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Topic: Introduction to Systems Biology (Read 17105 times) previous topic - next topic

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  • Photon
  • I interfere with myself
Re: Introduction to Systems Biology
Reply #3225
It's not that hard to understand. If copying fidelity is too high, the population will be too rigid and unable to adapt, and in changing environments, will likely go extinct.

But if copying fidelity is too low, the population will not be able to keep hold of any advantages it does gain, and in a competitive but static environment, will likely go extinct (depending both on costs for error-correction and the size of the gains).

That matches what Pingu said.
Anyway, either one is complete and utter horseshit because copying errors are not needed for diversity.

But copying errors do create novel DNA sequences, and therefore can lead to increased diversity in the population.  Right?

Your statement does not follow from what uncool or Pingu have said.

  • Photon
  • I interfere with myself
Re: Introduction to Systems Biology
Reply #3226
Dave, on a scale of 1 to 10 on how confused you are, I'd say you are approaching 11.  Militant confusion breaks the scale.

  • Fenrir
Re: Introduction to Systems Biology
Reply #3227
It's not that hard to understand. If copying fidelity is too high, the population will be too rigid and unable to adapt, and in changing environments, will likely go extinct.

But if copying fidelity is too low, the population will not be able to keep hold of any advantages it does gain, and in a competitive but static environment, will likely go extinct (depending both on costs for error-correction and the size of the gains).

That matches what Pingu said.
Anyway, either one is complete and utter horseshit because copying errors are not needed for diversity.

Coz diversity is created by stripey sticks.

Tremble at the power of the stripey stick you clueless heathens!
  • Last Edit: March 18, 2018, 10:07:24 PM by Fenrir
It's what plants crave.

  • Faid
Re: Introduction to Systems Biology
Reply #3228
Here's a layman's article explaining some details of the two experiments ...
Quote
Lenski and colleagues have proposed that the Cit+ mutants evolve through a three-step process: potentiation, actualization (promoter capture), and refinement (the addition of other mutations that improve citrate metabolism). In experiments in which they "replayed" evolution--by repeating the experiment with samples frozen at different time points--the researchers found that cells evolved the Cit+ phenotype from later generations, but not earlier ones, supporting the idea of historical contingency.

Suspecting that the rarity of the Cit+ phenotype might have been due to experimental conditions that could stall Cit+ evolution, Minnich and colleagues designed a study to test how long it would take Cit+ mutants to emerge under different conditions.

Minnich and colleagues grew the LTEE E. coli strain  (REL606) in the same glucose- and citrate-containing medium used in the LTEE, but allowed the bacteria to grow for a week before passaging. Under this condition, the team found, Cit+ mutants appeared much faster: as early as 63 days. In a separate experiment, the researchers grew several E. coli strains (excluding REL606) in a medium in which citrate was the only carbon source, to select for citrate-eating bacteria. Cit+ mutants emerged in fewer than 40 days in all but one strain tested, the researchers reported.

"What the new experiment has told us is [that] actually these phenotypes can evolve much more readily than we initially thought," said Rees Kassen, who studies evolution using microbial systems at the University of Ottawa but was not involved in the research. "To me [this] suggests that if we're going to make inferences about a species itself evolves over long periods of time, we have to be very careful about the ecology of how we do our experiments." https://www.the-scientist.com/?articles.view/articleNo/45423/title/Similar-Data--Different-Conclusions/
It also explains the creationist bias of one side. Did you bother to read what Lenski (and Blount ::) ) said in response? Rememer the slide presentation?
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Introduction to Systems Biology
Reply #3229
Science, baby.

Careful reading.

Careful, tentative statements.
Bookmarked.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

Re: Introduction to Systems Biology
Reply #3230
It's not that hard to understand. If copying fidelity is too high, the population will be too rigid and unable to adapt, and in changing environments, will likely go extinct.

But if copying fidelity is too low, the population will not be able to keep hold of any advantages it does gain, and in a competitive but static environment, will likely go extinct (depending both on costs for error-correction and the size of the gains).

That matches what Pingu said.
Anyway, either one is complete and utter horseshit because copying errors are not needed for diversity.

I wonder if it has crossed your mind that with this response, you openly admit that you consider things true or not true based on whether they are required for a design you have already decided exists.

  • Faid
Re: Introduction to Systems Biology
Reply #3231
"The point is that you cannot infer from the fact that an adaptive mutation occurs that it can't have occurred by "RM+NS". "

Of course you can't and if you would learn to read what I write, you would not think that I think that.

You wrote:

Quote
OK so if when mutants appear depends on the ecological context, then that means that NGE is occurring, not RM + NS + MOY.

What DID you mean if not that you were inferring that IF "when mutants appear depends on the ecological context" THEN "NGE is occurring, not RM + NS + MOY"?

Do you know what the words IF and THEN mean in English? 

But if you adopt an ID paradigm instead of a non-ID paradigm, you MIGHT be more likely to look for some computational mechanism inside the bugs whereby they can sense citrate and in effect say "Hey, citrate!  I have some tools I can deploy to utilize that!" 

Relax.  I'm not saying this definitely IS the case yet.  It might not be.  But it might be.  And given what we know of Shapiro's work, it's certainly worth looking into.

Well, if you aren't making an inference, don't make inferential statements.

And if you do make a stupid inferential statement, don't attack the messenger who points it out.
In general you cannot infer that r m + n s did not occur. But in a specific case where an Adaptive mutation arises very quickly and it's repeatable, then you ought to infer NGE rather than r m + n s. At least it appears that you should to me.
"It appears" has truly become your new 'tell'.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Introduction to Systems Biology
Reply #3232
And of course it's been shown now to be complete and utter horseshit and the third weighers have figured that out but they're not quite as outspoken as me cuz they still want to get invited to the cocktail parties. Sorry for the funky spelling and capitalization I'm using Siri
But not your brain.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Introduction to Systems Biology
Reply #3233
Another way to look at it this is the first wayers are like Jesus and the apostles. Second wayers are like John Tetzel selling indulgences for the corrupt papacy. And the third wayers are like Martin Luther nailing his 95 Theses on the door of the church.

There really is not much difference.
So Darwinists are like corrupt clergy, and Dave is like Jesus.

Classy as fuck.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Introduction to Systems Biology
Reply #3234
So as not to being accused of destroying straw men let me be clear...

I really don't have any quibbles with Darwin except his idea of a universal common ancestor and what some call "macroevolution."

What I have a problem with is the idea that random copying errors created everything in the biosphere. ( not Darwin's idea )
Which stems from your previous 'quibble' for a universal common ancestor and what some call "macroevolution."

If it wasn't for that "quibble", you would have no problem agreeing that genomic change can occur through "copying errors" and increase diversity. Shapiro clearly says so, and it's even compatible with your "organisms=machines" shtick. You could easily expand that to say "Look how COMPLEX  and SOPHISTICATED biological machinery is- They can even use RANDOM COPPYING ERRORS to their advantage! Like an artist ingenuously incorporating accidental changes to their masterpiece! Nature is amazing!".

But you stop short of that.

I wonder why.


(Not really)
  • Last Edit: March 19, 2018, 02:09:56 AM by Faid
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Introduction to Systems Biology
Reply #3235
I think this is the appropriate time to smack you in the head again with this baseball bat from Shapiro

"It has been a surprise to learn how thoroughly cells protect themselves against precisely the kinds of accidental genetic change that, according to conventional theory, are the sources of evolutionary variability."
Gonna repost this every page for awhile in the hopes that it will sink in.
Sure thing, "socrates".
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Introduction to Systems Biology
Reply #3236
Besides the error correction problem is the problem of not being able to build any kind of mechanism whatsoever by random accidents.  It's the most ridiculous idea ever.  The fact that people with PhDs espouse this stuff makes the mind reel.
I'm not sure how you'd define "mechanism" here, because I can think of several mechanisms that could be built through random accidents and pruning, a la natural selection.
Don't take my word for it. Take Shapiro's.

Quote
How all of this modularity, complexity, and integration arose and changed during the history of life on earth is a central evolutionary question. Localized random mutation, selection operating "one gene at a time" (John Maynard Smith's formulation), and gradual modification of individual functions are unable to provide satisfactory explanations for the molecular data, no matter how much time for change is assumed. There are simply too many potential degrees of freedom for random variability and too many interconnections to account for.

Shapiro's statement is much less wide-ranging than yours; I was commenting specifically in relation to your statement about "any kind of mechanism".
I may not be saying it right. He's a professional. Take his word not mine.
OK, we will.

His words and ideas attest to a concept of evolution that is dynamic and capable of major innovation. He makes evolution easier.

Why dpn't YOU take his word for it? Is it your "quibble"?
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Introduction to Systems Biology
Reply #3237
Quote from: Dave Hawkins
 
Quote from: Photon
And it is blindingly obvious that copying errors can, and do, introduce new genotypes (and subsequent phenotypes) into a population.
of course they do. Who said that they don't?

Umm. Dave. You should tell yourself your latest position.
Quoted for truth (and lulz)
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

Re: Introduction to Systems Biology
Reply #3238
It's not that hard to understand. If copying fidelity is too high, the population will be too rigid and unable to adapt, and in changing environments, will likely go extinct.

But if copying fidelity is too low, the population will not be able to keep hold of any advantages it does gain, and in a competitive but static environment, will likely go extinct (depending both on costs for error-correction and the size of the gains).

That matches what Pingu said.
Anyway, either one is complete and utter horseshit because copying errors are not needed for diversity.

But copying errors do create novel DNA sequences, and therefore can lead to increased diversity in the population.  Right?
Sure.  In exactly the same way that copying errors in the software controlling the machines at the Ford factory lead to increased diversity.

Re: Introduction to Systems Biology
Reply #3239
It's not that hard to understand. If copying fidelity is too high, the population will be too rigid and unable to adapt, and in changing environments, will likely go extinct.

But if copying fidelity is too low, the population will not be able to keep hold of any advantages it does gain, and in a competitive but static environment, will likely go extinct (depending both on costs for error-correction and the size of the gains).

That matches what Pingu said.
Anyway, either one is complete and utter horseshit because copying errors are not needed for diversity.

But copying errors do create novel DNA sequences, and therefore can lead to increased diversity in the population.  Right?
Sure.  In exactly the same way that copying errors in the software controlling the machines at the Ford factory lead to increased diversity.

exactly like counting piles of shit leads to a greater number of piles of shit?
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 #3240
now we know how many holes it takes to fill the albert hall?
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 #3241
This morning I was browsing through the Third Way of Evolution website and found this interesting little nugget ...
Quote
Wetware: A computer in every living cell
Author: Dennis Bray
How does a single-cell creature, such as an amoeba, lead such a sophisticated life? How does it hunt living prey, respond to lights, sounds, and smells, and display complex sequences of movements without the benefit of a nervous system? This book offers a startling and original answer.

In clear, jargon-free language, Dennis Bray taps the findings of the new discipline of systems biology to show that the internal chemistry of living cells is a form of computation. Cells are built out of molecular circuits that perform logical operations, as electronic devices do, but with unique properties. Bray argues that the computational juice of cells provides the basis of all the distinctive properties of living systems: it allows organisms to embody in their internal structure an image of the world, and this accounts for their adaptability, responsiveness, and intelligence.

In Wetware, Bray offers imaginative, wide-ranging and perceptive critiques of robotics and complexity theory, as well as many entertaining and telling anecdotes. For the general reader, the practicing scientist, and all others with an interest in the nature of life, the book is an exciting portal to some of biology's latest discoveries and ideas.

  • Faid
Re: Introduction to Systems Biology
Reply #3242
It's not that hard to understand. If copying fidelity is too high, the population will be too rigid and unable to adapt, and in changing environments, will likely go extinct.

But if copying fidelity is too low, the population will not be able to keep hold of any advantages it does gain, and in a competitive but static environment, will likely go extinct (depending both on costs for error-correction and the size of the gains).

That matches what Pingu said.
Anyway, either one is complete and utter horseshit because copying errors are not needed for diversity.

But copying errors do create novel DNA sequences, and therefore can lead to increased diversity in the population.  Right?
Sure.  In exactly the same way that copying errors in the software controlling the machines at the Ford factory lead to increased diversity.

And how do you know it's in "exactly the same way"?
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

Re: Introduction to Systems Biology
Reply #3243
It's not that hard to understand. If copying fidelity is too high, the population will be too rigid and unable to adapt, and in changing environments, will likely go extinct.

But if copying fidelity is too low, the population will not be able to keep hold of any advantages it does gain, and in a competitive but static environment, will likely go extinct (depending both on costs for error-correction and the size of the gains).

That matches what Pingu said.
Anyway, either one is complete and utter horseshit because copying errors are not needed for diversity.

But copying errors do create novel DNA sequences, and therefore can lead to increased diversity in the population.  Right?
Sure.  In exactly the same way that copying errors in the software controlling the machines at the Ford factory lead to increased diversity.

And how do you know it's in "exactly the same way"?
Because they are both computer controlled machines made from exactly the same "stuff".

Re: Introduction to Systems Biology
Reply #3244
I'm not aware of different chemistry / physics rules and a different periodic table of elements, are you?

  • VoxRat
  • wtactualf
Re: Introduction to Systems Biology
Reply #3245
It's not that hard to understand. If copying fidelity is too high, the population will be too rigid and unable to adapt, and in changing environments, will likely go extinct.

But if copying fidelity is too low, the population will not be able to keep hold of any advantages it does gain, and in a competitive but static environment, will likely go extinct (depending both on costs for error-correction and the size of the gains).

That matches what Pingu said.
Anyway, either one is complete and utter horseshit because copying errors are not needed for diversity.

But copying errors do create novel DNA sequences, and therefore can lead to increased diversity in the population.  Right?
Sure.  In exactly the same way that copying errors in the software controlling the machines at the Ford factory lead to increased diversity.

Only the fact that cars and factory machines don't reproduce makes it far from "exactly".

I believe this has been pointed out to you a few hundred times.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

Re: Introduction to Systems Biology
Reply #3246
It's not that hard to understand. If copying fidelity is too high, the population will be too rigid and unable to adapt, and in changing environments, will likely go extinct.

But if copying fidelity is too low, the population will not be able to keep hold of any advantages it does gain, and in a competitive but static environment, will likely go extinct (depending both on costs for error-correction and the size of the gains).

That matches what Pingu said.
Anyway, either one is complete and utter horseshit because copying errors are not needed for diversity.

But copying errors do create novel DNA sequences, and therefore can lead to increased diversity in the population.  Right?
Sure.  In exactly the same way that copying errors in the software controlling the machines at the Ford factory lead to increased diversity.
If there was a population of Ford factories, competing for resources and reproduction opportunities, that would work.
But there isn't.

  • Faid
Re: Introduction to Systems Biology
Reply #3247
It's not that hard to understand. If copying fidelity is too high, the population will be too rigid and unable to adapt, and in changing environments, will likely go extinct.

But if copying fidelity is too low, the population will not be able to keep hold of any advantages it does gain, and in a competitive but static environment, will likely go extinct (depending both on costs for error-correction and the size of the gains).

That matches what Pingu said.
Anyway, either one is complete and utter horseshit because copying errors are not needed for diversity.

But copying errors do create novel DNA sequences, and therefore can lead to increased diversity in the population.  Right?
Sure.  In exactly the same way that copying errors in the software controlling the machines at the Ford factory lead to increased diversity.

And how do you know it's in "exactly the same way"?
Because they are both computer controlled machines made from exactly the same "stuff".

But one is WAY more "sophisticated". Right?
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

Re: Introduction to Systems Biology
Reply #3248
It's not that hard to understand. If copying fidelity is too high, the population will be too rigid and unable to adapt, and in changing environments, will likely go extinct.

But if copying fidelity is too low, the population will not be able to keep hold of any advantages it does gain, and in a competitive but static environment, will likely go extinct (depending both on costs for error-correction and the size of the gains).

That matches what Pingu said.
Anyway, either one is complete and utter horseshit because copying errors are not needed for diversity.

But copying errors do create novel DNA sequences, and therefore can lead to increased diversity in the population.  Right?
Sure.  In exactly the same way that copying errors in the software controlling the machines at the Ford factory lead to increased diversity.

Just because Ford don't use machine learning to design the software in their factories doesn't mean they couldn't. There's no reason why they couldn't use it to design parts of the car either. Google uses it to do all sorts of things. So do many other companies.

Watch and learn Dave, watch and learn.

https://youtu.be/R9OHn5ZF4Uo
Why do I bother?

  • Faid
Re: Introduction to Systems Biology
Reply #3249
I'm not aware of different chemistry / physics rules and a different periodic table of elements, are you?
The same goes for stars, mountains, dirt, galaxies, clouds, geusers, all the rocks on earth and beyond, and the small piece of wood on my desk. but "machines" (biological or artificial) are capable of more under the same rules, right?
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.