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Topic: Introduction to Systems Biology (Read 17597 times) previous topic - next topic

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  • Pingu
Re: Introduction to Systems Biology
Reply #2450
Is Dave about to discover chemistry?

No, but he is about discover homeostasis. 

Which is cool.  Cognitive systems are in some senses homeostatic systems (though think it is more fruitful to think of cognition as a special case of homeostasis than homestasis as equivalent to cognition).

I did my training in a "Perception and Action" lab, which was essentially a cognitive science lab that investigating the neural mechanisms by which people (and often other animals) respond to incoming sensory stimuli, evaluate it, and take appropriate action.  And you can fairly easily set up virtual critters that do this, with relatively simple decision nodes that serve to maintain homeostasis.  So, for instance, the action the critter takes in response to a threat might be different depending on how hungry the critter is.  If the critter is very hungry, it might seek food even in the presence of predators.  If not so hungry, it won't seek food in the presence of predators, but will in the absence of predators.

That's a basic "cognitive" agent- what action the agent takes in response to one stimulus depends on a second external stimulus combined with internal signals from the agent itself. 

And cells certainly do this.  It's how development works in multicellular organisms - what a cell does next depends on signals coming in from other cells and from the external environment, and also from within the cell itself.

And it's a fractal system, so we as humans are systems of systems of systems. So in that sense, I agree with Shapiro that the cell is a cognitive unit. A population of cells is also a cognitive unit - but its cognition is not the same as the cognition of the cells of which it is made up, and may have quite different priorities.

One of my criticisms of Shapiro is that he is often unclear whether he is talking about a single cell being "cognitive" (which it can be - it can repair its own damage, for instance, or mount defenses and attacks) or about a population being "cognitive".  Because a population-level system that causes some cells to die is not in the interests of the individual cells.

And that's really what this thread, with its title, should be about.  But it's not :(

I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2451
By the way I do believe that Shapiro would categorize nhej under natural genetic engineering. I'd have to check, but I think that's correct.

Well it's not what he says in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048091/

As we've already discussed.  ::)
Good Lord.  NHEJ is a complex repair pathway. It can be categorized under natural genetic engineering. But yes it has errors which can be categorized under random change.
  • Last Edit: March 14, 2018, 10:44:18 AM by Dave Hawkins

Re: Introduction to Systems Biology
Reply #2452
By the way I do believe that Shapiro would categorize nhej under natural genetic engineering. I'd have to check, but I think that's correct.

Well it's not what he says in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048091/

As we've already discussed.  ::)
Good Lord.  NHEJ is a complex repair pathway. It can be categorized under natural genetic engineering. But yes it has errors which can be categorized under random change.
So NGE processes can result in random changes. So the two categories are not mutually exclusive.

Re: Introduction to Systems Biology
Reply #2453
You think that cell duplication that happened in lenski's lab Is Random. I think it's not. I think it was NGE.

Let's try to find out which is correct, shall we?

But then you've just re-defined "random" as: "Action not based on sensory data or analysis of same" which is clearly bullshit.

Please write in English, not Davinese.
No it's not clearly b*******. You just would like it to be b******* so that you don't have to be wrong.

  • Pingu
Re: Introduction to Systems Biology
Reply #2454
By the way I do believe that Shapiro would categorize nhej under natural genetic engineering. I'd have to check, but I think that's correct.

Well it's not what he says in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048091/

As we've already discussed.  ::)
Good Lord.  NHEJ is a complex repair pathway. They can be categorized under natural genetic engineering. But yes it has errors which can be categorized under random change.

Yes, but Shapiro doesn't.  And why should he?  NHEJ doesn't involve shunting mobile genetic elements around the genome and between cells.  Sure it's complex.  And sure it senses a problem, analysis the problem, and takes action. But so do other repair pathways that repair errors that occur during chromosome duplication.

Basically you are making shit up.

Both repair systems AND systems that recombine substantial stretches of DNA cause mutations.  All involve complex processes.  All involve mechanism that respond to signals with quite complex courses of action.

But you want to carve out any that are related to "copying" as "random" (by some bizarre definition) while any that are related to anything else, INCLUDING damage by, say oxidation or radiation, as "non-random".

I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2455
By the way I do believe that Shapiro would categorize nhej under natural genetic engineering. I'd have to check, but I think that's correct.

Well it's not what he says in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048091/

As we've already discussed.  ::)
Good Lord.  NHEJ is a complex repair pathway. It can be categorized under natural genetic engineering. But yes it has errors which can be categorized under random change.
So NGE processes can result in random changes. So the two categories are not mutually exclusive.
No one said anything about the processes being mutually exclusive. But also no one but desperate Neo darwinists talks this gibberish about something which is accidental being a "process." That's f****** deranged.

Re: Introduction to Systems Biology
Reply #2456
You think that cell duplication that happened in lenski's lab Is Random. I think it's not. I think it was NGE.

Let's try to find out which is correct, shall we?

But then you've just re-defined "random" as: "Action not based on sensory data or analysis of same" which is clearly bullshit.

Please write in English, not Davinese.
No it's not clearly b*******. You just would like it to be b******* so that you don't have to be wrong.
It's not useful in any way. It defines anything that isn't a product of thought as "random." It means that when an object falls down rather than up, that's random. The sun rising in the east instead of the west is random. It's nonsense.

  • Pingu
Re: Introduction to Systems Biology
Reply #2457
You think that cell duplication that happened in lenski's lab Is Random. I think it's not. I think it was NGE.

Let's try to find out which is correct, shall we?

But then you've just re-defined "random" as: "Action not based on sensory data or analysis of same" which is clearly bullshit.

Please write in English, not Davinese.
No it's not clearly b*******. You just would like it to be b******* so that you don't have to be wrong.

Of course it's bullshit.  It's not what "random" means to anyone but you.  You just made it up.

And even more hilariously if we took your bullshit definition of "random" then repair processes wouldn't be random either.  Because they are all based on sensing the damage, analysing the problem, and enacting an appropriate repair.
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2458
By the way I do believe that Shapiro would categorize nhej under natural genetic engineering. I'd have to check, but I think that's correct.

Well it's not what he says in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048091/

As we've already discussed.  ::)
Good Lord.  NHEJ is a complex repair pathway. They can be categorized under natural genetic engineering. But yes it has errors which can be categorized under random change.

Yes, but Shapiro doesn't.  And why should he?  NHEJ doesn't involve shunting mobile genetic elements around the genome and between cells.  Sure it's complex.  And sure it senses a problem, analysis the problem, and takes action. But so do other repair pathways that repair errors that occur during chromosome duplication.

Basically you are making shit up.

Both repair systems AND systems that recombine substantial stretches of DNA cause mutations.  All involve complex processes.  All involve mechanism that respond to signals with quite complex courses of action.

But you want to carve out any that are related to "copying" as "random" (by some bizarre definition) while any that are related to anything else, INCLUDING damage by, say oxidation or radiation, as "non-random".
It's not a bizarre definition. It's only bizarre to you because you live in this freakish Neo darwinist bubble that desperately wants mistakes to be creative because your whole stupid paradigm is based upon that ridiculous notion.

Mistakes are not a process. They are mistakes that happen in the course of processes.

The sooner you get that through your titanium helmet, the better.

  • Pingu
Re: Introduction to Systems Biology
Reply #2459
By the way I do believe that Shapiro would categorize nhej under natural genetic engineering. I'd have to check, but I think that's correct.

Well it's not what he says in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048091/

As we've already discussed.  ::)
Good Lord.  NHEJ is a complex repair pathway. It can be categorized under natural genetic engineering. But yes it has errors which can be categorized under random change.
So NGE processes can result in random changes. So the two categories are not mutually exclusive.
No one said anything about the processes being mutually exclusive. But also no one but desperate Neo darwinists talks this gibberish about something which is accidental being a "process." That's f****** deranged.

By the way I do believe that Shapiro would categorize nhej under natural genetic engineering. I'd have to check, but I think that's correct.

Well it's not what he says in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048091/

As we've already discussed.  ::)
Good Lord.  NHEJ is a complex repair pathway. It can be categorized under natural genetic engineering. But yes it has errors which can be categorized under random change.
So NGE processes can result in random changes. So the two categories are not mutually exclusive.
No one said anything about the processes being mutually exclusive. But also no one but desperate Neo darwinists talks this gibberish about something which is accidental being a "process." That's f****** deranged.


Please quote where some "desperate neo-Darwinist" talked about "something which is accidental being a 'process'".


I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2460
You think that cell duplication that happened in lenski's lab Is Random. I think it's not. I think it was NGE.

Let's try to find out which is correct, shall we?

But then you've just re-defined "random" as: "Action not based on sensory data or analysis of same" which is clearly bullshit.

Please write in English, not Davinese.
No it's not clearly b*******. You just would like it to be b******* so that you don't have to be wrong.

Of course it's bullshit.  It's not what "random" means to anyone but you.  You just made it up.

And even more hilariously if we took your bullshit definition of "random" then repair processes wouldn't be random either.  Because they are all based on sensing the damage, analysing the problem, and enacting an appropriate repair.
Bingo. Ding ding ding ding.

Repair processes are NOT random. Never have been, never will be. But all processes involve errors because no processes are perfect. But we don't call errors a "process."

Unless you're from Mars and have a third eye in the middle of your forehead. Then maybe you do.

Re: Introduction to Systems Biology
Reply #2461
By the way I do believe that Shapiro would categorize nhej under natural genetic engineering. I'd have to check, but I think that's correct.

Well it's not what he says in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048091/

As we've already discussed.  ::)
Good Lord.  NHEJ is a complex repair pathway. It can be categorized under natural genetic engineering. But yes it has errors which can be categorized under random change.
So NGE processes can result in random changes. So the two categories are not mutually exclusive.
No one said anything about the processes being mutually exclusive.
So the answer to your question about whether the mutation in Lenski's experiment was random or NGE might be that it was both.
But also no one but desperate Neo darwinists talks this gibberish about something which is accidental being a "process."
I'm sure the desperate Neo darwinists who said that in your imagination are very offended right now.
That's f****** deranged.
Tell that to those imaginary desperate Neo darwinists.

  • Pingu
Re: Introduction to Systems Biology
Reply #2462
By the way I do believe that Shapiro would categorize nhej under natural genetic engineering. I'd have to check, but I think that's correct.

Well it's not what he says in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048091/

As we've already discussed.  ::)
Good Lord.  NHEJ is a complex repair pathway. They can be categorized under natural genetic engineering. But yes it has errors which can be categorized under random change.

Yes, but Shapiro doesn't.  And why should he?  NHEJ doesn't involve shunting mobile genetic elements around the genome and between cells.  Sure it's complex.  And sure it senses a problem, analysis the problem, and takes action. But so do other repair pathways that repair errors that occur during chromosome duplication.

Basically you are making shit up.

Both repair systems AND systems that recombine substantial stretches of DNA cause mutations.  All involve complex processes.  All involve mechanism that respond to signals with quite complex courses of action.

But you want to carve out any that are related to "copying" as "random" (by some bizarre definition) while any that are related to anything else, INCLUDING damage by, say oxidation or radiation, as "non-random".
It's not a bizarre definition. It's only bizarre to you because you live in this freakish Neo darwinist bubble that desperately wants mistakes to be creative because your whole stupid paradigm is based upon that ridiculous notion.

It's a totally idiotic definition.  It's not what anyone else means by the word.  It's not what Shapiro means by the word, and it includes lots of things that nobody would call random. 


Mistakes are not a process. They are mistakes that happen in the course of processes.

The sooner you get that through your titanium helmet, the better.

The soon you get out of yours, the sooner you will actually start to understand what people are actually saying instead of flailing at straw men with straw flails.
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2463
"Please quote where some "desperate neo-Darwinist" talked about "something which is accidental being a 'process'"

Good Lord she doesn't even know she's doing it.

Re: Introduction to Systems Biology
Reply #2464
"So the answer to your question about whether the mutation in Lenski's experiment was random or NGE might be that it was both"

No.

Stop flailing and read for comprehension.

  • Pingu
Re: Introduction to Systems Biology
Reply #2465
You think that cell duplication that happened in lenski's lab Is Random. I think it's not. I think it was NGE.

Let's try to find out which is correct, shall we?

But then you've just re-defined "random" as: "Action not based on sensory data or analysis of same" which is clearly bullshit.

Please write in English, not Davinese.
No it's not clearly b*******. You just would like it to be b******* so that you don't have to be wrong.

Of course it's bullshit.  It's not what "random" means to anyone but you.  You just made it up.

And even more hilariously if we took your bullshit definition of "random" then repair processes wouldn't be random either.  Because they are all based on sensing the damage, analysing the problem, and enacting an appropriate repair.
Bingo. Ding ding ding ding.

Repair processes are NOT random. Never have been, never will be. But all processes involve errors because no processes are perfect. But we don't call errors a "process."

But we DO call error REPAIRS a process, right?


Unless you're from Mars and have a third eye in the middle of your forehead. Then maybe you do.

Calm down and stop making shit up.
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2466
You think that cell duplication that happened in lenski's lab Is Random. I think it's not. I think it was NGE.

Let's try to find out which is correct, shall we?

But then you've just re-defined "random" as: "Action not based on sensory data or analysis of same" which is clearly bullshit.

Please write in English, not Davinese.
Yes it's clearly b*******. I just would like it to be not b******* so that I don't have to be wrong.

fyp

  • Pingu
Re: Introduction to Systems Biology
Reply #2467
"Please quote where some "desperate neo-Darwinist" talked about "something which is accidental being a 'process'"

Good Lord she doesn't even know she's doing it.

Well, quote, please.

I'm fed up of you misrepresenting mine and other people's views, and then trying to beat us over the head for those misrepresentations with your misrepresentations of Shapiro's.
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2468
You think that cell duplication that happened in lenski's lab Is Random. I think it's not. I think it was NGE.

Let's try to find out which is correct, shall we?

But then you've just re-defined "random" as: "Action not based on sensory data or analysis of same" which is clearly bullshit.

Please write in English, not Davinese.
No it's not clearly b*******. You just would like it to be b******* so that you don't have to be wrong.

Of course it's bullshit.  It's not what "random" means to anyone but you.  You just made it up.

And even more hilariously if we took your bullshit definition of "random" then repair processes wouldn't be random either.  Because they are all based on sensing the damage, analysing the problem, and enacting an appropriate repair.
Bingo. Ding ding ding ding.

Repair processes are NOT random. Never have been, never will be. But all processes involve errors because no processes are perfect. But we don't call errors a "process."

But we DO call error REPAIRS a process, right?

Yes but it's the repair process that's the process. You don't call the motherfuking errors a process. Jesus Christ.

  • Pingu
Re: Introduction to Systems Biology
Reply #2469
Dave, think:  if a repair process results in a mutation it is usually a fairly small mutation.  You get repeated sections, or short deletions, or single nucleotide substitutions.

However, a mutation that involves wholesale duplication or rearrangement of entire segments are likely to have arisen from something like recombination.

So which of the two do you think is more likely to have caused the duplication that gave rise to citrate utilisation?
I have a Darwin-debased mind.

  • Pingu
Re: Introduction to Systems Biology
Reply #2470
You think that cell duplication that happened in lenski's lab Is Random. I think it's not. I think it was NGE.

Let's try to find out which is correct, shall we?

But then you've just re-defined "random" as: "Action not based on sensory data or analysis of same" which is clearly bullshit.

Please write in English, not Davinese.
No it's not clearly b*******. You just would like it to be b******* so that you don't have to be wrong.

Of course it's bullshit.  It's not what "random" means to anyone but you.  You just made it up.

And even more hilariously if we took your bullshit definition of "random" then repair processes wouldn't be random either.  Because they are all based on sensing the damage, analysing the problem, and enacting an appropriate repair.
Bingo. Ding ding ding ding.

Repair processes are NOT random. Never have been, never will be. But all processes involve errors because no processes are perfect. But we don't call errors a "process."

But we DO call error REPAIRS a process, right?

Yes but it's the repair process that's the process. You don't call the motherfuking errors a process. Jesus Christ.

And who called the errors a process, Dave? 
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2471
"Please quote where some "desperate neo-Darwinist" talked about "something which is accidental being a 'process'"

Good Lord she doesn't even know she's doing it.

Well, quote, please.

I'm fed up of you misrepresenting mine and other people's views, and then trying to beat us over the head for those misrepresentations with your misrepresentations of Shapiro's.
I'm not going to go out searching on my phone to prove what your cockamamie ideas used to be. If you don't subscribe to a particular cockamamie idea anymore, then fine. That's great and we can move forward.

Re: Introduction to Systems Biology
Reply #2472
"So the answer to your question about whether the mutation in Lenski's experiment was random or NGE might be that it was both"

No.

Stop flailing and read for comprehension.
I'm not the one who's flailing or failing to comprehend here, Dave...
So NGE processes can result in random changes. So the two categories are not mutually exclusive.
No one said anything about the processes being mutually exclusive.
Either they're mutually exclusive or they're not. Which is it?

  • Pingu
Re: Introduction to Systems Biology
Reply #2473
"Please quote where some "desperate neo-Darwinist" talked about "something which is accidental being a 'process'"

Good Lord she doesn't even know she's doing it.

Well, quote, please.

I'm fed up of you misrepresenting mine and other people's views, and then trying to beat us over the head for those misrepresentations with your misrepresentations of Shapiro's.
I'm not going to go out searching on my phone to prove what your cockamamie ideas used to be. If you don't subscribe to a particular cockamamie idea anymore, then fine. That's great and we can move forward.

I never did.  Perhaps if you actually read my posts instead of trying to listen to them on your phone while driving around selling windows you'd actually understand what I'm trying to say instead of making shit up.
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2474
"So the answer to your question about whether the mutation in Lenski's experiment was random or NGE might be that it was both"

No.

Stop flailing and read for comprehension.
I'm not the one who's flailing or failing to comprehend here, Dave...
So NGE processes can result in random changes. So the two categories are not mutually exclusive.
No one said anything about the processes being mutually exclusive.
Either they're mutually exclusive or they're not. Which is it?
You are not going to put me in your stupid Neo darwinist box. Processes are processes and they are non-random. And errors that occur during processes are errors and they are random. Period. End of story.