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Author Topic:   Gene duplication = information!
AnswersInGenitals
Member (Idle past 151 days)
Posts: 673
Joined: 07-20-2006


Message 1 of 11 (546782)
02-13-2010 8:03 PM


There have now been dozens of threads and hundreds of posts on this forum that try to address the issue of biological information and in particular, the information content and development of new information in the genome. These threads and posts always seem to get hung up on the definition of 'information' to the extent that they turn into unproductive shouting matches.
In many of their posts, evolutionists attempt to demonstrate an evolutionary mechanism for the production of new information that starts with the duplication of an existing gene, something that occurs and has been documented quite frequently, with one of the duplicates then undergoing a series of random mutations that eventually produces a new and useful gene. In this post I will (hopefully) demonstrate that gene duplication without further mutations in itself produces new information, and in doing so I will take a new tack on defining 'information'.
The main reason that information is so hard to define is that the kind of information we are talking about is very subjective, not only in determining its quantity, but also in even trying to define it in qualitative terms. For example, I am quite sure that creationists/bible-literalists and atheists would have very different opinions about the qualitative and quantitative information content of the bible and of Darwin's Origins of Species. Many disciplines use the term 'information' in many different ways that often have no relation to each other. One way to get around this impasse, when a community can't agree on a formal definition of a term, is to define the term by example. I. e., the community finds several examples that they generally agree fits the meaning of the term, and several examples of things that they agree don't meet the meaning of the term and leave aside several examples of things that are ambiguous or for which there is no general agreement. This is a very common practice in biology and is referred to as a 'consensus' definition. There might be no formal agreed upon definition of a particular fossil species, but there is often a consensus definition of what traits any member of that species must demonstrate and what it must not contain. So, I will show that gene duplication by itself can create information by defining information by example.
Suppose we have a book on the eating habits of primates. Each chapter discusses the eating habits of a particular primate. I would be surprised if anyone disputed that this book, and each of its chapters, contain information. If you did not know about the eating habits of primates, or if you had a job, such as a zoo attendant, that required that knowledge, this book would certainly inform you and raise your level of knowledge about that subject.
Now, let's discuss the gene for the digestive enzyme Amylase, and, in particular, the copy number of this gene in chimpanzees and humans. Amylase is the key enzyme for breaking down starches into sugar. Chimpanzees have one copy of this gene and humans have multiple copies, from two to nine. Chimpanzee diets are very restricted to low starch (and usually high sugar content) foods like fruits, nuts, berries, and other low starch foods. Humans often have staple diets of high starch foods such as rice, potatoes (my spell checker seems to be a Dan Quail fan), and starchy grains. In fact, the Amylase gene copy number variation in humans is very regional and correlates well with the starchiness of the regional diet.
An animal's genome contains as much information as the book I mentioned concerning that animals diet. And not only particular genes, but also those gene's copy numbers contain detailed information (using our example definition of information) of that diet. Note that this so far is not an argument for evolution, since we haven't discussed where the gene copy number came from, but if the copy number arose from ancestral gene duplication events (which some could argue are just "micro-evolutionary" processes), then those gene duplications produced new genetic information even in the absence of further mutation to a new function. Since gene duplication events have been observed in the lab to occur randomly demonstrates that that new genetic information can occur by purely natural means.
In this thread I hope to have other forum members comment and critique the above post and to offer other examples of evolutionary processes producing information where the specific type of information is defined by particular examples that (almost) all would agree has the meaning for 'information' that we generally assume. I also have a few further examples I hope to post in this thread if it is accepted (e. g., ACO: Ant Colony Optimization). I'll leave it to the admins to decide what forum should house this thread.
Note 1) Since this is ski season and the Sierras have tons of fresh new powder, I may be a little slow in responding to your posts.
Note 2) The idea for this thread and the details about the Amylase gene came to me from page 217 of Jerry Coyne's recent book, Why Evolution is True. Whatever your persuasion, your time would be far better spent reading that book than reading posts like mine.

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Message 2 of 11 (546792)
02-13-2010 9:25 PM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Gene duplication = information! thread in the Proposed New Topics forum.

  
Dr Adequate
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Posts: 16113
Joined: 07-20-2006


Message 3 of 11 (546810)
02-13-2010 11:22 PM
Reply to: Message 1 by AnswersInGenitals
02-13-2010 8:03 PM


So, I will show that gene duplication by itself can create information by defining information by example.
This seems painfully circular. You will show that gene duplication creates evolution by defining creation of information by the example of gene duplication.
I don't see why this should convince any creationist, and after all this blather about "information" is their thing, not ours. Let them define it.

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 Message 4 by Percy, posted 02-14-2010 6:13 AM Dr Adequate has replied

  
Percy
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From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 4 of 11 (546834)
02-14-2010 6:13 AM
Reply to: Message 3 by Dr Adequate
02-13-2010 11:22 PM


Dr Adequate writes:
I don't see why this should convince any creationist, and after all this blather about "information" is their thing, not ours. Let them define it.
I agree about the blather part, but "information" already has a definition. As with creationist definitions of evolution where the only way they can appear to have a leg to stand on is by mis-defining it, the same thing is true of information.
--Percy

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 Message 3 by Dr Adequate, posted 02-13-2010 11:22 PM Dr Adequate has replied

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 Message 5 by Dr Adequate, posted 02-14-2010 7:39 AM Percy has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 5 of 11 (546841)
02-14-2010 7:39 AM
Reply to: Message 4 by Percy
02-14-2010 6:13 AM


I agree about the blather part, but "information" already has a definition. As with creationist definitions of evolution where the only way they can appear to have a leg to stand on is by mis-defining it, the same thing is true of information.
Well, "information" can be defined in many ways. We are trying to get from a concept which is qualitative and intuitive to a definition which is qualitative and precise. There are a number of ways that we could do that. There are a number of ways that people have done that.
Shannon information is one way of measuring information. If I came up with a new way of measuring information and called it "Dr Adequate information", then so long as it had some sort of fit with what we intuitively mean by information, then you couldn't say that I was wrong by proposing my definition.
So let the creationists bring it on. Let John Smith claim that evolution can't increase "John Smith information". Let's analyze the claim. Let's see whether DNA contains any "John Smith information", and let's ask whether evolutionary processes can increase it.
But I don't see how AIG has got even that far. He doesn't say how we can quantify "AIG information", he just says that "AIG information" should be so defined such that that gene duplication is an increase in "AIG information", and then he triumphantly proclaims that gene duplication is an increase in "AIG information" --- by definition.
If we are going to talk about increases or decreases in information, then we need some way to measure how much information is in a given genome of an organism. Anyone who tries to come up with an idea of "information" which doesn't do that is blowing smoke.

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 Message 4 by Percy, posted 02-14-2010 6:13 AM Percy has replied

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 Message 6 by Percy, posted 02-14-2010 8:22 AM Dr Adequate has replied

  
Percy
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Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 6 of 11 (546845)
02-14-2010 8:22 AM
Reply to: Message 5 by Dr Adequate
02-14-2010 7:39 AM


Hmmm - wasn't expecting that answer. Letting creationists redefine information seems inconsistent with your position over in Why creationist definitions of evolution are wrong, terribly wrong. about not letting creationists redefine evolution.
--Percy

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 Message 5 by Dr Adequate, posted 02-14-2010 7:39 AM Dr Adequate has replied

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 Message 7 by Dr Adequate, posted 02-14-2010 5:02 PM Percy has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 7 of 11 (546881)
02-14-2010 5:02 PM
Reply to: Message 6 by Percy
02-14-2010 8:22 AM


Hmmm - wasn't expecting that answer. Letting creationists redefine information seems inconsistent with your position over in Why creationist definitions of evolution are wrong, terribly wrong. about not letting creationists redefine evolution.
Well, evolution has a clear-cut definition already. But I think anyone can come up with their own metric of "information". There may be more than one way to do so --- Shannon information and Kolmogorov complexity, for example.
So if someone wants to come up with a new metric of information, then we can think about it. If John Smith offers us a metric, then we can start talking about "Smith information". But if someone invents their own theory of evolution, then they're either right or wrong, and if they come up with their own definition of evolution, then they're definitely wrong --- by definition.

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 Message 6 by Percy, posted 02-14-2010 8:22 AM Percy has replied

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 Message 8 by Percy, posted 02-14-2010 5:42 PM Dr Adequate has replied

  
Percy
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Posts: 22392
From: New Hampshire
Joined: 12-23-2000
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Message 8 of 11 (546885)
02-14-2010 5:42 PM
Reply to: Message 7 by Dr Adequate
02-14-2010 5:02 PM


Moderator Back for Just One Message
Dr Adequate writes:
Well, evolution has a clear-cut definition already. But I think anyone can come up with their own metric of "information". There may be more than one way to do so --- Shannon information and Kolmogorov complexity, for example.
I think that both evolution and information have clear-cut definitions, and that anyone can come up with their own evolutionary mechanisms or information metrics that we can assess. Where information and evolution differ is that a layperson can be persuaded which definition of evolution properly applies within biology without too much difficulty, but this is not true for information. Convincing laypeople that meaning has no place in information is as difficult as convincing them that entropy isn't what makes rooms messy. Which makes a lot of sense since information and entropy are flip sides of the same coin.
--Percy
PS - Kolmogorov complexity is not another information metric. It combines Shannon information with computational concepts to form one approach for measuring algorithmic complexity.

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 Message 7 by Dr Adequate, posted 02-14-2010 5:02 PM Dr Adequate has replied

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 Message 9 by Dr Adequate, posted 02-14-2010 6:35 PM Percy has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 9 of 11 (546898)
02-14-2010 6:35 PM
Reply to: Message 8 by Percy
02-14-2010 5:42 PM


Re: Moderator Back for Just One Message
I think that both evolution and information have clear-cut definitions ...
Let's see your definition of information, then. Try to make it quantifiable.
PS - Kolmogorov complexity is not another information metric. It combines Shannon information with computational concepts to form one approach for measuring algorithmic complexity.
It can be used as an information metric, because it measures the complexity of an algorithm which generates the information. KC is in many ways closer to our intuition of information than Shannon information is.

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 Message 8 by Percy, posted 02-14-2010 5:42 PM Percy has replied

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 Message 10 by Percy, posted 02-14-2010 6:51 PM Dr Adequate has replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 10 of 11 (546903)
02-14-2010 6:51 PM
Reply to: Message 9 by Dr Adequate
02-14-2010 6:35 PM


Re: Moderator Back for Just One Message
Information is one message of a set of messages. Shannon information is my metric.
Concerning KC, Kolmogorov defined functions for both complexity and information. The functions are not identical. If you're thinking of Komogorov's function for information then I won't quibble, but Kolmogorov's function for complexity isn't really a measure of information.
--Percy

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 Message 9 by Dr Adequate, posted 02-14-2010 6:35 PM Dr Adequate has replied

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 Message 11 by Dr Adequate, posted 02-14-2010 7:59 PM Percy has seen this message but not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 11 of 11 (546905)
02-14-2010 7:59 PM
Reply to: Message 10 by Percy
02-14-2010 6:51 PM


Information
Information is one message of a set of messages. Shannon information is my metric.
It's a metric. But there's no reason to be partisan about it. It's not right, it's just useful.
Concerning KC, Kolmogorov defined functions for both complexity and information. The functions are not identical. If you're thinking of Komogorov's function for information then I won't quibble ...
Good.

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 Message 10 by Percy, posted 02-14-2010 6:51 PM Percy has seen this message but not replied

  
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