Discussing the gaps in evolution theory

a reply to: peter vlar

Shhh some people think giraffes got long necks by stretching

One correction, some people are born unable to deal with lactose (I'm one of them). So congenital alactasia, a total absence of lactase. Its another mutation. Minor quibble

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.

The difference is that one can theoretically reconstruct the entire strand of DNA just from the data. However one could clearly not reconstruct your wife with perfect accuracy just from a picture. If we couldn't reconstruct the DNA just from the digital information then clearly we missed something when sequencing the genome, but there's no theoretical reason we cannot accurately sequence a genome and reconstruct it with enough accuracy so that it could work as DNA without a biological system realizing it was artificially created. It's like if I modeled an electric circuit with perfect accuracy and it behaved exactly like the real world circuit, then what's the practical difference? Both systems contain the same information at the end of the day. Just because one seems more "real" to me doesn't make it any more real. We could be living in a computer simulation right now for all we know, every single particle in our universe could just be bits of information on a highly advanced computer. Once again I will say, everything is information at the end of the day.

a reply to: ChaoticOrder

"Theoretically" does not mean in actuality. Just because something is theoretically possible, it does not mean it is practically possible.

A biological system is not going to "know" it is "artificial" or "natural", because you don't need to anthropomorphize it. I say this as a polytheist, with pantheistic leanings.

Its nice to throw "what ifs" around. But that is philosophy, not science. I like philosophy. It is not science. Though before you say "but many scientists have Doctors of Philosophy" in, I've got one, the "philosophy" is not that sort.

DNA has low information content, from a digital perspective.

I suggest reading this: Nijhout, H. F. Bioessays, September 1990, vol. 12, no. 9; p.443

So I am going to bring this back to a couple of people (including the OP), as this has gone way (WAY) off topic.

These gaps in evolutionary theory. What are they again? How does this quibling over "Data" pertain to it? Come now, lets be on topic, rather than avoid it.

a reply to: Barcs

I'm not saying computational biology is wrong, I'm saying that Information theory describes computer software, not biological systems.

Your problem is clearly a lack of understanding in the field of information theory. Information theory describes any informational system, and it happens that all systems in nature are informational systems that obey very specific laws. If you study advanced fields of physics and cosmology you'll begin to hear of matter being described in terms of bits, for example the Planck length is defined as "the square root of the Planck area, which is the area by which a spherical black hole increases when the black hole swallows one bit of information". Information theory is probably the most low level subject one could study because it's applicable to essentially every other field of science. It's completely irrelevant that computers compute using wires and silicon processors and biological systems compute with chemical reactions and other molecular interactions, at the end of the day they are both information systems obeying very specific laws. Our computers could work completely differently to the way they do now if history went a bit differently, but it wouldn't matter, they would still be general turing machines and they would be able to solve any Turing complete problem, software would still be called software regardless of how the underlying computations were performed.

a reply to: Noinden

"Theoretically" does not mean in actuality. Just because something is theoretically possible, it does not mean it is practically possible.

It doesn't need to be physically possibly, just because we don't have tools with a high enough level of precision to build DNA molecule by molecule doesn't detract from the point I'm making. You're clearly just saying anything now to get around the point I'm making. I truly have no idea why you're so against the idea of DNA possessing digital information. Do you even believe it holds any type of information, and if so what type of information exists in this reality besides digital information?

a reply to: ChaoticOrder

Then demonstrate how Information Theory fits so well for DNA please.

Address:

Shannon information

Kolmogorov complexity

What the unit of measure in a biological system is.

Thanks in advance

a reply to: ChaoticOrder

(a) How is this pertenant to the OP?

Ok that aside.

I am against it being seen as digital information. Because I've worked with it. I've worked with the physical DNA, culturing it, cloning it, isolating it, and yes sequencing the bloody stuff. Its not clean digital data. When I whip out the code in R, if I get a correlation to something in the 80% range I'm happy. Speaking as someone with honors level (4th year papers) in Statistics, thats crap. Utter crap, for making conclusive comments on something. Why? Because it is biological, an intertwined with a dozen or more other things. SO you get dodgy data.

I'm not getting around any point you are making. I disagree that it contains digital information. Yes there is an information aspect to it, its not digitizable, its low information content (from a digital perspective).

Using your analogies, do you see the pharmaceuticals I help create as containing digital information? Given the alphabet which makes them up is over 100 "letters long", ok no I take it back, it could POTENTIALLY be taken from 100s of "letters" (the elements).

Information is not digital. It should at least be trinary to be useful.

a reply to: Noinden

Address:

Shannon information

Kolmogorov complexity

I don't see why this is so complicated for you to understand. The molecules in a strand of DNA can be defined using bits of information. The resulting information is a representation of the DNA, just because we're using magnetized particles on a HDD to store the data rather than 4 base pairs doesn't some how tarnish the information. If we can fully recreate the DNA strand from just the information then no information was lost. We could attempt to estimate the Kolmogorov complexity of DNA by attempting to compress the data representing the DNA and see how small we can make it, but actually it's an uncomputable problem for any set of data.

a reply to: ChaoticOrder

Again this is "hand waving" and "what ifs" not science.

DNA is a very complex molecule, with its structure deciding its functions in a living system. "Information" is just the term we use to make sense of it. Whjen DNA is used to create proteins, it does not sent "info" to RNA or the building blocks, it just reacts with them chemically. There is NO message, just molecules in a chemical reaction. Unlike information, DNA can change between copies, and be perfectly functional (as evidenced by you not being a clone of your parents (one assumes))
Information does not react chemically with your brain when you say read it. DNA does react chemically. Above all, there has never been a form of information we have observed which can copy its self. No book, no data file, nada. So a book has a predetermined end product in mind, life does not.

So no, DNA is not "information" in the digital sense. It is how we "think about it" and that is an imperfect model.

a reply to: Noinden

Information is not digital. It should at least be trinary to be useful.

This statement doesn't make sense. Any base, whether base-10 or base-3, can be represented with a base-2 (binary) system. If you encode a string in base64, it looks like it's using 64 different characters, but it's still just a bunch of 1's and 0's inside the computer memory. Bits are the fundamental building blocks of all information.

a reply to: ChaoticOrder

Hmm ok I did not type what I was thinking there. Let me redo it.

Useful information is not digital, it should be more than binary (digital), it should be trinary. Do you understand what that means? It needs to be more than yes and no, 1 and 0, it needs a "maybe" in there.

You seem stuck in the world of computers, yes that is ironic given the mode of communication we have here.

a reply to: Noinden

Useful information is not digital, it should be more than binary (digital), it should be trinary. Do you understand what that means? It needs to be more than yes and no, 1 and 0, it needs a "maybe" in there.

That would not be a trinary (base-3) system, that would be more like a qubit system.

a reply to: ChaoticOrder

No it is trinary, aka three valued logic.

en.wikipedia.org...

That is far more value than binary, and that is just a place to start.

The universe is not black and white, 1 and 0, yes and no.

a reply to: ChaoticOrder

SO I am assuming you are ignoring the rest of that post? Out of your area you wish to comment on? How about how does this fit in gaps in evolutionary theory?

a reply to: Noinden

Whjen DNA is used to create proteins, it does not sent "info" to RNA or the building blocks, it just reacts with them chemically. There is NO message, just molecules in a chemical reaction. Unlike information, DNA can change between copies, and be perfectly functional (as evidenced by you not being a clone of your parents (one assumes))
Information does not react chemically with your brain when you say read it. DNA does react chemically. Above all, there has never been a form of information we have observed which can copy its self. No book, no data file, nada.

Of course DNA its self doesn't "do" anything, it's simply an information storage mechanism as I've been saying. The layout of the DNA determines how those chemical reactions will occur. I never claimed DNA shouldn't be able to change, if the information held in the DNA is altered in some way by changing the layout of the DNA then it will change how those chemical reactions occur, it makes perfect sense and doesn't go against anything I've said. DNA is the biochemical algorithm instruction set. Just because it doesn't use the same instruction set as a computer doesn't mean we cannot understand it in terms of computer science and information theory. It's still just a deterministic system obeying specific rules which can be modeled and understood.

Also the DNA doesn't copy its self, systems in the cell make copies of the chromosomes and then divide with the use of microtubule networks. Once again this comes back to the idea you cannot have a self replicating system without already having a pre-built system which can build a copy of its self. It really comes down to the way a single cell self-replicates because all life started off as single cell organisms, and when a baby is created it starts from a single cell which then begins to divide rapidly. It's still a sort of chicken and egg problem and it's why many people find it hard to believe the first self-replicating life form just occurred by chance, but as I see it when given enough time and space anything is possible.

a reply to: Noinden

Read the wiki page:

# in balanced ternary, each digit has one of 3 values: −1, 0, or +1; these values may also be simplified to −, 0, +, respectively;[1]

# in the redundant binary representation, each digit can have a value of −1, 0, 0/1 (the value 0/1 has two different representations);

#in the ternary numeral system, each digit is a trit (trinary digit) having a value of: 0, 1, or 2;

There is no "maybe" answer in that system, it's a base-3 system at the end of the day. There may be some slight speed advantages to a computer physically built to compute using trinary logic but it wouldn't be able to compute anything a binary computer couldn't compute. A quantum computer which uses qubits is the only thing which can give a "maybe" answer, because you can have superposition between the 1 and 0 state.

a reply to: ChaoticOrder

As I said you seem to be stuck in the idea of computers. We are in something much more complex . Where there are seldom black and white answers. The phrase "some indeterminate third value" is the important bit

a reply to: ChaoticOrder

The chemistry is DNA seems to have eluded you.

a reply to: Noinden

Sure I'm open to the idea that evolution has exploited the laws of quantum mechanics to its advantage, but your argument about the trinary system is flawed because it's still a type of digital information. Also you talk about "hand wavy" theories being undesirable, well what you are saying is very vague and unsubstantiated as far as I can tell. You cannot just say there's some mysterious "indeterminate third value" and not explain how such a concept relates at all the 4 base pairs used by evolution. You're just going on gut feeling and acting like its hard science.