Creationist argument about DNA and information

JeanTate · Mar 6, 2016

Daniel said:
<snip>

Darwin123 said:

What is your background in science?

Click to expand...

None of your business.

<snip>

With respect, Daniel, it may not be any of Darwin123's (or any ISF member's) business. However, it is quite pertinent to what you've posted here (well, if expanded to "science and mathematics" perhaps).

For example, in your posts there seems to be quite significant use of what seems to be technical terms (e.g. 'Algorithmic', 'Cybernetic', 'CODING Schemes', 'Functional Sequence', and 'Specified Complexity'), but you do not reference any standard texts - from biology, chemistry, physics, computer science, for example - to help your readers understand what you mean (and whether or not you are using these terms with the same meanings that they have in those fields of science/mathematics).

Saying a few words about your science/mathematics background would help readers understand what you write, IMHO.

Reality Check · Mar 6, 2016

Daniel said:
1. It's not 'my way'. SEE Sir Francis Bacon et al.

What an abysmally ignorant "citation", Daniel. Francis Bacon, 1st Viscount St Alban was the "the father of empiricism". Bacon was instrumental in establishing the scientific method!
What makes the above statement a lie is

Bacon did not know abut ice cores.
If Bacon was presented with the ice core or tree ring data he would agree that the Earth is older than 6000 years old because Bacon could count and use the scientific method.
You are not following the scientific method or Bacon !

The "et. al" may be the millions of scientists who have followed the scientific method to produce the enormous amount of reliable information that we have about the universe.

Reality Check · Mar 6, 2016

Daniel: Why is *Something from Nothing*, special pleading

Daniel said:
Ok, *Something from Nothing*.

7 March 2014 Daniel: Is this parroting some creationist idiocy or can you explain why *Something from Nothing* is special pleading?

Some creationists lie about the Big Bang being the creation of something from nothing. The Big Bang is an existing universe being in a hot dense state and expanding. Even the emergence of matter is not "something from nothing", it is "something from something"!

Reality Check · Mar 6, 2016

Daniel: Please give coherent examples of QM begging the question

Daniel said:
Begging the Question Fallacy: where'd you get real/Reality?? Start here...

Followed with a rant about valid science which is arguments from ignorance, not begging the question, Daniel :jaw-dropp

!

The Schrodinger Equation is not really used in the "most successful branch of Physics in the History of Actual Science" (removed the idiocy of scare quotes because QM is actual science). Quantum field theory is the addition of relativity to QM and starts with the Dirac Equation to get to quantum electrodynamics whose equations are very different.

One interpretation of QM is that the amplitude of wave functions squared are probabilities and that measurements are a collapse of a wave function to a value (Copenhagen Interpretation). There are many other interpretations :eye-poppi

.

So rather than another incoherent post, why not give specific coherent examples from QM, Daniel?
7 March 2016 Daniel: Please give coherent examples of QM "begging the question", e.g. assuming the outcome and then deriving it.

Reality Check · Mar 6, 2016

Daniel said:
It's not only NOT Scientific, it Doesn't Exist.

4 March 2016 Daniel: It is a lie to state that the scientific theory of evolution does not exist since textbooks on TOE exist, etc.!

You do not even know what Intelligent Design is, Daniel - ID explicitly rules out any investigation of the nature of the designer.

There are many "Choices for HOW we (Universe/Us) are here"

Nature
Intelligent Design
Cheonjiwang Bonpuri
Enûma Eliš
Greek cosmogonical myth
etc. including the Genesis creation myth

Reality Check · Mar 6, 2016

Daniel said:
I said: "Historical Documentation".

Define "historical documentation" , e.g. is it documents written at the time of an event? Or documented rumors and second hand stories written well after the event?
Does "historical documentation" have to contain actual dates?
Does "historical documentation" include Viking, Germanic, etc. sagas?
Does "historical documentation" include religious texts such as the Rigveda, , Bible, etc. ?

Are you saying that only "historical documentation" can determine the age of anything, Daniel?

Can only humans write "historical documentation"?
What about the first layer of dark snow laid down in snow during the last summer. That tells a rational person that the layer is one year old. But there need not be anyone around during that summer to record that a dark layer was laid down - is that layer "historical documentation"?
What about the first tree ring in a tree trunk?

Daniel · Mar 6, 2016

JeanTate said:
Thanks.

I can't speak for anyone else (obviously), but my main impression is that you and many others who've posted in this thread (but not all) are 'speaking past each other'; in particular, I think rather a lot of other posters really do not understand many of the key words/terms you have used in many of your posts. Instead they have interpreted what you wrote using the language (words, terms) they are familiar with, here in the ISF.

That would be a fair assessment, I suppose. I've broken many of these concepts down as best I could; however, there has to be some semblance of an acumen on the other side...I have found very little of that.

In other words, If you wanna play Lumberjack then it behooves you to handle your side of the log.

I would have expected that "Algorithmic Cybernetic CODING and de-CODING Schemes" is something abstract, to do with algorithms, and coding (I don't know what extra meaning "cybernetic" would add, here).

Cybernetic has to do with "Information", communication..."Semiotics".

Instead, you seem to be defining it (entirely?) as something to do with DNA, and chemical processes (I use the term loosely).

Well DNA contains boat loads of "Information" i.e., it transcends the "Physical Molecule"/Medium.

Maybe this will help...

"Information"/Software is Semiotic i.e., it's not Physical (Material) or Physically a part of it's Medium of Conveyance. Letters, Numbers (Symbols) are just Pre-Arranged Conventions between the Transmitter and Receiver for communication and to understand the message.

SOFTWARE is the "Meaning", the CODE are the Symbols that represent the agreed upon "Meaning".

See this......C A T ? This is a "CODE". For what? ......

The Letters " C A T " aren't spelled out on it's fur. C A T is the "CODE" name "WE" (Intelligent Agents) gave it. The message is the agreed upon meaning "SOFTWARE"; It's semiotic.

Paul Revere...what's the "CODE" ? One Light or Two Lights, right? What's the Software? It was the Agreed Meaning between Paul and The Patriots. Who Created the Software/Message (The "1 if by Land and 2 if by Sea")....the Lights or Paul Revere and The Patriots ??

You're looking @ a "CODE" right now....it's called the English Language. The Software (Meaning) is the Preemptive Agreed upon Convention so we can Understand the Message, it's Semiotic. Without "Meaning"/Convention there is No Information/"CODE" it's utter noise.
CODE/Information/Software is always...ever ever ever, sourced by INTELLIGENT AGENCY, Without Exception!

The EXACT Same Concept here....

CCU, CCC, CCA, CCG = ....................... Proline.
CUU, CUC, CUA, CUG, UUA, UUG =.................... Leucine
UAA, UAG, UGA =................................... STOP!

There are NO Physico-Chemical links between the " CODE " and Amino Acid or Instruction. The Laws of Physics/Chemistry contain NO Symbolic Logic Functions.

The Medium/Convention is Arbitrary as long as it's Agreed Upon:

Ed Lewis PhD Genetics, Nobel Prize Genetics....

"The Laws of Genetics have never depended upon knowing what genes are chemically and would hold true even if they were made of green cheese". ---caltech.edu 7/22/2004

He's saying that "The Medium" (DNA/RNA) is basically irrelevant and arbitrary to the discussion which Ipso Facto means INFORMATION is the Key Driver.

I was unable to find what papers (published in peer-reviewed journals) cite this; does any reader know?

What is the significance of "Peer-Review" ??

Also, the abstract at least does not use the phrase "Algorithmic Cybernetic CODING and de-CODING Schemes", nor any part of it (except "code(s)"). So, at that level, it doesn't help me understand what you mean by "Algorithmic Cybernetic CODING and de-CODING Schemes".

DNA contains Algorithms "Programs".
DNA/Living Cells contains Cybernetic Systems (Information/communication networks)
DNA is "A CODE".
Cells contain "De-CODING machinery"...for "Translation".

These attributes are quite apodictic @ this point.

Further, the paper you cite comes from the journal "Computers & Chemistry", which, while pertinent, doesn't help me understand the broader - CS - context.

And? The Citation was just to introduce you to the comparisons between modern communication systems and DNA (Genetic Information Systems)

Sorry Daniel, but that doesn't seem - to me - to come anywhere close to bolstering your claim.

Well you need to bolster your knowledge of Gibbs Free Energy then.

Would you mind walking me through it, with particular emphasis on separating the "Physically IMPOSSIBLE" from the "Chemically IMPOSSIBLE"?

Physically --- Gibbs Free Energy.

Chemically --- Stereoisomerization, Sunlight, Hydrolysis/Brownian Motion, pH, Oxidation, Cross Reactions, Bi/Mono functional molecules et al.

Remember this is merely regarding the formation of the Physical Molecules "Naturally", it speaks nothing to "Information".

See Previous post to 'ehcks' in this thread discussing "Proteins".

But why are you limiting your scope to "LIFE"?

Because that's what we're discussing here.

The claim you made - "Nature/Natural Law causation CAN NOT create Algorithmic Cybernetic CODING and de-CODING Schemes" - does not refer to "LIFE" in any way at all, does it?

Yes, it most certainly does. SEE above

You have introduced a (two?) new term(s), "Functional Sequence/Specified Complexity". These too seem to be CS concepts, not limited to "LIFE". Would you please explain what you mean by these, in some detail? And provide references to relevant CS texts/papers too?

Functional Sequence Complexity:

There are 3 Types of Complexity 1) random sequence complexity (RSC), 2) ordered sequence complexity (OSC), or Functional Sequence Complexity (FSC)."

Random (RSC): fgskztosbclgdsk.

Order (OSC): hhhhhhdddddduuuuuu: Crystals, Snow Flakes, Sand Dunes, Fractals.

Functional Sequence Complexity (FSC): "It Puts The Lotion in the Basket", Sand Castles, The Genetic CODE, Barbecue Grills, Indy Cars, Hyper-NanoTech Machines and Robots (Kinesin, ATP Synthase, Flagellum, Cilia....ad nauseam) et al.

So RSC and OSC = "Nature" construct, "Shannon Information"

FSC = Intelligent Design Construct.

"In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity"
Leslie E. Orgel, The Origins of Life: Molecules and Natural Selection, pg. 189 (Chapman & Hall: London, 1973

"The attempts to relate the idea of order...with biological organization or specificity must be regarded as a play on words that cannot stand careful scrutiny. Informational macromolecules can code genetic messages and therefore can carry information because the sequence of bases or residues is affected very little, if at all, by [self-organizing] physicochemical factors".
H.P. Yockey; "A Calculation of Probability of Spontaneous Biogenesis by Information Theory"; Journal of Theoretical Biology 67, 1977; p. 390.

But, again, why should this be limited to "Proteins/DNA/RNA"?

Because that's what we're talking about; Primary and Secondary Structure are quintessential attributes of "Functional" Proteins/DNA/RNA.

Lastly, perhaps somewhat at a tangent: are viruses part of "LIFE"?

Nope. Viruses are Obligate Parasites i.e., they need LIFE Existing FIRST to exist; so, somewhat irrelevant to the discussion.

With respect, Daniel, it may not be any of Darwin123's (or any ISF member's) business.

It isn't.

However, it is quite pertinent to what you've posted here (well, if expanded to "science and mathematics" perhaps).

It's not. It would just be me saying it. I will not post Personal Information on forums so it can't be validated anyway.

Anyone with any Scientific Acumen @ all can tell instantly by the substance of my posts, what they're dealing with. I surely can tell.

(e.g. 'Algorithmic', 'Cybernetic', 'CODING Schemes', 'Functional Sequence', and 'Specified Complexity')

These terms are prolific throughout the Scientific Literature on the topics we're discussing here.

regards

Reality Check · Mar 6, 2016

Daniel said:
The Date of the Citation has NOTHING to do with the veracity of the message.

Yes it does, Daniel, as any one knows. The further back in the past a citation is the more likely it is to be a citation to something that has been invalidated. Go far enough back and you start to cite idiotically invalid things such as a flat Earth, Earth centric universe, an Earth that is 6000 years old, etc.

The quote itself is a lie by quote mining, Daniel.The Quote Mine Project Or, Lies, Damned Lies and Quote Mines Quote #57

"This was only one of Pasteur's experiments. It is no easy matter to deal with so deeply ingrained and common-sense a belief as that in spontaneous generation. One can ask for nothing better in such a pass than a noisy and stubborn opponent, and this Pasteur had in the naturalist Felix Pouchet, whose arguments before the French Academy of Sciences drove Pasteur to more and more rigorous experiments.

We tell this story to beginning students in biology as though it represented a triumph of reason over mysticism. In fact it is very nearly the opposite. The reasonable view was to believe in spontaneous generation; the only alternative, to believe in a single, primary act of supernatural creation. There is no third position. For this reason many scientists a century ago chose to regard the belief in spontaneous generation as a "philosophical necessity". It is a symptom of the philosophical poverty of our time that this necessity is no longer appreciated. Most modern biologists, having reviewed with satisfaction the downfall of the spontaneous generation hypothesis, yet unwilling to accept the alternative belief in special creation, are left with nothing.

I think a scientist has no choice but to approach the origin of life through a hypothesis of spontaneous generation. What the controversy reviewed above showed to be untenable is only the belief that living organisms arise spontaneously under present conditions. We have now to face a somewhat different problem: how organisms may have arisen spontaneously under different conditions in some former period, granted that they do so no longer."
[Wald, G. 1954. The Origin of Life. Scientific American August: 44-53.]

Wald uses the same term for two different phenomena. He starts with the spontaneous generation of existing life, e.g. rotting meat produces flies. He ends with what we now call abiogenesis (the spontaneous generation of original life).

Reality Check · Mar 6, 2016

Daniel: List the usage of Demski's specified complexity with citations

Daniel said:
..
There are 3 Types of Complexity 1) random sequence complexity (RSC), 2) ordered sequence complexity (OSC), or Functional Sequence Complexity (FSC).
...
"In brief, living organisms are distinguished by their specified complexity....

Lots of gibberish snipped, Daniel.
Assertions about what look like irrelevant phrases means nothing.

A phrase existing in the scientific literature does not mean that an invalid creationist concept is being used in the scientific literature :jaw-dropp

!
7 March 2016 Daniel: List the usage of Demski's specified complexity with citations to his definition in the scientific literature.

Also:
7 March 2016 Daniel: Quote the definition of random sequence complexity from the scientific literature .
7 March 2016 Daniel: Quote the definition of ordered sequence complexity from the scientific literature.
7 March 2016 Daniel: Quote the definition of functional sequence complexity from the scientific literature.
I do know what these are (concepts in gnetic algorithms) but do you?

Reality Check · Mar 6, 2016

Daniel: Explain why the difference in DNA between us and other apes matches fossils

Let us add more about the real world for Daniel to deny

!
In the real world creationists state that DNA contains information and then deny what that information means :jaw-dropp

!
7 March 2014 Daniel: Explain why the difference in DNA between us and other apes matches the fossil record.
A creationist excuse is admitting "God is a liar and faked the evidence" which leads into a bog of things like - how can we tell if God is lying to us?; the world was created last Tuesday (by a more powerful God than in the Bible!); etc.

7 March 2014 Daniel: Explain how the shared ERV in the same locations between us and other apes is not evidence of descent from a common ancestor.
There are at least seven different known instances of common retrogene insertions between chimps and humans, and this number is sure to grow as both these organism's genomes are sequenced (Bonner et al. 1982; Dangel et al. 1995; Svensson et al. 1995; Kjellman et al. 1999; Lebedev et al. 2000; Sverdlov 2000).
One creationist excuse is to ignore what this means and go on irrelevant rants, e.g. lying about ERV having functionality (some ERV partial functionality); the delusion that ERV can only infect apes.

JeanTate · Mar 6, 2016

I've time to respond, now, to only some of your lengthy post, Daniel (thanks for taking the time and trouble, by the way).

Daniel said:
That would be a fair assessment, I suppose. I've broken many of these concepts down as best I could; however, there has to be some semblance of an acumen on the other side...I have found very little of that.

Again, I can't speak of anyone else, but my impression is that several of the others who have responded to you feel the same about what you have posted.

JeanTate said:
<snip>

JeanTate said:

I would have expected that "Algorithmic Cybernetic CODING and de-CODING Schemes" is something abstract, to do with algorithms, and coding (I don't know what extra meaning "cybernetic" would add, here).

Click to expand...

Cybernetic has to do with "Information", communication..."Semiotics".

So it adds nothing to the phrase ("Algorithmic Cybernetic CODING and de-CODING Schemes"), right?

Instead, you seem to be defining it (entirely?) as something to do with DNA, and chemical processes (I use the term loosely).

Click to expand...

Well DNA contains boat loads of "Information" i.e., it transcends the "Physical Molecule"/Medium.

Indeed.

So do crystals, black holes, ... why, then, limit your scope to DNA and chemical processes?

Maybe this will help...

"Information"/Software is Semiotic i.e., it's not Physical (Material) or Physically a part of it's Medium of Conveyance. Letters, Numbers (Symbols) are just Pre-Arranged Conventions between the Transmitter and Receiver for communication and to understand the message.

SOFTWARE is the "Meaning", the CODE are the Symbols that represent the agreed upon "Meaning".

See this......C A T ? This is a "CODE". For what? ......

[qimg]http://i158.photobucket.com/albums/t97/jstunja/CAT_zpsfcoma0g6.jpg[/qimg]

The Letters " C A T " aren't spelled out on it's fur. C A T is the "CODE" name "WE" (Intelligent Agents) gave it. The message is the agreed upon meaning "SOFTWARE"; It's semiotic.

Paul Revere...what's the "CODE" ? One Light or Two Lights, right? What's the Software? It was the Agreed Meaning between Paul and The Patriots. Who Created the Software/Message (The "1 if by Land and 2 if by Sea")....the Lights or Paul Revere and The Patriots ??

You're looking @ a "CODE" right now....it's called the English Language. The Software (Meaning) is the Preemptive Agreed upon Convention so we can Understand the Message, it's Semiotic. Without "Meaning"/Convention there is No Information/"CODE" it's utter noise.

First, "Semiotic": do you intend this to have a meaning beyond that which exists in the brains of individuals of the species Homo sapiens? If so, what's the scope? If not, what does this add to this discussion?

Second, re this: "Without "Meaning"/Convention there is No Information/"CODE" it's utter noise": I think you're conflating two quite distinct concepts. Perhaps the best way I can illustrate this is by using black holes (crystals will work too): they have entropy (a physical quantity, albeit an abstract one), and a key question in black hole physics is whether they destroy information. In papers on this, no one (as far as I know) uses "information" and "CODE" as synonyms.

With DNA, accepting (for the moment) that "the CODE are the Symbols that represent the agreed upon "Meaning"", how can amino acid sequences have an "agreed upon" meaning?

Also, if "Letters, Numbers (Symbols) are just Pre-Arranged Conventions between the Transmitter and Receiver for communication and to understand the message", what is "the Transmitter", what is "the Receiver" (re DNA)?

CODE/Information/Software is always...ever ever ever, sourced by INTELLIGENT AGENCY, Without Exception!

What is the "INTELLIGENT AGENCY" which "sources" the information of black holes (and crystals)?

The EXACT Same Concept here....

CCU, CCC, CCA, CCG = ....................... Proline.
CUU, CUC, CUA, CUG, UUA, UUG =.................... Leucine
UAA, UAG, UGA =................................... STOP!

There are NO Physico-Chemical links between the " CODE " and Amino Acid or Instruction. The Laws of Physics/Chemistry contain NO Symbolic Logic Functions.

First, do you agree that "The Laws of Chemistry" can be derived, in their entirety, from "The Laws of Physics" (if only in principle)? If not, which of the laws (of chemistry) are not derivable?

Second, what do you mean by "Symbolic Logic Functions"? Please give some specific examples.

(to be continued)

Daniel · Mar 7, 2016

JeanTate said:
I've time to respond, now, to only some of your lengthy post, Daniel (thanks for taking the time and trouble, by the way).

You're welcome.

Again, I can't speak of anyone else, but my impression is that several of the others who have responded to you feel the same about what you have posted.

Well they need to start doing their homework to support their belief systems.

So it adds nothing to the phrase ("Algorithmic Cybernetic CODING and de-CODING Schemes"), right?

It adds nothing to what? What's "it" ??

Indeed.

So do crystals, black holes, ... why, then, limit your scope to DNA and chemical processes?

Neither contain "Information"; They don't send messages with a pre-arranged and agreed upon convention/medium/meaning. Frankly, the notion is absurd.

First, "Semiotic": do you intend this to have a meaning beyond that which exists in the brains of individuals of the species Homo sapiens? If so, what's the scope? If not, what does this add to this discussion?

Information is only ever ever ever sourced by Intelligent Agency, this may help...

CODE has information. (such as a Book, Morse Code, Instructions, they all have information)
Information has authors. (which we can show is ALWAYS the case)
DNA is a CODE.
Therefore DNA has an Author. <---- My position

Second, re this: "Without "Meaning"/Convention there is No Information/"CODE" it's utter noise": I think you're conflating two quite distinct concepts. Perhaps the best way I can illustrate this is by using black holes (crystals will work too): they have entropy (a physical quantity, albeit an abstract one), and a key question in black hole physics is whether they destroy information.

Well they don't have Information; (SEE: Above). So everything that follows is erroneous.

In papers on this, no one (as far as I know) uses "information" and "CODE" as synonyms.

You're looking @ the wrong papers...

"DNA has two types of digital information — the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes."
Hood, L., Galas, D.,: The Digital Code of DNA: Nature 421, 444-448 (23 January 2003) | doi :10.1038/nature01410

DNA contains: Information/CODE/SOFTWARE.

“DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff — hardware — but as INFORMATION, or SOFTWARE. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level.” {Emphasis Mine}
Paul Davies PhD Physics
Paul Davies PhD Physics http://www.guardian.co.uk/education/2002/dec/11/highereducation.uk

"Over the next sixty minutes I explained how life ultimately consists of DNA-driven biological machines. All living cells run on DNA SOFTWARE, which directs hundreds to thousands of PROTEIN ROBOTS. We have been digitizing life for decades, since we first figured out how to read the SOFTWARE of life by sequencing DNA. Now we can go in the other direction by starting with computerized digital code, designing a new form of life, chemically synthesizing its DNA, and then booting it up to produce the actual organism." {Emphasis Mine}
Craig Venter PhD Geneticist (NIH, Celera Genomics)
http://www.sciencefriday.com/blogs/10/24/2013/dna-the-software-of-life.html

With DNA, accepting (for the moment) that "the CODE are the Symbols that represent the agreed upon "Meaning"", how can amino acid sequences have an "agreed upon" meaning?

Pre-Programming.

Also, if "Letters, Numbers (Symbols) are just Pre-Arranged Conventions between the Transmitter and Receiver for communication and to understand the message", what is "the Transmitter", what is "the Receiver" (re DNA)?

Transmitter ---> DNA

Receiver ---> Ribosome (via mRNA/tRNA/Aminoacyl tRNA Synthetase's. Many others, but good for our purposes)

First, do you agree that "The Laws of Chemistry" can be derived, in their entirety, from "The Laws of Physics" (if only in principle)? If not, which of the laws (of chemistry) are not derivable?

Yes, many can.

Second, what do you mean by "Symbolic Logic Functions"? Please give some specific examples.

1. The sentence you just wrote.

2.

CCU, CCC, CCA, CCG = ....................... Proline.
CUU, CUC, CUA, CUG, UUA, UUG =.................... Leucine
UAA, UAG, UGA =................................... STOP!

There are no Physico-Chemical links (as mentioned, several times).

Maybe this will lift some of the fog...

CODES:
"We repeatedly consider the following scenario: a sender (say, A) wants to communicate or transmit some information to a receiver (say, B). The information to be transmitted is an element from some set X . It will be communicated by sending a
binary string, called the message. When B receives the message, he can decode it again and (hopefully) reconstruct the element of X that was sent. To achieve this, A and B NEED TO AGREE on a code or description method BEFORE communicating." {emphasis mine]
Grunwald, P., Vitanyi, P ; Algorithmic Information Theory; p. 10, 14 Sept 2005
http://www.illc.uva.nl/HPI/Algorithmic_Complexity.pdf

SEE: Paul Revere Example.

So you have 2 Choices:

1. Invalidate DNA as a "CODE"; Best wishes.

2. Reckon with an Intelligent Designer (Creator).

regards

Reality Check · Mar 7, 2016

steenkh · Mar 7, 2016

Daniel said:
Information is only ever ever ever sourced by Intelligent Agency, this may help…

Is this your private definition of information? You are sure you are not confusing 'information' with 'message'?

Information has authors. (which we can show is ALWAYS the case)

So information is not defined to have authors, you can show it! Go on, do it!

DNA is a CODE.

What is your definition of code?

Therefore DNA has an Author. <---- My position

Do you really think that a creator will pop into existence just because of an argument from incredulity?

CODES:
"We repeatedly consider the following scenario: a sender (say, A) wants to communicate or transmit some information to a receiver (say, B). The information to be transmitted is an element from some set X . It will be communicated by sending a binary string, called the message. When B receives the message, he can decode it again and (hopefully) reconstruct the element of X that was sent. To achieve this, A and B NEED TO AGREE on a code or description method BEFORE communicating." {emphasis mine]
Grunwald, P., Vitanyi, P ; Algorithmic Information Theory; p. 10, 14 Sept 2005
http://www.illc.uva.nl/HPI/Algorithmic_Complexity.pdf

So DNA is not code, because there is nobody sending any messages, and no communication - unless you want to anthropomorphize the proteins in the cell.

marplots · Mar 7, 2016

steenkh said:
So DNA is not code, because there is nobody sending any messages, and no communication - unless you want to anthropomorphize the proteins in the cell.

Yep, that's exactly what was done.

JeanTate · Mar 7, 2016

(continued)

Daniel said:
<snip>

The Medium/Convention is Arbitrary as long as it's Agreed Upon:

Ed Lewis PhD Genetics, Nobel Prize Genetics....

"The Laws of Genetics have never depended upon knowing what genes are chemically and would hold true even if they were made of green cheese". ---caltech.edu 7/22/2004

He's saying that "The Medium" (DNA/RNA) is basically irrelevant and arbitrary to the discussion which Ipso Facto means INFORMATION is the Key Driver.

Hmm ... I think there may be a pretty deep gulf in our mutual understanding of some key concepts here; I'll explore them later.

JeanTate said:
JeanTate said:

I was unable to find what papers (published in peer-reviewed journals) cite this; does any reader know?

Click to expand...

What is the significance of "Peer-Review" ??

Peer review (no caps, you don't need the hyphen here either) is a process used in science (and mathematics, and ...). While it certainly has some shortcomings, it does a pretty good job of ensuring that papers which are published in peer-reviewed journals are worth reading, in terms of their science content.

Also, the abstract at least does not use the phrase "Algorithmic Cybernetic CODING and de-CODING Schemes", nor any part of it (except "code(s)"). So, at that level, it doesn't help me understand what you mean by "Algorithmic Cybernetic CODING and de-CODING Schemes".

Click to expand...

DNA contains Algorithms "Programs".
DNA/Living Cells contains Cybernetic Systems (Information/communication networks)
DNA is "A CODE".
Cells contain "De-CODING machinery"...for "Translation".

Daniel, I'm struggling to grasp what you're trying to say here; I hope you can help me.

First, why the caps? the quote marks? For example, what are you trying to convey by writing "Algorithms "Programs"" rather than "algorithmic programs"? Ditto re ""A CODE"", rather than "a code"?

Second, what do you mean by "Algorithms "Programs""? Did you, for example, mistype (perhaps you meant to write "algorithmic programs"?)

Third, assuming that your use of quote marks in "A CODE" refers to a special, non-standard meaning (this is one common use of quote marks), what is this special meaning?

Finally - and most importantly - I still cannot work out what connection you seem to have made between "Algorithmic Cybernetic CODING and de-CODING Schemes" (with all its caps etc) and the content of the abstract of the Yockey paper you cited.

These attributes are quite apodictic @ this point.

I do not doubt that, for you, this is true.

However, as I have no real understanding of what you have written, it is certainly not for me.

I hope you can clarify.

And? The Citation was just to introduce you to the comparisons between modern communication systems and DNA (Genetic Information Systems)

In that regard, it succeeded, at least somewhat. So thanks for that.

However, the more papers I read of such papers, the more confused I have have become. Not so much by the content of such papers (though there's an awful lot to learn, some of it quite subtle, much of it very technical), but by the apparent disconnect between what I read and what you have posted, here in this (and one other) ISF thread.

Sorry Daniel, but that doesn't seem - to me - to come anywhere close to bolstering your claim.

Click to expand...

Well you need to bolster your knowledge of Gibbs Free Energy then.

Would you mind walking me through it, with particular emphasis on separating the "Physically IMPOSSIBLE" from the "Chemically IMPOSSIBLE"?

Click to expand...

Physically --- Gibbs Free Energy.

Chemically --- Stereoisomerization, Sunlight, Hydrolysis/Brownian Motion, pH, Oxidation, Cross Reactions, Bi/Mono functional molecules et al.

Remember this is merely regarding the formation of the Physical Molecules "Naturally", it speaks nothing to "Information".

I'll address just the first, for now.

I do have some familiarity with Gibbs free energy (without the caps; what difference, may I ask, does adding caps make to its meaning?). But I have no clue as to how Gibbs free energy makes the natural, spontaneous formation of functional DNA, RNA, and/or proteins, outside already existing cells, from sugars, bases, phosphates, and amino acids (my attempt to re-write your "Functional DNA/RNA/Proteins NEVER spontaneously form "naturally", outside already existing cells, from Sugars, Bases, Phosphates, and Aminos, respectively") physically impossible (without the caps).

Would you please have another go? This time start with a definition of Gibbs free energy.

See Previous post to 'ehcks' in this thread discussing "Proteins".

Link please.

Because that's what we're discussing here.

Yes, it most certainly does. SEE above

Thanks for the clarifications.

I had not appreciated the extent to which you are using special meanings for what I took to be standard, if technical, terms (all those quote marks, and caps).

And I also had not appreciated just how different at least some of your special meanings are from those standard, technical, meanings. My lack of appreciation for how you have been using so many terms, in this thread (and one other) has - IMHO - seriously hindered my attempts to understand what you have written.

May I make a suggestion? Please try much harder to be clear about the meanings of key words/terms/phrases you use, and where you use them in ways that are, in important respects, different from the standard, technical, meaning(s), spell those differences out. In as much detail, and as clearly, as you can.

You have introduced a (two?) new term(s), "Functional Sequence/Specified Complexity". These too seem to be CS concepts, not limited to "LIFE". Would you please explain what you mean by these, in some detail? And provide references to relevant CS texts/papers too?

Click to expand...

Functional Sequence Complexity:

There are 3 Types of Complexity 1) random sequence complexity (RSC), 2) ordered sequence complexity (OSC), or Functional Sequence Complexity (FSC)."

Random (RSC): fgskztosbclgdsk.

Order (OSC): hhhhhhdddddduuuuuu: Crystals, Snow Flakes, Sand Dunes, Fractals.

Functional Sequence Complexity (FSC): "It Puts The Lotion in the Basket", Sand Castles, The Genetic CODE, Barbecue Grills, Indy Cars, Hyper-NanoTech Machines and Robots (Kinesin, ATP Synthase, Flagellum, Cilia....ad nauseam) et al.

So RSC and OSC = "Nature" construct, "Shannon Information"

FSC = Intelligent Design Construct.

"In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity"
Leslie E. Orgel, The Origins of Life: Molecules and Natural Selection, pg. 189 (Chapman & Hall: London, 1973

"The attempts to relate the idea of order...with biological organization or specificity must be regarded as a play on words that cannot stand careful scrutiny. Informational macromolecules can code genetic messages and therefore can carry information because the sequence of bases or residues is affected very little, if at all, by [self-organizing] physicochemical factors".
H.P. Yockey; "A Calculation of Probability of Spontaneous Biogenesis by Information Theory"; Journal of Theoretical Biology 67, 1977; p. 390.

Thanks for this.

I've been reading up on this, and - so far - I have concluded that you do not seem to be using the terms Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC), and Functional Sequence Complexity (FSC) quite in the same way as, for example, Durston et al. do (source). In particular, your gloss "FSC = Intelligent Design Construct" seems wildly inaccurate and inappropriate.

<snip>

Lastly, perhaps somewhat at a tangent: are viruses part of "LIFE"?

Click to expand...

Nope. Viruses are Obligate Parasites i.e., they need LIFE Existing FIRST to exist; so, somewhat irrelevant to the discussion.

<snip>

I'll stop here, and my next post - in response to what you, Daniel, have written - will likely not address the rest of yours. Nor, perhaps, your other one, written in response to a later one of mine.

What is an "Obligate Parasite"? To be clear, I know something about what an obligate parasite is, but not your caps version of the term. Ditto, what is "LIFE", as opposed to life?

Are obligate parasites other than viruses also irrelevant to our discussion? What about autotrophs? Lithotrophs? Are they also irrelevant to our discussion?

JeanTate · Mar 7, 2016

I'll start this post of mine here:

Daniel said:
<snip>

JeanTate said:

Daniel said:

Well DNA contains boat loads of "Information" i.e., it transcends the "Physical Molecule"/Medium.

Click to expand...

Indeed.

So do crystals, black holes, ... why, then, limit your scope to DNA and chemical processes?

Click to expand...

Neither contain "Information"; They don't send messages with a pre-arranged and agreed upon convention/medium/meaning. Frankly, the notion is absurd.

<snip>

When I first read this, I thought I'd respond with boatloads of references to papers (published in relevant peer-reviewed journals) on black holes and information.

Then I realized that you, Daniel, seem to have a personal, idiosyncratic definition of information (or "Information"), one that is quite inconsistent with any of the standard, technical meanings widely used in the relevant scientific literature. So lots of references would be largely irrelevant.

Some of your apparent confusion may stem from the way entropy is used/defined in thermodynamics and information theory. I found this WP article quite helpful. Among other things it shows that the two concepts are (or can be) equivalent. Also that information can be regarded as physical, clearly the opposite of what you have written in many posts.

Then there's this:

Daniel said:
<snip>

However, it's quite telling that the people "screaming from the rooftops" about their "belief" systems which are "Allegedly" grounded in "SCIENCE" haven't a fleeting glimpse of a clue about that which they profess (Blindly Parrot).

<snip>

I have been reading the Why millions of apes and humans, but nothing between? thread, and found this post of yours, Daniel, to be quite informative:

Daniel said:
Since requesting the "Scientific Theory of evolution" appears to be the acme of foolishness (It's a Fairytale!), I suppose we can expand and discuss other fairytales...

So Relativity, sr and gr via different mechanisms (Speed vs. Gravity), can: Dilate/Bend/Warp...TIME ??

TIME is a "Conceptual" relationship between 2 motions. Specifically, it's based on a single rotation of the Earth on it's axis in respect to the Sun (A Day).
It's a "CONCEPT" (Non-Physical). It is without Chemical Formula/Structure, no Dimensionality/Orthogonality, and no Direction or Location. You can't put some in a jar and paint in red.

I mean c'mon now, let's reason together....can you Dilate/Bend Warp Non-Physical "Concepts"??

That which you are using to measure....isn't the thing you're measuring.

** A Football Field is 100 Yards long but a Football Field isn't Yardsticks!! If I bend a Yardstick...does the Football Field Bend also? **

So if something affects say...Cesium Atomic Clocks, or any modern "Clock" for that matter, does that then IPSO FACTO mean the Earth's rotation is Affected?
These Two matheMagical Fairytales (sr and gr) were falsified 30 seconds after their respective publications by 3rd graders @ recess, for goodness sakes.
IN TOTO, each are Massive Reification Fallacies on Nuclear Steroids!!

I really don't know why you'd need anymore but Quantum Mechanics (The most successful branch of Physics in the History of Science) has taken both to the Woodshed and Bludgeoned them Senseless !!! "Non-Locality" and Delayed Choice Experiments (in the literal thousands without exception) have annihilated "Space-Time".

Even Einstein later in Life, after 30 years of playing with UFT reckoned with it...

"I must confess that I was not able to find a way to explain the atomistic character of nature. My opinion is if that the objective description through the field as an elementary concept is not possible then one has to find a possibility to AVOID the continuum (together with SPACE and TIME) ALTOGETHER but I have not the slightest idea what kind of elementary concepts could be used in such a theory".--- Letter from Albert Einstein to David Bohm, 28 October 1954.

Albert Einstein, Endorsed (See Foreword)...
"Hence it is clear that the space of physics, is not in the last analysis, anything given in nature or Independent of human thought. It is a function of our conceptual scheme [mind]."
Max Jammer; The Concepts of Space, 1954, p. 171

"Reality is merely an illusion, albeit a very persistent one." --- Albert Einstein

I have some familiarity with Special Relativity (SR; yes, caps are often used) and the General Theory of Relativity (GTR, or GR; in this case caps are usually used), and found your characterization of them, um, irrational. And ignorant.

So what is this ""SCIENCE"" (yes, in caps, and with quote marks) you refer to?

I think MikeG nailed it, in this post: it's Danielscience.

IMHO, you (Daniel) have invented some private, highly idiosyncratic idea, and chose to call it ""SCIENCE"" (yes, in caps, and with quote marks). It seems to resemble the science that most (all?) of the others who've posted to these two thread seem to understand (e.g. it has, at some level, the same letters), but as your post on GR clearly shows, it is fundamentally different.

In my next post I'll give a concrete example of where, to me, you showed just how huge the communications gulf is, between us.

(to be continued)

Tolls · Mar 7, 2016

Daniel said:
“DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff — hardware — but as INFORMATION, or SOFTWARE. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level.” {Emphasis Mine}
Paul Davies PhD Physics
Paul Davies PhD Physics http://www.guardian.co.uk/education/2002/dec/11/highereducation.uk

That's a rather disingenuous choice of quote from that article.
Here's the paragraph beforehand:

There is a fundamental reason for this impasse. Life, as we now know it, is not magic matter. It isn't something that can be incubated by the methods of 19th-century chemistry. Nor can it be conjured up by infusing matter with energy, such as a bolt of electricity, à la Dr Frankenstein. There is no life force over and above normal intermolecular forces.

And the whole article is discussing how to go about creating life in the lab, and arguing that it makes more sense to work backwards (top-down) from a functioning lifeform (eg bacteria or a virus) than to go the Miller-Urey (bottom-up) way of zapping chemicals to create the real basics.

Darwin123 · Mar 7, 2016

Daniel said:
It's not. It would just be me saying it. I will not post Personal Information on forums so it can't be validated anyway.

Then why did you ask me whether I had ANY scientific background.

Note that I answered your question. I know that you can't check my answer. However, I wanted you to CONSIDER the possibility that many of the replies come from people with more formal, informal and a formal background than you do.

Note I broke my answer into formal, informal and aformal components. Perhaps you can point out which is which in my reply!

A

Daniel said:
nyone with any Scientific Acumen @ all can tell instantly by the substance of my posts, what they're dealing with. I surely can tell.
These terms are prolific throughout the Scientific Literature on the topics we're discussing here.

regards

Yes. I can tell by the substance of your posts that you have very little education in most scientific subject matter. However, I can tell that you are a computer programer of some type.

You have some background in that computer programming. However, you didn't go very deeply into information theory. You are pretending to have a large background in information theory. You haven't studied probability theory. You take all your probability theory from Creationist literature. You use words common to both fields in a creative manner.

JeanTate · Mar 7, 2016

(continued)

Again, I'll start by quoting something you posted, Daniel:

Daniel said:
MikeG said:

I'm not sure that astronomy is big on experiments.

Click to expand...

<snip>

“Cosmology may look like a science, but it isn’t a science. A basic tenet of science is that you can do repeatable experiments, and you can’t do that in cosmology.” {emphasis mine}
Gunn, J., cited in: Cho, Adrian, A singular conundrum: How odd is our universe? Science 3171848–1850, 2007.

Go and learn what REAL "Science" is, then Re-compute. <snip>

As hecd2 subsequently noted, "Gunn, J." is James Gunn (WP), among whose achievements is a leading role in the Sloan Digital Sky Survey (SDSS). "Daniel is indulging in the old YEC tactic of quote mining." - that's hecd2. And there seems to be some concrete evidence for this; for example, the quote appears in a website called creation.com.

But the most relevant thing is that Gunn obviously considers himself to be a scientist (someone who is doing science), and that many of the papers based on SDSS' published results are about tests of various cosmological models ... and Gunn is an author of some of these*!

So?

Well, to me, Daniel, you seem to be using so many key terms/phrases with meanings that are non-standard (and possibly highly idiosyncratic too) that meaningful dialog between us has been, up to now, largely illusory.

Is there a way forward, or should I simply drop out of any discussion with you (at least in this thread)?

One possibility: you sit down, think long and hard, and write out your core ideas again. This time making very sure you're using the key terms with their standard meanings (by all means ask for help on this), and where you're not, spell out exactly what you mean (in as much detail as any and all ISF readers need). And wherever you use caps or quote marks - except where caps are usually used, or when you are actually quoting - make crystal clear what specific meaning you intend (that differs from the standard one(s)).

Perhaps, as a trial, you could start with the terms 'information' and 'code', particularly as they are used in the relevant scientific literature on DNA?

* To give just one, recent, example, "Cosmological implications of baryon acoustic oscillation measurements" (ADS source)

Creationist argument about DNA and information

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