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Topic: Introduction to Systems Biology (Read 17610 times) previous topic - next topic

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  • Pingu
Re: Introduction to Systems Biology
Reply #25
My own suspicion is that it is most unlikely that, if we could turn the clock right back and let the process run again, we would end up with anything like the range of species we have today on earth (Gould, 2002).
Here's a sentence ripe for Davining. On my plain reading of it, it looks like he is saying exactly what Dave does not want him to be saying: that there is plenty of "randomness" (at least in the sense of unpredictability) inherent in evolutionary processes. My prediction, however, is that Dave will home in on the word "unlikely" and try to argue that Noble is making some sort of teleological argument here.

Or alternatively, he may start to smell a rat, especially given the fact that i recommended Noble to him, and just drop the whole thread.

I suspect he's just hawkinsed both Shapiro and Noble enough to pick up nuggets about ...Darwinism...wrong.... to thinks they must be closest IDist/Creationists.
I have a Darwin-debased mind.

  • fredbear
  • Militantly Confused
Re: Introduction to Systems Biology
Reply #26
Hey Dave, can you summarize your review in three words? 'Cause sheesh!. And if you cant ....
"...without considering any evidence at all - that my views are more likely - on average - to be correct.  Because the mainstream is almost always wrong" - Dave Hawkins

  • Pingu
Re: Introduction to Systems Biology
Reply #27
Here's another interesting passage:

Quote from: Denis Noble
Much better, therefore, to let the genetic influences of natural selection be exerted on undifferentiated cells, leaving the process of differentiation to deal with the fine-tuning required to code for the pattern of gene expression appropriate to each type of cell. If this explanation is correct, we would not necessarily expect it to be 100% effective. It is conceivable that some germ-line changes in gene expression patterns might be so beneficial for the organism as a whole, despite deleterious effects on a few cell lines, that the result would favour selection. This could explain the few cases where germ-line 'Lamarckian' inheritance seems to have occurred. It also motivates the search for other cases. The prediction would be that it will occur in multicellular species only when beneficial to overall intercellular harmony. It might be more likely to occur in simpler species. That makes sense in terms of the few examples that we have so far found (Maynard Smith, 1998). Notice that, in contrast to the central dogma, this explanation is a systems level explanation.

Noble is suggesting that it makes sense for there to be systems to prevent epigenetic marking of germ-line cells, but that "we wouldn't necessarily expect it to be 100% effective" i.e. we would expect it to make "errors" by Dave's defnition.

And that it is those "errors" that pave the way for Lamarckian inheritance.

hehe
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #28
That's right. I don't read someone's book until I am sold on the idea that I should read it for whatever reason. Life is too short.

And you aren't yet sold on the idea of reading Shapiro's book? Even though you think he's a saint?
Getting closer, thanks to Denis Noble's video yesterday.

So you went all in for Noble because he agreed with your assessment of Shapiro as a "saint".  And yet that assessment was based on NOT reading Shapiro's actual book or papers???

wtf Dave?

What made you adopt Shapiro as your saint in the first place if you still aren't "sold" on him enough to even read his book?  And if you still aren't sold on him enough to read his book, whay should Noble's approval of Shapiro's book make you think that Noble is worth reading?

Not that you have, yet, apparently.

When is your review going to be posted?
There's plenty of saints whose books I haven't read.

Re: Introduction to Systems Biology
Reply #29
Hey Dave, can you summarize your review in three words? 'Cause sheesh!. And if you cant ....
Yeah.

NeoDarwinism

Is

Dead

  • fredbear
  • Militantly Confused
Re: Introduction to Systems Biology
Reply #30
Hey Dave, can you summarize your review in three words? 'Cause sheesh!. And if you cant ....
Yeah.

NeoDarwinism

Is

Dead
ok, that summary was a bit lossy. Can you perhaps elaborate a tad?
"...without considering any evidence at all - that my views are more likely - on average - to be correct.  Because the mainstream is almost always wrong" - Dave Hawkins

Re: Introduction to Systems Biology
Reply #31

There's plenty of books I haven't read.

Obviously.

  • Pingu
Re: Introduction to Systems Biology
Reply #32
Hey Dave, can you summarize your review in three words? 'Cause sheesh!. And if you cant ....
Yeah.

NeoDarwinism

Is

Dead

OK. So how is that newsworthy?  What are the implications, in your view?

And what do you think "neo-Darwinism" actually is (or was, I should say, now it's dead)?
I have a Darwin-debased mind.

  • VoxRat
  • wtactualf
Re: Introduction to Systems Biology
Reply #33
Hey Dave, can you summarize your review in three words? 'Cause sheesh!. And if you cant ....
Yeah.

NeoDarwinism

Is

Dead
Though not nearly as dead as pre-Darwinism.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • Pingu
Re: Introduction to Systems Biology
Reply #34
That's right. I don't read someone's book until I am sold on the idea that I should read it for whatever reason. Life is too short.

And you aren't yet sold on the idea of reading Shapiro's book? Even though you think he's a saint?
Getting closer, thanks to Denis Noble's video yesterday.

So you went all in for Noble because he agreed with your assessment of Shapiro as a "saint".  And yet that assessment was based on NOT reading Shapiro's actual book or papers???

wtf Dave?

What made you adopt Shapiro as your saint in the first place if you still aren't "sold" on him enough to even read his book?  And if you still aren't sold on him enough to read his book, whay should Noble's approval of Shapiro's book make you think that Noble is worth reading?

Not that you have, yet, apparently.

When is your review going to be posted?
There's plenty of saints whose books I haven't read.

But how did you know he was a saint?  After all YOU were the one who canonised him, so what made you do it, without first reading his books or papers?
I have a Darwin-debased mind.

  • Pingu
Re: Introduction to Systems Biology
Reply #35
Hey Dave, can you summarize your review in three words? 'Cause sheesh!. And if you cant ....
Yeah.

NeoDarwinism

Is

Dead
Though not nearly as dead as pre-Darwinism.

But deader than post neo-Darwinism.
I have a Darwin-debased mind.

  • VoxRat
  • wtactualf
Re: Introduction to Systems Biology
Reply #36
But how did you know he was a saint?  After all YOU were the one who canonised him, so what made you do it, without first reading his books or papers?
Dave knows what authors really mean better than the authors themselves.
Why bother slogging through the actual words, which will be, at best, an approximation of what Dave knows is the Real Meaning?
Like seeing through a glass darkly, if you will.

"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • Sea Star
  • Not an octohatter
Re: Introduction to Systems Biology
Reply #37
I don't have the impression that you were the one that introduced me to Noble. I think I ran across him because of my interest in Shapiro which goes back a long time. I guess we should call him Saint Shapiro now. You guys may not recognize him as such but I have for a long time and one of the reasons I'm all of a sudden more interested in Denis Noble is because it appears that Denis Noble also seems to regard him as Saint Shapiro.

So I think rather than me thanking you for introducing me to Noble, you should probably be thanking me for introducing you to the whole Third Way movement via Shapiro. And yes, Denis Noble seems to be a prominent Third Wayer that we should listen to.
Preaching.
Quote from: Dave Hawkins on Today at 07:50:40 AM
Lol
Sea Star has been trolling me this whole time.

  • Peez
Re: Introduction to Systems Biology
Reply #38
Hey Dave, can you summarize your review in three words? 'Cause sheesh!. And if you cant ....
Yeah.

NeoDarwinism

Is

Dead
Though not nearly as dead as pre-Darwinism.

But deader than post neo-Darwinism.
The Relativity of Wrong

  • Pingu
Re: Introduction to Systems Biology
Reply #39
But how did you know he was a saint?  After all YOU were the one who canonised him, so what made you do it, without first reading his books or papers?
Dave knows what authors really mean better than the authors themselves.
Why bother slogging through the actual words, which will be, at best, an approximation of what Dave knows is the Real Meaning?
Like seeing through a glass darkly, if you will.

yabbut he knew enough about the book without reading it to know that Shapiro was a saint, but not enough to "sell him on" actually reading it.

:dunno:

Until someone he didn't know much about cited the book approvingly.  Maybe.
I have a Darwin-debased mind.

  • VoxRat
  • wtactualf
Re: Introduction to Systems Biology
Reply #40
I don't have the impression that you were the one that introduced me to Noble.
The first time you mentioned Noble was here:
http://talkrational.org/archive/showthread.php?p=2579359#post2579359
six years after Pingu brought him to your attention.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • Pingu
Re: Introduction to Systems Biology
Reply #41
OK, this is getting boring, let's have a go:

Noble's Ten principles of systems biology and how they kill neo-Darwinism:

Quote
First principle: biological functionality is multilevel.

Yes indeed.  neo-Darwinism was quite narrowly focussed, not just on genes but on coding genes.  A multi-level approach doesn't "kill" neo-Darwinism on this score, but it makes it just part of the picture.  Which is how science generally proceeds of course.  Shoulders of Giants and all that.  So a casualty, I'd say, rather than a fatality here.

Quote
Second principle: transmission of information is not one way.

Yes, Crick was pretty silly to call his principle a "dogma" - asking for trouble.  It was a hypothesis.  And probably mainly true rather than wholly true. McClintock and Shapiro would seem to scotch the absolutism of the dogma for somatic cells.  As far as the germline goes, though, it looks like Noble is talking about epigenetics here, though, so that doesn't violate the dogma. But yes, the dogma, qua dogma is dead.  Cool.  One fatality so far.

And that's of course quite apart from the fact that information flows into the genome from the environment via natural (and indeed artificial) selection, but then that was Darwin's point (even though he didn't know what a genome was) and neo-Darwinists never disputed it. Far from it.

Quote
Third principle: DNA is not the sole transmitter of inheritance

Indeed. But no casualties here in the neo-Darwinism ranks because nobody ever thought otherwise.  However, good to be reminded, and of course the role of the egg and of epigenetics is new since their day.

Quote
Fourth principle: the theory of biological relativity; there is no privileged level of causality

Indeed.  Anyone who thought so was a fool.  Not aware that anyone thought so, though Dawkins trails his coat a bit.  A flesh-wound maybe.

Quote
Fifth principle: gene ontology will fail without higher-level insight

Yes indeed.  But again, this is merely a welcome enlargement and change of emphasis, not a fatality.  Not even a flesh-wound.

Quote
Sixth principle: there is no genetic program

Yes, this is important. The idea of DNA as a program was always a poor metaphor (though one beloved of IDists), and although molecular biologists have always been smart enough not to be overly misled, there's been a certain amount of misleading popularisation of this idea.  Which is regrettable.  Glad that one is dead, even though it's a bit unfair to call it a neo-Darwinist casualty.  But the popular idea that DNA "programs" us is a destructive one, IMO.

Quote
Seventh principle: there are no programs at any other level

Right.  A worthwhile point.  Nothing to do with neo-Darwinism though. 

Quote
Eighth principle: there are no programs in the brain

Indeed.  But again, nothing to do with neo-Darwinism.

Quote
Ninth principle: the self is not an object

My favorite.  But again, nothing to do with neo-Darwinism.

Quote
Tenth principle: there are many more to be discovered;

Nice.  The principle that there are always more principles is always worth having.

Pingu's conclusion:  Crick's Central Dogma isn't a dogma.

In other news; Newton's Laws of Motion aren't laws.
I have a Darwin-debased mind.

  • fredbear
  • Militantly Confused
Re: Introduction to Systems Biology
Reply #42
OK, this is getting boring, let's have a go:

Noble's Ten principles of systems biology and how they kill neo-Darwinism:

Quote
First principle: biological functionality is multilevel.

Yes indeed.  neo-Darwinism was quite narrowly focussed, not just on genes but on coding genes.  A multi-level approach doesn't "kill" neo-Darwinism on this score, but it makes it just part of the picture.  Which is how science generally proceeds of course.  Shoulders of Giants and all that.  So a casualty, I'd say, rather than a fatality here.

Quote
Second principle: transmission of information is not one way.

Yes, Crick was pretty silly to call his principle a "dogma" - asking for trouble.  It was a hypothesis.  And probably mainly true rather than wholly true. McClintock and Shapiro would seem to scotch the absolutism of the dogma for somatic cells.  As far as the germline goes, though, it looks like Noble is talking about epigenetics here, though, so that doesn't violate the dogma. But yes, the dogma, qua dogma is dead.  Cool.  One fatality so far.

And that's of course quite apart from the fact that information flows into the genome from the environment via natural (and indeed artificial) selection, but then that was Darwin's point (even though he didn't know what a genome was) and neo-Darwinists never disputed it. Far from it.

Quote
Third principle: DNA is not the sole transmitter of inheritance

Indeed. But no casualties here in the neo-Darwinism ranks because nobody ever thought otherwise.  However, good to be reminded, and of course the role of the egg and of epigenetics is new since their day.

Quote
Fourth principle: the theory of biological relativity; there is no privileged level of causality

Indeed.  Anyone who thought so was a fool.  Not aware that anyone thought so, though Dawkins trails his coat a bit.  A flesh-wound maybe.

Quote
Fifth principle: gene ontology will fail without higher-level insight

Yes indeed.  But again, this is merely a welcome enlargement and change of emphasis, not a fatality.  Not even a flesh-wound.

Quote
Sixth principle: there is no genetic program

Yes, this is important. The idea of DNA as a program was always a poor metaphor (though one beloved of IDists), and although molecular biologists have always been smart enough not to be overly misled, there's been a certain amount of misleading popularisation of this idea.  Which is regrettable.  Glad that one is dead, even though it's a bit unfair to call it a neo-Darwinist casualty.  But the popular idea that DNA "programs" us is a destructive one, IMO.

Quote
Seventh principle: there are no programs at any other level

Right.  A worthwhile point.  Nothing to do with neo-Darwinism though. 

Quote
Eighth principle: there are no programs in the brain

Indeed.  But again, nothing to do with neo-Darwinism.

Quote
Ninth principle: the self is not an object

My favorite.  But again, nothing to do with neo-Darwinism.

Quote
Tenth principle: there are many more to be discovered;

Nice.  The principle that there are always more principles is always worth having.

Pingu's conclusion:  Crick's Central Dogma isn't a dogma.

In other news; Newton's Laws of Motion aren't laws.
Nice, If a bit sparse.

Dave, are you able to do something like Pingu did here and summarize, IN YOUR OWN WORDS, your understanding of each of the 10 points, and how they impact neo-darwinism?
"...without considering any evidence at all - that my views are more likely - on average - to be correct.  Because the mainstream is almost always wrong" - Dave Hawkins

Re: Introduction to Systems Biology
Reply #43
I don't have the impression that you were the one that introduced me to Noble. I think I ran across him because of my interest in Shapiro which goes back a long time. I guess we should call him Saint Shapiro now. You guys may not recognize him as such but I have for a long time and one of the reasons I'm all of a sudden more interested in Denis Noble is because it appears that Denis Noble also seems to regard him as Saint Shapiro.

So I think rather than me thanking you for introducing me to Noble, you should probably be thanking me for introducing you to the whole Third Way movement via Shapiro. And yes, Denis Noble seems to be a prominent Third Wayer that we should listen to.
You are really a peach
Love is like a magic penny
 if you hold it tight you won't have any
if you give it away you'll have so many
they'll be rolling all over the floor

Re: Introduction to Systems Biology
Reply #44
That's right. I don't read someone's book until I am sold on the idea that I should read it for whatever reason. Life is too short.
Remember that time you claimed to have read Darwin's Origin of Species, cover to cover?


Lol. Good times. Well, I've never actually held the book in my hands but...
Love is like a magic penny
 if you hold it tight you won't have any
if you give it away you'll have so many
they'll be rolling all over the floor

Re: Introduction to Systems Biology
Reply #45
This is nicely put:

Quote from: Denis Noble
Ninth principle: the self is not an object In brief, the mind is not a separate object competing for activity and influence with the molecules of the body. Thinking in that way was originally the mistake of the dualists, such as Sherrington and Eccles, led by the philosophy of Descartes. Modern biologists have abandoned the separate substance idea, but many still cling to a materialist version of the same mistake (Bennett & Hacker, 2003), based on the idea that somewhere in the brain the self is to be found as some neuronal process. The reason why that level of integration is too low is that the brain, and the rest of our bodies which are essential for attributes such as consciousness to make sense (Noble, 2006; chapter 9), are tools (back to the database idea again) in an integrative process that occurs at a higher level involving social interactions. We cannot attribute the concept of self-ness to ourselves without also doing so to others (Strawson, 1959). Contrary to Crick's view, therefore, our selves are indeed much 'more than the behaviour of a vast assembly of nerve cells and their associated molecules' precisely because the social interactions are essential even to understanding what something like an intention might be. I analyse an example of this point in much more detail in chapter 9 of The Music of Life. This philosophical point is easier to understand when we take a systems view of biology, since it is in many ways an extension of that view to the highest level of integration in the organism.

One of the big drivers of systems neuroscience has been the discovery that the brain is a network rather than a set of modules. Which makes a lot more sense than the hyper-regionalism of the nineties.  There was even a plug-in for one of the major brain imaging software packages called "what does this bit do?" - when you clicked on a brain region you'd get links to all the functional imaging papers that referenced that region.  It was quite clever, but also reveallingly silly.
Not to get too far out there, but self also requires society as meaning is socially constructed.
Love is like a magic penny
 if you hold it tight you won't have any
if you give it away you'll have so many
they'll be rolling all over the floor

  • Pingu
Re: Introduction to Systems Biology
Reply #46
This is nicely put:

Quote from: Denis Noble
Ninth principle: the self is not an object In brief, the mind is not a separate object competing for activity and influence with the molecules of the body. Thinking in that way was originally the mistake of the dualists, such as Sherrington and Eccles, led by the philosophy of Descartes. Modern biologists have abandoned the separate substance idea, but many still cling to a materialist version of the same mistake (Bennett & Hacker, 2003), based on the idea that somewhere in the brain the self is to be found as some neuronal process. The reason why that level of integration is too low is that the brain, and the rest of our bodies which are essential for attributes such as consciousness to make sense (Noble, 2006; chapter 9), are tools (back to the database idea again) in an integrative process that occurs at a higher level involving social interactions. We cannot attribute the concept of self-ness to ourselves without also doing so to others (Strawson, 1959). Contrary to Crick's view, therefore, our selves are indeed much 'more than the behaviour of a vast assembly of nerve cells and their associated molecules' precisely because the social interactions are essential even to understanding what something like an intention might be. I analyse an example of this point in much more detail in chapter 9 of The Music of Life. This philosophical point is easier to understand when we take a systems view of biology, since it is in many ways an extension of that view to the highest level of integration in the organism.

One of the big drivers of systems neuroscience has been the discovery that the brain is a network rather than a set of modules. Which makes a lot more sense than the hyper-regionalism of the nineties.  There was even a plug-in for one of the major brain imaging software packages called "what does this bit do?" - when you clicked on a brain region you'd get links to all the functional imaging papers that referenced that region.  It was quite clever, but also reveallingly silly.
Not to get too far out there, but self also requires society as meaning is socially constructed.

Absolutely.  Which is a timely reminder that despite the fact that I am officially on strike right now, I need to get back to preparing a grant application to investigate just that :)
I have a Darwin-debased mind.

  • Pingu
Re: Introduction to Systems Biology
Reply #47
That's right. I don't read someone's book until I am sold on the idea that I should read it for whatever reason. Life is too short.
Remember that time you claimed to have read Darwin's Origin of Species, cover to cover?


Lol. Good times. Well, I've never actually held the book in my hands but...

The online searchable is really neat.

ETA: from which one discovers that Darwin NEVER uses the word "random".  He uses "error" but only about ideas.   He does use "mutation" but to refer to changing phenotypes over time.
  • Last Edit: February 27, 2018, 09:12:52 AM by Pingu
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #48
This is nicely put:

Quote from: Denis Noble
Ninth principle: the self is not an object In brief, the mind is not a separate object competing for activity and influence with the molecules of the body. Thinking in that way was originally the mistake of the dualists, such as Sherrington and Eccles, led by the philosophy of Descartes. Modern biologists have abandoned the separate substance idea, but many still cling to a materialist version of the same mistake (Bennett & Hacker, 2003), based on the idea that somewhere in the brain the self is to be found as some neuronal process. The reason why that level of integration is too low is that the brain, and the rest of our bodies which are essential for attributes such as consciousness to make sense (Noble, 2006; chapter 9), are tools (back to the database idea again) in an integrative process that occurs at a higher level involving social interactions. We cannot attribute the concept of self-ness to ourselves without also doing so to others (Strawson, 1959). Contrary to Crick's view, therefore, our selves are indeed much 'more than the behaviour of a vast assembly of nerve cells and their associated molecules' precisely because the social interactions are essential even to understanding what something like an intention might be. I analyse an example of this point in much more detail in chapter 9 of The Music of Life. This philosophical point is easier to understand when we take a systems view of biology, since it is in many ways an extension of that view to the highest level of integration in the organism.

One of the big drivers of systems neuroscience has been the discovery that the brain is a network rather than a set of modules. Which makes a lot more sense than the hyper-regionalism of the nineties.  There was even a plug-in for one of the major brain imaging software packages called "what does this bit do?" - when you clicked on a brain region you'd get links to all the functional imaging papers that referenced that region.  It was quite clever, but also reveallingly silly.
Not to get too far out there, but self also requires society as meaning is socially constructed.

Absolutely.  Which is a timely reminder that despite the fact that I am officially on strike right now, I need to get back to preparing a grant application to investigate just that :)
It's pretty much a given that the evidence will lead to the realization that the system is never closed, at least up to the point of Gaia.
Love is like a magic penny
 if you hold it tight you won't have any
if you give it away you'll have so many
they'll be rolling all over the floor

  • Pingu
Re: Introduction to Systems Biology
Reply #49
This is nicely put:

Quote from: Denis Noble
Ninth principle: the self is not an object In brief, the mind is not a separate object competing for activity and influence with the molecules of the body. Thinking in that way was originally the mistake of the dualists, such as Sherrington and Eccles, led by the philosophy of Descartes. Modern biologists have abandoned the separate substance idea, but many still cling to a materialist version of the same mistake (Bennett & Hacker, 2003), based on the idea that somewhere in the brain the self is to be found as some neuronal process. The reason why that level of integration is too low is that the brain, and the rest of our bodies which are essential for attributes such as consciousness to make sense (Noble, 2006; chapter 9), are tools (back to the database idea again) in an integrative process that occurs at a higher level involving social interactions. We cannot attribute the concept of self-ness to ourselves without also doing so to others (Strawson, 1959). Contrary to Crick's view, therefore, our selves are indeed much 'more than the behaviour of a vast assembly of nerve cells and their associated molecules' precisely because the social interactions are essential even to understanding what something like an intention might be. I analyse an example of this point in much more detail in chapter 9 of The Music of Life. This philosophical point is easier to understand when we take a systems view of biology, since it is in many ways an extension of that view to the highest level of integration in the organism.

One of the big drivers of systems neuroscience has been the discovery that the brain is a network rather than a set of modules. Which makes a lot more sense than the hyper-regionalism of the nineties.  There was even a plug-in for one of the major brain imaging software packages called "what does this bit do?" - when you clicked on a brain region you'd get links to all the functional imaging papers that referenced that region.  It was quite clever, but also reveallingly silly.
Not to get too far out there, but self also requires society as meaning is socially constructed.

Absolutely.  Which is a timely reminder that despite the fact that I am officially on strike right now, I need to get back to preparing a grant application to investigate just that :)
It's pretty much a given that the evidence will lead to the realization that the system is never closed, at least up to the point of Gaia.

Yes indeed.  Which is why free will is perfectly compatible with materialism :)
I have a Darwin-debased mind.