Insofar as “more reader interaction” is one of our strategic priorities, then that is a good thing. But of course there is a context for that too. If all we wanted was more reader interaction, then we’d post articles about NFL protests and gun control. We want more reader interaction within the confines of our mission and values, which is (in part) showing the harmony of evolutionary science and Christian faith through gracious dialogue. If the only way to increase reader interaction is by giving up the gracious dialogue, then we shouldn’t do it.
Yes, competing priorities always must be balanced. Just offering a different perspective. I think it would be a strategic mistake to eliminate your forums, but why should I care? I have no emotional investment in this place …
Good luck. Not an easy problem to solve.
I have enjoyed our convsersations, and I reiterate my appreciation for your responses to these posts. I am sure that your time is precious and I hope that you would never feel compelled to continue any conversation beyond what you are comfortable with.[quote=“agauger, post:39, topic:36875”]
It’s a catch-22. According to received wisdom, you have to retrace history, rewind the clock, to be able to interconvert protein function. This suggests evolutionary paths are locked in by epistasis, and there are only one or a few ways to move forward. The fitness landscape may be so rugged that only one or a few paths exist. That’s a very thin needle for unguided evolution to thread, especially if the emerging new function is very weak, and therefore not accessible to selection.
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If you are challenging received wisdom then it would seem that you should start with the ancestral sequence. It’s a bit like challenging the idea that French and Italian evolved from Latin, and then running an experiment where you try to see if French can evolve into Italian. Axe’s assertion that it shouldn’t matter if you start with the derived or ancestral sequence is just that, an assertion. Not only that, it is an assertion that is contradicted by a lot of other work demonstrating that epistasis is real.
I can see how your study could be useful from a stance where you are just looking at protein function and the effects of mutations. However, your conclusions seem to go beyond that, as do the claims made by ID supporters who reference your work. You are trying to say that your study makes the evolution of a protein very improbable, and I think the it is right to criticize that conclusion given the fact that your model was incapable of supporting that conclusion.
One more criticism that I have is that you only test for one possible function. If you are looking for the emergence of new function then it doesn’t make sense to focus on just one possible function out of millions. You speak of epistasis locking in specific protein function, but this applies at the organismal level as well. The emergence of a new function can be helpful when it first emerges, but as other functions are removed or become dependent on that new function it can lock the new function in as a required function. Therefore, if you are arguing that new function can not emerge through mutation then you need to look for a much wider array of functions, even those that would only be slightly beneficial at first.[quote=“agauger, post:39, topic:36875”]
What I’m saying is that evolutionary pathways to new enzyme function appear to be incredibly fine-tuned. We shouldn’t just say “and this thing was coopted to a new function” without testing whether it’s possible. It’s not easy at all. Joe Thornton can tell you about it. So can David Baker and Daniel Weinreich. Should evolutionary geneticists worry about higher-order epistasis? - PMC
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They only appear fine tuned because of the Sharpshooter fallacy. Using the same logic, the lottery is fine tuned because of the near impossibility of specific people winning specific lotteries. If we calculate the odds of 5 specific people winning 5 specific lotteries the odds of it happening are so astronomical that someone would argue that it was impossible. What we are seeing are the functions that did evolve. What we don’t see in modern populations is all of the functions that didn’t evolve, just as the lottery example ignores all of the people who didn’t win.
As to Thornton, I mentioned one of his recent Nature papers (Starr et al. Sept. 2017). In that paper, there were 160,000 total combinations of mutations in a functional fold, and more than 800 of those had the same or better function than the protein that did evolve. On top of that, the function that did evolve is one of perhaps millions that could have evolved and become fixed in the population.[quote=“agauger, post:39, topic:36875”]
P.S. T_aquaticus, I hope you read the whole paper.
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I will, and I wish you well in your own research which I look forward to reading in the future. Although I may lob criticisms at what you have done thus far, you deserve much praise for actually doing the work and publishing it.
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That’s you. I for one would not care to have anybody audit how much time I’ve spent here in the last years. The cartoon below could be modified to read: “life before the Biologos forum came online.”
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STATS
850 days visited
24d read time
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It should be possible to predict when Merv is on holiday and burgle his house, then.
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Does he visit more or less frequently when he’s on holiday?
I heard flat-earther today say that evolution is a conspiracy to make it look like the Bible teaches that slavery is okay. And he used ID science to prove it.
…that’s gotta work to derail this thread …
Wait a minute! Did I type that last part out loud?
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Oh, but the computer overlords are keeping track. Click on your avatar and go to summary. 24 days of your life reading BioLogos, Merv.
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Okay, okay already! That was 24 days worth, none of which involved me noticing that this information was dangling out there for me and you all to see! There isn’t some stored and displayed idiot coefficient that I should know about is there? Are the overlords meeting in some sinister back room to discuss posters who have the top snarkiness quotients?
Okay --I’m out of here. Gotta turn out the lights and deadlock the doors. I think I hear helicopters.
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I do have to wonder, though… I mean, it regularly tells me it will take X number of hours to catch up on a thread, and instead of reading every post meticulously, I’ll scroll through it for bits that interest me, or sort of sample a random comment here and there to see if the thread is interesting, and my eyes will glaze over when I see a post that’s a whole screen long, so I’ll keep scrolling… I wonder if the algorithm thinks I really spent 3 hours reading it all word by word??
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…and, in the other direction, it probably doesn’t count all the clicking away to BioLogos-discussion-related links and reading those…
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No, that was 24 “yoms” worth, because we all know that when you sit at the computer to read BL, a day is like a thousand years …
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If you can hear the helicopters… that isn’t the Overlord choppers. You can never hear those.
Maybe it’s Putin’s men?
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My earlier joke about a flat-earther prompted someone to ask me if I had actually met a flat-earther recently; (that was attempted silliness in that post --similar to the “nuke the gay whales for Jesus” variety).
But joking aside, that wasn’t totally disconnected from reality. I recently did have a discussion with someone who told me her father was indeed now into flat-earther conspiracy theory – a growing movement, I guess.
I think such topics actually do relate to the topic of this thread, even if along tangential topics. Part of group clustering on social media these days is probably fueled by a persecution complex. Ad hominem attacks may or may not qualify as fallacious or relevant, but whether any alleged case is warranted or not, it probably does help fuel paranoid sentiments on the part of fringe-view proponents. And they also use ad hominem in their own way by writing off experts as part of some large deceitful establishment.
If such belief is growing today, then that could be informative to observe --though the condescension implicit in that last statement
is, I propose, part of the very fuel for the problem being addressed. I think we all have varying degrees of conspiracy enthusiasm or tolerance in us. And we probably find our own version of it to be eminently defensible of course.
You forgot the aliens and Trump.
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Oh, and I count it successfully derailed.
…or even just restored back to its original topic would be great too. As much as I enjoy being the center of attention, that was a bit much. I guess I asked for it though.
The discussion over what constitutes ad hominem was enlightening I thought. And perhaps it is even more important whether or not something is perceived as ad hominem? After all, being attacked isn’t the only thing that sends a person or group into militant mode. Just thinking you have been attacked suffices. That may send all discussion south with all the same negative results as ad hominem even if ad hominem had not technically been committed.
There is probably no way to avoid this, though, short of shutting up completely. Plenty of prophets through history could probably be accused, whether rightly or wrongly of ad hominem attacks.
I agree. And for some reason I am reminded of this saying of St. John of the Cross:
Never take a man for your example in the tasks you have to perform, however holy he may be, for the devil will set his imperfection before you. But imitate Christ, who is supremely perfect and supremely holy, and you will never err.
I think the problem may arise in the (mis)perception of the one using ad hominem (sensu strictu or not) attacks., and their motivation. Someone who sees what he thinks is a lie may out of indignation call out “Liar!” even when there is no lie. And others may pick up the chant. The victim may or may not be able defend himself.
If the person crying “Liar” does so maliciously, even if it seems to justify his argument, then I submit it should called an ad hominem attack.
In any case, there are ways of saying someone has misrepresented the facts without using inflammatory words.
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