Origin of Proteins

Now you’re trying to escape again and put the burden of proving your claims wrong on me. I don’t have to prove your claims wrong. When you make them, you have to prove them right.

You’re not going to get out of this. Stop making claims you can’t support.

Cells can’t get simpler is your claim.

No, that’s yours.

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This is my claim. Can you refute it without invoking a straw-man.

This is a text book example of shifting the burden of proof. As the Hitch said, “What can be asserted without evidence can be dismissed without evidence”.

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Its an example of demonstrating the weaknesses of your claim.

And now you are passing your claims onto others. This isn’t an improvement.

But you don’t care about experiments. You are fine with inference to the best explanation, it’s just that there are some inferences that lead to conclusion you don’t like. So the first thing we need to point out here is your hypocritical and inconsistent demand for experimental evidence.

So far the model is not being supported by the evidence.

Phylogenetics. There are many examples of lineages evolving greater levels of complexity over time during the history of life, even around the root of the tree of life. So there is actually, demonstrably, empirical evidence for that.

But we don’t know how life originated, so we dont’t know how simple it was when it did. Scientists are working on trying to figure that out. Until and if they do so, there is not a default answer we must go to, like “Oh gee we don’t yet know so until and if we figure it out it must be design”. No, when we don’t know, we don’t know and then we try to figure it out and wait for answers, we don’t just jump straight to vacuous placeholders in the mean time.

Simple life is not an empirically demonstrated hypothesis.

Depending on how simple “simple life” is in your view, that might be true. There are hypotheses and models that have not been tested, or experimentally demonstrated. That doesn’t tell us anything about whether those models could work, or whether other such scenarios are possible. We just don’t know enough about it.

Sadly it is Bill’s usual method of dodging when he has no evidence to support his claims.

I will stop here. I think you are correct that there is some evidence of the model of increasing complexity over time. You are also right the weakness in my argument is defining simple.

At this point empirically the simplest cell it is around 400 genes which I would define as a very complex structure relative to human technology.

That cell is also at the end of a 3.5 billion year old lineage.

Not exactly. It is that cell reduced to the edge that it could still self replicate.

That only tells us what we can remove from that cell. It doesn’t tell us how simple or complex cells in the past could be.

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In the lastest paper where they describe their simplest-yet cell they explicitly state there are some genes they decided to keep in the organism despite the fact that they could technically dispense with them, because the cells had very long doubling times that made it impractical to work or do experiments with them. A particular gene they mention as an example, if removed, increased the doubling time by over 3 hours. They decided to keep that gene for practical reasons.

We know there are possible routes to simpler cells still but which would require an enormous amount of work to construct. To highlight a particular example, the cells have all the genes encoding tRNAs for all codons of the genetic code(and their associated aaRS enzymes), but a streamlined genome could restrict all codons to one for each amino acid. That would reduce the number of required tRNA genes from 64 to somewhere around 20. Same goes for the aaRS genes. That’s a potential reduction of about 80 genes there.

Then there are enzymes the organisms use which use the entire modern amino acid alphabet, but we know that reduced amino acid alphabets can still produce functional, correctly folding proteins, so that could potentially reduce the number of required tRNA genes even further, down to maybe 12 or even 8. That’s another 16-20 fewer genes required.

But this would require an enormous amount of work to completely rewrite the protein coding genes of for all the proteins encoded in it’s the organisms genome, and the proteins in turn need to be evolved (probably by artifical selection) towards reduced alphabets too. Some of the routes to simpler cells have not been taken for practical reasons. They are extremely laborious(people need to get paid to do work that will only really pay off decades down the line), and the cells grow very slowly. Not because such cells aren’t possible.
A 6-month doubling time may be of no consequence on geological timescales, the timescales over which large-scale evolutionary change occurs. But it’s just not practical to human researchers.

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It is not an opinion but a scientific fact that IC is a serious problem for evolution, a good example being the ATP synthase. There is no credible evolutionary scenario for this extraordinary but vital nanomachine.

By all means, offer your rebuttal of papers like this:
https://www.nature.com/articles/nrmicro1767

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Is a living self replicating cell probable without ATP synthase?

Fair enough. You’re right here and I was wrong to formulate your dispute with Bill as I did.
So yes, as a general principle, the burden of proof is on the shoulders of the person making a proposition.
But did you notice that evolutionary biologists keep claiming that all extant proteins have evolved to their present forms through some unguided and blind natural process when for many of them (the ATP syntase for example) they have zero evidence to support their claim. Worse, this unsupported claim is even sometimes asserted in college biochemistry textbooks!

Thank you, I appreciate that.

But did you notice that evolutionary biologists keep claiming that all extant proteins have evolved to their present forms through some unguided and blind natural process when for many of them (the ATP syntase for example) they have zero evidence to support their claim.

No I haven’t noticed that. There is of course actual evidence that ATP synthase evolved, some of which is elucidated in the paper evograd linked above.

Worse, this unsupported claim is even sometimes asserted in college biochemistry textbooks!

What claim specifically, that ATP synthase evolved?

Given that the paper shows actual evidence that ATP synthase has an evolutionary history, the implication is: yes.

It is probably also important to remember that there are huge numbers of organisms that can generate ATP without oxidative phosphorylation (and the ATP synthase complex).

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I have never actually had any of my professors or anybody I have worked with ever say those words.

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