Chemical evolution:

[Write4U]

Bioinorganic Pattern Formation in Diatoms.
A Story of Polarized Trafficking, Chiara Zurzolo, Chris Bowler
Published December 2001. DOI: https://doi.org/10.1104/pp.010709

• Copyright © 2001 American Society of Plant Physiologists

The world's oceans cover 70% of the surface of our planet. The photosynthetic organisms living within its photic zone are responsible for about one-half of global primary productivity. The most successful organisms are thought to be photosynthetic prokaryotes (cyanobacteria and prochlorophytes) and a class of eukaryotic unicellular algae known as diatoms (Norton et al., 1996; Van Den Hoek et al., 1997; Falkowski et al., 1998).

Diatoms are likely to have arisen around 280 million years ago following an endosymbiotic event between a red eukaryotic alga and a heterotrophic flagellate related to the Oomycetes (Medlin et al., 1997,2000). As a consequence, their only phylogenetic similarity to green algae and higher plants is derived from the primary endosymbiotic event, which is thought to have occurred at least 700 million years ago (Kowallik, 1992). ........much more!

http://www.plantphysiol.org/content/127/4/1339#:

continued in the Microtubule thread

 

[Write4U]

continued from post # 658

Diatoms

Therefore, diatom cells have a range of features that make them highly divergent from the classical cellular structure of higher plants, including:
(a) The use of the brown carotenoid pigment fucoxanthin for light energy transfer within the light-harvesting complexes of photosystems I and II.
(b) The presence of four membranes around their plastids. The inner two membranes are equivalent to the membranes that normally surround higher plant chloroplasts, whereas the second membrane (as counted from the outside) is thought to be derived from the endosymbiont's plasma membrane, and the outer membrane is continuous with the endoplasmatic reticulum of the host cell.

(c) The presence of a rigid cell wall composed largely of amorphous silica (i.e. glass). The exquisite lacework-like patterning of diatom cell walls (see example in Fig. 1) is reproduced with high fidelity from generation to generation and is species specific. For these reasons, it has been used since the last century for taxonomic classification.

Fig 1.
Electron micrograph of the diatomCampylodiscus sp. at 890× magnification. Photograph courtesy of Masahiko Idei.

http://www.plantphysiol.org/content/127/4/1339#:

Mitosis of amorphous silica (i.e. glass)?

 

[iceaura]

Mitosis of amorphous silica (i.e. glass)?

?
The glass shell normally comes in two pieces, one fitting inside the other - like an oldfashioned shoebox.
That is produced by a functioning, living diatom - both "halves". These shells, once constructed, do not normally grow.

In the first couple of reproductive duplications of a standard diatom that two piece glass shell divides along its seam, into a cover half and a box half, so to speak - and each half is used as the cover half for a new shell: that means the two new diatoms are different sizes, one daughter being smaller than the mother.

Sooner or later the new generation diatom has to recover the original size, or the entire growing population runs out of nutrients or favorable circumstances - so the reproduction produces a (sometimes temporarily free-swimming) amoeba stage, which in turn generates the walls of a kind of "spore" or "auxopsore" that rests, sometimes feeds, and grows until it's big enough (and circumstances allow it) to make both halves of an initial size shell.

Hence an overheard comment from a diatom researcher: "Sometimes when I see an amoeba, I wonder - what am I looking at?"

 

[Write4U]

Hence an overheard comment from a diatom researcher: "Sometimes when I see an amoeba, I wonder - what am I looking at?"

Abiogenesis?

 

[iceaura]

To suppose any of your 'millions of environments' could replicate human ability to purify and maintain requisite chemical purity is wholly unrealistic.

That may be why nobody does.

And re the first highlighted - those millions of base units long DNA strands are only safe within a whole living cell.

That is not true - sections of them are quite durable, and can be recovered from all kinds of environments.

The magical jump required to go from foreign encapsulating bag to highly selective semi-permeable membrane integrally connected to the interior cell factory is just that - magical wishful thinking.

Yes.
That's a major reason ID or other forms of creationism have never worked as developmental theories, or plausibly explained abiogenesis. Too much magical thinking is involved.
Avoiding that kind of impossible jump is exactly what Darwinian evolution does best.

Without the latter those hypothetical self-replicating strands will degrade quickly.

Once again you need reminding: DNA is not self-replicating.

Meanwhile: Most researchers think DNA was a later addition to the earliest emergent quasi-living or partially replicating molecular arrangements.
Meanwhile, strands of DNA are quite durable, and have been recovered from all kinds of environments - including the extra-cellular stuff of mammalian digestive tracts, the residue of degraded cellular protoplasm in fossils, samples of ocean water, mud cores under arctic lakes, and so forth.

And there is so much more required that only a living whole cell can provide. For instance continued cell division is impossible unless the cell membrane/wall is an integral not foreign entity.

Which is one reason very few researchers think the first living beings were modern cells, with their billion years of evolved complexity.

Once again: the central and recurrent and common task of anyone dealing with creationists in a science-based discussion of life on this planet is correcting their false claims and assertions involving Darwinian theory and the biology of evolution.

As a rule of thumb, and without exception in my direct experience, no one who rejects Darwinian theory understands it.

 

[Write4U]

Q-reeus said: ↑ : And re the first highlighted - those millions of base units long DNA strands are only safe within a whole living cell.

You are looking at abiogenesis but refuse to see. Viruses are the "missing link" between non-living and living organisms.

Define Virus

All living things have DNA, but technically speaking, viruses aren't living things because they can't maintain themselves or reproduce on their own. They also aren't technically cells because virus structure doesn't have organelles -- cellular machinery -- of their own. They don't fit into any of the kingdoms of life -- they aren't plants, animals, fungi, protists, bacteria or archaea -- but there are types of virus that infect every one of these life forms. Viruses exist only as infectious agents. They're made up of a nucleic acid -- either DNA or RNA -- surrounded by a protein capsule. They only become active after entering a host cell.

Many viruses are not cellular and use the host's mitotic mechanism to duplicate.

DNA Viruses

DNA viruses have deoxyribonucleic acid. They invade the cells of host organisms and use the host cells' machinery to create more viral capsules. They also use the host cells' energy to "feed" themselves. DNA viruses essentially turn host cells into virus factories. These host cells fill with newly manufactured viral packets and then release them, usually by bursting, to infect other cells. DNA viral infections -- such as colds and flus -- are usually highly communicable because they spread by broadcasting new viral packets into the environment.

https://sciencing.com/virus-dna-4058.html

This is why viruses occupy a special intermediate status in the abiogenetic evolution of non-living bioinorganic organisms into living bioorganic organisms.

 

[Write4U]

Meanwhile, strands of DNA are quite durable, and have been recovered from all kinds of environments - including the extra-cellular stuff of mammalian digestive tracts, the residue of degraded cellular protoplasm in fossils, samples of ocean water, mud cores under arctic lakes, and so forth.

Remarkable!

How Long Does DNA Last?
BY ROMA PANGANIBAN, FEBRUARY 13, 2013

Scientists have estimated that under the most ideal conditions, DNA can theoretically survive for a maximum of one million years. Although a team of researchers recently claimed to have discovered 419 million-year-old genetic material belonging to prehistoric bacteria in the Michigan Basin, others in the field have loudly contested the claim, especially in light of an earlier sample thought to be 250 million years old, but later proven contaminated by the presence of modern DNA.

The oldest actual DNA samples hail from Greenland (the icy one, as opposed to Iceland, the green one), extracted from beneath a mile of ice, a “perfect, natural freezer” for DNA preservation. The 450,000 to 800,000-year-old samples provide evidence of green life on the now largely barren landmass.

https://www.mentalfloss.com/article/48815/how-long-does-dna-last#:

 

[James R]

paddoboy:

In your latest string of rants responses, you deliberately avoided responding to the most important question. You know, the one that repeatedly torpedoes your silly claim. Here's what I wrote, again. When you respond, make sure you don't oops accidentally forget to respond to this again, because it makes you look like a dishonest hack.

I say there is no theory of abiogenesis. You say I'm wrong. Easily settled. Point me towards the theory. Provide a link, a reference, anything that will show us all the full theory.
​

The reason why you don't respond is clear: you have no response. There is no link or reference to any full theory of abiogenesis, because such a thing does not exist. In fact, by repeatedly pretending that you don't have to respond to this, you effectively concede the point, every time you do it. This is a dead argument. You're spinning your wheels. At this stage, you're making yourself look like a fool. And for what? Only to protect your overblown ego, once again.

Whether you call Abiogenesis a theory, a process, or an assumption, I don't really care.

Don't tell lies. If you didn't really care, you'd have given up this pointless battle hundreds of posts ago.

I say your claim about abiogenesis is an unjustified assumption you make. You say that, on the contrary, there is a scientific theory of abiogenesis that explains the natural origin of live.

This is the only reason why you and I are arguing about this. This is our major point of difference on the specifics of this topic. You are wrong. I am right. You can't handle that I'm right and you're wrong. There's really nothing much more to say.

Obviously, if there was such a thing as a scientific theory (N.B. not a disparate set of part-answers or tentative hypotheses) about abiogenesis, you would have been able to produce at least ONE reference to such a thing by now. The fact that you can't - and that you KNOW you can't - means I win and you lose this round. The rest is just you grumbling about how many times I end up being proven right while you're wrong.

But please, feel free to repeat your false claim for the umpteenth time, all the while knowing that you're telling a lie. All it does is to highlight your lack of integrity and maturity. The only other possible reason you'd want to do that would be if you're actually much stupider than you appear to be, so that you can't actually understand the simple ideas that have been taught to you here.

Is there?
So we have the fact that once there was no life, then there was and either one of the following.....

1. Life arose from non-living stuff by itself.
2. A magical creature from who-knows-where magicked it all into existence.

What are the other thousands of possibilities? So as to not put you to too much trouble, 10 of that thousands will do.

Notice that (1) doesn't even make any sense. If there was no life, then life couldn't have created life - life couldn't have arisen "by itself" (i.e. due to something that life did to itself). If there was no life, then something else must have caused life to start.

Other possibilities include:

3. We all live in a simulation, so life (and everything else we're aware of) is just part of the simulation.
4. [Read this one carefully.] Chemical processes created life from non-living things by some as-yet-unknown process (that we don't yet have a theory for).
5. A god created life.
6. Two or more gods created life.
7. Machine intelligences somehow evolved from non-living material, and they somehow created life.
8. Extradimensional beings came into our universe and created life.
9. Life has always existed.
10. The entire universe has some kind of undiscovered "life essence", that caused life-as-we-know-it to start.
11. Life was formed from an (unknown) incredibly-unlikely chemical accident.
12. An undiscovered "fifth force" allowed life to start.

You said 10 would be enough, so there's 10. Notice that numbers 5 and 6 could easily be subcategorised into thousands, just for starters. I've been generous with this short list, shooshing several complex sets of possibilities into one or two deceptively-simple categories.

Bingo James!!! Now you're getting it!!! It happened, but as yet we don't know exactly how it happened.

You're just repeating what I taught you. Now that you know this, you will agree we with me that not knowing how it happened means there's no complete scientific theory of abiogenesis. Right?

You can post your agreement when you quote this bit in your next response. I'm sure you won't dishonestly ignore it (again). Or will you?

 

[Q-reeus]

That is not true - sections of them are quite durable, and can be recovered from all kinds of environments.

Yes - sections of them. Already, a necessarily whole dna strand has become irreversibly lost re biological efficacy. In most environments, DNA degrades relatively fast.Check out fig.1 here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218555/

Yes.
That's a major reason ID or other forms of creationism have never worked as developmental theories, or plausibly explained abiogenesis. Too much magical thinking is involved.
Avoiding that kind of impossible jump is exactly what Darwinian evolution does best.

Really? But you offer no Darwinian explanation as to how it could plausibly happen. Noted.

Q-reeus said: ↑
Without the latter those hypothetical self-replicating strands will degrade quickly.

Once again you need reminding: DNA is not self-replicating.

That was your interpolation. I never mentioned DNA, and earlier referred to RNA as the supposed early self-replicators. Try and be accurate.

As a rule of thumb, and without exception in my direct experience, no one who rejects Darwinian theory understands it.

Is that so. You seem to claim to understand it. So explain what the first life was, and how it could tightly organize and be robust against attack without a protective membrane.
Additionally, explain how an integral cellular membrane arose without invoking mysterious Teleological direction.

 

[Michael 345]

Modern abiogenesis hypotheses are based largely on the same principles as the Oparin-Haldane theory and the Miller-Urey experiment

https://www.britannica.com/science/abiogenesis

 

[James R]

Yazata:

In response to Paddoboy trying to set up his false dichotomy, I asked, "So what's wrong with just admitting that nobody currently knows how life originated?"

Paddoboy repeats his mantra once again as if the strength of an argument is a function of repetition...

Once he gets outside his comfort zone of what's on wikipedia, he is often reduced to repeating himself uselessly.

He generally assumes that his first thoughts on any topic must be correct, and will defend them at all costs. He is unwilling to change his mind about anything, especially when it involves admitting he made a mistake. His ego won't allow it.

Can support what? Your conclusion? How does one get from simply observing that life appears to have had an initial origin (somehow, somewhere) to a never-clearly-stated conclusion that you seem to believe is absolutely devastating against the creationists?

Did you notice his response to this question? Instead of answering it, he tries to ignore it, answering with a distraction:

paddoboy: Is that what's troubling for you? The fact that it is absolutely devastating for our creationists/IDer friends?
​

He's trying to make it about you rather than facing up to the fact that he can't support his own claim. His ego won't let him do that, apparently.

If you want to make progress from the place where you are currently stuck you will need to clearly state what your conclusion is and then argue for it as best you can, making clear all your hidden assumptions.

It's like he is blind to his own assumptions. I can't actually tell whether it is stupidity or pretense, at this point. Maybe he wants his readers to conclude that he's stupid. Bizarre, but possible.

Why must the true answer to life's origins be "scientific"? What prevents these other sorts of accounts of life's origins from being true?

That's a good question to ask him, Yazata. Of course, he tried to avoid answering that one, too:

paddoboy: Interesting question...so we have a choice, science and a scientific answer, based on some evidence and chemical processes, or ancient mythical faith based answers, that evolved in ancient times, before that terrible discipline of science reared its head.
​

Instead of answering you, he merely repeated what you already pointed out to him, as if you were unaware of it.

I honestly think that paddoboy has a huge blind spot when it comes to his own assumptions about the world. He has decided at some point "Science good; religion bad", so anything that has the whiff of religion must be wrong, for him. No need to investigate. No need for disproof. Just assume it's wrong. And on the reverse side, never mind if science doesn't actually have an answer. If it doesn't, pretend it does and hope that religion goes away.

If you want to slay creationism you will need to answer that one. I don't think that you can without making clear your implicit unstated premise of metaphysical naturalism -- your apparent belief that reality and the scope of natural science are coextensive, such that nothing can possibly exist that science can't at least in principle explain using purely natural principles.

Notice how far paddoboy got with this one? He understood the first 6 words, then ignored the rest.

I don't think he understands what "metaphysical naturalism" means. Probably, he tunes out as soon as he sees a term like that, dismissing it in his own mind as "philosophical claptrap". In spite of the fact that it is the assumption he continually makes himself.

Of course, justifying that metaphysical naturalism premise would seem to be impossible. So it looks like a statement-of-faith not unlike the creationist's belief in divine agencies. Both would seem to be making assertions about the ultimate nature of reality that exceed knowledge and justification.

paddoboy won't ever be able to bring himself to admit that his beliefs are directly comparable to creationist beliefs in the sense you point out. When you write this, his mind just sees blank space.

"Abiogenesis" seemingly just serves you as an occasion for slipping in your own metaphysical belief about the nature of reality as your initial premise without stating it openly, so that you can triumphantly pull it out again with all of the supposed authority of "science" behind it in order to slay the evil creationists.

That's paddoboy's position in a nutshell. He doesn't recognise it as such. He will never acknowledge it. He acts like he can't even see it. But obviously, that's the problem we're dealing with here.

 

[Write4U]

paddoboy said: ↑ Is there? So we have the fact that once there was no life, then there was and either one of the following.....

1. Life arose from non-living stuff by itself.
2. A magical creature from who-knows-where magicked it all into existence.

Notice that (1) doesn't even make any sense. If there was no life, then life couldn't have created life - life couldn't have arisen "by itself" (i.e. due to something that life did to itself). If there was no life, then something else must have caused life to start.

IMO, that is not a strict interpretation of what paddo proposed. His argument is that Life did indeed arise from Non-Life by an evolutionary process or causality, the very definition of Abiogenesis.

Abiogen·e·sis,

/ˌābīōˈjenəsəs/, noun

• 1.the original evolution of life or living organisms from inorganic or inanimate substances: "to construct any convincing theory of abiogenesis, we must take into account the condition of the Earth about 4 billion years ago"

He admits that the exact process of transformation is as yet unknown, but that does not negate the argument that Abiogenesis is the logical conclusion based on our "known" science of the early universe.

 

[James R]

Because it involves only chemical transmutation, not any extraneous ID or other exterior interference .

Your answer is a non sequitur to the one that Yazata asked you.

I think there is a category error being committed in this entire conversation...

Not by Yazata or myself.

There is no Elan Vital. That's old stuff!

Explain how you know there is no "Elan Vital". What makes you so sure?

Abiogenesis is a chemical process and therefore falls in the domain of Science, not spirituality.

"Abiogenesis" is a just a label for whatever process started life from non-life. It can be scientific or spiritual, conceptually.

You haven't ruled out a spiritual explanation. Neither has paddoboy, or anybody else.

Nor have any of you guys who are so convinced there is a scientific explanation managed to actually provide one. The reason is, as I keep pointing out to paddoboy, there currently is no scientific theory of abiogenesis. We might have pieces of the puzzle, but that's all.

 

[Write4U]

Explain how you know there is no "Elan Vital". What makes you so sure?

Because we know the science of cellular formation. (see Anil Seth)

 

[James R]

Is that what's troubling for you? The fact that it is absolutely devastating for our creationists/IDer friends?

A non-explanation - or a pretend explanation that isn't actually real - is not devastating for creationists, or anybody else.

I advise you to talk to James about assumptions.

Be specific. If you believe I'm making false assumptions about something, set them out and I'll respond. Stop with the snide asides.

All I'm saying is that Abiogenesis is the only scientific answer to how life arose. That's not an assumption, until someone can give me another scientific process about how life arose.

What do you mean "another process"? You haven't given us the first process, yet.

I'm still waiting for you to outline the process of abiogenesis.

The floor is yours. Go.

I'm not out to slay creationism. People are free to accept what they will.

Those are two different matters.

But I will argue when people come to a science forum, preaching fire and brimstone, as opposed to a logical scientific answer.

You have no scientific answer, logical or otherwise.

yes I do see science as the only answer, and yes, I certainly am not a scientist that can give you a nitty gritty blow by blow account of biological processes.

You're in good company. Nobody can give a nitty gritty account, because there isn't one (yet).

I do read some though, and see answers and assumptions re life and the universe that I find much much more logical, and natural then some inner comforting, creative myth, to warm the cockles of someone's heart, and help them forget about the finality of death and the indifference of the universe as a whole, to all life.

All you're saying is that you prefer your own comforting myth that warms the cockles of your heart, over some other myths.

But hey, Yazata, don't despair...I still find you a heaps better philosopher then iceaura or James!

Don't damn Yazata with your faint praise.

You're obviously completely unqualified to rank philosophers.

 

[Write4U]

"Abiogenesis" is a just a label for whatever process started life from non-life. It can be scientific or spiritual, conceptually.

You haven't ruled out a spiritual explanation. Neither has paddoboy, or anybody else.

Yes, that's true. But logically the concept of ID is so much more complicated than normal evolutionary processes, that Occam would turn in his grave. (Do you really want to be questioned on the physical properties of spiritual causality?)

Did anything else other than Life in the universe require the presence of an Intelligent Designer?

That leaves only the very simple explanation of probabilistic evolutionary processes over enormous time spans and spaces with available chemical elements.

I believe that I provided possible examples of known "evolutionary transmutations" in my posts on Diatoms and viruses.

 

[James R]

Because we know the science of cellular formation. (see Anil Seth)

That doesn't rule out the possible existence of an "elan vital".

 

[James R]

Yes, that's true. But logically the concept of ID is so much more complicated than normal evolutionary processes, that Occam would turn in his grave.

Did anything else other than Life in the universe require the presence of an Intelligent Designer?

That leaves only the very simple explanation of probabilistic evolutionary processes over enormous time spans and spaces with available chemical elements.

I believe that I provided possible examples of known "evolutionary transmutations" in my posts on Diatoms and viruses.

I agree with you, in part. There's no good evidence for ID, which means nobody has good reason to claim that ID happened.

On the other hand, when you allude to a "very simple explanation" of abiogenesis, I say: if you have a very simple explanation, why haven't you produced it yet?

I don't think there's a very simple explanation of abiogenesis. I think that the "nitty gritty", as paddoboy puts it, is likely to be quite complicated. My whole argument with him here is that he seems to think that we have a complete theory of abiogenesis. We don't. Do you agree with me, or with paddoboy?

 

[Write4U]

That doesn't rule out the possible existence of an "elan vital".

OK, you are asking to explain the evolutionary process of Abiogenesis . Can you explain the process of "Elan Vital"?

 

[Write4U]

On the other hand, when you allude to a "very simple explanation" of abiogenesis, I say: if you have a very simple explanation, why haven't you produced it yet?

I have produced 2 examples of apparent abiogenesis. Diatoms which are more crystal chemistry than bio-chemistry and viruses which are "partly" living organisms.
IMO, these are evidentiary examples of being "not quite alive".

If there is something wrong with those examples, I sure want to hear them.