Evolution is Still Not a Theory in Crisis, but Neo-Darwinism Might Be

[benkirk (Benjamin Kirk)]

@Sy_Garte

Ribozymes are not great replicators or great catalysts, and there are other major problems with how RNA based life would work, not the least of which is evolution.

Hello Sy,

Then why is the enzyme currently catalyzing virtually every peptide bond in your body a ribozyme?

[glipsnort (Steve Schaffner)]

@Eddie

I like to see this sort of academically qualified statement, one which makes a point while avoiding over-claims in the opposite direction. Very well done! A model for scientifically-trained people who debate about origins issues! Thank you.

Uh oh. Does this mean I have to reevaluate my position?

[Sy_Garte]

@benkirk

Then why is the enzyme currently catalyzing virtually every peptide bond in your body a ribozyme?

I am not saying that there are no effective ribozymes. Of course the ribosome works extremely well, (as do other current ribzymes). But that fact does not negate what I said. RNA life implies that all cellular functions (or at least the minimum required for a cell to live) be catalysed by ribozymes, which lack the chemical diversity available to proteins. In other words, ribozymes can be great specialists (like the rrbosome) but cannot compete with proteins for breadth of activity. Again, I dont dispute the possibility of RNA world. But there is a reason we dont see it. DNA world is much better.

[Biosemiosis.org]

@glipsnort

Good question, and dumb hypothetical by me

This is hardly a dumb hypothetical; in fact it’s not dumb at all. It puts the investigator in immediate contact with the issues at hand. How does a nucleotide specify an amino acid? How can a sequence of nucleotides specify a particular sequence of amino acids, as well as any alternative sequences of amino acids?

If you’ll attempt to answer that question – after all it is the question – then you’ll no longer need anyone to clarify the issues. And if we fast-forward through this conversation, you will find yourself in Francis Crick’s shoes in 1955, knowing that an adapter of some sort is a logical necessity (and a prediction confirmed three years later).

@glipsnort

My understanding of your positions:

1. Life requires a representational medium.
2. Life may be possible on RNA in RNA world.
3. RNA world does not include a representational medium.Those three claims are inconsistent, so presumably I’ve failed to understand something.

1. Yes, a representational medium is required to organize the heterogeneous cell.

2. The value of this question is limited by the fact that it can’t be falsified. In any case, the system will require a representational medium and a reading frame code in order to organize the heterogeneous cell and record itself into memory.

3. The RNA world can include a representational medium if it is organized to be so. Again, there is nothing about the physical properties of RNA, or DNA, or protein that makes them a representation. They must be organized in a system that establishes them as representations, where the details of the system’s construction are simultaneously encoded in the representations being created.

[glipsnort (Steve Schaffner)]

@Biosemiosis.org

This is hardly a dumb hypothetical; in fact it’s not dumb at all.

Since it did not raise the question I wanted to raise, it was indeed dumb.

@Biosemiosis.org

Yes, a representational medium is required to organize the heterogeneous cell.

This is the claim for which I have seen you present no evidence. RNA world could have a lot of complexity and still have no representational medium.

[Biosemiosis.org]

@glipsnort

Since it did not raise the question I wanted to raise, it was indeed dumb.

It raised the question that cannot be avoided, unless avoiding it is the point…

Yes, a representational medium is required to organize the heterogeneous cell.

This is the claim for which I have seen you present no evidence.

I’ve presented it several times now. Each time I answer, you avoid the issue and ask me again. But it is always interesting to see someone say there’s no evidence that the heterogeneous cell requires a genome. If there is no evidence for that, then there is no evidence for anything.

[glipsnort (Steve Schaffner)]

@Biosemiosis.org

It raised the question that cannot be avoided, unless avoiding it is the point…

Don’t be ridiculous. I wanted to raise a question, and for that purpose, my hypothetical was inappropriate. If you want to ask a different question, knock yourself out.

@Biosemiosis.org

I’ve presented it several times now. Each time I answer, you avoid the issue and ask me again. But it is always interesting to see someone say there’s no evidence that the heterogeneous cell requires a genome. If there is no evidence for that, then there is no evidence for anything.

I assume your reason for writing here is to persuade people of your ideas. If so, I have to say that you’re doing quite a poor job of it. I have indeed seen you present a number of assertions, but nowhere in what you’ve written to me have you presented any evidence that a heterogeneous cell requires a representational medium. You may think you’ve presented that evidence, but you haven’t. If it is possible to have an arbitrarily complex set of chemical reactions without a representational medium, then why is a representational medium required?

[Biosemiosis.org]

@glipsnort

Don’t be ridiculous. I wanted to raise a question, and for that purpose, my hypothetical was inappropriate. If you want to ask a different question, knock yourself out.

I did ask it. You did not respond. Twice.

Let us be clear, you asked directly for evidence, and I answered it directly. In your very next post you did not respond to a single word of it. Instead, you asked the question again.

Since it has been demonstrated that it makes no difference what I say, I’ll ask you a question:

In your counter-example to the heterogeneous living cell, you’ve described it as “an arbitrarily complex set of chemical reactions without a representational medium”, and you’ve offered more details here:

@glipsnort

Suppose a cell contains an RNA molecule that promiscuously copies RNA molecules, a second RNA that encodes a useful protein and a third RNA that translates RNA into protein, along with lots of other RNAs.

In your scenario, how does the RNA encode a protein, and how does the other RNA translate it?

[glipsnort (Steve Schaffner)]

@Biosemiosis.org

In this scenario, how does the RNA encode a protein, and how does the other RNA translate it?

It doesn’t. There is no protein in RNA world.

[Biosemiosis.org]

So you are not actually talking about a heterogeneous living cell. You are talking about an assumption, which we will then assume can create a set of spatially-oriented representations and the constraints of a reading frame code, and get those simultaneously encoded into the representations its creates – so that it can then become a heterogeneous cell?

Is that correct?

How does this falsify anything I’ve said?

Q: Life requires a representational medium.
A: Yes, a representational medium is required to organize the heterogeneous cell.

Q: Life may be possible on RNA in RNA world.
A: The value of this question is limited by the fact that it can’t be falsified. In any case, the system will require a representational medium and a reading frame code in order to organize the heterogeneous cell and record itself into memory.

Q: RNA world does not include a representational medium.
A: The RNA world can include a representational medium if it is organized to be so. Again, there is nothing about the physical properties of RNA, or DNA, or protein that makes them a representation. They must be organized in a system that establishes them as representations, where the details of the system’s construction are simultaneously encoded in the representations being created.

[glipsnort (Steve Schaffner)]

@Biosemiosis.org

So you are not actually talking about a heterogeneous living cell

Incorrect. I’m talking about a heterogeneous living cell that does not use proteins and does not rely on a representational medium. I want to know why it is impossible.

[Biosemiosis.org]

So your assumption is a “heterogeneous cell” made up of nothing but RNA? Great.

[glipsnort (Steve Schaffner)]

@Biosemiosis.org

So your assumption is a “heterogeneous cell” made up of nothing but RNA? Great.

Since that’s been the most common hypothesis in origin-of-life research for years, yeah, I think that would be a good possibility to address. Now, can you tell me why it is impossible? You’ve said that there are universal physical principles that prohibit it. What are they?

[Biosemiosis.org]

You do realize, don’t you. that a heterogeneous cell is an organization made up of a lot more than RNA?

het·ero·ge·neous

: made up of parts that are different

: consisting of dissimilar or diverse ingredients or constituents

[glipsnort (Steve Schaffner)]

@Biosemiosis.org

You do realize, don’t you. that a heterogeneous cell is an organization made up of a lot more than RNA?

Sure. An RNA world cell would undoubtedly include a lipid membrane and a range of small molecules, as well as a wide variety of RNA molecules. Maybe other things, too. In any case, your original claim was about the primordial condition of life, not about the first heterogeneous cell. That’s why I asked about it.

[Biosemiosis.org]

@glipsnort

your original claim was about the primordial condition of life, not about the first heterogeneous cell.

From my first post: “To organize the heterogeneous cell requires the ability to specify a thing among alternatives and to place it under temporal control.”

You first addressed me on this thread by claiming I was making a mere assumption. Tell me, which of these two is the real assumption about life:

a) that life requires nucleic acids, proteins, lipids, etc., in a coherently-orchestrated organization, or

b) that it only needs “an arbitrarily complex set of chemical reactions” of RNA?

And even if I were to grant your many assumptions, you still have to deal with the semiotic requirements I’ve discussed in order to actually address the question on the table – the extant cell. Suddenly, everything I have been telling you is front and center. The real issues hadn’t changed a bit.

Thanks for the conversation.

[glipsnort (Steve Schaffner)]

@Biosemiosis.org

From my first post: “To organize the heterogeneous cell requires the ability to specify a thing among alternatives and to place it under temporal control.”

Also from your first post: “Irreducible complexity can be shown to be the primordial condition of life. It is the necessary material condition that enables the organization of the cell. Without it, you have nothing.” That is a general claim about life – “without it you have nothing.” I am asking you to support that claim. Are you doing to do so or not?

@Biosemiosis.org

You first addressed me on this thread by claiming I was making a mere assumption. Tell me, which of these two is the real assumption about life:

a) that life requires nucleic acids, proteins, lipids, etc., in a coherently-orchestrated organization, or

b) that it only needs “an arbitrarily complex set of chemical reactions” of RNA?

They’re both assumptions. I have never claimed that RNA world ever existed or is even possible. I’m asking you to support your claim.

@Biosemiosis.org

And even if I were to grant your many assumptions, you still have to deal with the semiotic requirements I’ve discussed in order to actually address the question on the table – the extant cell.

Look, you made a sweeping statement about universal physical principles that constrain possible life. I’m a physicist and a biologist, and universal physical principles that constrain life would be very interesting to me. That was the claim I was interested in, and it’s the claim I’ve been asking you about. It doesn’t seem to be a claim you can support.

[Biosemiosis.org]

@glipsnort

It doesn’t seem to be a claim you can support.

You must be one of those people who believes that if you repeat the denial of something enough times, it’ll make it go away. So you repeat it over and over and over and over again – even on a page where every word is recorded for anyone to see.

. . . . . . . . . . .

Earlier in this thread …

Bio: Yes, I have explained it. To organize the heterogeneous cell requires the capacity to specify something and place it under temporal control

Steve: You have not explained why a heterogenous cell requires a representational system

The following text is the part of my comment that you specifically clipped from your response above. It is a physical reality that you’ve avoided throughout this entire thread, while demanding I tell you what it is:

“Yes, I have explained it. To organize the heterogeneous cell requires the capacity to specify something and place it under temporal control. Why does it take two objects to specify something within a system? Because nothing in this material universe inherently specifies anything else. It requires one object to act as a representation, and a second object to establish what is being represented. And indeed, this is exactly what is found inside the cell.”

[glipsnort (Steve Schaffner)]

@Biosemiosis.org

You must be one of those people who believes that if you repeat the denial of something enough times, it’ll make it go away. So you repeat it over and over and over and over again – even on a page where every word is recorded for anyone to see.

No, I’m someone who doesn’t accept assertions without evidence. It’s a scientific approach.

@Biosemiosis.org

“Yes, I have explained it. To organize the heterogeneous cell requires the capacity to specify something and place it under temporal control. Why does it take two objects to specify something within a system? Because nothing in this material universe inherently specifies anything else. It requires one object to act as a representation, and a second object to establish what is being represented. And indeed, this is exactly what is found inside the cell.”

That statement isn’t evidence of anything. It’s an assertion, or rather, a series of assertions, and the first one seems to be false. To organize the kind of heterogeneous cell I’m talking about does not require the capacity to specify something in the sense you are using. Lipid membranes organize themselves. RNA molecules copy themselves. No external specification required. And RNA molecules have molecular functions, of course, without external specification. (Personally, I would call that being inherently specified, but that’s not important.)