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Author Topic:   Irreducible Complexity, Information Loss and Barry Hall's experiments
RAZD
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Posts: 15475
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.4


Message 76 of 136 (515136)
07-15-2009 5:58 PM
Reply to: Message 65 by traderdrew
07-15-2009 10:05 AM


adaptation? start another thread.
Hi traderdrew,

Adaptation is not IC. I will attempt to explain this to someone who is interested in what I am thinking. I have the impression that you are not.

Of course adaptation does not (necessarily) result in IC systems, nobody said it doesn't.

The issue, however, is that an IC system has evolved. Mutations occurred, natural selection occurred, and the result was an IC system, a system where the removal of one component rendered the other components incapable of metabolizing lactose.

If you want to discuss adaptation, please start another thread.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 65 by traderdrew, posted 07-15-2009 10:05 AM traderdrew has not yet responded

Replies to this message:
 Message 78 by DevilsAdvocate, posted 07-15-2009 6:44 PM RAZD has responded

  
DevilsAdvocate
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Posts: 1535
Joined: 06-05-2008
Member Rating: 3.3


Message 77 of 136 (515139)
07-15-2009 6:42 PM
Reply to: Message 70 by traderdrew
07-15-2009 12:31 PM


Re: Sticking to the topic/s, and avoiding deceptions.
Trader writes:

I don't have to admit it. I would freely declare it. Haven't you ever read any of Michael Behe's books?

Actually I have Darwin's Black Box sitting upstairs on my bookshelf in my home office with the rest of the Christian apologetic books I have accumulated over the years. BTW, I wasn't asking Behe, I was asking you; for reasons of clarity of your position on this issue.

Trader writes:

Myself writes:

So do you agree that natural selection occurs and weeds out the defective 'structures'?

I believe it potentially can. I wouldn't say that natural selection would be the only process.

True there other factors such as genetic drift and gene flow (migration) but natural selection is more directive in its nature in weeding out genetic variation that may be harmful to that population of organisms.

Trader writes:

Myself writes:

If so why could cumulative genetic mutation guided by natural selection not produce a 'novel structure'?

If I can briefly explain it. It is because in the random world of neo-Darwinism, a single mutation would have to be preserved by natural selection. So what are the chances of two or more ("complimentary or coherent") mutations that can occur at pinpoint areas of the informational areas of DNA or proteins of occurring?

That is a simplistic way of looking at it.

I assume by "informational areas of DNA" you are talking about areas of the genome that are used in protein replication aka coding vs non-coding ("junk") DNA. Other portions of the genome may serve other purposes that can be beneficial to an organism i.e. gene regulatory functions, etc.

Why does it have to occur first in informational areas of DNA? Could not these mutations occur anywhere in the genome and later be incorporated into the coding region of the genome and then be able to replicate new proteins?

Trader writes:

The odds start to greatly decrease when you have to simultaneous mutations.

You are throwing a lot of bogus criteria for the ability of mutations in the genome being able to create new proteins that really do not exist. Why do all the mutations have to occur simultaneous? Again buildup of mutations guided by natural selection and other evolutionary mechanisms (genetic drift) can result in a small step by step advancement of simple structures into more complex structures. Simultaneous mutations is not necessary. If so please explain why? Give me an real-life example.

And what about three or more? I wouldn't say that it is impossible. The mutations have to be integrated and provide specific functions.

No, they don't have to provide specific functions much less beneficial ones all at one time. Some of these proteins can be co-opted from other simpler structures. That is why Behe's IC argument fell completely apart at the Dover Trial. Some genetic mutations may result completely different structures/functions that later may be combined to form totally different structures/functions. This was exemplified by Dr. Ken Miller's example that many of the proteins that constitute the flagellum that serve a different purpose in a protein pump.

So if the odds start to become astoundingly great, how can neo-Darwinism explain a severely IC system?

Because #1 they are not necessarily IC systems but rather are systems in which we still have gaps in our knowledge of exactly how they evolved and #2 the odds you present are contrived and unfounded.


For me, it is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring.
Dr. Carl Sagan
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 Message 70 by traderdrew, posted 07-15-2009 12:31 PM traderdrew has not yet responded

  
DevilsAdvocate
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Posts: 1535
Joined: 06-05-2008
Member Rating: 3.3


Message 78 of 136 (515140)
07-15-2009 6:44 PM
Reply to: Message 76 by RAZD
07-15-2009 5:58 PM


Re: adaptation? start another thread.
RAZD writes:

The issue, however, is that an IC system has evolved.

If an IC system evolved from simpler structures can you really call it IC? I think not.


For me, it is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring.
Dr. Carl Sagan
This message is a reply to:
 Message 76 by RAZD, posted 07-15-2009 5:58 PM RAZD has responded

Replies to this message:
 Message 80 by RAZD, posted 07-15-2009 7:21 PM DevilsAdvocate has responded

  
RAZD
Member
Posts: 15475
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.4


Message 79 of 136 (515142)
07-15-2009 6:59 PM
Reply to: Message 67 by traderdrew
07-15-2009 11:35 AM


Re: Sticking to the topic/s, and avoiding deceptions.
Hi again traderdrew, we've all had trouble with disappearing posts.

Message 66

Darn it. I had this nice long response and it got wiped out just as I finished it. Login was required.

I recommend using wordpad or some other text program on your computer for composing long posts, then should anything happen to your internet connection, or accidental hitting of buttons, you still have the post. I usually transfer to wordpad when a post gets long.

Does anyone else see what is wrong with this?

Apparently not: please elucidate. Is that or is that not what happened?

Then tell me why this is the case:

The sole function of the IPTG is to induce synthesis of the lactose permease, and thus to deliver lactose to the inside of the cell. Neither the constitutive nor the inducible evolved strains grew on lactose in the absence of IPTG. (Hall 1982b)

It seems you have trouble with the concept of an environment and the effect of the environment on natural selection. ITPG does not force the bacteria to mutate, nor does it force the bacteria to adapt (again) to the use of lactose. What it does is provide an opportunity to use lactose permease. Every environment provides an opportunity for evolution, some favor some organisms, while others favor different organisms. This is why speciation occurs.

In this instance we have an original bacteria that could not survive on the lactose alone, but it can utilize lactose, the ITPG allows this original bacteria to survive and reproduce. As Phage0070 said in Message 27:

I might not be getting the idea here, but doesn't this say that neither of the strains were capable of growing on lactose in the absence of IPTG? That is to say, both the original and the evolved strains lacked this capability?

... The bacteria developed the ability to metabolize lactose, a seemingly irreducibly complex system. They did not develop the ability to transfer the lactose through their cell membrane, a different matter altogether. ...

They just used the lactose permease that was readily available due to the environment they were in, however neither the original strain, nor the evolved strain could do so without the genes that are the issue of this discussion.

http://mbe.oxfordjournals.org/cgi/reprint/12/3/514.pdf

quote:
The wild-type enzyme, whose function in nature is unknown, is a very feeble β-galactosidase whose activity toward lactose (galactosyl-β- 1,4-D-glucose) and its analog lactulose (galactosyl-β- 1,4-D-fructose) is so ineffective that, in ΔlacZ strains, those sugars cannot be utilized for growth even when the operon is expressed constitutively (ebgR-) at a level such that EBG enzyme constitutes 5% of the cellís soluble protein (Hall 1982).

In other words, lactose provides a marginal resource for the organisms. Thus we have bacteria grown on a culture with two marginal resources - lactose and IPTG.

http://en.wikipedia.org/wiki/Isopropyl_%CE%B2-D-1-thiogalactopyranoside

quote:
Isopropyl β-D-1-thiogalactopyranoside, abbreviated IPTG, is a molecular biology reagent.

This compound is used as a molecular mimic of allolactose, a lactose metabolite that triggers transcription of the lac operon. Unlike allolactose, the sulfur (S) atom creates a chemical bond which is non-hydrolyzable by the cell, preventing the cell from "eating up" or degrading the inductant; therefore the IPTG concentration remains constant.


Oh my gosh,,,
now I am being accused of something I never stated. I never stated that I thought that this experiment was the result of "unguided" multiple coherent mutations.

Curiously, I quoted you directly. Here it is again, as quoted:

Re: Irreducibly Complexity and a True Acid Test (Message 42)

At least it would have not been done without simultaneous multiple coherent mutations and that would arguably be entering into the realm of metaphysical miracles.

Is that not what you said? Of course the one option you left out was the one that is substantiated by the facts: that an IC system evolved.

I intend to show you that some IC systems can be mutated but not evolve into novel structure.

and Message 42
Adaptation is not IC. I will attempt to explain this to someone who is interested in what I am thinking.

So mutations do occur and they lead to adaptation of the organism to the environment. Curiously, that is evolution. Of course, not every mutation is selected for increased survival and reproduction, as many are neutral in their current environment, and even potentially lethal mutations can piggy-back on heavily selected traits, however not every mutation results in a novel structure, so what you have is a straw man argument.

And, interestingly, and IC system was still seen\observed\documented to evolve in a petri dish.

You spend a lot of time yapping, but little time addressing the issues of this thread: the evolution of an IC system and the evolution of increased "information" in the process.

Perhaps you need to start a thread of your own.

Enjoy.

Edited by RAZD, : mid


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 67 by traderdrew, posted 07-15-2009 11:35 AM traderdrew has responded

Replies to this message:
 Message 92 by traderdrew, posted 07-17-2009 12:28 PM RAZD has responded

  
RAZD
Member
Posts: 15475
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.4


Message 80 of 136 (515143)
07-15-2009 7:21 PM
Reply to: Message 78 by DevilsAdvocate
07-15-2009 6:44 PM


Re: adaptation? start another thread.
Hi Dr Adequate,

If an IC system evolved from simpler structures can you really call it IC? I think not.

There seems to be a popular misconception that if a system can be explained how it evolved that it cannot be an IC system. This is false, an IC system is defined as one that has several interrelated parts necessary to function in a specific manner, where the removal of any one part renders the whole system inoperable.

So to answer your question, it does not matter how simple the basal structures are, what matters is the final configuration into an interrelated complex of parts that all are needed for a specific function to occur.

A mortar-less stone arch is composed of simple parts, but they all have to act together, you can't build the arch a stone at a time as it will fall down.


Click to enlarge

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 78 by DevilsAdvocate, posted 07-15-2009 6:44 PM DevilsAdvocate has responded

Replies to this message:
 Message 82 by DevilsAdvocate, posted 07-15-2009 8:54 PM RAZD has acknowledged this reply

  
RAZD
Member
Posts: 15475
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.4


Message 81 of 136 (515144)
07-15-2009 7:26 PM
Reply to: Message 72 by Perdition
07-15-2009 12:56 PM


Neutral mutations as a platform for later novel features
Hi Perdition, this is a little to the side of the topic, but it does address how IC systems can evolve.

All you need is a mutation to occur at a spor that doesn't do any harm to the organism. Then that mutation will be passed down in that family line. At some point, perhpas hundreds of years later, you have another mutation that builds on the previous one. It may help, it may do nothing, but as long as it doesn't hurt the survival of an organism, again, it gets preserved. How would it be difficult for mutations to build up? Especially if the area they're building up in is an unused copy of another gene, and if one of those mutations reactivates the copy, and the new process is better than the original, how would that not make a novel feature?

Again, this very thing has been observed, where a later mutation enabled a bacteria (e.coli again I believe, a common lab organism) evolved an ability to utilize a new substrate, however only the ones descended from a specific generation of one branch evolved the ability, and this was tracked back to a mutation in that generation population that was the foundation for the new feature.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 72 by Perdition, posted 07-15-2009 12:56 PM Perdition has responded

Replies to this message:
 Message 84 by Perdition, posted 07-16-2009 12:33 PM RAZD has acknowledged this reply

  
DevilsAdvocate
Member
Posts: 1535
Joined: 06-05-2008
Member Rating: 3.3


Message 82 of 136 (515146)
07-15-2009 8:54 PM
Reply to: Message 80 by RAZD
07-15-2009 7:21 PM


Re: adaptation? start another thread.
RAZD writes:

There seems to be a popular misconception that if a system can be explained how it evolved that it cannot be an IC system. This is false, an IC system is defined as one that has several interrelated parts necessary to function in a specific manner, where the removal of any one part renders the whole system inoperable.

Sorry I guess I misunderstood how your were defining IC. Makes sense now. Thanks.

RAZD writes:

A mortar-less stone arch is composed of simple parts, but they all have to act together, you can't build the arch a stone at a time as it will fall down.

I am not sure if this is what you intended by this is a great analogy for biological evolution.

Just as a natural arch made out of rock is caused by the gradual wearing away of underlying material by natural causes (i.e. the erosive power of flowing water over millions of years) so to is the evolution of seemingly irreducibly complex biological structures caused by the gradual build-up of mutational changes to the genome and shaped by natural selection.


For me, it is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring.
Dr. Carl Sagan
This message is a reply to:
 Message 80 by RAZD, posted 07-15-2009 7:21 PM RAZD has acknowledged this reply

  
Peepul
Member (Idle past 1302 days)
Posts: 206
Joined: 03-13-2009


Message 83 of 136 (515226)
07-16-2009 10:30 AM
Reply to: Message 75 by RAZD
07-15-2009 5:55 PM


Re: Logic and reality please.
Thanks for the clarification, RAZD, appreciated.
This message is a reply to:
 Message 75 by RAZD, posted 07-15-2009 5:55 PM RAZD has acknowledged this reply

    
Perdition
Member (Idle past 155 days)
Posts: 1592
From: Wisconsin
Joined: 05-15-2003


Message 84 of 136 (515234)
07-16-2009 12:33 PM
Reply to: Message 81 by RAZD
07-15-2009 7:26 PM


Re: Neutral mutations as a platform for later novel features
Again, this very thing has been observed, where a later mutation enabled a bacteria (e.coli again I believe, a common lab organism) evolved an ability to utilize a new substrate, however only the ones descended from a specific generation of one branch evolved the ability, and this was tracked back to a mutation in that generation population that was the foundation for the new feature.

I know. I was responding to traderdrew and explaining why his little rant on mutations was wrong.


This message is a reply to:
 Message 81 by RAZD, posted 07-15-2009 7:26 PM RAZD has acknowledged this reply

    
Admin
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Message 85 of 136 (515312)
07-17-2009 6:49 AM
Reply to: Message 66 by traderdrew
07-15-2009 10:56 AM


Re: IC or not
traderdrew writes:

Darn it. I had this nice long response and it got wiped out just as I finished it. Login was required.

I'm curious how this happened. If one isn't logged in, then clicking on the "reply" button takes you to the login page. You cannot get to the "reply" page without first being logged in. The only way I can imagine this happening is if you went to the "reply" page in one browser window, then before submitting the reply clicked on "Logout" in another browser window. Can you recall the specifics of what happened?


--Percy
EvC Forum Director

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Replies to this message:
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traderdrew
Member (Idle past 1438 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 86 of 136 (515330)
07-17-2009 10:30 AM
Reply to: Message 85 by Admin
07-17-2009 6:49 AM


Re: IC or not
I really thought I logged into the system. I think I spent about 25 minutes typing out a response to NoseyNed. I hit the submit reply tab and then the page blanked out. I guess it was an anomaly due the occasional chaos within or between computer systems.

But it is all good. I am writing a larger and more general article on this subject and hopefully it will answer some other questions from other forum participants as well.


This message is a reply to:
 Message 85 by Admin, posted 07-17-2009 6:49 AM Admin has not yet responded

    
traderdrew
Member (Idle past 1438 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 87 of 136 (515331)
07-17-2009 10:50 AM
Reply to: Message 72 by Perdition
07-15-2009 12:56 PM


Re: Sticking to the topic/s, and avoiding deceptions.
All you need is a mutation to occur at a spor that doesn't do any harm to the organism. Then that mutation will be passed down in that family line. At some point, perhpas hundreds of years later, you have another mutation that builds on the previous one. It may help, it may do nothing, but as long as it doesn't hurt the survival of an organism, again, it gets preserved.

The problem I have with this senario are two different reasons. In a post that I am writing for this thread shows that the preservation of such "nonessential" mutations that create would need energy to maintain. Due to the complexities of DNA and the cell, a lot of things can go wrong. It would seem to me that if your explanation was plausible, then bacteria would be carrying about a lot of luggage around with them. Do you really think that these bacteria are so poorly organized?

Why haven't the staunch supporters of Darwin such as Kenneth Miller and Jerry Coyne proposed such a theory in their books??? I don't think they have the luxury of giving casual step by step explanations for irreducibly complex structures like we do here on this forum. They have all of science reading what they say. Instead we see this:

There is no doubt that many biochemical systems are dauntingly complex. But biologists are beginning to provide plausible scenarios for how "irreducibly complex" biochemical pathways might have evolved. - Jerry Coyne

Edited by traderdrew, : No reason given.


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 Message 72 by Perdition, posted 07-15-2009 12:56 PM Perdition has responded

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Perdition
Member (Idle past 155 days)
Posts: 1592
From: Wisconsin
Joined: 05-15-2003


Message 88 of 136 (515338)
07-17-2009 11:17 AM
Reply to: Message 87 by traderdrew
07-17-2009 10:50 AM


Re: Sticking to the topic/s, and avoiding deceptions.
Why haven't the staunch supporters of Darwin such as Kenneth Miller and Jerry Coyne proposed such a theory in their books???

If you don't mind, may I ask where you learned biology. The process I told you is pretty much exactly what I was taught in Biology class in high school.

preservation of such "nonessential" mutations that create would need energy to maintain. Due to the complexities of DNA and the cell, a lot of things can go wrong.

Preservation doesn't require as much energy as "pruning" would. If something changes in an unused piece of DNA, why would our cells waste energy trying to ferret out those minor changes and remove them? Even if they did, what makes you think they'd be perfect in their execution.

As it turns out, not only can a lot of things go wrong, but a lot of things do go wrong. That's why we have miscarriages, cancer, genetic diseases, and general cell death.

Let's see you read through billions of lines of letters and find the one change that occured, like those pictures in kids' magazines where you have to circle the things that change from one to the other. If you can't reliably do it every time, what makes you think an automated process could do better?


This message is a reply to:
 Message 87 by traderdrew, posted 07-17-2009 10:50 AM traderdrew has responded

Replies to this message:
 Message 89 by traderdrew, posted 07-17-2009 11:54 AM Perdition has responded

    
traderdrew
Member (Idle past 1438 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 89 of 136 (515348)
07-17-2009 11:54 AM
Reply to: Message 88 by Perdition
07-17-2009 11:17 AM


Re: Sticking to the topic/s, and avoiding deceptions.
If you don't mind, may I ask where you learned biology. The process I told you is pretty much exactly what I was taught in Biology class in high school.

Where I learned biology is irrelevant to the issue at hand. If you are so confident in what you are claiming, then why not just give us an article that totally supports your explanation?

Even if they did, what makes you think they'd be perfect in their execution.

I never said that the world is perfect. I am starting to get the impression that you attempting to equivocate my points.

As it turns out, not only can a lot of things go wrong, but a lot of things do go wrong. That's why we have miscarriages, cancer, genetic diseases, and general cell death.

Obviously we are more sophisticated than E. coli. Has any bacteria ever developed cancer?

Edited by traderdrew, : No reason given.


This message is a reply to:
 Message 88 by Perdition, posted 07-17-2009 11:17 AM Perdition has responded

Replies to this message:
 Message 91 by Rahvin, posted 07-17-2009 12:23 PM traderdrew has responded
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traderdrew
Member (Idle past 1438 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 90 of 136 (515353)
07-17-2009 12:15 PM
Reply to: Message 57 by DevilsAdvocate
07-14-2009 9:06 PM


Re: Irreducibly Complexity and a True Acid Test
Here is someone else who is attempting to play a game of deception by equivocating the information in my post.

If you look at the post that this post is responding to, you will see that I was mostly kidding. Aren't we all wasting time with attempting to equivocate each others points?

If you want to, you can take the historical account of junk DNA from the Devil's Advocate, an interesting avatar by the way, or you can take it from the Natural Standard below:

http://www.naturalstandard.com/index-abstract.asp?create-abstract=/monographs/genomics/genomic-junkdna.asp

Researchers originally called these sections of DNA "junk DNA" because they thought they served no functional purpose.

Better Yet

http://www.sciencedaily.com/releases/2009/05/090528203730.htm

Scientists used to believe that most of the DNA outside of genes, the so-called non-coding DNA, is useless trash that has sneaked into our genome and refuses to leave. One commonly known example of such 'junk DNA' are the so-called tandem repeats, short stretches of DNA that are repeated head-to-tail. "At first sight, it may seem unlikely that this stutter-DNA has any biological function," says Marcelo Vinces, one of the lead authors on the paper. "On the other hand, it seems hard to believe that nature would foster such a wasteful system."

Why would they think it is "junk"? Because the theory that says life emerged by unintelligent causes says that it there should be evidence that supports it. Hence, junk DNA is evidence for neo-Darwinism.

Edited by traderdrew, : No reason given.

Edited by traderdrew, : No reason given.


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