Skip to main content

TR Memescape

  • Talk Rational: All are welcome, but not all will be welcomed!

Topic: Introduction to Systems Biology (Read 19617 times) previous topic - next topic

0 Members and 1 Guest are viewing this topic.
  • Photon
  • I interfere with myself
Re: Introduction to Systems Biology
Reply #2250
DendroFakeChronology

Lol
Oh? Perhaps you'd like to present your objections?
You're not interested. You like your fake beliefs.
Never has Dave written anything more clearly that shows he is not interested in truth.

Re: Introduction to Systems Biology
Reply #2251
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 #2252
Well excuuuuse me ... for daring to talk about a DNA error rate for an individual bacterium dividing.

Why do you even care about this anyway?  What difference does it make?  The error rate is something like 1 in 10 billion for E coli is it not?  And I forget how many bases E coli has in it's genome but you're going to get quite a bit of dividing before you get your first error are you not?
The point is that the deleteriousness or beneficialness should be measured over the whole population, not individuals. It's a correction to your statement that it is deleterious for cells.
OK fine.  Doesn't matter as you will see.

yes it does. As you won't.
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 #2253
Well excuuuuse me ... for daring to talk about a DNA error rate for an individual bacterium dividing.

Why do you even care about this anyway?  What difference does it make?  The error rate is something like 1 in 10 billion for E coli is it not?  And I forget how many bases E coli has in it's genome but you're going to get quite a bit of dividing before you get your first error are you not?
4.6 million bp.  Something like 1 in 100 ends up with a base pair substitution from replication

For the most part neither Lenski's not Minnish's E. coli are going to be dividing.  But as I showed for Minnish's bugs they differ from the parental strain at about 3000 locations.
Right.

Do you know how quickly that occurred?  It was a 40 day experiment right?  Do we know if there was a huge spike in the mutation rate in the first 2 days?  Or 10 days?  Then not much change for the balance of time?
  • Last Edit: March 13, 2018, 02:54:54 PM by Dave Hawkins

Re: Introduction to Systems Biology
Reply #2254
Well excuuuuse me ... for daring to talk about a DNA error rate for an individual bacterium dividing.

Why do you even care about this anyway?  What difference does it make?  The error rate is something like 1 in 10 billion for E coli is it not?  And I forget how many bases E coli has in it's genome but you're going to get quite a bit of dividing before you get your first error are you not?
4.6 million bp.  Something like 1 in 100 ends up with a base pair substitution from replication

For the most part neither Lenski's not Minnish's E. coli are going to be dividing.  But as I showed for Minnish's bugs they differ from the parental strain at about 3000 locations.
Right.

Do you know how quickly that occurred?  It was a 40 day experiment right?  Do we know if there was a huge spike in the mutation rate in the first 2 days?  Or 10 days?  Then not much change for the balance of time?
If you read the paper ( ::) ) you'll see that they only sequenced the endpoints.
While you were getting your PhD in virology, I got my PhD in truth detection. :wave:  Dave Hawkins

  • JonF
Re: Introduction to Systems Biology
Reply #2255
Anyway, let's move on ...

Next you say ...
Quote
A mutation rate is bad for a well-adapted population, as most of the mutations will be worse than the status quo.  However, a high mutation rate is good for a population under streess, as it increases the chance that a novel variant will be better than the status quo.

Which is one of Shapiro's two big points: that cell mechanisms are such that stress induces a higher error rate in stressed populations, thus increasing diversity and thus opening possibilities for natural selection.
Now here is where we need to get specific about what you mean when you say "a high mutation rate is good for a population under stress" ... which of the following do you mean?

1) An increased rate of single base errors is good? Like swapping A's for G's or T's?  Or ...
2) An increased rate of larger "errors" like a gene being duplicated?
3) Something else?

All mutations. Any situation in which the DNA sequence changes.
"I would never consider my evaluation of his work to be fair minded unless I had actually read his own words." - Dave Hawkins

Re: Introduction to Systems Biology
Reply #2256
Maybe someday I'll learn to read RSPL

  • uncool
Re: Introduction to Systems Biology
Reply #2257
You should. Understanding language is often a key point in understanding mentality.

Re: Introduction to Systems Biology
Reply #2258
Anyway, let's move on ...

Next you say ...
Quote
A mutation rate is bad for a well-adapted population, as most of the mutations will be worse than the status quo.  However, a high mutation rate is good for a population under streess, as it increases the chance that a novel variant will be better than the status quo.

Which is one of Shapiro's two big points: that cell mechanisms are such that stress induces a higher error rate in stressed populations, thus increasing diversity and thus opening possibilities for natural selection.
Now here is where we need to get specific about what you mean when you say "a high mutation rate is good for a population under stress" ... which of the following do you mean?

1) An increased rate of single base errors is good? Like swapping A's for G's or T's?  Or ...
2) An increased rate of larger "errors" like a gene being duplicated?
3) Something else?

All mutations. Any situation in which the DNA sequence changes.
Thanks for your answer ... anyone else?

  • Pingu
Re: Introduction to Systems Biology
Reply #2259
Well excuuuuse me ... for daring to talk about a DNA error rate for an individual bacterium dividing.

Sure you are excused.  Just stop strutting around with your franoogle in the air like you know more than anyone else.

Why do you even care about this anyway?  What difference does it make?  The error rate is something like 1 in 10 billion for E coli is it not?  And I forget how many bases E coli has in it's genome but you're going to get quite a bit of dividing before you get your first error are you not?

And every time a cell divides, there are two where there was one.

So the error rate is per division.  It makes no sense to talk about the error rate for a single cell.

Just as it makes no sense to talk about diversity for a single cell.  Or about a single cell "adapting"  - well, it might, but in biology when an individual adapts scientists use different words - development is one, or homeostasis sometimes.  Adaptation is what a population does.

So if you have a bunch of identical bacteria with identical genomes you have a population with no diversity.  If, every one in a billion divisions, a mutation occurs, then you have a mutation RATE of 1/billion IN THAT POPULATION.

After a while, as in Lenski's experiment, you have a DIVERSE population, i.e. a population of cells in which the genomes are NOT identical.

A population that is DIVERSE is more able to ADAPT to an environmental challenge.  That doesn't mean that the individual cells adapt by doing something more suitable and beneficial for them in that environment. It means that the variants that do better in that environment will (by definition) become more common and outcompete the others.

That is why I say that mutations are good for the population, but not so good for the individual cells that get one (talking about bacteria here - with multicellular organisms a whole different set of values apply - a mutation that is good for an individual cell is often lethal for the organism).

And THAT is why Shapiro is saying that bacterial populations "sense" environmental stress and respond with adaptive mutations.  He's not saying that the cells adapt to cope with the stressor.  He's saying the POPULATION adapts,  first by upping its mutation rate and thus increasing its diversity, and secondly by natural selection i.e. by one or two of the new variants being better than the original population at coping with the stressor.

And he gives a couple of ways in which the mutation rate can be increased.  At it's crudest it's just that stressors cause DNA damage, resulting in more error-prone repairs, and thus more mutations, and thus more diversity.


I have a Darwin-debased mind.

  • Pingu
Re: Introduction to Systems Biology
Reply #2260
Maybe someday I'll learn to read RSPL

Well, if you want to be able to read scientific papers, yes.  No point in reading papers in a language you don't understand.  And the RSPL is there for a reason.  It's precise.  English is much sloppier.  And Davinese is positively soup.
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2261
Are you going to answer my question? Or would you prefer to continue preaching these long sermons?

Re: Introduction to Systems Biology
Reply #2262
Are you going to answer my question? Or would you prefer to continue preaching these long sermons?
Says the guy endlessly posting long sections of St Shapiro's writings...   ::)
While you were getting your PhD in virology, I got my PhD in truth detection. :wave:  Dave Hawkins

Re: Introduction to Systems Biology
Reply #2263
Are you going to answer my question? Or would you prefer to continue preaching these long sermons?
her long sermon there was an answer to your question.
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 #2264
Are you going to answer my question? Or would you prefer to continue preaching these long sermons?
Says the guy endlessly pointlessly posting long sections of St Shapiro's writings...   ::)
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 #2265
Are you going to answer my question? Or would you prefer to continue preaching these long sermons?

Who are you talking to? And which question are you referring to?  And why can't you use the fucking quote function like everybody else? 
I have a Darwin-debased mind.

  • Pingu
Re: Introduction to Systems Biology
Reply #2266
Anyway, let's move on ...

Next you say ...
Quote
A mutation rate is bad for a well-adapted population, as most of the mutations will be worse than the status quo.  However, a high mutation rate is good for a population under streess, as it increases the chance that a novel variant will be better than the status quo.

Which is one of Shapiro's two big points: that cell mechanisms are such that stress induces a higher error rate in stressed populations, thus increasing diversity and thus opening possibilities for natural selection.
Now here is where we need to get specific about what you mean when you say "a high mutation rate is good for a population under stress" ... which of the following do you mean?

1) An increased rate of single base errors is good? Like swapping A's for G's or T's?  Or ...
2) An increased rate of larger "errors" like a gene being duplicated?
3) Something else?

All mutations. Any situation in which the DNA sequence changes.
Thanks for your answer ... anyone else?


I mean that a diverse population enables a population to adapt more readily.  But adaptation results in loss of diversity.

Therefore some rate of mutation is important to replace diversity lost to during adaptation. And as bacterial populations tend not to be very diverse (because they clone) then it makes sense that an increased mutation rate when diversity is needed to help a population adapt will help because it will increase diversity.

And this is what Shapiro is claiming happens - mutation rates increase when diversity is most needed.

Feel free to ask me if you find any of this ambiguous or unclear.
I have a Darwin-debased mind.

  • Pingu
Re: Introduction to Systems Biology
Reply #2267
Are you going to answer my question? Or would you prefer to continue preaching these long sermons?
her long sermon there was an answer to your question.

inorite?
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2268
Anyway, let's move on ...

Next you say ...
Quote
A mutation rate is bad for a well-adapted population, as most of the mutations will be worse than the status quo.  However, a high mutation rate is good for a population under streess, as it increases the chance that a novel variant will be better than the status quo.

Which is one of Shapiro's two big points: that cell mechanisms are such that stress induces a higher error rate in stressed populations, thus increasing diversity and thus opening possibilities for natural selection.
Now here is where we need to get specific about what you mean when you say "a high mutation rate is good for a population under stress" ... which of the following do you mean?

1) An increased rate of single base errors is good? Like swapping A's for G's or T's?  Or ...
2) An increased rate of larger "errors" like a gene being duplicated?
3) Something else?

All mutations. Any situation in which the DNA sequence changes.
Thanks for your answer ... anyone else?


I mean that a diverse population enables a population to adapt more readily.  But adaptation results in loss of diversity.

Therefore some rate of mutation is important to replace diversity lost to during adaptation. And as bacterial populations tend not to be very diverse (because they clone) then it makes sense that an increased mutation rate when diversity is needed to help a population adapt will help because it will increase diversity.

And this is what Shapiro is claiming happens - mutation rates increase when diversity is most needed.

Feel free to ask me if you find any of this ambiguous or unclear.
all I asked you to do was answer the following questions. I just want a 1 or 2 or 3.

I didn't ask for a long sermon.

Now here is where we need to get specific about what you mean when you say "a high mutation rate is good for a population under stress" ... which of the following do you mean? 

1) An increased rate of single base errors is good? Like swapping A's for G's or T's?  Or ... 
2) An increased rate of larger "errors" like a gene being duplicated?
3) Something else?

Re: Introduction to Systems Biology
Reply #2269
1?

2?

Or

3?

Re: Introduction to Systems Biology
Reply #2270
yes
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 #2271
Anyway, let's move on ...

Next you say ...
Quote
A mutation rate is bad for a well-adapted population, as most of the mutations will be worse than the status quo.  However, a high mutation rate is good for a population under streess, as it increases the chance that a novel variant will be better than the status quo.

Which is one of Shapiro's two big points: that cell mechanisms are such that stress induces a higher error rate in stressed populations, thus increasing diversity and thus opening possibilities for natural selection.
Now here is where we need to get specific about what you mean when you say "a high mutation rate is good for a population under stress" ... which of the following do you mean?

1) An increased rate of single base errors is good? Like swapping A's for G's or T's?  Or ...
2) An increased rate of larger "errors" like a gene being duplicated?
3) Something else?

All mutations. Any situation in which the DNA sequence changes.
Thanks for your answer ... anyone else?


I mean that a diverse population enables a population to adapt more readily.  But adaptation results in loss of diversity.

Therefore some rate of mutation is important to replace diversity lost to during adaptation. And as bacterial populations tend not to be very diverse (because they clone) then it makes sense that an increased mutation rate when diversity is needed to help a population adapt will help because it will increase diversity.

And this is what Shapiro is claiming happens - mutation rates increase when diversity is most needed.

Feel free to ask me if you find any of this ambiguous or unclear.
all I asked you to do was answer the following questions. I just want a 1 or 2 or 3.

I didn't ask for a long sermon.

I know you didn't.  That's because you don't actually want to know the answer.  You just want confirmation of your prior beliefs.

The answer is "something else" and I told you the "something else". Which I had already told you.

Now here is where we need to get specific about what you mean when you say "a high mutation rate is good for a population under stress" ... which of the following do you mean?

1) An increased rate of single base errors is good? Like swapping A's for G's or T's?  Or ...
2) An increased rate of larger "errors" like a gene being duplicated?
3) Something else?


Something else, namely what I told you.
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2272
Dave, what sort of thing would you expect to find if your religious model would turn out to be wrong and what impact would that have on your life?
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

  • Faid
Re: Introduction to Systems Biology
Reply #2273
DendroFakeChronology

Lol
Nice witty zinger, champ! Did you come up with it yourself?

If only you had some substance to go with that slander...
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 #2274
Pingu that's a non-answer. It's your favorite kind!