The Complexity of Evolution

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Burning ghost
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The Complexity of Evolution

Post by Burning ghost » October 12th, 2018, 6:04 am

Note: This post was made by LuckyR


The build up to this can be seen here: viewtopic.php?f=12&t=15797&p=321710#p321710

Moved due to an inappropriate thread title (which cannot be editted once posted.) If anyone would like any particular posts above thread placed here please PM me and I’ll copy and paste where appropriate. Anyway, back to LuckyR’s post:
ThomasHobbes wrote:
October 11th, 2018, 4:37 pm
LuckyR wrote:
October 11th, 2018, 11:59 am


Microbes? The ability of mammals to gestate using placentas is of retro-viral origin, not mammalian origin.
Prove it!
Here is an entertaining synopsis geared to the lay public:

The Virus and the Placenta
Boston in the mid-1990s was humming with the activity of the Human Genome Project. Sequencing technologies had advanced to the point where scientists were incorporating gene discovery into even the most basic research. Since the American courts had thus far allowed companies to patent the genes they discovered, companies like the Genetics Institute (now a part of Pfizer) saw a chance to cash in. There, molecular biologist John McCoy was looking for proteins secreted by cells since they seemed good targets for developing potential drugs.

All was going as planned until McCoy’s bioinformatics specialist Steve Howes rushed into his lab in 1997 to show him the sequence of a gene they called syncytin, which their work showed was secreted by placenta tissue.

Before McCoy could go public with his discovery, he needed to figure out exactly what syncytin did, a job he passed to bench scientist Sha Mi, who everyone called Misha. Misha’s experiments seemed to be going as planned until, a few months later, she, too, rushed into McCoy’s lab with findings of her own.

Syncytin is produced only by certain cells in the placenta, and it directs the formation of the cellular boundary between the placenta and maternal tissue. Approximately one week after fertilization, the egg, now a hollow ball of cells called a blastocyst, implants itself into the uterus, stimulating the formation of the placenta, which provides the fetus with oxygen and nutrients while removing carbon dioxide and other wastes. It also serves as a barrier to prevent infection and keep maternal and fetal blood separate. (Mixing the two could cause a fatal autoimmune response.) The cells in the outer layer of the blastocyst form the outer layer of the placenta, and those in direct contact with the uterus are the only ones that made syncytin.

When the scientists looked closer at the DNA sequence of syncytin, they found that it was nearly identical to a viral protein called env that caused the virus to fuse with its host cell. In the placenta, syncytin performed helped the fetus fuse with its mother. At last McCoy, Howe, and Mi knew what syncytin did.

“This was a bona fide retroviral envelope protein that had somehow been captured during evolution and been trained to operate in human biology,” McCoy says.

The two other retroviral genes next to syncytin, gag and pol, were completely non-functional, McCoy says. Only env remained intact. “Everything else about that retrovirus had been trashed,” he says. The team published a paper in Nature in 2000.

“An important step in mammalian evolution was accomplished by capturing this viral envelope gene,” McCoy says. “There’s plenty of examples of viruses picking up human genes, but this is one of the first examples of the reverse.”

Humans aren’t the only species with a placenta, however. All mammals have placentas, including marsupials and egg-laying mammals. Although all of these mammals have a syncytin gene, they don’t all have the same syncytin gene. The syncytin produced by mice is completely different from the two syncytins found in humans and other primates. At numerous points in mammalian evolution, symbiotic retroviruses entered the genome and steered different groups of mammals along different evolutionary paths, according to a 2012 paper in PNAS by virologist Harmit Malik at the Fred Hutchinson Cancer Research Center in Seattle. Nor was syncytin the only driver
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ThomasHobbes
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Re: The Complexity of Evolution

Post by ThomasHobbes » October 12th, 2018, 12:33 pm

Burning ghost wrote:
October 12th, 2018, 6:04 am
Note: This post was made by LuckyR


The build up to this can be seen here: viewtopic.php?f=12&t=15797&p=321710#p321710

Moved due to an inappropriate thread title (which cannot be editted once posted.) If anyone would like any particular posts above thread placed here please PM me and I’ll copy and paste where appropriate. Anyway, back to LuckyR’s post:
ThomasHobbes wrote:
October 11th, 2018, 4:37 pm


Prove it!
Here is an entertaining synopsis geared to the lay public:

The Virus and the Placenta
Boston in the mid-1990s was humming with the activity of the Human Genome Project. Sequencing technologies had advanced to the point where scientists were incorporating gene discovery into even the most basic research. Since the American courts had thus far allowed companies to patent the genes they discovered, companies like the Genetics Institute (now a part of Pfizer) saw a chance to cash in. There, molecular biologist John McCoy was looking for proteins secreted by cells since they seemed good targets for developing potential drugs.

All was going as planned until McCoy’s bioinformatics specialist Steve Howes rushed into his lab in 1997 to show him the sequence of a gene they called syncytin, which their work showed was secreted by placenta tissue.

Before McCoy could go public with his discovery, he needed to figure out exactly what syncytin did, a job he passed to bench scientist Sha Mi, who everyone called Misha. Misha’s experiments seemed to be going as planned until, a few months later, she, too, rushed into McCoy’s lab with findings of her own.

Syncytin is produced only by certain cells in the placenta, and it directs the formation of the cellular boundary between the placenta and maternal tissue. Approximately one week after fertilization, the egg, now a hollow ball of cells called a blastocyst, implants itself into the uterus, stimulating the formation of the placenta, which provides the fetus with oxygen and nutrients while removing carbon dioxide and other wastes. It also serves as a barrier to prevent infection and keep maternal and fetal blood separate. (Mixing the two could cause a fatal autoimmune response.) The cells in the outer layer of the blastocyst form the outer layer of the placenta, and those in direct contact with the uterus are the only ones that made syncytin.

When the scientists looked closer at the DNA sequence of syncytin, they found that it was nearly identical to a viral protein called env that caused the virus to fuse with its host cell. In the placenta, syncytin performed helped the fetus fuse with its mother. At last McCoy, Howe, and Mi knew what syncytin did.

“This was a bona fide retroviral envelope protein that had somehow been captured during evolution and been trained to operate in human biology,” McCoy says.

The two other retroviral genes next to syncytin, gag and pol, were completely non-functional, McCoy says. Only env remained intact. “Everything else about that retrovirus had been trashed,” he says. The team published a paper in Nature in 2000.

“An important step in mammalian evolution was accomplished by capturing this viral envelope gene,” McCoy says. “There’s plenty of examples of viruses picking up human genes, but this is one of the first examples of the reverse.”

Humans aren’t the only species with a placenta, however. All mammals have placentas, including marsupials and egg-laying mammals. Although all of these mammals have a syncytin gene, they don’t all have the same syncytin gene. The syncytin produced by mice is completely different from the two syncytins found in humans and other primates. At numerous points in mammalian evolution, symbiotic retroviruses entered the genome and steered different groups of mammals along different evolutionary paths, according to a 2012 paper in PNAS by virologist Harmit Malik at the Fred Hutchinson Cancer Research Center in Seattle. Nor was syncytin the only driver
Interesting but purely speculative.
The assumption is that the cause has an effect, but what is seen as a effect might just as well be the cause.
The retro-virus' origin is as likely to be the placenta as the other way round. And there is no possible evidence to say if the chicken is an egg.

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Re: The Complexity of Evolution

Post by ThomasHobbes » October 12th, 2018, 12:35 pm

I think the case for mitochondria seems clearer though. But we just cannot know one way or the other.

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LuckyR
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Re: The Complexity of Evolution

Post by LuckyR » October 18th, 2018, 1:53 am

ThomasHobbes wrote:
October 12th, 2018, 12:33 pm
Burning ghost wrote:
October 12th, 2018, 6:04 am
Note: This post was made by LuckyR


The build up to this can be seen here: viewtopic.php?f=12&t=15797&p=321710#p321710

Moved due to an inappropriate thread title (which cannot be editted once posted.) If anyone would like any particular posts above thread placed here please PM me and I’ll copy and paste where appropriate. Anyway, back to LuckyR’s post:



Here is an entertaining synopsis geared to the lay public:

The Virus and the Placenta
Boston in the mid-1990s was humming with the activity of the Human Genome Project. Sequencing technologies had advanced to the point where scientists were incorporating gene discovery into even the most basic research. Since the American courts had thus far allowed companies to patent the genes they discovered, companies like the Genetics Institute (now a part of Pfizer) saw a chance to cash in. There, molecular biologist John McCoy was looking for proteins secreted by cells since they seemed good targets for developing potential drugs.

All was going as planned until McCoy’s bioinformatics specialist Steve Howes rushed into his lab in 1997 to show him the sequence of a gene they called syncytin, which their work showed was secreted by placenta tissue.

Before McCoy could go public with his discovery, he needed to figure out exactly what syncytin did, a job he passed to bench scientist Sha Mi, who everyone called Misha. Misha’s experiments seemed to be going as planned until, a few months later, she, too, rushed into McCoy’s lab with findings of her own.

Syncytin is produced only by certain cells in the placenta, and it directs the formation of the cellular boundary between the placenta and maternal tissue. Approximately one week after fertilization, the egg, now a hollow ball of cells called a blastocyst, implants itself into the uterus, stimulating the formation of the placenta, which provides the fetus with oxygen and nutrients while removing carbon dioxide and other wastes. It also serves as a barrier to prevent infection and keep maternal and fetal blood separate. (Mixing the two could cause a fatal autoimmune response.) The cells in the outer layer of the blastocyst form the outer layer of the placenta, and those in direct contact with the uterus are the only ones that made syncytin.

When the scientists looked closer at the DNA sequence of syncytin, they found that it was nearly identical to a viral protein called env that caused the virus to fuse with its host cell. In the placenta, syncytin performed helped the fetus fuse with its mother. At last McCoy, Howe, and Mi knew what syncytin did.

“This was a bona fide retroviral envelope protein that had somehow been captured during evolution and been trained to operate in human biology,” McCoy says.

The two other retroviral genes next to syncytin, gag and pol, were completely non-functional, McCoy says. Only env remained intact. “Everything else about that retrovirus had been trashed,” he says. The team published a paper in Nature in 2000.

“An important step in mammalian evolution was accomplished by capturing this viral envelope gene,” McCoy says. “There’s plenty of examples of viruses picking up human genes, but this is one of the first examples of the reverse.”

Humans aren’t the only species with a placenta, however. All mammals have placentas, including marsupials and egg-laying mammals. Although all of these mammals have a syncytin gene, they don’t all have the same syncytin gene. The syncytin produced by mice is completely different from the two syncytins found in humans and other primates. At numerous points in mammalian evolution, symbiotic retroviruses entered the genome and steered different groups of mammals along different evolutionary paths, according to a 2012 paper in PNAS by virologist Harmit Malik at the Fred Hutchinson Cancer Research Center in Seattle. Nor was syncytin the only driver
Interesting but purely speculative.
The assumption is that the cause has an effect, but what is seen as a effect might just as well be the cause.
The retro-virus' origin is as likely to be the placenta as the other way round. And there is no possible evidence to say if the chicken is an egg.
You are free to voice your opinion, though I will take the life's work of a group of professional researchers and leaders in the field, over the thoughts of an internet commenter who perhaps took a minute and a half to reach his conclusion.
"As usual... it depends."

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ThomasHobbes
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Re: The Complexity of Evolution

Post by ThomasHobbes » October 18th, 2018, 2:58 am

LuckyR wrote:
October 18th, 2018, 1:53 am
ThomasHobbes wrote:
October 12th, 2018, 12:33 pm


Interesting but purely speculative.
The assumption is that the cause has an effect, but what is seen as a effect might just as well be the cause.
The retro-virus' origin is as likely to be the placenta as the other way round. And there is no possible evidence to say if the chicken is an egg.
You are free to voice your opinion, though I will take the life's work of a group of professional researchers and leaders in the field, over the thoughts of an internet commenter who perhaps took a minute and a half to reach his conclusion.
Blind faith is about as useful as a chocolate fire-guard. Are you also quite religious too?

Since the article makes unfounded assumptions we are free to ask questions about them.
Try and think about what you are saying here! What sort of unambiguous evidence could there be to assert that human evolution has co-opted this genetic material? NONE.

Yet the anecdotal evidence that the source of all human-like viruses is in fact originally from humans is vast.

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JamesOfSeattle
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Re: The Complexity of Evolution

Post by JamesOfSeattle » October 18th, 2018, 2:18 pm

ThomasHobbes wrote:
October 18th, 2018, 2:58 am
Since the article makes unfounded assumptions we are free to ask questions about them.
I missed something. What are the unfounded assumptions?
Try and think about what you are saying here! What sort of unambiguous evidence could there be to assert that human evolution has co-opted this genetic material? NONE.
Hmmm. If I looked in the human genome and found a gene that was expressed in a particular way, and that gene was extremely similar to a retrovirus gene which had a very similar function, that would seem like good evidence. Now if the DNA on both sides of the human gene looks a lot like the DNA on both sides of the retrovirus gene, except that the human version is so mutated as to render that DNA non-functional, that would be compelling evidence. That’s because we know how natural selection works. Mutations that are bad get removed. Mutations that don’t make any difference can hang around.
Yet the anecdotal evidence that the source of all human-like viruses is in fact originally from humans is vast.
Not sure you really mean “anecdotal” here. But yes, there is evidence (I assume) that retroviruses pick up human DNA. But that activity does not produce the pattern described above.

So, TH, I guess I’m not really sure what your point is.

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Re: The Complexity of Evolution

Post by ThomasHobbes » October 18th, 2018, 4:22 pm

JamesOfSeattle wrote:
October 18th, 2018, 2:18 pm
ThomasHobbes wrote:
October 18th, 2018, 2:58 am
Since the article makes unfounded assumptions we are free to ask questions about them.
I missed something. What are the unfounded assumptions?
Try and think about what you are saying here! What sort of unambiguous evidence could there be to assert that human evolution has co-opted this genetic material? NONE.
Hmmm. If I looked in the human genome and found a gene that was expressed in a particular way, and that gene was extremely similar to a retrovirus gene which had a very similar function, that would seem like good evidence. Now if the DNA on both sides of the human gene looks a lot like the DNA on both sides of the retrovirus gene, except that the human version is so mutated as to render that DNA non-functional, that would be compelling evidence.
When Copurnicus asked what would it look like if the sun rather than the earth were the centre of the universe, it turned out it was exactly the same.

The claim that humans co-opted an existing virus looks the same as a virus being originating from the host in the first place.
The point is that the original source of retro-viruses tend to be the host that they inflict. For rather obvious reasons viruses are so similar to their hosts as they would otherwise be unable to infect cells of that host.
The likelihood of the human genome getting hold of spare genetic material is low, since it would have to involve the haphazard adoption by gametes for something useful. Let me know how you think this might happen!
Conversely the likelihood that this virus originated FROM the human ; from the mega-tonnes of waste placenta that has been ejected from humans and their forebears for millions of years is very high indeed.
I'm pretty sure when they boys in the lab do their homework and discover that mammalian placenta also use the same genetic material the case of the bleeding obvious will be shown.

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Re: The Complexity of Evolution

Post by JamesOfSeattle » October 18th, 2018, 6:06 pm

TH, I’m curious as to your background regarding molecular biology, because a lot of what you’re saying doesn’t make sense to me. Just to be clear, my undergraduate degree was Biochemistry/Molecular Biology/Cell Biology (that was the name of the one department, not three). I have a Master’s in immunology, so some extra virology, much molecular biology.
ThomasHobbes wrote:
October 18th, 2018, 4:22 pm
The claim that humans co-opted an existing virus looks the same as a virus being originating from the host in the first place.
This might be true, except when extra genes come along for the ride and mutate out of functionality. If the virus had other human-like genes that lost functionality by mutation, that would be evidence of the human -> virus direction. In this case, the reverse is true, suggesting virus -> human.
For rather obvious reasons viruses are so similar to their hosts as they would otherwise be unable to infect cells of that host.
This makes no sense to me at all. In what way are viruses similar to their hosts and dissimilar from non-hosts?
The likelihood of the human genome getting hold of spare genetic material is low, since it would have to involve the haphazard adoption by gametes for something useful. Let me know how you think this might happen!
How this would happen is called natural selection. Mutation in the germ line and selection. In this case we get mutation in the germ line via infection in the germ line. I expect the most likely place for such infection is in utero, i.e., when the “germ line” is just one or a few cells in the uterus. Now, as we all know from how natural selection works, the vast majority of mutations are either nonfunctional or dysfunctional, and so don’t get selected. So yes, the likelihood of adoption of spare genetic material is low. If the mutation/infection is useful, it gets selected (and accompanying non-functional DNA will tend to mutate randomly).
Conversely the likelihood that this virus originated FROM the human ; from the mega-tonnes of waste placenta that has been ejected from humans and their forebears for millions of years is very high indeed.
Not sure what you mean by “originated” here. Do you mean there was placenta before any of this particular type of virus existed, and the virus came into existence by co-opting the functional syncytin/env gene plus non-functional gag and pol genes from the human, and then somehow fixed the gag and pol genes so they would be functional for the virus? I hope you see how implausible that is.

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Re: The Complexity of Evolution

Post by LuckyR » October 19th, 2018, 1:17 am

ThomasHobbes wrote:
October 18th, 2018, 2:58 am
LuckyR wrote:
October 18th, 2018, 1:53 am


You are free to voice your opinion, though I will take the life's work of a group of professional researchers and leaders in the field, over the thoughts of an internet commenter who perhaps took a minute and a half to reach his conclusion.
Blind faith is about as useful as a chocolate fire-guard. Are you also quite religious too?

Since the article makes unfounded assumptions we are free to ask questions about them.
Try and think about what you are saying here! What sort of unambiguous evidence could there be to assert that human evolution has co-opted this genetic material? NONE.

Yet the anecdotal evidence that the source of all human-like viruses is in fact originally from humans is vast.
Sorry to interrupt. article ? Perhaps you missed my description of the piece I quoted: "Here is an entertaining synopsis geared to the lay public". There is little to no hard data with which to make a decision on the veracity of the conclusions of the researchers, it is a fluff piece.

I will now return you back to the previously scheduled: James taking Thomas to the woodshed...
"As usual... it depends."

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ThomasHobbes
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Re: The Complexity of Evolution

Post by ThomasHobbes » October 19th, 2018, 3:46 am

JamesOfSeattle wrote:
October 18th, 2018, 6:06 pm
The likelihood of the human genome getting hold of spare genetic material is low, since it would have to involve the haphazard adoption by gametes for something useful. Let me know how you think this might happen!
How this would happen is called natural selection.
You are joking??
What are they teaching you in college these days??
LOL

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Re: The Complexity of Evolution

Post by Burning ghost » October 19th, 2018, 3:58 am

Something I watched a couple of years ago:

https://m.youtube.com/watch?v=3wy6EmhhR7I
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ThomasHobbes
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Re: The Complexity of Evolution

Post by ThomasHobbes » October 19th, 2018, 4:17 am

Burning ghost wrote:
October 19th, 2018, 3:58 am
Something I watched a couple of years ago:

https://m.youtube.com/watch?v=3wy6EmhhR7I
How can you watch something so dumbed down?

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ThomasHobbes
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Re: The Complexity of Evolution

Post by ThomasHobbes » October 19th, 2018, 4:43 am

My objection is with this statement:

"...protein that had somehow been captured during evolution and been trained to operate in human biology"

Somehow, somewhere, over the rainbow!
Please elucidate!
And NO, natural selection will not do it - for obvious reasons.

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JamesOfSeattle
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Re: The Complexity of Evolution

Post by JamesOfSeattle » October 19th, 2018, 2:50 pm

ThomasHobbes wrote:
October 19th, 2018, 4:43 am
And NO, natural selection will not do it - for obvious reasons.
Again with the obvious reasons. Count me as dim, because they’re not so obvious to me. Care to be explicit?

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ThomasHobbes
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Re: The Complexity of Evolution

Post by ThomasHobbes » October 19th, 2018, 3:40 pm

JamesOfSeattle wrote:
October 19th, 2018, 2:50 pm
ThomasHobbes wrote:
October 19th, 2018, 4:43 am
And NO, natural selection will not do it - for obvious reasons.
Again with the obvious reasons. Count me as dim, because they’re not so obvious to me. Care to be explicit?

*
Because any genetic material would have to be sequestered into the human genome and directed into either a human egg or sperm without disrupting its code. This would have to happen randomly.
If you want to roll back genetic science to Darwin's gemmules, which he failed to demonstrate, then please tell us all about it.
Maybe you have another mechanism in mind for the human genome acquiring viruses?

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