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Author Topic:   Examples of new information
dan4reason
Junior Member (Idle past 2222 days)
Posts: 25
Joined: 01-03-2010


Message 1 of 31 (656312)
03-16-2012 12:30 PM


I would like some examples of how the process of natural selection and mutations created new information. This must not occur by playing around with gene switching.

Preferably this should occur by mutating a protein to gain a new function.

Examples must be specific in exactly what gene was mutated, what the gene does, and what it did.


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Message 2 of 31 (656313)
03-16-2012 2:17 PM
Reply to: Message 1 by dan4reason
03-16-2012 12:30 PM


If you describe the math you'd like to use for quantifying information I'll go ahead and promote this thread.

--Percy
EvC Forum Director

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dan4reason
Junior Member (Idle past 2222 days)
Posts: 25
Joined: 01-03-2010


Message 3 of 31 (656314)
03-16-2012 7:30 PM
Reply to: Message 2 by Admin
03-16-2012 2:17 PM


I am not too stingy with the definition of information.

I am specifically looking for a novel adaptation that performs a new task through natural selection and mutations. These mutations could for example change the DNA coding for an enzyme, in order for the enzyme to perform another useful function.

One can also show mutational adaptations conforming to information theory.
This link shows some mathematics behind information theory.
http://www.cs.cmu.edu/~dst/Tutorials/Info-Theory/


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Message 4 of 31 (656315)
03-16-2012 8:46 PM
Reply to: Message 3 by dan4reason
03-16-2012 7:30 PM


dan4reason writes:

This link shows some mathematics behind information theory.
http://www.cs.cmu.edu/~dst/Tutorials/Info-Theory/

Hey, my alma mater! How would you go about measuring the amount of information in a gene? For example, let's say the gene was this:

CAGTAGCCTAAC

How would you calculate its information content?

Edited by Admin, : Remove sig.


--Percy
EvC Forum Director

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dan4reason
Junior Member (Idle past 2222 days)
Posts: 25
Joined: 01-03-2010


Message 5 of 31 (656316)
03-16-2012 9:19 PM
Reply to: Message 4 by Admin
03-16-2012 8:46 PM


I have no clue, which is why I gave the first definition: Performing some new function not involved with gene switching. That should be a lot easier.
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Message 6 of 31 (656317)
03-16-2012 9:47 PM
Reply to: Message 5 by dan4reason
03-16-2012 9:19 PM


One common answer to your question about a new function is nylon eating bacteria, but the usual response is that the behavior was caused by a deletion rather than an addition. If your criteria is merely new function, then your question has already been answered. But if your criteria is new function by adding information to the genome then we need to know how you're measuring information. If by the number of nucleotides, a rather simplistic measure, then nylon eating bacteria do not qualify. But if by the number of alleles for the gene in the bacterial population, then nylon eating bacteria do qualify.

Your understandable reaction is probably, "Sheesh, I was just trying to ask a simple question." But as you must have guessed by now, the question has been raised here before, so I was hoping for a little clarification.

Edited by Admin, : Grammar.


--Percy
EvC Forum Director

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dan4reason
Junior Member (Idle past 2222 days)
Posts: 25
Joined: 01-03-2010


Message 7 of 31 (656318)
03-16-2012 10:51 PM
Reply to: Message 5 by dan4reason
03-16-2012 9:19 PM


How do you know that this came about by mutation instead of gene switching or from plasmids?
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Message 8 of 31 (656319)
03-17-2012 7:46 AM
Reply to: Message 7 by dan4reason
03-16-2012 10:51 PM


Hi Dan4Reason,

We're just going through the thread proposal process, not having a pre-discussion about your topic. Nylon-eating bacteria was just the example I chose to explain why the approach used to measure information is important. If we don't agree on the method for measuring genetic information then we'll have no criteria for judging success or failure in answering your question. If you can describe how you're measuring information I can promote your thread.

Or we can take the other approach you suggested of providing examples of mutations that produce new proteins.


--Percy
EvC Forum Director

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dan4reason
Junior Member (Idle past 2222 days)
Posts: 25
Joined: 01-03-2010


Message 9 of 31 (656320)
03-17-2012 4:20 PM
Reply to: Message 8 by Admin
03-17-2012 7:46 AM


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.


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Admin
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Message 10 of 31 (656322)
03-17-2012 4:34 PM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Examples of new information thread in the Proposed New Topics forum.
    
RAZD
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(1)
Message 11 of 31 (656325)
03-17-2012 4:47 PM
Reply to: Message 9 by dan4reason
03-17-2012 4:20 PM


Barry Hall experiment
Hi dan4reason

from Irreducible Complexity, Information Loss and Barry Hall's experiments, Message 136:

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 invalidated. 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.


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Dr Adequate
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(1)
Message 12 of 31 (656328)
03-17-2012 5:13 PM
Reply to: Message 9 by dan4reason
03-17-2012 4:20 PM


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.

In many experiments, we can check this very easily. We can see that gene switching is not a possibility by looking at the actual DNA sequence and finding the mutation; and we can check that it is not a result of lateral gene transfer (of plasmids or anything else) by using a clonal line --- that is, you do the experiment starting with just one bacterium, yeast cell, or whatever.

In the case of the nylon-eating bacteria which Percy mentioned, the first condition holds but not the second, since this development occurred in nature and not in the laboratory. (However, one might in lieu of it consider the fact that prior to the invention of nylon, a nylon-eating bacterium would have starved to death, so common sense suggests that the development of the gene must involve a novel mutation.)

However, there are plenty of experiments where both conditions apply --- we can identify the mutation, and we can be certain that the founder of the population didn't have it. One example would be Lenski's experiment, which you may have read about.

Afterthought added by edit: another way we can rule out gene switching is if we can watch the process of change and know that it didn't happen immediately. If it was a pre-programmed response to environmental factors, then it would take place on introduction to the organism into the new environment, whereas if the change is a result of genuine evolution this will hardly ever be the case. So it is not always necessary to look at the gene directly.

For example, when we watch the evolution of multicellularity in chlorella, not only does it not happen instantly, but we can observe several steps in the process as the first crude mutation is progressively refined to the optimal form. If this change was pre-programmed, then we'd see every organism in the experiment switch to the optimal form within the first generation, would we not? If it looks like evolution and quacks like evolution, it's probably evolution.

Edited by Dr Adequate, : No reason given.


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Coragyps
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Posts: 5377
From: Snyder, Texas, USA
Joined: 11-12-2002


(1)
Message 13 of 31 (656333)
03-17-2012 6:24 PM
Reply to: Message 1 by dan4reason
03-16-2012 12:30 PM


There's a 2001 paper by Ritz, et al., that describes a precisely known mutation in a strain of E. coli that "created" an enzyme that breaks disulfide bonds from a previous enzyme that reduced peroxides. The change in activity was from adding a single amino acid into the peroxiredoxin enzyme - Coragyps's guess is that the change made the active site of the enzyme large enough to accomodate a sulfur-sulfur bond rather than its original oxygen-oxygen.

Abstract:

Pathways for the reduction of protein disulfide bonds are found in all organisms and are required for the reductive recycling of certain enzymes including the essential protein ribonucleotide reductase. An Escherichia coli strain that lacks both thioredoxin reductase and glutathione reductase grows extremely poorly. Here, we show that a mutation occurring at high frequencies in the gene ahpC, encoding a peroxiredoxin, restores normal growth to this strain. This mutation is the result of a reversible expansion of a triplet nucleotide repeat sequence, leading to the addition of one amino acid that converts the AhpC protein from a peroxidase to a disulfide reductase. The ready mutational interconversion between the two activities could provide an evolutionary advantage to E. coli.

Science 5 October 2001:
Vol. 294 no. 5540 pp. 158-160
DOI: 10.1126/science.1063143

It should be publically available if you want to read the whole thing - www.sciencemag.org


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Trixie
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Posts: 1011
From: Edinburgh
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(1)
Message 14 of 31 (656334)
03-17-2012 6:31 PM
Reply to: Message 13 by Coragyps
03-17-2012 6:24 PM


HIV-1 Vpu
There's also the HIV-1 Vpu which can now act as an ion channel. This link will get you started on the Vpu story

http://pandasthumb.org/...ives/2007/11/an-open-letter-6.html


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Dr Adequate
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Posts: 16086
Joined: 07-20-2006
Member Rating: 10.0


(1)
Message 15 of 31 (656338)
03-17-2012 6:51 PM
Reply to: Message 14 by Trixie
03-17-2012 6:31 PM


Re: HIV-1 Vpu
I love the last comment on that page. You could show it to kids and explain that this is why they shouldn't get into ID --- "this is your brain, and this is your brain on creationism ..."
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