DNA and Information

[TRoutMac]

Using Shannon, it is enough with a mere duplication to increase information, but since you seem to require "new meaning" in addition, subsequent mutations in the duplicated sequences leading to a difference in functions should qualify as a difference in "meaning"

 

Forget about Claude Shannon. It's not that his principles cannot be applied to the information content in DNA, it's just that this isn't the aspect of the information which is important to this discussion. Shannon information in this context is a smoke screen aimed at obfuscating and confusing the issue. We're talking about specific instructions, not just bits of generic information.

 

New features with new functions in an organism which make the organism more complex require more instructions. An illustration of this is software. (since DNA has been described by some as a software program) Let's say you have software which performs function A, and you want to add function B. You cannot gain function B without adding specific instructions to the existing source code. This is an increase in information. A single-celled organism operates on x quantity of information, or instructions. A human is thousands upon thousands of times more complex and consequently, the volume of instructions which comprises the human genome is commensurately more complex as well. It takes a greater volume of instructions to build a more complex machine. There are millions of examples of this in our every day lives, but some of us want to throw that experience out the window when we talk about the information in DNA, like as though it's not pertinent.

 

Since you're a later arrival to this thread, how do you respond to Questor's initial comments and quotes which began this thread? How can science account for the arrival of information (NOT Shannon) in the first cell?

[MortenS]

I did not forget Shannon, read my sentence after ", but"

 

New features with new functions in an organism which make the organism more complex require more instructions.

 

... which can be aqquired by duplication, and then subsequent diversification of functions....one gene give rise to two genes in the same organism (or rather descendants of that organism).

 

As far as I know, one gene can be counted as one instruction, two genes can therefore be counted as two instructions, hence increase in information according to your concept.

[TRoutMac]

... which can be aqquired by duplication, and then subsequent diversification of functions....one gene give rise to two genes in the same organism (or rather descendants of that organism).

 

If a gene is literally "duplicated", then that's merely redundancy… the same information twice. Not a new instruction. If I'm selling you a car and you ask me what kind of engine it has, and I say it's a V-8, and then you ask me for "more information" and I tell you its engine is a V-8 again, have I given you "more information"? No.

 

As far as I know, one gene can be counted as one instruction, two genes can therefore be counted as two instructions, hence increase in information according to your concept.

 

If each new gene provides different instructions, then yes, that's an increase in information. But again, "duplicate" genes are "duplicates". You can repeat the same instruction a million times, but there's no new information there.

 

Complex specified information expresses an idea and an intent. A radio beacon broadcast from another planet expresses the idea of "Here we are." The instructions for assembling and operating a remote control car express an idea. (lots of them) If you express the same idea over and over again, that's not new information.

 

Besides which, you still have to account for how the first instruction came to be, which is more along the lines of what Questor was asking as he began this thread.

[MortenS]

What is this practice you are doing, selective reading?

 

 

 

 

which can be aqquired by duplication, and then subsequent diversification of functions....one gene give rise to two genes in the same organism (or rather descendants of that organism).

 

The clue here is diversification, which occur by substitution, or even frameshift mutations. Since the gene is duplicated, mutations in one of the copies are not as harmful as they would be if there was only one copy. This makes it possible for the copy of the gene to aqquire a new function, and keep the function of the old gene.

 

This is really straight forward..and I would appreciate if we actually talked about DNA, not cars, jpegs and other stuff. Analogies can be useful at times, but they allways break down at some time. Better to talk about the real thing

[TRoutMac]

This makes it possible for the copy of the gene to aqquire a new function, and keep the function of the old gene.

 

"Acquire" a new function? And it just so happens there is a new function which can be "acquired" by that specific copying error, just waiting for that copying error to occur, is that right?

 

This is really straight forward..and I would appreciate if we actually talked about DNA, not cars, jpegs and other stuff.

 

The great thing about analogies is that they tend to help clear away the smoke and mirrors put up by evolutionary biologists and people who are themselves invested in an evolutionary world view. That's why there's so much objection to my use of analogies.

 

Analogies help to establish the flow of logic. The great thing about logic is that it's consistent… like algebra. You can plug in different "values" for the variables and the result is always predictable and consistent. If you're reaching a different conclusion with another set of variables, then somewhere along the line you must have made an error in logic, or arithmetic.

 

And again, you have not explained where the first set of instructions came from, and this appears not to interest you too much.

[MortenS]

Well, I am not particulary interested in going down that road. I know where it leads, been there done that, I would have quoted Questor if I felt for that. I was merely interested in giving my views on how DNA can increase its information content (by whatever definiton of information you choose).

 

Obviously however, I am of the opinion that all of todays DNA ultimately originated from one ancestral sequence, that went through a whole series of chromosome duplications, genome duplications, horisontal gene transfers, substitutions, insertions, deletions, gene losses, fusions of chromosomes, and fission of chromosomes until we got the diversity we have today (and the genomes still undergo radical changes from time to time).

 

As for what that ancestral sequence was, I have no idea. I do think RNA came before DNA, and that the early sequences had a much greater mutation rate than today, perhaps to the degree that the chance of getting a perfect copy of a sequence was almost 0. I also suspect that there might have been a replicator before RNA, but what this replicator was, I have no idea about.

 

Origin of life questions are bound to have lots of question marks around them.

 

 

 

"Acquire" a new function? And it just so happens there is a new function which can be "acquired" by that specific copying error, just waiting for that copying error to occur, is that right?

 

It certainly seems to be that way.

 

Proteins are all about 3-D structure. If you change the structure a little in the binding site of a protein, it might not fit the original molecule that was supposed to bind in the site, or it might still fit the original molecule, but another one in addition, it might not fit the original molecule at all, but it might fit some other molecule, or it might not fit any molecule at all. There are many possibilites, and not all will lead to a new functional gene.

 

But you know what, it is not necessary for all mutations to result in new information. It is enough that some do.

[TRoutMac]

Obviously however, I am of the opinion that all of todays DNA ultimately originated from one ancestral sequence, that went through a whole series of chromosome duplications, genome duplications, horisontal gene transfers, substitutions, insertions, deletions, gene losses, fusions of chromosomes, and fission of chromosomes until we got the diversity we have today.

 

Understood. But the problem is that you can find no other context in every day life, in all of human experience, where information (instructions which express an idea or an intent) is understood to increase by accident and produce complex, functional machines.

 

Changing the plans for a single-story house to a 2-story house requires more information. Copying the blueprints over and over again doesn't give you more information, it gives you less information. (or a degradation of existing information) Copying and recopying blueprints for a house won't even give you a single additional electrical outlet. If you've written a software program which browses the Internet and you want to add the function of an e-mail client, you cannot add the necessary information (source code) by merely copying and recopying the source code. Plans for a 2 seat sportscar cannot change into plans for a 4 seat sedan via copying errors.

 

This demonstrates something exceedingly basic and easy to understand about this kind of information: It doesn't arise by accident.

 

Now please… If Richard Dawkins can use analogies to illustrate the concept of DNA, then so can I. Refer to Dawkins' quote posted by Questor in the first post.

 

As for what that ancestral sequence was, I have no idea. I do think RNA came before DNA, and that the early sequences had a much greater mutation rate than today, perhaps to the degree that the chance of getting a perfect copy of a sequence was almost 0. I also suspect that there might have been a replicator before RNA, but what this replicator was, I have no idea about.

 

Let me be very clear… In this thread, nobody asked anyone what the original sequence might have been. You're addressing a question that was never even asked. This thread has been about DNA and its information content, and about properly understanding what kind of information DNA contains and, ultimately, how that information came to be in the first instance. In a broader sense, we can ask how can this kind of information increase? (or appear out of nowhere, which is also an "increase")

 

Origin of life questions are bound to have lots of question marks around them.

 

Yes, I think that's why they're called "questions". But those questions will never be answered if you adhere to methodological naturalism… (limiting your explanations of natural phenomena to natural explanations) Logically, this philosophy of science guarantees that the origin of life question can never be answered.

 

It certainly seems to be that way.

 

Well, it has to "seem that way" if you reject the simpler, more obvious conclusion. But I simply do not have enough faith to believe these mutations just happened to find a specific function.

[MortenS]

Understood. But the problem is that you can find no other context in every day life, in all of human experience, where information (instructions which express an idea or an intent) is understood to increase by accident and produce complex, functional machines.

 

That is no problem for me. And it is no problem for DNA. However, I do have an example that comes very close to what you are asking for, and it is pretty everyday.

 

Making food!

 

Many new recipes have been created because of accidents.

There are many errors that can occur when you follow a recipe. You can read it wrong, and add the wrong amount of an ingredient, or you can forget an ingredient. It is also possible that you do not have a particular ingredient, so you have to try and find a substitute, not to forget that you might heat the food too short, or too long, or not at all. You can chop the ingredients up in varying sizes, or you can prepare them whole. You might not have a frying pan, so you decide to try and boil it instead. The possibilites are endless with food, and the end result can be quite different if you throw in some random "mutations" to the recipe :cup:

 

I have tried for so long not to enter this discussion....and now I failed...

 

And yes, I know, food is not a machine...

[questor]

Welcome Morten. it is one thing to rearrange macroscopic globules of food

even this takes information from the chef. it is quite another thing to consider the sub-microscopic activity necessary for genetic influences, which

is self generating with no human influence.

[MortenS]

Welcome Morten. it is one thing to rearrange macroscopic globules of food

even this takes information from the chef. it is quite another thing to consider the sub-microscopic activity necessary for genetic influences, which

is self generating with no human influence.

 

I know perfectly well questor, and if you read my previous entry, you will see that I am of that opinion. You cannot compare DNA, cells and bodies with machines, cars or houses when it comes to how they get built, and how they change through time (but if you do, you have to perfectly clear about when the analogy breaks down). It can sometimes be ok to compare how they function when they are fully developed. You have to go directly to the source, and study DNA, genetics and biochemistry.

 

I am a biologist by training, and I would rather discuss the intricasies of biology with you all, instead of conjuring up analogies. The word recipe describes DNA's function much better than the word blueprint does, though. That was all I wanted to demonstrate with my example, that and the power of trial and error, and keeping the results of the successful trials.

[MortenS]

So, can I rearrange some chromosomes instead of food, questor?

 

Or at least some DNA or protein sequences. I did mention (and show a few of them) some sequences of a protein family where every protein is related to each other in sequence, but have somewhat different functions in the body.

 

You might of course claim that they have allways had that sequence, but the fact is that the differences can, without to much difficulty be explained by duplication of genes, combined with later substitution of aminoacids (via nucleotide substitutions of course), thus an overall increase in information, measured from before duplication took place.

[Boerseun]

Analogies are incredibly useful, and incredibly senseless if you pick the wrong ones.

 

Thanks, Morten - I've been getting rather tired of TRout's selective application of irrelevant analogies and arbitrary dismissal of equally valid/irrelevant analogies, only because it supports the other side.

 

I can't wait for their 'Yes, but...' post, about to follow.

 

Wait...

[TRoutMac]

Thanks, Morten - I've been getting rather tired of TRout's selective application of irrelevant analogies and arbitrary dismissal of equally valid/irrelevant analogies, only because it supports the other side.

 

Were you going to explain, Boerseun, why it is that it's acceptable for Richard Dawkins to employ an analogy between computer files and DNA, while it's an irrelevant and inappropriate analogy if I empoy it? Were you going to enlighten me on that? I'd sure appreciate it if you would.

 

The word recipe describes DNA's function much better than the word blueprint does, though.

 

So you'd like to compare DNA with a recipe. Not a bad analogy… far from arbitrarily dismissing it, as Boerseun seems to think I would do, I must say I like this analogy. After all, a recipe is a set of instructions. And, they are instructions that are devised by an intelligent agent. (presumably a chef, or possibly your grandmother). A recipe is an example of information produced by intelligence.

 

That was all I wanted to demonstrate with my example, that and the power of trial and error, and keeping the results of the successful trials.

 

Sure. Just one problem. You need intelligence to develop a recipe which is edible and does not make someone puke.

 

I also like this recipe analogy because it reminds me of when my friend made pancakes one morning but accidentally used baking soda instead of baking powder!! That "mutation" in the recipe for pancakes was definitely selected for extinction!!

[Boerseun]

Sure. Just one problem. You need intelligence to develop a recipe which is edible and does not make someone puke.

Why?

Any 'edible' disaster in the kitchen, that happens to be 'tasty' or any other variable you care to mention that satisfies the requirements for replication, will be made again. Those that make you puke, won't. Unless you're some sort of masochist.

 

Intelligence has nothing to do with it. The fact that replication happens (reading a tried and tested recipe from a book, and duplicating it) and the opportunity for a 'mutation' to happen (mistaking the pepper shaker for the cinnamon) will result in change that might be either awesomely tasty or a complete disaster.

 

Replication in the kitchen needs intelligence, in order to read the pages.

Replication on the DNA level requires zero intelligence.

The mechanism for replication failure to occur, in other words mutations, requires zero intelligence in either case. It simply needs a mechanism.

[TRoutMac]

Why? Any 'edible' disaster in the kitchen, that happens to be 'tasty' or any other variable you care to mention that satisfies the requirements for replication, will be made again.

 

Are you denying that your intelligence reacts to such "disasters" and then makes decisions in the future as to whether that recipe will tried again? Are you actually going to deny that? You guys are just too freakin' funny. You ask why intelligence is necessary, and then you describe a process which involves your intelligence. Do you think a "tasty" disaster will simply happen at a later date by magic? No, you would record that recipe, with the mistake, and then at a later date you would decide, using your intelligence, to make it again. Come on, Boerseun… you're makin' this too easy.

 

Replication in the kitchen needs intelligence, in order to read the pages. Replication on the DNA level requires zero intelligence.

The mechanism for replication failure to occur, in other words mutations, requires zero intelligence in either case. It simply needs a mechanism.

 

First of all, an intelligence is not only needed to read the recipe, but an intelligence is also necessary to first develop and then record the recipe in a form that another intelligence can then read.

 

Secondly, replication isn't the question. Replication presupposes that there's something to replicate. The question is how did the information originate in the first place? I realize that the replication of DNA happens without intelligent input. But how did the information in any of the "original" genomes come about? That's the problem Questor expressed in his original post and thus far you guys are avoiding that question like the plague. No mystery as to why.

 

You also "forgot" to explain why only evolutionists like Richard Dawkins are allowed to compare computer files to DNA, but when Intelligent Design proponents use the same analogies, we're told they are irrelevant, illegitimate, faulty, false, etc.

[Edge]

I actually think that analogies should not be used as evidence. You can make up any analogy to prove whatever...

 

Now, back to topic... I'll reply later, TRoutMac, I have been busy as of lately, sorry for that

[TRoutMac]

I actually think that analogies should not be used as evidence. You can make up any analogy to prove whatever...

 

No one's using analogies as evidence. I'm using analogies to show what a reasonable interpretation of that evidence is. If it's reasonable to interpret the evidence in one way over here, then it must also be reasonable to interpret the evidence over there in the same way.

 

When Richard Dawkins, for example, likened DNA to the files on his computer, he wasn't offering that as evidence. He was using it to help us understand something important about DNA. It's a great analogy. It's just too bad that the folks on Dawkins' side of the issue will only allow Dawkins to use that analogy.

 

The information in DNA, according to Dawkins, is a digital code just like a file on a computer. Now, we all know very well that the digital code that comprises any computer file was devised by an intelligence. We also know that you could never randomly throw down 1s and 0s by the millions and come up up with, for example, complete plans for a two-story house. Fortunately, the software that we've devised has a clever user interface that lets us determine in what sequence those 1s and 0s will be without ever having to choose them directly. We don't have to write the code… the software writes the code for us every time we choose "Save" from the File menu. Moving on… if DNA is like a file on a computer, like a DXF file which describes a house, and the DXF file describing the house had to come from an intelligence, then logic dictates that the digital code in DNA also came from an intelligence. We just know that intelligence isn't human.

 

See, the evidence isn't the analogy. The analogy just helps us understand and interpret the evidence in the most reasonable fashion.

 

Now, back to topic... I'll reply later, TRoutMac, I have been busy as of lately, sorry for that

 

Hey, no apologies needed here. You're certainly not the only one with a "life" besides this silly forum!! :cup: