Was that on RuBisCo? I remember this paper from a few years back, but it’s definitely not the only study that uses ancestral sequence reconstruction (not even the only one that’s about RuBisCo specifically).
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No but that’s a great paper, was gonna post about it at some point but forgot about it.
Especially interesting how the seven substitutions that created the binding interface between the small and large subunits are actually beneficial even without the small subunit, demonstrating a rare case where positive selection also created the conditions for increased complexity, and where the increased complexity(gain of small subunit) in turn also afforded a significant increase in fitness.
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Ancestral reconstruction is now a regular occurrence in the literature – Joe Thornton and his colleagues are still at it but they have excellent company. This recent one from Thornton, Dickinson, Pu, and colleagues is worth a writeup sometime:
Then there’s the paper below: this excellent work examines ancestral states that are almost 2 billion years in the past (“…near the origin of the α-proteobacteria ~1900 million years (Ma) ago.”) Super interesting, about how signaling pathways can become “insulated” from each other after their birth in a duplication event.
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There’s this cool database with a list of publications on resurrected/reconstructed proteins where authors can upload their results:
https://revenant.inf.pucp.edu.pe/browse
I like the timeline view.
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Hello Alan Fox! I hope you and your family are well.
Yes, I am here, stirring the pot it seems. There was something I wanted to get and understand, and I knew I would likely get it here on Peaceful Science. Fortunately, I was able to get it before being thrown off the site as a … “a troll” I believe is the term that was used.
It is a very interesting thing. I came here and made some statements that are confirmed scientific facts. They are undeniably true. I mentioned that these issues I was discussing were predicted in 1948 (by John Von Neumann, using the logical organization of Alan Turing’s Machine of 1933), and again in 1955 (put into biological context by Francis Crick in the Adapter Hypothesis), and then confirmed via experimental result in 1956-58 (Hoagland and Zamecnik). Oddly enough, no on asked me even a single solitary question about those things. (They weren’t discussed at all).
Instead, I have been accused of trying to “sneak in creationism”, told that my communication skills are lacking (some truth there I admit), explicitly reminded that the use of the word “code and all its derivatives” is strictly metaphorical in biology, and given a couple rather thorough dress downs. However for me, the facts, the physics, and the history of science remains.
The concept of the gene as a symbolic representation of the organism is a fundamental feature of the living world. Arguably the best examples of Turing’s and von Neumann’s machines are to be found in biology.
I believe out in the grand ether of human history, there is a very very old book. Perhaps the oldest trick in that book is to feign incredible confusion about something being said, so that one might take the opportunity to beat it to death as the means to avoid it.
This page from that book is on full display here.
Hmm… okay, I’ll bite… how is it that the idea that RNA can both “carry information… and be a catalyst at the same time” was falsified (which was your original claim) before Woese even proposed that RNA could act as a catalyst (in 1968 according to Wikipedia)?
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Since people have built Turing machines, which differ from Turing’s specification only in that their tape is not infinite, whatever argument you have that the best ones are biological needs to be exceptionally good.
P.S. 1933? Turing was still a student then.
Hard to tell, because nobody knows what those facts are supposed to be, and you refuse to explain. It’s not even possible to tell whether your communication skills are lacking or you just won’t try. And tone trolling isn’t getting you anywhere.
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This guy isn’t here to have an actual interaction. He ignores most questions posed to him and generally dismisses them with the excuse that he once read a book that said that if people ask for clarification they are feigning “incredible confusion.” With a heuristic like that it’s difficult to see how he distinguishes cases of him simply being an unclear communicator from genuine confusion, etc.
He has outright ignored every one of my posts. It would have been simple for him to just respond to my first post in this thread by explaining that he had been misunderstood, that he is not disputing the possibility of an RNA molecule simultaneously being able to contain a coding region while also functioning as a ribozyme, but instead meant something else (and then just take more care to explain what that was in more standard terminology.)
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All fine, thanks. Same wishes to you. I have often wondered what the former commenters at UD are doing these days. I did hope some might have called in at The Skeptical Zone.
As you have found, there are some very well-informed people here. With respect, your commenting style can be a bit abrasive, but the humour helps. “Losing their shorts” 
Well, what is known about biochemistry and genetics has expanded hugely since the 1950s. As an interested layman, I’ve revised my previous skepticism about RNA world and the subsequent gradual evolution of the DNA-based genetic code. Someone downthread has asked for details, I see.
Why not present those facts? What could possibly go wrong?
Well, you already know I disagree about the symbolism. All the biochemical processes are physical. There is no symbolism, though it may do no real harm to visualize protein synthesis, etc, in this way. And Turing and von Neumann were both brilliant in their fields though neither were biochemists
You have sustained a good argument over the years. I have changed my view in light of new evidence and research, seeing RNA world as practically irrefutable. Are you open to the possibility you could be wrong?
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That hypothesis is easily tested.
Had you been “thrown off” you wouldn’t be here to write that. I believe the phrase I used was, “If you behave as a troll you will be treated accordingly.” I am delighted to see you are capable of interacting in a normal manor. Please continue.
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It seems to have been tested at length already.
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Yes, that’s objectively true.
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I mean, this would answer your and your brother’s question:
Such amazing results from evolutionary biology is just a regular occurrence at this point. Eventually it won’t become very newsworthy. “Oh look, yet another ancestral reconstruction showing us amazing details of the past. Oh look, yet another transitional fossil discovered that we can add to the thousands we already have”.
Really, evolutionary biology is just a victim of it’s own success… kinda like vaccines are.
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I think there is truth in that but I’m still worried about the point @Rumraket made about the stuff that gets “covered” in the “news.” Rum’s brother didn’t know about ancestral reconstruction and I would bet he’s overwhelmingly typical in that regard. Endless dino fossils and other stuff that “rewrites textbooks” (UGH) are what “evolution” is to many, perhaps most.
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I can only find 8 comments, the latest in mid 2019, from appsandorgs alter ego.
Who cares how many years you have studied. In that time, how many striking revelatory papers have you published? Notable researchers want to know.
Are you referring to “Upright Biped”? What evidence do you have that they’re the same person? At any rate, we have sufficient evidence from the current thread that @appsandorgs is uninterested in actual interaction.