I recently created a video (sorry, it’s a long one) covering what I view as the evidence that cells direct their own evolution. I’m curious what feedback others have on it.
Sorry about the length, but I cover a large number of topics, and try to explain it in light of all of the misunderstandings about the subject which I have seen.
This is interesting…
Do you mention in the video the quantum tunneling mutations or any other mechanism?
I’m sorry but I don’t have the time to watch it now…
I posted a similar OP on the theme a while back…
I have new info on the theme as well… including how QM must be involved in processes involving enzymes… Dr. Axe would probably be interested in that..but he will not post here because of the obvious reasons… 🙁
Feedback:
It is about 55 minutes too long.
Could you post a transcript? That might motivate people to stay the course.
Just posting the text of your slides would get you 90% of the way there…
There is evidence that some few mutations involved in particular processes in particular species are directed. But as a general phenomenon, no.
Really??? Directed by what???
Yes, it is too long.
I watched (or listened) for 34 minutes of tedium. At that point I was interrupted. And I did not go back.
I’m not a biologist. But, as far as I can tell, there is nothing new there. You are playing what I call “the construal game”. You are construing the evidence in such a way as to force it to support your own beliefs.
I don’t recall every hearing a biologist use the term “haphazard” for mutations. It is usually the creationists who choose that sort of language. I’ll stick with “random”.
Yes, biologists describe their work in a detached manner. That’s how science is done.
So about half the time it takes someone to slog through one of Vj Torley’s posts.
Not that I think anyone has actually ever done that.
Half? I have a hard time getting through the summaries… 😉
Neil Rickert,
The reason for the “haphazard” language is that, if I use the term “random”, I usually get complaints – even more strongly than yours. Usually, if the term “random” is used, there will be endless complaints saying, “are you saying that mutations follow a uniform standard distribution, because that’s ridiculous.” Any attempt to clarify is considered “moving the goalposts”. I chose “haphazard” because it seems to be the clearest, most succinct way of describing the phenomena of mutations being not related to organismal need. For instance, you seemed to know exactly what I was talking about.
Other cellular processes. Like an environmentally regulated, highly sequence-specific methylation and excision-repair pathway, just to pick an example.
The environmental trigger could be sugar. Literally. If sugar molecules are detected in the environment, they attach to some regulatory element, that then binds a particular stretch of DNA and initiates expression of some downstream gene. That downstream gene could be involved in sequence-specific methylation, which can trigger excision repair, causing a particular mutation.
So the ultimately the mutation is “directed” by the interaction of sugar with intracellular reaction cascades.
However, “haphazard” seems to fit the creationist misunderstanding of evolution. Several creationist posters here at TSZ describe evolution in terms of “dumb luck” — which fits “haphazard” but is not how I understand evolution.
I walk into a dark cave. I turn on a flashlight, so that I can look around. I don’t know what’s in the cave, so I am looking around to see if there is anything interesting.
I can describe the use of a flashlight as randomly spraying photons around. But it seems wrong to describe it as haphazardly spraying photons. There’s nothing haphazard about it. I’m spraying the photons to help me look around and explore the cave. The spray is random, because I don’t know what I am looking for — that’s the nature of exploration.
I see random mutations as something like that. The population is exploring its environment, and randomly (but not haphazardly) spraying mutations helps in that exploration.
I would say that mutations exhibit no bias toward any particular goal.
It seems odd that creationists on one hand assert that mutations are mostly deleterious and lead to genetic meltdown, and on the other hand, say that they appear to be directed.
I’d suggest this isn’t “directing” mutations, it is triggering mutations, the mutation caused is still random. Haven’t watched the video but “directed” suggests a biased outcome to the mutation rather than post facto selection being the bias.
Indeed!
This.
There are some really interesting bits of biology out there. Transposons that only jump if they find themselves in a zygote that lacks their suppressor. Transposons that jump when heat-shocked, etc.
Also, defining “any particular goal” might be challenging, as phase variation might be viewed as ‘particular’, even if antigenic variation is not.
If someone wishes to argue that any of these processes present a problem for the MES, they are welcome to try and make that argument.
Alluding to them and saying “Darwin was wrong” is not compelling.
DNA_Jock,
I still maintain that this is not directed mutation in that it is the triggering or accelerating of mutation that is involved, not mutation with a direction, just mutation with a difference.
Interesting…but nothing new-methylation: i.e. epigenetics…
What are the other processes?
Directed, adaptive mutations (quantum mutations) require the optimal path…each step being advantageous to the previous one…there is no going back though…
No I meant what I wrote quite literally. There really are examples known of highly specific and “targeted” mechanisms of inducing particular mutations. It is a very rare and isolated phenomenon, and a few handful of examples are known.
As in, some extracellular stimulus is detected, and this has the effect that, reliably and consistently given that stimulus and context, chromosome nucleotide number 1.134.082 on E coli strain whatever, is mutated to C instead of A. I’ll have to go digging for the reference because I don’t remember it off the top of my head.
But again I emphasize, this is NOT a general phenomenon and does NOT explain mutations in general. The people who advocate for a generalized phenomenon are doing EXTREME extrapolations from a handful of examples.
Methylation can have epigenetic consequences yes, but they can also have classically heritable consequences in nucleotide sequence.
I mean literally that somewhere in the sequence AGACTGATAGTCGATCGT, there’s an A nucleotide that will be “directed” to mutate to a C nucleotide for example, and that mutation is then passed on.
Rumraket,
OK, wow. Be interested to hear more.
There was a long discussion at PS of the technical meaning of ‘random mutation’ but I understood that mutations induced by environmental stimuli as discussed in that thread were related to the evolutionary model used in the immune response, not evolution of whole organisms.
I don’t recall an example like this coming up. So I am also interested in any further details you have time to dig up.
For the one you have in mind, does that mutation likely confer a fitness benefit in the presence of some environment change which has led to the external the stimulus?
Is there a biochemical mechanism we understand which explains how the stimulus reliably causes that specific mutation?
ETA: Link to PS. There is a lot of less interesting stuff earlier in the thread but I think the material relevant to this discussion starts here
https://discourse.peacefulscience.org/t/perry-marshall-what-is-random/1419/162
Rumraket,
I’m not sure it is quite so rare and isolated as you suppose. First of all, as I note in my video, it currently takes zero experiments for someone to declare in the literature that a mutation was random. However, it takes numerous experiments to prove that a mutation is not random. This introduces a huge bias in the literature. As an example, see this paper. If this much time/money/effort is spent tracking down an individual mutation to determine if it was the result of a mechanism or not, then no wonder there are so few known.
As I also point out in the video, there is an additional bias that one major source of knowledge about mutations is medicine. Just like bacteria were originally thought to be entirely harmful, because the people tracking them were primarily interested in disease, so those were the ones they knew most about. Now it is known that most bacteria are good. I think we will see the same trend with mutation.
Finally, there is the problem of understanding *what* it means to be for a mutation to be directed. Many people have the idea that a directed mutation should make the right mutation exactly the first time. However, direction can come in the form of simply reducing the mutation space. As long as the reduction in mutation space matches the biology of the selection pressure, it is direction.
Anyway, I go into more depth in the video, and touch on more mechanisms, some of which are very interesting. Sadly, I did not have a chance to go into all of the mechanisms (nor do I know them all), but they are truly fascinating. For instance, some bacteria use pseudogenes to store alternate sequences for their outer coat protein, and recombine different pieces from a set of pseudogenes in together to make a new outer coating.
petrushka,
Here’s what I see as the issue. Sanford’s approach is population genetics that is based on the mutation theory from the modern synthesis. If the modern synthesis’ view of the origin of mutations is true, then Sanford’s Genetic Entropy is definitely a simple outgrowth of that picture, which is consonant with the claims that creationists have been making for a long time.
However, if this view of mutation is not the whole picture, then Sanford’s models are incomplete.
So, in short, Sanford shows why the modern synthesis cannot be the cause of evolutionary progression, but, if we discard the modern synthesis, then there is a lot more that has to be considered.
This is entirely wrong.
Sanford’s Genetic Entropy is counterfactual.
A gambler purposefully rolls the dice in the game of Craps. The results of that roll are still random with respect to the chips on the table. This is analogous to “directed” mutations.
These experiments were done in the 1940’s and 50’s, and their results stand to this day.
Luria and Delbruck’s fluctuation assay:
https://en.wikipedia.org/wiki/Luria%E2%80%93Delbr%C3%BCck_experiment
Ester and Joshua Lederbergs’ plate replica experiment:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169282/
In the modern theory a lethal mutation will be selected against very strongly which puts a limit on how many slightly deleterious mutations can build up in the genome. This is the simple reason why Sanford’s ideas fail. This has been further confirmed in living populations where nucleotide substitution rates decrease over time.
https://www.ncbi.nlm.nih.gov/pubmed/19305500
In my estimation Sanford highly selectively cherrypicks the literature on the frequency and magnitude of deleterious-to-beneficial mutations in order to arrive at this conclusion. IIRC he picked references detailing a range in the ratio going from 1 beneficial for every 1 million deleterious mutations, to 1 in every 1000.
Yet one can rather easily find references detailing evidence on the other end of that spectrum, with estimations from experiments on yeast that as much as 16% of mutations in novel environments are beneficial.
Further, again going from memory Sanford also seems to have ruled out strongly adaptive mutations. Basically implying that Sanford considers it somewhere between impossible or, speaking figuratively, at least “miraculously” rare that a mutation could yield a fitness increase of something like 10% or more.
I would simply say that Sanford ignores the fact that genetic meltdown doesn’t happen. His model is wrong. Bumblebee’s do fly.
You are probably referring to the mutation bias , which is NOT a rare phenomenon… It’s quite the opposite to petrushka’s unfounded claim…
“Recently, numerous genome analyses revealed the existence of a universal G:C→A:T mutation bias in bacteria, fungi, plants and animals. To explore the molecular basis for this mutation bias, we examined the three well-known DNA mutation models, i.e., oxidative damage model, UV-radiation damage model and CpG hypermutation model. It was revealed that these models cannot provide a sufficient explanation to the universal mutation bias. Therefore, we resorted to a DNA mutation model proposed by Löwdin 40 years ago, which was based on inter-base double proton transfers (DPT). Since DPT is a fundamental and spontaneous chemical process and occurs much more frequently within GC pairs than AT pairs, Löwdin model offers a common explanation for the observed universal mutation bias and thus has broad biological implications.”
https://www.ncbi.nlm.nih.gov/pubmed/21586276
If this is the case, what’s the stimulus?
I hope you still remember your little comment to me?
J-mac: Can some please give me one reason why further discussions would not a waste of time?
Alan Fox: I think you’ve supplied ample evidence for that already. 🙂
Now you provided more than ample evidence that you are confused about your own beliefs… I’m glad that it wasn’t me who provided you with the rope…
Too bad you don’t believe in shame…
Little? What does that mean in this context?
I think I acknowledged my ignorance of the phenomenon mentioned by Rumraket. Let’s see more details before we rush to judgement whether “directed” in this phenomenon really means predictable or involving foresight. Ignorance is what you don’t know, finding out something you didn’t know cures it.
Well, let’s see what turns up. I’ve Googled a few phrases and I haven’t managed to come across anything yet. Have you?
Rubbish. Human emotions are well understood as hormone induced responses to certain stimuli. I’m quite capable of being ashamed and I bet you are too. Whether I should be because I’m unaware of a process that could be fairly described as “directed mutation” is something you can argue if you want. Seems a bit premature before we have more information on the process.
Just to clarify:
Question 1.
What do we mean by “directed mutation”?
Question 2
Are there documented examples of the process fitting the definition of “directed mutation” given as an answer to question 1?
J-Mac’s “shaming” of Alan Fox is particularly ironic in view of this piece of misplaced condescension [addressing Rumraket]:
Far be it from me to speak for Rumraket, but he has a track record of knowing what he’s talking about, and he is very very obviously NOT talking about common-or-garden mutation bias. Notice that his example was a directed A to C mutation. That you, J-Mac, thought otherwise is a demonstration of your inability to read for comprehension and your D-K failure to recognize same.
DNA_Jock is correct, I was not talking about transition bias.
I think those are good questions. I would want to make a distinction between a mutation being guided by intent, as in some sentient being WANTS with some level of comprehension a particular mutation to happen.
And then mutations being caused by some highly specific, but ultimately blind, biochemical process that homes in on a particular genetic locus and reliably causes a particular mutation to happen there. The type of directed mutations I think of are of the 2nd kind.
And I would distinguish mutations caused by such “targeted” or “directed” biochemical mechanisms, from “undirected” mutations caused by stochastic elements, like random brownian motion affecting DNA polymerase, or ionizing radiation.
In any case, when we speak of random mutations we are of course not saying mutations happening without some physical cause. For any given mutation that happens, even for the “random” ones that are caused by water or other molecules bumping into DNA polymerase hard enough to cause misincorporation of a nucleotide, or ionizing radiation, those are physical causes that explain why those mutations happened.
And yes there are documented cases of mutations happening according to my latter case of directed. As in directed by a highly specific, “targeted” but ultimately blind biochemical process. And they are few and far between, and the people who argue otherwise are extrapolating from the few known cases, and as we can see up above earlier also seem to rely in part on ignorance. As if our ignorance of what “really” cased many recorded mutations was itself evidence that renders their extrapolation plausible.
Laughable, is all I have to say to that.
Of course… How stupid of me?!
Here is proof that Rumkert’s record of “knowing” what he is talking about never fails…
Directed highly specific mutations targeted ultimately by blind biochemical processes…
In other words: oxymoron…which speaks volumes for another kind of blindness…
Both Rum and Jock should read about the all known ways of catalytic enzyme capabilities… You can start with quantum superposition… lol
Alan Fox,
In the video, the definition of “direction” we are using is that it (a) reduces the mutational range, and (b) this reduction in mutational range corresponds with biological function or need. Several examples are given. A very simple one is this paper where a very specific DNA sequence is inserted in response to very specific biological needs. Another highly specific one, not mentioned in the video, is here.
However, even more than the highly-specific examples, I am also talking about more generalized mechanisms. The point I make is that there has been an extreme amount of bias introduced in the theoretical understandings of mutations that essentially prevents cell-directed mutations from being seen. A non-evolutionary example I give is somatic hypermutation. This process reduces the mutation space from 3,000,000,000 base pairs (i.e., the whole genome) to 1,000 base pairs (the correct half of the correct gene). This process is over 99.9999% directionalized, yet, because it doesn’t pick out one specific set of mutations, it is considered “random”.
There are many other, similar processes, but I like to use somatic hypermutation because it is relatively unambiguous what is happening, and has been rigorously studied for almost half a century now, so there is little doubt as to the details.
Other mutational processes may not hit a specific gene, but a specific gene class (i.e., metabolic genes). It even looks like the genome has certain parts of the DNA marked for mutation, though the alignment of these markings and propensity towards functional mutants has not yet been established.
A great book on the cell’s ability to direct mutation is Caporale’s The Implicit Genome.
Thanks JohnnyB for sharings this video here. I think you are right in saying that we should be looking at mutations in diffent ways. I would say that there is much in biology that should be looked at in different ways. Here is an excerpt from New Scientist (Journal reference: Science, DOI: 10.1126/science.aat9077):
To my mind this way of looking at this process is totally wrong, and we often see mutations written about in similar ways. What is it that is making the ‘mistake’ and why should it be classed as a mistake?
If it weren’t for ‘mistakes’ like this, we may not have arrived here to witness the diversity of life on earth.
As you pointed out in the video, bacteria and virus like elements aren’t all detrimental, and mutations aren’t all detrimental. All living beings are alive because they have the ability to maintain a fine balance between destructive and constructive forces. The aim is not to annihilate destructive forces, but to control the interplay of destructive and constructive forces, because what is destructive and detrimental on a lower level could very well be beneficial on a higher level. For example cancer is not more prevalent because the cells that lead to cancer are destroyed before they can become a problem.
Anyway I hope that this thread can stimulate some more interesting discussions.
Nobody in the right frame of mind, other then theistic evolutionists like Swamidass, have even alluded to it…
Your (and Jock) being afraid to even imply that tells me that your bias has reached a limit very hard to comprehend…
Why? I really would like to know why people like you are so afraid of supernatural implications…
ETA: You don’t have to answer this question…
Rumraket,
While these are not incontrovertible, these are actually fairly standard numbers coming from the standard literature. Especially when you look at theoretical mutation space (i.e., the rate of beneficial mutations from mutating an arbitrary base pair).
So, as you are saying, the observed mutation space is significantly more beneficial than the theoretical mutation space. This is itself indicating cell-directed mutations. Otherwise, there would be no reason for even a biased mutation space to be significantly better than the theoretical mutation space (we often forget, it is also possible for a biochemical bias to be a bias towards the negative – however, when we repeatedly find bias in the positive direction, that should tell us something).
Additionally, you are pointing out that organisms in “new environments” (i.e., changing selection pressures) are more likely to produce beneficial mutations. In other words, the cell is shifting the bias of mutations in a direction that is advantageous in the new environment. Sounds like cell-directed mutations on a global scale.
Also, by the way, I am not familiar with that specific paper on yeast, though it sounds extremely interesting. Can you send me a link? Thanks.
Lol.
Jock is acting as he knew the mechanism for the molecular bias for the common-or-garden mutations…
He probably has a patent on it so we will hear not details…-;)
IMO this is a poor analogy.
A better way of putting it would be: All the gamblers that throw the dice at that table suffer any losses personally but donate whatever winnings they get towards the communal good. So we have losses at a lower level but gains at the higher level.
A similar analogy would be the seeds of a dandylion. The seeds are scattered randomly or if you prefer haphazardly, and there are more lost than produce new plants. The losses are unimportant, it is the few that germinate that ensure the continued existence of the species. And of course any that are lost to the plant are of benefit to various other species. Individual seeds may be destroyed before they can produce more dandylions, but overall, life gains from the destruction.
Do you know how this ties in with the comparison of overall mutation rates in the different environments?
So what in your opinion is preventing genetic meltdown?
Well, I do understand a number of mechanisms that contribute to mutation bias. You have even cited some of them yourself.
I will note that science cannot rule out the possibility that a God-like designer is responsible for every single mutation that occurs. It’s just that parsimony leads one away from this explanation: we have perfectly reasonable ‘natural’ explanations for the patterns of mutations that we do observe. Theology also leads one away from the “God of Mutation” explanation: that would be a very busy and malevolent deity…
Finally, insult, you are doing it wrong:
If I had a patent on {subject X}, then I would be motivated to discuss it publicly.
If I did NOT have a patent on {subject X}, but had some cool ideas, then I would be motivated to NOT discuss it publicly.
You might want to educate yourself about how patents work…
😉
Perhaps it’s time for a neologism. Or call them needless mutations.. 🙂
Your analogy, however is quite flawed. You, presumably, are intelligent enough to not repeatedly spray the photons in the same direction hoping to see something different. You are more likely to spray the photons in an area where you have not already looked.
Evolution, they say, is not like that.