RSS 2.0 Feed

» Welcome Guest Log In :: Register

Pages: (16) < ... 4 5 6 7 8 [9] 10 11 12 13 14 ... >   
  Topic: For the love of Avocationist, A whole thread for some ID evidence< Next Oldest | Next Newest >  
argystokes



Posts: 766
Joined: Jan. 2006

(Permalink) Posted: Jan. 29 2007,01:06   

Quote
My understanding of antibiotic resistance is 1) that it is being found that bacteria have a way of turning on mutations that are directed toward solving a problem

I'd be very interested in your source which states that any mutation is specifically directed. I am aware of papers that show an increased mutation rate under certain stress situations (such as application of antibiotics), which would naturally lead to a faster rate of "finding" an antibiotic resistance mutation. But I am not aware of any that show specifically directed mutations in bacteria.

--------------
"Why waste time learning, when ignorance is instantaneous?" -Calvin

  
avocationist



Posts: 173
Joined: Feb. 2006

(Permalink) Posted: Jan. 29 2007,01:24   

Creeky Belly,

Quote

Me:  In the end, I can see only two choices. Ether there is a mind involved in the whole process of this cosmos, or there isn't. They aren't the same at all, and they won't look the same. I would just not worry too much about diminishing God by finding natural explanations. The question is, do we live in a universe with a mind or not. The idea that God shrinks is downright silly. Supposedly, people were real deflated when they figured out angels didn't push the planets around. So they said God lost a job. What nonsense. Isn't the truth more magnificent, the planning more impressive? The old way of looking at things was like a fairy tale, with a magic-wand God. God's domain can never shrink. It is a nonproblem.

You:  I agree, but what you've just stated is not a theory of ID, it's a creationist (philosophical) argument, all or nothing. ID wants to have it both ways: X can be observed naturally, therefore supernatural explanation. It masquerades as science until it draws a conclusion. Unfortunately for ID, scientists can see through the bullshit. (I should say, to keep with the logical fallacies, true scientists can see through the bullshit)



I'm not sure which part you agree with, and which is creationist bullshit. Yes, it was a philosophical answer, because your original question was philosophical: you worry that if we find naturalistic explanations for things, God's domain shrinks. I find it hard to relate to this. On one hand, I do not believe in the supernatural, and I don't think there is such a thing as disrupting the laws of physics. On the other hand, if we manufacture a car, we have definitely designed something that nature alone could not, but neither have we gone against the laws of nature. I also resent being called a creationist because it is usually pejoriative and often refers to Biblical literalists. Whatever poor sap wrote Genesis probably never dreamed humanity would descend to such an extremity of foolishness as to take it literally.

Deadman,

Quote
there are two possibilities. Either things are accidental or they are designed, and the two can be told apart.


How? Be precise. Don't just point to Dembski's mathemagical tripe.
I don't point to his tripe because I haven't read it. But I have read some explanations of information from an ID viewpoint in the Meyer paper, probably Spetner and perhaps also Dembski in a short essay. Generally, we don't have too much trouble discerning when things are designed or not. There may be some ambiguous cases, but ID would not focus on those. There comes a point of complexity, when the probability of unguided processes producing the result just becomes untenable. Where it becomes more rational and reasonable to infer design. That people who believe in an omnipotent and moralizing God argue against that, not just as to whether we have reached that point, but whether we ever can, is puzzling to say the least.

It's important to realize that because we aren't sure, we speak as if we had a choice of universes, whereas in fact there is only one kind. Either we live in a God universe or we don't, and they are mutually exclusive. If there is a God, then existence without God is a nonpossibility. If there is no God, then God is a silly notion, and there is not possibility of one. If we live in a God universe, it is a designed universe, and if it is a designed universe then a nondesigned one cannot have any existence and therfore cannot be rationally postulated.

Wesley,(or anyone)

I read down quite a bit on the link about falsifiability, but I never found the point made that I am looking for. So why is it that ID is not falsifiable if we could account for IC and CSI?

Altabin,

Very disappointing post. I thought we had established a bit of rapport, but apparently not. I'm sorry you didn't realize my remark about people disappearing was meant to be a joke. Probably you haven't read through the history of this thread, in which I made it clear I'm unhappy about the moderation over there.

The alien thing comes from a genre of books about it.

Quote

[Cedric's jaw drops open. His drink falls from his suddenly useless fingers onto the floor and rolls under the sofa.]

Not sure why.
****************
I made several replies to all the entropy nonsense. Won't go over it again in detail. My points were:

I never did have any 'argument' regarding the second law.
My interest in the second law has nothing to do with the ID debate, never did, it was a side issue that struck me at the time, largely due to a book I'm reading on a different topic.
Entropy is not only defined as a variable, but as a process and a result.
How can you say that we cannot discuss entropy unless we have the ability to plug in the actual numerical values? Do the laws of physics only work if we have learnt to understand and quantify them?
Everything Improvius said in post 633 is obviously true.

I find it VERY odd that people keep thinking I'm worried that the SLOT prevents evolution. I do realize that has been done by creationists, but how many times do I have to make myself clear, and if you guys don't listen well to that, why should I expect you to listen to what else I say?

Quote
But please note that Berlinski's beef is with the thermodynamics of abiogenesis, not evolution proper. None of the observed mechanisms driving evolution run contrary to the Second Law so long as the animals eat.  :)
You too, Paley? sigh

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Jan. 29 2007,01:43   

Quote
I'm not sure which part you agree with, and which is creationist bullshit. Yes, it was a philosophical answer, because your original question was philosophical: you worry that if we find naturalistic explanations for things, God's domain shrinks.

I don't think it shrinks and I'm not particularly worried, since I don't think we can empirically support the supernatural. If we could, then we could rule out God from natural processes and in that sense God's domain would necessarily diminish. That's why I spoke in the domain of philosophy; since in science, the answer is simple: God gets dropped by Occam's Razor.

  
Altabin



Posts: 308
Joined: Sep. 2006

(Permalink) Posted: Jan. 29 2007,03:14   

Quote (avocationist @ Jan. 29 2007,08:24)
Altabin,

Very disappointing post. I thought we had established a bit of rapport, but apparently not. I'm sorry you didn't realize my remark about people disappearing was meant to be a joke. Probably you haven't read through the history of this thread, in which I made it clear I'm unhappy about the moderation over there.

Apologies - nuances can be lost in this medium, and ironic inflections are usually the first to go.  And, as you may have noticed, what gets people riled up here is not ignorance (in the sense of simply not knowing something) but dishonesty.  We can be hyper-sensitive to apparent dishonesty simply because we have seen so much of it.  If I falsely accused you of something, again I apologize.  I hope we can continue our conversation.

 
Quote
The alien thing comes from a genre of books about it.

Not sure I got that.

--------------

  
demallien



Posts: 79
Joined: Jan. 2007

(Permalink) Posted: Jan. 29 2007,05:05   

Quote (avocationist @ Jan. 29 2007,00:47)
...

The bacteria were examined and compared with others of their species and it was discovered that a particular frame shift mutation (which means that a gene got read at a slightly different starting point and slightly different ending point) allowed that bacteria to break down the nylon and obtain energy from that process. But not a LOT of energy. It wasn't a highly competent design because the bacteria weren't extracting a lot of energy from the process, just enough to get by. And it was based on a simply frame shift reading of a gene that had other uses. But with a simple frame shift of a gene that was already there, it could now "eat" nylon. Future mutations, perhaps point mutations inside that gene, could conceivably heighten the energy gain of the nylon decomp process, and allow the bacteria to truly feast and reproduce faster and more plentifully on just nylon, thus leading perhaps in time to an irreducibly complex arrangement between bacteria who live solely on nylon and a man-made fiber produced only by man.

You see, right there is a fine example of the disconnect that occurs in the brains of IDists, and I for the life of me cannot see how the disconnect happens.

You describe in detail the mutation (a frame shift).  You acknowledge that the gene that has been frame-shifted was in fact originally used for other purposes.  You acknowledge that with further point mutations to this gene we could arrive at a highly specialised organism that is apparently (according to the measures "defined" by Behe) irreducibly complex, yet arrived at by simple random mutation and natural selection.  In your own words, you have just completely invalidated ID, showing that irreducibly complex organisms can evolve naturally.

But then, something weird happens in your head.  Instead of saying "oh!  Hang on!  ID can't be right then", as would be the logical thing to do at this point, you go on defending it?!?!?!  Huh!?!?!?!  Please explain!

Don't be sidetracked by speciation.  Speciation is just the accumulation over time of lots of these mutations in reproductively separated groups, until the two groups can no longer interbreed - voilà, new species...  Anyway, ID doesn't contest speciation, it contests evolution of cell-level machinery, such as the machinery to permit a bacteria to digest nylon.

  
Serendipity



Posts: 28
Joined: Jan. 2007

(Permalink) Posted: Jan. 29 2007,06:30   

Hello, Avocationist.

Quote
I never did have any 'argument' regarding the second law.


It would require the equation (maths).

Quote
My interest in the second law has nothing to do with the ID debate, never did, it was a side issue that struck me at the time, largely due to a book I'm reading on a different topic.


If you don't mind my asking, what book is that? I remember how excited i got reading Shannon's Entropy.

Quote
Entropy is not only defined as a variable, but as a process and a result.


Entropy is meaningless outside of the equation thus making it a variable. It remains a variable due to process. Even its result is a variable. For example: entropy and chemistry (as was mentioned earlier by Creeky) would render a different mathematical application, to say Entropy and Information Theory (again, Shannon), or Entropy and Quantum Mechanics, or Entropy and Classical Thermodynamics. In classical Clausius Thermodynamics, Entropy is representative of S based on heat (Q) and temperature (T) which is applicable (S that is) for systems/states in thermodynamical equilibrium. However, if applied to statistical mechanics then entropy is equal to the probability of a particle in a microstate, compared to the macrostate of its system, added to determine all of the particles in that system. Defining its entropic measure using Boltzmann's constant rendering an arbitrary result (based on a probability of 0 and/or 1). While I can understand a need to apply reductionism to a simple "word" that actual word "entropy" is representative of a myriad of mathematical applications, where outside that application, is meaningless. Thus you have pseudophilosophers then utilise standard definitions and jigsaw together something that pulls away from the maths of it - making it USELESS for anything than philosophical jargon.

Quote
How can you say that we cannot discuss entropy unless we have the ability to plug in the actual numerical values?


Read above. I have no idea how much clearer it can be made for you. If you wish to discuss entropy outside of maths, then thats your prerogative (totally) but it is a meaningless, obselete cause because it means having to redefine its application, thus its entire meaning.

Quote
Do the laws of physics only work if we have learnt to understand and quantify them?


The Laws of Physics work regardless of our understanding them or not. For those that take the time to understand them - it makes things easier. For those that don't, it makes it harder for those who do who are presented by those who don't but wish to give them meaning without understanding.

Quote
I find it VERY odd that people keep thinking I'm worried that the SLOT prevents evolution. I do realize that has been done by creationists, but how many times do I have to make myself clear, and if you guys don't listen well to that, why should I expect you to listen to what else I say?


Besides stating previously that all biological systems apply thermodynamics there really isn't an argument per se. But its an interesting conversation to have outside of "creationism" if I must say so myself.

Ciao.

Serendipity.

--------------
Without question or false modesty, no success has owed more to serendipity than ours. (Fischer)

  
mitschlag



Posts: 236
Joined: Sep. 2006

(Permalink) Posted: Jan. 29 2007,06:59   

Quote (avocationist @ Jan. 29 2007,00:47)
Then ther's the problem I can't cut and paste from the article because it's in pdf. I was going to ask for clarification of a couple of things.

To cut and paste from a pdf file, go to the Tools menu, click on "Select and Zoom."  If the tool is checked, you can select text with the I-beam cursor.  Right-click on the selected text to copy.

--------------
"You can establish any “rule” you like if you start with the rule and then interpret the evidence accordingly." - George Gaylord Simpson (1902-1984)

  
"Rev Dr" Lenny Flank



Posts: 2560
Joined: Feb. 2005

(Permalink) Posted: Jan. 29 2007,07:14   

Quote (avocationist @ Jan. 29 2007,00:47)
Nor does this address the problems associated with speciation

(sigh)


You know, I'm not at all surprised when creationists like Avo prove themselves to be crushingly uneducated and ignorant about basic biology and evolution.  But I *am* mildly surprised (and a little annoyed) when they turn out to be too stupid and uninformed to even get the basic CREATIONIST arguments straight.

This is from the website of Answers in Genesis, one of the largest creationist organizations in the world:

"Poorly-informed anti-creationist scoffers occasionally think they will 'floor' creation apologists with examples of 'new species forming' in nature. They are often surprised at the reaction they get from the better-informed creationists, namely that the creation model depends heavily on speciation."

Let me repeat that, in case you're not bright enough to get it.  Answers in Genesis says that not only does creationism itself "depend heavily on speciation", but they also say that those who argue that there are NO "new species forming in nature" are "poorly informed".

Guess that means YOU, huh.  By arguing to me that new species cannot evolve, you are not only demonstrating that you are completely ignorant of basic biology, but you're also demonstrating that you're too stupid and uninformed to even understand the most elementary CREATIONIST arguments.

But hey, if you think speciation is such a "problem", perhaps you could explain to me why speciation has been DIRECTLY OBSERVED, both in the wild and in the lab, over one hundred times in the past 20 years . . . .?

You are a pig-ignorant buffoon, Avo.  I see no reason why anyone should pay the slightest attention to anything you babble about.  Fortunately, though, it appears that no one --either ID or "evolutionist" -- DOES pay any attention to your babbling.  (shrug)

--------------
Editor, Red and Black Publishers
www.RedandBlackPublishers.com

  
"Rev Dr" Lenny Flank



Posts: 2560
Joined: Feb. 2005

(Permalink) Posted: Jan. 29 2007,07:18   

Quote (avocationist @ Jan. 29 2007,00:47)
My understanding of antibiotic resistance is 1) that it is being found that bacteria have a way of turning on mutations that are directed toward solving a problem, and 2) that they usually involve either a reshuffling of some sort or actually a loss of information or functionality.

Your understanding is wrong.  Not surprising, actually, since you don't understand anything that you presume to babble about.

Thanks for once again demonstrating to everyone that you are just an uninformed uneducated pig-ignorant buffoon who has no idea at all what she is talking about.

--------------
Editor, Red and Black Publishers
www.RedandBlackPublishers.com

  
mitschlag



Posts: 236
Joined: Sep. 2006

(Permalink) Posted: Jan. 29 2007,07:58   

Quote (avocationist @ Jan. 29 2007,01:24)
...I do not believe in the supernatural, and I don't think there is such a thing as disrupting the laws of physics...

Either we live in a God universe or we don't, and they are mutually exclusive. If there is a God, then existence without God is a nonpossibility. If there is no God, then God is a silly notion, and there is not possibility of one. If we live in a God universe, it is a designed universe, and if it is a designed universe then a nondesigned one cannot have any existence and therfore cannot be rationally postulated.

Avo, you present yourself as a sincere seeker of truth, and your efforts to understand the science involved in nylon-eating bacteria speak to that.  But I have trouble interpreting your thoughts excerpted above.  You seem to be able to hold contradictory positions simultaneously.  If you don't believe in the supernatural, how can you believe in design of the universe by a god?

--------------
"You can establish any “rule” you like if you start with the rule and then interpret the evidence accordingly." - George Gaylord Simpson (1902-1984)

  
k.e.



Posts: 40
Joined: Jan. 2006

(Permalink) Posted: Jan. 29 2007,09:06   

Quote (mitschlag @ Jan. 29 2007,07:58)
Quote (avocationist @ Jan. 29 2007,01:24)
...I do not believe in the supernatural, and I don't think there is such a thing as disrupting the laws of physics...

Either we live in a God universe or we don't, and they are mutually exclusive. If there is a God, then existence without God is a nonpossibility. If there is no God, then God is a silly notion, and there is not possibility of one. If we live in a God universe, it is a designed universe, and if it is a designed universe then a nondesigned one cannot have any existence and therfore cannot be rationally postulated.

Avo, you present yourself as a sincere seeker of truth, and your efforts to understand the science involved in nylon-eating bacteria speak to that.  But I have trouble interpreting your thoughts excerpted above.  You seem to be able to hold contradictory positions simultaneously.  If you don't believe in the supernatural, how can you believe in design of the universe by a god?

Here's how it works (HenryJ I'll channel Reciprocating bill for a change).

If something is supernatural it isn't, and everyone knows that. Supernatural is like UFO's they never show up to the best parties uninivited and bring extra nachos and Stolichnaya or zap the fuzz when they catch you driving home on the wrong side of the road.

So supernatural is very unreliable and so are the people who are abducted and analy probed by them.

Given the choice between supernatural and electro shock treatment for shop lifting most people would take supernatural, it passes the least harm test and remains the logical choice for any intelligent shop lifter.

Now given the brand  awareness of supernatural and its usefulness as the product of choice by various spivs,hucksters, piss artists and purveyors of flim flam for g$d to actually exist it would be much easier to deny her superness and make her just natural.

'K?

  
avocationist



Posts: 173
Joined: Feb. 2006

(Permalink) Posted: Jan. 29 2007,11:21   

Creeky,

Quote

I don't think it shrinks and I'm not particularly worried, since I don't think we can empirically support the supernatural. If we could, then we could rule out God from natural processes and in that sense God's domain would necessarily diminish. That's why I spoke in the domain of philosophy; since in science, the answer is simple: God gets dropped by Occam's Razor.
See, I don't think there is a divide between nature and God. If there is a God, I don't think this God is outside of natural processes. If I could drown Occam in the deepest ocean it would be a boon to philosophy. People get away with all sorts of lazy thinking by invoking the poor ghost, and we should let him rest in peace. No, we do not drop God due to Occam. Either there's a God or there isn't. And accounting for existence and a highly complex universe without recourse to any sort of mind or causation is actually the more difficult route.

Quote
You seem to be able to hold contradictory positions simultaneously.  If you don't believe in the supernatural, how can you believe in design of the universe by a god?
I don't consider God to be supernatural. I don't think the situation is one where God is here but not there. I think it is a lot like the idea of two dimensional beings seeing a third dimensional being jump up and down. When he jumps up off the flat plane, he disappears, so he is supernatural and has magical powers. It seems obvious enough that we are also like these two dimensional beings, and when we see only dimly or not at all or by clues and inferences, we consign the phenomenon to a realm called supernatural.

Lenny,

Quote
Answers in Genesis says that not only does creationism itself "depend heavily on speciation", but they also say that those who argue that there are NO "new species forming in nature" are "poorly informed".
What they mean by speciation is not the arisal of totally new kinds. They consider one kind to have given rise to dogs and wolves and jackals and foxes, that sort of thing. they do not think that amoebas became fish became reptiles, etc.

Quote

You describe in detail the mutation (a frame shift).  You acknowledge that the gene that has been frame-shifted was in fact originally used for other purposes.  You acknowledge that with further point mutations to this gene we could arrive at a highly specialised organism that is apparently (according to the measures "defined" by Behe) irreducibly complex, yet arrived at by simple random mutation and natural selection.  In your own words, you have just completely invalidated ID, showing that irreducibly complex organisms can evolve naturally.

I didn't show that mutations could lead to IC - I show that whoever wrote what I quoted, believes that. But is a frame shift new information?  

Quote
Speciation is just the accumulation over time of lots of these mutations
A lot of people think that is an unwarranted extrapolation from minimal data.

  
The Ghost of Paley



Posts: 1703
Joined: Oct. 2005

(Permalink) Posted: Jan. 29 2007,11:29   

Avocationist:

     
Quote
     
Quote
 
But please note that Berlinski's beef is with the thermodynamics of abiogenesis, not evolution proper. None of the observed mechanisms driving evolution run contrary to the Second Law so long as the animals eat.  :)  

You too, Paley? sigh


Well, think about gene duplication + mutation of the extra copy. That's a good way to build complexity in the system, and this process has been observed in a mosquito, and seems to have played a large role in shaping the human genome. Obviously, the process can't be contrary to the Second Law because it's been observed. So where does the energy come from? The calories the animal consumes. If the animal stops eating, the animal's body doesn't have enough energy to perform meiosis (let alone anything else), and the animal dies. Remember, animal bodies are not closed systems. Now as to how meiosis and retrotransposition came to be in the first place....that's a different question. Nevertheless, gene duplication itself is uncontroversial.

Sun's energy -> plants -> herbivores -> food.

:D  :D  :D

--------------
Dey can't 'andle my riddim.

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Jan. 29 2007,13:29   

Quote
I don't consider God to be supernatural. I don't think the situation is one where God is here but not there. I think it is a lot like the idea of two dimensional beings seeing a third dimensional being jump up and down. When he jumps up off the flat plane, he disappears, so he is supernatural and has magical powers. It seems obvious enough that we are also like these two dimensional beings, and when we see only dimly or not at all or by clues and inferences, we consign the phenomenon to a realm called supernatural.

You should be very careful when you start talking about dimensions; did you mean it in the scientific sense or as an analogy? If you're interested in the scientific aspect of multi-dimensions, I can direct you to a wealth of information on String Theory.
What I meant by God is removed by Occam's; it's not that his existence is disproved, but that God is removed as an explanation for a natural process (extraordinary claims require extraordinary evidence). Either God is supernatural, or he isn't.

Quote
And accounting for existence and a highly complex universe without recourse to any sort of mind or causation is actually the more difficult route.

This is an argument from incredulity, and unless you're going to provide some evidence for this you're going to be stuck in the realm of philosophy. I don't mind, since I agree with you there. To say that it's more difficult to justify a natural universe than one created by God is to ignore the body of work in chemistry, physics, and biology.

  
avocationist



Posts: 173
Joined: Feb. 2006

(Permalink) Posted: Jan. 29 2007,14:02   

Anyway, I found where somebody had asked Spetner about the nylon bug:

Comments by Lee Spetner, November 19, 2002

It's interesting, first of all, that the URL you pointed to picked the "nylon bug" as an example of a random mutation yielding a gain of information. (The short answer is, the mutation does yield an increase of information, but was it random?) It's interesting because the "nylon bug" is exactly what I used in my letter #7 to Jim Crow (of which you got a copy) as a possible example of a nonrandom mutation triggered by the environment. To respond to your query, I shall have to elaborate on this more than I did in that letter, which was not polemical.

Let me point out two important facts that the URL ignores. First, there are two altered enzymes, not just one.  Both these enzymes are needed to metabolize the 6-aminohexanoic-acid-cyclic-dimer (6-AHA CD) found in the waste water of the nylon factory. Neither of these enzymes alone is effective. Both are needed. The first enzyme, which I shall call enzyme 1, is 6-aminohexanoic-acid-cyclic-dimer hydrolase (6-AHA CDH) and catalyzes the conversion of 6-AHA CD to 6-aminohexanoic-acid-oligomer (6-AHA LO). The second enzyme, which I shall call enzyme 2, is (6-aminohexanoic-acid-oligomer hydrolase (6-AHA LOH) and catalyzes the conversion of 6-AHA LO  to 6-amino-hexanoic acid [Kinoshita et al. 1981].  Only enzyme 2 is the product of a frame shift. Enzyme 1, whose DNA sequence I have not seen, is probably the product of only point mutations. [Okada et al. 1983, Ohno 1984]

Second, enzyme 2 is not just the product of a frame shift, it is also the product of 140 point mutations. Many of these mutations are silent, but many are not. 47 amino acids out of 392 of the enzyme have been changed.

It seems to me that many of these altered amino acids are essential to the catalytic effect of the enzyme. How many, I don't know. In my above cited letter to Jim, I calculated the probability of getting multiple random mutations in the 30 years it took to evolve these enzymes. If the evolution of this enzyme had to rely on random point mutations, it could have never evolved. Thus, if only 6 of these 47 mutations were essential for the evolution, the probability of achieving it in 30 years is about 3 x 1035. So, if the evolution could not be random, then it would have to be nonrandom, and as I have suggested in my book, they would be triggered by the environment. That is, the capability is built into the bacterium and the environment triggers the mutations.

I have ignored the evolution of enzyme 1, and the random evolution of that enzyme makes for an even less probable event.

Now, why should there be a built-in capability to metabolize nylon, which did not exist until 1937 or so? The answer is there shouldn't be. But there could have been a built-in capability to metabolize some other substrate. Kinoshita et al. (1981) tested enzyme 2 against 50 possible substrates and found no activity, but that does not mean that it doesn't have activity on some substrate not tested. The activity of enzyme 2 was small, but enabled the bacteria to metabolize the nylon waste.

  
avocationist



Posts: 173
Joined: Feb. 2006

(Permalink) Posted: Jan. 29 2007,14:09   

Quote
I'd be very interested in your source which states that any mutation is specifically directed. I am aware of papers that show an increased mutation rate under certain stress situations (such as application of antibiotics), which would naturally lead to a faster rate of "finding" an antibiotic resistance mutation. But I am not aware of any that show specifically directed mutations in bacteria.

It gets turned on in response to the environment, is confined to speific loci in the genome, and is turned off when it's job is done. The mutations which occur under those conditions are random. Thus it took (if I understood the article) 3 months to produce the nylon eating mutation(s) but apparently that was not the only time it occurred. Spetner mentions it being discovered accidentally 30 years after nylon was invented.

  
argystokes



Posts: 766
Joined: Jan. 2006

(Permalink) Posted: Jan. 29 2007,14:21   

Quote (avocationist @ Jan. 29 2007,12:09)
Quote
I'd be very interested in your source which states that any mutation is specifically directed. I am aware of papers that show an increased mutation rate under certain stress situations (such as application of antibiotics), which would naturally lead to a faster rate of "finding" an antibiotic resistance mutation. But I am not aware of any that show specifically directed mutations in bacteria.

It gets turned on in response to the environment, is confined to speific loci in the genome, and is turned off when it's job is done. The mutations which occur under those conditions are random. Thus it took (if I understood the article) 3 months to produce the nylon eating mutation(s) but apparently that was not the only time it occurred. Spetner mentions it being discovered accidentally 30 years after nylon was invented.

What gets turned on? And the letter above does not describe any experiments showing directed mutations. Spetner asserts that the enzyme could not have evolved "randomly," but makes no note of how selection might impact the evolution of the enzyme.

Are you interested in discussing papers that actually test whether or not directed mutations exist (in given experimental conditions, of course)?

--------------
"Why waste time learning, when ignorance is instantaneous?" -Calvin

  
The Ghost of Paley



Posts: 1703
Joined: Oct. 2005

(Permalink) Posted: Jan. 29 2007,14:21   

This link addresses a few of Spetner's claims.

--------------
Dey can't 'andle my riddim.

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Jan. 29 2007,14:29   

Re "they do not think that amoebas became fish became reptiles, etc."

Do scientists think a kind of amoeba was predecessor to animals?

Henry

  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: Jan. 29 2007,15:50   

Quote (Henry J @ Jan. 29 2007,14:29)
Re "they do not think that amoebas became fish became reptiles, etc."

Do scientists think a kind of amoeba was predecessor to animals?

Henry

Not specifically, as far as I can tell, but unicellular eukaryotes  are our ancestors. For a creationist, that means "ameobas".  ???

  
mitschlag



Posts: 236
Joined: Sep. 2006

(Permalink) Posted: Jan. 29 2007,16:23   

Quote (avocationist @ Jan. 29 2007,11:21)
 
Quote
You seem to be able to hold contradictory positions simultaneously.  If you don't believe in the supernatural, how can you believe in design of the universe by a god?
I don't consider God to be supernatural. I don't think the situation is one where God is here but not there. I think it is a lot like the idea of two dimensional beings seeing a third dimensional being jump up and down. When he jumps up off the flat plane, he disappears, so he is supernatural and has magical powers. It seems obvious enough that we are also like these two dimensional beings, and when we see only dimly or not at all or by clues and inferences, we consign the phenomenon to a realm called supernatural.

Wow, thanks for clarifying that!

OK, God is not supernatural.  We just think it [he/she] is beyond nature because it [he/she] exists in  another dimension that we can't perceive, because it's beyond nature.  But it's not supernatural.  
Sure, I get it!

--------------
"You can establish any “rule” you like if you start with the rule and then interpret the evidence accordingly." - George Gaylord Simpson (1902-1984)

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Jan. 29 2007,16:37   

Hmm. Quantum physicists also put a bunch of stuff in other dimensions too. Wonder how that fits in with the natural/supernatural distinction?

  
mitschlag



Posts: 236
Joined: Sep. 2006

(Permalink) Posted: Jan. 29 2007,16:42   

Quote (Henry J @ Jan. 29 2007,16:37)
Hmm. Quantum physicists also put a bunch of stuff in other dimensions too. Wonder how that fits in with the natural/supernatural distinction?

Henry, you are so pedestrian.

There's dimensions and then there's D!I!M!E!N!S!I!O!N!S.

--------------
"You can establish any “rule” you like if you start with the rule and then interpret the evidence accordingly." - George Gaylord Simpson (1902-1984)

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Jan. 29 2007,16:48   

Re "Henry, you are so pedestrian."

Well, foot!  :p

  
GCT



Posts: 1001
Joined: Aug. 2005

(Permalink) Posted: Jan. 29 2007,17:01   

Quote (mitschlag @ Jan. 29 2007,17:23)
 
Quote (avocationist @ Jan. 29 2007,11:21)
     
Quote
You seem to be able to hold contradictory positions simultaneously.  If you don't believe in the supernatural, how can you believe in design of the universe by a god?
I don't consider God to be supernatural. I don't think the situation is one where God is here but not there. I think it is a lot like the idea of two dimensional beings seeing a third dimensional being jump up and down. When he jumps up off the flat plane, he disappears, so he is supernatural and has magical powers. It seems obvious enough that we are also like these two dimensional beings, and when we see only dimly or not at all or by clues and inferences, we consign the phenomenon to a realm called supernatural.

Wow, thanks for clarifying that!

OK, God is not supernatural.  We just think it [he/she] is beyond nature because it [he/she] exists in  another dimension that we can't perceive, because it's beyond nature.  But it's not supernatural.  
Sure, I get it!

No see god is natural because the universe is god and the universe that god created is god and god is a part of everything so when you are measuring gravity you are measuring god and this proves that IDdidit because goddidit is the answer for everything and there's no need to test for it because it's what I believe and what I believe is truth because I'm also part of god and I can see in higher dimensions than all of you sorry people that haven't studied and been touched like I have which enables me to see other dimensions which I already said and why aren't you listening to me because you need to see god like I do so that you'll throw your stupid evolution aside and know the evidence that I just know even though I have no clue what any of the science actually is or means but I don't have to because god is everywhere and there is only one possibility for god because that's the only one I can think of because if god were just an observer or something that wouldn't make sense because I can't conceive of it but that's not an argument from incredulity because my incredulity is good because I'm a skeptic of everything except god because I know god is real and god is everything and you people should just agree with me and what was I talking about again?

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Jan. 29 2007,17:08   

breathe, GCT, breathe... ;)

  
"Rev Dr" Lenny Flank



Posts: 2560
Joined: Feb. 2005

(Permalink) Posted: Jan. 29 2007,18:11   

Quote (avocationist @ Jan. 29 2007,11:21)
Quote
Answers in Genesis says that not only does creationism itself "depend heavily on speciation", but they also say that those who argue that there are NO "new species forming in nature" are "poorly informed".
What they mean by speciation is not the arisal of totally new kinds. They consider one kind to have given rise to dogs and wolves and jackals and foxes, that sort of thing. they do not think that amoebas became fish became reptiles, etc.

No, Avo, what they mean by "speciation" is . . . well . . . "speciation".

Idiot.  No WONDER the ID/creationists think you're just as nutty and pig-ignorant as WE do.  (shrug)

--------------
Editor, Red and Black Publishers
www.RedandBlackPublishers.com

  
avocationist



Posts: 173
Joined: Feb. 2006

(Permalink) Posted: Jan. 29 2007,21:50   

Quote
What gets turned on?
The hypermutation state.
Quote
And the letter above does not describe any experiments showing directed mutations. Spetner asserts that the enzyme could not have evolved "randomly," but makes no note of how selection might impact the evolution of the enzyme.
As I said, the mutations themselves are not directed, but the search for a solution is turned on. The hypermutation state is under control of the cell. Of course selection, after the fact, will reinforce keeping the enzyme which works.
***
Quote
OK, God is not supernatural.  We just think it [he/she] is beyond nature because it [he/she] exists in  another dimension that we can't perceive, because it's beyond nature.  But it's not supernatural.
Other dimensions are not supernatural. They are very much part of your reality. I personally think the subquantum, sub-planck-length may be a divide into another, smaller dimension. That you can't perceive it means little. Can you hear a dog whistle? Can you see xrays?

Lenny, you provide me a link where the answers in genesis people think species spontaneously arise from one another, and they do not mean 'Biblical kinds."

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Jan. 29 2007,22:06   

Quote
Other dimensions are not supernatural. They are very much part of your reality. I personally think the subquantum, sub-planck-length may be a divide into another, smaller dimension.

What you just described is the basis for string theory. As we increase the power of our particle colliders, we will be able to probe such scales. In fact, it's thought that the reason gravity is so weak might derive from the fact that it could operate in such extra dimensions. The new Large Hadron Collider is designed to test some of the basics of string theory in a non-trivial way. See: LHC

 
Quote
That you can't perceive it means little. Can you hear a dog whistle? Can you see xrays?

You might want to save yourself the embarrassment and not post drivel like this.

  
Mike PSS



Posts: 428
Joined: Sep. 2006

(Permalink) Posted: Jan. 29 2007,22:08   

Quote (avocationist @ Jan. 29 2007,01:47)
As regards the nylon eating bacteria, the paper cited was a bit technical (and also I'm having trouble with pdf links and I think it is the reason my computer shut down), but in this article they stated they didn't know how the bacteria aquired their ability. If we don't know that, I don't think we can assess the situation. Then ther's the problem I can't cut and paste from the article because it's in pdf. I was going to ask for clarification of a couple of things.

Yeesh.  It sucks being you.  :O

SORRY!  Sorry.  Shouldn't say things like that.

   
Quote
The bacteria were examined and compared with others of their species and it was discovered that a particular frame shift mutation (which means that a gene got read at a slightly different starting point and slightly different ending point) allowed that bacteria to break down the nylon and obtain energy from that process. But not a LOT of energy. It wasn't a highly competent design because the bacteria weren't extracting a lot of energy from the process, just enough to get by. And it was based on a simply frame shift reading of a gene that had other uses. But with a simple frame shift of a gene that was already there, it could now "eat" nylon. Future mutations, perhaps point mutations inside that gene, could conceivably heighten the energy gain of the nylon decomp process, and allow the bacteria to truly feast and reproduce faster and more plentifully on just nylon, thus leading perhaps in time to an irreducibly complex arrangement between bacteria who live solely on nylon and a man-made fiber produced only by man.

O.K. You got the main points of the paper.  
And you realized that the nylon digestion/conversion function, although "primative" was still functional enough for the organism to survive.
AND you realized that this function COULD be improved with further "evolution" (my word, not yours).

Here's a few more points from the paper that will be important in a second. Nylon eating bug paper.
Quote
We have previously isolated two microorganisms, Flavobacterium sp. strain KI72 (7) and Pseudomonas sp. strain NK87 (6), that grow with the Ahx cyclic dimer (Acd) as the sole source of carbon and nitrogen.
...
In this study, we investigated the possibility of creating a new metabolic activity that would degrade the Ahx oligomer in a strain that is not inherently capable of such degradation.
...
If a new metabolic ability could be directly evolved under laboratory conditions,
...
Pseudomonas aeruginosa PAO was clinically isolated in New Zealand and has been well studied biochemically and genetically as a standard strain of Pseudomonas (5). The wild-type PAO1 did not use Acd (Fig. 1) and the Ahx linear dimer (Ald) (data not shown); therefore, this strain was used to study whether microorganisms can acquire the ability to metabolize nylon oligomers experimentally.

So the experimenters identified that there existed two DIFFERENT bacteria strains that digested nylon.  But they wanted to see if a strain that DIDN"T have the nylon digesting mutation could be developed under laboratory conditions.

So the experimenters took a well identified strain PAO1 and subjected it to conditions where nylon was the only food available.

The results found two NEW bacterial strains (PAO5501 and PAO5502) where PAO5502 was actually derived from an isolated solution of PAO5501.  Tests were done on all three strains (-1, -5501, -5502) and it was confirmed that the two NEW strains were true derivatives of the original PAO1 strain.  The PAO5502 strain was the active strain that actually digested nylon.  THIS IS A KEY POINT.

The PAO5502 strain was compared to one of the originally discovered strains mentioned and found to have similar enzymatic funtions (although the rates of activity differed).

This was ALL the data.  Everything.  In three months this was the reported testing (measuring, cleaning, recording, observing, etc...) that was done.

NOW comes the hard part.  The experimenters have to answer the questions;
How does the data fit into the established theory of evolution?
What mechanisms within the theory are available to explain this data?
Are there any data discrepencies that don't fit the theory?


So the experimenters reported thus;  
Quote
The adaptation of microorganisms to nonphysiological substrates has been extensively studied, and several molecular bases have been proposed: (i) alteration of substrate specificity of an enzyme (amidase/P. aeruginosa) (1), (ii) activation of a cryptic gene by mutation in the promoter region (evolved b-galactosidase/Escherichia coli) (3), and (iii) alteration of regulator specificity (xylS/Pseudomonas sp.) (16). Though a molecular basis for the emergence of nylon oligomer metabolism in PAO5502 is still unknown, it is probable that the basic mechanisms acting during environmental stress are involved in this adaptation.

So the experimenters are making what we call an "educated guess" with "modifiers" and "clarification".  Notice that the suggested mechanism is supported by references to previous work.

Guess what, someone else could run this experiment again and set up a sampling regime to actually test and measure the molecular changes from generation to generation of this bug to see what actual mechanism occurs.  Maybe if I go back to school and pursue a biology doctorate this could be my thesis.

So when you say  
Quote
but in this article they stated they didn't know how the bacteria aquired their ability. If we don't know that, I don't think we can assess the situation.
I think that is a bit disingenuous to the work done and support given to the "educated guess" of the experimenters.

I'll reference this post from another when I take down Spetner's objections.

Mike PSS

  
  459 replies since Jan. 22 2007,04:54 < Next Oldest | Next Newest >  

Pages: (16) < ... 4 5 6 7 8 [9] 10 11 12 13 14 ... >   


Track this topic Email this topic Print this topic

[ Read the Board Rules ] | [Useful Links] | [Evolving Designs]