Abiogenesis - The Impossible Theoretical Miracle

a reply to: cooperton

Coop, where's your response??

a reply to: cooperton

Coop, are you ending this discussion? You asked for a civilized discussion. Now that we have one, you disappear into the aether.

originally posted by: Phantom423

It's been demonstrated many times in the lab that nucleic acids can self assemble into amino acids.

You're mistaken here. Nucleic acids have not been shown to form into amino acids.

The self assembly process is driven by thermodynamics and kinetics. There are many research papers discussing the dynamics. Self assembly is a well known phenomenon.

Yet there is no evidence that the self-assembly process can create even one gene outside of an already established biological organism. Let alone the hundreds of genes required for the first living organism. Even if it did manage to create one gene, there would be nothing to replicate it. Without the ability to replicate, it would be lost. This theory, therefore, calls for hundreds of miracles to happen at once.

a reply to: cooperton

You're mistaken here. Nucleic acids have not been shown to form into amino acids.

Poorly worded, I admit. But nucleic acids play a major role in the self assembly of amino acids and hence proteins.

Self-assembly of proteins and their nucleic acids.
Fletcher G1, Mason S, Terrett J, Soloviev M.

Abstract

We have developed an artificial protein scaffold, herewith called a protein vector, which allows linking of an in-vitro synthesised protein to the nucleic acid which encodes it through the process of self-assembly. This protein vector enables the direct physical linkage between a functional protein and its genetic code. The principle is demonstrated using a streptavidin-based protein vector (SAPV) as both a nucleic acid binding pocket and a protein display system. We have shown that functional proteins or protein domains can be produced in vitro and physically linked to their DNA in a single enzymatic reaction. Such self-assembled protein-DNA complexes can be used for protein cloning, the cloning of protein affinity reagents or for the production of proteins which self-assemble on a variety of solid supports. Self-assembly can be utilised for making libraries of protein-DNA complexes or for labelling the protein part of such a complex to a high specific activity by labelling the nucleic acid associated with the protein. In summary, self-assembly offers an opportunity to quickly generate cheap protein affinity reagents, which can also be efficiently labelled, for use in traditional affinity assays or for protein arrays instead of conventional antibodies.

CELL ORIGINS AND METABOLISM
An Evolutionary Perspective on Amino Acids

Amino acids are one of the first organic molecules to appear on Earth. What are they made of and how have they evolved?

Amino acids play a central role in cellular metabolism, and organisms need to synthesize most of them (Figure 1). Many of us become familiar with amino acids when we first learn about translation, the synthesis of protein from the nucleic acid code in mRNA.To date, scientists have discovered more than five hundred amino acids in nature, but only twenty-two participate in translation. In 1943, Gordon, Martin, and Synge used partition chromatography to separate and study constituents of proteins (Gordon, Martin, & Synge 1943), a major breakthrough that contributed to the rapid identification of the twenty amino acids used in proteins by all living organisms. After this initial burst of discovery, two additional amino acids, which are not used by all organisms, were added to the list: selenocysteine (Bock 2000) and pyrrolysine (Srinivasan et al. 2002).

_______________________________________________________________

Yet there is no evidence that the self-assembly process can create even one gene outside of an already established biological organism. Let alone the hundreds of genes required for the first living organism. Even if it did manage to create one gene, there would be nothing to replicate it. Without the ability to replicate, it would be lost. This theory, therefore, calls for hundreds of miracles to happen at once.

There are a number of research articles in the literature which describe the self assembly of chromosome/gene components. Below are a few examples.

Self assembly of functional macromolecules is a well known phenomenon. Your requirement that all the components be put in a jar and out pops a functional chromosome with genes in place is wrong. Nowhere in molecular biological research has it ever been suggested that this is the way functional macromolecules were synthesized by nature.

A process is a process - nothing happens "at once" or in a vacuum. And there's no requirement that all components come together simultaneously.

Replication is part of the evolutionary process. The component parts obviously replicate or we wouldn't be here. The systematic acquisition of new genetic traits and speciation is also an example of the evolutionary process. As far as I know, there's nothing in the literature which describes a unique organism popping out of nowhere. That fact, in and of itself, points to the process of evolution. The "miracles" that you refer to happen every day - as an ongoing process, not a rubber stamp.


Self-Assembly of Thin Plates from Micrococcal Nuclease-Digested Chromatin of Metaphase Chromosomes

The three-dimensional organization of the enormously long DNA molecules packaged within metaphase chromosomes has been one of the most elusive problems in structural biology. Chromosomal DNA is associated with histones and different structural models consider that the resulting long chromatin fibers are folded forming loops or more irregular three-dimensional networks. Here, we report that fragments of chromatin fibers obtained from human metaphase chromosomes digested with micrococcal nuclease associate spontaneously forming multilaminar platelike structures. These self-assembled structures are identical to the thin plates found previously in partially denatured chromosomes. Under metaphase ionic conditions, the fragments that are initially folded forming the typical 30-nm chromatin fibers are untwisted and incorporated into growing plates. Large plates can be self-assembled from very short chromatin fragments, indicating that metaphase chromatin has a high tendency to generate plates even when there are many discontinuities in the DNA chain. Self-assembly at 37°C favors the formation of thick plates having many layers. All these results demonstrate conclusively that metaphase chromatin has the intrinsic capacity to self-organize as a multilayered planar structure. A chromosome structure consistent of many stacked layers of planar chromatin avoids random entanglement of DNA, and gives compactness and a high physical consistency to chromatids. (PDF) Self-Assembly of Thin Plates from Micrococcal Nuclease-Digested Chromatin of Metaphase Chromosomes. Available from: www.researchgate.net... [accessed Oct 24 2018].

Dynamic plasticity of large-scale chromatin structure revealed by self-assembly of engineered chromosome regions

In this study, we extend this experimental approach to create engineered chromosome regions tens to hundreds of megabase pairs in size formed entirely by tandem arrays of specific, ∼200 kbp gene loci. We apply this approach to compare and contrast the folding of the α-globin, β-globin, and Dhfr gene loci in undifferentiated mouse embryonic stem (ES) cells versus ES cell–derived fibroblasts and erythroblasts. We show that several of the aforementioned properties of genome architecture are recapitulated in the self-assembly of these engineered chromosome regions. We also demonstrate a dramatic plasticity of large-scale chromatin structure, varying as a function of cell differentiation, with linear interphase configurations formed from nonlinearly compacted, topologically complex, looping architectures.

jcb.rupress.org...

Synergistic self-assembly of RNA and DNA molecules
www.nature.com...

originally posted by: Phantom423

Poorly worded, I admit. But nucleic acids play a major role in the self assembly of amino acids and hence proteins.

Self-assembly of proteins and their nucleic acids.
Fletcher G1, Mason S, Terrett J, Soloviev M.

In this experiment they use an already existent gene from Streptomyces avidinii, which defeats the goal of self assembly. The scientists still had to undergo regular transcription and translation (referred to as T & T in the methods section of the paper) in vitro to create this protein, meaning that all the necessary tools of transcription and translation described in the OP would still be necessary. Therefore, this does not by-pass the difficulty expressed in the OP.

Don't you see? Even scientists trying to emulate this original condition need the transcription and translation methods to artificially create proteins. It would require a miracle for the component parts of the transcription and translation mechanisms to self-assemble. You will see in all these experiments they take transcription and translation for granted, because there is no way around it as a requirement for biological assembly.

originally posted by: Phantom423

Here, we report that fragments of chromatin fibers obtained from human metaphase chromosomes digested with micrococcal nuclease associate spontaneously forming multilaminar platelike structures.

Same issue as above. The protein solution they used to dissolve the chromosomes was Micrococcal nuclease, which is an enzyme (protein) that requires transcription and translation for it to be created. I do not have access to the article, but chromatin folding into chromosomes is a quaternary process, meaning it is the folding of already existent tertiary nucleic acid chains through electromagnetic forces and histone proteins (again, histone proteins require transcription and translation).

The real question would be how does a logical nucleic acid sequence form at random? And even if against all odds it formed a logical sequence, how would it replicate without transcription and translation (which require nucleic acid sequences to work)?

We apply this approach to compare and contrast the folding of the α-globin, β-globin, and Dhfr gene loci in undifferentiated mouse embryonic stem (ES) cells versus ES cell–derived fibroblasts and erythroblasts.

Again, they are using already-existent structures to create what they call self-assembly. This doesn't address the dilemma in the OP. α-globin, β-globin, and Dhfr, the components used in the experiment, are all genes that would require transcription and translation. They are also housing them in stem cells - complete stem cells would not be present for the theoretical abiogenesis pass from non-life to life.

All these experiments take transcription and translation as a given, because there is no way around it as a requirement for biological assembly.

a reply to: cooperton

Well then you have to name the first component of any of these structures and we'll see if it can be self assembled. Basic molecules can self assemble - |C=C| ... bonding, fusion, fission - all these processes are generated independently of any human input.

Yes, they use scaffolding in these experiments so that the molecule can assemble. But nature also uses substrates to build molecules so it isn't that much different. Of course, we don't know what substrate was used (if any) for the first molecules to self assemble. Carbon and hydrogen assemble very readily due to the ease of bonding. From there, all sorts of isomers assemble by themselves. So it's not unreasonable to think that complex structures with a variety of atoms could mimic the process. Again, it's the kinetic and thermodynamic properties of the atoms and the stability of the molecule that define the result. The Periodic Table can be used to figure out which atoms should produce stable bonds between each other.

There's all sorts of bonding configurations that can result in supramolecular structures - hydrophobic forces, p-bonding, van der Waals forces, electrostatic forces. These in turn can independently form micelles, liquid crystals, etc. This is not unusual in nature. Lipids self assemble into membranes. So I don't see why it's so outlandish to think that large, macromolecular structures could form, including the DNA which codes for the molecule. Nucleic acids have been found in meteorites so unless there's some chemical/physical reason why these simple compounds wouldn't build a macromolecular structure, then the probability is that they do assemble naturally in nature.

a reply to: cooperton

you know, at any time you feel like sharing, we would be happy to see you propose an alternative mechanism for life being initiated on earth. provided your hypothesis has greater experimental backing than the evolution/abiogenesis documentation already provided throughout this forum. reproducible tests with measurable data is encouraged.

i only say this because your extensive attempts to sink the theory of modern evolutionary synthesis have so far come to nothing. it would be fun to see you take a turn in the hot seat and defend your theories.

originally posted by: Phantom423
a reply to: cooperton

Well then you have to name the first component of any of these structures and we'll see if it can be self assembled.

ATP Synthase is integral to every living organism. It creates energy for all known organisms. ATP synthase, as well as many other proteins, would be necessary for life. ATP synthase has two main regions - one being 8890 nucleic acid base pairs, and the other being 4737 nucleic acid base pairs. Is there any evidence that a nucleic acid chain can spontaneously form over 10,000 monomers in length? Even so, it would need transcription and translation to make anything of it. So all the proteins necessary for transcription and translation also have to occur spontaneously.

Such monumentous self-assembly is totally unfounded in the scientific literature because it does not happen

originally posted by: TzarChasm
a reply to: cooperton

you know, at any time you feel like sharing, we would be happy to see you propose an alternative mechanism for life being initiated on earth. provided your hypothesis has greater experimental backing than the evolution/abiogenesis documentation already provided throughout this forum. reproducible tests with measurable data is encouraged.

i only say this because your extensive attempts to sink the theory of modern evolutionary synthesis have so far come to nothing. it would be fun to see you take a turn in the hot seat and defend your theories.

The Copenhagen Interpretation of Quantum Physics is the first main clue. The observer or measurement is the cause of wave functions substantializing or "collapsing" into matter.

a reply to: cooperton

Is there any evidence that a nucleic acid chain can spontaneously form over 10,000 monomers in length? Even so, it would need transcription and translation to make anything of it. So all the proteins necessary for transcription and translation also have to occur spontaneously.

Nothing forms "spontaneously". It's a process. I don't know where you get the idea that things have to drop out of nowhere. Is there anything in the literature that says self assembly is a spontaneous or occurs instantly? No. What it does say is that the process of self assembly is well understood. Nucleic acids can self assemble. Precursors to amino acids can self assemble. Peptides can self assemble. Proteins can self assemble. You're avoiding the word "process".

Transcription and translation are also part of the process. The whole kit and caboodle can most likely self assemble from its parts.

Can you cite anything in the literature which says that self assembly is an instantaneous process? Can you find anything which suggests that it is impossible for macromolecules to self assemble? You use the word "impossible" as though science was a dead end street - that everything that's discoverable has been discovered and, therefore, whatever we don't know now should be attributed to some being. If everyone followed that train of thought, nothing would ever be discovered and nothing would ever get done. We should all give up and go home.

originally posted by: Phantom423

Nothing forms "spontaneously". Can you cite anything in the literature which says that self assembly is an instantaneous process?

Many reactions occur spontaneously. The spontaneity of a reaction is determined by the Gibbs Free Energy Equation. The purpose of Enzymes is to catalyze spontaneous reactions. For example, DNA ligase is necessary for nucleic acid chain formation, Ribosomes enzymatically catalyze peptide bonds, etc, etc. Citing a source would be silly, because this necessity is ubiquitous among all enzymatic reactions

Transcription and translation are also part of the process. The whole kit and caboodle can most likely self assemble from its parts.

There are over 80 proteins involved in the transcription process alone. These could not have all self-assembled and began working in synchrony without a pre-existent comprehensive code that generated these proteins.

You use the word "impossible" as though science was a dead end street

No, science is not a dead end street, evolutionary theory is a dead end street.

a reply to: cooperton

No, science is not a dead end street, evolutionary theory is a dead end street.

But with Christ there is life eternal.

Right?

And all you gotta do is believe.

Oh, and repent.

originally posted by: Phage

And all you gotta do is believe.

The placebo effect is based on it

and repent.

Changing your mind away from toxic behavior can do wonders for your health

a reply to: cooperton

I'm pretty darned healthy for my age. I have to admit I have to take a short break while mowing my lawn nowadays though.

But maybe it's the chemotherapy I had 30 years ago. Yeah. That's it. I'm not old. It's the chemo.

a reply to: Phage

I was saying it is good advice in general. I was not directing it at you implying you were unhealthy

a reply to: cooperton

And I was implying that, in spite of my "toxic behavior" (sin?), I'm doing fine, thank you.

Actually, I was overtly saying it. Not implying it. It's a bad sin too; I don't believe.


I know, I know. I've surrendered eternal life. You can give me a big neener neener, some day. Real soon, from what I hear.

originally posted by: Phage
I don't believe.

You don't believe what? You believe what you believe, and things work in that manner for you.

And I was implying that, in spite of my "toxic behavior" (sin?), I'm doing fine, thank you.

Again, I was not implying your behavior was toxic. Your self-certainty is a form of belief and you are content with your current mindset. This is much better than hypocrisy.

a reply to: cooperton

You don't believe what?

In an almighty creator. That my "sins" will be forgiven if I truly believe.

I'm doomed. I know. Guess what? So are you.

Here’s some food for thought on creation...
Anything and everything that comes into existence is created...
That’s the bottom line...
The process or the credit for it matters not...

a reply to: Phage

You are eternal if you believe or not...
To believe in God does not have to mean you know him as Christ or any other name...
Because to stand for what he stands for will play a much bigger role in your path after this little test...

originally posted by: cooperton
Some examples of irreducible complexity in humans:

Show me a heart working without lungs/gills. Show me a stomach without an acid-resistant stomach lining. Show me bones without tendons. Testes without vas deferens. Actin without myosin. spindle fibers without a kinetochore. A Retina without an optic nerve. A Spinal cord without vertebrate. A blood cell without hemoglobin. Mammary glands without a child with lactase. Adrenal glands without adrenoreceptors. etc, etc

Again, nothing you said has been proved to be irreducibly complex. As I said in the other thread, it's a complete straw man that shows zero understanding of evolutionary mechanisms. Evolution says they incrementally developed over time, not that you could remove a piece today and it would still function. That's completely nonsensical and only applies to machines assembled from parts, not ones that incrementally developed, thus the IC is a complete fallacy and demonstrates nothing about evolution, just a waste of time.