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Author Topic:   Who Owns the Standard Definition of Evolution
Percy
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Posts: 22456
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.5


Message 541 of 671 (915934)
02-20-2024 2:05 PM
Reply to: Message 539 by Taq
02-20-2024 1:31 PM


Taq writes:
and then apply present processes to explain the past
NO!!! We run tests to see if these processes were active in the past. Those are the tests I have been showing you.
A lot's been said, so I'm not sure which tests you mean, and K.Rose might not be sure either.
--Percy

This message is a reply to:
 Message 539 by Taq, posted 02-20-2024 1:31 PM Taq has replied

Replies to this message:
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Taq
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Posts: 10012
Joined: 03-06-2009
Member Rating: 6.3


(3)
Message 542 of 671 (915941)
02-20-2024 3:50 PM


How the Scientific Method Works
1. Background information
2. Hypothesis
3. Experiment
4. Conclusion
These are the 4 basic steps of the scientific method. Let's see how it applies to the DNA differences between humans and other apes.
1. Background information: We observe mutations happening in humans by comparing up to three generations of parents and offspring. When we categorize these mutations we put them into 4 buckets due to different factors, such as DNA being double stranded. Those buckets are: 'T<>C/G<>A', 'G<>C', 'A<>T', and 'A<>C/G<>T'. Just to make this clear, a mutation of a G to an A would fall into the first bucket, as would a A to a G, C to a T, or a T to C. A G to a C or a C to a G would fit into the 2nd bucket.
If there were an equal chance of a base mutating into one of the 3 other bases then we can predict what the pattern should be. In fact, I wrote a Python script that ran a simulation of 2,200 mutations across 60 million bases in a genome with 41% GC content which is the case in humans (41% of the sequence is GC while 59% is AT) and across 4 trials. Here are my results:
T<>C/G<>A = 0.342 +/- 0.00812225796070065
G<>C = 0.133 +/- 0.008323272163286037
A<>T = 0.19290909090909092 +/- 0.009450829689407263
A<>C/G<>T = 0.3320909090909091 +/- 0.007340592450249576
This is what we would expect if there was an equal chance of every mutation. So what do we actually see when we look at new mutations (de novo mutations) in humans?
That's not at all what we would expect from equal chances (new measured mutations in green). The first bucket is clear up to almost 0.7 instead of 0.33. Both the 2nd and 3rd buckets are below where they should be (0.13 and 0.19 expected) as is the 4th bucket (0.33 expected).
What's going on? Well, we know that there are two mechanisms in action. First, some nucleotides are closer to one another at a molecular level than others:
There are bases with one ring and bases with two rings. From a biochemical point of view, it is more likely that an enzyme will mistake the similar bases for one another. We call these transition mutations. Mutations between dissimilar bases are called transversions, and there are two transversions and only one transition possible for each substitution mutation. Even though there is a 1:2 ratio between transition and transversion mutations there are still way more transition mutations than transversion mutations. There is also deamination of methylated cytosines at CpG's. This is a fancy way of saying that a C is converted to a T at CG's because of C's are often methylated at CG's.
Bucket 1 are all of the transition mutations that include CpG mutations. They are WAY overrepresented compared to equal chance. This is the fingerprint of natural mutation.
2. Hypothesis: If naturally occurring mutations are responsible for the differences between humans AND between humans and other ape species then we should see this same ratio of mutations.
3. Experiment: We compare human genomes to one another and to the genomes of other apes. We count the mutations in each bucket and graph it.
4. Conclusion: The graph above shows the same pattern between de novo (new mutations) mutations and differences between human genomes (Human SNP's). We also see the same pattern when we compare human and ape genomes:
Our hypothesis is supported. We have scientific evidence that humans and other apes share a common ancestor, and that the differences between our genomes are the product of naturally occuring mutations.
I am not assuming common ancestry, nor am I assuming that current processes produced these differences. Instead, I am TESTING to see if this is the cause.

  
Taq
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Posts: 10012
Joined: 03-06-2009
Member Rating: 6.3


Message 543 of 671 (915942)
02-20-2024 3:53 PM
Reply to: Message 541 by Percy
02-20-2024 2:05 PM


Percy writes:
A lot's been said, so I'm not sure which tests you mean, and K.Rose might not be sure either.
The three tests are:
1. Nested hierarchy
2. More differences in introns than in exons
3. More transitions than transversions

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 Message 541 by Percy, posted 02-20-2024 2:05 PM Percy has not replied

  
Taq
Member
Posts: 10012
Joined: 03-06-2009
Member Rating: 6.3


Message 544 of 671 (915943)
02-20-2024 3:58 PM
Reply to: Message 540 by Phat
02-20-2024 1:48 PM


Re: To Thine Own Self Be True
Phat writes:
People have always been free to believe whatever they want. Science and religion can always coexist if each discipline "stays in its own lane".
I completely agree. I disagree with my fellow atheists when they say evolution disproves Christianity. There are tons and tons of Christian scientists and clergy alike who see no conflict.

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Replies to this message:
 Message 547 by dwise1, posted 02-20-2024 5:09 PM Taq has replied
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dwise1
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Posts: 5941
Joined: 05-02-2006
Member Rating: 6.4


Message 545 of 671 (915947)
02-20-2024 4:49 PM
Reply to: Message 533 by Percy
02-20-2024 11:20 AM


A few quick responses.
There have been PhD biologists trying unsuccessfully to make the same case you're trying to make, such as Michael Behe and Jonathan Wells.
Jonathan Wells is the better example, since he self-admittedly pursued his doctorate for the express purpose of "disproving evolution". And he stayed on target, shooting to destroy "evolution" regardless of what he had learned.
In contrast, we have Dr. Mary Schweitzer, PhD Biology, who as a young-earth creationist entered her doctorate for the express purpose of gathering evidence to "disprove evolution." Instead, she now accepts evolution because of the evidence. And is really pissed off at the creationists who lie about her work.
Wells continued on his mission despite the evidence, while Schweitzer dropped that same mission because of the evidence.
This reads like a proposal to disregard scientific knowledge that doesn't have everyday practical applications. Aside from the possibility that one never knows what practical applications might emerge from any scientific investigation, what is wrong with scientific study for the sake of knowledge?
Science, technology, and engineering are not the same things! I am a retired engineer (AKA "intelligent designer") so I know the differences!
Recently in another topic, ICANT praised "science" for what it has done for him, only he was actually talking about advances in technology developed by engineering. Similarly, after having filmed for The Final Countdown (1980) which was filmed in part on an actual US aircraft carrier (USS Nimitz), star Kirk Douglas raved in an interview about the "marvels of science" he saw on that ship. Sorry, no, not science, but rather technology realized through engineering. Not the same things!
We can achieve technology without science. Even other apes and birds can achieve technology without science. You find something that works (eg, pounding a coconut with a rock, poking a stick into a termite hill), so you teach your children, etc. In the case of ravens, they seem to be able to work out the stick tricks on their own without being taught. Technology itself can be a literal no-brainer.
Engineering is basically taking the accrued technology and organizing it into a system that we can use. Basically: we know these things work, so if we extend them to a new problem can we make it work too?
Back to basics for a moment. Science is basically figuring out how everything works. Id est, we can know that something works, but why or how does it work?
Engineering cares nothing for science. It does not care how or why anything works, but rather what does it take to make our project work? The goal, the end result, is the only thing that matters and they couldn't care less why it works.
An example came up in my Linear Circuit Analysis class (Electrical Engineering (EE) -- while working on my Computer Science degree, I took some EE classes "for fun", though also to complement my electronic technician training). We had been spending all this time building frequency-domain models for circuits, so now we needed to study how those models reacted to driving forces. Key to the driving functions was the delta function (AKA "unit impulse"), which was a force of one unit being applied instantaneously (extremely quickly, the total impulse force being applied is the area under the force curve over a period of time (Δt); reducing the delta-time to zero drives the amplitude to infinity so you're slamming your system with an instantaneous pulse of infinite amplitude and watching to see how it rings).
Our professor had been a practicing engineer (unlike our department head who had never left academia to practice in the real world, but that's another story). At this point he reveled in the fact that it was engineers who had come up with that delta function and had been using it successfully for a century before the scientists could figure it out ("those stupid scientists couldn't keep up with us!").
Engineers (especially the creationists) will shout out how much they love science, but only so far as science can provide them with new tools. As soon as they get their new toys, they don't want to have anything more to do with science. Is it then a wonder that so many on that "scientists who are creationists" list are engineers (and theologians and even a couple "food scientists")?
Indeed, one of the worst insults you can give an engineer is to accuse him of turning his assignment into a "science project". Rather than try to figure out how it works and how you should make it work, you are expected to find the quickest (and usually dirtiest) way to solve that immediate problem.
Every-day applications have very little to do directly with science, so most people don't see it. Kind of like their not realizing where the meat and dairy and produce in their grocery stores actually come from.
The purpose of public school science education is to teach children our current scientific understandings in all the major fields of science. Some of it has practical everyday applications, some of it doesn't.
From the Science Framework for California Public Schools Kindergarten Through Grade Twelve, 1990, pg 206, the Anti-Dogmatism Statement:
quote:
"State Board of Education Policy on the Teaching of Natural Sciences, adopted 13 Jan 1989 [emphasized in original]:
Nothing in science or in any other field of knowledge shall be taught dogmatically. A dogma is a system of beliefs that is not subject to scientific test and refutation. Compelling belief is inconsistent with the goal of education; the goal is to encourage understanding."
Later, the Framework makes this statement:
"We repeat here the fundamental conviction of this framework: Education does not compel belief; it seeks to encourage understanding. Nothing in science, or in any other field, should be taught dogmatically. But teaching about something does not constitute advancing it as truth. In science, there is no truth. There is only knowledge that tests itself and builds on itself constantly. This is the message that students should take away with them."

References:
As I have often done here, in 1982 the Air Force Communications Command Leadership School (part of the NCO Academy) instructed us in Marxism and Communism and the Soviet system. To a fundie like K.Rose who thinks that all "education" is instead indoctrination to compel the student to believe in what is taught, that would have meant that the US Air Force was trying to turn its NCOs into Commies! Not hardly! (John Wayne quote)
In my own decades-long experience, I have literally encountered creationists who absolutely refused to learn anything about evolution "because that would require that I believe in it." LITERALLY! -- I ain't shittin' ye! How is any rational person supposed to deal with such a completely screwed up mindset?

This message is a reply to:
 Message 533 by Percy, posted 02-20-2024 11:20 AM Percy has not replied

Replies to this message:
 Message 546 by Taq, posted 02-20-2024 5:00 PM dwise1 has replied

  
Taq
Member
Posts: 10012
Joined: 03-06-2009
Member Rating: 6.3


Message 546 of 671 (915950)
02-20-2024 5:00 PM
Reply to: Message 545 by dwise1
02-20-2024 4:49 PM


dwise1 writes:
Science, technology, and engineering are not the same things!
At the same time, engineers use the scientific method all of the time in the same way that plumbers, carpenters, and car mechanics use the scientific method. For example, if you hypothesize that a car won't start because of a faulty fuel pump then you can test your hypothesis by replacing the fuel pump, or testing its output. When you get down to it, the scientific method is a combination of troubleshooting and puzzle solving.

This message is a reply to:
 Message 545 by dwise1, posted 02-20-2024 4:49 PM dwise1 has replied

Replies to this message:
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dwise1
Member
Posts: 5941
Joined: 05-02-2006
Member Rating: 6.4


Message 547 of 671 (915951)
02-20-2024 5:09 PM
Reply to: Message 544 by Taq
02-20-2024 3:58 PM


Re: To Thine Own Self Be True
I disagree with my fellow atheists when they say evolution disproves Christianity. There are tons and tons of Christian scientists and clergy alike who see no conflict.
Not only that, but there is no inherent reason to perceive any conflict between evolution and Divine Creation. Ask any number of creationists that you want to (and I have) and none of them can give you any reason. Or at least they refuse to give any (mainly because they don't know themselves).
Evolution is implicit in how life works; if you have life, then you also have evolution -- the two are inseparable.
Regardless of how life got started, be it through natural processes or through purely supernatural means or through natural processes set up through supernatural agency (the one that creationists always ignore since they cannot abide the actual Divine Creation), then the moment that life got started it also started evolving.
IOW, evolution happens and would still happen regardless of whether the Creator ever existed or not. It's part of nature, which we know does exist and happen -- we're just not agreed on how it happens and, sadly, on whether it does even happen (that's just the messed up creationist view).
But if they want to redefine (as they do everything else) Christianity to be something completely different, something that depends on Reality not being Realty (ie, which makes required assertions of the universe which are contrary-to-fact), then, yeah, not only evolution but also the rest of science would "disprove Christianity", as would just about everything else we know.

This message is a reply to:
 Message 544 by Taq, posted 02-20-2024 3:58 PM Taq has replied

Replies to this message:
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Tangle
Member
Posts: 9501
From: UK
Joined: 10-07-2011
Member Rating: 5.4


(1)
Message 548 of 671 (915954)
02-20-2024 5:38 PM
Reply to: Message 544 by Taq
02-20-2024 3:58 PM


Re: To Thine Own Self Be True
Taq writes:
I completely agree. I disagree with my fellow atheists when they say evolution disproves Christianity. There are tons and tons of Christian scientists and clergy alike who see no conflict.
I have never met an atheist that says that evolution disproves Christianity and I don't even know anyone here that says that. Evolution certainly doesn't disprove Christianity - even the Pope says that.
Evolution defeats the primitive biblical idea of the immutability of species - that god created species as we see them today. That's a minority Christian view. (nb Christianity is not an American concept - Americans are really weird.)

Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien. I am Mancunian. I am Brum. I am London. Olen Suomi Soy Barcelona. I am Ukraine.

"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.


This message is a reply to:
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Taq
Member
Posts: 10012
Joined: 03-06-2009
Member Rating: 6.3


(1)
Message 549 of 671 (915955)
02-20-2024 5:38 PM
Reply to: Message 547 by dwise1
02-20-2024 5:09 PM


Re: To Thine Own Self Be True
dwise1 writes:
But if they want to redefine (as they do everything else) Christianity to be something completely different, something that depends on Reality not being Realty (ie, which makes required assertions of the universe which are contrary-to-fact), then, yeah, not only evolution but also the rest of science would "disprove Christianity", as would just about everything else we know.
I often get the feeling that Creationists think evolution is just something people choose to believe in. At least for me, accepting reality is not a choice. Some people live in a post-fact post-modernist world where reality can be whatever they want it to be, apparently. This is probably where we get the flat Earthers, 5G causes viral infections, moon landing conspiracy theorists, and young Earth creationists. Perhaps some think that intellect and reason are something to be sacrificed on the altar of Christianity.
YEC also makes a mockery of the church in general. It's like telling people that they have to believe in a flat Earth in order to be a Christian. As Francis Collins put it:
quote:
Professor Darrel Falk has recently pointed out that one should not take the view that young-earth creationism is simply tinkering around the edges of science. If the tenets of young earth creationism were true, basically all of the sciences of geology, cosmology, and biology would utterly collapse. It would be the same as saying 2 plus 2 is actually 5. The tragedy of young-earth creationism is that it takes a relatively recent and extreme view of Genesis, applies to it an unjustified scientific gloss, and then asks sincere and well-meaning seekers to swallow this whole, despite the massive discordance with decades of scientific evidence from multiple disciplines. Is it any wonder that many sadly turn away from faith concluding that they cannot believe in a God who asks for an abandonment of logic and reason?
--Francis Collins, "Faith and the Human Genome"
https://www.asa3.org/ASA/PSCF/2003/PSCF9-03Collins.pdf

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dwise1
Member
Posts: 5941
Joined: 05-02-2006
Member Rating: 6.4


Message 550 of 671 (915956)
02-20-2024 5:41 PM
Reply to: Message 546 by Taq
02-20-2024 5:00 PM


When you get down to it, the scientific method is a combination of troubleshooting and puzzle solving.
Yes, if you analyze the methodology. But the rigor of that approach degrades as you dig deeper into practice.
I am a partner dancer. As we learn some new footwork, I realize that we think much more slowly than we move (I've made the mistake of saying "We move faster than we think" which is unfortunately very ambiguous), so if we have to depend on thinking our way through every part of a new move, then we could not possibly be able to accomplish it -- hence the need for repetitive practice in order to set that move in "muscle memory".
We technicians (eg, tradesmen, mechanics) are taught procedures. Troubleshooting protocols. The most basic one we learned as US Air Force Electronic Systems Repairmen (though not necessarily restricted to that deprecated AFSC) -- a form of bisection search:
  1. The unit does not produce output.
  2. After verifying everything else is in order (including that the inputs are there), then the problem must be inside the box.
  3. Go to the test point in the exact middle of the signal pathway and scope for the signal. If the signal is present, then the problem is after that point, but if the signal is not present then the problem is before that point.
  4. Repeat Step #3 similarly bisecting each segment of the signal pathway until you've narrowed the failure down to the location of the failure.
Similarly in troubleshooting digital circuits, if an output is grounded then it's at zero volts and will show up as a "zero", but if the output is open then you see the applied voltage, hence it will show up as a "one". No scientific method being applied; you just know it and think in those terms.
In a skills knowledge exam, I was presented with a digital circuit and the erroneous outputs due to a fault which I was to identify. The first time I encountered that problem I was baffled since none of the answers were right to my way of thinking. Then later I realized that the logic levels had been defined to completely turn around how I had been trained to think: if zero volts was a "one" and -12V a "zero, then a ground would be a "one" and an open a "zero", completely reversed.
And back to the dancing example, to use the scientific method to create an entire approach to solving a specific common problem would take far too much time. Certain many hours longer than an employer would want to have to pay you for trivial tasks that any journeyman could do immediately in minutes. They need to know what to do immediately. They are not following the scientific method, but rather are following their training.
Yes, much of the protocols had been constructed through the scientific method, but the point is that all that scientific work has already been done. So based on the scientific method, but not always employing it (except when there's something the protocols can't handle).
ABE:
When I had just started working as a technician (c. 1977), Issac Asimov offered me some insight when I read Foundation for the first time.
Early in the story, the Foundation had been established as a repository for all Imperial (a galactic empire) knowledge and technology. After that Galactic Empire collapsed (as the Foundation had predicted) and neighboring star systems started to crawl back out of barbary to interstellar travel, the Foundation was there to guide them in rebuilding civilization in the galaxy.
Here's how they did it, in the spirit of Clarke's Third Law ("Every sufficiently advanced technology is indistinguishable from magic") they started exporting their technology, their only resource, in the form of a highly ritualistic religion. Foundation "priests" would set everything up and manage it. Your world would sent acolytes for training to become technician-priests: "To start up: Say this particular prayer and press that red button."
I realized that I was seeing many of the same things in my fellow technicians. We even had one training NCO who maintained that we have no idea how electronics work, but rather it's all FM ("F**king Magic") or even PFM ("pure f***ing magic").

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Percy
Member
Posts: 22456
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.5


(1)
Message 551 of 671 (915957)
02-20-2024 8:47 PM
Reply to: Message 550 by dwise1
02-20-2024 5:41 PM


dwise1 in Message 550 writes:
When I had just started working as a technician (c. 1977), Issac Asimov offered me some insight when I read Foundation for the first time.
I read the trilogy in 1965 and met Asimov in 1973.
--Percy

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 Message 552 by Tanypteryx, posted 02-20-2024 9:06 PM Percy has replied

  
Tanypteryx
Member
Posts: 4401
From: Oregon, USA
Joined: 08-27-2006
Member Rating: 6.4


Message 552 of 671 (915958)
02-20-2024 9:06 PM
Reply to: Message 551 by Percy
02-20-2024 8:47 PM


I think I read them in 1961, freshman in high school.
and met Asimov in 1973.
I'm probably going to hate you forever now!
The story is so great that I still can suspend disbelief. The TV series is like a completely different story about a few of the same characters. My daughter and son-in-law like it, so I watch it. It's funny how you almost feel violated somehow, when a movie diverges drastically from the book.

Stop Tzar Vladimir the Condemned!
What if Eleanor Roosevelt had wings? -- Monty Python
One important characteristic of a theory is that it has survived repeated attempts to falsify it. Contrary to your understanding, all available evidence confirms it. --Subbie
If evolution is shown to be false, it will be at the hands of things that are true, not made up. --Percy
The reason that we have the scientific method is because common sense isn't reliable. -- Taq
Why should anyone debate someone who doesn't know the subject? -- AZPaul3

This message is a reply to:
 Message 551 by Percy, posted 02-20-2024 8:47 PM Percy has replied

Replies to this message:
 Message 553 by Omnivorous, posted 02-21-2024 5:13 AM Tanypteryx has seen this message but not replied
 Message 554 by Percy, posted 02-21-2024 6:49 AM Tanypteryx has replied

  
Omnivorous
Member
Posts: 3983
From: Adirondackia
Joined: 07-21-2005
Member Rating: 8.3


(1)
Message 553 of 671 (915962)
02-21-2024 5:13 AM
Reply to: Message 552 by Tanypteryx
02-20-2024 9:06 PM


Tanypteryx writes:
It's funny how you almost feel violated somehow, when a movie diverges drastically from the book.
Bookmarks handed out at my local library say "Don't hold the movie against the book."

"If you can keep your head while those around you are losing theirs, you can collect a lot of heads."

Homo sum, humani nihil a me alienum puto.
-Terence


This message is a reply to:
 Message 552 by Tanypteryx, posted 02-20-2024 9:06 PM Tanypteryx has seen this message but not replied

  
Percy
Member
Posts: 22456
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.5


Message 554 of 671 (915963)
02-21-2024 6:49 AM
Reply to: Message 552 by Tanypteryx
02-20-2024 9:06 PM


Tanypteryx in Message 552 writes:
and met Asimov in 1973.
I'm probably going to hate you forever now!
He spoke to a crowded auditorium and then met with a small group of students in a dorm lounge for a couple more hours, which is where I met him. He never flew and I think had driven down from New York City. He was with a male traveling companion who stood slightly off to the side in a trench coat that he never removed, and he never spoke a word that I recall though he frequently gave a half smile that said, "Well, I've heard this one before."
He told story after story and answered question after question. I thought he was charming but my girlfriend couldn't stand him because he would drop in occasional comments like, "But we should get together later and discuss this, girls. But don't worry, I'm not virile." She found him too dirty-old-manish.
The only other things I remember now is in the auditorium describing his oft-told story of the dinner with the female book agent where afterwards he thought he would be accompanying her into her hotel room and suddenly found himself on one side of the door and her on the other with no idea how it happened. And in the lounge how he extended his ideas for thiotimoline after the first story.
--Percy

This message is a reply to:
 Message 552 by Tanypteryx, posted 02-20-2024 9:06 PM Tanypteryx has replied

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 Message 555 by Dr Jack, posted 02-21-2024 8:01 AM Percy has not replied
 Message 557 by Tanypteryx, posted 02-21-2024 10:14 AM Percy has replied

  
Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 10.0


Message 555 of 671 (915965)
02-21-2024 8:01 AM
Reply to: Message 554 by Percy
02-21-2024 6:49 AM


Percy writes:
I thought he was charming but my girlfriend couldn't stand him because he would drop in occasional comments like, "But we should get together later and discuss this, girls. But don't worry, I'm not virile." She found him too dirty-old-manish.
Asimov was a famous creep, noted for groping women. It was so well known about him that he was once jokingly invited to give a talk on "The Positive Power of Posterior Pinching".

This message is a reply to:
 Message 554 by Percy, posted 02-21-2024 6:49 AM Percy has not replied

  
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