DNAunion: First, this post is too long to fit into a single e-mail, so it
will be broken up into 2 posts.
Second, Before getting into my position as it relates to David's statements
to Richard (which both clearly referenced statements made by me), I would
like to state how I see our positions. I feel that there are 2 major
"issues" between David and me.
First, he does not like my word choice, i.e., my use of the word "overcome".
To me, this seems like a minor detail (for example, I don't think David
disagrees with me that amino acids thrown into a empty beaker would not
spontaneously form polypeptides, and that for them to become assembled into
polypeptides, something else would have to influence them. He just appears
to disagree with my saying that the something else is overcoming the original
tendency).
Second, we appear to look at the same thing from different perspectives. For
example, I consider it valid to look at individual components/processes and
determine whether or not they themselves are spontaneous, while David
apparently feels that doing this is wrong, and that the aggregate as a whole
must be considered. I consider this too to be a minor point because when I
look at the composite picture, as David does, he and I seem to be seeing the
same thing.
David, feel free to respond to my statements above (and of course those
below) if you see things differently.
[…]
>>>David Bowman: This is quite true. But we certainly don't have to
consider anything as esoteric as the solar interior for such a
counterexample. Such examples occur at the *simplest* level of all
thermodynamic processes. One of the most trivial thermodynamic processes
imaginable is the flow of heat from a region at higher temperature to a
region at a lower temperature. In such a process the higher temperature
region has its entropy *decrease* with time as the entropy of the lower
temperature region increases by an amount which is greater than the decrease
that occurs in the high temperature region. There is *no* need for any
"code-driven energy-conversion system" for such an entropy decrease to take
place in the region of high temperature. This process does *not* "overcome"
the 2nd law. In fact, it is one of the simplest imaginable manifestations of
that law operating as normally and simply as possible.
*********************
DNAunion: Okay, but bioenergetics is not about the *simplest* of
thermodynamic processes, like cups of hot tea cooling. I didn't state that
such simple processes required a coupling mechanism. I would, however, like
to see someone here - anyone, not you specifically - give a full explanation
of the operations of a CELL, or the origin of the first CELL, without
involving multiple coupling mechanisms.
*********************
>>>David Bowman: The simple fact is that the 2nd law does not require, nor
even address the issue of, the
existence of such an "energy conversion system".
******************
DNAunion: Not meaning to be blunt, but *bioenergetics* does require, and
does address the issue of, the existence of coupling mechanisms. And since
this board does concentrate on biology (and not on "hot cups of tea cooling")
then coupling mechanisms are perfectly within the topic of discussion (even
though they are not part of thermodynamics itself).
******************
>>>David Bowman: To append such arequirement to the second law *is*
inventing one's own idiosyncratic (and incorrect) formulation of
thermodynamics.
*****************
DNAunion: Your statement is unclear to me. If you meant that I am appending
requirements for coupling mechanisms to thermodynamics itself, then you have
misunderstood my statements. If on the other hand you are saying that
coupling mechanisms cannot be discussed in relation to thermodynamics, I (and
apparently many Ph.Ds in biology), would have to respectfully disagree.
*****************
>>>David Bowman: Also, it is a simple demonstrable fact that many instances
of local entropy decrease are *not* accomplished via such an "energy
conversion system"; many other instances of local entropy decrease *are*
accomplished with such a system that itself spontaneously forms in situ; and
some instances *do* require a previously constructed such system. Sometimes
such a "energy conversion system" is used for the production of a local
*increase* in entropy. Whether or not such a system is needed for a given
process or not is a function of the particular process at hand. It is *not* a
concern of the 2nd law.
*******************
DNAunion: Yes, but it is a concern when the second law is applied to biology.
*******************
>>>David Bowman: Whether or not a given system will spontaneously form
varying degrees of complexity with or without an externally previously built
special apparatus is simply *not relevant* to the 2nd law.
*******************
DNAunion: Okay, but it is relevant when the second law is applied to biology.
*******************
>>>David Bowman: No matter what apparatus is or is not needed to enable a
given process, the 2nd law is obeyed as usual, and isn't violated nor
"overcome".
***************
DNAunion: I already addressed the near conflation of the words "overcome"
and "violate" by David and others as related to my statements. The quick
summarization (details in other posts) is that nowhere, at no time, do my
statements hold that the second law is violated, defied, broken, or done away
with.
***************
>>>David Bowman: The formation of complexity is *not* necessarily
thermodynamically "uphill". Sometimes it is "downhill" (such as in the
spontaneous formation of Prigogine's "dissipative structures" in
far-from-equilibrium systems whose disequilibrium is maintained via
externally imposed gradients across the system of one or more intensive
thermodynamic potentials).
***************
DNAunion: Okay, but note all the requirements needed for that complexity to
arise "spontaneously": "such as in the spontaneous formation of Prigonine's
"dissipative structures" in *far-from-equilibrium* systems whose
*disequilibrium is maintained* via *externally imposed gradients* across the
system of *one or more intensive thermodynamic potentials*."
That seems to me to be similar to saying that a many-ton object can
"spontaneously" rise from the ground if it has wings, of appropriate size, a
streamlined body, powerful engines, suitable fuel, a trained pilot, wheels,
and is moving forward fast enough. In that sense, everything that ever
occurred, occurs today, or ever will occur is "spontaneous": the term loses
its *common* meaning. I doubt many people would consider it correct to say
that a many-ton object could *spontaneously* rise from the Earth. They would
admit that that object could rise, provided a long list of prerequisite
conditions were met, but then the object or its surroundings would be
contrived and/or manipulated (unnatural in a sense) and it wouldn't seem to
be very "spontaneous". In addition, those contrivances should be included
in the statement of spontaneity or else the statement would be incorrect (I
am not saying you did not do this: you did include the special conditions in
your statements).
Of course the term has a different meaning in bioenergetics/physics.
Something that is thermodynamically spontaneous in bioenergetics is something
that CAN occur (something that is not thermodynamically spontaneous can NOT
occur). This is the sense you were using. I am *not* trying to charge you
with equivocation - you used the term in only one way and that way was
correct. I am pointing out to others that the term spontaneous as used
(correctly) by you above can include contrived and manipulated conditions
(something most people do not consider valid in claims of things occurring
spontaneously) as long as they are mentioned (to be correct in saying that
something occurs spontaneously, one would need to include all contrivances
and manipulations in the statement - as you did).
*****************
>>>David Bowman: All naturally occuring processes are, by the very operation
of the 2nd law, thermodynamically "downhill". But to see that it really is
"downhill" one has to consider all the relevant interactions associated with
the process, because *any* such process will involve some entropy-increasing
aspects and other entropy-decreasing aspects. The net generation of
thermodynamic entropy in a physical process (being related to the relevant
microscopic degrees of freedom in the process) is quite unrelated to whether
or not various patterns of complexity or order do or do not form at the
macroscopic level. I do not know how to make this any more plain.
****************
DNAunion: But let me ask this. The Ph.Ds who authored my two cell biology
college texts, and origin of life researchers such as Noam Lahav, say that
amino acids bonding to form polypeptides is an "uphill" process and will not
occur spontaneously: and they are correct. Yet polypeptides are in fact made
by the linking together of amino acids.
If I have not misunderstood you, it appears to me that you are implying that
they are wrong (since you apparently do not like their looking at just amino
acid polymerization and stating that it is not spontaneous - yet it occurs).
But to say that amino acids will form polypeptides "spontaneously", one
would need to include, "… because there is DNA to code the rRNA that composes
the small subunit and the large subunit of a ribosome, and these join
together to form a complex, along with mRNA (which was also transcribed from
DNA - with transcription itself requiring specific large protein complexes),
and the mRNA and LSU and SSU and any needed initiation factors come together
to form a ribosome ready to accept a tRNA, and aminoacyl-tRNA-synthetases
have attached amino acids to tRNA molecules with that aid of hydrolysis of
ATP, and elongation factors (EF-Tu) binds GTP and bonds to the incoming tRNA,
and there are an aminoacyl site, and peptidyl site, and an exit site on the
ribosome, and the charged tRNA has a complementary anticodon - which must be
in a single, specific 3-nucleotide position in the tRNA - and the rRNA forms
peptidyl transferase- the catalytic site where the amino acids are bonded -
and that after two amino acids are bonded, the growing polypeptide is
transferred to the tRNA in the A site, then the tRNA in the E site exits
through a tunnel, and the tRNA in the P site moves to the E site, and the
tRNA in the A site moves exactly 3 spaces to the P site, and the mRNA
advances exactly 3 nucleotides, and then the all the steps involved in
elongation are repeated over and over, until one of the stop codons is read,
after which the polypeptide is freed, and the LSU, SSU, and mRNA
disassociate".
So even though the overall process is spontaneous - because ANYTHING that
does occur MUST be spontaneous - look at all the contrivances, manipulations,
and accessory structures involved in bonding amino acids together to form
polypeptides (and believe me, mine was a short description). It IS accurate
to say that amino acids will not spontaneously form polypeptides, and it IS
inaccurate to simply say that they will. To leave off the details is to turn
a true statement into a false one (again, you did not do so: I am taking this
opportunity, since the discussion is going along lines similar to this, to
inform the other readers what to look for in statements about spontaneous
processes).
When people hear a phrase like "amino acids spontaneously form polypeptides"
they imagine that a scientist "picks up a handful of amino acids, throws them
into an empty beaker, and presto! - you've got polypeptides". This does not
occur. Yes, the overall synthesis of polypeptides from amino acids is a
spontaneous process, but amino acids forming polypeptides is not.
I believe one reason you and I keep talking past each other (on various
topics) is that I am looking at a specific individual step and you are
looking at the overall process, composed of multiple parts and/or processes.
****************
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