Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 78 (8896 total)
Current session began: 
Page Loaded: 03-22-2019 10:09 AM
46 online now:
AZPaul3, Diomedes, JonF, Meddle, PaulK, Phat (AdminPhat) (6 members, 40 visitors)
Chatting now:  Chat room empty
Newest Member: WookieeB
Post Volume:
Total: 848,542 Year: 3,579/19,786 Month: 574/1,087 Week: 164/212 Day: 6/25 Hour: 0/1


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Prev1
2
3Next
Author Topic:   Question on genetic information
Arithus
Inactive Member


Message 16 of 32 (373797)
01-02-2007 6:41 PM
Reply to: Message 9 by platypus
01-02-2007 2:18 AM


Re: macro and genetic information
PlatipusFollowing up on what Paul said,

A good way to tell when a creationist is pulling from thin air is when they talk about information increase in an organism, but don't define information, and switch between some sort of macroinformation and genetic information definition, as I have begun to call them. They will talk about genetic information in things like new genes and genes that switch traits on and off. But we can give actual mathematical descriptions of genetic information in the same way that we can describe the information in the digital bytes of your hard drive. Problem is that genetic information increased if the length of the DNA sequence increases. And there are several known mechanisms which cause the length of the DNA sequence to increase.

This causes them to switch to a macroinformation concept, which seems to be looking for new "functions" in an organism, though function often isn't defined and really can't be measured in any effective way. Additionally, we have examples of opposite trends in macroinformation, for example where one group of organisms evolves to bigger sizes and one evolves to smaller sizes. Both of these changes can't be a decrease in information.

A commonly cited example used by creationists is snakes. Creationist mostly accept that snakes have lost their legs, there is fossil evidence of such a transition occurring and some snakes still have vestigil legs. Snakes lost their legs, which is the loss of an appendage and function, obviously a loss of information. But if function is our concern, their are several forms of snake locomotion that have evolved after the limbs have been lost, lateral undulation, sidewinding, concertina, rectilinear, and slide pushing are all forms of ground locomotion, while some snakes have adapted the ability to climb trees and glide trough the air. Several of these forms of locomotion involve changes in the snakes body, which are neccessary for these locomotions to occur. In other words, a mutation in design which causes a new function, or an increase in information.

I'd be happy to direct you to more information concerning these examples, just let me know. The basic point is that information is a useful metaphor for what is stored in DNA, but that evolutionary changed care not for information- the concept is foreign. Things change, that's it.

Please, I would love to know as much as possible...

Edited by Arithus, : No reason given.


I only want the truth, whatever it leads to is fine by me...
This message is a reply to:
 Message 9 by platypus, posted 01-02-2007 2:18 AM platypus has responded

Replies to this message:
 Message 18 by platypus, posted 01-03-2007 1:46 AM Arithus has responded

  
RAZD
Member
Posts: 19756
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.5


Message 17 of 32 (373864)
01-02-2007 11:50 PM
Reply to: Message 14 by Percy
01-02-2007 10:05 AM


Re: macro and genetic information
This year's Nobel prize in biology was for research into gene regulation and expression, and when I read your post I wondered if perhaps the snake's loss of legs was due to regulatory changes rather than to loss of actual genes.

Doesn't this just shift the issue of {gain\loss} to the gene regulatory part of the DNA?

This would be similar to the {off\on\off\on} expression of wings in the walkingstick insects.

Thanks.


Join the effort to unravel AIDS/HIV, unfold Proteomes, fight Cancer,
compare Fiocruz Genome and fight Muscular Dystrophy with Team EvC! (click)


we are limited in our ability to understand
by our ability to understand

RebelAAmericanOZen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.


This message is a reply to:
 Message 14 by Percy, posted 01-02-2007 10:05 AM Percy has not yet responded

  
platypus
Member (Idle past 3830 days)
Posts: 139
Joined: 11-12-2006


Message 18 of 32 (373890)
01-03-2007 1:46 AM
Reply to: Message 16 by Arithus
01-02-2007 6:41 PM


Re: macro and genetic information
A lot of the information all ready exists in links on other posts on this website. Confidence argues the genetic information position and is refuted by examples in Message 41. I would suggest reading through the entire thread starting with message 41 and following interesting links. Towards the end of this thread are a few examples showing a changed in organisms in two different directions, in particular towards small sizes and large sizes.

Also, Can random mutations cause an increase in information in the genome? discusses the problems with defining information in a measurable way. This thread got off-topic pretty quickly, but the first couple pages are relevant and informative.

As for gene switching, look at Message 18. This is what RAZD is refering to in the previous post, and is also refered to in your opening post. When new features do appear, creationists try to explain it away by saying that the gene was present from the begining, but was switched on by another regulatory gene. Still, the switch gene must still be activated, which presumably works by an increase in some sort of information.

DNA increases in length can be caused by gene duplication , linked to a wikipedia entry.

As for snakes, here you can read about the various forms of ground locomotion. The most interesting from an information standpoint is rectilinear motion. From the webpage

Rectilinear locomotion is movement in a straight line. It is used mainly by large snakes such as large vipers, boas, and pythons. In rectilinear locomotion, the belly scales are alternately lifted slightly from the ground and pulled forward, and then pulled downward and backward. But because the scales "stick" against the ground, the body is actually pulled forward over them. Once the body has moved far enough forward to stretch the scales, the cycle repeats. This cycle occurs simultaneously at several points along the body. Static friction is the dominant type of friction involved in rectilinear locomotion. Unlike lateral undulation and sidewinding, which involve unilateral muscle activity that alternates from one side of the body to the other, rectilinear locomotion involves bilateral activity of the muscles that connect the skin to the skeleton. One set of these muscles lifts the belly scales up and pulls them forward and another set of muscles pulls the them downward and backward.

This sort of motion is caused by large changes to body structure, which confer a benefit to the snake- the ability to move while being extremely large. The structure and arrangements of skeletal muscles has changed in these snakes, opening up a new form of locomotion.

My favorite example of information increase is in flying snakes. Similar to rectilinear motion, there is a definite change to the snakes skeletal flexibility and muscular arrangement. These changes allow the snake's body to assume a more aerodynamically efficient shape, thus allowing these snakes to glide through the air.

I like these examples because they are not just genetic changes, they are major changes to an organism's shape and structure which open up the possibility of new fuctions that confer a selective advantage to that organism. It's hard to see how these changes can be viewed as decreases in information, or losses of function.

Hope that helps!


This message is a reply to:
 Message 16 by Arithus, posted 01-02-2007 6:41 PM Arithus has responded

Replies to this message:
 Message 19 by Arithus, posted 01-04-2007 6:43 AM platypus has not yet responded

    
Arithus
Inactive Member


Message 19 of 32 (374324)
01-04-2007 6:43 AM
Reply to: Message 18 by platypus
01-03-2007 1:46 AM


Re: macro and genetic information
Awsome!

Haha some people would find it funny, but I get excited over this stuff.


I only want the truth, whatever it leads to is fine by me...
This message is a reply to:
 Message 18 by platypus, posted 01-03-2007 1:46 AM platypus has not yet responded

  
Dr Adequate
Member
Posts: 16085
Joined: 07-20-2006
Member Rating: 10.0


Message 20 of 32 (374642)
01-05-2007 4:59 AM


As has been pointed out, creationists making this argument don't give a quantitative defintion of "information". This means that we can't test the claim that mutations don't increase "information"; and we can't analyse the claim that evolution requires the increase of "information".

So it would seem at first glance that like so much creationist rhetoric, it's so ill-defined as to be completely meaningless.

For example, the particular article you cite defines "information" as follows:

INFORMATION - What is conveyed or represented by a particular arrangement or sequence of things : genetically transmitted information.

This does not allow us to compare the quantity of "information" in two genomes, or to decide whether a given mutation increases or decreases the "information". This same author writes that:

[Information] has to be increased for the theory of evolution to be plausible.

(My emphasis).

And yet this author doesn't say how we can measure how much "information" is contained in a genome, nor how we may calculate whether this "information" is created or destroyed by any particular mutation.

He demands that evolution should "increase" the amount of "information", but doesn't trouble to tell us how to measure the amount of "information".

---

It seems almost as though the creationists are simply mouthing meaningless phrases. However, we can show that creationist claims are false according to any reasonable definition of "information". Stop me if I'm, wrong, but I would say that:

By any reasonable definition of "information", two completely identical genomes must contain the same amount of "information".

What follows from this?

Well, every mutation has an inverse. A point mutation can be undone by an opposite point mutation. An insertion can be undone by a deletion. A frame shift can be reversed by another frame shift. And so forth.

In general, if there is a series of mutations which gets you from genome (a) to genome (b), then there is also a series of mutations which gets you from genome (b) to genome (a).

So, if it is claimed that some series of mutations --- from (a) to (b) --- destroys "information", then the reverse sequence of mutations which get you from (b) to (a) must create "information". Because otherwise you could go from (a) to (b) and then back to (a) with a net destruction of "information". But (a) and (a) are the same genome, and so must have the same amount of "information", by the principle we set down above --- two completely identical genomes must contain the same amount of "information"..

So if some mutations detroy "information", other mutations must create "information".

---

If you are astute, you might think that you see a loophole here. A creationist might argue that in fact "information" can neither be created nor destroyed by mutation, but must be conserved. Now, if this was true, it would be true, in particular, of any series of deletion mutations. If mutation could neither create nor destroy information, then deleting any part (or the whole) of a genome would not destroy any "information".

But if that is true, then no genome contains any "information", and then the claim that "mutations can't create information" is irrelevant, since in that case mutations can create any genome you please without creating "information" as so defined.

---

In summary, if "information" is defined in any way we can measure, either there is no "information" in the genome, and so we don't have to explain how it got there; or there is "information" in the genome, and mutation can increase it as well as decrease it.

And if, as is invariably the case, "information" is not quantatively defined, then the creationists don't even have an argument.

Edited by Dr Adequate, : No reason given.

Edited by Dr Adequate, : No reason given.


Replies to this message:
 Message 21 by platypus, posted 01-07-2007 9:10 PM Dr Adequate has responded

  
platypus
Member (Idle past 3830 days)
Posts: 139
Joined: 11-12-2006


Message 21 of 32 (375196)
01-07-2007 9:10 PM
Reply to: Message 20 by Dr Adequate
01-05-2007 4:59 AM


Dr. Adequate
The argument has one more possibility, stemming from the origin of the information argument, which was in the second law of thermodynamics. Namely, Information (like entropy) can only stay teh same or decrease, it can never increase. Since point mutuations are reversible, creationists can argue that point mutations conserve information (like reversible thermodynamic transitions converse entropy). But major changes will only cause a decrease in information. The analogy to thermodynamics is uncanny.

Not that I think this gives this argument any more validity, but I seem to gather that this is what they are arguing, or trying to argue. They still have the problems of not defining information, and dealing with gene duplication.


This message is a reply to:
 Message 20 by Dr Adequate, posted 01-05-2007 4:59 AM Dr Adequate has responded

Replies to this message:
 Message 22 by fallacycop, posted 01-16-2007 11:36 PM platypus has responded
 Message 30 by Dr Adequate, posted 01-18-2007 5:58 PM platypus has not yet responded

    
fallacycop
Member (Idle past 3597 days)
Posts: 692
From: Fortaleza-CE Brazil
Joined: 02-18-2006


Message 22 of 32 (377469)
01-16-2007 11:36 PM
Reply to: Message 21 by platypus
01-07-2007 9:10 PM


Re: Dr. Adequate
The analogy to thermodynamics is uncanny.

Not that I think this gives this argument any more validity, but I seem to gather that this is what they are arguing

If that`s what they are arguing, then they are wrong again bacause the afirmation that entropy is always increasing is only true for isolated systems. A system that is in contact with the external world can indeed have its entropy decrease over time.


This message is a reply to:
 Message 21 by platypus, posted 01-07-2007 9:10 PM platypus has responded

Replies to this message:
 Message 23 by platypus, posted 01-17-2007 1:10 AM fallacycop has not yet responded

  
platypus
Member (Idle past 3830 days)
Posts: 139
Joined: 11-12-2006


Message 23 of 32 (377481)
01-17-2007 1:10 AM
Reply to: Message 22 by fallacycop
01-16-2007 11:36 PM


Re: Dr. Adequate
If that`s what they are arguing, then they are wrong again bacause the afirmation that entropy is always increasing is only true for isolated systems. A system that is in contact with the external world can indeed have its entropy decrease over time.

Right. The creationist argument was originally formed on entropy, as I understand it. They argued that things must be designed because the world is highly ordered, and entropy can only increase with time based on the second law of thermodynamics. Then they realized this was wrong because the earth is not a closed system, so they quickly exchanged "entropy" for "information" and made a similar argument, except with no information increase in time. This argument works remarkably better, mainly because no one is quite sure what information is, so it is unclear whether information should increase or decrease with time, and whether this decrease depends on the system being open or closed. Many arguments have learned from this mistake- creationists have learned not to use scientific terms anymore, because it makes the flaws in their arguments too obvious. Now they make up their own terms (like information or "kinds"- why talk about cat "kinds" when cat have already have a taxonomic grouping?), or they simple redefine scientific terms to mean what they want (like the terms "evolution" and "science").

edit- Wiki has a pretty good section on this:
http://wiki.cotch.net/index.php/List_of_creationist_arguments
Look at the section based on the second law of thermodynamics. The entropy argument is given initially, and then there are several arguments that attempt to relate information theory to entropy. All these areguments are refuted by talkorigens.

Edited by platypus, : No reason given.


This message is a reply to:
 Message 22 by fallacycop, posted 01-16-2007 11:36 PM fallacycop has not yet responded

    
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 24 of 32 (377528)
01-17-2007 11:16 AM


Keep in mind a few things about Chase - he is 20, Christian, and in college.
The old adage:

When you earn a Bachelors, you think you know everything
When you earn a Masters, you realize how littl eyou knew
When you earn a Doctorate, you realize how little everyone knows

Chase is at the 'I know everything, I am in college' phase.

His replies at the Myspace forum show that in spades - he was/is completely unwilling to even entertain the possibility that he is wrong and basically ignores all the explanations and questions presented to him.


    
Jaderis
Member (Idle past 1502 days)
Posts: 622
From: NY,NY
Joined: 06-16-2006


Message 25 of 32 (377671)
01-17-2007 9:58 PM


INFORMATION - What is conveyed or represented by a particular arrangement or sequence of things : genetically transmitted information.

Oh...wow. That definition sure clears things up.

Seriously..."Sequence of things"??? How on earth does anyone accept this as anything resembling a scientific or testable definition? It disheartens me to think that the wool can be so thick over so many people's eyes that they would accept this definition as having any meaning at all.


Replies to this message:
 Message 26 by Percy, posted 01-17-2007 10:35 PM Jaderis has responded

    
Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 26 of 32 (377677)
01-17-2007 10:35 PM
Reply to: Message 25 by Jaderis
01-17-2007 9:58 PM


Jaderis writes:

INFORMATION - What is conveyed or represented by a particular arrangement or sequence of things : genetically transmitted information.

Oh...wow. That definition sure clears things up.

Seriously..."Sequence of things"??? How on earth does anyone accept this as anything resembling a scientific or testable definition?

I was wondering if/when things would get to this point.

Information does have a formal definition. In fact, there is a branch of science called Information Theory, and the field was founded by Claude Shannon over half a century ago with his seminal paper titled A Mathematical Theory of Communication.

As Shannon points out, the problem of communications is one of transmitting a message from a fixed set of messages. For example, a very simple message might consist of a single letter. The set of all possible messages in that case would be the set of all letters, which for ASCII is 256 different letters (a good number of them non-printing, but we'll ignore that and keep this example simple).

How much information is contained in a single message is a function of how many bits it takes to represent the message. In the case of a single letter of 256 different letters, it takes 8-bits. So the information contained in a single ASCII letter is 8-bits. For those already familiar with information theory, keep in mind I'm just trying to communicate the general principle of information theory and am purposely avoiding all nuances such as noise, redundancy, etc.

I was actually heading off to bed when I saw this message so I'm not going to go beyond that brief explanation. I'd be glad to answer any questions tomorrow.

--Percy


This message is a reply to:
 Message 25 by Jaderis, posted 01-17-2007 9:58 PM Jaderis has responded

Replies to this message:
 Message 27 by Jaderis, posted 01-17-2007 10:53 PM Percy has responded

    
Jaderis
Member (Idle past 1502 days)
Posts: 622
From: NY,NY
Joined: 06-16-2006


Message 27 of 32 (377683)
01-17-2007 10:53 PM
Reply to: Message 26 by Percy
01-17-2007 10:35 PM


I can see how Information Theory can be applied to genetics, in a vague sort of way since I am not very schooled in this theory.

Could you perhaps elaborate on the what this theory might imply with regards to transmitting genetic information?

Is the definition of information as presented in Information Theory pretty much the same as the definition I quoted in my post?

Are we (evos) being disingenious when we state that the creationists won't or haven't yet defined information (IOW do they actually use the definition presented by Information Theory and can it be applied accurately to genetics)?

Have a nice rest, Percy :)


This message is a reply to:
 Message 26 by Percy, posted 01-17-2007 10:35 PM Percy has responded

Replies to this message:
 Message 28 by Wounded King, posted 01-18-2007 8:33 AM Jaderis has not yet responded
 Message 29 by Percy, posted 01-18-2007 10:04 AM Jaderis has responded

    
Wounded King
Member (Idle past 2171 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 28 of 32 (377752)
01-18-2007 8:33 AM
Reply to: Message 27 by Jaderis
01-17-2007 10:53 PM


Could you perhaps elaborate on the what this theory might imply with regards to transmitting genetic information?

The most obvious implications would be in relation to the likelihood of changes in the genetic 'message' due to the 'noise' of random mutations, specifically in terms of the transgenerational transmission of genetic information.

Are we (evos) being disingenious when we state that the creationists won't or haven't yet defined information (IOW do they actually use the definition presented by Information Theory and can it be applied accurately to genetics)?

No, creationist and ID proponents do not simply refer to Shannon information or Shannon entropy in their arguments. That doesn't mean that it can't be applied to genetics however and indeed it has been in a number of ways, including searching for regions of genetic complexity, and it has been shown that there is more shannon information in genomes than in an equivalent set of random sequences (Chen et al, 2005).

Someone whose work relates to information theory and who has often been co-opted by anti-evolutionists is Hubert Yockey. Yockey has argued that there is reason to doubt whether we can ever fully understand the actual processes which gave rise to the early life and proto-genetics which preceeded life on Earth (Yockey, 2000). Yockey has also put forward some calculations of the kind creationists love regarding the probabilities of Cytochrome C forming spontaneously . Yockey has made some explicit analogies between Shannon information theory regarding communication and elements of the processes involved in translation and transcription. To see how one creationist approaches Yockey's work go here.

Other Id proponents prefer making their own definitions of information up such as Gitt's form of information which has its own thread, The value of Gitt information.

William Dembski starts with a similar calculation for information as Shannon but uses a different definition to fit in with his own ideas of complex specified information which seem to involve conflating shannon information and another measure known as Kolmogorov complexity.

TTFN,

WK

Edited by Wounded King, : Because I just can't type


This message is a reply to:
 Message 27 by Jaderis, posted 01-17-2007 10:53 PM Jaderis has not yet responded

    
Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 29 of 32 (377768)
01-18-2007 10:04 AM
Reply to: Message 27 by Jaderis
01-17-2007 10:53 PM


Jaderis writes:

Could you perhaps elaborate on the what this theory might imply with regards to transmitting genetic information?

WK already alluded to noise, which in the case of genetics is most often caused by replication error (copying mistakes during cell division). It is this error-prone process that leads to increasing amounts of information in the genome.

As I said earlier, the amount of information contained in a message is the number of bits required to represent the message. If there are only five possible messages, then it takes only three bits to encode a single message, like this for example:

000 Blue eyes
001 Brown eyes
010 Green eyes
011 Hazel eyes
100 Yellow eyes

In reproduction the goal is to pass the genetic information from the parents to the offspring, but what if there is a copying error? What if one of the parents has the genetic code for brown eyes (001 in my example, not an actual genetic code, of course), but during reproduction there was a copying error and the 001 became 101. Well, there was originally no code for 101, but now there is, so now our table now looks like this:

000 Blue eyes
001 Brown eyes
010 Green eyes
011 Hazel eyes
100 Yellow eyes
101 ???

Genetically we don't know what the new code will do until we see what it does to the individual. The codes are instructions for building proteins, which are the workhorses of the body. Will the 101 code produce one of the already existing eye colors, or a new eye color. Body chemistry is usually too complex to predict what would happen ahead of time. That's why medicine is full of animal trials before they actually begin testing on humans.

But notice that the mutation (that's what a copying error is) has caused our message set size to increase from five messages to six. The mathematical way to calculate information is to take the log base 2 of the number of messages in the message set. So the amount of information communicated when sending a single message from a set of messages of size five is:

log25 = 2.32 bits

When the message set size increases to six the amount of information communicated by a single message is:

log26 = 2.585 bits

So the mutation has caused an increase in information in the genome of 0.265 bits.

(Keep in mind that this is just a simple example to get the principle of how Information Theory can be applied to genetics - it's not a real world example. I used binary bits instead of nucleotide triplets, and eye color determination is actually spread amongst a number of genes, not just one.)

Is the definition of information as presented in Information Theory pretty much the same as the definition I quoted in my post?

The definition you quoted is very imprecise for purposes of understanding Information Theory.

Are we (evos) being disingenious when we state that the creationists won't or haven't yet defined information (IOW do they actually use the definition presented by Information Theory and can it be applied accurately to genetics)?

WK covered this pretty well. I wouldn't be so kind myself. Both Gitt and Dembski information are just made up definitions of information drawn from thin air with occasional references to real world theories to lend them an air of legitimacy.

--Percy


This message is a reply to:
 Message 27 by Jaderis, posted 01-17-2007 10:53 PM Jaderis has responded

Replies to this message:
 Message 31 by Jaderis, posted 01-18-2007 6:36 PM Percy has not yet responded

    
Dr Adequate
Member
Posts: 16085
Joined: 07-20-2006
Member Rating: 10.0


Message 30 of 32 (377865)
01-18-2007 5:58 PM
Reply to: Message 21 by platypus
01-07-2007 9:10 PM


Re: Dr. Adequate
The argument has one more possibility, stemming from the origin of the information argument, which was in the second law of thermodynamics. Namely, Information (like entropy) can only stay teh same or decrease, it can never increase. Since point mutuations are reversible, creationists can argue that point mutations conserve information (like reversible thermodynamic transitions converse entropy). But major changes will only cause a decrease in information.

But the same "major change", whatever that consists of, would, in reverse, increase information.If the major change consists of a reduplication, a frame shift, five point mutations and a deletion, and it decreases "information", then a "major change" involving an insertion, five point mutations, a frame shift and a deletion will increase information.

...

Now, if the creationists wish to concede that mutations which increase information are possible in principle, but that as at matter of fact, they do not occur, then we have to ask: how the heck does that happen? Mutations are random. There aren't enough zeros in the world to express the odds against that --- which I could calculate if only they produced a definition of "information".

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 21 by platypus, posted 01-07-2007 9:10 PM platypus has not yet responded

  
Prev1
2
3Next
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2019