Why punctuated equilibrium happens

Originally posted by C Hess
I've already explained how that figure of speech is poorly chosen in other posts. You've
failed to counter my arguments. Please don't reuse already failed arguments.

DNA computing is a form of computing which uses DNA, biochemistry and molecular biology, instead of the traditional silicon-based computer technologies. DNA computing, or, more generally, biomolecular computing, is a fast developing interdisciplinary area. Research and development in this area concerns theory, experiments, and applications of DNA computing.

DNA computing is fundamentally similar to parallel computing in that it takes advantage of the many different molecules of DNA to try many different possibilities at once.

http://en.wikipedia.org/wiki/DNA_computing

Originally posted by DeepThought
Prove that the genetic code does not work in the same way as an event driven program.

The problem with reffering to DNA as "code" is that you typically think of code as programs
that will run exactly the same on every run, producing completely predictable results. They
do this because the machines they run on are built by intelligent humans who made sure
that there's a defined language that the machine can execute, and the program is written
by an intelligent programmer who understands that language. But DNA doesn't have to
follow any linguistic rules. Any sequence of guanine, adenine, thymine or cytocine will do
(well actually there's the chemical restriction that only allows them to pair in certain ways,
but any sequence of such pairs will do). What that means is that the cell will happily work
with any DNA. You can just randomly jumble the DNA pairs around and you'll still get some
kind of protein factory going.

So genetic "code" is an event based programming like any chemical process in nature is an
event-based program, in that certain things happen that is somewhat predictable. But
unlike human made programs and machines, the DNA and the cell will not always yield the
exact same results, for obvious reasons. If you build a computer with free-floating parts
that will gladly "run" any "code" they recieve, you're bound to have mistakes happening
every now and then. Hardly what you'd call a well written program running on intelligently
designed hardware.

Well, maybe microsoft produce comparable systems, but you know what I'm saying, right?

Originally posted by C Hess
The problem with reffering to DNA as "code" is that you typically think of code as programs
that will run exactly the same on every run, producing completely predictable results. They
do this because the machines they run on are built by intelligent humans who made sure
that there's a defined language that the machine can execute, and the program is wri ...[text shortened]... ware.

Well, maybe microsoft produce comparable systems, but you know what I'm saying, right?

Where do you get this idea that you can just randomly jumble the DNA pairs around and you'll still get some kind of protein factory going? Probably out of your arse.

Originally posted by RJHinds
DNA computing is a form of computing which uses DNA, biochemistry and molecular biology, instead of the traditional silicon-based computer technologies. DNA computing, or, more generally, biomolecular computing, is a fast developing interdisciplinary area. Research and development in this area concerns theory, experiments, and applications of DNA computing. ...[text shortened]... f DNA to try many different possibilities at once.

http://en.wikipedia.org/wiki/DNA_computing

I've already explained this to you. When intelligent humans decide to use DNA as
information storage they do it quite differently from how DNA is used by a cell. What you're
saying is the equivalent of saying that trees are chairs, because we can take trees and
make them into chairs. It's ludicrous to suggest that because DNA, being such a tiny and
lengthy molecule, can be manipulated to hold information for our purposes, that therefore
the cell and the way it "uses" DNA is a natural computer of some sort. It's so wrong it's
almost funny.

DNA computing is when you build machines using enzymes (and other molecules) to
execute code stored in DNA, but again it's machines built by people. They build logic gates
using organic material. These machines are similar to cells only in that they use some of
the same material.

This whole DNA as code and the cell as a machine running that code only works as a
figure of speech, to better understand what's going on inside a cell without going into too
much detail. The natural cell really isn't that precise a "technology" that you would think of
it as such.

Originally posted by RJHinds
Where do you get this idea that you can just randomly jumble the DNA pairs around and you'll still get some kind of protein factory going? Probably out of your arse.

I should probably clarify that. The ribosomes in cells that produce proteins will happily
accept any order of G, A, T and C, and produce proteins. They won't stop working if the
"syntax" is not right. That doesn't mean that the cell can survive on just any sequence, but
it will happily produce the proteins, even if it's suicide for the cell. This is yet another
example of a poorly designed "machine". It's what you'd expect if the cell evolved through
natural, unguided processes, but if it's designed that way poof-style by a superintelligence,
well that's just embarrassing.

Originally posted by C Hess
I should probably clarify that. The ribosomes in cells that produce proteins will happily
accept any order of G, A, T and C, and produce proteins. They won't stop working if the
"syntax" is not right. That doesn't mean that the cell can survive on just any sequence, but
it will happily produce the proteins, even if it's suicide for the cell. This is yet ...[text shortened]... ut if it's designed that way poof-style by a superintelligence,
well that's just embarrassing.

I don't think so. What is you explanation of the following quoted articles, if they don't mean that the DNA has been programmed for life?

So, what is life from the perspective of a genetic engineer whose team programmed DNA in a computer in the first attempt to build a synthetic organism? Venter told the packed audience in Dublin that life is DNA-software-driven machinery that operates protein robots.

Here's the key passage in the article:

"All living cells that we know of on this planet are 'DNA software'-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions," said Venter. "We are now using computer software to design new DNA software."

That's a remarkable statement. It has intelligent design written all through it.

http://www.evolutionnews.org/2012/07/software_machin062211.html

“With the proper computer tools, biologists can write their own genetic code -- and then turn that code into life,” said biochemist Omri Amirav-Drory, who founded Genome Compiler Corp., the company that built the software.

He demonstrated for FoxNews.com at a Starbucks early one morning by manipulating a bacteria's genes on his MacBook.

App lets scientists build custom DNA using gene sequences from existing life forms.

As the price of reading genomes drops, biologists have sequenced thousands of organisms.

It would cost a few billion dollars to write a human genome DNA, but bacterial DNAs cost a few thousand.

The left side of the Genome Compiler app lists folders for known viruses, bacteria and other organisms, each storing files of genome sequences, the unique biological stamp encoded in an organism's DNA. The software offers tools to add extra genes, mutate proteins, or toss in a few amino acids.

If a particular genetic sequence is not in the list, the compiler downloads it from a library at the National Institute of Health. Once satisfied with the results, a scientist can save her invention to a file, click the order button and ship the virtual creature’s specs to a DNA synthesizing lab such as GenScript or GeneArt, which can assemble actual physical DNA based on the specs.

A Fulbright Scholar with a Ph.D. from Tel Aviv University, Amirav-Drory has simply merged two fields: computer science and biochemical engineering.

“Computers understand code and living things understand the language of DNA,” he said. The software has built-in biosecurity measures to stop someone from building Ebola and other deadly agents, Amirav-Drory said, and assembling complex creatures that think is still far, far off. But it will let scientists program simple new microorganisms that can clean our air and water or produce energy just by coding their DNA in a certain way.

John Cumbers, a synthetic biologist at the NASA Ames Research Center who has been using the genome compiler, says it speeds up his DNA work approximately ten times.

http://www.foxnews.com/science/2013/02/27/programming-life-with-click-mouse/

Originally posted by RJHinds
I don't think so. What is you explanation of the following quoted articles, if they don't mean that the DNA has been programmed for life?

So, what is life from the perspective of a genetic engineer whose team programmed DNA in a computer in the first attempt to build a synthetic organism? Venter told the packed audience in Dublin that life is DNA-softwar ...[text shortened]... ately ten times.

http://www.foxnews.com/science/2013/02/27/programming-life-with-click-mouse/

You just don't get the concept of figure of speech, do you?

http://en.m.wikipedia.org/wiki/Figure_of_speech

Originally posted by C Hess
You just don't get the concept of figure of speech, do you?

http://en.m.wikipedia.org/wiki/Figure_of_speech

he also doesn't get this:

http://www.thefreedictionary.com/analogy

and this;

http://en.wikipedia.org/wiki/Science

and this;

http://en.wikipedia.org/wiki/Evolution

and this;

http://en.wikipedia.org/wiki/Occam%27s_razor

and this;

http://en.wikipedia.org/wiki/Equivocation

and a whole lot more but the above are some of the main things you just never gets.

Originally posted by C Hess
The problem with reffering to DNA as "code" is that you typically think of code as programs
that will run exactly the same on every run, producing completely predictable results. They
do this because the machines they run on are built by intelligent humans who made sure
that there's a defined language that the machine can execute, and the program is wri ...[text shortened]... ware.

Well, maybe microsoft produce comparable systems, but you know what I'm saying, right?

An electronic computer is expected to be precise in the sense that the same code run twice with the same inputs (and timings of inputs if that matters) will produce the same outputs. This kind of reliability isn't automatically relevant to a cell. There's a fair amount of interest in this kind of approximate logic. I don't think there's a problem of thinking about it as a program. To conclude from that that there necessarily must be an independent programmer is an induction too far.

Originally posted by humy
But I suppose it might be a reasonable analogy to think of a genetic code as being like a program so long as one understands this is not pure software we are talking about because the genetic code is made of the ordering of DNA bases which, unlike computer software, does not consist of just pure abstract information but has a material physical existence.

I disagree. Computer software is also stored on physical materials.
However, large parts of DNA should be thought of as data not software - it is blueprints for creating specific amino acids which are then used for building proteins.
Also the cell is not quite like a CPU which runs only one set of instructions at once, but rather does parallel processing with various signaling molecules and other environmental factors triggering the running of different cellular machinery and transcription from the DNA.
So the software should more correctly be thought of as being throughout the cell, not just in the DNA.

Originally posted by twhitehead
I disagree. Computer software is also stored on physical materials.
However, large parts of DNA should be thought of as data not software - it is blueprints for creating specific amino acids which are then used for building proteins.
Also the cell is not quite like a CPU which runs only one set of instructions at once, but rather does parallel processin ...[text shortened]... software should more correctly be thought of as being throughout the cell, not just in the DNA.

This is the first time you have ever said anything that makes me think you might understand something about computers. You must have been doing your homework. Too bad these so-called scientists, like humy, don't understand it.

Originally posted by DeepThought
I don't think there's a problem of thinking about it as a program. To conclude from that that there necessarily must be an independent programmer is an induction too far.

It is a problem because that's the conclusion creationists draw from this
analogy. Creationists believe that cells are tiny little organic computer
systems, equivalent (or even superior) in computational reliability to
human-built systems and that DNA is some kind of information
storage/programming. Of course, if cells were really that reliable, even I
would have to stop and wonder if there's not some kind of programmer/
engineer behind it all, so you can see why analogies like "code" and
"blueprint for life" would be confusing to someone who's a priori decided
that there's a creator who chose to create all forms of life after their own
"kind".

Originally posted by C Hess
It is a problem because that's the conclusion creationists draw from this
analogy. Creationists believe that cells are tiny little organic computer
systems, equivalent (or even superior) in computational reliability to
human-built systems and that DNA is some kind of information
storage/programming. Of course, if cells were really that reliable, even ...[text shortened]... decided
that there's a creator who chose to create all forms of life after their own
"kind".

You must not forget that the Second Law of Thermodynamics or entropy is working on those cells.

(Dr. Sarfati's Chicken & Egg)

YouTube

Originally posted by RJHinds
(Dr. Sarfati's Chicken & Egg)

http://www.youtube.com/watch?v=CmB4uLANCBo

Case in point. 😵