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Topic: Introduction to Systems Biology (Read 17102 times) previous topic - next topic

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Re: Introduction to Systems Biology
Reply #2575
Okay Pingu I'm going to have another go of trying to figure out what you actually think, but I'm going to do it in small bite-sized chunks. Please do not respond with long sermons or you will definitely lose me.

Question number one... you are familiar No Doubt with Shapiro's discussion of DNA replication in bacteria which he says has something like a 1 in 10 billion error rate. I may be off a zero or two One Direction or the other but the exact figure isn't important. Here's my question.

Are these errors...

1) Random?
2) random with respect to Fitness?
3) random with respect to time?
4) random with respect to physiology?
5) all 3, answers 2 3 and 4?
6) all four, answers 1 through 4?
7) none of the above?

Simple answer first please, then you can post a long sermon afterwards if you please.

  • fredbear
  • Militantly Confused
Re: Introduction to Systems Biology
Reply #2576
Okay Pingu I'm going to have another go of trying to figure out what you actually think, but I'm going to do it in small bite-sized chunks. Please do not respond with long sermons or you will definitely lose me.

Question number one... you are familiar No Doubt with Shapiro's discussion of DNA replication in bacteria which he says has something like a 1 in 10 billion error rate. I may be off a zero or two One Direction or the other but the exact figure isn't important. Here's my question.

Are these errors...

1) Random?
2) random with respect to Fitness?
3) random with respect to time?
4) random with respect to physiology?
5) all 3, answers 2 3 and 4?
6) all four, answers 1 through 4?
7) none of the above?

Simple answer first please, then you can post a long sermon afterwards if you please.
I have a test for you, Dave, to assess your capacity for learning. And don't worry, the question is less than 50 words. Don't want to tax that high-speed mind of yours too much, do we.

Nested Hierarchies. Do you still stand by your statement:
Quote from: Dave Hawkins
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.
?
"...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 #2577
Okay Pingu I'm going to have another go of trying to figure out what you actually think, but I'm going to do it in small bite-sized chunks. Please do not respond with long sermons or you will definitely lose me.

Well, you would be less ignorant if you could actually read things that were a page or so long.  But I will do my best.

Question number one... you are familiar No Doubt with Shapiro's discussion of DNA replication in bacteria which he says has something like a 1 in 10 billion error rate. I may be off a zero or two One Direction or the other but the exact figure isn't important. Here's my question.

Are these errors...

1) Random?

Depends what definition of random you are using.

2) random with respect to Fitness?

Yes.  I am not aware of any mutagenic process that is unambiguously non-random with respect to fitness, although that tryptophan thing is sort of intriguing.
3) random with respect to time?

Probably not.  I expect that under stress, all mutations will tend to become more common than under benign conditions.
4) random with respect to physiology?

Partly.  Some DNA sequences are more prone to mutations during chromosome duplication than others.  That means some physiological processes are more likely to be affected than others.

5) all 3, answers 2 3 and 4?
6) all four, answers 1 through 4?
7) none of the above?

Simple answer first please, then you can post a long sermon afterwards if you please.

I've given you specific answers to the ones that require specific answers.  You can work out the math on the remainder yourself.
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2578
Yeah, we'd noticed.
Who is we? Would that be a group in our nested hierarchy that I would label the Darwin Club? Or should we label it the Dave Hawkins PhD awarding committee? Or what?

Re: Introduction to Systems Biology
Reply #2579
Okay Pingu I'm going to have another go of trying to figure out what you actually think, but I'm going to do it in small bite-sized chunks. Please do not respond with long sermons or you will definitely lose me.

Well, you would be less ignorant if you could actually read things that were a page or so long.  But I will do my best.

Question number one... you are familiar No Doubt with Shapiro's discussion of DNA replication in bacteria which he says has something like a 1 in 10 billion error rate. I may be off a zero or two One Direction or the other but the exact figure isn't important. Here's my question.

Are these errors...

1) Random?

Depends what definition of random you are using.

2) random with respect to Fitness?

Yes.  I am not aware of any mutagenic process that is unambiguously non-random with respect to fitness, although that tryptophan thing is sort of intriguing.
3) random with respect to time?

Probably not.  I expect that under stress, all mutations will tend to become more common than under benign conditions.
4) random with respect to physiology?

Partly.  Some DNA sequences are more prone to mutations during chromosome duplication than others.  That means some physiological processes are more likely to be affected than others.

5) all 3, answers 2 3 and 4?
6) all four, answers 1 through 4?
7) none of the above?

Simple answer first please, then you can post a long sermon afterwards if you please.

I've given you specific answers to the ones that require specific answers.  You can work out the math on the remainder yourself.
Please try again with the assumptions that I'm talking about bacteria and only bacteria. And I'm talking about benign conditions, not stress conditions. And I'm only talking about normal DNA replication, not other kinds of change like Gene duplication or whatever else.

  • Pingu
Re: Introduction to Systems Biology
Reply #2580
Yeah, we'd noticed.
Who is we? Would that be a group in our nested hierarchy that I would label the Darwin Club? Or should we label it the Dave Hawkins PhD awarding committee? Or what?

It was minuted at the last AGM of the Darwin Club that Davinese speakers tend to have a problem with numbers, and that we should seek ways of making them more accessible to the Davinese people.
I have a Darwin-debased mind.

  • Pingu
Re: Introduction to Systems Biology
Reply #2581
Okay Pingu I'm going to have another go of trying to figure out what you actually think, but I'm going to do it in small bite-sized chunks. Please do not respond with long sermons or you will definitely lose me.

Well, you would be less ignorant if you could actually read things that were a page or so long.  But I will do my best.

Question number one... you are familiar No Doubt with Shapiro's discussion of DNA replication in bacteria which he says has something like a 1 in 10 billion error rate. I may be off a zero or two One Direction or the other but the exact figure isn't important. Here's my question.

Are these errors...

1) Random?

Depends what definition of random you are using.

2) random with respect to Fitness?

Yes.  I am not aware of any mutagenic process that is unambiguously non-random with respect to fitness, although that tryptophan thing is sort of intriguing.
3) random with respect to time?

Probably not.  I expect that under stress, all mutations will tend to become more common than under benign conditions.
4) random with respect to physiology?

Partly.  Some DNA sequences are more prone to mutations during chromosome duplication than others.  That means some physiological processes are more likely to be affected than others.

5) all 3, answers 2 3 and 4?
6) all four, answers 1 through 4?
7) none of the above?

Simple answer first please, then you can post a long sermon afterwards if you please.

I've given you specific answers to the ones that require specific answers.  You can work out the math on the remainder yourself.
Please try again with the assumptions that I'm talking about bacteria and only bacteria. And I'm talking about benign conditions, not stress conditions. And I'm only talking about normal DNA replication, not other kinds of change like Gene duplication or whatever else.

Well try examining your assumptions. 
I have a Darwin-debased mind.

  • Pingu
Re: Introduction to Systems Biology
Reply #2582
Okay Pingu I'm going to have another go of trying to figure out what you actually think, but I'm going to do it in small bite-sized chunks. Please do not respond with long sermons or you will definitely lose me.

Question number one... you are familiar No Doubt with Shapiro's discussion of DNA replication in bacteria which he says has something like a 1 in 10 billion error rate. I may be off a zero or two One Direction or the other but the exact figure isn't important. Here's my question.

Are these errors...

1) Random?
2) random with respect to Fitness?
3) random with respect to time?
4) random with respect to physiology?
5) all 3, answers 2 3 and 4?
6) all four, answers 1 through 4?
7) none of the above?

Simple answer first please, then you can post a long sermon afterwards if you please.

Please try again with the assumptions that I'm talking about bacteria and only bacteria. And I'm talking about benign conditions, not stress conditions. And I'm only talking about normal DNA replication, not other kinds of change like Gene duplication or whatever else.

OK, let me try again:
Quote
1) Random?

Depends what you mean by random.

Quote
2) random with respect to Fitness?

Most likely.

Quote
3) random with respect to time?

Well, if the environment isn't changing over time, then this question doesn't make sense.  If it is, then quite possibly no.

Quote
4) random with respect to physiology?

No.  Some physiological functions are likely to be less susceptible to mutation than others.

Quote
5) all 3, answers 2 3 and 4?
6) all four, answers 1 through 4?
7) none of the above?

See my specific responses.
I have a Darwin-debased mind.

Re: Introduction to Systems Biology
Reply #2583
Okay Pingu I'm going to have another go of trying to figure out what you actually think, but I'm going to do it in small bite-sized chunks. Please do not respond with long sermons or you will definitely lose me.

Well, you would be less ignorant if you could actually read things that were a page or so long.  But I will do my best.

Question number one... you are familiar No Doubt with Shapiro's discussion of DNA replication in bacteria which he says has something like a 1 in 10 billion error rate. I may be off a zero or two One Direction or the other but the exact figure isn't important. Here's my question.

Are these errors...

1) Random?

Depends what definition of random you are using.

2) random with respect to Fitness?

Yes.  I am not aware of any mutagenic process that is unambiguously non-random with respect to fitness, although that tryptophan thing is sort of intriguing.
3) random with respect to time?

Probably not.  I expect that under stress, all mutations will tend to become more common than under benign conditions.
4) random with respect to physiology?

Partly.  Some DNA sequences are more prone to mutations during chromosome duplication than others.  That means some physiological processes are more likely to be affected than others.

5) all 3, answers 2 3 and 4?
6) all four, answers 1 through 4?
7) none of the above?

Simple answer first please, then you can post a long sermon afterwards if you please.

I've given you specific answers to the ones that require specific answers.  You can work out the math on the remainder yourself.
Please try again with the assumptions that I'm talking about bacteria and only bacteria. And I'm talking about benign conditions, not stress conditions. And I'm only talking about normal DNA replication, not other kinds of change like Gene duplication or whatever else.

Well try examining your assumptions.
I'm just focusing on a specific organism and a specific process with that specific organism.

E coli.

Normal, non stressed replication.

  • Pingu
Re: Introduction to Systems Biology
Reply #2584
Okay Pingu I'm going to have another go of trying to figure out what you actually think, but I'm going to do it in small bite-sized chunks. Please do not respond with long sermons or you will definitely lose me.

Well, you would be less ignorant if you could actually read things that were a page or so long.  But I will do my best.

Question number one... you are familiar No Doubt with Shapiro's discussion of DNA replication in bacteria which he says has something like a 1 in 10 billion error rate. I may be off a zero or two One Direction or the other but the exact figure isn't important. Here's my question.

Are these errors...

1) Random?

Depends what definition of random you are using.

2) random with respect to Fitness?

Yes.  I am not aware of any mutagenic process that is unambiguously non-random with respect to fitness, although that tryptophan thing is sort of intriguing.
3) random with respect to time?

Probably not.  I expect that under stress, all mutations will tend to become more common than under benign conditions.
4) random with respect to physiology?

Partly.  Some DNA sequences are more prone to mutations during chromosome duplication than others.  That means some physiological processes are more likely to be affected than others.

5) all 3, answers 2 3 and 4?
6) all four, answers 1 through 4?
7) none of the above?

Simple answer first please, then you can post a long sermon afterwards if you please.

I've given you specific answers to the ones that require specific answers.  You can work out the math on the remainder yourself.
Please try again with the assumptions that I'm talking about bacteria and only bacteria. And I'm talking about benign conditions, not stress conditions. And I'm only talking about normal DNA replication, not other kinds of change like Gene duplication or whatever else.

Well try examining your assumptions.
I'm just focusing on a specific organism and a specific process with that specific organism.

E coli.

Normal, non stressed replication.


Well, I don't know specific answers for e-coli, Dave, and I'm not a bacteriologist.  But obviously NORMAL replication of bacteria doesn't have mutations.  Mutations are, as you say, rare, and therefor ABnormal. What causes any given mutation is impossible to know unless you see it happening, which we don't.

It's like you are asking how often a normal human delivery goes wrong. It's a non-question. Because a human delivery that goes wrong isn't a normal delivery.
I have a Darwin-debased mind.

  • Faid
Re: Introduction to Systems Biology
Reply #2585
Wait- Is dave saying that gene duplication is not associated with DNA replication?
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 #2586
Also, why insisting on "benign" conditions of replication? Shapiro certainly does not.
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.

  • Pingu
Re: Introduction to Systems Biology
Reply #2587
This is the problem with your narrow blinkered view of the world, Dave.  Your questions are framed so narrowly that a "simple" answer will either confirm your prior belief that you are right or that we are wrong, while you dismiss any more complex answer as "squid ink".  As a result you never actually find out what anyone else thinks.

So you are stuck with your straw men. 

And you do the same with reading.  You only read for answers you either want to see, or want to hold up as wrong. So you think that Shapiro is saying something that none of the rest of us are willing to accept.  That's your straw flail.

In fact, none of us hear have a big issue with anything Shapiro is saying, and VoxRat apparently teaches some of Shapiro's work.  I've posted a couple of papers making even more Lamarckian claims than Shapiro's. And as you know, I've been trying to get you to read Denis Noble for years.

But your rigidity prevents you from actually learning.  Stop framing your questions so narrowly, and open your mind to the possiblity that what you think that the Darwin Club believes isn't actually a view anyone holds.  You may still disagree with it, but at least you'd be right about what you disagree with.
I have a Darwin-debased mind.

  • Pingu
Re: Introduction to Systems Biology
Reply #2588
Wait- Is dave saying that gene duplication is not associated with DNA replication?

:itsamystery:
I have a Darwin-debased mind.

  • nesb
Re: Introduction to Systems Biology
Reply #2589
Dave might (or might not) like to think about cancer cells.  Cancer cells are cells that have a mutation that is really really good for the cell - causes it to reproduce at a much higher rate than their fellows.

But cancers generally are really really bad for the population of cells they belong to i.e. the person with the cancer.

Dave, do you think cancer cells INTEND to mutate in a way that helps them reproduce so efficiently?  Or do you think those mutations happen BY ACCIDENT?  And, if the latter, how come an ACCIDENT is so good for a cell?  What if the a similar accident happened to a bacterial cell?

And if you think that cancer cells INTEND to mutate so as to out-compete their fellows, what "cell mediated" process made them do this?  And who designed that process for them?



Dave?
I think an accidental mutation (or mutations) occurs in a particular region of the genome that causes the cell to "intend" things that it would not otherwise have intended had the accidental mutation not occurred.  Sorta like a person with a mental problem. Perfectly understandable.

And some of those mutations are situationally beneficial. Dave has conceded the point. Disavowed himself of creationism, and will soon change his last name to Dawkins, in celebration of the biologist. Hooray

  • nesb
Re: Introduction to Systems Biology
Reply #2590
As a personal note, I'm not the biggest fan of Dawkins, but to each their own.

Re: Introduction to Systems Biology
Reply #2591
Leave it to pingu to give a complicated answer for a simple question like will you get wet if you walk out in the rain with no umbrella.

Re: Introduction to Systems Biology
Reply #2592
I really thought I had simplified the question enough to where I could finally, for once in my life, nail the Jell-O to the wall. But alas, no.

Re: Introduction to Systems Biology
Reply #2593
I really thought I had simplified the question enough to where I could finally, for once in my life, nail the Jell-O to the wall. But alas, no.
Perhaps your assumption that Jell-O can be nailed to the wall is the problem.

Re: Introduction to Systems Biology
Reply #2594
Quote
And it would help if you could finally get your head round the idea that genetic DIVERSITY denotes, in English, a property of a population, not an individual.
Diversity is a property of sets, is it not?  Individuals have a "set" of genes, do they not?

:facepalm:

And, just like that, it's 2006 again.
Quote
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.

ETA: unbelievable. this was ninja'd. Multiple times!
  • Last Edit: March 15, 2018, 09:11:49 AM by Testy Calibrate
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 #2595
Yeah, we'd noticed.
Who is we? Would that be a group in our nested hierarchy that I would label the Darwin Club? Or should we label it the Dave Hawkins PhD awarding committee? Or what?
I just got the funniest vignette of your oral defense
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 #2596
I really thought I had simplified the question enough to where I could finally, for once in my life, nail the Jell-O to the wall. But alas, no.
IOW, you were trying for a "gotcha" and failed.

What part of Pingu's response confuses you?
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.

  • uncool
Re: Introduction to Systems Biology
Reply #2597
Quote
And it would help if you could finally get your head round the idea that genetic DIVERSITY denotes, in English, a property of a population, not an individual.
Diversity is a property of sets, is it not?  Individuals have a "set" of genes, do they not?

You can torture it to make it make sense for an individual, but its natural expression is as something about a population; the torture effectively remakes an individual into a population.

  • Pingu
Re: Introduction to Systems Biology
Reply #2598
Leave it to pingu to give a complicated answer for a simple question like will you get wet if you walk out in the rain with no umbrella.

Well, that tends to happen, Dave, if you ask a question to which there is no simple answer, or which assumes its conclusion.

Consider the possiblity tht the reason you don't like my answers is that mind is too rigid and narrow to formulate a question with any other answer than ones you like.
I have a Darwin-debased mind.

  • nesb
Re: Introduction to Systems Biology
Reply #2599
I really thought I had simplified the question enough to where I could finally, for once in my life, nail the Jell-O to the wall. But alas, no.

Hmm... Pingu must have somehow sussed out that you aren't trying to discuss this in good faith.