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!
DNA_Jock,
So are you sweeping the above under the rug? You’re not called math genius for nothing. Now will you reply or it this too inconvenient to you?
No one is denying you know some biology. So you settle “evolutionary” “science” in the court of law and betting and the cancel culture. Do you smack each other too? Or fling feeces like “cousins”? Haha.
Anyway, you can start by explaining how you would analyze and label a new mutation never seen before as either “beneficial” or “deleterious” or “neutral”. If you can’t, the whole classification fails.
Sorry. This doesn’t make any sense.
You’re not answering the question. Are you referring to an absolute or a conditional? You seem to search for an absolute whereas now you talk about “conditions”.
I must insist: as a math genius, would you say a ‘conditional beneficial’ is not the same as ‘beneficial’? A simple Yes or No is needed. Then an explanation if ‘No’ (meaning ‘they are the same’). Thanks.
Not sure what you’re talking about. But this is moot as I ask above for your method (if any) to determine if a mutation will be “beneficial” or “deleterious” or “neutral”.
Not running away from anything Hit-and-run. Show me the link, and you get an answer. You’re hilarious, Guy-that-doesn’t-have-a fitness-function-but-pretends-“evolution”-works-without.
Sorry. That’s a negative. And before “the spread”, let’s talk about how you come to know a mutation to be “beneficial”. Hopefully not by its spread. Just to be safe, you do know what circular logic is, right?
I don’t want to misrepresent your dogma, so correct me if I’m wrong: I do believe – in your dogma – a “beneficial” mutation spreads to the whole (100%) of the population given enough time, like 100% of the whale that can swim, 100% of the cats that can meow (no obscure reference to cat that doesn’t meow please) and so on. And yes, 100% of the e coli. Correct? And, in the mythical TOL, this will also spread to 100% of all descending “species”, right? In light of this, your “every living thing” makes no sense whatsoever. Is this, gasp, a joke?
Said the guy-that-pretends-he’s-going-to-publish.
The fastest runner won the race…..
Good grief!
Mutations can be lethal. In such cases, context, the niche, is irrelevant.
Let’s!
Alan wrote that AFTER your demand for entire planet coverage. The original context was Lenski’s experiment. Nice trick to point to a comment that occurred after you made a fool out of yourself refusing to understand that evolution is about the interplay between variability and the environment. Your particular definitions for beneficial are your problem, not evolution’s. You did not read anything by Darwin, and you cannot read for comprehension. QED.
I read it. See above (if you can read at all).
You made a fool out of yourself claiming that Darwin taught about context-independent beneficial mutations. Darwin did not teach anything about mutations, and he talked about the interplay between a population’s variability and the environment. Noticed that? The fucking environment! That makes evolution dependent on both, the population’s variability and the environment! Got it now or you prefer to continue making a fool out of yourself?
Mung was not answering that comment. Click the link by the end of your own comment Nonlin. You’ll notice, unless you cannot read for comprehension (it seems you cannot), that you agreed with me that beneficial is always context dependent.
You did not understand what Mung was answering. Therefore you’re illiterate. Now you fail time and again in checking your own comment and the comment by Mung you were answering: therefore you’re illiterate.
Oh, sorry, most probably you don’t understand what illiterate means: it means you cannot understand what you try and read. It means that you fail to put words within their context. Maybe you think that words have only absolute meanings, and that if they depend on the context they’re just meaningless words. I would not be too surprised.
Nope. Not by its spread. The spread is one step in their identification, but other tests have to be made in order to fully identify a beneficial mutation. For example, checking the effect of the mutation would be an excellent thing to do.
Mutation effect testing is not circular logic, it’s a task. To identify a beneficial mutation, for example, you proceed through some steps checking for what a beneficial mutation should do. You notice that a mutation is spreading in a population, whereas a sister population, or populations, lack it. You check if the carriers have some characteristic that’s advantageous in their niche compared to where the sister population(s) thrive. Etc. The more you can check the better. But spreading alone is not enough. Evolutionary biologists already know this, so do not act surprised. Remember that your ignorance and misunderstanding of science and evolution are yours, not theirs.
Circular logic is when some imbecile defines “design” as anything that’s not random to try and conclude design. Like when philosophers use the word “necessity” against “random”, and the imbecile redefines “necessity” as “design”, and then concludes that everything is designed.
ETA: I don’t expect you to understand this, given your profound illiteracy and your resistance to correction and learning. But maybe it helps someone else.
ETA2:
The demand for context-independent effects is your misunderstanding. Whether people can or cannot give you examples that comply with your nonsensical demands doesn’t matter. Evolution is not about magic. It’s about the interplay between the population’s variability and the environment.
We can identify antibiotic cassettes as beneficial to the bacteria that carry them against antibiotic-infested environments due to human overuse. Yet, we can still find bacteria that do not carry those cassettes. That doesn’t mean that the cassettes are not beneficial to the bacteria exposed to the antibiotics. Again, semantic games, based on your profound ignorance and nonsensical mind, have no effect on evolutionary phenomena. The problem remains in your mind, while evolutionary theory carries on. Cry. Yell. Sob. Make as many tantrums as you like. The only effect of your misunderstandings and refusal to learn will continue to be just you looking pathetically stupid. I suspect that’s not what you want, but that’s all you’re gonna get.
I know that you make me want to have nothing to do with Intelligent Design. 🙂
nonlin,
This is a very important point.
I am providing you with examples of context-independent effects, not to defend evolution in any way (it matters not at all, except in your confused view), but rather because it’s funny. Your ignorance is so deep and profound that it becomes entertaining.
Here goes. ‘Deleterious’, ‘beneficial’, and ‘neutral’ are not three distinct categories. There is in fact a continuum, ranging from highly beneficial, through beneficial, slightly beneficial, very slightly beneficial, very slightly deleterious, slightly deleterious… you get the idea, I hope.
Just how beneficial or deleterious a given mutation might be varies, depending on context. Context includes the external environment (that ‘niche’ thingy), and the allele frequencies of other genes in the breeding population. Whether CCR5Δ32 is beneficial depends on the amount of HIV out there. Whether beta-globin-S is beneficial depends on how much malaria is out there and also the frequency of the S-allele in the breeding population (phoodoo may be able to explain why).
None of this represents any problem for evolution at all.
However, I enjoy pointing out your more egregious errors — it’s a weakness of mine, and rather unchristian of me.
In that vein, here goes: in addition to those mutations that might be beneficial, or might not, depending on the context, there also exist mutations whose effects range from the very very deleterious to the very deleterious. In any context imaginable, they are always deleterious. You keep claiming that such mutations do not exist. The mutant alleles are unimpressed…
Let us consider two mutations in the human IDS (iduronate 2-sulfatase) gene:
mutation W is the change:codons 84-85 from allele A (TGCGCC, Cys-Ala) to allele B (TACGCC, Tyr-Ala)
mutation X is the change:codons 84-85 from allele A (TGCGCC, Cys-Ala) to allele C (TGCTCC, Cys-Ser).
I know (because I know about sulfatases), that mutation W is deleterious under all circumstances. It (and the other five missense mutations to codon 84) is always deleterious. “Absolute”, as you would put it. No such mutation has ever been observed, but statistically speaking its a safe bet that such a mutation has occurred.
Mutation X (Cys-Ala -> Cys-Ser) is a different kettle of fish in terms of my predictive skills; from first principles, I do not know whether mutation X would be deleterious or not. I would suspect it might be rather deleterious, but it could be in that near-neutral zone too. If I wanted to make a prediction, I would synthesize the mutant protein and test its enzyme activity, stability, and intra-cellular trafficking. Evolution, on the other hand, is entirely unconcerned by my ignorance. If allele C is defective in sulfatase activity, boys carrying it will suffer from Hunter syndrome, whether I was able to predict this or not. [It is and they do, btw]
Final source of confusion for you.
Mutation W is deleterious under all circumstances; I predicted this. Mutation X is deleterious under all circumstances; researchers have observed this.
Consider the following two mutations
Mutation W* is the mutation from allele B to allele A (it is the back-mutation that reverses the effect of mutation W.)
Mutation X* is the mutation from allele C to allele A (it is the back-mutation that reverses the effect of mutation X.)
Mutation W* and mutation X* are beneficial under all circumstances. Do you see?
E2clarify intended recipient…
Here you go.
This is beneath you. Don’t let nonlin lead you into spouting nonsense.
If you’re arguing that something can be both beneficial and not beneficial (deleterious or neutral) then you need to explain how it can be so rather than just declare it to be so.
Light and dark may be a continuum, but it does not follow that at some point darkness becomes the complete absence of light.
If there is no distinction, then the terms are meaningless. Yet evolution requires such distinctions. Say it isn’t so.
Mung,
DNA_Jock did not say there’s no distinction in mutation effects. DNA_Jock said that the range of mutation effects is a continuum. You might need to read a tad better.
Of course not. Evolution eagerly embraces contradiction.
Pointing out error is not unChristian. So perhaps it’s the “enjoyment” of pointing out error that you think “unchristion.” But why should that be so?
Why on earth would you even suggest that you are a Christian?
FFS. What he wrote was that:
“in addition to those mutations that might be beneficial, or might not, depending on the context, there also exist mutations whose effects range from the very very deleterious to the very deleterious”
He’s making clear distinctions while claiming that such distinctions do not exist.
In the spirit of Christian charity, I encourage you to read to the end a comment before responding. That might reduce the frequency of “This is beneath you”-style failures on your part.
I am a Christian in that I try to follow Christ’s teachings re how to treat fellow human beings. With mixed success.
I just don’t think that Jeshua ben Joseph was “The Son of God”. If that were true, then the moral of the Gospel would be
uplifting, it ain’t.
Mung,
Or not, I guess.
Yikes.
It’s a continuum, Mung FFS.
Effect can range from plus 100 to minus 100.
Some mutations have (depending on context) effect between plus 20 and minus 30: could be beneficial or not, depending on context…
Others have a range from minus 100 to minus 70: always, unconditionally, “absolutely” deleterious.
And for the back mutation, reverse the sign.
It is merely the difference between a continuous and a categorical variable.
Yikes!
E2vary range size
In the spirit of Christian charity, I encourage you to to admit that your participation in my removal as an admin here at TSZ was unChristian.
Those were the good days, when hundreds of people weren’t dying needlessly everyday and we could be outraged at moderation issues.
Sorry, but your private opinion does not annul how the terms are correctly used.
Entropy already answered this and I agree with him. To pile on: this is how the Lenski lab determined whether mutant alleles were beneficial in the LTEE; By demonstrating the observed rate of increase of specific variants was statistically highly unlikely in a neutral scenario. Your insistence that this is somehow invalid is bizarre.
For comparison: can you tell beforehand whether any person you encounter for the first time will be friendly? Does your inability to reliably predict so mean that “nicety” does not exist and is a conclusion from a circular argument?
I am sorry, but what makes you say that “e coli” is a natural group? Is it a created kind? How can you tell?
You seem to have missed Alan’s previous remark about asexuality. That may prove to be germane to finding out why your representation of my “dogma” is misguided.
And you’ve encountered Joe G!
The demand for identification of a novel beneficial allele prior to its spread ‘in the wild’ seems akin to demanding identification of an effective medication prior to its administration to anyone.
New drugs are developed by producing variant molecules and testing them for activity, sieving them, testing for safety and effectiveness, iterating.
It’ll never catch on.
Oh, that starving unemployed publisher again. I feel your pain, but don’t call me, I’ll call you.
Haha. This goes beyond anecdotes. Is there a method to the madness? Don’t see any. And a conditional “beneficial” is NOT THE SAME as “beneficial”. Let’s start with the clear, logical basis and in short order you’ll see “evolution” is impossible.
False. Why would I expect a full population spread out of a flask? You can’t read. Haha.
Then we’re in agreement that the mutation itself cannot be “beneficial” if “interplay” and all that?
I said that much. And nothing else. Enough time wasted with you.
False. “Interplay”!
Haha! Inteplay – yes. “Evolution” – no.
Haha. Ask the chicken to explain relativity and this is what you get.
Then can I interest you in “evolution”? You’re almost there it seems.
The mutation by itself is neither. Right? If context-dependent. Right? It’s elementary. RIGHT?
Haha. Have you tried for stand-up comedian? Hilarious!
Who gives a fuck? Let’s try explaining you methodology. Do you even have one? You know the drill: new mutation without references – “beneficial”, deleterious” “neutral”? How much? How would you know? HOW? No method, no more bullshit.
Is this your method then? Because this kind of looks like a method. This isn’t bad. But you must agree (as you already did) this will not be enough to label a mutation B/D/N. Hence, mutations – by themselves – are neither. B/D/N that is. Clear and simple?
That’s all I’m trying to establish lately: you can’t speak of B/D/N mutations if whatever outcome is context dependent. Why is this like pulling teeth? Sheesh.
Wait a minute. Researches have observed “ALL” circumstances? Isn’t that impossible? And whatever happened to “context dependent”? And if so bad, how do those organisms live to reproduce? Isn’t reproduction a leisure in terms of survival? This is very, VERY fishy.
Are you fucking kidding? Is this logical hocus-pocus what “evolution” is all about? Reversing a disaster in a highly theoretical argument?!? Haha. You must be really desperate, math genius.
No. The bullshit story goes like this: everything was fine with dinosaurs and then “beneficial” mutation Y and now all dinosaurs turned into birds because, you see, birds are superior to dinos and ate their lunch. But that kind of NOVEL “beneficial” mutation is NOWHERE to be found. Haha. Because there never was any and never will be one. Very important: in the real, observable life that is.
Your turn.
Math genius, what’s wrong with you? You just link to yourself. In support of your own claim? I asked you to link said claim to something I said. And do you know what “link” means in this context? Hint: it includes proving a LOGICAL link actually exists.
Too many beers over the weekend? Not good, math genius. Not good.
Yeah, Mung. What’s so hard to understand a mutation is “beneficial” and “deleterious” at the same time? And that’s how you get “neutral”, you see? Just add 30 and subtract 30 and you get what? Think! That’s right, you get “neutered”.
The terms are correctly used sometimes. Definitely not interchangeable. Else why the different words? But then again, in Lala land…
But you’re the one insisting the person will be friendly. I am merely trying to discourage that. And even so, your analogy fails because you’re trying to forecast how successful that parson is by him/herself based on the encounter since a mutation has nothing to do with a relationship to you. Get it?
Did I say “natural group”? What does that even mean?
So asexual organisms live in separate “niches”? No interactions? No competition? Ever? HGT anyone? Wow! Then no “evolution”, either, right? How could they “evolve” if no interaction ever?
False. You’re the one bragging about your “effective medication” when in fact it’s “context dependent” and most often just snake oil. Haha.
Very Intelligent. Like by Design.
Goodness me!
Non-lin has managed to max out on incoherence.
@ non-lin
Mutations happen.
Variation is enhanced by sexual reproduction.
Selection happens.
Denying these well-established, evidenced facts is perverse in the extreme. Whilst your minority (of one, I suspect) view has generated some insightful responses, the repetition is becoming tedious.
https://ghr.nlm.nih.gov/condition/sickle-cell-disease
You see Frankie, according to Nonlin ID is anti-evolution.
Yes. That’s basic logic. Do you need a link?
You suggested it was improper to bring up adaptation when discussing beneficial mutations. That’s just wrong.
No, I am claiming that using the spread of a mutant allele as a clue that it might be beneficial is not circular reasoning.
You tell me. You said that “in my dogma”, a beneficial mutation would spread to 100% of the “e coli”. I do not see why it would spread to all microbes with that name but stop there. What made you say that, I wonder?
No, asexual organisms do not have sex (shocker!). That affects what we consider to be a population. So what exactly is an “e coli”? Can you tell me?
Nonlin.org,
Wrong.
Here you are.
You will have to re-read, and understand, the comments by Corneel and myself on pages 1 and 2 of that thread to see the connection between your “grammatical” confusion and your schoolboy howler equating P(null|result) with P(result|null). The only tenable explanation at this juncture is that you do not understand the P(A|B) notation. Hence my P(A|B) ÷ P(B|A) question, which is easily answered by any moderately intelligent High School student.
So an allele (aren’t all alleles mutant? Careful Jock is going to scold you for using words for convenience and then tell you its used for convenience) can spread throughout a population and become fixed and be deleterious? And beneficial mutations can provide no survival advantage at all as well?
If that is true then I guess it is not circular after all. But then we are going to have to figure out why you call them beneficial and deleterious. Convenience?
LOL phoodoo,
Corneel is consistently precise in his use of language. He is re-iterating, for nonlin’s benefit, a point made by Entropy earlier.
To understand Entropy or Corneel, one must be capable of conceptual thought. Not all humans are.
An allele is advantageous in a genotype if that genotype has higher fitness than the genotypes that existed without the allele. This is in theory to be judged by the expected fitness, which would be the fitness averaged over an infinite set of individuals.
That means that we don’t know the fitness, but can estimate it from a suitably large sample. And this is not circular reasoning, as one can estimate the fitness and then check this out by further sampling of individuals from the same population or from future generations.
Similarly, the weight of an object can be estimated by weighing it, and that’s not circular since it predicts what we would find using more observations on the same scale or a different scale. So weight is not a vacuous concept.
And an advantageous allele, which has higher fitness in all the genotypes in which it is likely to be found, will not necessarily rise in frequency to fixation if it is in a finite population in which it mght be lost due to genetic drift. We can caluate the frequency with which that would happen, in simple cases.
Joe this is just such bad logic.
First what do you mean you can “estimate” an objects weight by weighing it? Do you really mean to say that?
Second, this idea that the fitness of an allele is determined by its “expected” fitness, rather than by its ACTUAL prevalence in the population is further nonsense. Are you really going to claim that its “expected” fitness takes precedence over actual observations? And if expected simply means observed, then expected is a totally meaningless phrase.
Don’t be silly. If someone told you the life expectancy of a dog breed is say, 15 years, how do you think it was estimated other than by sampling enough dogs? Joe told you exactly what it means to say that you can estimate an attribute by measuring it. It’s really not that hard.
How accurate are your scales?
OMagain,
Actually, even before phoodoo arrived with his predictable failure to comprehend, I was thinking of extending Joe’s analogy (and perhaps helping with the measurement issue…) by saying that if we want to know the mass of an object, we can estimate it by measuring its volume and density, or by weighing it on a scale, or by measuring its mass using a balance. The device in your bathroom and the device Justitia holds measure quite different things, but they are related.
Of course he meant to say that, for all weight is context dependent.
The expected fitness must be based on something actual, one would think.
Sample enough dogs and you might arrive at a figure that has nothing to do with the life expectancy of any particular breed of dog.
Good point. In that case you would simply add some squirrels to the sample for good measure
Here is a very clever way to avoid that: sample enough dogs of that particular breed.
phoodoo is welcome to give the name “fitness” to something else of phoodoo’s choosing. Just keep in mind that this is not what biologists call fitness, and when they talk about it they are not using phoodoo’s private terminology.
Alan Fox,
So the bullshit never ends? Haha.
Can you be anti-nonsense? Anti-unicorns and anti-leprechauns? Haha.
Basic illogical. Yes, I do need a link. Is a number both positive and negative? Haha.
You wish.
Huh? Is your friend a mutant now? You’re a very, very confused little chameleon.
Something something struggle for survival and something something “survival of the fittest”. Ain’t that mutation “the fittest”? How can the old un-“evolved” e coli even dare to compete with the new mutant?
Yes, but don’t forget the “millions and trillions of years”. Eventually they MUST encounter one another. And when they do, the mutant always wins per the old man’s myth. Am I missing something?
DNA_Jock,
I read your nonsense then and it didn’t make much sense. Why would it make any sense now? Be brave enough and try again. New words, maybe better clarity. Who knows, maybe you actually got something there (but doubtful). Corneel, would you help him if he’s lost for words?