Talk:DNA/archive 3

• archive 1
• archive 2

Contents

1 Sentence 1 1.1 Tangent on "Information" 2 Sentence 2A 3 Sentence 2B

Sentence 1

Perhaps a paragraph is too much, maybe we can agree on the first sentence.

• A: Deoxyribonucleic acid (DNA) is a nucleic acid which carries the genetic "instructions" for the biological development of all known organisms.
  • I would accept removing "is a nucleic acid which"; if the second sentence began "This nucleic acid..." Lirath Q. Pynnor
    • The suggestion is raised below that we state "instructions" and link information -- We should just link to instructions then, the instructions article states that an instruction is a type of information. One person said "information", another said "instructions" -- Im not overly concerned about the issue, either way is probably fine with me.
    • If you feel a general statment of DNA's actual chemical structure is necessary for the first sentence, it is probably best to retain nucleic acid. Biochemical would be acceptable to me, but the nucleic acid article explains that nucleic acids are biochemicals. As for the obscure nature of the term, that is not reason not to use it. The word biochemical links to the page on biochemistry, that should be sufficient for the reader to understand. In any case, I think "nucleic acid" suffices, at least for the introduction.

---

I just made some comments about your version, but there was an edit conflict and afterwards some weren't relevent because you'd modified it -- for this first sentence:

1. I say that we don't need links to either information or instructions, but this version has both! I'd suggest "...carries the genetic instructions for..."

[Peak:] My proposal was, and remains genetic instructions, that is, [genetics|genetic] [information|instructions]. That way, the link to information is there, but very discretely. Seems like a pretty good compromise to me. Peak 22:04, 16 Jan 2004 (UTC)

2. If the nucleic acid link is moved to the next sentence, this first sentence should have some reference to what DNA actually is, i.e. it's a chemical/biochemical/compound/biopolymer/complex/macromolecule/whatever. I'd prefer biochemical (with link to biochemistry), but will accept anything.

3. I'm agnostic about whether a nucleic acid link is required (provided point 2 is satisfied). I could accept a version with or without it.

Stewart Adcock 17:42, 16 Jan 2004 (UTC)

Stewart, would you do me a favor? I'd ask you to look up "biochemical" in a dictionary. To save you some work, I will tell you it's not in the American Heritage Dictionary, 2000 edition. I would like to know if you find a definition that says something like "a biological chemical." I predict you won't find such a definition, but I'd be very interested to know if you do. 168... 17:56, 16 Jan 2004 (UTC)

For your delectation I give you http://dictionary.reference.com/search?q=biochemical -- Cyan 20:33, 16 Jan 2004 (UTC)

You're right. I goofed. My own preferred source, the AHD, says there is a noun form. I overlooked it the first three times I looked! So, I guess I owe people an apology for writing with such assurance about that. Still, the AHD supports the original objection that (I think it was) Peak and I made, which is that "biochemical" is obscure. The AHD doesn't actually honor it with a definition, only mentions it as a derivative of biochemistry and says it can be a noun or an adjective. In fact, one of the definitions at the link you gave defines it only as an adjective, suggesting that the noun form (which mistakenly I thought wasn't even recognized by the AHD as vernacular) is even more obscure than the adjective. So I don't withdraw my objection, although I do concede to some mud on my face. 168... 21:12, 16 Jan 2004 (UTC)

[Peak:] To attest further to the obscurity:

• WordNet and other online sources do not recognize it as a noun at all.
• The online AHD has a full entry for chemical as a noun, in stark contrast to the "adj and noun" description given for the subentry at "biochemical". Peak 22:04, 16 Jan 2004 (UTC)

I actually didn't read the entry very carefully; I was just providing it for all and sundry. (I would have completely overlooked the fact that it lists "biochemical" as a noun if 168 hadn't pointed it out...) -- Cyan 21:24, 16 Jan 2004 (UTC)

To be honest, I haven't opened a dictionary for at least 2 years and 4 months, given that all of my dictionaries are in storage on the opposite side of the atlantic. But, I wasn't really intending to suggest its use as a noun here, I apologise for giving that impression (maybe I should read what I type before clicking on submit). If you look way back up through the prior discussions, at that earlier time I was suggesting it in the sense "relating to biochemistry". When I listed all of the options more recently, I wasn't ultimately trying to indicate which word(s) to use but to give some possibilities. If you really want to known my prefered choice for this intro -- it's "biochemical compound". Incidently, I regularly use the word biochemical as a noun in my own speech, but I wouldn't necessarily try to claim that it is acceptable in formal documents. Stewart Adcock 02:21, 18 Jan 2004 (UTC)

I have addressed both raised points above, directly under Sentence 1:A. (see above) Lirath Q. Pynnor

Okay. If, in your first sentence, you replace "genetic "information" and "instructions"" with Peak's version (or something very similar to it) then I'll happily accept that sentence. Stewart Adcock 02:21, 18 Jan 2004 (UTC)

Ok, so I edited it so that it only contains genetic "instructions" -- is that ok? Note that the instruction does define an instruction as a form of information. Lirath Q. Pynnor

I suppose so. Is there any particular reason for the quotation marks though? What do the other people, who aren't ignoring you, think?

• My reasoning is that information is technically something created by intelligent thought. The information article seems to agree with this at points: it explicitly refers to pheremones as "information" and states, "neural processes are seen as a form of information by some" -- the article also refers to DNA as information (no quotes) but only after it noted that the "non-intelligence" view of information is only held "by some".
  • Basically, intercellular communication is really a chemical reaction between interacting components -- true information is not really being sent. I feel the same notion applies to DNA. One might argue that the brain's stored information is also a chemical process; however, such information is in the brain -- it is associated with intelligent thought. DNA is more metaphorically viewed as information. Lirath Q. Pynnor

Argh! This is the "information can of worms" I alluded to back on 15th Jan. Complete codswallop most of that. However, DNA is metaphorically viewed as storing information. So, can we consider sentence 2 now? Stewart Adcock 00:34, 19 Jan 2004 (UTC)

Well, Im not sure whether you are for or against using the " ". But lets move on to sentence 2 and we can come back to this minor issue later, if need be. Lirath Q. Pynnor

P0M: Sorry to horn in on what appears to be an ongoing discussion of some length. Since 1950 when Claude Shannon published work on information theory, that word has taken on a technical meaning in contexts such as DNA. One speaks, for instance, of the content of any signal that conveys a report of the conditions of one system to another system as the "information" in the signal. If one is doing remote sensing on the temperatures and wind speeds present on the top of K-2, for instance, one would speak of the data sent out by the automatic monitoring equipment as the information that it is transmitting. Bursts of static or other problems with the transmission of the monitoring stations signals would cause losses of information.

Right, but the information article seems to indicate that this technical usage is not universally used -- even within the technical fields. Even you, in your above paragraph, stated, "One speaks, for instance, of the content of any signal that conveys a report of the conditions of one system to another system as the "information" in the signal." Just as in your paragraph you felt it appropriate to use ""; during the first such usage, so should we here. I like your paragraph and will add it to information. Lirath Q. Pynnor

P0M's use of quotes around the word information is the use-mention distinction. I believe this has a different purpose from the quotes in our proposed text. Specifically, P0M is just mentioning the word information, whereas we propose to use it and/or the word instructions, possibly with quotation marks. (Note that P0M uses, rather than mentions, the word information in his last sentence, and leaves it unquoted there.) -- Cyan 18:12, 20 Jan 2004 (UTC)

Regardless, there is not scientific agreement that this is a form of information. Lirath Q. Pynnor

P0M: The convention I was taught was that when you say something like, "The word light has five letters," you are supposed to put quotation marks around the word to indicate you are talking about the word and not its referent.

P0M: According to my understanding of this term, it could also be used (i.e., it would communicate meaning clearly) in the following kind of description:

"Primordial gravitational waves are thus direct probes of the inflationary epoch and the initial Planck-scale singularity, and can even transmit information from a pre-Big-Bang collapsing universe in 'bounce' cosmologies."

P0M: "Scientific agreement" is different from "agreement among all scientists.

---

Tangent on "Information"

[Peak:] Whether the DNA article uses the word "information" or "instructions" is of little consequence as far as I'm concerned, but since it was I who first proposed using the word "information" in the preamble, I would like to point out that the idea that DNA is the "substance carrying organism’s genetic information" is hardly new or uncontroversial. In fact, I now see that that's how the Encarta entry for DNA begins.

Perhaps to stir up some controversy, Lir claims that:

• "information is technically something created by intelligent thought"

As P0M has already pointed out, this is manifestly untrue - in fact, the most "technical" meanings of the word (in physics and communications engineering) are distinctive precisely because there is no presumption of "meaning", let alone "intelligent thought".

Of course if Lir simply meant that some would define information as requiring intelligence, then there would be no cause for disagreement.

The real reason for this tangent, however, is that I came across a 2003 revision of the April 1997 Scientific American article "BLACK HOLES and the INFORMATION PARADOX". For your reading please, therefore, I offer you [1] (http://www.physics.utoronto.ca/~peet/media/SciAmEdge/Q103018C.pdf) Peak 08:15, 21 Jan 2004 (UTC)

Sentence 2A

• Sentence 1A was, "*A: Deoxyribonucleic acid (DNA) is a nucleic acid which carries the genetic "instructions" for the biological development of all known organisms."
  • Although the indicator "instructions" may be debatable, it appears that Adcock, Peak, and Pynnor have no real issue with the above.

• Sentence 2A could be: This nucleic acid is sometimes referred to as the "molecule of heredity" and the "genetic code of life".
  • A quick look on yahoo/google will find that both phrases are not uncommon. The latter phrase is used both to refer to the human genome and DNA. This sentence gives a link to nucleic acid, it links to important concepts such as heredity and genetics, and it gives the reader two generally accepted nicknames. In case the reader is truly ignorant of the subject, it also informs the reader that DNA is a molecule and that it is associated with the life processes. Lirath Q. Pynnor

I don't think this sentence adds anything useful, whatsoever, to the introduction. The reader has already been informed that DNA is involved in genetics. By virtue of the mention of nucleic acid in sentence 1, we have already indicated to the reader that it is a molecule. As Lir suggests, the reader may indeed be completely ignorant, but that doesn't mean that we need to insult their intelligence in the introduction. By avoiding this sentence entirely, we don't need to discuss the, controversial, merits of using those two phrases. (I think they do deserve a mention in the article, however) Stewart Adcock 21:25, 20 Jan 2004 (UTC)

Where would you put it, if not in the introduction? Lirath Q. Pynnor

The "molecule of heredity" phrase is already in the main body of the article. The "genetic code of life" phrase could, perhaps, be mentioned along with the history of DNA research near the end of the article. Stewart Adcock 22:41, 20 Jan 2004 (UTC)

[Peak:] The genetic code link is already mentioned in the DNA article; the phrase is actually already used twice. Would Lir be content if we said something like "DNA uses the genetic code of life"? (I've already tried to explain to Lir that there's a difference between a "code" and an "encoded message." Would someone else perhaps like to explain why the phrase "DNA is the genetic code of life" is simply wrong?) Peak 07:08, 21 Jan 2004 (UTC)

Sentence 2B

• I don't really care whether or not the phrase is technically wrong. It is used; thus, we must include it. For now, lets decide to put it down where "molecule of heredity" is at in the article.
  • DNA is inherited and used to propagate traits; during reproduction, it is replicated and transmitted to offspring.
    • Lirath Q. Pynnor 16:31, 21 Jan 2004 (UTC)

This one is going to be more tricky. First, I think we should decide what we actually want to say here before we select an exact wording. I think that it is important to introduce DNA replication, but inheritance of traits might already implied be by the reference to genetics. I was going to suggest (2 sentences):

• During reproduction, organisms transmit replicated DNA to offspring. This is the primary mechanism of biological inheritance.

But it is possible that the second sentence is completely redundant. What do you others think? Nonetheless, this is very similar to T5.2 (IIRC) which wasn't deemed suitable so I doubt it is acceptable now.

A more concise alternative is:

• The primary mechanism of biological inheritance is the DNA replication occuring during reproduction.

Stewart Adcock 06:58, 22 Jan 2004 (UTC)

biological inheritance is linked to by inherited Lirath Q. Pynnor

Yes it is... but in the preceeding dicussions someone pointed out that the term "biological inheritance" is less ambiguous than "inheritance". This is especially true since saying "DNA is inherited" means something that is very different from saying "biological inheritance" and I think we want to say the later. Yes? Stewart Adcock 00:50, 24 Jan 2004 (UTC)

I'm not sure, surely we can expect that the reader will either know that by "inherited" we mean "biological inheritance"; in which case, they don't want to read the full phrase -- or, the reader will say, "DNA can be inherited, like when my grandma dies she can leave it to me in her will?"; and they will find that notion to be so strange that they just have to click on the link and learn more about inheritance laws...at which point they will say, "oh". Is there any usage of the word "inheritance", in biology, physics or chemistry; which one could possibly confuse biological inheritance with? Lirath Q. Pynnor

You could inherit, for example, a chemical dependancy which has nothing to do with genetics and we don't want to imply that DNA is involved in that. (I've never come across a technical meaning for the term "inheritance" in chemistry or physics outside their overlap with the computational sciences.) Stewart Adcock 18:39, 24 Jan 2004 (UTC)

Our addiction articles do not use the term "inheritance". My search on yahoo found a lot of articles talking about the inheritance of drug addictions; but the context was always that of an inherited genetic predisposition. Dictionary.com really doesn't imply that the term has a non-genetic usage. While it is worthwhile to note the term's alternate usages; I don't think there is any need to do this here -- inheritance should always be understood as either "biological/genetic inheritance" or "economic inheritance"; unless designated otherwise (such as: inheritance (computer science)). So there is no real need to use the full "biological inheritance" term. Lirath Q. Pynnor

[Peak:] "Inheritance" has plenty of meanings outside biology, economics and computer science (consider e.g. "the cultural inheritance of Rome"). Here's the AHD entry for the non-biological meanings:

1a. To receive (property or a title, for example) from an ancestor by legal succession or will. b. To receive by bequest or as a legacy. 2. To receive or take over from a predecessor: The new administration inherited the economic problems of the last four years. 4. To gain (something) as one's right or portion.

Peak 05:07, 25 Jan 2004 (UTC)

Yes, those would be 4 examples of economic inheritance, which I noted above. Since this isn't an article about economics (or computer science), the reader will have no trouble understanding that by "inheritance" we are referring to "biological inheritance". Lirath Q. Pynnor

So law == economics == politics == culture? That's an impressive bit of oversimplification. Peak 06:17, 30 Jan 2004 (UTC)~

Anything involving property is a form of economic activity. Economics has legal, cultural, and political subfields. Lirath Q. Pynnor