Beneficial Mutations

[Tanj]

So I have another question about this topic of "specificity" in genes. I want to see what people think.

So, in the lenski experiments regarding e.coli. Ive heard some Creationists suggest that an observed mutation involved the removal of a part of a system, or the turning off of some kind of "operon" that was otherwise used for metabolism of ribose.

The purpose of the statement being that the population "lost" something, which allowed them to then grow faster.

So, I invision this biological system, almost like a 4 sided square. Where a population "loses" a side, and becomes a three sided square (which is no longer a square at all).

So my question is, does my analogy using a square accurately represent what actually occurred with respect to one of the mutations observed in the lenski experiments?

No, it doesn't. I'd like to provide a similar but better one, but it's too flawed a simile.

And beyond that, are there ever examples of mutations that result in the production of proteins with a greater quantity of pieces, or in which produced proteins gain volume, as a product of mutations?

It's not a particularly meaningful question. Not even sure what "gain volume" means. "Gaining quantity of pieces" is a natural side effect of random mutation due to increased protection of internal hydrophobic residues, aka "useless complexity"

A simple rule drives the evolution of useless complexity: New study shows that proteins become biochemically addicted to complex interactions without adaptation.


For a great story on evolution, have a look at DDT resistance in fruit flies. There's no one good paper, but it's an outstandingly good example of many aspects of evolution

google evolution of ddt resistance fruit flies

 

[Job 33:6]

No, it doesn't. I'd like to provide a similar but better one, but it's too flawed a simile.



It's not a particularly meaningful question. Not even sure what "gain volume" means. "Gaining quantity of pieces" is a natural side effect of random mutation due to increased protection of internal hydrophobic residues, aka "useless complexity"

A simple rule drives the evolution of useless complexity: New study shows that proteins become biochemically addicted to complex interactions without adaptation.


For a great story on evolution, have a look at DDT resistance in fruit flies. There's no one good paper, but it's an outstandingly good example of many aspects of evolution

google evolution of ddt resistance fruit flies

Thanks for acting as my poking bag. This is what I am looking for.

So let's say, in the case of the Lenski experiments, we have a mutation which "turned off" this regulating operon, thereby allowing the e.coli to digest citrate under aerobic conditions.

This is what intelligent design advocates appear to be describing in their summaries of the Lenski experiments.

If the mutation stopped an operon from functioning, it is described or viewed by ID advocates as, almost like...well, I'll just take a quote from creation.com:

"So what happened? It is not yet clear from the published information, but a likely scenario is that mutations jammed the regulation of this operon so that the bacteria produce citrate transporter regardless of the oxidative state of the bacterium’s environment (that is, it is permanently switched on). This can be likened to having a light that switches on when the sun goes down—a sensor detects the lack of light and turns the light on. A fault in the sensor could result in the light being on all the time. That is the sort of change we are talking about."

So first I wonder, if this is an accurate picture of what one of the observed mutations of the Lenski experiments is.

My second question is, do we also have instances of mutations in which operons are "unjammed"? In which case, some source of energy would then only be able to be consumed under limited conditions?

Sometimes these arguments seem kind of relative. Because I wonder, if e.colo originally could consume citrate under both aerobic and anaerobic conditions, but then mutated and could then only process citrate under anaerobic conditions (the reverse of what actually appears to have happened), I wonder if creationists would then just say "well, it's a loss of function, and is therefore not evolution because now the population can only do less than what it could before".

Like, if a fish evolves to walk on land, then it's a loss of function that the land animal can no longer swim as good and breath under water. But if a land animal evolves to live in the ocean, well now it's lost its ability to feed off of terrestrial trees and has lost its ability to hunt land animals.

As if, no matter what change happens, anyone could call it a "loss of function".

This is the impression I get from ID advocates arguments.

And, I still wonder, what about the other hundreds of beneficial mutations identified in Lenski's research? How come nobody seems to talk about them?

 

[Hans Blaster]

David Berlinski also rips evolutionary theory to shreds. He's not a biologist.

And that's why we don't give his claims or arguments any credence. (As I recall his argument wasn't particularly original or compelling.)

 

[sfs]

Tour has over 715 research publications and over 140 patent families, with an h-index = 150 with total citations of >107,000. Tour became a Fellow of the Royal Society of Chemistry in 2020 and in the same year was awarded the Royal Society of Chemistry’s Centenary Prize for innovations in materials chemistry with applications in medicine and nanotechnology. Based on the impact of his published work, in 2019 Tour was ranked in the top 0.004% of the 7 million scientists who have published at least 5 papers in their careers. He was inducted into the National Academy of Inventors in 2015. Tour was named among “The 50 Most Influential Scientists in the World Today” by TheBestSchools.org in 2019; listed in “The World’s Most Influential Scientific Minds” by Thomson Reuters ScienceWatch.com in 2014; and recipient of the Trotter Prize in “Information, Complexity and Inference” in 2014; and was the Lady Davis Visiting Professor, Hebrew University, June, 2014. He was named “Scientist of the Year” by R&D Magazine, 2013.

In other words, no, no qualifications relevant to evolution.

How does your CV compare?

59,000 citations and an h-index of 59 -- which means what, exactly? Unlike Tour, I study the selective effects of mutations.

 

[pitabread]

David Berlinski also rips evolutionary theory to shreds. He's not a biologist.

You don't think it's a little weird that you lend credibility to people criticizing a field they have no proficiency in, but you completely ignore those in the field with relevant expertise? Can't you see the gaping disconnect there?

A gentleman who calls himself Do-while Jones (real name David R Pogge)

I remember reviewing some of Mr Pogge's stuff you previously linked on the forum. I remember it involved a woefully pitiful attempt at criticizing a scientific paper and it was obvious he lacked even the basic knowledge to understand what he was criticizing.

The fact that these are the people you think are credible should really tell you something. You're getting your information from terrible sources.

Now maybe you don't *care* about that (and it's obvious you don't), but that doesn't lend any credibility to your own position. It just reinforces that creationists thrive on ignorance.

 

[sjastro]

What makes you think that he is not? How many fields was Leonardo da Vinci skilled in? Benjamin Franklin? This idea that an individual has to specialise to know anything is a modern construct that is false. David Berlinski also rips evolutionary theory to shreds. He's not a biologist. There are other scientists who put their minds to examining evolution. A gentleman who calls himself Do-while Jones (real name David R Pogge) is an ADA programmer and spent many years working with the US defence forces. He is responsible for the effectiveness of the AIM-9 air to air missile, having solved the problems that made it near useless in combat. He is also an expert in closed loop systems such as temperature control. He explains why the idea that a reptile could evolve into a mammal is preposterous. I have some knowledge of closed loop temperature control, and I have to agree. I don't need to be a biologist in order to see how implausible it is.

The idea of a polymath in the form of a "Renaissance Man" doesn't exist these days due to the high level of specialization and expertise required.
The closest example of a modern day Renaissance Man is Ed Witten the physicist who won the Fields Medal in Mathematics.

Nobel Prize winners can look quite silly when they stray outside their field of expertise.
Here are some examples.

Linus Pauling
Pauling won the 1954 Nobel Prize in Chemistry. A decade before winning the prize, he was diagnosed with Bright's disease which he treated in part by ingesting vitamin supplements, which he claimed dramatically improved his condition. He later espoused taking high doses of vitamin C to reduce the likelihood and severity of experiencing the common cold. Pauling himself consumed amounts of vitamin C on a daily basis that were more than 120 times the recommended daily intake. He further argued that megadoses of vitamin C have therapeutic value for treating schizophrenia and for prolonging cancer patients' lives. These claims are not supported by the best available science.[6][1][2]

Kary Mullis
Mullis won the 1993 Nobel Prize in Chemistry. Mullis has disagreed with the accepted, and scientifically verified, view that AIDS is caused by the HIV virus, has questioned the evidence for human contributions to global warming, professed a belief in astrology, and claims that he once encountered a fluorescent raccoon that spoke with him.[3][6][7][8]

Luc Montagnier
Montagnier won the 2008 Nobel Prize in Physiology or Medicine. In 2009, in a non-peer-reviewed paper in a journal that he had founded, Montagnier claimed that that solutions containing the DNA of pathogenic bacteria and viruses could emit low frequency radio waves that induce surrounding water molecules to become arranged into “nanostructures”. He suggested water could retain such properties even after the original solutions were massively diluted, to the point where the original DNA had effectively vanished, and that water could retain the “memory” of substances with which it had been in contact -- claims that place his work in close alignment with the pseudoscientific tenets of homeopathy.[2][9][7]He has supported the scientifically discredited view that vaccines cause autism and has claimed that antibiotics are of therapeutic value in the treatment of autism.[6]

Nikolaas Tinbergen
Tinbergen won the 1973 Nobel Prize in Physiology or Medicine. During his Nobel acceptance speech, Tinbergen promoted the widely discredited[10] "refrigerator mother" hypothesis of the causation of autism, thereby setting a "nearly unbeatable record for shortest time between receiving the Nobel Prize and saying something really stupid about a field in which the recipient had little experience.”[2] In 1985, Tinbergen coauthored a book with is wife[11] that recommended the use of "holding therapy" for autism, a form of treatment that is empirically unsupported and that can be physically dangerous.[6][1][7]

Brian Josephson
Josephson won the Nobel Prize in Physics in 1973. Josephson has promoted a number of scientifically unsupported or discredited beliefs, including the homeopathic notion that water can somehow "remember" the chemical properties of substances diluted within it, the view that transcendental meditation is helpful for bringing unconscious traumatic memories into conscious awareness, and the possibility that humans may be able to communicate with each other through the use of telepathy.[6][7][3]

 

[Tanj]

So first I wonder, if this is an accurate picture of what one of the observed mutations of the Lenski experiments is.

Probably.

My second question is, do we also have instances of mutations in which operons are "unjammed"? In which case, some source of energy would then only be able to be consumed under limited conditions?

Again, probably, It's a huge experiment spanning decades, I don't have the time to parse all of it to find specific instances.

As if, no matter what change happens, anyone could call it a "loss of function".
This is the impression I get from ID advocates arguments.

Sounds about right.

And, I still wonder, what about the other hundreds of beneficial mutations identified in Lenski's research? How come nobody seems to talk about them?

As I said, look beyond Lenski.

 

[Job 33:6]

Probably.



Again, probably, It's a huge experiment spanning decades, I don't have the time to parse all of it to find specific instances.



Sounds about right.



As I said, look beyond Lenski.

I'll see if I can find an instance in which operons become more active in some instances then. Or perhaps become functional under new conditions that they previously had not.

Maybe that can help then.

Otherwise, thanks!

 

[Kylie]

What makes you think that he is not? How many fields was Leonardo da Vinci skilled in? Benjamin Franklin? This idea that an individual has to specialise to know anything is a modern construct that is false. David Berlinski also rips evolutionary theory to shreds. He's not a biologist. There are other scientists who put their minds to examining evolution. A gentleman who calls himself Do-while Jones (real name David R Pogge) is an ADA programmer and spent many years working with the US defence forces. He is responsible for the effectiveness of the AIM-9 air to air missile, having solved the problems that made it near useless in combat. He is also an expert in closed loop systems such as temperature control. He explains why the idea that a reptile could evolve into a mammal is preposterous. I have some knowledge of closed loop temperature control, and I have to agree. I don't need to be a biologist in order to see how implausible it is.

Evolution is a biological process. If a scientists is to be considered an expert on evolution, they will need to have some formal education in evolution. Since he has not had such an education in a relevant field, his opinions about evolution aren't worth much.

The fact he is a scientists in other fields does not mean he understands fields outside his area of expertise.

 

[Hans Blaster]

Nobel Prize winners can look quite silly when they stray outside their field of expertise.
Here are some examples.

Then there is the old favorite of this board, a Nobel prize winner who stubbornly refused to accept something in his own field. Hannes Alfven insisted that magnetic recombination could not exist, yet it does.

Science works on evidence, not authority. One gains credence in science by discovering and explaining evidence, and recognizing the limits of one's own knowledge.

 

[sjastro]

Then there is the old favorite of this board, a Nobel prize winner who stubbornly refused to accept something in his own field. Hannes Alfven insisted that magnetic recombination could not exist, yet it does.

Science works on evidence, not authority. One gains credence in science by discovering and explaining evidence, and recognizing the limits of one's own knowledge.

How could I forget our old friend Alfven who is now revered as a demigod in pseudoscience circles.
I wonder if he was alive today how he would react to the recent news of solar scientists finding more evidence of corona heating being caused by magnetic reconnection.

 

[Aussie Pete]

Evolution is a biological process. If a scientists is to be considered an expert on evolution, they will need to have some formal education in evolution. Since he has not had such an education in a relevant field, his opinions about evolution aren't worth much.

The fact he is a scientists in other fields does not mean he understands fields outside his area of expertise.

How come you have to be a biologist to know anything about evolution yet countless non-scientists say they believe in evolution. What would they know? They are obviously too dumb to understand the concepts, so they should just leave alone what they do no understand.
Seriously, any intelligent person can have a look at evolution and work out for themselves if it is what they want to believe or not. Of course, that is dependent on giving them the opportunity to decide for themselves. The Evolutionary Gestapo make sure that there is as little opportunity as possible. Funny how a supposedly proven theory is so fragile that scrutiny must be avoided at all costs.

I know something about closed loop temperature control. I'm not an expert, but I know the basics. For a reptile to somehow evolve into a mammal is simply impossible. Reptiles are cold blooded. Something within them enables them to seek out heat to maintain body temperature. Mammals are self regulating. Do you have any idea what that involves? Not only that, every new creature must evolve a mate in the same geographic location and at the same time. Current listing of mammal species is 6,495. No. Just no.

 

[SelfSim]

Seriously, any intelligent person can have a look at evolution and work out for themselves if it is what they want to believe or not. Of course, that is dependent on giving them the opportunity to decide for themselves. The Evolutionary Gestapo make sure that there is as little opportunity as possible. Funny how a supposedly proven theory is so fragile that scrutiny must be avoided at all costs.

Why are you ranting about freedom of belief when the topic is about the effect of mutations in the process of Evolution?

 

[pitabread]

Seriously, any intelligent person can have a look at evolution and work out for themselves if it is what they want to believe or not. Of course, that is dependent on giving them the opportunity to decide for themselves. The Evolutionary Gestapo make sure that there is as little opportunity as possible. Funny how a supposedly proven theory is so fragile that scrutiny must be avoided at all costs.

It's the other way around. The reason you're perceiving so much controversy around evolution is the fact that religious fundamentalists have been trying to for decades to suppress it as a science out of fear over said religious beliefs. I don't know about Australia, but in the U.S. at least there were even laws prohibiting its teaching. Heck, in some countries there are still efforts to sabotage its teaching.

You ought to ask yourself, if creationist religious beliefs weren't so fragile, why all the fearmongering over evolution? What are creationists so afraid of when it comes to learning about science?

FWIW, awhile back I did an informal poll about whether evolutionists would allow creationist books in a public library and vise-versa for creationists allowing books on evolution in the same. The only people advocating censorship (e.g. not allowing books on evolution) were creationists: What would you allow in a public library?

I know something about closed loop temperature control. I'm not an expert, but I know the basics. For a reptile to somehow evolve into a mammal is simply impossible. Reptiles are cold blooded. Something within them enables them to seek out heat to maintain body temperature. Mammals are self regulating. Do you have any idea what that involves? Not only that, every new creature must evolve a mate in the same geographic location and at the same time. Current listing of mammal species is 6,495. No. Just no.

These types of comments (among others) aren't a criticism of evolution. It's a commentary on the lack of understanding thereof.

It's like saying, "How can the equation x + 10 = 2 mean that x = -8? How can numbers be negative? No. Just no."

Do you think they should teach alternative math?

 

[Ophiolite]

FWIW, awhile back I did an informal poll about whether evolutionists would allow creationist books in a public library and vise-versa for creationists allowing books on evolution in the same. The only people advocating censorship (e.g. not allowing books on evolution) were creationists: What would you allow in a public library?

In fairness, I have to admit I've considered surreptitiously moving the Creationist books in the local bookstore into the humour section, as a form of Public Service. It's not censorship, but it is disingenuous, so I abandoned the idea.

 

[Hans Blaster]

In fairness, I have to admit I've considered surreptitiously moving the Creationist books in the local bookstore into the humour section, as a form of Public Service. It's not censorship, but it is disingenuous, so I abandoned the idea.

I did this once, well, sort of...

For a long time in our bookstore the science and certain religious books were on opposite sides of the same aisle. It was "Science; Nature; Animals/Pets" on one side and "Religious history, theology, apologetics; Christian Fiction; Christian Advice" on the opposite. One day I was browsing the science section and there was a book of appologetics in the science section. It might have been just placed on the wrong side of the aisle by error, or someone may have been planting it amongst the "atheistic science books". I don't know. It needed to be moved (certainly out of the science section), so I put it in "Christian Fiction".

(I never "misfiled" a book that was in the section the bookstore designated, though.)

 

[tas8831]

David Berlinski also rips evolutionary theory to shreds. He's not a biologist.

And it shows.
Are you thinking of his claim re: 50,000 changes to get a whale from a camel? Yeah, that was pretty stupid, actually.

A gentleman who calls himself Do-while Jones (real name David R Pogge) is an ADA programmer and spent many years working with the US defence forces. He is responsible for the effectiveness of the AIM-9 air to air missile, having solved the problems that made it near useless in combat. He is also an expert in closed loop systems such as temperature control. He explains why the idea that a reptile could evolve into a mammal is preposterous.

Are you familiar with the the fallacy of the appeal to false authority?
Pogge is actually kind of a fool - he tries to compare evolution to to upgrades in brackets at one point. He like to edit and distort emails and comments he gets to make himself look better. He doesn't - he relies on people like you who have even less of a science background than he does.
Tell you what, take one of Pogge's claims that impress you and present it here to see if it impresses us.

I have some knowledge of closed loop temperature control, and I have to agree. I don't need to be a biologist in order to see how implausible it is.

Right.... I don't have to be a religionist to see that deity tales are nonsense.

 

[sfs]

How come you have to be a biologist to know anything about evolution

You don't. Most people can understand at least the basics of evolution if they're willing to put in the work.

That's not the question here, though, is it? You were suggesting that Tour be treated as an authority on evolution because of his status as a scientist. To be an expert in a field, you have to have acquired the necessary expertise. Tour hasn't.

Not only that, every new creature must evolve a mate in the same geographic location and at the same time. Current listing of mammal species is 6,495. No. Just no.

This provides a good example of why it's important to know something about the field. Your argument here suggests that you have a very confused understanding of how evolution works. In the real world (which is where evolution operates), every creature is a new creature, and yet they can still mate with existing members of the species. That's how evolution works: tiny changes that accumulate slowly. Only after many, many generations would animal be born that couldn't mate successfully with a member of the earlier generation. (In animals, that is -- plants are sometimes different.)

 

[FrumiousBandersnatch]

The idea of a polymath in the form of a "Renaissance Man" doesn't exist these days due to the high level of specialization and expertise required.
The closest example of a modern day Renaissance Man is Ed Witten the physicist who won the Fields Medal in Mathematics.

Nobel Prize winners can look quite silly when they stray outside their field of expertise.
Here are some examples.

Linus Pauling
Pauling won the 1954 Nobel Prize in Chemistry. A decade before winning the prize, he was diagnosed with Bright's disease which he treated in part by ingesting vitamin supplements, which he claimed dramatically improved his condition. He later espoused taking high doses of vitamin C to reduce the likelihood and severity of experiencing the common cold. Pauling himself consumed amounts of vitamin C on a daily basis that were more than 120 times the recommended daily intake. He further argued that megadoses of vitamin C have therapeutic value for treating schizophrenia and for prolonging cancer patients' lives. These claims are not supported by the best available science.[6][1][2]

Kary Mullis
Mullis won the 1993 Nobel Prize in Chemistry. Mullis has disagreed with the accepted, and scientifically verified, view that AIDS is caused by the HIV virus, has questioned the evidence for human contributions to global warming, professed a belief in astrology, and claims that he once encountered a fluorescent raccoon that spoke with him.[3][6][7][8]

Luc Montagnier
Montagnier won the 2008 Nobel Prize in Physiology or Medicine. In 2009, in a non-peer-reviewed paper in a journal that he had founded, Montagnier claimed that that solutions containing the DNA of pathogenic bacteria and viruses could emit low frequency radio waves that induce surrounding water molecules to become arranged into “nanostructures”. He suggested water could retain such properties even after the original solutions were massively diluted, to the point where the original DNA had effectively vanished, and that water could retain the “memory” of substances with which it had been in contact -- claims that place his work in close alignment with the pseudoscientific tenets of homeopathy.[2][9][7]He has supported the scientifically discredited view that vaccines cause autism and has claimed that antibiotics are of therapeutic value in the treatment of autism.[6]

Nikolaas Tinbergen
Tinbergen won the 1973 Nobel Prize in Physiology or Medicine. During his Nobel acceptance speech, Tinbergen promoted the widely discredited[10] "refrigerator mother" hypothesis of the causation of autism, thereby setting a "nearly unbeatable record for shortest time between receiving the Nobel Prize and saying something really stupid about a field in which the recipient had little experience.”[2] In 1985, Tinbergen coauthored a book with is wife[11] that recommended the use of "holding therapy" for autism, a form of treatment that is empirically unsupported and that can be physically dangerous.[6][1][7]

Brian Josephson
Josephson won the Nobel Prize in Physics in 1973. Josephson has promoted a number of scientifically unsupported or discredited beliefs, including the homeopathic notion that water can somehow "remember" the chemical properties of substances diluted within it, the view that transcendental meditation is helpful for bringing unconscious traumatic memories into conscious awareness, and the possibility that humans may be able to communicate with each other through the use of telepathy.[6][7][3]

This is common enough that it's known as 'The Nobel Disease', although it happens to many others after they reach the peak of their careers; people who have been used to success can come to expect it outside their field of expertise - it's like a lateral Dunning-Kruger effect.

"Preliminary evidence further suggests that intelligent people may have a somewhat larger bias blind spot than other people, meaning they are less aware of their propensity toward biases (Stanovich et al. 2013). Some authors have further argued that high levels of intelligence may exacerbate the risk of critical thinking failures; for instance, Sternberg (2004) proposed that several cognitive errors prevalent among the highly intelligent can predispose to irrationality; several may account for the weird ideas of some Nobel laureates. Unrealistic optimism occurs when people believe that because they are smart, they need not worry about intellectual errors. The sense of omniscience arises when people believe they are so intelligent that they know virtually everything. The sense of invulnerability emerges when people believe they are so smart that they are essentially immune to mistakes. If Sternberg is correct, by virtue of their high intellect Nobel laureates may be at risk for peculiar ideas, especially if they are not sufficiently intellectually humble."​

 

[Job 33:6]

I'll see if I can find an instance in which operons become more active in some instances then. Or perhaps become functional under new conditions that they previously had not.

Maybe that can help then.

Otherwise, thanks!

So I was continuing on with this question about operons and I found the following:

The Life-Cycle of Operons

"Second, some operons have undergone accelerated evolution, with multiple new genes being added during a brief period. "

"new operons often comprise functionally unrelated genes that were already in proximity before the operon formed."

"For example, new operons often arise by deleting the DNA between functionally unrelated genes that happen to be near each other. "

The idea of new operons forming, sounds like it would have an opposite effect as operons being "jammed" or stopped from acting, as per the creation.com description.