DNA as a programming language

[Vaccine]

In this peer-reviewed publication they find the "redundancy of the genetic code enables translational pausing". Which alone is fascinating, but in reading about how they found this out was the interesting part:

"Previously, evolutionary biologists have not been aware of the conceptual complexity required for genomic programming"

"We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties."

"Within the genome domain, executable operations format, read, write, copy, and maintain digital Functional Information (FI)"

"They reveal the ribosome, among other things, to be not only a machine, but an independent computer-mediated manufacturing system"

"We show in this paper that the bit patterns representing TP instructions follow logical and linguistic rules that support their use in a non-ambiguous way."

"We posit that the operation of the ribosome can be viewed as a type of physical multi-core processor in terms of concurrently executing amino acid elongation and pausing control to enable protein folding."

"The ribosome functions as a multi core processing protein synthesis machine."

"The ribosome can be thought of as an autonomous functional processor of data that it sees at its input."

"Such an iterative process nicely lends itself to an algorithmic process should geneticists experiment with writing their own genetic code."

"It has been shown that both the genetic code and TP code are decoupled allowing simultaneous decoding and dual functionality within the ribosome using the same alphabet (nucleotides) but different languages."

"The TP code also exhibits a syntax or grammar that obeys strict codon relationships that demonstrate language properties."


Not just a metaphor, it demonstrates language properties. And all that was just to show:
"The functionality of condonic redundancy denies the ill-advised label of “degeneracy.”
Because:
"Redundancy of the genetic code enables translational pausing"

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033003/

 

[sfs]

It's always a hoot when Abel gets one of his papers published -- as creationists are wont to point out, peer review really does often do a lousy job(*). For anyone who isn't familiar with him, Dr. David Abel, of the Department of ProtoBioCybernetics/ProtoBioSemiotics at The Origin of Life Science Foundation, Inc, is a retired large-animal veterinarian. His department consists of him, and the foundation is his house.

Based on a quick look, the actual science in this paper (i.e. the research that's been done by other people) seems sound enough. Amino acids are coded for by several alternative strings of DNA bases, and some strings yield faster protein synthesis (mostly because of varying abundance of the associated tRNAs). For some proteins, slower synthesis yields better results, since it minimizes misfolding. Not surprisingly, bacteria tend to use the slower DNA string for those proteins, since that would be selectively favored. Abel wrapped this information, which is interesting but not surprising, in some bafflegab about information and coding systems, and presto! another Intelligent Design publication is born.

(*) In this case, the article was handled by an editor who seems to be a long-time graduate student in a psychiatry department; the editor also served as one of the two reviewers. Clearly the kind of expertise that's needed to evaluate information theory and genetics.

 

[durangodawood]

The people who think He couldn't create a universe with evolution in it. They are scared of a God that capable......

No they arent.

They are scared of a Bible that demands interpretation.
.

 

[ecco]

DNA as a programming language

Not a very good programming language. Every human generation contains, on average, about 60 mutations.
Over 25% of pregnancies end in miscarriage. Due, in part, to more severe "copying" errors.

 

[ecco]

Name one thing in nature you observed mutate from something else?

• Name one time you have seen a hair grow.
• Name one time you have seen fingernail grow.
• Name one time you have seen a blade of grass grow.

That is what I thought.

 

[morse86]

DNA is a hoax:
Read the research: http://cluesforum.info/viewtopic.php?f=25&t=1487

 

[The Barbarian]

Physical causes-and-effect have been tested since Crick proposed the sequence hypothesis in 1958. They've come to the conclusion: "Nucleotide, and eventually amino acid, sequencing are both physicodynamically indeterminate." Intelligent design theory unshackles scientists from materialistic chains.

Your error here, is to assume that natural processes must be determinate. But they often are not. Radioactive decay, for example. Chemical reactions are, at the molecular level, stochastic processes; in organic reactions, you can't predict which molecule will end up in a particular isomer, when the result is a mix of isomers. Are you beginning to realize why the story they told you is flapdoodle?

Barbarian observes:
Actually, they do. I don't know of a long-lived concept that didn't.

Explain how the concept 7 evolves.

Primitive people often count like this; 1, 2,3, many. And so the concept many eventually became 4,5,6,7... and so on. Try again?

That concepts don't evolve is the difference between rational and irrational.

Let's take the concept of the United States of America. It has changed greatly from the time it became a nation. Let's talk about the concept of justice. That is continually changing. And yes, it is irrational to deny that they do change.

 

[[serious]]

That language seem vague to me. Can you elaborate on what you mean?

Sure, say you have an ancestral vertebrate. It reproduces and evolves. Eventually you have an eel and a tuna. Now, they are different from each other, but they are still vertebrates just like that common ancestor. Occasionally you will have someone presented with a clear example of a new species evolving and they will respond "but it's still just a fruit fly (or a mouse, or a whatever)", which of course it is since it's ancestor was a fruit fly (or a mouse, or a whatever). Likewise, humans are still in every parent group our ancestors were in all the way back to a little eukaryotic swimming around in some puddle.

 

[ecco]

DNA is a hoax:
Read the research: http://cluesforum.info/viewtopic.php?f=25&t=1487

How do you arrive at that conclusion from an article that states...

This amazing 3-D twisted ladder I was once introduced to on the cover of Time magazine as a positive discovery for the advancement of the human race, now tells the story of your very being. Is it real science or quackery? Why don't all criminals prepare for their ultimate fate in incarceration and why aren't all of them found out
​

... and references Dr. Josef Mengele?

 

[David4223]

MOD HAT ON

This thread has undergone a cleanup.

Please remember to stay on topic!

Thank you.

MOD HAT OFF​

 

[The Barbarian]

This...

"This amazing 3-D twisted ladder I was once introduced to on the cover of Time magazine as a positive discovery for the advancement of the human race, now tells the story of your very being. Is it real science or quackery? Why don't all criminals prepare for their ultimate fate in incarceration and why aren't all of them found out"

...makes no sense at all, particularly for humans. Genes can give a disposition to certain behaviors, but it has been long known that environment, particularly from a very early age, is far more important in determining behavior. This is true of all higher vertebrates, but is particularly true of humans, who seem to have the fewest innate behaviors, and are most plastic with regard to learned behavior.

 

[The Cadet]

DNA is a hoax:

We can directly observe the DNA molecule with microscopes. Have you ever tried to do that?

 

[pshun2404]

Definitely not a hoax..I've seen them, extracted them, spliced them...and more...it real...no DNA ever found outside of a cellular environment in nature...no FUNCTIONAL DNA outside of a living system...no functional DNA no cell/no cell no functional DNA, but even some evolutionists see the similarity to a program language (explore Pre-Coded Equilibrium)

 

[Paul of Eugene OR]

In this peer-reviewed publication they find the "redundancy of the genetic code enables translational pausing". Which alone is fascinating, but in reading about how they found this out was the interesting part:

"Previously, evolutionary biologists have not been aware of the conceptual complexity required for genomic programming"

"We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties."

"Within the genome domain, executable operations format, read, write, copy, and maintain digital Functional Information (FI)"

"They reveal the ribosome, among other things, to be not only a machine, but an independent computer-mediated manufacturing system"

"We show in this paper that the bit patterns representing TP instructions follow logical and linguistic rules that support their use in a non-ambiguous way."

"We posit that the operation of the ribosome can be viewed as a type of physical multi-core processor in terms of concurrently executing amino acid elongation and pausing control to enable protein folding."

"The ribosome functions as a multi core processing protein synthesis machine."

"The ribosome can be thought of as an autonomous functional processor of data that it sees at its input."

"Such an iterative process nicely lends itself to an algorithmic process should geneticists experiment with writing their own genetic code."

"It has been shown that both the genetic code and TP code are decoupled allowing simultaneous decoding and dual functionality within the ribosome using the same alphabet (nucleotides) but different languages."

"The TP code also exhibits a syntax or grammar that obeys strict codon relationships that demonstrate language properties."


Not just a metaphor, it demonstrates language properties. And all that was just to show:
"The functionality of condonic redundancy denies the ill-advised label of “degeneracy.”
Because:
"Redundancy of the genetic code enables translational pausing"

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033003/

Well, the next thing to do is examine the nature of the coding. Is it straightforward, logical in the order of the way things are coded for, or is the implementation confusing and tangled? Is it tight and economical, or are there huge swaths of unused sequences? Are the instructions for a given protein kept together in order, or scattered around and needing to be grabbed from several places to finish putting it together?

An omniscient designer hypothesis would be supported by one outcome for these questions, a random evolutionary source would be supported by the other outcome for these questions. So what are the answers?

 

[Loudmouth]

Definitely not a hoax..I've seen them, extracted them, spliced them...and more...

When you are writing computer software, do you use restriction enzymes to change the program? Is the software ever in any physical form?

 

[ecco]

Is the software ever in any physical form?

Yep. Punched cards. Oooops, did I just show my age?

 

[sfs]

When you are writing computer software, do you use restriction enzymes to change the program?

Does successful execution of the program depend on widely separated lines of code lying near one another on the hard drive?

 

[Loudmouth]

Does successful execution of the program depend on widely separated lines of code lying near one another on the hard drive?

I like that one.

 

[Loudmouth]

Yep. Punched cards. Oooops, did I just show my age?

Does anyone use enzymes to join and cut the punched cards?

 

[ecco]

Anything as vague and unpredictable and error prone as DNA is not a good choice for a language for writing computer programs.


I pondered on...

A possible exception to my above statement might be a highly advanced artificial intelligence program designed to mimic human thought. In such a program, it would be reasonable to intentionally allow the program to make mistakes.​

...but concluded that it was invalid. Using DNA to write even such a program could easily lead to the program malfunctioning to the point of being irrelevant.