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Author Topic:   Semiotic argument for ID
Capt Stormfield
Member
Posts: 251
From: Vancouver Island
Joined: 01-17-2009


(1)
Message 211 of 223 (725475)
04-27-2014 3:37 PM
Reply to: Message 208 by Ed67
04-27-2014 3:10 PM


Re: AZPaul3 Reveals Contreversy in the Darwinian Camp
You might try reading the WHOLE article...

Wise words. You might consider reading the abstract of the paper itself instead of just the PR fluff about the paper.

"Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution."

They seem to have left out the part about the "code" being designed.


This message is a reply to:
 Message 208 by Ed67, posted 04-27-2014 3:10 PM Ed67 has responded

Replies to this message:
 Message 213 by Ed67, posted 04-27-2014 3:48 PM Capt Stormfield has responded

  
Ed67
Member (Idle past 947 days)
Posts: 159
Joined: 04-14-2014


Message 212 of 223 (725476)
04-27-2014 3:39 PM
Reply to: Message 209 by Omnivorous
04-27-2014 3:16 PM


Re: The plain truth about the function of DNA

Ed writes:

If they mean 'metaphorical code' they will say it.


I noticed that. Every time I encounter metaphorical language in English, hey, there it is! A big fat red METAPHOR printed right next to it!

Thank God, huh? Otherwise some folks could METAPHOR make asses of themselves.

Hey, buddy, if your only contribution is to INSULT, you're better off waiting to comment until you have something INTELLIGENT to say.


This message is a reply to:
 Message 209 by Omnivorous, posted 04-27-2014 3:16 PM Omnivorous has responded

Replies to this message:
 Message 214 by Omnivorous, posted 04-27-2014 4:13 PM Ed67 has not yet responded

    
Ed67
Member (Idle past 947 days)
Posts: 159
Joined: 04-14-2014


Message 213 of 223 (725477)
04-27-2014 3:48 PM
Reply to: Message 211 by Capt Stormfield
04-27-2014 3:37 PM


Re: AZPaul3 Reveals Contreversy in the Darwinian Camp
Capt writes:

You might try reading the WHOLE article...
Wise words. You might consider reading the abstract of the paper itself instead of just the PR fluff about the paper.

"Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution."
They seem to have left out the part about the "code" being designed.

Actually, Capt, I already quoted this paragraph from the abstract on this thread or the other one on this topic. When I did, I did NOT claim that the researchers believed the two codes in the genome to be DESIGNED. So where did you get that idea?

You are throwing useless RED HERRINGS into the discussion in an attempt to harass me. Any more of this an I will be reporting this to the administrators.


This message is a reply to:
 Message 211 by Capt Stormfield, posted 04-27-2014 3:37 PM Capt Stormfield has responded

Replies to this message:
 Message 217 by Capt Stormfield, posted 04-27-2014 6:59 PM Ed67 has not yet responded
 Message 218 by AZPaul3, posted 04-27-2014 8:14 PM Ed67 has not yet responded

    
Omnivorous
Member (Idle past 585 days)
Posts: 3808
From: Adirondackia
Joined: 07-21-2005


(1)
Message 214 of 223 (725481)
04-27-2014 4:13 PM
Reply to: Message 212 by Ed67
04-27-2014 3:39 PM


Re: The plain truth about the function of DNA
Ed67 writes:

Hey, buddy, if your only contribution is to INSULT, you're better off waiting to comment until you have something INTELLIGENT to say.

Then where would you be?

Besides, it's not just an insult. You totally missed the mockery.

And what about the entertainment value? You have to take that into account. Don't be so selfish.

You don't reply to serious problems pointed out in your own position, preferring rather to ridicule questions and objections you cannot handle. You've got a METAPHORone-trick, incredulity pony, and it gets tedious watching you ride around in circles.

METAPHORSo as far as I'm concerned, buddy, it's open season on boringly stupid. My restraint heretofore has been herculean...but every once in a while your empty pinata head will swing by, and I'll whack it.

Aw, go ahead. Say something smugly ignorant again.

You know you want to.


"If you can keep your head while those around you are losing theirs, you can collect a lot of heads."

This message is a reply to:
 Message 212 by Ed67, posted 04-27-2014 3:39 PM Ed67 has not yet responded

    
Ed67
Member (Idle past 947 days)
Posts: 159
Joined: 04-14-2014


Message 215 of 223 (725485)
04-27-2014 5:22 PM
Reply to: Message 188 by RAZD
04-26-2014 9:08 AM


Re: in your own words
RAZD writes:

Can you please elucidate in your own words any specific difference in quality rather than quantity between DNA and salt molecules?

Really, you don't understand?

In HIGH SCHOOL, we were taught that, in my own words, the DNA molecule has INTERCHANGEABLE PARTS (the 4 bases) within its structure. These interchangeable parts are ordered in different ways to produce different specific results.

Where do you see this happening in salt crystals?

Edited by Ed67, : No reason given.


This message is a reply to:
 Message 188 by RAZD, posted 04-26-2014 9:08 AM RAZD has responded

Replies to this message:
 Message 221 by RAZD, posted 04-28-2014 7:56 AM Ed67 has not yet responded

    
Ed67
Member (Idle past 947 days)
Posts: 159
Joined: 04-14-2014


Message 216 of 223 (725491)
04-27-2014 6:44 PM
Reply to: Message 185 by Omnivorous
04-26-2014 6:26 AM


Re: The plain truth about the function of DNA
Omnivorous writes:

There are other concepts on that page relevant to Ed.
quote:
Instead, Fremdscham (the noun) describes the almost-horror you feel when you notice that somebody is oblivious to how embarrassing they truly are. Fremdscham occurs when someone who should feel embarrassed for themselves simply is not, and you start feeling embarrassment in their place.
Personally, I'm mortified.

Hey, let's keep the personal insults out of this, guys. It's against the rules of the thread.

Edited by Ed67, : No reason given.


This message is a reply to:
 Message 185 by Omnivorous, posted 04-26-2014 6:26 AM Omnivorous has not yet responded

    
Capt Stormfield
Member
Posts: 251
From: Vancouver Island
Joined: 01-17-2009


Message 217 of 223 (725493)
04-27-2014 6:59 PM
Reply to: Message 213 by Ed67
04-27-2014 3:48 PM


Re: AZPaul3 Reveals Contreversy in the Darwinian Camp
You are throwing useless RED HERRINGS into the discussion in an attempt to harass me. Any more of this an I will be reporting this to the administrators.

Hey, I've got an idea, why don't you report that I've invited you to kiss my ass, you unresponsive troll.

Edited by Adminnemooseus, : Note: Suspension for this and other messages.


This message is a reply to:
 Message 213 by Ed67, posted 04-27-2014 3:48 PM Ed67 has not yet responded

  
AZPaul3
Member
Posts: 3428
From: Phoenix
Joined: 11-06-2006


Message 218 of 223 (725501)
04-27-2014 8:14 PM
Reply to: Message 213 by Ed67
04-27-2014 3:48 PM


Consider this harassment. Report away.
so you think that we shouldn't listen to science reporting
but we should listen to you instead.

No, not me. You might want to consider the sources, though. One of which has the actual abstract linked.

He confirms that 'additional layers of complexity' have been found, and that the UW scientists have added 'additional knowledge to this growing field'.

So your claim "there is no second code!" is all hype.

With your research methods and reading comprehension I'm not surprised you have missed the whole side of the barn. Yes, scientists have continued to find additional complex operations of the genome such as enhancers, promoters, HOX genes, as well as the transcription binding factors the UofW work was studying. None of these equate to any "second code hidden within the first (non-existent) DNA code".

What the UofW work did was not find any new levels of complexity, let alone any hogwash like a hidden second code, but did add new knowledge showing the breadth of use of the (already found and analysed) transcription binding factors.

[aside]
Not that you would understand, but a lot of the rest of the folks here will; the significance of the UofW paper is that it will help track the transcription paths, especially the multi-gene paths, for a lot of proteins. This will impact proteomics to a great extent.
[/aside]

So, in addition to there being no first code, in the sense you wish "code" to be defined, there now is no second code within the same DNA molecular structure. Who'd a thunk?

The release also contains gems such as “The genetic code uses a 64-letter alphabet called codons.” This sentence makes me sad...

Your smart-pants 'contributor' thinks she knows better than to use literary terms to describe the codon...

Wow. How damn dense can one human be and still function across the internet?

Her statement has nothing to do with using "literary terms." The statement she points to:

“The genetic code uses a 64-letter alphabet called codons.”

is just plain wrong even given the literary analogy.

Do you understand why?

yet in the SAME PARAGRAPH, gloating after showing up a research scientist, she gets a little too 'wordy' for her own good (pardon the pun):

your second link writes:

...Some amino acids get more than one word to designate them.

... which is correct and you probably still do not know why. The only one screwed here is not Dr. Emily Willingham, Ph.D., Biology, U of Texas, Austin, the author of that second link, but (no surprise) you.

With the typical Missouri mule you have to take a 2x4 to their butt to get their attention. Here, you were walloped up 'long side the head and you still carried on, dumb as a stump, like nothing ever happened.

As for your message to Capt Stormfield for quoting from the actual study paper from the UofW, the actual paper which is now the (sub)topic of discussion in this thread:

You are throwing useless RED HERRINGS into the discussion in an attempt to harass me. Any more of this an I will be reporting this to the administrators.

Please consider my responses to your continued inanity as harassment of your poor, helpless, little self.

Report away.


This message is a reply to:
 Message 213 by Ed67, posted 04-27-2014 3:48 PM Ed67 has not yet responded

  
Ed67
Member (Idle past 947 days)
Posts: 159
Joined: 04-14-2014


Message 219 of 223 (725503)
04-27-2014 8:19 PM
Reply to: Message 189 by JonF
04-26-2014 10:20 AM


Make up your mind...
Thanks for reminding me about your posts, Jon. I have been distracted by dog-and-pony shows but I finally got back to looking for some reasonable posts on this forum, and yours are two of them. In reply to this:
JonF writes:

And what did University of Washington researchers mean when they use the word "code" in this 2013 research report?

quote:
quote:

Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long.



The standard meaning... the "rules" "imposed" by natural chemical reactions that govern the translation from DNA to protein. There's no code in DNA, and the "genetic code" is just chemistry. Cool and complex chemistry, but just chemistry.

Make up your mind:
Either 'code' means

JonF writes:

the "rules" "imposed" by natural chemical reactions that govern the translation from DNA to protein.


...or it doesn't exist in biology.

Which is it?

Edited by Ed67, : No reason given.


This message is a reply to:
 Message 189 by JonF, posted 04-26-2014 10:20 AM JonF has responded

Replies to this message:
 Message 222 by JonF, posted 04-28-2014 8:43 AM Ed67 has not yet responded

    
Ed67
Member (Idle past 947 days)
Posts: 159
Joined: 04-14-2014


Message 220 of 223 (725505)
04-27-2014 8:33 PM
Reply to: Message 190 by JonF
04-26-2014 10:25 AM


Re: I agree - same old argument, different name
JonF writes:


As I've already explained, I don't invoke any special meaning by using the term. I simply mean information which is complex and specified

The definitions you have offered are useless. They involve too many subjective evaluations and are not operational definitions. Two people could easily disagree whether some system possesses CSI because your definitions do not invoke objective measures.

Fail.

{ABE} Your definitions boil down to "it sure looks like CSI to me!"

Point taken. I don't have mastery of Dembski's math. That's why I'm fine with using different wording; I don't mean to conflate what I'm arguing with what Dembski argues. I don't understand the guy - it's not just the math, but the very technical language he uses is way above my head.

At the same time, I was not convinced of my viewpoint by Dembski's work; it was mainly Stephen Meyer and Michael Behe whose books speak directly to the topic of CSI (and its synonym, Specified Complexity) that have been most convincing to me about the implications of the existence of a code in DNA.

Edited by Ed67, : No reason given.


This message is a reply to:
 Message 190 by JonF, posted 04-26-2014 10:25 AM JonF has responded

Replies to this message:
 Message 223 by JonF, posted 04-28-2014 8:50 AM Ed67 has not yet responded

    
RAZD
Member
Posts: 19329
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.2


Message 221 of 223 (725535)
04-28-2014 7:56 AM
Reply to: Message 215 by Ed67
04-27-2014 5:22 PM


Re: in your own words
RAZD writes:

Can you please elucidate in your own words any specific difference in quality rather than quantity between DNA and salt molecules?

Really, you don't understand?

In HIGH SCHOOL, we were taught that, in my own words, the DNA molecule has INTERCHANGEABLE PARTS (the 4 bases) within its structure. These interchangeable parts are ordered in different ways to produce different specific results.

Where do you see this happening in salt crystals?

In natural salt crystals there are several "interchangeable parts" -- different elements that can take their place in the crystal structure and otherwise occupy space in the crystals:

quote:
... The mineral content also affects the taste. The colors and variety of flavors are due to local clays and algae found in the waters the salt is harvested from. For example, some boutique salts from Korea and France are pinkish gray, some from India are black. Black and red salts from Hawaii may even have powdered black lava and baked red clay added in.[8] Some sea salt contains sulfates. It may be difficult to distinguish sea salt from other salts, such as pink "Himalayan salt", Maras salt from the ancient Inca hot springs, or rock salt (halite).

... However, a study found the amount of trace elements, such as titanium, silver, cobalt, and lead in synthetic sea salt are much higher than those in sea water. ...

Iodine, an element essential for human health,[14] is present only in small amounts in sea salt,[15] although the concentration varies according to its provenance.[citation needed]


Lots of interchangeable parts ... all based on basic chemical bonding ...

... the DNA molecule has INTERCHANGEABLE PARTS (the 4 bases) within its structure. These interchangeable parts are ordered in different ways to produce different specific results.

This is still just chemical bonds and chemical reactions -- just a difference in quantity and not a difference in quality as I requested.

Curiously I've also raised this same issue on the other thread where you keep asserting some magical difference to DNA from basic chemistry:

Message 285, copied in full for your pleasure:

quote:
Valence Bond Theory

quote:
In chemistry, valence bond (VB) theory is one of two basic theories, along with molecular orbital (MO) theory, that were developed to use the methods of quantum mechanics to explain chemical bonding. It focuses on how the atomic orbitals of the dissociated atoms combine to give individual chemical bonds when a molecule is formed. In contrast, molecular orbital theory has orbitals that cover the whole molecule.[1]

Information that is complex and specific (your "definition" of csi) to how all molecules are formed from elements.

Note that this is general basic knowledge in chemistry.

What you have failed to show (yet) is that there is an entirely different sort/quality of "csi" in DNA, rather than just a difference in degree/quantity due to the quantity of molecular bonds.

There is a larger number of bonds, and hence "information that is complex and specified" regarding the molecular formation in Sodium Sulfate ( Na2SO4) crystals than in Salt (NaCl) crystals ... a difference in the degree of "csi" (based on the coded information specified by the valence bonds) but not any difference in the sort of "csi".

If I have one apple in one basket and 10 apples in another then I have a difference in the degree of fruit in the baskets. If I have one apple in one basket and one pear in the other then I have a difference in the sort of fruit in the baskets.

Please identify something that makes it a different sort of "csi" in DNA from the chemical bonding sort of "csi" in salt and sodium sulfate and other molecules -- this is your assertion to support.


So I'll repeat, now that I have made my point a little clearer:

Can you please elucidate in your own words any specific difference in quality rather than quantity between DNA and salt molecules?

Something that is not merely based on chemical bonding via the basic rules of chemistry?


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This message is a reply to:
 Message 215 by Ed67, posted 04-27-2014 5:22 PM Ed67 has not yet responded

  
JonF
Member
Posts: 4001
Joined: 06-23-2003
Member Rating: 3.0


Message 222 of 223 (725536)
04-28-2014 8:43 AM
Reply to: Message 219 by Ed67
04-27-2014 8:19 PM


Re: Make up your mind...
The former.

Edited by JonF, : No reason given.

Edited by JonF, : No reason given.


This message is a reply to:
 Message 219 by Ed67, posted 04-27-2014 8:19 PM Ed67 has not yet responded

  
JonF
Member
Posts: 4001
Joined: 06-23-2003
Member Rating: 3.0


(2)
Message 223 of 223 (725537)
04-28-2014 8:50 AM
Reply to: Message 220 by Ed67
04-27-2014 8:33 PM


Re: I agree - same old argument, different name
Dembski argues. I don't understand the guy - it's not just the math, but the very technical language he uses is way above my head.

Then why are you asking for references to mathematicians who have analyzed and demolished Dembski's arguments? There are plenty, but you wouldn't have a chance of understanding them.

At the same time, I was not convinced of my viewpoint by Dembski's work; it was mainly Stephen Meyer and Michael Behe whose books speak directly to the topic of CSI (and its synonym, Specified Complexity) that have been most convincing to me about the implications of the existence of a code in DNA.

CSI and SI are not synonyms. Since you (and Dembski and Meyer and Behe and anyone) have never been able to produce an operational definition for what CSI is or detecting it, there's no point in using the term; it's just meaningless noise.


This message is a reply to:
 Message 220 by Ed67, posted 04-27-2014 8:33 PM Ed67 has not yet responded

  
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