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----- Original Message -----
From: "Denys Beauchemin" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Friday, April 29, 2005 11:01 AM
Subject: Re: [HP3000-L] Evolution, Question 1


> Finally, back home for a little bit with a few minutes to respond.
>
> I printed your response for reading on the plane.  I also visited the
> sites
> you mentioned.
>
> Now, your answer raises a few questions:
>
> You say that "... DNA-based life extends back at least as far 3.6 Ga, and
> may go to 3.8 Ga. This is the point in time at which the machinery of life
> that inhabits this planet was invented..."
>
> You did not explain how it was invented or by whom or what.
>
> Next you state: "... but then becoming obligate symbionts and eventually
> so
> well integrated into the working of the protoeukaryotic cells that they
> became organelles. This evolution took an additional 2 Ga, and we have no
> idea why it took so long.
>
> The next great step required another 2 GA, occurring only 570 Ma ago, and
> that was the evolution of task-partitioned, complex multicellularity. This
> evolution was the "Cambrian Explosion" of animals, plants and fungi, and
> again, we have no idea why it took so long..."
>
> I hear what you are saying about "... why it took so long..."  But I would
> like to ask, "why did it happen at all?  How did it happen?"
>
> Second set of questions coming right up.
>
> Denys
> -----Original Message-----
> From: [log in to unmask] [mailto:[log in to unmask]]
> Sent: Friday, April 08, 2005 10:44 PM
> To: [log in to unmask]; [log in to unmask]
> Subject: Re: Evolution, Question 1
>
> Denys asks:
>
> [Please note: In order for this response to make sense, you will have to
> take
> the time to look at each of the referenced pages or images. For some
> things,
>
> pictures are worth a thousand words.]
>
>> It is my understanding that Charles Darwin is, if not the originator, he
> is
>>  at least the scientist that first formulated this theory in his book
>> "The
>>  Origin of Species." The basis of the theory is that all current life
> forms
>>  on planet Earth have evolved from prior forms that in turn evolved from
>>  prior forms and so on until the very beginning of life in the primordial
>>  soup.  I believe the current theory is that evolutionary changes occur
> due
>>  to environment changes and the natural selection of the more adapted
> forms
>>  in the continuing struggle for existence.
>
> That's basically correct, but with a few caveats. The notion of all life
> being connected is at least as old as the Greeks, and the idea of
> biological
>
> evolution was very much in the air prior to Darwin. Darwin's great
> accomplishment
> was that he provided, for the first time, a plausible mechanism, natural
> selection, by which lineages could adapt in form and behavior over time.
>
> Aristotle, biologist/philosopher, spoke of the "scala naturae", or "the
> great
> chain of being", which you can see schematized in this figure:
>
>  http://web.clas.ufl.edu/users/rhatch/images/greatChain.gif
>
> Clearly, Aristotle had some of the basic order correct: minerals lead to
> life, which lead to plants, which leads to animals, which leads to man,
> and
> then
> inevitably to demons, angels and god, but Darwin's idea was much simpler
> and
>
> much more obvious. He specified an algorithm:
>
>     o given self-reproduction, all populations expand in Malthusian
> fashion
>
> to the limit of their boundaries.
>     o error in reproduction is inevitable, thus there will be variation.
>     o all competitive arenas are finite.
>     o when the limits of those arenas are met, the competitive exclusion
> of
>
> the least appropriate variants must occur due to an inevitable competition
> for
> resources, leaving the most appropriately matched individuals to
> differentially reproduce and become the basis set for the next generation.
>
> This simple statement of three premises and one inescapable conclusion
> came
> as a thunderclap to the 19th Century scientific community, only because it
> was
> so obvious, yet no one had so clearly outlined it before.
>
> Darwin also perfectly well understood the philosophical implications of
> his
> work, and it was his intent to have "Origin" published after his death, if
> for
> no other reason than to spare his wife, who was devoutly religious, the
> travails of a long public argument.
>
> But he also understood that the exquisite perfection we see in nature was
> purchased on the back of enormous destruction, and that may have bothered
> him as
> much anything. In the final paragraph of "Origin," he wrote to both
> concerns,
> the destruction implicit in the process and the physics of the algorithm
> that
> is represented by natural selection:
>
> =======================================
>
> "It is interesting to contemplate a tangled bank, clothed with many plants
> of
> many kinds, with birds singing on the bushes, with various insects
> flitting
> about, and with worms crawling through the damp earth, and to reflect that
> these elaborately constructed forms, so different from each other, and
> dependent
> upon each other in so complex a manner, have all been produced by laws
> acting
> around us. These laws, taken in the largest sense, being Growth with
> Reproduction; Inheritance which is almost implied by reproduction;
> Variability from the
> indirect and direct action of the conditions of life and from use and
> disuse:
> a Ratio of Increase so high as to lead to a Struggle for Life, and as a
> consequence to Natural Selection, entailing Divergence of Character and
> the
> Extinction of less-improved forms. Thus, from the war of nature, from
> famine
> and
> death, the most exalted object which we are capable of conceiving, namely,
> the
> production of the higher animals, directly follows. There is grandeur in
> this view
> of life, with its several powers, having been originally breathed by the
> Creator into a few forms or into one; and that, whilst this planet has
> gone
> cycling on according to the fixed law of gravity, from so simple a
> beginning
> endless
> forms most beautiful and most wonderful have been, and are being evolved."
>
> ========================================
>
> Reading this passage, it's easy to see why the robber baron capitalists of
> 19th Century America took such pleasure in his writings. It was only a
> small
>
> step from this passage to their justifications of the exploitations of the
> lesser
> fit. But Nazi Germany used much the same rationales to justify racial
> purity,
> as did Marx and Lenin to justify the proletariat's overthrow of their
> oppressors. George Bernard Shaw ultimately said that Darwin had the great
> fortune to
> be useful to anyone with an ax to grind.
>
> But Darwin intended none of this.
>
> The first major reinterpretation of this Darwinian biological physics was
> Boltzmannian thermodynamics. Boltzmann wrote that he dreamed of the
> becoming
> the
> "Darwin of Matter," and that the 19th Century should be named the "Century
> of
> Darwin." The second major reinterpretation was Shannon's information
> theory.
>
> The connection between the three ideas is not accidental. Each part of the
> link
> was purposefully intended by each of its participants.
>
>
>
>>  I believe the age of the planet is currently pegged at about 4.5 billion
>>  years old.  IIRC, for the first two billion years or so, Earth was
>> barren
>>  without either an atmosphere or with an atmosphere radically different
> than
>>  what we have now.  I think the current theory is for one large ocean
>> with
>
> an
>>  original super continent or archipelago, called Columbia, which broke
> apart
>>  about 2 bya.  The landmass was later reassembled into another
> supercontinent
>>  called Rodinia.  Then that one broke apart.  The landmass reformed into
>>  Pangea which then broke apart about 300 mya.
>>
>>  During this breakup and assembly cycle, life appeared somewhere on the
>>  planet, perhaps in the oceans and one of the by-product of this life is
>>  oxygen, which explains how the atmosphere was transformed over time.
>>
>>  This life, which somehow started in the "primordial soup", evolved over
> time
>>  into something like 100 million or is it a billion, species over about 2
>>  billion years.  Of this huge number, about 98% is now extinct.   For
>>  example, the dinosaurs were by all accounts, a very successful and
> diverse
>>  group of species which existed for over 400 million years, before
> hurriedly
>>  disappearing about 65 mya.  If I remember, there have been "great
>> dyings"
>>  going back eons.  It's almost as if on some type of schedule, the slate
> is
>>  wiped almost clean and a bunch (sorry for the technical term here,) of
> new
>>  critters emerges, and these new life forms do not seem to have much
> relation
>>  with the prior occupants.  There seems to be a rather large jump and
>> then
>>  ordinary evolution runs its course.
>
> Again this basically correct, but with a few caveats. I have never heard
> of
> Columbia. Nor can we track the continents back much further in time than
> 750
> Ma.
>
> [Ma = megannum, or millions of years before the present. Because this
> usage
> is still relatively new, other people write it as Mya (million years ago).
> Similarly, Ga is equivalent to Bya and ka is equal to kya].
>
> The person doing the best work in this area at the moment is Chris
> Scotese.
> He works as an independent scientist, thus he earns his living by
> producing
> educational materials. Nonetheless, the pages you will want to look at are
> a
>
> series of maps that he has produced:
>
>     http://www.scotese.com/earth.htm
>
> It takes a little while to go through each of the eras that the maps
> represent, but it's well worth the time.
>
> [Here, btw, is a picture of Chris taken at a meeting that I attended a
> couple
> of years ago:
> http://www.biogeography.org/Mesquite%20IBS%20Photo%20Tour/image6.html ]
>
> The earth is 4560 Ma old, but the crust of the planet is in constant
> motion.
>
> As a consequence, our capacity to say something meaningful increasingly
> erodes
> with the passing of each 100 Ma. Anything said about the shape of the
> earth
> much older than 750 Ma becomes more speculation than known fact.
>
> Although we can be more certain of which land mass was next to which one
> at
> which time, and which land mass was submerged or not at any epoch (that
> record
> is reasonably clearly written in the rocks), our understanding of the
> lattitudes at which the continents appeared at any one time also grows
> substantially
> fuzzier the farther back in time we go.
>
> Nonetheless there is another record that's also very clearly written in
> the
> rock: the impact that life has had on the geochemistry of the earth.
> Molecular
> oxygen (O2) simply did not exist on the primordial earth, nor does it
> exist
> now in the atmospheres of any of the other planets. On the earliest earth,
> molecular oxygen represented only 0.0000000000001 of the atmospheric
> population it
> does today. In an equilibrial chemistry, a chemistry characteristic absent
> of
> life, oxygen, because its reactivity, immediately disappears. But life
> changed
> that chemistry, several times. The following timeline is from David
> Catling
> (Univ. Washington, Seattle):
>
> http://67.41.4.238/lectures/earlymars/em-catling/resources/em-catling018.jpg
>
> The chart is divided into the three primary epochs: the Archaen, the
> Proterozoic ("first life", although don't take that interpretation
> literally), and the
> Phanerozoic ("visible life," life large enough to be seen by the human
> eye).
>
> The Phanerozoic encompasses the Cambrian Explosion of 540-570 Ma, the time
> of
> the origination of the various body plans used by plants, animals and
> fungi,
>
> and itself is broken into three eons: Paleozoic ("old life"), Mesozoic
> ("middle
> life") and Cenozoic ("recent life").
>
> Superimpose, at least in your mind, Catling's chart with this one from
> David
>
> Des Marais (NASA Ames):
>
> http://67.41.4.238/lectures/aslcnm/atmar-030919/resources/atmar-030919015.jp
> g
>
> This is the biological clock for the planet Earth. From it we derive one
> extraordinary fact: the machinery of life formed on the planet almost as
> soon as
> it possibly could. For the first few hundred million years, life would
> have
> been impossible. The crust/mantle/core of the earth was still in the
> process
> of
> fractional distillation. Simultaneous to that time the earth and the other
> planets were sweeping the inner solar system free of the debris of the
> initial
> protoplanetary disc that formed simultaneously with the origin of the sun.
> Life-extincting impacts would have been common, if life did have the
> fortune
> to
> arise then.
>
> We only have this one example of a solar system, and we only have this one
> example of life in the universe, and we have to make as much of these two
> exemplars as we can, knowing full well that we could easily becoming to
> erroneous
> conclusions. Prior to the discovery of the first extrasolar planets in
> 1995,
>
> based on what we knew about our on solar system, we believed that the
> planets
> nearest their host stars would inevitably be stony-iron planets, planets
> that
> have had their volatiles blown away by a vigorous solar wind. Planets that
> were
> within about 2 AU of their central star would be like earth, venus and
> mars.
>
> Planets further out would be similar to our gas giants, Jupiter and
> Saturn.
>
> It came as a great shock therefore to find that the first extrasolar
> planets
>
> we discovered were very close-in "hot Jupiters", orbiting just off of the
> surface of their host stars. No one expected this result, but due to
> observational
> selective bias in the technology used, these were the easiest planets to
> detect, and thus were the first to be found. We still can't detect planets
> as
> small as the Earth, but we're moving in that direction. But we're also
> having
> trouble in explaining the origin of the hot Jupiters.
>
> We have anticipations of being just as surprised at the kind of life we
> will
>
> discover elsewhere in the universe, once we find it, but for now, we only
> have
> the kind of life that we know on this planet, and we base all of our best
> guesses on what we know of it.
>
> DNA-based life extends back at least as far 3.6 Ga, and may go to 3.8 Ga.
> This is the point in time at which the machinery of life that inhabits
> this
> planet was invented. It was only bacterial, but it was the same kind of
> life
> that
> we are now.
>
> Two great events occurred in the history of life on this planet, and you
> can
>
> see those events clearly marked in the geochemistry of the planet in
> Catling's
> diagram. The first was the evolution of the eukaryotes. Bacteria are
> simple
> cells, composed of an outer cell wall and loosely stuffed with a fair
> amount
> of
> DNA. By contrast, eukaryotes are complex and highly organized cells,
> containing a distinct nucleus and organelles, such as mitochondria,
> cloroplasts, Golgi
> bodies, etc. The eukaryotes apparently evolved through the symbiotic
> aggregation of a number of types of bacteria, first being only facultative
> symbionts,
> but then becoming obligate symbionts and eventually so well integrated
> into
> the working of the protoeukaryotic cells that they became organelles. This
> evolution took an additional 2 Ga, and we have no idea why it took so
> long.
>
> The next great step required another 2 GA, occurring only 570 Ma ago, and
> that was the evolution of task-partitioned, complex multicellularity. This
> evolution was the "Cambrian Explosion" of animals, plants and fungi, and
> again, we
> have no idea why it took so long.
>
> Des Marais' biological clock outlines these steps very clearly, but the
> diagram is a bit misleading. The sun and the earth will last about 12 Ga.
> So
> far
> we're about 1/3 of the way through that span, but life itself won't last
> that
> long. One of two hells await us: either a wet hell, where the oceans
> evaporate
> into the atmosphere and we have a Venus-like planet, or the oceans
> evaporate
>
> and are lost to space, and we become a barren planetary surface, much like
> the
> moon or Mercury. At the moment, we don't know.
>
> In either case, life on the planet is expected to last only 0.5 Ga more.
> In
> about the same time we've gone from trilobite to astronaut, it appears
> that
> it's all going to be over.
>
>
>>  What I would dearly like to see is a solid chain that shows the ancestry
> of
>>  man going back a lot further than apes.  The step from apes to man is,
>> in
>
> my
>>  estimation very small, compare to the whole concept.  All the talk on
>>  evolution to which I have ever been exposed, seems to focus on small
>>  changes, like skin color, or teeth or bone formation.  What I want to
>>  understand is the progression from something say, a half inch long
> swirling
>>  blindly in a mud puddle to a human being able to build computers,
> airliners
>>  and spaceships.
>
> In this, you're in luck. An extraordinarily solid chain has come into
> existence in the last 20 years. The process is called phylogenetics ("the
> origin of
> families"), and it's a mechanism that any computer person would understand
> in
> five minutes. It is the biological equivalent of a versioning control
> system
>
> for code development.
>
> Phylogenetics is possible because we've learned to reliably and rapidly
> sequence the genomes of the life on this planet, and because of that, we
> can
> very
> rapidly sort all life on this planet and say based solely on the content
> of
> its
> code what is most like which else, and what changes must have occurred to
> get
> us from this species to that.
>
> The following diagram is a supertree of the extant mammals, humans
> included:
>
> http://67.41.4.238/lectures/evolution/sanderson-04ev/resources/sanderson-04e
> v0
> 02.jpg
>
> Like all supertrees, you can't even read the names of the species on the
> chart. The deepest common ancestor lies at the center, while the most
> recently
> derived species sit near the outer ring.
>
> The process is completely objective, and it will work with any kind of
> code.
>
> You don't even need to know what the code does, only what has changed. You
> could just as easily create a phylogenetic tree of all of the UNIX
> variants
> and
> backtrack to a hypothetical common ancestor.
>
> Phylogenetics hasn't provided any real surprises. Based on other, more
> physical characters, people had pretty much worked out these relationships
> over the
> last century with surprising accuracy, but it has allowed us to settle
> some
> long-standing squabbles, such as whether the macrochiroptera ("large hand
> wings", the large bats such as flying foxes) were derived from the rodents
> as a
> second, convergently evolved flying mammal or were merely an offshoot of
> the
>
> microchiroptera ("small hand wings"). Although good evidence existed for
> both
> points of view, it now appears certain that it was the second.
>
> Nor is the process limited in time. We can create phylogenetic trees of
> the
> most ancient relationships, as you can see in this enormously simplified
> diagram:
>
> http://67.41.4.238/lectures/earlymars/em-mckay/resources/em-mckay023.gif
>
> These trees work because all life on this planet is descended from a
> common
> ancestor. What we are attempting to do in our search for life elsewhere in
> the
> universe is to find something that isn't on this tree, a true second
> genesis
>
> of life.
>
> Wirt Atmar
>
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