Discussing the gaps in evolution theory

a reply to: Noinden

originally posted by: Noinden
a reply to: ChaoticOrder

Demonstrate that they are closely related. Saying that it is, and the fact that it is are two different things. I've degrees in Chemistry, Biochemistry and Bioinformatics, the last one if you don't know is a hybrid of Biochem/Genetics with COmp Sci, and Statistics. I'll say again, they are not that closely related.

I've already given multiple examples: redundancy, error correction, modularity. If you want more concrete examples of how we build algorithms based on biological systems then just look at neural networks. Deep neural networks are some of the most powerful algorithms known for solving high dimensional problems are they based on how real neural networks work. Of course they are very much simplified compared to the way real neural networks work but there is a lot of progress being made on understanding exactly how real neurons process information. There are also more clear cut examples, like algorithms for protein folding which generalize to several different problems.

Just like how nature was the inspiration for velcro, biological systems can very much help to inspire the development of algorithms. The wiki page for bio-inspired computing has a list of many more great examples. For example cellular automata algorithms are very useful for self-organizing systems and the way our cells and our nervous systems transmit information around our body can be very useful for developing ideas in the field of networking. Another example is the creation of artificial immune systems, which can prove useful for developing ideas in the field of virus detection and prevention.

I'm sorry but if you cannot see the relationship between these two topics then you're clearly not looking very hard. If you are a student of bioinformatics then you of all people should understand the relationship between biology and computer science. Just the other day I was reading "An introduction to Bioinformatics Algorithms" by Neil Jones and Pavel Pevzner, and I couldn't help but note the relation between the algorithms discussed in that book and real world algorithms which are used to solve many practical problems. Here's a quote from the book which is of particular relevance to this discussion:

Over the last forty years, computer scientists have discovered that many algorithms share similar ideas, even though they solve very different problems. There appear to be relatively few basic techniques that can be applied when designing an algorithm, and we cover some of them later in this book in varying degrees of detail.

a reply to: Noinden

It's a question of translation, interpretation and coding into another language. It is possible. DNA may not be binary code now, but that doesn't mean that the programming language of DNA cannot be elucidated and translated into other languages.
It's no different than translating a unique foreign language into your own language. It's just a matter of interpretation.
Think Rosetta stone.

a reply to: ChaoticOrder

See this is not how science works. You can "see" all the things you like, but they will still not be so. Feeling something is so, so "truthiness" is not part of science.

What is part of science?

Facts.

Facts which do not change with how you feel.

Thus Biology, and compsci are still completely separate.

Just as (for example) Swahili and tocharan are separate languages.

a reply to: Phantom423

Actually, you are correct. Code is code. It comes down to a question of translation, interpretation and confluence. The article below describes how DNA can store digital information. Binary code to a 4 letter code - a big leap technologically, but not a big leap when you realize that codes can be broken and reprogrammed into an entirely different language.

Exactly, the fact that DNA is encoded using 4 base pairs is proof right there it can be stored as digital information, and in fact we can and do store DNA sequences as bits of information on HDD's. There is absolutely no debating that DNA stores some type of information, and all information is measured with bits.

originally posted by: ChaoticOrder
a reply to: Phantom423

Actually, you are correct. Code is code. It comes down to a question of translation, interpretation and confluence. The article below describes how DNA can store digital information. Binary code to a 4 letter code - a big leap technologically, but not a big leap when you realize that codes can be broken and reprogrammed into an entirely different language.

Exactly, the fact that DNA is encoded using 4 base pairs is proof right there it can be stored as digital information, and in fact we can and do store DNA sequences as bits of information on HDD's. There is absolutely no debating that DNA stores some type of information, and all information is measured with bits.

of course dna stores information. that is the purpose of dna. but it sounds to me like you are suggesting that the storage of information implies some type of importing agency that updates dna information as desired. thats a bit of a leap.

a reply to: Phantom423

Actually it does mean it can not be translated into other languages. DNA codes for proteins (yes that is a gross over simplification). You can't type "four score and twenty years...." in English, and translate that to a living creature, similarly you can't wack your DNA into an Illumina HiSeq X Series and read a good novel.

Just because you are envisioning something to be so, does not make it thus.

The analogy of DNA as code is faulty, and limiting. Your DNA is doin what it does, doe to kinetics and thermodynamics, not because it is a language you can read.

a reply to: Noinden

All languages can be traced to a root - even if it's only categorically a "language". Language is language. If binary code is the language of current computer technology, then any other code, including DNA, is related to binary code because it is a language. Codes are languages. Nothing new here. It's just that the language of DNA hasn't been elucidated.
When it is, it will fall into the same category as other languages, no matter how complex it turns out to be.

Python, C+, Ruby on Rails, Java - these are all based on binary code. But they are all languages.

DNA will have its own root and other languages will be developed as subsets of the original.

a reply to: TzarChasm

Which is faulty, just because you need mathematics to do the sequencing. I also need mathematics to do the thermochemical calculations on my chemistry before I scale up. It does not mean Scale up Chemistry is mathematics

People seem to want to simplify things to wooden blocks and hope to put them in Square pegs do not go into round holes any better in adulthood do they chaps?

a reply to: Noinden

You are dead wrong here. It certainly IS mathematics.
You're a chemist and you don't understand scaling i.e. ratios? Please don't tell me that....

originally posted by: Phantom423
a reply to: Noinden

You are dead wrong here. It certainly IS mathematics.

it is math, but not supervised math. math doesnt require a foreman.

originally posted by: Noinden
a reply to: Phantom423

Actually it does mean it can not be translated into other languages. DNA codes for proteins (yes that is a gross over simplification). You can't type "four score and twenty years...." in English, and translate that to a living creature, similarly you can't wack your DNA into an Illumina HiSeq X Series and read a good novel.

Just because you are envisioning something to be so, does not make it thus.

The analogy of DNA as code is faulty, and limiting. Your DNA is doin what it does, doe to kinetics and thermodynamics, not because it is a language you can read.

Then you don't understand the word "code". Code is translational. Codes are written to convey meaning. It's a system of communication. DNA is no different. The code is translated into meaningful products. It communicates.

a reply to: TzarChasm

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

On another note...

It's good to see people questioning the suppositions of evolutionists....

a reply to: Noinden

Square pegs fall right through larger round holes...

a reply to: Noinden

See this is not how science works. You can "see" all the things you like, but they will still not be so. Feeling something is so, so "truthiness" is not part of science.

Seems to me that you feel there is some sort of "truthiness" to the idea DNA can not be digital information, although any serious scientist would clearly not agree with that statement and would see it as pseudoscience, that I guarantee you. So let me see the hard science behind such a claim if you want me to believe it.

Thus Biology, and compsci are still completely separate.

Yes the two subjects are separate things, but that doesn't mean there's no overlap between them. Didn't you just state bioinformatics is a "hybrid of Biochem/Genetics with COmp Sci, and Statistics"? Throughout history many seemingly unrelated fields have merged to form new subfields. The human body is a biological machine and it behaves according to biological algorithms, so of course the field of biology is going to have some bearing and some usefulness in the fields of computer science and information theory. People working in the field of artificial intelligence are expected to have quite a strong interdisciplinary background if they want to make good progress in the field.

a reply to: Noinden

And nucleotides are not called "codons" for no reason. It functions as information storage.
I don't see why this is such a far-fetched idea. It may be complex, but its essence is certainly
that of a code.

a reply to: Noinden

Also, I think you're confused on what "digital" actually means. It only means that two values are different and can be distinguished between each other. Hence, 0 and 1 - they are different - they are coded in such a way as to distinguish different things. It's more complex than that, but I suggest you look up the meaning of "digital".

a reply to: Noinden

The analogy of DNA as code is faulty, and limiting. Your DNA is doin what it does, doe to kinetics and thermodynamics, not because it is a language you can read.

So the rate constants and heat transfer to energy and work govern DNA mechanisms? How does that work?
Temperature, energy and entropy are inherent in all systems - think your teapot on the stove.
What you forget (or don't understand) is that systems - organic and inorganic - have structure and energy functions i.e. bonding angles,etc.
But systems which can REPRODUCE themselves, which are translational, and produce a product are systems governed by a language - i.e. a code. A rose doesn't bloom because of its kinetic or thermodynamic properties. It blooms because there's a code that programmed the plant to produce a rose. The temperature, energy, entropy - whatever are ancillary

a reply to: Noinden

The analogy of DNA as code is faulty, and limiting. Your DNA is doin what it does, doe to kinetics and thermodynamics, not because it is a language you can read.

It's not limiting at all, in fact it's a very powerful way of looking at DNA. You're looking at the human body as a physical system made of molecules and then abruptly concluding such a system has no relationship to a computer because it functions very differently, but that is a flawed conclusion. Evolution is simply using what it has available to it, and that happens to be molecules and the laws of chemistry. So it comes up with biological algorithms which exploit the laws of chemistry to achieve very specific results. Technically I could program a very accurate model of particle physics and simulate real biological life if I had enough computing power. Once again I will say, everything is information at the end of the day.

The thing which really makes biological systems such as humans hard to conceptualize in terms of information is that you cannot build a human without already having an adult human female and some sperm. The female reproductive and incubation system is required to construct the new baby human from the DNA in the egg and sperm. But this is still an entirely algorithmic process. The cells divide and multiply according to very specific rules, new proteins and molecules are produced according to data encoded in the DNA. Little molecular machines build new amino acids and proteins based on the instructions encoded in the DNA. This is an algorithmic process, regardless of whether it uses chemical potentials or what ever, it doesn't matter, computers are general turing machines and can algorithmically simulate these processes.

a reply to: ChaoticOrder

So it comes up with biological algorithms which exploit the laws of chemistry to achieve very specific results.

Bravo. Well said.

originally posted by: ChaoticOrder
a reply to: Noinden

The analogy of DNA as code is faulty, and limiting. Your DNA is doin what it does, doe to kinetics and thermodynamics, not because it is a language you can read.

It's not limiting at all, in fact it's a very powerful way of looking at DNA. You're looking at the human body as a physical system made of molecules and then abruptly concluding such a system has no relationship to a computer because it functions very differently, but that is a flawed conclusion. Evolution is simply using what it has available to it, and that happens to be molecules and the laws of chemistry. So it comes up with biological algorithms which exploit the laws of chemistry to achieve very specific results. Technically I could program a very accurate model of particle physics and simulate real biological life if I had enough computing power. Once again I will say, everything is information at the end of the day.

The thing which really makes biological systems such as humans hard to conceptualize in terms of information is that you cannot build a human without already having an adult human female and some sperm. The female reproductive and incubation system is required to construct the new baby human from the DNA in the egg and sperm. But this is still an entirely algorithmic process. The cells divide and multiply according to very specific rules, new proteins and molecules are produced according to data encoded in the DNA. Little molecular machines build new amino acids and proteins based on the instructions encoded in the DNA. This is an algorithmic process, regardless of whether it uses chemical potentials or what ever, it doesn't matter, computers are general turing machines and can algorithmically simulate these processes.

would you care to explain how this constitutes as a "gap in evolution"?