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GÖDEL, ESCHER, BACH (1988)
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"As development of an organism takes place, can it be said that
the information is being "pulled out" of its DNA? Is that
where all of the information about the organism's structure
reside;
DNA and the Necessity of Chemical Context
In one sense, the answer seems to be yes, thanks to experiments li
Avery's [1]. But in another sense, the answer seems to be no, because so
much of the pulling-out process depends on extraordinarily complicated
cellular chemical processes, which are not coded for in the
DNA itself. The DNA relies on the fact that they will
happen, but does not seem to contain a code which brings them about. Thus
we have two conflicting views on the nature of the information in a
genotype. One view says that so much of the information is
outside the DNA that it is not reasonable to look upon the
DNA as anything more than a very intricate set of triggers, like a
sequence of buttons to be pushed on a jukebox; another view says that
the information is all there, but in a very implicit form.
Now it might seem that these are just two ways of saying the same thing,
but that is not necessarily so. One view says that the DNA is quite
meaningless out of context; the other says that even if it were taken out
context, a molecule of DNA from a living being has such a
compelling inner logic to its structure that its message could be
deduced anyway. To put it as succinctly as possible, one view says that in
order for DNA to have meaning, chemical context is
necessary; the other view says that only intelligence is necessary
to reveal the "intrinsic meaning" of a strand of DNA."
Quote from chapter 6 'The Location of Meaning'.
My copy of Douglas Hofstadter's famous book 'Gödel, Escher, Bach' (Dutch translation, 1985) stood gathering
dust on my bookshelf for some 30 years. A few days ago when I was
searching for artwork of M. C. Escher in Hofstadter's book, I unexpectedly
came across arguments against the 'DNA-centric view' of life. I have
blogged about DNA-centrism many times over the past several months. It is
extraordinary to find the same ideas you have been developing in a book
that was written 47 years ago. As far as I can see, Hofstadter was not
participating in an ongoing discussion among biologists about
DNA-centrism. He wrote his ideas as part of an investigation of formal
languages. DNA was an example of such a language. Probably the two
mutually exclusive points of view –'DNA-centric' and 'cell-centric'– did not exist at the time. Likely, mainstream biology was DNA-centric. For example, Hofstadter
writes: "Gunther Stent has characterized the nucleus as the 'throne room' of the
cell, with DNA acting as the ruler." (page 509). Hofstadter wrote this in passing and without further
comment! Stunning remark! If this isn't DNA-centrism, then I don't know what is!
Hofstadter accepts it as if it were merely a neutral description of what
DNA is. Probably it reflects mainstream scientific thinking at the time.
Hofstadter is a computer scientist and investigated coded messages, and the concept of information and meaning. It appears he had a detailed knowledge of what
DNA is and how it functions. In chapter 16 Hofstadter gives detailed
description of the structure of DNA, the Genetic code [2], transcription, translation, proteins, Transfer RNA and
Ribosomes. Furthermore, he understood that knowing the Genetic Code, that is how a
particular DNA sequence is translated in to a protein, is far from
sufficient to understand how a genotype is translated in to a phenotype
[1]. This truth still holds today!
An important question for Hofstadter was:
Where is the meaning of a coded message located?
Applied to DNA, attempts to answer this question yield important insights. Interestingly, he proposed two possible answers: the intrinsic and
extrinsic view of meaning. The intrinsic view means that DNA has 'a
compelling inner logic' that enables an intelligent (extraterrestrial)
investigator to decode the DNA message. This sounds rather vague.
Hofstadter doesn't explain what 'inner logic' means [4], [5]. The
extrinsic view is that the meaning of DNA is not stored in DNA itself, but
that "extraordinarily complicated cellular chemical processes" are
required.
Although he never rejects the intrinsic meaning hypothesis explicitly, I
conclude from his statement "extraordinarily complicated cellular chemical processes, which are not
coded for in the DNA itself", that he favours the extrinsic view. This is further confirmed by the
heading "DNA and the Necessity of Chemical Context" and this (charming!)
statement:
"they [an extraterrestrial civilization]
might to try to deduce from its chemical structure what kind
of chemical environment it seemed to want, and then supply such an
environment." (under the section heading How Universal Is DNA's Message?).
(page 183).
Another wonderful statement:
"On the other hand, DNA is itself a passive molecule which
undergoes manipulation at the hands of various kinds of enzymes; in this
sense, a DNA molecule is exactly like a long piece of data, as
well." (page 542) (my emphasis). I love this. This is exactly what I argued on
several previous blogs. And: "But most of the 'living' in a cell goes on outside of the nucleus,
namely in the cytoplasm..." (page 512). Well said! I fully agree. In other words: DNA is dead,
the cell is alive! However, Hofstadter does not note there is a certain
degree of contradiction between DNA 'sitting on a throne' and being
dead.
Bootstrap problem
Continuing with the intrinsic and extrinsic point of view. There is a
problem with the distinction. The tRNAs contain the translation key of DNA
to protein. Since the information for producing tRNAs is stored in DNA
(necessarily, because it must be inherited), one could say that the meaning
of DNA is intrinsic to DNA. That's OK. However, in order for that
information in DNA to be used, it must first be read by cellular
machinery. Hofstadter is aware of the problem [3]: "...
there is no way for the DNA to hoist itself by its own bootstraps. Some
amount of knowledge of the Genetic Code must already be present
in the cell beforehand." (page 519) (my italics). Excellent remark! Remarkable insight! However,
it appears that the concepts intrinsic and extrinsic
meaning are ambiguous. In one sense, DNA has an intrinsic meaning because
DNA encodes for tRNAs, but on the other hand the meaning is
extrinsic because machinery outside DNA is necessary to get the
whole process started. In other words: a bootstrap problem [6]. The information is there, but one can not get it
out!
Think about this: 47 years ago a smart computer scientist clearly understood that a DNA 'message' is
meaningless without its cellular context! So, the cell-centric view is
certainly not a modern invention. It was kept alive in the fringes of
science. Hofstadter did not fully realize that his anti DNA-centric
views contradicted the prevailing view of DNA as 'the Ruler on the
throne'. Since Watson and Crick (1953) DNA-centrism has experienced stormy growth. Today, more and more scientists
reject the DNA-centric view of life.
Notes
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My note:
Avery
(1944) was the first to demonstrate that DNA and not protein was the
vehicle of heredity.
-
The Genetic Code table is on page 515. Furthermore: "The curious
fact is that the Genetic Code is stored-where
else?-in the DNA itself." (page 517).
-
quote: "(Warning: Understanding this "language" would not at all be the same
as cracking the Genetic Code, something which took place in the early
1960s. ... The cracking of the Genetic Code was a vital step on the
way
to extracting the meaning of DNA strands, but it was only the first on
a long path which is yet to be trodden.)" page 168.
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An argument against the intrinsic meaning of DNA is: the genetic code
is a rather arbitrary association of 61 base triplets with 20 Amino
Acids and 3 base triplets with STOP signals. Hofstadter did not mention
this in this book. But 3 years later, in his 1982
Scientific American "Metamagical Themas" column, titled "Is the genetic code an arbitrary one, or would another code work as
well?" Hofstadter argued that the genetic code is not fundamentally dictated
by chemical necessity, suggesting that many other codes could
theoretically work. (answer by Google AI!). The conclusion must be:
there is no compelling logic in DNA.
-
A further problem with 'intrinsic meaning': how to find the translation
keys in a code script with the length of billions of symbols? The code
for the tRNAs are scattered all around DNA and there are many
duplicate keys. In other words: how to locate the meaning of DNA?! That's the fundamental question.
Sources
The paperback edition is still available on Amazon. The PDF of the book
can be found on several websites, such as
this
one. I discovered the Dutch translation of the book at my bookshelves,
which so it appears was a birthday present.
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