Over at the “IDM collapse” thread I rather churlishly rejected CharlieM’s invitation to read an extensive piece by Stephen L. Talbott. Discovering he is a fan of Velikovsky did little to encourage me (that is, I fully realise, an argument from authority, but life is short and authors many. One needs a filter). What did catch my eye, however, is the fact that he is a contributor to Third Way of Evolution. This, on their front page, is what one might term their ‘manifesto’.
The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon intervention by a divine Creator. That is clearly unscientific because it brings an arbitrary supernatural force into the evolution process. The commonly accepted alternative is Neo-Darwinism, which is clearly naturalistic science but ignores much contemporary molecular evidence and invokes a set of unsupported assumptions about the accidental nature of hereditary variation. Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis. Many scientists today see the need for a deeper and more complete exploration of all aspects of the evolutionary process.
That puzzles me. We need a root-and-branch rethink because of the widely-accepted phenomena of endosymbiosis, HGT, transposons and epigenetics? I honestly don’t get it. These are refinements easily, and already, accommodated. Neo-Darwinists do not ‘ignore’ these phenomena, nor consider them unimportant. They may fall outside a strict framework of genetic gradualism by ‘micromutation’, but are hardly keeping anyone awake nights.
Perhaps, on reflection, I should punt them my musings on the Evolution of Sex. It is non-Darwinian in the sense they appear to mean, so it should be right up their street!
So “time” accounts for both the differences and the lack of differences? That’s quite some theory you guys have.
You can’t just blithely attribute it to “time.”
ETA: Well, you can, but you shouldn’t.
If a pair of descendants from a common ancestor has arrived at 99% similarity, it has also arrived at 1% difference, in the same amount of time. It’s like magic.
Not just time – rate matters too. But fundamentally, if there is a mutational process active, then in lineages descended from a particular branch point, the longer it goes on, the more differences will accumulate. This seems uncontroversial to me.
In the statistical models in molecular phylogenetics, the branch length is rate multiplied by time. What it is, is not the total change, or the change per site, but the expected change per site. The branch lengths may be expected to be clocklike (resulting in an “ultrametric” tree), or not, and the rates that differ among branches may also differ among sites, and even among molecules. Which gets messier. The phylogeny is a tree in that it is somewhat like a tree. Just as some graphs are trees, even though they do not have bark.
Wait a minute. Are you saying Lenski personally made that a “beneficial mutation”? And you don’t see a problem?
Isn’t that what “beneficial mutation” means? Otherwise, shouldn’t be a “trade-off mutation” or simply “a mutation”?
Then what makes a mutation “beneficial” and another “deleterious”?
False. I read it end to end. It was very funny.
Then how can the mutation be “beneficial” if “it depends”? Shouldn’t the environment be “beneficial” rather than the mutation?
And isn’t this like exactly what I said some time ago:
In a small farm, only organisms closely related to their wild cousins survive, but agribusinesses select for chickens with oversize breasts and research labs select for populations with specific genetic mutations requiring tight environments to survive. As shown, all these different organisms may or may not survive regardless of their phenotype.
How subtle is it? Explain how you reconcile “beneficial”, “it depends”, and “deleterious”? And anyway, I asked for a “beneficial” mutation to which you confidently replied with CCR5 Δ32, to later find out said mutation is sometimes “deleterious”? WTF, dude? Did I ever disappoint you like that?
And in general, if you’re presented with mutation A and mutation B on one particular gene, both never documented before, what process will you use to forecast “beneficial” and or “deleterious” on one vs the other? I’m just trying to understand the logic and the process, if any.
But wait. Wasn’t this about “science vs. religion”? Now you’re saying it’s “religion vs religion”? Or is it “science vs science”? Either way, will the disappointments never end? I thought I was learning something about biology.
Ah, but let’s not forget the most important assumption, which it turns out to also be a conclusion, just like an authentic 100% aboriginal boomerang, that “evolution” is true. But I repeat myself. Remember?
Btw, some guy Koonin is citing you in his very funny book (well if you skip all the boring stuff which is like 90%). Congrats, dude! Too bad at some point he rather agrees with me and not with you on the TOL. Member that discussion? I member.
See Allan Miller? The third rail link was very helpful as now I enjoy Koonin. Excellent humor indeed. Rest assured, I didn’t pay for that.
Of course not. Richard Lenski designed an experiment in which there was a very simple, stable and specific niche that allowed E. coli populations to grow in controlled temperature and identical nutrient broth, sampled and re inoculated daily into fresh broth. He had no idea what would transpire over time. Lenski provided the niche, chance provided mutations and selection made the citrate-digesting mutant prevail.
I’d be interested (in an ironical sense) to hear what you think is the problem.
The niche! Did I not mention this already?
Good grief how does one respond to this…
this…
Words fail me!
The niche is where you live. If it’s water and you can’t swim you die. If it’s desert and you can, you die. How can anyone not grasp this?.
Glad you get amusement from reading me. I find you incomprehensible. But we can leave it at that.
Yes, a few folks, from time to time, do cite my work. That is not new.
No you didn’t. You think that Darwin taught about mutations that are beneficial regardless of the environment. That means you did not read anything by Darwin.
Nice to see you missing the point and resisting correction as expected. You’re that predictable.
Good thing I’m not cynical, otherwise I’d predict that Nonlin will miss it again.
Then he was the god of that e coli.
More importantly, do you believe this is the first time ever the e coli underwent that mutation? And if not, and if said mutation is “beneficial”, how come it did not spread to 100% of the e coli population? It stands to reason that the mutation is not ubiquitous because it is not “beneficial”. It’s just a mutation that is neither good nor bad. Logical.
Then the “niche” (whatever that means) is “beneficial”, not the mutation. But more likely neither the “niche” nor the mutation as per the e coli saga above.
What’s your “niche” btw? Any “niche”?
So what has water to do with a “beneficial” mutation?
WTF does this even mean? Is that because you eat too many sweets and get diabetes? And you forgot to mutate into a ninja turtle?
Not reading you, but Koonin. Poor sap is trying desperately to make sense out of nonsense. With hilarious results. Not sure being cited in that mess is “beneficial” or “deleterious”. Perhaps a “niche”.
Stands to reason that a mutation dependent on something else cannot be “beneficial”
Anyway, I asked the lot of you to forecast whether a brand new (undocumented) mutation is “beneficial” and crickets. So no method to the madness.
No, that doesn’t stand to reason. I truly do not know how to explain something this obvious to you, precisely because it’s too obvious. The word “beneficial” is always context dependent. If unqualified, the proper question is: beneficial for what? As someone else told you, the ability to swim is beneficial if you live in water, not so much if you live in a desert. Antibiotic resistance is only beneficial for an organism it it is exposed to antibiotics that would kill it otherwise.
You still think that Darwin taught about environmentally-independent beneficial mutations, therefore you did not read anything by Darwin. Darwin insisted on the environment shaping the organisms’ populations. Who could be illiterate enough to miss that if they actually read anything by Darwin? The very idea of natural selection depends on understanding the interplay between population variability and the environment. I have to conclude that either you’re that illiterate, which would not be too surprising, or that you did not read anything by Darwin. I lean towards the latter, but neither is good news about you.
Well, that’s a profoundly incoherent question, how could anybody tell if a mutation is beneficial if it hasn’t been reported? The madness is all yours.
You appear not to be following along. I see Entropy has written an explanation about genome changes being either beneficial, deleterious, neutral depending on context – the niche. Richard Lenski designed the niche for his bacteria. He did not create mutations and he sampled populations, he did not select individual bacteria.
As Entropy points out, this makes no sense whatsoever.
The niche is the immediate environment of the population of organisms. This is not at all complicated. Your obtuseness is… unmatched in my experience.
Quite a bit. There are no organisms that I know of that can grow and reproduce without it, though some do survive desiccation and persist in suspended animation during droughts.
Oh but it did. 🙂
Minor quibble: the word “beneficial” is nearly always context-dependent.
A while back nonlin wanted examples of mutations that we could predict would be ‘deleterious’ without the (perceived) circularity of seeing how the offspring did, or knowing anything about the environment…
When he was supplied with examples, all he could manage was sputtering, so we never got to discuss the back mutations.
Plus ca change…
Not really.
Maybe. Maybe not. You may tell a story about how swimming is beneficial and someone else may tell a story about why it is not beneficial. Storytelling isn’t science.
Mung,
You’re not helping. At least try and get the point before “helping” Nonlin make an imbecile out of him/herself.
Good point. On a similar note, if water “runs downhill”, how come it hasn’t all ended up in the oceans yet?
When a bacterial strain gains antibiotic resistance, it is the antibiotic that is beneficial? LMAO!
You need to look up what “adaptation” means, laddie.
You’re on a roll again, Nonlin. This is priceless stuff.
A mind did it.
Right. How can you tell if its beneficial if it doesn’t exist?
If it does exist, it is by definition beneficial. Until it doesn’t exist anymore. Then of course it is deleterious.
Mutations don’t exist.
</Mung>
They happen…
And I can point to examples of mutations that are unequivocally beneficial, and ones that are unequivocally deleterious, without any knowledge of relative reproductive success.
You guys sound like you are talking about alleles.
Oh, then I guess mutations aren’t heritable.
Interesting.
Very good, phoodoo, the mutation is not inherited.
It is the DNA that results from the mutation that is inherited.
If TGC mutates to TAC, then it is TAC that is inherited, NOT T(G>A)C.
And if that’s codon 84 of human I2S, then it’s deleterious.
Of course, sometimes people use verbal shortcuts to describe a situation, using “the mutation” to signify “the DNA resulting from the mutation”. Grown-ups are not confused, and it does not affect the underlying reality one iota.
I try to not engage in pointless pursuits. Well, except for posting at TSZ.
https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation
LoL
*chuckles*
I edited out “or lethal” from my earlier comment, deciding it would be confusing to non-lin. Mea culpa.
As Jock remarked:
Of course, sometimes people use verbal shortcuts to describe a situation, using “the mutation” to signify “the DNA resulting from the mutation”.
You forgot the bit most relevant to Mung.
LoL indeed. But at you for thinking you caught somebody out. Sad really, but that’s ID supporters for you, all word games no actual substance.
Great. So nothing wrong with saying mutations are inherited or heritable. Glad we settled that.
Oh, and alleles aren’t heritable/inherited either. And the idea of mutation-driven evolution is nonsense.
😀
I never said I could. You might be mistaking Nonlin’s comment for mine.
Nope, it could be anywhere from not-deletereous-enough-to-care to beneficial.
If it doesn’t exist any more and we witnessed it being there and then going extinct, it could be anywhere from not-deletereous-enough-to-care to beneficial-but-not-essential. Unless we also witnessed its effect. Then we could tell which in that range.
Don’t bother. Your “obvious” is mathematically stupid. But then again is anything “evolution” not entirely stupid?
Exactly! Then a mutation cannot be “beneficial” and the predictive power of “evolution” is zero. QED.
Ok, so not god, but farmer.
We’re not talking about a flask, right? We’re talking about all e coli everywhere.
That’s the thing, math genius. Something that is ALWAYS (not “nearly always”) context-dependent is by itself neither “beneficial” nor “deleterious” nor “neutral”. It’s just a mutation. Now be kind enough and present the mathematical proof to them ignorants. I know you got it because you’re a math genius. Right, math genius?
What do you know? I side with Entropy and against you and math genius on this one.
Hey, look who’s back. Let me be the first to welcome you from your Moon trip. This being said, your absence hasn’t been all positive. For instance, right here you’re mixing apples and oranges. Or is it apples and cats? Maybe you’ll get better after you recover…
No idea what you mean. But anyway, there is no “beneficial” anywhere. Maybe that wasn’t a Moon trip after all… Was it Wuhan flu?
Wait, where is that even coming from? The topic is mutation, not adaptation. Go check.
Well, math genius, I went back and checked your other comment. But there are problems:
1. You only offered your prediction which is not really scientific until backed by data
2. This time we were talking specifically about “beneficial” mutations which you have yet to offer any.
3. You do make it clear in your own comment that you’re referring to ‘absolute’ not ‘conditional’ on anything stupid like “the niche”. Therefore you must present (to the ignorants) the math proof as to why a ‘conditional beneficial’ is not the same as ‘beneficial’.
4. It’s kind of unrealistic to talk about mutations that do not result in live births. After all, we’re playing the “evolution” drama here, so let’s stay in character.
Your illiteracy is your fault, not mathematics’.
You’re looking at yourself in the mirror again. Illiteracy doesn’t lead to understanding Nonlin. First learn to read for comprehension, then take a good course on logic. Then, after you truly master those, you might be ready to give us a real criticism of evolution. Right now you’re just ridiculing yourself. Oh, but that you do really well.
Don’t be silly. Your incoherent questions are not evidence of anything except your illiteracy and lack of reasoning abilities.
Why not? The flask is the environment and Darwin taught about the interplay between the environment and a population variability! You’d know this if you had read Darwin, but you can only read wikipedia, and not that well. Why are you refusing to admit that you didn’t read Darwin? You happily and honestly admitted that you were unable to read Paley because it was too advanced for you.
Of course it can. It’s beneficial under that condition “genius.” You just agreed to that look:
Unless you wrote that because you cannot read for comprehension.
Just wait for math genius. He will explain it to you.
Illiteracy means something else than what you think. The other side to “incoherent” is a reader that lacks in reading comprehension.
That discussion was with someone else. To not make a fool of yourself, read that background.
OMG! I feel your embarrassment. But you don’t, right? Like I said before, to not make a fool of yourself, read that background. Hint: on what exactly did I agree with you and against the other two? Think!
I read the background “genius”. Obviously you did not understand that very background. It seems like you feel pride about being an illiterate.
I read the background “genius”, you answered Mung’s answer to me, and in doing so you agreed with my point that “beneficial” is always context dependent. Holy crap, you could not be more illiterate if you did it on purpose!
I am sure that you’d feel embarrassed if you could understand any of this. But surely you won’t notice even if you took another look. I suspect that the word context is very hard for you to grasp. “Read that background” “genius”. If you have the ability that is.
Nonlin.org,
Ah yes, “mathematically stupid”. It’s a technical term, meaning “that which nonlin disagrees with, but is completely unable to argue against”. Usually due to his inability to comprehend even the simplest of High School Math.
Well, I could also offer up mutations in I2S that are KNOWN to be deleterious (like ARG468LEU), but then you and phoodoo would complain that I was ‘cheating’, because I had data about the phenotype of offspring carrying said mutations. Thanks to the fact that I know some biology, I will happily bet my $1,000,000 against your $100,000 that my prediction is correct. Care to wager?
You missed my coy references to the ‘back-mutations’. If the forward mutation is unequivocally deleterious, then the back-mutation is unequivocally beneficial.
I explained the necessary conditions in my December comment. Patients with I2S null mutations rarely if ever reach puberty. Procreation is extremely unlikely.
Patients with I2S null mutations rarely reach puberty, but they do survive birth.
I am not responsible for your ignorance, whether of biology or math.
Have you figured out my P(A|B) ÷ P(B|A) question yet, or are you still running away from that?
ETfix $
Thanks. It was the only place that offered sufficient social isolation.
I believe you were talking specifically about the spread of beneficial mutations. That’s adaptation.
Why stop there? How come the mutation didn’t spread to every living thing in existence? That’s what I’d like to know.
“We” means “you”. How are the mutations that occurred in Lenski’s experiment going to take over the entire planet? E. coli are asexual. They exist in separate niches. You seem to have yet another misconception about how biology works.
He only does math questions.
Let’s see who didn’t understand: and what is that background, aka the point of contention?
Another one that doesn’t understand what’s being discussed. Think. Is Lenski’s experiment the whole discussion? Hint: no. Go back and read.
Yes. And that’s the end of the agreement. Not this: “Of course it can.”
in reply to
Nonlin.org:
That’s the thing, math genius. Something that is ALWAYS (not “nearly always”) context-dependent is by itself neither “beneficial” nor “deleterious” nor “neutral”.
Yawn, how long till you publish? The less time you spend here the faster that’ll happen you get that right?
I don’t think I’ve noticed you engaging anyone in discussion. Your incomprehension seems a fixed asset.