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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