DNAunion

DNAunion: Uhm, you are talking about thermodynamics as it applies to organisms. That too is what I have been talking about – the application of thermodynamics to biology. We are both talking about bioenergetics.

If you want to talk about thermodynamics without relating it to life, then be my guest. But in these exchanges, you have been discussing bioenergetic concepts.

Oh, and Boltzman’s statistical mechanics’ view of entropy is part of bioenergetics. So I am not getting confused and “mixing them up”.

Okay, here’s a slew of quotes from various types of college-level texts (microbiology, molecular cell biology, organic chemistry, general chemistry, etc.) that support my position that “Thermodynamics only says what can and can't happen; it doesn't say something that CAN happen WILL actually happen: it might not, or it might occur so slowly as to be imperceptible”.

DNAunion: Is that enough for you?

[ August 15, 2002: Message edited by: DNAunion ]</p>

DNAunion

DNAunion: Uhm, why did you switch your statement? Originally you said the proteins melt in the stomach into amino acids. That was one of the things I was objecting to, and the reason I brought enzymes into the picture. Ingested proteins in the stomach do not melt into amino acids – they are enzymatically hydrolyzed (by pepsin) into shorter peptides.

And even now that you have improved by saying the ingested proteins would be acted upon by “digesting acids”, you still don’t have it right. The stomach – where the environment is highly acidic – is not where the majority of protein digestion occurs. As I said before, the majority of protein digestion occurs in the small intestine, where the pH is near neutral (i.e., not strongly acidic as is the stomach). And it is ENZYMES (such as carboxypeptidase, trypsinogen, etc.) in the small intestine that digest the ingested peptides/proteins into free amino acids.

DNAunion: Uhm, where did I say k log(I/D) was invalid? Nowhere.

In reply to your statement, “Thus the proteins in a beef … ordinary melting through logD, into free amino acids in the stomach…”, I said, “Proteins do not melt in the stomach through log D. …” followed by explaining that enzymes are involved (i.e., it is not a case of melting) and that the proteins are not digested into free amino acids in the stomach. Nothing I stated means that “log D” or “k log(I/D)” is invalid.

DNAunion: Uhm, we aren’t using “daily language” here. How many days do you walk down the street and somebody comes up to you in normal conversation and starts talking about entropy, Boltzman’s constant, the second law of thermodynamics, etc. We – including you - are being rather technical here.

And it is simply wrong to call the small intestine the stomach: they are two separate organs with different shapes, different sizes, different functions, different pH’s, different enzymes, etc.

DNAunion: Could you try again? The first part makes little sense and it is a bit difficult to answer a question that is only half intelligible.

DNAunion: I didn’t object to log(I/D) occurring during protein synthesis; I objected to your statement, “…and the amino acids syntheses back again through log(I/D) into proteins, for instance haemoglobins in our blood”.

It is neither the amino acids themselves nor log(I/D) that synthesizes amino acids into proteins. It is the information stored in DNA (that encodes the three types of RNA used during protein synthesis), and the mRNA for that particular protein, and the rRNAs and proteins that come together to form a ribosome, and the multiple tRNAs that get charged by tRNA-specific enzymes, and the genetic code, and the energy liberated by other processes that are coupled to the steps of interest, … Those are the things responsible for protein synthesis.

An increase in order does not drive the process of protein synthesis at all. In fact, the decrease in entropy associated with polymerization hinders the process, which is why it requires an input of sufficient information (DNA) and sufficient energy (by coupling the energy-requiring processes to energy-liberating processes).

[ August 15, 2002: Message edited by: DNAunion ]</p>

DNAunion

DNAunion: Sure it does, because you said, and I quote:

DNAunion: As I correctly pointed out, reaching thermal equilibrium with the environment does not equate to death. If you claim it does, then you believe in resurrection because organisms can be frozen solid in nature for months and then “become alive again” when thawed.

What you actually said was wrong; I was right when I pointed that out.

By the way, contrary to what a lot of your statements imply, organisms are not mere “combustion machines”, or mere heat engines, or merely beakers with chemicals in them. Sure organisms follow the laws of thermodynamics, but the organismal complexity and organization that controls the multitude of thermodynamic processes in living entities is something many (arm-chair) physicists just can’t seem to come to grips with.

I guess next you’ll try to tell me that aerobic respiration is merely

C6H12O6 + 6O2 -&gt; + 6CO2 + 6H2O + E(out)

Peter Soderqvist

TO DNA UNION

Hi!
Your reply is big! So I suggest that we take one message at a time!

Soderqvist1: An algorithm is an stochastic computational procedure, for instance, to throw a dice! The process need an answer let's say 5 in order to count as an algorithm! An "endless process" without any answer, is thus not an algorithm! As you probable understand, the algorithm is a very broad description, and includes many subjects!

The earth is 4.6 billion years old, and the first replicator is approximately 3.5 – 4.0 billion years old. So the stochastic algorithmic process toke at least 0.6 billon year to generate the first replicator, and for the same reason, "your pre-biotic experiment" is not possible, because we will be gone, before the experimental result is generated!

Natural selection is an equally broad description, it is simply an waste and regard mechanism, for instance, water is naturally selected to go through a strainer, but heavier things like stones are not! Or your "river metaphor" The river in Eden is naturally selected by the environmental structure (riverbanks) to flow in some direction, in this case; out of Eden, but swimming birds on the river, are normally naturally selected to overcome, or cross the riverbanks!

Soderqvist1: A strainer is a physical object, with some internal chemical structure, hence physicochemical! And the strainer is the stones, and water's selecting environment!

Soderqvist1: algorithms and natural selection was at work in the primordial soup. Different chemicals, started to jostle together with energy from the sun, and these chemical reactions became more compounded, and complex through time. Richard Dawkins has even used Cairns-Smith's theory of inorganic "low-tech replicator 's of crystal silicates, as an precursor to DNA-replicators. However the details are not in dispute here, so I will leave it for the moment. Richard Dawkins has a cumulative natural selection explanation about it, thus contrary to what you have alleged!

1986 The Blind Watchmaker online Chapter 3 - Accumulating small change
We have seen that living things are too improbable and too beautifully 'designed' to have come into existence by chance. How, then, did they come into existence? The answer, Darwin's answer, is by gradual, step- by-step transformations from simple beginnings, from primordial entities sufficiently simple to have come into existence by chance. Each successive change in the gradual evolutionary process was simple enough, relative to its predecessor, to have arisen by chance. But the whole sequence of cumulative steps constitutes anything but a chance process, when you consider the complexity of the final end-product relative to the original starting point. The cumulative process is directed by nonrandom survival. The purpose of this chapter is to demonstrate the power of this cumulative selection as a fundamentally nonrandom process.

Chapter 5 - The power and the archives
It is raining DNA outside. On the bank of the Oxford canal at the bottom of my garden is a large willow tree, and it is pumping downy seeds into the air. ... The whole performance, cotton wool, catkins, tree and all, is in aid of one thing and one thing only, the spreading of DNA around the countryside. Not just any DNA, but DNA whose coded characters spell out specific instructions for building willow trees that will shed a new generation of downy seeds. Those fluffy specks are, literally, spreading instructions for making themselves. They are there because their ancestors succeeded in doing the same. It is raining instructions out there; it's raining programs; it's raining tree-growing, fluff-spreading, algorithms. That is not a metaphor, it is the plain truth. It couldn't be any plainer if it were raining floppy discs

Cairns-Smith believes that the original life on this planet was based on self-replicating inorganic crystals such as silicates. If this is true, organic replicators, and eventually DNA, must later have taken over or usurped the role.
<a href="http://www.world-of-dawkins.com/Dawkins/Work/Books/blind.htm" target="_blank">http://www.world-of-dawkins.com/Dawkins/Work/Books/blind.htm</a>

You should review Dawkins answer to Alabama's state board of education!
<a href="http://www.world-of-dawkins.com/Dawkins/Work/Articles/alabama/1996-04-01alabama.htm" target="_blank">http://www.world-of-dawkins.com/Dawkins/Work/Articles/alabama/1996-04-01alabama.htm</a>

Soderqvist1: I am close to never in front of my computer at weekends, but I will be back at Monday and review about what you have to say about this message. I have tried to be as simple as possible, though correct, and I hope you will rend me same service! Werner Heisenberg has said something very interesting in the issue!

The physicist may be satisfied when he has the mathematical scheme and knows how to use for the interpretation of the experiments. But he has to speak about his results also to non-physicists who will not be satisfied unless some explanation is given in plain language. Even for the physicist the description in plain language will be the criterion of the degree of understanding that has been reached.
Physics and Philosophy
<a href="http://www-groups.dcs.st-and.ac.uk/~history/Quotations/Heisenberg.html" target="_blank">http://www-groups.dcs.st-and.ac.uk/~history/Quotations/Heisenberg.html</a>

Best regards

[ August 16, 2002: Message edited by: Peter Soderqvist ]</p>

Peter Soderqvist

DNA Union, where are you?

DNAunion

DNAunion: I am going to stop replying to you for several reasons. First, because of your “broken English”, it is often times difficult for me to understand exactly what your point or counterpoint is. Second, you don’t fully understand the biology being discussed, making it even more difficult for me to communicate with you. Third, you are frequently being pejorative/condescending. And fourth, school started back today so I will not have as much free time to “play on the internet”.

However, I will reply to the one post you had made last time I checked in.

DNAunion: And therefore you confirm my position. You see, you asserted your conclusion as fact. Look again.

DNAunion: There’s no, “Many believe that…”. There’s no, “I think that…”. There’s no, “some theories suggest that…”. There’s no, “Although different camps disagree, one school of thought holds that…” Nope, you stated it as straight out fact.

Not only can you not show that it is fact, you have now admitted that you can’t even show that it is actually possible. Yet you must show that it actually could have occurred that way before you can even think about stating that it actually did occur that way.

[ August 19, 2002: Message edited by: DNAunion ]</p>

DNAunion

DNAunion: No, that is wrong. Even Dawkins – in the very book you quote – demonstrates that your usage is wrong.

Note what Dawkins says natural selection is all about.

DNAunion: Note that Dawkins statements indicate that NS requires competition between multiple (self-)replicating entities (the organisms that contain the DNA). Just as I said.

And here is something else that Dawkins says about natural selection, when discussing the very topic you bring up later. That is, Dawkins is talking about “self-replicating” crystals here.

DNAunion: Dawkins is discussing the effects of variations among “populations” of “self-replicators”, and yet he still qualifies his statement by saying “a simple kind of natural selection”.

Now what you described – simple sieving of stones with a strainer – is NOT even a “simple kind of natural selection”. There are no self-replicators in your sifting of stones, nor is there any differential growth in your sifting of stones.

In fact, go back and reread pages 43-44. Here is something nearly identical to your example, and Dawkins does not label it as NS, but as simple sieving.


DNAunion: But Dawkins says that cumulative NATURAL SELECTION IS enough to account for those things. Simple sieving is not NS.

DNAunion: The strainer attempt fails, as I showed above.

Besides, you still have it “backwards” anyway (which was the main point I was making at that time).

Even IF we go out of our way and accept the simple sifting of stones from water using a strainer as being natural selection – WHICH WE SHOULD NOT – even then, natural selection is not a physicochemical environment. The physicochemical environment would be the strainer: that which produced (what you wrongly claim is) natural selection. NS is a process, not a physicochemical environment. Your confused statement is kind of like saying, “Emission of light is a filament”.

Third, as with several other terms, you are misusing the term physicochemical. Only the physical properties of the strainer matter in your straining-rocks-from-water example. It is the physical size of the hole that determines what makes it through and what doesn’t: it is the physical “environment” that does the sifting. The chemical part is irrelevant to the sorting in your example. You are just trying to dress up your arguments in impressive-sounding words that you apparently don’t fully understand (yet later you claim to be keeping things simple!?).

DNAunion

DNAunion: Okay, but that has nothing to do with selfish genes. Hopefully you finally get on track with the rest of your response.

DNAunion: So? Even if we accept that Dawkins’ term “selfish genes” applies to (self-)replicating clays, we would still have (self-)replicators before we would have selfish “genes” (now the word genes has to be enclosed in quotes to indicate its nonstandard usage). So you still haven’t successfully defended your position (no surprise, because you can’t)

DNAunion: The details of WHAT are not in dispute? That self-replicating clays were the first life forms, and gave rise to the first organic life forms? If so, then I guess you are pretty much right; that idea isn’t much in dispute anymore because it has been largely cast aside in favor of more plausible or simpler (Ockham’s razor!) models for the origin of life.

DNAunion: Dawkins does not have a cumulative natural selection explanation for the origin of life. Go back and reread the beginning of chapter 6 – Origins and Miracles. There you will see Dawkins pondering how much luck one can incorporate into the formation of the first self-replicator/origin of life.

Here are a few quotes for you to examine.

DNAunion: That one quote resolves nearly every point of contention between us, in favor of me.

There are also statements on pages 140 and 141 that confirm the above quote (but my carpal is starting to act up – you’ll need to look them up yourself).

Oh wait – look what I just happened upon. Note what Dawkins says here (not from the same book, but there is no requirement that everything we say sticks to The Blind Watchmaker).

DNAunion: Uhm…. Game, set, and match…again!

Although it has all been settled now, here is something else from the end of the chapter in The Blind Watchmaker.

DNAunion: Dawkins offers cumulative natural selection as an explanation for the vast diversity of life – GIVEN THE FIRST LIFE FORM EVER. Cumulative natural selection does not explain the origin of the first (self-)replicator, just what came afterwards.

DNAunion

DNAunion: Now let my dissect the long quote from The Blind Watchmaker that you provided.

DNAunion: When Dawkins says that living things are too improbable to come into existence by chance, he is talking about bat sonar (chapter 2), eyes (pages 16-17), earwigs (page 6), dogs (page 7), humans (page 7), moles (page 9), monkeys (page 9), swallows (page 8 & 9), whales (page 8 & 9), earthworms (page 9), elephants (page 14), etc. Dawkins is talking highly complex EVOLVED things.

Nowhere in the above passage does Dawkins say that cumulative selection accounts of the origin of life. In fact, he says those things evolved “…from primordial entities sufficiently simple to have come into existence by chance.”

DNAunion: “Nonrandom survival” implies life. Again, Dawkins is saying that the very complex things found in living entities – things like eyes and bat sonar -evolved by cumulative selection. Cumulative selection does not explain the origin of the starting point.

DNAunion: And...?

DNAunion

DNAunion: Cairns-Smith’s belief is irrelevant; it reduces to the standard origin of life theories based on mineral catalysts.

The “information” that would be contained in the imperfections of a crystal that allowed it to spread through “cumulative selection” (because it was a better dam builder, or whatever) would be totally incompatible with the information needed for RNA to self-replicate (It would kind of be like taking the English instructions for building a car and throwing them into a non-English-speaking Japanese assembly plant and expecting them to produce a car from only those instructions – it wouldn’t work). Meaningful “self-replicating” information transfer would not occur between the “Self-replicating” clays and the RNA.

What we are left with is the same thing that the mainstream origin of life theories based on on "clays". Inorganic minerals/clays – such as montmorillonite – would have adsorbed monomers from the aqueous phase, thereby concentrating them, and would have oriented them properly to accelerate their combining, and would have helped shield the formed molecules from degradation, etc.

Neither version based on clays explains where the specific information required for RNA to self-replicate comes from. It can explain where “information” comes from: imperfections in the mineral surfaces – but it is vastly improbable that that type of random and meaningless “information” is sufficient to produce a self-replicating RNA.

All theories of the origin of life that I am aware of still rely upon CHANCE to produce a proper sequences of monomers in order to get the first self-replicator (just as Dawkins has said).

*NOTE: The term “self-replicator”, as used in origin of life discussions, usually implies that it is organic, and that it can evolve via (proto-)natural selection.

DNAunion: Doesn’t really matter – the discussion is over.

DNAunion: Unfortunately, you failed. You have not been correct about many things; and you have “simplified” definitions down to the point where they no longer mean what they mean (examples: sifting stones out of water with a strainer is NS; NS is a physicochemical environment; life is just a "combustion engine", etc.)