DNA information

[momo666]

First of all, Hello ! I am new here, I've found this forum due to MarsCydonia in his recent exchange about the cosmological argument.

I thought to ask here some questions I have since I got the impression some of you guys are well versed in biology ( among other fields ).

1) Can someone explain me how information works in the DNA? I hear this point repeated over and over by creationists; information can only come from a mind; we have never observed an increase in information due to genetical mutations.

The closest I've come to find an answer was Professor Lenski long-term E.coli experiment but this article basically tells that it wasn't really an increase of information but merely a "recycle" of the old one or if I understood it correctly, a genetic inhibitor was deactivated thus there wasn't really any "new" information added.

Admittedly it is a creationist website but you can see why a person not educated in the field of biology can take their points seriously. As far as I know they've also been beaten in court so that doesn't help their credibility "In 2005, a federal judge banned Pandas outright from science classrooms in Dover, Pennsylvania

— Casey Luskin, Evolution News & Views, Discovery Institute"

2)I've recently heard a creationist claim that epigenetics pose a threat to the theory of evolution but I'm kind of confused here. As far as I know epigenetics studies what turns off/on some genes, how the environment affects the genes. Hoes does that pose a thread to the theory?

Moreover, I've heard him claim something along the lines " Epigenetic information is not in the DNA; is in the structure of the cell itself, how could it be there if it didn't come from a mind?"

3) I've also heard him use the phrase "semiotic information in the DNA" but as far as I know semiotics has nothing to do with biology so I'm really lost here.

Although you don't need to watch it in order to answer my questions, I will post the youtube link so those interested can take a look at the exchange I'm talking about. Please note I'm not a participant there, I merely picked some questions from the discussion.
https://www.youtube.com/watch?v=w7FhphWDokA

The topic is the one Ian G started, the exchange is between Tyson Guess and Robbie Kay.


Lastly, I've skimmed through the board index a bit to see if my questions were asked before but I got no luck even though I'm sure this is not the first time someone asks something along these lines so if this was already answered and you don't want to lose time just direct me to the said topic. Hopefully I've posted this in the correct topic.

Thanks.

 

[Deleted member 619]

Hi, and welcome.

You're in luck, because there are good minds with knowledge not just of biology, but robust treatments of information. Here's a post that covers pretty much all the relevant bases, and it's a good idea to pay close attention to my signature as well.

If you have specific questions not covered therein, or you require any clarification, ask away.

 

[tuxbox]

Welcome to the forum, mom666. I hope you stay awhile.

 

[he_who_is_nobody]

he_who_is_nobody[/url]"]

Typically regarding creationists using DNA as evidence to there position comes in a misrepresentation of the term 'information'. By twisting it make it sound like it literally is some sort of message from a/the creator in regards to it's 'complexity' it all comes down to a form of special pleading fallacy. Knowing the refutation to the specific fallacy is the key to destroying such arguments, and subsequent dismissal of it.

You hit the nail on the head with that. I am going to link the best takedown of the argument "DNA equals information" I have ever come accross.

​

 

[tuxbox]

​

:facepalm:

 

[Dragan Glas]

Greetings,

Welcome to LoR, momo666!

Kindest regards,

James

 

[Elshamah]

First of all, Hello ! I am new here, I've found this forum due to MarsCydonia in his recent exchange about the cosmological argument.

I thought to ask here some questions I have since I got the impression some of you guys are well versed in biology ( among other fields ).

1) Can someone explain me how information works in the DNA? I hear this point repeated over and over by creationists; information can only come from a mind; we have never observed an increase in information due to genetical mutations.

The closest I've come to find an answer was Professor Lenski long-term E.coli experiment but this article basically tells that it wasn't really an increase of information but merely a "recycle" of the old one or if I understood it correctly, a genetic inhibitor was deactivated thus there wasn't really any "new" information added.

Admittedly it is a creationist website but you can see why a person not educated in the field of biology can take their points seriously. As far as I know they've also been beaten in court so that doesn't help their credibility "In 2005, a federal judge banned Pandas outright from science classrooms in Dover, Pennsylvania

— Casey Luskin, Evolution News & Views, Discovery Institute"

2)I've recently heard a creationist claim that epigenetics pose a threat to the theory of evolution but I'm kind of confused here. As far as I know epigenetics studies what turns off/on some genes, how the environment affects the genes. Hoes does that pose a thread to the theory?

Moreover, I've heard him claim something along the lines " Epigenetic information is not in the DNA; is in the structure of the cell itself, how could it be there if it didn't come from a mind?"

3) I've also heard him use the phrase "semiotic information in the DNA" but as far as I know semiotics has nothing to do with biology so I'm really lost here.

Although you don't need to watch it in order to answer my questions, I will post the youtube link so those interested can take a look at the exchange I'm talking about. Please note I'm not a participant there, I merely picked some questions from the discussion.
https://www.youtube.com/watch?v=w7FhphWDokA

The topic is the one Ian G started, the exchange is between Tyson Guess and Robbie Kay.


Lastly, I've skimmed through the board index a bit to see if my questions were asked before but I got no luck even though I'm sure this is not the first time someone asks something along these lines so if this was already answered and you don't want to lose time just direct me to the said topic. Hopefully I've posted this in the correct topic.

Thanks.

here you will find extensive writings about the issue :

http://elshamah.heavenforum.org/f16-information-theory-coded-information-in-the-cell

 

[he_who_is_nobody]

here you will find extensive writings about the issue :

http://elshamah.heavenforum.org/f16-information-theory-coded-information-in-the-cell

 

[Deleted member 619]

here you will find extensive writings plagiarism, quote-mines, lies and general ignorant bollocks about the issue

FIFY.

This poster is a liar.

 

[momo666]

Thank you all for the information and the welcomes. Sorry for the late reply.

I understand better now the information argument. I still have a few questions however.

1) Did the E.coli experiment (or any sort of experiment for that matter ) showed that mutations can add new "things" ? The most common argument I hear about that experiment is that the mutations merely switched ON a gene that allowed E.coli to digest "whatever they began to digest". That sounds rational.

It seems to me, that in order for mutations to add new information ( I shouldn't say " new information" I know...I don't know how else to put it), they need to add a "new thing" or replace/modify an existing gene by adding "new things". Switching a gene on/off doesn't really address the point of how the DNA got from simple to complex right?


I would also like you to add your opinion on the following arguments, if you can call it that. This, seems to me to be that last meaningful exchange there was between the two participants. I will put in green the points of the person that was arguing with the creationist.

" in most cases offspring contain different information to their parents"

So are you saying that information theory is incorrect?

"The very simple fact of the matter is that if an organic life form goes from a simple state to a more complex state it DEMANDS that new information is added"

I know many lay persons are under the impression that variation is the expression of new information but that simply isn't the case. Consider these comments from mostly atheist/agnostic sources: (taken from my library so I did put a modest amount of work in locating these statements). I will then do a little explaining of information theory.

I'll start with Darwin: "The number of intermediate varieties, which have formerly existed on the earth should be truly enormous. Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such graduated orgainic chain; and this, perhaps is the most obvious and gravest objection which can be urged against my theory" - The origin of species


"The extreme rarity of transitional forms, in the fossil record persists as the trade secret of paleontology" Stephen J. Gould

"We now have a quarter of a million fossil species, but the situation hasn't changed much. The record of evolution is s still surprisingly jerky and ironically, we have even frewer examples of evolutionary transition than we had in darwin's time" David Raup - Field Museum of Natural History


"When we do see the introduction of evolutionary novelty, it usually shows up with a bang, and often with no firm evidence that the fossils did not evolve elsewhere. Evolution cannot forever be going on somewhere else. Yet that's how the fossil record has struck many a forlorn palaeontologist looking to learn something about evolution. We Palaeontologists have said that the history of life supports the story of gradual adaptive change knowing all the while it does not" Niles Eldredge - American Museum of natural history


These statements by unbelievers are consistent with information systems.

If you were waiting on a text message then the probability of receiving any symbol (letter or space) is 1/27. The information added by each text is log2^27, so that information conveyed by a text 'm' symbols long will be mLog2^27. This should demonstrate that the amount of information conveyed is relative to the known size of the alphabet. If we add numbers it becomes now log2^37.

Suppose the message received is ZXXTRQ NJOPW TRP (16 Symbols including spaces).

The information content would be: 16log2^27 bits. We have just calculated the total possible syntactic information content possible. So then any system that has a finite number of parts and therefore a finite number of pieces of information has a limit to it's syntactic information. Now when we turn to the genetic code it too in any living system has a finite number of syntactical expressions but the semiotic meaning of the syntactical expressions are enormous (but also finite). The re-arrangement of one single syntactical piece of information could seemingly produce a totally different effect. It could, in fact, seem totally new but it is still just the re-arrangement of existing syntactical information. Just as if you received a text message "Throw the trash out when you get home" - there wasn't new information added syntactically (to the alphabet). It was just arranged in a way to carry a specific meaning (semiotics) which brings us to the final point. We only have evidence of semiotic information arising from intelligent sources and closed syntactic systems are by definition not capable of increasing their syntactical content.

So, when you say:

"a more complex state it DEMANDS that new information is added"

You are implying that closed systems can increase their syntactical informational content and we don't have any evidence to support that notion. It is effectively, 'wishful thinking' on the part of the atheist (regardless of any capitalized emphasis)

"A machine does not create any new information, but it performs a very valuable transformation of known information" - Leonard Brillouin


This is the first one. You don't need o address the quotes the creationist wilfully cherry-picked, the other guy already pointed that out and I myself did some research and saw the dishonesty the creationist displayed.

The second one is:

"The point I made was that information increases as life forms evolve into more complex organism"


This is a presupposition. We have no evidence that natural selection causes any increase in information. In fact, we only have evidence to the contrary. Now I agree that atheist biologists expect to find this, but so far we haven't. So yes, I disagree. You can say such a thing is so, but the moment you do you have to also say that Information theory and the law of decay are false. (as demonstrated with E. Coli and fruit flies even the slightest mutation causes death in an organism) Furthermore, mutation and natural selection can only happen in organisms that already have genetic information. The very word 'selection' implies there's something to select (that can't be accounted for by natural forces). Physics and chemistry no more determine the order of the information of the genetic code than it does the order of the english letters in the sentence you are reading. MInds determine messages and codes (semiotic information). We only have evidence of information arising from intelligent sources so we can safely conclude that any message had to be the product of intelligence. Why you might ask? Because natural laws don't create information rich messages. For example, If you told me - 'i'd believe in God if I walked out side and the stars arranged themselves in a message that said, Robbie, there is a god so quit being silly'. The underlying question is why would that be striking to you? The answer is exactly what I'm pointing to: Natural forces do not create information rich messages. Just as you would know that nature could not have done that on it's own we can say the same thing with the genetic code. But hold on, what supports this notion? 20 of the 26 animal phyla (representing distinct body plans) appear without any ancestral lineage in the cambrian explosion. Darwin was also unaware of the inner workings of the cell. He had no idea of the complexity of the machinery within it. But the problem doesn't stop there because DNA isn't the only controlling factor. There is also epigenetic information. DNA is involved in 5 levels of function, but levels 2-5 can't be performed by DNA alone. DNA is the instructions but it also requires precise structures, tissues, organs (epigenetic information). If you're building a house simply mutating the instructions doesn't build a more sophisticated building, just as mutating dna doesn't build a new body plan. There has to be both genetic and epigenetic information - information that is not stored in DNA and thus cannot be generated by DNA mutation.


Thank you for the responses you gave me. As soon as i have more time, I will take a look at other topics too, this forum seems to have alot of goodies. Can't decide from where to start reading

 

[SpecialFrog]

Just briefly, whenever you see a creationist quote Darwin, Gould or any other scientist, you should look here:
http://www.talkorigins.org/faqs/quotes/mine/contents.html

The quote is almost always a quote mine. More recent people -- such as Gould -- specifically rebutted most of the quote-mined versions of their statements.

On mobile so haven't gone through the quotes in detail but the Gould quote definitely doesn't mean what creationists pretend it does.

 

[Deleted member 619]

I'm on my hols at the mo, and posting from my mobile, hence the brevity of my responses, so more detail may have towait a couple of days till I'm home, but a couple of points.

1st, Lenski's E. coli experiments: What was added was a brand new gene that coded for a new protein that allowed them to digest citrates (see also nylonase, which had never been digested by any organism, because nylon was a brand new invention). If that's not 'new information,I don't know what is, and I feel like I have some expertise in information theory (Shannon-Nyquist theorem is central to my profession).

2nd, generally, every time two sexually procreating organisms reproduce, their offspring constitutes a brand new, never seen before, combination alleles, and that's even before we talk about the brand new mutations that occur with every single new organism (some 350 per generation for humans, if memoery serves). DNA is a pure Kolmogorov information system, which means that ANY cgange in the genes constitutes new information, regardless of whether the genome increases.

I'll come back to the rest when I have leisure, if you don't get satisfactory coverage in the interim but, suffice it to say for now that anybody who raises objections to evolution on the basis of information are ignorant twonks who know fuck all about either evolution or information.

 

[momo666]

I can't wait for your response. Take as much time as you need, I'm not in a hurry.

Also, perhaps a better way to phrase my 1st question would be "How does the genome increases?". Did Lenski's E. coli experiments increased the genome? Or any other experiment for that matter?

@SpecialFrog, thanks for the link, I visited it a few times already in the past. All in all, of course I knew from the very start he is not being honest, a bit of research confirmed my hypothesis.

 

[SpecialFrog]

I can't wait for your response. Take as much time as you need, I'm not in a hurry.

Also, perhaps a better way to phrase my 1st question would be "How does the genome increases?". Did Lenski's E. coli experiments increased the genome? Or any other experiment for that matter?

Short response: https://en.wikipedia.org/wiki/Evolution_by_gene_duplication

 

[Rumraket]

Thank you all for the information and the welcomes. Sorry for the late reply.

I understand better now the information argument. I still have a few questions however.

1) Did the E.coli experiment (or any sort of experiment for that matter ) showed that mutations can add new "things" ? The most common argument I hear about that experiment is that the mutations merely switched ON a gene that allowed E.coli to digest "whatever they began to digest". That sounds rational.

It seems to me, that in order for mutations to add new information ( I shouldn't say " new information" I know...I don't know how else to put it), they need to add a "new thing" or replace/modify an existing gene by adding "new things". Switching a gene on/off doesn't really address the point of how the DNA got from simple to complex right?

That is a deliberate and clever kind of lie creationists use about the experiment. Quite simply it isn't true.

You have to understand what happened in the experiment to see why it is wrong.

When the experiment started about 20 years ago, the E coli bacteria they used had a gene for transporting citrate into the cell, but it only got activated when there was no oxygen in the environment. So as long as the cells were growing and living in their little flasks, since there was oxygen in the air and mixed into their medium, the oxygen there was keeping the transporter gene inactive.

In other words, the genetic regulator that controlled when E coli would take up citrate and use it to make energy required that there was no oxygen present. If there was oxygen present, they could not use citrate and would instead use glucose in the growth-medium.

What happened over the course of the experiment was that some genes were duplicated(a type of mutation, called gene-duplication) and rearranged(inserted in other spots in the genome). One of those genes was the citrate transporter.

So the gene was duplicated (copied so there was 2 of them instead of 1), and the copy happened to be inserted in a place in the genome where it became under control of a different regulator. The regulator under the control of which it was placed, is a regulator that is active under aerobic conditions(when there is oxygen present).

So suddenly the researchers could see that the bacteria could grow in medium that contained citrate, but no glucose, even when oxygen was present.

Now you might argue, correctly, that both the citrate transporter and the regulator both existed before the experiment began. But what has been created is a new association between them that did not exist before. The gene has been put into another context where it now gives the organism a function it did not have before. This is both new information and a new function.

Lets take an analogy with written language. Suppose I write a book in English, only using normal English words. Have I not created any new information simply because the words already exist in other books? And all I did was move words around and copy them, putting them into a different order to create new sentences and new stories? That would of course be silly to claim. If the association between the words create new sentence structures, then the information conveyed by those sentences is new even if the words already existed in other books.

In this way the information created in the genome during the course of the experiment is also new, while the individual genes (from this particular example) all remained pretty much unaltered. But they were copied and put into new places so they could interact in ways they did not before.

The information conveyed by these two sentences is quite different, but they use the same "already existing words".
Will you do it?
Do you will it?

Googling around a bit(i copied all these from the internet) you see many clever examples(this one just move the position of "only" in the sentence):
Only he told his mistress that he loved her.
He only told his mistress that he loved her.
He told only his mistress that he loved her.
He told his only mistress that he loved her.
He told his mistress only that he loved her.
He told his mistress that only he loved her.
He told his mistress that he only loved her.
He told his mistress that he loved only her.
He told his mistress that he loved her only.

You can even modify these into conveying new information by just copying and inserting one of the words in a new place in the sentence, proving once again that making new word associations is in fact enough to create new information.
He told his mistress that only he loved her.
He told his only mistress that only he loved her.
There I just copied the word only and inserted it in another place.

Man bites dog.
Dog bites man. (this one is easy and you can make pretty much endless variations on this, they all convey different and new meanings)

 

[Rumraket]

I will be back later with a more comprehensive answer to your first post in this thread. I will try to cover all the topics.

 

[momo666]

Awesome. Now that you put it that way it does sure sounds nonsensical to say mutations don't bring any new information.

Can't wait for your next comment.

 

[Elshamah]

here you will find extensive writings plagiarism, quote-mines, lies and general ignorant bollocks about the issue

FIFY.

This poster is a liar.

point out where i lied, or retract.

 

[Elshamah]

Awesome. Now that you put it that way it does sure sounds nonsensical to say mutations don't bring any new information.

Can't wait for your next comment.

Mutations CANNOT produce a increase of information in the genome. Thats a lie you are being feeded with.

http://elshamah.heavenforum.org/t1664-mutations-cannot-produce-new-information?highlight=information

and even IF it could do so, it cannot account for the change of body plans.



Darwins doubt : pg. 204

Genes alone do not determine the three-dimensional form and structure of an animal. so-called epigenetic information—information stored in cell structures, but not in DNA sequences—plays a crucial role. The Greek prefix epi means "above" or "beyond," so epigenetics refers to a source of information that lies beyond the genes. "Detailed information at the level of the gene does not serve to explain form." "epigenetic" or "contextual information" plays a crucial role in the formation of animal "body assemblies" during embryological development.

Recent discoveries about the role of epigenetic information in animal development pose a formidable challenge to the standard neo-Darwinian account of the origin of these body plans—perhaps the most formidable of all. "the neo-Darwinian paradigm still represents the central explanatory framework of evolution," it has "no theory of the generative." neo-Darwinism "completely avoids the question of the origination of phenotypic traits and of organismal form." 1

Neo-Darwinism lacks an explanation for the origin of organismal form precisely because it cannot explain the origin of epigenetic information.

 

[SpecialFrog]

Awesome. Now that you put it that way it does sure sounds nonsensical to say mutations don't bring any new information.

Can't wait for your next comment.

Mutations CANNOT produce a increase of information in the genome. Thats a lie you are being feeded with.

http://elshamah.heavenforum.org/t1664-mutations-cannot-produce-new-information?highlight=information

By what measure of "information"?