Code as an Analogy of DNA?

Science

(John Mercer) #1

This. 100x.

It just amazes me that some can be so gullible that they will assert that something that involves absolutely zero abstractions somehow must be a code, just because we use the term metaphorically to describe it.


Perry Marshall: What is Random?
(John Mercer) #2

It must not be a very strong argument if you are reduced to simply asserting its truth.

Where, exactly, is the abstraction in the alleged code?


#3

I think that’s far from grasping the significance of transposition, epigenetic changes, or symbiogenesis. But I suppose it’s a start.

@Mercer

I can only tell you that I found Perry’s argument plausible. I have not studied it enough to repeat the ins and outs of it myself. If you are interested, here is a blog about it.


(Retired Professor & Minister.) #4

Yes indeed.

I think people get confused by the fact that not only is “code” a convenient analogy, many people assume that everything and anything which can be displayed or explained in a this-means-that code chart (or code table) is a literal code in the scientific sense. Thus:

Zip Code…City

60007…Chicago, IL
77001…Houston, TX
84044…Salt Lake City, UT

…and…

Atomic Number…Element

1…Hydrogen
2…Helium
3…Lithium

An area of Chicago, IL can be specified by the zip code 60007 and it is a totally arbitrary abstraction. (Any uniquely assigned number could have served that purpose.) But Hydrogen being linked to “1” is not an arbitrary abstraction. It is a description of Hydrogen’s number of protons in the nucleus. Even though one could imagine writing an unconventional (and potentially very confusing) chemical formula (i.e., a kind of “code” in popular parlance) using atomic numbers as stand-ins for atomic symbols, the atomic numbers are not codes assigned as abstractions.


(John Mercer) #5

From the post:

“Is DNA a Code?” makes zero sense. Right away, you know semantic precision has been thrown out the window!

" 1. Code is defined as the rules of communication between an encoder (a “writer” or “speaker”) and a decoder (a “reader” or “listener”) using agreed upon symbols."

Nothing in molecular biology meets that definition. If you truly find this convincing, where exactly is there any symbolism outside of our human descriptions? Where’s the symbolism in base pairing and charging of tRNAs? Who agreed on them?

How can anyone find that to be plausible, much less strong, without a massive dollop of wishful thinking?


(Retired Professor & Minister.) #6

I say this not as a linguist but as just another person possessing reasonable common sense about words and their multiple definitions: Never assume that the most common definition of a word in routine English language usage by the general population of native speakers is the same definition that scientists use for the same word.

In fact, I think I made that point to Perry Marshall some years ago. (Of course, I made that same point to many others—all within the context of many other scientific topics, such as with the word “theory.”)


(John Mercer) #7

True, and maybe more are confused because we use it in a literal way in our 3-letter and 1-letter codes for amino acids. There’s no such symbolism nor abstraction in the cell, though.


#8

“The most common computer code is a language called ASCII. ASCII is a simple scheme your keyboard uses to talk to your PC, in which different combinations of seven bits (0’s or 1’s) are mapped to the English alphabet.
There are 128 ASCII characters—lowercase and capital letters, numbers, and punctuation marks. “A” is “1000001,” “B” is “1000010,” and “Z” is “1011010.” You can look up the whole table at www.asciitable.com or on Wikipedia.
ASCII is a code because when you press the letter “A” on your keyboard, your keyboard encodes it as “1000001,” sends it down the cable and into your computer, and your computer then decodes the “1000001” to display the letter “A” on your screen.
In the same way, DNA is a code (304, 318) because the codons on DNA strands are encoded into messenger RNA (ribonucleic acid) and decoded into amino acids and proteins (326). For example, the base pairs GGG (guanine- guanine-guanine) are instructions that the ribosomes use to make the amino acid glycine.
This process follows the rules of the genetic code. GGG encodes glycine, CGG encodes arginine, AGC encodes serine, and so forth."

Excerpt From: Marshall, Perry. “Evolution 2.0.” BenBella Books, Inc. iBooks.
This material may be protected by copyright.

Check out this book on the iBooks Store: Evolution 2.0 by Perry Marshall on Apple Books

That’s part of it.


(Timothy Horton) #9

Yep. “Code” also can mean any process in which the outputs are mapped to the inputs. That is the only definition of “code” applicable to DNA. Equivocation over the definition of “code” has been a mainstay argument for ID-Creationists for decades.


#10

"“As I’ve stated elsewhere in the book, another reason why DNA is literally and not figuratively a code is that DNA has features only found in sophisticated codes: codes within codes (675), redundancy (326), checksums (316), and error correction (307). Hubert Yockey’s book Information Theory, Evolution, and the Origin of Life (326) is a definitive text on this subject. (For a rigorous definition of codes, see appendix 4.) Again, everything in genetics, bioinformatics, and this book is based on this crucial fact.
When a cell reads instructions from DNA, an enzyme called a polymerase encodes data from the DNA into messenger RNA. Then the ribosomes decode it into proteins. The chaperones (special proteins that assist folding) organize these proteins into 3-D physical structures.
This decoding process is very similar to what happens when your friend prints out the Word document you just sent her. Your document is encoded into the USB cable connecting her computer to her printer, which decodes the 1’s and 0’s and prints the result on a physical piece of paper.”

Excerpt From: Marshall, Perry. “Evolution 2.0.” BenBella Books, Inc. iBooks.
This material may be protected by copyright.

Check out this book on the iBooks Store: Evolution 2.0 by Perry Marshall on Apple Books


#11

Can you explain what is so wrong-headed about that?


(Retired Professor & Minister.) #12

Definitely. And when such “letter codes” are obvious and highly mnemonic, it is very easy to ignore whether or not abstractions are involved.

Words as labels are also abstractions. After all, the amino acid lysine doesn’t somehow sound like the name assigned to it as its label in English and many other languages. And lysine doesn’t make a sound that is similar to the word when doing what lysine does—so the label lysine is not onomatopoeia. Somebody made the decision years ago to assign the name lysine to that amino due to various perceived mnemonic advantages. ( I assume it refers to its role in cataLYSis.) Yet, many other labels/names could have been equally reasonable. None of those names in any way effects how it functions in organisms.


(John Mercer) #13

ASCII is a code because we agree on the symbolism. There’s no symbolism in biology, and no one to agree on it.

You’re not bothering to reply my post, and you are reiterating the “DNA is a code” gibberish.

If you can’t even start by being be accurate enough to say that the codons in DNA might represent a code, I don’t see how sufficient semantic precision will be possible.


(Timothy Horton) #14

Sorry but that is just wrong. ASCII uses symbols as abstract representations of the information to be passed. There is no abstraction in DNA --> protein process, none at all. It’s just a complex chemical reaction following the laws of chemistry and physics. If you don’t believe it, try creating a gene from Lego or Tinkertoys, see if if produces a Lego or Tinkertoy amino acid.


(Retired Professor & Minister.) #15

My first reaction is that wording like “codes within codes” and “redundancy” and “checksums” and “error corrections” are themselves either analogies or simply descriptive within their routine English definitions.

For example, there are no actual “literal” checksums within organisms! There may be processes which function comparably to checksums—but I would challenge anyone to tell me where the numbers serving as checksums appear in a typical genome, for example. (Now I would be the first to agree that anything which functions comparably to a checksum inside of an organism is an amazing and fascinating phenomenon—but that doesn’t mean that I accept that actual checksums are stored in DNA as unambiguous numeric quantifications.)


#16

Very good. Thanks everyone.

What do you make of this?

“Note that GGG is not literally glycine, because the GGG nucleotides never end up in the glycine (221). Instead, the nucleotides merge back into the original DNA strand after it is read. GGG are the symbolic instructions to make glycine. The cell’s machinery reads these instructions and obeys”

Excerpt From: Marshall, Perry. “Evolution 2.0.” BenBella Books, Inc. iBooks.
This material may be protected by copyright.

Check out this book on the iBooks Store: Evolution 2.0 by Perry Marshall on Apple Books

Would you guys say that a genetic code is even possible? What WOULD constitute a genetic code for you guys? Again, I think all this could have come about through a natural self-organizing process. That’s fine.


#17

I find it interesting that I probably have a more liberal view of scripture than most Christians on here but am more “conservative” and minority-ish on biology than most people on here.


(Retired Professor & Minister.) #18

A thought comes to mind when I read Marshall’s description. Is a Periodic Table containing valence information a set of “codes” which tells inorganic matter how to form molecules? Are valences all part of a “coded language” (i.e., a set of instructions) which is embedded within matter such that combining various chemicals produces predictable “coded results” to form the resulting products?


(Timothy Horton) #19

It’s nonsense written by someone who doesn’t understand biochemistry. A GGG codon is not symbolic of anything except in human produced nomenclature.


#20

@Timothy_Horton

What WOULD constitute a genetic code for you? What would it look like? Is it possible?