:35 pm 

I'm not a huge fan of Niels deGrasse-Tyson by any stretch. But at this juncture I am thinking this thread stands as a testament to something which deGrasse-Tyson said during a TV interview.

This, over time, has been described by philosophers as the God-of-the-gaps. If that's how you, if that's where you're going to put your God in this world, then God is an ever-receding pocket of scientific ignorance.

If that's how you're going to invoke God. If God is the mystery of the universe, these mysteries, we're tackling these mysteries one by one. If you're going to stay religious at the end of the conversation, God has to mean more to you than just where science has yet to tread. So to the person who says, "Maybe dark matter is God," if the only reason why you're saying it is because it's a mystery, then get ready to have that undone.

I would like to emphasize the phrase "God is an ever-receding pocket of scientific ignorance."

The OP of this thread needs to stop implying things and beating around the bush. He needs to take a hard, concrete position regarding where in the chain of early pre-biotic chemistry, did God intervene and perform magic?

Just tell us straight up where God did the magic on the chemicals. Did he intervene in the transition from RNA to DNA? And what exact magical trick did he perform there? Like draw a diagram -- show us on that diagram of molecules where exactly "And then God does this here" and draw a little arrow.

I get increasingly worn down and tired of these sideways implications of "the realms of God that I won't get into". No. Stop it. Get into it and get into it with a coherent claim. Stop the fence-sitting and adopt a strong, concrete position on this. Tell us what you are claiming and we will answer to that claim.
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Re: Origins of the First Living Cell and Evolution

Postby Braininvat on August 11th, 2017, 6:05 pm 

He knows he can't "get into it" because this is a science forum, and that departure from the topic would end the thread. God is not a scientific hypothesis or explanation or anything, so it would be discussed in the PCF side, in metaphysics and/or religion. In science, as the sayiing goes, "extraordinary claims require extraordinary evidence."
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Re: Origins of the First Living Cell and Evolution

Postby hyksos on August 11th, 2017, 6:19 pm 

moleculemiracle.png
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