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Author Topic:   Can mutation and selection increase information?
CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 136 of 222 (816825)
08-11-2017 6:03 PM
Reply to: Message 133 by Taq
08-10-2017 10:37 AM


Re: random and non-random mutations
If it is a random search then it is not goal directed. Goal directed means making specific mutations to a specific gene with a known specific outcome.

You can have a search that is goal directed but can be random, systematic, or guided.

A friend of mine found a journal written by the notorious pirate, Short Jim Pewter. This recorded how SJP buried his treasure on a certain island, but unfortunately the last page with the map to the precise location was missing. Searching for this treasure is goal directed but it is also a blind search. It could be a random search or systematic but it would still be blind. When my friend started digging random holes looking for the treasure a very old parrot sitting in a tree started calling out "colder" or "warmer" with each hole. Relying on the parrot it now became a guided search and soon my friend found the treasure; 1000 jars of Vegemite. My friend took the parrot home and kept it in parrot luxury until it died.

Now consider the bacteria responding to an environmental stress. It begins to hypermutate certain regions of the genome in order to adapt. The goal is to adapt to the stress; although I don't suggest the bacteria has a conscious intention to to do this. The search space is restricted to certain parts of the genome. Within this space we assume the search is blind and random.


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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 139 of 222 (816888)
08-13-2017 2:01 AM
Reply to: Message 138 by Taq
08-11-2017 6:15 PM


Re: random and non-random mutations
In biology, a goal directed mutation is one that is non-random. It is a specific change to a specific base in a specific gene that results in a specific outcome. That is what "goal directed" means in biology.

Perhaps it does but I couldn't find it in a glossary of biological terms.
Perhaps you could supply a link to a suitable definition.

However I think you might be confusing "goal directed search" with a "guided search". In fact if the organism can go to a specific base in a specific gene to get a specific outcome it's not a search at all.

I tried to show the differences in my story about Short Jim Pewter.

Another example is the immune system. In response to an infection the immune system starts producing many variations looking for an antibody for the invader. This is goal directed but the immune system can't go directly to the specific mutation that will produce the antibody and it might have to use a blind search to find an antibody that works. (Not a perfect analogy since the immune system starts with a library of antibodies that have worked for past infections.)

In a blind search humans will often use a systematic search instead of a purely random search but this is still different to a guided search in which information is supplied to enable the search target to be reached more efficiently. A blind search can still have a goal as in "A blind search (also called an uninformed search) is a search that has no information about its domain. The only thing that a blind search can do is distinguish a non-goal state from a goal state." ref.


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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 141 of 222 (816933)
08-13-2017 7:21 PM
Reply to: Message 140 by JonF
08-13-2017 8:23 AM


Re: random and non-random mutations
goal–directed: aimed toward a goal or toward completion of a task.

As I have explained a search can have a goal while still being a blind search, as opposed to a guided search. And a blind search can be a random search.
(Maybe I should be writing "goal-directed" rather than "goal directed".)


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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 147 of 222 (817345)
08-16-2017 6:51 PM
Reply to: Message 145 by Taq
08-14-2017 11:09 AM


Re: random and non-random mutations
Taq writes:

CRR writes:

goal–directed: aimed toward a goal or toward completion of a task.
As I have explained a search can have a goal while still being a blind search, as opposed to a guided search. And a blind search can be a random search.
(Maybe I should be writing "goal-directed" rather than "goal directed".)

There is already a term that describes this process. It is called random mutagenesis.

All you are doing is redefining terms to make them sound more guided when they aren't.

I have already made the distinction between a goal-directed search and a guided search. A search can be goal-directed and unguided, completely random, at the same time. The mistake you are making is to assume that a random search is necessarily not goal-directed. Rather than "redefining terms" I am using already established terms in their normal way.

But the question is Can mutation and selection increase information?


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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 149 of 222 (817357)
08-16-2017 9:36 PM
Reply to: Message 148 by JonF
08-16-2017 7:42 PM


Re: random and non-random mutations
You have admitted you have no evidence that particular "search" is related to a goal in any way.

Incorrect.

This is relating to hypermutation of selected areas of the genome in response to an environmental stress trigger.
It appears this is a mechanism to adapt to the event and that makes it goal-directed; the goal being to adapt. I also pointed out that some parts of the genome are preferentially targeted for mutation rather than being random across the entire genome. It might be that the mutations within those target areas are random, but maybe not. At this stage I don't think there is specific evidence either way.


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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 153 of 222 (817626)
08-18-2017 6:02 PM
Reply to: Message 151 by Percy
08-17-2017 8:49 AM


Re: random and non-random mutations
Random mutation increases information, ...

Only if you're talking about Shannon Information and even Shannon acknowledged that had nothing to do with meaning.

... selection reduces it.

Yes.

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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 156 of 222 (817848)
08-21-2017 4:37 AM
Reply to: Message 154 by Percy
08-19-2017 8:33 AM


Re: random and non-random mutations
Think of it this way.
I have a copy of Origin of Species which contains information.
I buy another copy. Do I now have twice as much information? Or 2 copies of the same information?
I tear a page out of one copy and glue in a page of random numbers. That's a deletion and an insertion. Does that give me more information?

Werner Gitt in In the Beginning Was Information distinguishes 5 levels of information of which Statistical (Shannon Information) is the lowest level.


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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


(1)
Message 159 of 222 (817950)
08-22-2017 2:44 AM
Reply to: Message 157 by Percy
08-21-2017 8:47 AM


Re: random and non-random mutations
Werner Gitt confuses information with meaning.

No, he just uses a different definition of information than Shannon; must people do. Shannon's definition is very restrictive but suited for the purpose for which he was using it.

random mutation increases information, selection reduces it.

Random mutation degrades existing information. Take a page from a book and start randomly mutating the letters and pretty soon it is unreadable and any information on that page is lost.

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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 169 of 222 (818220)
08-25-2017 1:49 AM
Reply to: Message 167 by Percy
08-24-2017 8:57 AM


Measuring Information
There are various ways of measuring various aspects of information but I don't think any of them is complete, and maybe never will be. One reference I've given before is by Durston et al; although I don't think this will be the last word on the subject.
Measuring the functional sequence complexity of proteins
quote:
Abstract

Background
Abel and Trevors have delineated three aspects of sequence complexity, Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC) and Functional Sequence Complexity (FSC) observed in biosequences such as proteins. In this paper, we provide a method to measure functional sequence complexity.

Methods and Results
We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families. Considerations were made in determining how the measure can be used to correlate functionality when relating to the whole molecule and sub-molecule. In the experiment, we show that when the proposed measure is applied to the aligned protein sequences of ubiquitin, 6 of the 7 highest value sites correlate with the binding domain.

Conclusion
For future extensions, measures of functional bioinformatics may provide a means to evaluate potential evolving pathways from effects such as mutations, as well as analyzing the internal structural and functional relationships within the 3-D structure of proteins.


Note that the authors highlight the distinction between functional information and Shannon information.


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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 170 of 222 (818221)
08-25-2017 2:09 AM
Reply to: Message 164 by ringo
08-23-2017 3:48 PM


Re: random and non-random mutations
How can you know whether the information is "degraded" before it is filtered by selection? What if a mutation makes an organism fitter in a new environment while the unmutated individuals remain fitter in the old environment? Isn't that an effective increase in information?

We already know that most evolution happens by the loss of information. As Behe says “The First Rule of Adaptive Evolution” is “Break or blunt any functional coded element whose loss would yield a net fitness gain.”

However he does say

quote:
As seen in Tables 2 through 4, the large majority of experimental adaptive mutations are loss-of-FCT or modification-of-function mutations. In fact, leaving out those experiments with viruses in which specific genetic elements were intentionally deleted and then restored by subsequent evolution, only two gain-of-FCT events have been reported.
https://www.researchgate.net/...t_rule_of_adaptive_evolution

So that would appear to be a qualified yes to the question "Can mutation and selection increase information?".

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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 193 of 222 (818522)
08-30-2017 12:22 AM
Reply to: Message 189 by Tangle
08-27-2017 11:04 AM


Re: Cells
Tangle writes:

Nevertheless, you now know that cells can differentiate - that is, start as one kind of cell and divide and specialise to become another. And you know that it's absolutely routine because it's simply the birth and growh process.


However in this case the original cell has ALL of the genetic and extra-genetic information for EVERY cell including the information to switch off the un-needed functions in each specialist tissue. That is the difference between a complex organism and a single celled organism.

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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 198 of 222 (818584)
08-30-2017 6:15 PM
Reply to: Message 196 by Percy
08-30-2017 9:09 AM


Re: Cells
Percy writes:

the amoeba genome is a hundred times larger than the human genome


Over 200 times in the case of Amoeba dubia.

My conclusion is that size is not a good measure of information content. I have found that with books. You can't determine the value of the content by weighing a book or by doing a word count.


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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 208 of 222 (818665)
08-31-2017 7:24 PM
Reply to: Message 201 by Percy
08-31-2017 8:39 AM


Re: Information
You're still confusing Shannon Information with Information. Shannon Information is only a metric for a message.
See https://en.wikipedia.org/wiki/Information
Information is that which informs, so it will have meaning.

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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


(1)
Message 209 of 222 (818667)
08-31-2017 7:26 PM
Reply to: Message 202 by Taq
08-31-2017 10:38 AM


Re: Cells
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

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CRR
Member (Idle past 1482 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 211 of 222 (818672)
08-31-2017 8:25 PM
Reply to: Message 207 by jar
08-31-2017 3:11 PM


Re: Information
jar writes:

But still, no one has presented the working definition of information, how to recognize information or how to determine increase in information.


It's less than 100 years since Claude Shannon published The Mathematical Theory of Communication. A lot of work has been done on how to define information and how to measure it. I have previously given examples. This work is continuing although I suspect since information is a non material thing it might never be possible to define and measure it exactly.

But we can all recognise information in everyday life, and distinguish different kinds of information and whether there is an increase or not. e.g. Hollandaise Sauce.

We could look it up in a dictionary and get some information. We can read a recipe and get more information. We can taste it and get more information. We now know what it is, how to make it, and what it tastes like. We know that we have acquired and increased information; we can qualitatively say we have more information even if we can't quantitatively say how much.

Claude Shannon no more had the last word on information than Charles Darwin did on evolution.


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