Discussing the gaps in evolution theory

a reply to: Phantom423

Excuse me, where did I say I don't understand those things?

What I said, (rather than what you read) is that they are not the same thing. Mathmatics is a simple blunt tool. Chemistry on scale requires understanding of kinetics, thermodynamics, mechanisms, rates of addition, sheer of the impeller etc. It is why there are no simple formulae for scaling up chemistry.

Similarly when one does bioinformatics, one uses complex statistics. Even then the level of correlation is statistically dubious. Why? Because it is complex.

Thus they are not the same thing.

So in short, you can't apply the same rules.

a reply to: ChaoticOrder

What pray-tell is "digital DNA"? You are confusing the use of DNA as a storage medium for data, with the biological function of DNA.

I don't care what you believe, I post here as a counterpoint to those who don't actually do the science.

You make the claim that DNA can be digitial information. Post the peer reviewed articles. Not a news blurb, not a popular science feel good piece. Post the actual science.

a reply to: Phantom423

Codons were named such, before the complete function of DNA was understood. So the name has stuck, while they are more than just CODE.

a reply to: Phantom423

I am not confused what digital means neighbour. I understand the language very well. I can code. Thus if you look at the "code" which DNA is involved in, it is not digital.

a reply to: Phantom423

What part of "I hold degrees in Chemistry and Biochemistry' was not clear.

Tell me do you not get, DNA does what DNA does, because of the chemistry. Because of bonds forming, and breaking, because of bond angles. That is kinetics (how fast), thermodynamics (how much energy). Not because it reads as such. That last bit, is people trying to grasp bits they can't understand, and make it simpler. It remains the chemistry is what governs what goes on.

a reply to: ChaoticOrder

See here is the thing. Models are not reality. All that matters here is REALITY. You can model something to infinity, then because it is simple, it misses something, and it does not work. Thats why computational chemistry (let alone biochemistry or Genetics) is pretty much limited to academia.

a reply to: TzarChasm

It does not. Its someones pet project or wishes. Wishes do not science or reality make.

a reply to: Noinden

What pray-tell is "digital DNA"? You are confusing the use of DNA as a storage medium for data, with the biological function of DNA.

Sequence a human genome. Store it as bits. That's DNA as digital information. When you have a child with a member of the opposite sex, the child gets half their genes from you and half from the other parent, information is preserved and propagated in that process. Like I said you still need a living human to interpret the DNA and use it to create a new human, but this is something virtual evolution can simulate. I didn't really want to reveal this information, but I will just to explain why your argument is flawed. The way I plan to design my next genetic/evolution algorithm is to build the creatures out of components analogous to the way real creatures are built out of molecular components. However instead of using molecules the components are more abstract building blocks for performing different types of computational operations but I don't want to go into too much detail. Essentially each creature has a DNA sequence which it can pass onto offspring and the DNA describes how to build a new creature.

However the DNA itself contains instructions for building the reproduction system, so in order to create a new offspring you first need a creature which has been built with a reproduction system. When a creature is fed the DNA sequence of a new offspring, it will use its reproduction/incubation system to build a new creature. So the process for building a new creature is encoded in the DNA, but first you need a fully built creature to interpret the DNA and use it to build a new creature. This is some what related to the chicken and the egg problem which arises when attempting to create a compiler in the source programming language that it intends to compile so that the compiler can compile its own source code. We could even go a step further and allow the algorithm for generating offspring DNA when given DNA from two parents to also be encoded in the DNA. The point I'm making is, these levels of DNA functionality do not detract from the point DNA holds information at the end of the day.

The way I like to think of it, DNA is the software which contains instructions for building the hardware and how that hardware should behave once it has been constructed. All information requires a physical medium for storage, certain types of molecules are the medium used by DNA. By its self the DNA is useless because it requires existing hardware to interpret the code. An analogy would be, if computers could self replicate, they would store the DNA code on their storage drive and it would contain instructions for building a whole new computer, such as how the circuits should be laid out and where things like capacitors and resistors should be located. Then parts of the DNA would also act as a sort of operating system, being used by the hardware to determine how the computer functions, what it should do in different situations, etc. In order to produce offspring the computers would also need hardware capable of building new hardware, which wont happen with real computers obviously, but can be simulated in a more abstract fashion.

See here is the thing. Models are not reality. All that matters here is REALITY. You can model something to infinity, then because it is simple, it misses something, and it does not work. Thats why computational chemistry (let alone biochemistry or Genetics) is pretty much limited to academia.

It's limited to academia because the computations require super computers. You're skipping around the core point I made and also nothing in nature has infinite precision due to QM, a fact you seem to totally ignore. Not everything needs to be modeled with perfect accuracy either, computers aren't limited to chemical reactions like biological systems are, the ability to solve problems analytically and algorithmically with the use of random access memory allows many complex real world systems to be simplified into tractable computational problems. Also just because a problem is very hard to model doesn't mean there's something mystical happening and we will never be able to simulate it.

originally posted by: Noinden
a reply to: Phantom423

What part of "I hold degrees in Chemistry and Biochemistry' was not clear.

Tell me do you not get, DNA does what DNA does, because of the chemistry. Because of bonds forming, and breaking, because of bond angles. That is kinetics (how fast), thermodynamics (how much energy). Not because it reads as such. That last bit, is people trying to grasp bits they can't understand, and make it simpler. It remains the chemistry is what governs what goes on.

The part that's not clear is - how can you hold a degree in chemistry and/or biochemistry and not understand the basic concept of a code? If there wasn't a code, the DNA molecule could not translate or replicate. And it does both.

Transcription: DNA to RNA to AMINO ACIDS

Translation: RNA to AMINO ACIDS and PROTEINS

If there was no information packed into the DNA molecule, none of that would be possible. Chemistry IS NOT a code. Chemistry is the interaction of matter and energy. Chemistry is formulaic - it requires the correct information as input to obtain the correct output. That information comes from the CODE INHERENT IN THE DNA MOLECULE.

And you are wrong on "codons". The four bases - adenine, guanine, cytosine, thymine - still form base pairs.

How Much Information Does DNA Encode?

The simplest answer to “How much information does DNA encode?” is “enough data to completely specify an organism’s particular genome and epigenome.” That involves the number of base pairs and the number of possible sites for adding a suppressor. Human DNA has approximately 3 billion base pairs, according to the National Human Genome Research Institute. That means 4^3,000,000,000 possible base sequences. For simplicity, let’s say that each gene is either suppressed, or not, in the epigenome. That would be a binary choice for each gene. Most humans have between 20,000 and 25,000 genes. Let’s say the average is about 2^22,500 more choices. The length of DNA varies for different species. Humans, with about 3 billion base pairs, have neither the largest nor smallest genome. Normally we specify the “amount of information” in bits; so 2^n choices requires n bits. Note that 4^j = (2*2)^j = 2^(2*j). Therefore human DNA genome encodes 4^(3 billion) = 2^(6 billion) choices, or 6 billion bits of information. The epigenome encodes at least 2^22,500 choices, or 22,500 bits. The total information is 6,000,022,500 bits, or approximately 6 Gb (gigabits). We usually discuss computer storage in bytes rather than bits. 6 Gb would amount to 6/7 = 0.857 GB (gigabytes), or 857 MB (megabytes), using ASCII code.

a reply to: ChaoticOrder

I understand that DNA functions LIKE computer software, but that doesn't make it computer software.

I'm not saying computational biology is wrong, I'm saying that Information theory describes computer software, not biological systems. If you can prove that it is actual software rather than biological functions being performed, I'm all ears. Maybe we haven't recognized it yet, and we'll discover that it is software one day, but for now it's still a mystery, and it relies heavily on our interpretation of the code.

Is there evidence of codes that control the functions of the software? Thus far the only coding is in the nucleotides which relate to the gene sequences that get passed down, but what about the codes that should control the things you mentioned like transcription. Where do we find those? Everyone just looks at the nucleotides, and sees the code, but where is the code that controls the actual functionality? DNA contains code, but it isn't a code in itself and isn't computer software (as far as we know). Humans interpret the arrangement of the nucleotides as a code, but we create this meaning. What I'd like to see is evidence of programming, which means finding the programming language of DNA if it exists.

The big issue with computer simulation theory is that it is not logical to waste code, which is what is happening when you look at the 99.9% of the universe that is hostile toward life and just takes up space. Why program quasars, supernovas, gamma ray bursts and other things that can instantly wipe out entire civilizations? Why program 400 billion stars in a single galaxy and several hundred billion galaxies, when most of those stars can't even support life? As somebody with experience in programming, it is highly illogical from a programming standpoint to waste such an exorbitant amount of memory on such things that would ultimately compromise the integrity and efficiency of the program? And then you have to figure out how to program consciousness which is a riddle in itself. I'm not saying it's impossible, it just doesn't make sense from a programming perspective to add all kinds of irrelevant things that waste space.

originally posted by: 5StarOracle
a reply to: TzarChasm

DNA is constantly being scanned and rewritten removing any errors ensuring it stays the way it is...

Except for the FACT that numerous genetic mutations are caused by errors in copying. Woops!

a reply to: Phantom423

Again, you saying I don't understand it, does not mean I do not. What I am saying is and read very closely:

DNA is not like computer code. Thus information science does not apply too it.

So stop applying the big lie technique to what I say. mmK?

a reply to: ChaoticOrder

I've sequenced a few genomes in my day. The data is not the genome. The genome is the actual DNA, the sequence is the equivalent to a picture of the DNA. Using your logic here, I can take a picture of my wife, and that picture IS my wife. Clearly that is wrong.

originally posted by: Noinden
a reply to: Phantom423

Again, you saying I don't understand it, does not mean I do not. What I am saying is and read very closely:

DNA is not like computer code. Thus information science does not apply too it.

So stop applying the big lie technique to what I say. mmK?

You haven't provided any evidence that contradicts what was already posted. If the genetic code illustration I posted above is incorrect, then it's up to you to explain - by example - why it is so. You say you understand "it", but you only say it - you explain your alternative interpretation. If you were in a lab and you understand how sequencing works, to include the instrumentation, then explain why the sequence below DOES NOT code for specific amino acids. If it isn't a code, why does the order of bases result in those specific amino acids.

originally posted by: Noinden
a reply to: ChaoticOrder

I've sequenced a few genomes in my day. The data is not the genome. The genome is the actual DNA, the sequence is the equivalent to a picture of the DNA. Using your logic here, I can take a picture of my wife, and that picture IS my wife. Clearly that is wrong.

What is the human genome? A genome is the complete set of nucleic acid sequence for humans encoded as DNA within 23 chromosomes.

What is a nucleic acid sequence? A nucleic acid sequence is a succession of letters that indicate the order of nucleotides within a DNA (using GACT) or RNA (GACU) molecule.

Is DNA a code? Yes. It is a four-letter language, which contains the information needed to build the entire human body.

What is a gene? A gene is a unit of DNA that carries the instructions for making a specific protein or set of proteins.

Now - if the sequence is only a "picture" of DNA, what is the significance of the order of nucleotides? If the succession of nucleotides is meaningless and does not code for specific amino acids and peptides, where does that information come from? If the information is not a set of instructions i.e. a code, what is it and where is it???

originally posted by: Noinden
a reply to: ChaoticOrder

I've sequenced a few genomes in my day. The data is not the genome. The genome is the actual DNA, the sequence is the equivalent to a picture of the DNA. Using your logic here, I can take a picture of my wife, and that picture IS my wife. Clearly that is wrong.

BTW, what instrumentation were you using to sequence and why were you doing it? Did it relate to some protein product that that particular sequence was associated with or was it just a random jumble of nucleotides?

a reply to: Phantom423

Stop interpreting what I write. DNA is not computer code, the "laws" of information technology do not apply.

End of statement. We've had this very same debate in other threads. Go read my responses there.

But in short

www.npr.org...

rationalwiki.org...

a reply to: Phantom423

When one tries to grossly oversimplify a complex idea, one looses resolution. Your explanation is about as resolved as an 8bit picture.

a reply to: Phantom423

I was using some next generation sequencing (Illumina and a Roche 454). Why? We were looking for a synthetic lethal sequence in a form of cancer, so as to silence one of the genes, and thus selectively kill the cancer, over the healthy cells. Its propitiatory beyond that, and I'm not going to say more. I work in a CRO if that explains why I'm being cagey over the details

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...