Discussing the gaps in evolution theory

a reply to: ChaoticOrder

Once again you focus in on computers. You ignore the chemistry, you ignore the science. This is a thread on evolution. Your thread no less.
My point is the five bases involved in genetics (yes 5 RNA us involved which adds a fifth) are not on it off. Thus for digital DNA you need the equivalent of a 1 and a 0! You can't even say what the simplest unit of data in DNA is. Yes you dodged that question!

You are seeking confirmation for your simulated reality. All you get is confirmation bias! Stay on topic!
So talk evolution.

a reply to: Noinden

Thus for digital DNA you need the equivalent of a 1 and a 0! You can't even say what the simplest unit of data in DNA is. Yes you dodged that question!

The point you cannot seem to grasp is that by arranging molecules in a certain order you are storing digital information. There's a finite number of ways the molecules can be ordered together so it's perfectly possible to describe such a system as a method of storing digital information. The simplest unit of data is always a bit in any system which has a finite number of arrangements. This is not me "focusing on computers", this is a low level interpretation from the perspective of information theory. I'm obviously not an expert on how DNA is structured, but it's clearly made of a limited number of molecular components, and by arranging those components in different ways it's able to contain information. The hexadecimal system (base16) has 16 different symbols which can be arranged in different ways to store data, but the base we use to represent the data is irrelevant because it's possible to convert base16 into base10 or base64 or any other base, including base2 (binary), because all information is fundamentally made of bits.

a reply to: ChaoticOrder

Yep you dodged the questions to go right to information theory. Either talk evolution and start a new thread or admit you never intended this to be a Thread for anything else but information theory

originally posted by: Noinden
a reply to: ChaoticOrder

Yep you dodged the questions to go right to information theory. Either talk evolution and start a new thread or admit you never intended this to be a Thread for anything else but information theory

Dude you're the one who came in here trying to use my thread as a platform to push your nonsensical theories about DNA. I just rebutted your posts I didn't agree with and allowed the thread to go where the conversation was naturally heading because that's how I like to handle my threads. As long as the discussion is some what related to the initial topic of the thread I don't mind if it drifts a little bit. When ever I make a solid point your only response is to tell me I'm going off topic in my own thread. Try harder.

Edit: Also I'm not dodging the question, I'm giving you a very clear answer. Just because the molecules which make up DNA are not little 1's and 0's doesn't mean DNA cannot be represented using binary data. If I have some match sticks in 5 different colors I can create a base5 system and create a message by lining up the matchsticks in different orders. It doesn't really matter what I'm using, different types of molecules will work just as well. The binary data is not exactly the same thing as the physical DNA, just like the data describing the order of matchsticks would not capture the physical structure of the wood in the matchsticks.

I do understand the point you are trying to make, but it's simply not a valid point when you view it from an informational perspective. DNA does nothing more than act as an information storage and propagation unit. It's the complex systems in the cell which made use of the DNA to generate amino acids or whatever, by reading along certain DNA sequences which causes certain reactions to occur. DNA its self has no motive or independency, and although it may interact with the cell components in many complex ways, none of that detracts from the underlying point that the DNA is an information storage mechanism and instruction set.

a reply to: Noinden

originally posted by: Noinden
Where exactly is it ever stated DNA will replicate with perfect fidelity. The mechanisms in cells, to maintain the fidelity of genetic material, are flawed, because it is a natural process. So anyone who states "DNA is supposed to remain perfectly the same" has never moved away from models, and looked at reality.

I don't know where that would be stated, perhaps nowhere. But you touched on my point (see underlined).

If mutations are considered to be "errors" then DNA is supposed to replicate with perfect fidelity, otherwise they wouldn't be classified as errors. Interestingly, it is these "errors" (mutations) that play a significant role in the evolution of life. If DNA actually replicated with perfect fidelity then there would be little to no evolution (assuming the role of epigenetics plays no significant role). So it's either DNA is supposed to mutate (in which case not all mutations are necessarily errors), or it isn't. Which is it?

Also, is It really an error if the mutation confers a benefit [or remains neutral] to the organism thereby ensuring further propagation of that gene? Isn't this what is supposed to happen?

originally posted by: Noinden
Again this is why you can't use information theory to properly model DNA. For one, have you ever seen computer code that self replicates, as a consequence of its chemsitry? Oh wait no you have not. Back to the fact, DNA is more than Data, it is chemical potential. It by its very nature replicates.

Regardless, there is still information in DNA. That part really shouldn't be debated. You want to call it chemical potential, okay fine maybe it is. But how does this translate into different types of functional self-sustaining self-replicating intelligent biological systems many of which are perfectly suited to survive in their environment?

originally posted by: Noinden
a reply to: ChaoticOrder

The chemistry is DNA seems to have eluded you.

Why don't you write that out in chemical notation?

a reply to: Noinden

My point is the five bases involved in genetics (yes 5 RNA us involved which adds a fifth) are not on it off. Thus for digital DNA you need the equivalent of a 1 and a 0! You can't even say what the simplest unit of data in DNA is. Yes you dodged that question!

The researchers at Microsoft's Molecular Information Systems don't seem to have the problems you have with digital DNA:

"First, the researchers developed a novel approach to convert the long strings of ones and zeroes in digital data into the four basic building blocks of DNA sequences — adenine, guanine, cytosine and thymine.

“How you go from ones and zeroes to As, Gs, Cs and Ts really matters because if you use a smart approach, you can make it very dense and you don’t get a lot of errors,” said co-author Georg Seelig, a UW associate professor of electrical engineering and of computer science and engineering. “If you do it wrong, you get a lot of mistakes.”

The digital data is chopped into pieces and stored by synthesizing a massive number of tiny DNA molecules, which can be dehydrated or otherwise preserved for long-term storage."

www.washington.edu...

In order for this storage mechanism to work, the reverse process must work - in other words, the DNA sequences which were initially digitized must be read back with fidelity from the digitized nucleotide sequences. That says everything you need to know about DNA. It can be digitized forward and backward.

a reply to: ChaoticOrder

Moving of goal posts has commenced.... yep it was that time.

a reply to: Phantom423

Yet more goal post moving.

The topic of the thread,

Gaps in the theory of evolution...

a reply to: PhotonEffect

So enumerate these other "self functioning self replicating intellegent biological systems" which don't use DNA.

The fact remains, saying DNA is "information" is a gross understatement, and poor understanding of what DNA is and does.

It is also off topic for this thread.

originally posted by: Noinden
a reply to: Phantom423

Yet more goal post moving.

The topic of the thread,

Gaps in the theory of evolution...

You can't answer the posts - so yes, back to gaps in evolution.

You also can't write out your chemical hypothesis in notation. Nor can you respond to the research that Microsoft's Molecular Information Group has done. That research effectively cancels your theories of DNA as some mysterious chemical entity that functions all by itself and has no relationship
to a code.

originally posted by: Noinden
a reply to: PhotonEffect

So enumerate these other "self functioning self replicating intellegent biological systems" which don't use DNA.

The fact remains, saying DNA is "information" is a gross understatement, and poor understanding of what DNA is and does.

It is also off topic for this thread.

The fact remains, saying DNA is "information" is a gross understatement, and poor understanding of what DNA is and does.

Should we send that to the Microsoft group???

originally posted by: Noinden
a reply to: PhotonEffect

So enumerate these other "self functioning self replicating intellegent biological systems" which don't use DNA.

It would be helpful if you responded based on what I actually said and not what you think I said. Please go back and read it.

originally posted by: Noinden
a reply to: PhotonEffect
The fact remains, saying DNA is "information" is a gross understatement, and poor understanding of what DNA is and does.

Again, go back a reread slowly what I actually said. No one here is saying DNA is information, only that it stores it or is within it.

Oh and DNA doesn't do anything. It's a completely passive molecule

originally posted by: Noinden
a reply to: PhotonEffect
It is also off topic for this thread.

Have you also added ATS moderator to your laundry list of credentials? Perhaps I missed it?

originally posted by: 5StarOracle
a reply to: Barcs

That sounds good and all but it's the mutations that affect the copying... And that's not a good thing...
But what you said is false or at least rather misleading...
While I am sure replication errors occur I believe it is because of other variables such as radiation for example which hinder the natural process... Like a virus causing problems in the code leading to abnormal function and improper performance and function... Or in other words causing a mutation from the norm...

No, it's not false or misleading. Error in copying is one of the CAUSES of genetic mutations. Sometimes they just don't copy properly, it has been studied and confirmed. For an advanced code written by an intelligent designer, that doesn't sound very advanced.

evolution.berkeley.edu...

a reply to: Phantom423

No you refuse to acknowledge the replies. There is a difference.

What exactly do you think "chemical notation is" neighbour. A stoichometrically balanced equation? Perhaps a reaction mechanism? What? This is not a media which deals well with chem draw.

originally posted by: Noinden
a reply to: Phantom423

No you refuse to acknowledge the replies. There is a difference.

What exactly do you think "chemical notation is" neighbour. A stoichometrically balanced equation? Perhaps a reaction mechanism? What? This is not a media which deals well with chem draw.

You're the one who should answer that question. You said that DNA was all chemistry, that code was impossible, that it didn't exist. So it's for you to describe the chemical reaction you have stated over and over again. This should be a simple matter for you - even though you have zero references to support your position.

And what do you want a reply to? You don't ask questions. You only make statements. Ask a question. I guarantee an answer.

a reply to: ChaoticOrder

I'm curious how the coding of DNA is a gap in evolution. I'll agree to disagree about information theory. I'm more interested in how this all applies to evolution and constitutes as a gap. A few people asked you this already and I don't think I saw an answer. If you already addressed that I apologize.

Thanks,

a reply to: Barcs

I was thinking perhaps the OP's title "....Gaps in Evolutionary Theory" is misunderstood. Here's a quote from the OP's first post:

The real reason is because one of my main interests as a programmer is designing systems which can simulate the process of evolution in order to generate solutions to problems without any input from the programmer. In order to design the best possible simulations I must have a very good understanding of how evolution actually works.

I think what he/she is looking for is a way to strip down DNA to a very basic set of algorithms - perhaps even just one algorithm - program the algo and let it run. The problem, as the OP acknowledges, is that the impact of variables can't be programmed into the model. You could certainly test a bunch of variables i.e. program catastrophic events, no events for millions of years, too much water, too little water - ad infinitum, and then observe what happens. But the design of the experiment would have to start with single stranded RNA and observe how double stranded RNA evolved and then on to DNA as the major storage molecule complete with code.

By necessity, the program would have to be able to solve its own problems i.e. how does it adapt to its environment and how does it replicate. There are self replicating programs called quines - don't know anything about them - but I also remember something from robotics a while back which may be related. I have to look it up.

Just my thoughts - at the end of the day, the OP is actually proposing to program life because if he/she could elucidate the language of single stranded RNA, then the sky's the limit, I guess.

a reply to: Barcs

I never said the coding of DNA is a gap in evolution. I'm saying that if we have a gap in our understanding of evolution then we also have a gap in our understanding of how the informational and algorithmic processes behind DNA work.

a reply to Phantom423

But the design of the experiment would have to start with single stranded RNA and observe how double stranded RNA evolved and then on to DNA as the major storage molecule complete with code.

Yes you're pretty much understanding how I want to approach this problem but it's not necessary to simulate things like RNA or actual particle physics. Computers have much more efficient ways of copying and computing information so the best approach is to take advantage of the strong points a computer has. The way I like to think of it, anything in nature can be simulated using a Turing machine, the problem is finding the right algorithm and the most efficient algorithm to solve the problem. The end goal is to create a system which will evolve algorithms which can solve specific tasks, concepts like food and water never come into play because we're talking about virtual life forms, and there's not much practical benefit to judging them on how well they can find food and water. The creatures can essentially be thought of as computing systems, so rather than building them out of virtual molecules, we use more abstract building blocks, things which are more akin to virtual electrical components.

The creature would be made of up components such as virtual transistors and virtual wires which connect different components together and form virtual circuits. However when you actually start thinking about it, these virtual electrical components are really just performing some basic mathematical operation. For example a resistor will simply multiply the input by some value between 0-1 depending on the amount of resistance. A capacitor will simply keep adding the input to some temporary memory until the number in that memory reaches a threshold. At that point the output of the capacitor is activated and set to the value of the temporary memory, and the temporary memory is reset to reflect the idea the capacitor has discharged its stored energy. Essentially any electrical component has this type of simplified mathematical representation; a diode only allows either negative or positive numbers as input, a wire simply outputs the input, etc.

This is why I say it's best to think of the components as abstract building blocks for performing different types of computational operations. There's still some details I haven't talked about, like how these components can be used to interact with some memory array allocated to each creature and how that helps make the system capable of solving any computable problem, but you should get the general point I'm trying to convey here. Basically the idea is to evolve virtual computers, but they should have their own system of self replication, like a computer that can build new copies of its self. Of course I will have to design the very first reproduction system myself because it'll be very unlikely to arise without my help, I mean who knows how many billions of years it took before the first self replicating life appeared by chance on Earth, I don't have that kind of time. This is why I said it's kind of like designing a compiler which can compile its own source code, although it may be more like designing the very first compiler in machine code before we even had programming languages.

a reply to: ChaoticOrder

I found some interesting research related to your project. I'm wondering whether the program Adami wrote, "Avida", could be considered a "Turning complete" program? It would be interesting to know how he programmed replication.


Virtual Life-Forms Mutate, Shedding Light on Evolution
By John Roach
for National Geographic News
May 7, 2003

(Excerpts)

Digital Evolution

Ever since Charles Darwin theorized about evolution in the 19th century, biologists have believed that complex features such as eyesight must have arisen through many steps and that some of the intermediate steps must have served different functions from what is observed today.
But while functions change, biologists have assumed that each step along the path to a complex new function is a step up—an improvement—in terms of producing an organism that is better adapted to its environment.
The problem is that evolution in the natural world is a slow process, making it difficult to watch the process play itself out and thus test these assumptions, said Lenski.
To speed things up, he and his colleagues placed digital organisms in a computer environment that was programmed to allow the organisms to replicate, mutate, and compete.
"We created a world in which these things are possible and the right organisms can take advantage of it," said Adami, a physicist, who designed the simulated environment to allow the evolutionary process to work as it does in the natural world.

The researchers use the computer program designed by Adami, which is called Avida. The program is basically an artificial petri dish in which organisms reproduce and if they evolve the right skills, can perform mathematical calculations to obtain rewards.

The digital organisms solved the most complicated problem by borrowing and modifying bits and pieces of the "genetic code" that their ancestors had used to solve the simpler tasks, just as predicted by Darwin.

The surprise, says Lenski, is that the evolutionary process is not a ladder in which the fittest organisms are descended from the fittest organisms in earlier generations. Instead, some mutations are harmful in the short term but can set up subsequent changes that are quite beneficial.

"What we are able to do is show how all components of the evolutionary process, the random and non-random, get together to form a highly complex gene which could not have evolved by random drift," said Adami.
This research is funded by a grant from the U.S. National Science Foundation.


Link to Adami's lab and publications: adamilab.msu.edu...

My question is does this research really give us any additional information as to how RNA/DNA is coded? Does it give us any clues to the language? Adami describes a very mechanical process - similar to what you were referring to with electronics - but to me the real question is what is the most fundamental algorithm which can be written which would lead to the same outcome AND could we code the algorithm into an RNA molecule and discover how it actually develops.