Creationist argument about DNA and information

[abaddon]

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

Except that DNA is nothing special. Several other different molecules can perform the function just as well.

 

[marplots]

(much cnipped)
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?

I too am interested in Daniel's conceptualization of information. (Thankfully, also the subject of this thread.)

So far, I've gathered that:
1) Information is not part of the material world (doesn't consist of matter nor energy) and thereby is not amenable to scientific (naturalistic) laws or explanations.

2) Information is the footprint (or fingerprint) of an intelligent designer and where we observe information of a particular complexity (maybe "form?"), we can reliably infer an agent created it.

I think I have those correct but welcome any dilation by Daniel.

My first question is then if information is immaterial, why should we care about thermodynamics when deciding if it arose naturally or not? And my second question is about the existence of information itself - if it can be created, can it be destroyed? Is it conserved in some manner? I gather it can be passed along somehow, since it is an ingredient in functioning DNA.

Daniel, can you talk about your concept of what information is, does, and how it operates a bit more?

ETA: I don't care if Daniel's use of the term is non-standard, I'm just trying to get at his meaning.

 

[Daniel]

Except that DNA is nothing special. Several other different molecules can perform the function just as well.

"There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences. The existence of a genome and the genetic code divides living organisms from non-living matter."
Yockey, HP; Origin of life on earth and Shannon's theory of communication. In open problems of computational molecular biology. Computers and Chemistry; 24(1):105-123, Jan 2000
http://www.ncbi.nlm.nih.gov/pubmed/10642883


regards

 

[Daniel]

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

It was Rhetorical.

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.

Exactly the Opposite.



Do you have a response...

Daniel: I do however have another Null Hypothesis for the Antithetical Position: Functional DNA/RNA/Proteins NEVER spontaneously form "naturally", outside already existing cells, from Sugars, Bases, Phosphates, and Aminos, respectively.

This "Default Position" (Null Hypothesis) is TRUE, unless you can show it to be FALSE.

"The null hypothesis is the conclusion that is considered the default – you will accept this hypothesis if you fail to find sufficient support for the alternative hypothesis."-- csun.edu

I have searched High and Low and have failed to find any "Functional" DNA/RNA/Proteins wickering themselves together spontaneously "Naturally" from their respective building blocks, OUTSIDE already Existing Cells/Organisms.

Ergo...

This Formation ("Naturally")...is the Foundation of your Entire World-View, so you need to SUPPORT/Validate IT....? It's just that simple.


2. So Computer Engineers can't make Computers because they don't have Silicon Micro-Processors in their Cells??



regards

 

[Jrrarglblarg]

2: Rule of So

 

[Daniel]

(continued)


Peer review (no caps, you don't need the hyphen here either) is a process used in science (and mathematics, and ...).

1. Quibbling Fallacy. (hyphens/caps et al, are you an English Teacher?)

2. Peer-Review in it's pristine state (Evaluating Study Methods and Design/Conclusions) I have no problem with. But it has become a fiasco with many abuses...

"Research on bias in peer review also suggests that peer review is social in ways that go beyond the social categories to which authors and reviewers belong: Relationships between individuals in the process impact outcomes (e.g., affiliation bias), and individuals make decisions conditioned on beliefs about what others value (e.g., publication bias)."
-(Lee CJ, Sugimoto CR, Zhang G & Cronin B (2013) ‘Bias in Peer Review’, Journal of the American Society for Information Science and Technology, Vol. 64(1), pp. 2-17.)

"So we have little evidence on the effectiveness of peer review, but we have considerable evidence on its defects. In addition to being poor at detecting gross defects and almost useless for detecting fraud it is slow, expensive, profligate of academic time, highly subjective, something of a lottery, prone to bias, and easily abused."
-(Smith R (2006) ‘Peer review: a flawed process at the heart of science and journals’, Journal of the Royal Society of Medicine, Vol. 99, pp. 178-182.)


" Editors of scientific journals and program officers at the funding agencies have the most to gain from peer review, and they steadfastly refuse to believe that anything might be wrong with the system. Their jobs are made easier because they have never had to take responsibility for decisions. They are also never called to account for their choice of referees, who in any case always have the proper credentials. Since the referees perform a professional service, almost always without pay, the primary responsibility of the editor or program officer is to protect the referee. Thus referees are never called to account for what they write in their reviews. As a result, referees are able, with relative impunity, to delay or deny funding or publication to their rivals. When misconduct of this kind occurs, it is the referee who is guilty, but it is the editors and program officers who are responsible for propagating a corrupt system that makes misconduct almost inevitable.
This is the kind of misconduct that is, I fear, rampant in all fields of science, not only biomedical science. Recently, as part of a talk to a large audience of mostly young researchers at an extremely prestigious university, I outlined this analysis of the crisis of peer review. The moderator, a famous senior scientist, was incredulous. He asked the audience how many disagreed with my heresy. No one responded. Then he asked how many agreed. Every hand in the house went up."
Goodstein, D; Conduct and Misconduct in Science: Caltech, 2002.
http://www.its.caltech.edu/~dg/conduct_art.html

First, why the caps? the quote marks?

I use them for emphasis. Try and focus on the substance of the arguments presented. thanks

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

Nonsensical Quibbling (Fallacy). Algorithms are "Programs".

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.

I've already explained this to you TWICE.

Do you have any semblance of a "Substantive" argument or position?

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.

Then it's time to educate yourself, eh?

I do have some familiarity with Gibbs free energy (without the caps; what difference, may I ask, does adding caps make to its meaning?).

Nonsensical Quibbling (Fallacy), again. And if you did have "some familiarity" with it, you surely wouldn't have asked this...

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...

Here's a clue.... SPONTANEOUS Formation.

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

dG = dH - TdS

Link please.

It's post# 453, in this very thread...

http://www.internationalskeptics.com/forums/showpost.php?p=11161974&postcount=453

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.

Really?? You forgot the "How/Why So" part. So go ahead....?

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?

Ahhh, either stop Quibbling nonsensically (it smacks of desperation) or our conversation will be over... QUICK!!

Are obligate parasites other than viruses also irrelevant to our discussion?

Yes. We are discussing How you get "LIFE". Obligate Parasites NEED Life established first, to exist. They are irrellevant to this discussion.

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

At this point, it's probably a good idea to drop out.


regards

 

[Son of Inigo]

It's not. SUPPORT ??





So we can add reading comprehension issues to your list, which is getting quite long.

You asked: "Just how does one go about determining the age of something in your world?"

I said: "Historical Documentation".

This doesn't then give you Carte Blanche authority to Incoherently Staple "Daniel Science = Historical Documentation" motif to anything you wish. It smacks of reading comprehension issues and/or deliberate misrepresentation. <--- I'm leaning here.

Rest snipped

Seems I am not the only one with reading comprehension issues, Daniel. I asked you specifically, if not, WHY not.

You give me quotes from other people. I don't care what anyone else thinks about this Daniel. I want to know what you think. I am not debating them, I am debating your views on science.

So again, if not, why not?

Also, of the three examples I asked about, why is germ theory the only one that you label real science? You didn't label the other two as real science.

And I use "Daniel' science when discussing your views because it must be modified due to the fact the only one that understands it is you. No one else in this thread (and several of them are practicing scientists) would label what you are saying as science. Therefore the qualification when speaking to that which you say. That way other readers of this thread will not be confused, as there is a big difference between 'Daniel' science and science.

Please Daniel, prove to me that you don't suffer from the same reading comprehension you accuse me of. If not, WHY not. Why do you accept those particular theories?

I, on pins and needles, are ever yours, ect, ect......

 

[Reality Check]

Daniel: I do however have another Null Hypothesis for the Antithetical Position: Functional DNA/RNA/Proteins NEVER spontaneously form "naturally", outside already existing cells, from Sugars, Bases, Phosphates, and Aminos, respectively.

This "Default Position" (Null Hypothesis) is TRUE, unless you can show it to be FALSE.

"The null hypothesis is the conclusion that is considered the default – you will accept this hypothesis if you fail to find sufficient support for the alternative hypothesis."-- csun.edu

And I have another null hypothesis which according to you must be TRUE, Daniel !
Null Hypothesis for the Rational Position: Functional DNA/RNA/Proteins DID spontaneously form "naturally", inside already existing cells, from Sugars, Bases, Phosphates, and Aminos, respectively.
This is obviously true: Earth was formed 4.5 billion years ago without any Functional DNA/RNA/Proteins. Functional DNA/RNA/Proteins appeared in the early history of the Earth.
Of course the

But you are wrong.
A null hypothesis is a default position that is presumed to be currently true when supported by evidence.
A null hypothesis is not a fantasy or unsupported assertion.
Testing a single alternative hypothesis tells us nothing about the truth of the null hypothesis.

www.csun.edu/~dgw61315/ECON309lect7Bhypotesting.doc

ECON 309
Lecture 7B: Hypothesis Testing

To do a hypothesis test, you will actual have two hypotheses: the null hypothesis and the alternative hypothesis, which are stated in such a way that they are mutually exclusive (you can’t have both hypotheses be true). The null hypothesis is the conclusion that is considered the default – you will accept this hypothesis if you fail to find sufficient support for the alternative hypothesis.

This is important: it means you are placing the burden of proof on those who support the alternative hypothesis. The null hypothesis is essentially “innocent until proven guilty” – it can be accepted with little support from the evidence, simply because the evidence doesn’t strongly indicate something else. For this reason, researchers will usually use the alternative hypothesis to represent their own position – what they wish to prove – in order to put their claim to the strongest test. But sometimes researchers put their own position as the null, in which case they’ve made things very easy on themselves.

 

[Reality Check]

2. Peer-Review in it's pristine state (Evaluating Study Methods and Design/Conclusions) I have no problem with. But it has become a fiasco with many abuses...

We know that there is bias in peer review, Daniel. That does not invalidate science that has been evaluated again and again over centuries, e.g. the age of the Earth being much greater than 6000 years was recognized from geology starting from the 17th century.

I have to tell you a basic fact about computer science: Algorithms are not Programs !
Programs are implementations of Algorithms in specific languages.

 

[Daniel]

Daniel. I asked you specifically, if not, WHY not.

And I've already told and SHOWED you numerous times; One Last Time, Ready....

I don't know the AGE of the Earth or Universe. It can't be Scientifically VALIDATED because you don't have any Viable...."Independent Variables".

In fact, it's Non-Sequitur Fallacy with The Scientific Method...since it's goal is to elucidate "Cause and Effect" relationships, for goodness sakes.

Is there something here that's particularly confusing you need me to elaborate on??

Also, of the three examples I asked about, why is germ theory the only one that you label real science?

1. What were the other two?

2. Because Germ Theory has the "Process/Mechanism" (The Cause) of "The Effect" which has been repeatedly supported/Validated by Experiment for ~200 Years.

That's what a Scientific Theory is...

A Scientific Theory summarizes a hypothesis or group of hypotheses that have been supported with repeated testing. {Emphasis Mine}
http://chemistry.about.com/od/chemistry101/a/lawtheory.htm

A Scientific Theory consists of one or more hypotheses that have been supported with repeated testing. {Emphasis Mine}
http://www.fromquarkstoquasars.com/hypothesis-theory-or-law/

A Scientific Theory represents an hypothesis, or a group of related hypotheses, which has been CONFIRMED through REPEATED EXPERIMENTAL TESTS. {Emphasis Mine}
http://teacher.nsrl.rochester.edu/phy_labs/appendixe/appendixe.html

See the connection??


regards

 

[Reality Check]

Are you referring to Miller-Urey??

If so, they didn't produce any "Proteins"..

Definitely laughable and irrelevant, Daniel - no one claims that Miller-Urey produced proteins. The experiment also did not produce millions of other organic molecules !
The experiment produced amino acids which are the first step to RNA or DNA which leads to the production of proteins.

 

[Reality Check]

Daniel: Cite the DeltaG for reaction of Nucleosides forming from bases and sugars.

The DeltaG for Nucleosides wickering themselves together from bases and sugars is "POSITIVE" as is the Phosphorylation into Nucleotides.

Unsupported assertions followed by a Gish Gallop from here to Christmas and what looks like the creationist idiocy about 2LOT.
8 March 2016 Daniel: Cite the value of DeltaG for reaction of Nucleosides forming from bases and sugars.
Scientists who study abiogenesis know about science, e.g. Gibbs free energy, and have no problem with Nucleosides forming from bases and sugars. So I have to start with this being yet another creationist myth !

N.B. I do know abut Gibbs energy (an important part of my Honors year work) which you may want to learn about.
Processes such as chemical reactions are not prohibited by an increase in Gibbs energy. They are disfavored. Their rates are lower than favored processes. Given the millions of years during which life arose on the Earth, a delataG > 0 is not an issue.

 

[JeanTate]

<snip>

"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.

<snip>

On a whim, I used Google to see where some of the various quotes Daniel has used in this thread have also appeared.

Call me naive, but I had expected that what Daniel was presenting was his own ideas, based on his own research (well, at least to some extent).

I've certainly not checked all Daniel's sourced quotes in this thread, but in the sample (of ~ten) I've so far checked, I found all but one also appears on various creationist websites (and I'm not sure that that one doesn't; I only checked the first page of Google's results)!

While such an - apparently - deceitful approach is not exactly verboten here in ISF (as far as I know), I think it's fair to say that it's regarded by almost all ISF members are pretty bad form. It's certainly not what one expects in a science-based discussion.

It also may go some way to explaining why Daniel seems so reluctant to engage in a meaningful dialog.

Now back to Danielscience ....

 

[JeanTate]

<snip>

A Scientific Theory summarizes a hypothesis or group of hypotheses that have been supported with repeated testing. {Emphasis Mine}
http://chemistry.about.com/od/chemistry101/a/lawtheory.htm

A Scientific Theory consists of one or more hypotheses that have been supported with repeated testing. {Emphasis Mine}
http://www.fromquarkstoquasars.com/hypothesis-theory-or-law/

A Scientific Theory represents an hypothesis, or a group of related hypotheses, which has been CONFIRMED through REPEATED EXPERIMENTAL TESTS. {Emphasis Mine}
http://teacher.nsrl.rochester.edu/phy_labs/appendixe/appendixe.html

<snip>

So, on this basis, we can be very confident that the theory of evolution, Special Relativity, the General Theory of Relativity, the Standard Model (of particle physics), Quantum Electrodynamics, the Big Bang theory (with some caveats about exactly what it is), ... are all "Scientific Theories".

I'm glad to see that we seem to have agreed on something concrete, Daniel.

 

[Reality Check]

I don't know the AGE of the Earth or Universe. It can't be Scientifically VALIDATED because you don't have any Viable...."Independent Variables".

Repeating nonsense does not stop us determining that the age of the Earth is greater than 6000 years, Daniel.
Any one who can count can Scientifically VALIDATE AS HAS ALREADY BEEN DONE MANY TIMES the number of layers in ice cores.
Any one with a basic knowledge of mathematics can Scientifically VALIDATE AS HAS ALREADY BEEN DONE MANY TIMES the dating of tree rings to ages of ~10,000 years.

We have not got to the geological record, sediments, radiometric dating (C14, etc.) other dating techniques, etc. yet !

That's what a Scientific Theory is...

A Scientific Theory summarizes a hypothesis or group of hypotheses that have been supported with repeated testing. {Emphasis Mine}
http://chemistry.about.com/od/chemistry101/a/lawtheory.htm...

Well Duh, Daniel !
Scientific theories include that there has been repeated testing, e.g. the repeated testing of the scientific theory of evolution.

 

[marplots]

On a whim, I used Google to see where some of the various quotes Daniel has used in this thread have also appeared.

Call me naive, but I had expected that what Daniel was presenting was his own ideas, based on his own research (well, at least to some extent).

I've certainly not checked all Daniel's sourced quotes in this thread, but in the sample (of ~ten) I've so far checked, I found all but one also appears on various creationist websites (and I'm not sure that that one doesn't; I only checked the first page of Google's results)!

While such an - apparently - deceitful approach is not exactly verboten here in ISF (as far as I know), I think it's fair to say that it's regarded by almost all ISF members are pretty bad form. It's certainly not what one expects in a science-based discussion.

It also may go some way to explaining why Daniel seems so reluctant to engage in a meaningful dialog.

Now back to Danielscience ....

It may not be nefarious. If I wanted to find a literature review pro-creation, I might take a look at creationist websites, since they've probably already done the work. Just as I might look at skeptic websites about evolution (TalkOrigins comes to mind) to find the opposite.

I see nothing wrong with the method, so long as Daniel is evaluating the quotes on his own to see if they support his argument.

 

[abaddon]

"There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences. The existence of a genome and the genetic code divides living organisms from non-living matter."
Yockey, HP; Origin of life on earth and Shannon's theory of communication. In open problems of computational molecular biology. Computers and Chemistry; 24(1):105-123, Jan 2000
http://www.ncbi.nlm.nih.gov/pubmed/10642883


regards

You are out of date.

https://www.newscientist.com/article/dn21720-move-over-dna-six-new-molecules-can-carry-genes/

What a surprise.

 

[abaddon]

And I've already told and SHOWED you numerous times; One Last Time, Ready....

I don't know the AGE of the Earth or Universe. It can't be Scientifically VALIDATED because you don't have any Viable...."Independent Variables".

So you don't know that it is 6,000 years old because because you cannot scientifically validate that either. Thank you for that admission.

In fact, it's Non-Sequitur Fallacy with The Scientific Method...since it's goal is to elucidate "Cause and Effect" relationships, for goodness sakes.

And it does. What was your question?

Is there something here that's particularly confusing you need me to elaborate on??

Yes. You have advocated a young earth, yet conceded an ancient earth and universe in various posts. It cannot be both.

1. What were the other two?

Didn't you read the post in question?

2. Because Germ Theory has the "Process/Mechanism" (The Cause) of "The Effect" which has been repeatedly supported/Validated by Experiment for ~200 Years.

Just like the other two which you cannot identify because you failed to actually read that post. I read it. I am not about to enable laziness. Does not the holey babble have words to say about sloth?

That's what a Scientific Theory is...

A Scientific Theory summarizes a hypothesis or group of hypotheses that have been supported with repeated testing. {Emphasis Mine}
http://chemistry.about.com/od/chemistry101/a/lawtheory.htm

A Scientific Theory consists of one or more hypotheses that have been supported with repeated testing. {Emphasis Mine}
http://www.fromquarkstoquasars.com/hypothesis-theory-or-law/

A Scientific Theory represents an hypothesis, or a group of related hypotheses, which has been CONFIRMED through REPEATED EXPERIMENTAL TESTS. {Emphasis Mine}
http://teacher.nsrl.rochester.edu/phy_labs/appendixe/appendixe.html

See the connection??

Everyone sees the connection bar one.

 

[JeanTate]

It may not be nefarious. If I wanted to find a literature review pro-creation, I might take a look at creationist websites, since they've probably already done the work. Just as I might look at skeptic websites about evolution (TalkOrigins comes to mind) to find the opposite.

The difference is, I think, that you'd be quite open about what you had done, fairly close to the start of such a presentation. Daniel, on the other hand, has never said anything about his direct sources (as far as I can see).

I see nothing wrong with the method, so long as Daniel is evaluating the quotes on his own to see if they support his argument.

Indeed.

From the research I did, into the sources he quoted, many of the snippets he quotes are "quote mining" (per hecd2). And - as has also been pointed out - when you look at the full context of many of his quotes, they not only do not "support his argument", but directly contradict it (e.g. the one by James Gunn).

IMHO, it's not only a pretty silly approach to use here in ISF, but a self-defeating one too ... of course many an ISF member will dig into the material he writes - including the quotes - so he can reasonably expect that his direct sources, and the "quote mining", will be discovered.

 

[marplots]

From the research I did, into the sources he quoted, many of the snippets he quotes are "quote mining" (per hecd2). And - as has also been pointed out - when you look at the full context of many of his quotes, they not only do not "support his argument", but directly contradict it (e.g. the one by James Gunn).

I have to admit I'm not entirely clear on what exactly his argument is. I've tried to narrow the scope without much success.

IMHO, it's not only a pretty silly approach to use here in ISF, but a self-defeating one too ... of course many an ISF member will dig into the material he writes - including the quotes - so he can reasonably expect that his direct sources, and the "quote mining", will be discovered.

True enough. I think it's often the case that someone wanders onto the field here, thinking to have a good game, not realizing it's pro baseball being played.

"But I killed 'em in West Podunk!"

"Yeah kid, you did. You certainly did."