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Author Topic:   Irreducible Complexity, Information Loss and Barry Hall's experiments
cavediver
Member (Idle past 1260 days)
Posts: 4129
From: UK
Joined: 06-16-2005


Message 121 of 136 (548377)
02-27-2010 7:52 AM
Reply to: Message 120 by Feathertail
02-27-2010 5:55 AM


Re: This discussion
Welcome to EvC. And you are not alone in losing your religious beliefs. I arrived at EvC five years ago as an evangelical Christian, and had been one for 20+ years, and I am now essentially agnostic atheist for most purposes. Many others here are in a similart position so you are among like-minded individuals

Your depiction of evolution seems to contain only part of the story - that of random mutation. Yes, random mutation creates noise - that is the whole point. It is the random number generator of a Monte-Carlo simulation. Evolution is driven by imperfect reproduction operated on by the filter of natural selection. Random mutation creates the myriad of possible changes between generations, and natural selection filters these changes, weeding out those that are sufficiently detrimental to future reproductive success. It really is that simple.

Have a look at this video to see how the process of evolution could begin, operating on nothing but random strings of polymers. It's worth diving in to 2min 40 secs on first viewing...

So, what do you think?


This message is a reply to:
 Message 120 by Feathertail, posted 02-27-2010 5:55 AM Feathertail has responded

Replies to this message:
 Message 122 by Feathertail, posted 02-27-2010 3:37 PM cavediver has not yet responded

  
Feathertail
Junior Member (Idle past 2759 days)
Posts: 2
Joined: 02-27-2010


Message 122 of 136 (548419)
02-27-2010 3:37 PM
Reply to: Message 121 by cavediver
02-27-2010 7:52 AM


Re: "It really is that simple"
Hello!

Yes; I know that's how evolution works. I'm not arguing with that at all (I'm not even really trying to argue!). I agree 100%, and I think you for your kind response.

I think you're missing what seems to me obvious, though (either that or I'm very deluded): The DNA molecule is not just an organic compound, but an informational storage medium. Because the genome can be transcribed onto other media (other molecules; modern computers) with minimal loss in signal.

I don't deny that this loss in signal is how profound biological innovation comes about, or that out of the numerous creatures to whom it proves harmful some of them are "blessed" with the ability to survive and reproduce in their environments. I just see the biological and informational processes separately.

  • The organism adapts to its environment;

  • The genome degrades and wears away.
I've discussed this before with others, and only ever received the same response: Dismissing the informational content of the genome, and concentrating solely on biological innovation as the measure of evolution. RAZD's (second?) post even suggested that biological innovation equals new informational content, when -- as I understand it -- it's really just line noise that happens to produce a beneficial result for the organism which carries it. Unlike the many other mutations that have no effect, or even a detrimental one.

I may be unique in seeing the genome as equivalent to a computer program. If this premise could be falsified (in a way that respects how information and matter differ) I'd like to hear it. Again, thank you for your response, as I'm very glad for the help.

Edited by Feathertail, : No reason given.


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Wounded King
Member (Idle past 1711 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 123 of 136 (548432)
02-27-2010 4:22 PM
Reply to: Message 122 by Feathertail
02-27-2010 3:37 PM


What does Information mean to you?
I may be unique in seeing the genome as equivalent to a computer program.

You aren't but that doesn't necessarily make it a genuine equivalence.

The problem with the 'information content of the genome' argument you are making is that by any actual usable metric of information, i.e. Shannon information, Kolmogorov complexity or Szostak's functional information, it clearly can be shown that mutation can add information to the genome and selection can lead to its preservation and accumulation.

The usual ID counterargument is based on the assumption that some arbitrary genetic sequence they have chosen is the maximal one for 'Genetic Information' and that any change to the sequence must therefore lead to a decrease. The problem with this is there is no evidence for such a platonic informationally maximised genome.

You seem to be just the latest person to be joining the ongoing list of ID supporters we try to pin down on exactly how they measure 'the information content of the genome'.

TTFN,

WK


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lyx2no
Member (Idle past 2333 days)
Posts: 1277
From: A vast, undifferentiated plane.
Joined: 02-28-2008


Message 124 of 136 (548433)
02-27-2010 4:23 PM
Reply to: Message 122 by Feathertail
02-27-2010 3:37 PM


Still That Simple"
I think you're missing what seems to me obvious, though (either that or I'm very deluded): The DNA molecule is not just an organic compound, but an informational storage medium. Because the genome can be transcribed onto other media (other molecules; modern computers) with minimal loss in signal.

All chemical reactions can be "transcribed onto other media": 2NH3(g) + CO2 ⇌ NH2CONH2(aq) + H2O(l) media: screen pixels. Dow Chemical doesn't do all its work with test tubes.

The genome degrades and wears away.

Since it clearly hasn't warn away, what has kept it from wearing away?

Edited by lyx2no, : Typ0.


You are now a million miles away from where you were in space-time when you started reading this sentence.
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RAZD
Member
Posts: 19324
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.2


Message 125 of 136 (548448)
02-27-2010 5:58 PM
Reply to: Message 120 by Feathertail
02-27-2010 5:55 AM


Reasons and Understandings
Hi Feathertail, and welcome to the fray,

Most of this is off topic, but I will answer briefly. If you want to discuss in greater depth then ask and we can move to an appropriate thread.

I came here because I've been questioning my personal religious beliefs. I have already thrown out the specific religion I belong to as being false. I am starting to find evidence that the whole family of religions it belongs to is based on a lie as well.

I understand that religion has no place in a scientific discussion. I just wanted to explain the reason why I came here. And the fact that I'm not married to any particular belief system, and am looking at everything with newly skeptical eyes.

When I was religious, I believed in Intelligent Design. My faith made it an attractive proposition. More than that, though, I could not see the logic behind evolution. Order arising from chaos without an intelligent mind to guide it? Where is that seen in our world? How often, over what duration and on what scale? Is it really the likeliest explanation?

In my personal opinion, the best approach is one of open-minded skepticism - willing to consider new ideas, but unwilling to accept just any concept without some validation for it. Often there are ideas where I cannot judge one way or the other, and so I wait for more information.

Can order rise out of chaos? Mandelbrot diagrams come to mind, as does crystal formations.

Crystals occur because chemicals do not combine in genuinely random ways, but according to their molecules and the ion valences.

I considered the informational content of the genome to be the ultimate evidence. At the macroscopic level, natural selection produces new biological innovation. But at the genetic level, it's just accumulated copying errors, like scratches on a CD. One can't write a new program from scratch by recording static. Right?

Ultimate evidence of what?

Certainly the genome carries a lot of information about ancestry, about the genetic history that resulted in the current genome.

Natural selection does not produce new innovation, it only selects among the variations currently within populations for those that improve the possibilities of survival and reproduction versus the variations that hinder the possibilities of survival and reproduction. The new information is provided by mutations.

If you want to discuss evolution several threads are open, and you may be interested in one of these:
Evolution and Increased Diversity
Evolutionary Theory Explains Diversity
Rapid Evolution in Lizards
Evolving New Information

A lot of very intelligent people believe that it's just a fallacy. After finding out the myths behind my cherished belief systems -- discoveries made this last month, which have shaken me to my core -- I needed to know whether or not this was true. So I decided to read the discussions again. That's how I found this thread. I have to say a lot of it's over my head.

A lot of ID is based on poor logical and unsupported assumptions, but there are other threads to discuss this, such as:
A Designer Consistent with the Physical Evidence
What exactly is ID?
Is ID properly pursued?

I'm glad your search came here, as this forum (not just this thread) can help a person willing to learn, as there are many people that really know what they are talking about.

I'm a bit disappointed, however, to see

Because of that, it probably won't surprise anyone that ... I'm still convinced of intelligent design. I read RAZD's first few posts. He did two things that convinced me of it:
...
The second thing was his attitude. ... I just want to say that if it appears that somebody's ego is invested in defending a particular position, that's going to speak a lot louder to me than any words that they use. It really is.

So says your ego and your continued emotional attachment to ID?

It seems you skipped over the logic of the issue and focused on a perception of ego rather than look at the facts involved.

First, he conflated the physical expression of the genome -- observable biological features -- with the informational content thereof.

I'm not sure what you mean here. You have genetic information, and the observed ability to use, or not use, Lactose. I'm not aware of any other "biological features" involved in this issue.

Are you saying that the ability of an organism to use, or not use, Lactose is a "physical expression of the genome" that is somehow separate from and distinct from the information content of the genome? ie that such ability can occur without any information in the genome? I hope you realize that such a case would mean that "information" then is irrelevant to evolution.

So I think that I've made up my mind about this, but if there's something I'm missing then please let me know.

An open-minded and skeptical evaluation of the evidence. You've jumped backwards to your a priori conclusion that ID is valid based on rejection of argument that IC is invalidated (not ID btw) because of your reaction to an assumed attitude?

I have to say a lot of it's over my head.

So therefore it is wrong?

Enjoy.

... as you are new here, some posting tips:

I notice you used html commands, which is fine, but dBcode is simpler with no loss in information. See Posting Tips for some other formatting tips.

type [qs]quotes are easy[/qs] and it becomes:

quotes are easy

or type [quote]quotes are easy[/quote] and it becomes:

quote:
quotes are easy

also check out (help) links on any formatting questions when in the reply window.

Edited by RAZD, : wrdng


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 120 by Feathertail, posted 02-27-2010 5:55 AM Feathertail has not yet responded

  
RAZD
Member
Posts: 19324
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.2


Message 126 of 136 (548452)
02-27-2010 6:10 PM
Reply to: Message 122 by Feathertail
02-27-2010 3:37 PM


TOPIC please
Hi again Feathertail,

I just see the biological and informational processes separately.
  • The organism adapts to its environment;

  • The genome degrades and wears away.
I've discussed this before with others, and only ever received the same response: Dismissing the informational content of the genome, and concentrating solely on biological innovation as the measure of evolution. RAZD's (second?) post even suggested that biological innovation equals new informational content, when -- as I understand it -- it's really just line noise that happens to produce a beneficial result for the organism which carries it.

Can you focus on the topic (see Message 1) and then talk about how you think things work and what happened in those experiments?

We generally like to keep topics focused so they don't wander all over the place.

If you can't find a topic you want to address directly, you can start one:

Go to Proposed New Topics to post new topics.

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:
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RAZD
Member
Posts: 19324
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.2


Message 127 of 136 (622673)
07-05-2011 10:09 PM


for Chuck77
Message 73 of Dog piling: ... Once it's deemed a PRATT that's it huh? So does Michael Behe or Stephen Meyer now this dissapointing news? Im not sure they recieved the memo, because there still strong advocates of ID.

Dover doesn't mean ID is "false" or "junk Science". A battle was lost not the war

Seriously tho, once a PRATT always a PRATT? Or until someone with a brain can "UN-PRATT" it?

First, it is IC that is falsified, not ID - they are not the same thing.

Second, we can compare this to how theories are used\handled in science:

  • A scientific theory is a tested hypothesis, tested against objective empirical evidence and deductions of what should be seen and not seen if true, and what should be seen and not seen if false:

    if trueif false
    should seeab
    should NOT seecd

    where 'a' or 'd' would be confirming evidence if found, and 'b' and 'c' are invalidating evidence if found,

  • Falsified theories are discarded or modified to account for information that invalidates the original formulation,

  • No amount of validating\conforming evidence can prove that a theory is true,

  • Tested but not invalidated theories are regarded as tentative explanations of the known evidence, and

  • An hypothesis is regarded as having the potential to explain the evidence, but is (or should be) regarded with skepticism and doubt.

So we can say that a PRATT is an invalidated concept, one where there is evidence that falls into the 'b' and 'c' categories. In science this type of concept would be discarded or modified to account for the 'b and 'c' evidence.

... because there still strong advocates of ID.

That they (and others) have not discarded IC demonstrates that they are NOT behaving in a manner appropriate for science.

There may be some tacit recognition that IC is falsified as evidence of design (because it can and has evolved), but I don't know of anyone that has come out and said that it is a failed concept and should be discarded.

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)

Replies to this message:
 Message 131 by Chuck77, posted 07-08-2011 4:49 AM RAZD has acknowledged this reply

  
Chuck77
Inactive Member


Message 128 of 136 (623084)
07-08-2011 2:35 AM
Reply to: Message 1 by RAZD
12-05-2006 9:46 PM


RAZD, the experiments were dona in a lab right? I think IC is using "real" life evidence as being complex? So shouldn't a test to falsify it use "real" life as well?

Isn't this the same as me sticking a rabitt fossil in the pre-cambrian?

Also, I can see where IC can be falisified with there strick guidelines. And if it MAY or MAY not have happened isn't good enough or "we don't know". Isn't tho, there some things about Gravity, or the BB that we don't know 100%?, but still qualifies as a theory?


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Replies to this message:
 Message 129 by Dr Adequate, posted 07-08-2011 3:09 AM Chuck77 has responded

  
Dr Adequate
Member
Posts: 15987
Joined: 07-20-2006
Member Rating: 4.0


Message 129 of 136 (623087)
07-08-2011 3:09 AM
Reply to: Message 128 by Chuck77
07-08-2011 2:35 AM


RAZD, the experiments were dona in a lab right? I think IC is using "real" life evidence as being complex? So shouldn't a test to falsify it use "real" life as well?

Life continues to be real even if you put it in a laboratory.

The question was: can mutation and selection achieve such a thing. The answer is yes. Unless there is some magical property of laboratories that should make us think that the answer is "yes, but only in laboratories", then this observation is relevant to things that happen outside laboratories, and would not have been more relevant by virtue of being made in a pizzeria, a football stadium, or a bicycle repair shop. Why should the location of the observation matter in the slightest?

Isn't this the same as me sticking a rabitt fossil in the pre-cambrian?

No.

Also, I can see where IC can be falisified with there strick guidelines. And if it MAY or MAY not have happened isn't good enough or "we don't know". Isn't tho, there some things about Gravity, or the BB that we don't know 100%?, but still qualifies as a theory?

Your question is hard to follow.


This message is a reply to:
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Replies to this message:
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Chuck77
Inactive Member


Message 130 of 136 (623094)
07-08-2011 4:40 AM
Reply to: Message 129 by Dr Adequate
07-08-2011 3:09 AM


Dr Adequate, im talking about this:

RAZD writes:

Let's review the logic of this argument:

(P1) complex systems exist in biological organisms where there are multiple parts involved in a process, feature or function, and where the removal of any part of the system renders the whole process non-functional.
(P2) if NO such system can evolve then it must be developed by some other process, and then, AND ONLY THEN, the existence of any "IC" system is evidence that "some other process"MUST have occurred.
(C1) Therefore such a system MUST be made, designed, created by some other process.

Leaving aside for now the logical fallacy of the false dichotomy (and the fact that precept (P2) of this argument is basically based on ignorance or denial of how such systems could have formed), we can still show that the concept is falsified if we can show that ONE such "IC" system HAS evolved: if ONE such "IC" system evolves then it invalidates the "then AND ONLY THEN" condition that is necessary in order that "some other process" MUST be involved.

I guess what I mean is, if ONE such "IC" system has NOT evolved is that a case for "IC" ? Is Behe or others putting themselves in a "box" with their definitions?

Also, even with questions concerning the BB that Science is still learning or will always be discovering, it still is a strong theory is what I mean. Maybe the two aren't comparable in anyway. Im sure there not, im just trying to relate it to a current theory(which is RAZD's point, it doesnt stand up to the Scientific method) I guess im confused as to the standard for evidence for 'IC".

Have any systems ever shown possibly not to have evolved? Are there any in question? Have any systems ever been shown to "possibly" be designed? Forgive these questions if they don't make sense. Im in no way an expert on "IC".

Edited by Chuck77, : No reason given.


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Chuck77
Inactive Member


Message 131 of 136 (623095)
07-08-2011 4:49 AM
Reply to: Message 127 by RAZD
07-05-2011 10:09 PM


Re: for Chuck77
RAZD, I understand. I guess I was always under the impression that 'IC" was "evidence" for (ID) or was a "branch" of (ID).

It's confusing. And I admit, I don't understand a lot of it, as you can see. I read some of Stephen Myeres paper on the "higher taxonomic categories" and got lost. Is it that complicated or am I an idiot? Is it just smoke and mirrors IYO?

IYO, is there a better way they could present ID in Philosophy class? Would you change it as opposed to it is now? What im asking is, is there a better way to present it that would make more sense that would give it a little more validity? This is really a question for the other thread, sorry.

Edited by Chuck77, : No reason given.

Edited by Chuck77, : No reason given.


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Dr Adequate
Member
Posts: 15987
Joined: 07-20-2006
Member Rating: 4.0


Message 132 of 136 (623105)
07-08-2011 6:12 AM
Reply to: Message 130 by Chuck77
07-08-2011 4:40 AM


I guess what I mean is, if ONE such "IC" system has NOT evolved is that a case for "IC" ? Is Behe or others putting themselves in a "box" with their definitions?

Well, there argument goes like this:

(1) IC can't evolve.
(2) Some things are IC.
(3) These things can't evolve.

Now their conclusion depends on (1) being a true generalization. If IC can evolve, then their logic is broken.

This is not to say that they couldn't come up with some argument why such-and-such a thing can't evolve, but it can't be founded solely on the observation that the thing is IC.

Compare:

(1) Mammals don't lay eggs.
(2) This is an egg.
(3) This was not laid by a mammal.

Since the discovery of the platypus and the echidna, point (1) is known to be false, so (3) doesn't follow from (2). (3) could still be true (the egg could have been laid by a chicken) but we can no longer prove (3) by an appeal to (1) because (1) is now known to be false.


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Wounded King
Member (Idle past 1711 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 133 of 136 (623106)
07-08-2011 6:32 AM
Reply to: Message 131 by Chuck77
07-08-2011 4:49 AM


What does IC mean?
I know this wasn't addressed to me, but I've never let that stop me before.

Irreducible Complexity is an attribute of a system. The existence of such systems is put forward by advocates of Intelligent Design as evidence for the insufficiency of current evolutionary theory.

The problem is that there are several different definitions of irreducible complexity kicking around the ID debate, even from the same ID proponent.

Behe, 1996 writes:

By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.

This seems a fairly straightforward definition and if we take a 'part' to be a specific gene or protein we can probably find examples of such systems in living organisms.

Despite this most of the examples usually given (the eye, the bacterial flagellum and the blood clotting cascade) don't really stand up as IC by this definition and ID proponents often argue that such systems have an 'IC core' of proteins/parts which is what remains when all the non-essential parts have been removed form the putatively IC system.

However this doesn't really represent a problem for standard evolutionary models, there is no reason why a system can't evolve which relies on such a set of interconnected 'parts', there are several models based on exaptation and scaffolding which can account for them.

In response to this Behe 'refined' his definition ...

Behe, 2002 writes:

An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.

Clearly this is a completely different argument and requires a much greater depth of historical knowledge of the evolution of the system to be able to actually define any system as IC. Indeed it is hard to see how any ID proponent could confidently claim that a system was IC under this definition assuming it also has to satisfy the original definition.

If it doesn't have to satisfy the original definition as well then there are plenty of experimental examples of apparently unselected steps being required for the development of a functional system/trait, including any 2 step mutation in the classical antibiotic/phage resistance experiments using replicate plates. Indeed there is considerable weight to the argument that deleterious mutations can provide important intermediates to the evolution of a more beneficial state.

is there a better way they could present ID OR IC?

IC would be better presented if it had a clear and concise definition and some examples which actually matched the necessary criteria or at least an understandable way to discern if a system matches the criteria. At the moment IC is one of those things like increases in genetic information, IDists can't really define it but they will know it when they see it and they never see it in any of the examples they are provided.

TTFN,

WK


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RAZD
Member
Posts: 19324
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.2


Message 136 of 136 (656324)
03-17-2012 4:43 PM
Reply to: Message 1 by RAZD
12-05-2006 9:46 PM


regarding the proposed Examples of new information thread
dan4reason Message 9 on his proposed Examples of new information thread:

My issue with the example is that I want to make sure that adaptation actually came about by natural selection and mutations, not something else.

I not necessarily looking for mutations that make new proteins, I am looking for mutations that make proteins with new functions.

I can leave out the information part, and just ask for the above.

See below:

quote:

2. Information Loss


Another argument common to creationism and IDology is that mutations only result in the loss of "information", and that without a mechanism to gain "information" new systems, functions or features cannot evolve.

Let's review the logic of this argument:

  • (P1) mutations cannot cause an increase in "information."
  • (P2) an increase in "information" is necessary for new mechanisms or functions to evolve.
  • (C1) Therefore new mechanisms or functions cannot evolve.

Leaving aside the fact that "information" is not defined in any way to measure whether or not there is an increase or a decrease in any evolved changes in species over time, we can still show that the concept is falsified if we can show that ONE such mechanism or function has evolved that would require such an increase. In other words, if we can show that either (P1) or (P2) must be invalid then we have shown that the conclusion is invalid.

Now let's look at Barry Hall's experiments again in light of this concept:

An existing "irreducibly complex" system is intentionally disrupted and ceases to function.

According to the equation of new information with the evolution of new functions or mechanisms by precept (2), the intentional loss of a function or mechanism must then also involve the loss of AT LEAST SOME information for that function or mechanism:

quote:
In 1982, Barry Hall of the University of Rochester began a series of experiments in which he deleted the bacterial gene for the enzyme beta-galactosidase. The loss of this gene makes it impossible for the bacteria to metabolize the sugar lactose.

Thus the deletion of the beta-galactosidase gene MUST have involved the loss of AT LEAST SOME information for the function or mechanism of that gene.

Next what we see is that a DIFFERENT "IC" system evolves to replace the original -- the original "IC" system is not repaired or recovered, but a new and different "IC" system evolved.

Ergo new "information" MUST have evolved that was not in the original organism, the "information" for that organism MUST have been increased. Again, this is the principle of falsification used by science - it invalidates either precept (P1) or precept (P2), and therefore invalidates ALL conclusions based on their combination.

We started with a system with some quantity of "information" that -- according to precept (2) -- must have been lost to render it dysfunctional, and then a replacement system evolved.

Either "information" was added (invalidates precept (P1)) OR added "information" was not necessary for the evolution of a feature, function or system (invalidates precept (P2)).

Thus either precept (P1) OR precept (P2) is invalidated, falsified, refuted and ALL conclusions based on their combination are invalidate. Q.E.D.


Information was either added or the concept of information is irrelevant to what can or cannot evolve.

The proteins that were available once the beta-galactosidase gene was deleted were modified to permit the new galactose metabolism - it was not there before - and the rapid growth of the bacteria with this modification show selection.

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)

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