On the Origin of Species.

[Kai]

Just wondering if anyone would be interested in seeing some notes and things from my seminar. We're reading On the Origin of Species, probably one of the most central books to the biological sciences. I've got a number of links and things.

First, if you are gonna read Origin for more than just a passing interest, please read the first edition. The later editions have many changes, some of them good, but some of them were concessionary statements. Darwin had a number of mental breakdowns in his lifetime, especially after publishing this book. You can imagine, with such a revolutionary idea in such a non abreviated form (Wallace's paper was very short and overlooked by comparison, and failed to present as convincing of a mechanism as the Origin), he was ridiculed. There were many people who wrote on biological evolution between 1800 and 1850, but none of them addressed it so well as Darwin did, and most were creationists. Even Wallace could not be convinced that the human brain was a product of change over time. The prevailing thought before Darwin was that there are types, and that variation within these types occurs, but only within set boundaries. Darwin tore that idea appart by proposing that types (ie species) could become more and different types over time, and he used natural selection as the justification of this hypothesis. This shook the worldview of most scientists of the time, including his good friend and collegue Lyell. Since what happened to him was akin to scientific beatdown, he made several consessions in later editions (as I said above). One of the most memorable was the placement of the words "survival of the fittest", and "evolution". He hated both those terms, and only grudgingly placed them in the 6th and final edition. The first edition of On the Origin is therefore his raw ideas before they were assaulted, and because of this they are much more interesting than the later editions, and much more true to his original thoughts.

Here is a full fascimile of the First edition, in PDF: http://darwin-online.org.uk/pdf/1859_Origin_F373.pdf

Also, some other interesting documents related to the history of evolutionary hypotheses:

The first chapter of Lyell's Principles of Geology, whereas he in depth covers the ideas of Lamarck. Most of what people learn about Lamarck is very cartoonish. People tend to forget he was a very intelligent person that had some very interesting ideas and remember only his idea that the neck of the giraffe became long from stretching. http://www.esp.org/books/lyell/principles/facsimile/contents/lyell-v2-ch01.pdf

Wallace's publication on "the tendency of varieties to depart indefinitely from their original type". You can see it is much shorter than Darwin's On the Origin, and the points have little supportive evidence. He was taken less seriously than Darwin mostly because of the short length. http://www.zoo.uib.no/classics/varieties.html

A short piece Darwin wrote about the history of "evolutionary theory". http://www.victorianweb.org/science/darwin/darwin_sketch.html

A very recent science mag article defending the originality of Darwin's work. http://www.sciencemag.org/cgi/content/full/323/5911/223

And, some quotes from notes the professor handed out:

Argument of Lamarck
P36: "The machinery of the Lamarckian system" (Lyell). Bring fixity of species into doubt, and then introduce a mechanism to explain transformation of species.
Step1. Argue against fixity of type.
P6: Old definition "...every collection of similar individuals, produced by other individuals like themselves." Cites Linnaeus that individuals from one stock "...have remained the same since the creation of each species."
and moreover that they are produced with a lineage derived from an unvarying "stock",
"...all the individuals propagated from one stock have certain distinguishing characters in common which never vary, and which have remained the same since the creation of each species."
BUT, Lamarck suggests that this definition is not an accurate picture of nature, because in many cases there is debate whether an individual is a species or a variety, because
P8: "...we see almost every void filled up..." & "...everything passes by insensible shades into something else..."
   Step 2: emphasize variation in nature
   P12: "...difference of situation and exposure causes individuals to vary..."
"...at the end of many successive generations, these individuals, which originally belonged to another species, are transformed into a new and distinct species." [transmutation]
P13: description of phenotypic plasticity and microselection
P15, 16: artificial selection yields products that vary widely from one another, and differences in 'circumstances' also yields some change
also, we are made aware of the changes in nature by consulting the geological record
The "Machinery"
P18: "...alteration in local circumstances...causes a change in their wants, and these new wants excite them to new actions and habits."
Use: "...greater development follows as a consequence of their more frequent use."
Disuse: "...organs no longer in use are impoverished and diminished."
[P19-21: Lyell interlude with an objection: no 'entirely new sense, faculty, or organ']
P22, 23: How does use and disuse work?
"...habits, its manner of living...have determined the form of its body...".
Examples:
water-fowl are web-footed because 'the wants' of ancestors drove them to the water where they were able to stretch their toes
giraffe has a long neck "...(not) because it was destined to live in Africa, but because it contracted the habit of stretching itself up to reach..."
   In sum, the repeated expression of a new want or habit eventually leads to that organ, sense, or faculty becoming hereditary (note mode of hereditary is not addressed, but presumably a form of Pangenesis, as it will be called by Darwin)
P24: Against the fixity of type continued and another mode of their creation hybridism.
"Hybrids have sometimes proved prolific...and varieties may be gradually created by near alliances..."
P25: Question- where did it all come from if modern animals and plants are descendants of 'single stocks'?
P27: Answer- "...series passes progressively from more simple to those more compound..."
& the  geological record attests to progression from 'simple to complex':
P30: In fact, the sequence goes: inert matter-vitality-(irrational) sensation-rational.
P31: But why are there still "...beings of the simplest structure."?
P32: Because Nature is lawful and "...is obliged to proceed gradually...(and) must always begin by the formation of the most simple kinds...", out of which more complex forms arise.
P33: This we would call spontaneous generation
P34: "...the higher and more perfect classes" arise due to the "...tendency to progressive advancement..." and "...the force of external circumstances...", broadly exposure to biotic and abiotic forces.
P35: How do these two actions conspire to create new kinds? The "progressive development" tends to produce a finely "graduated scale of being", but 'retarding' and 'accelerating' effects disrupt the progression, and "...chasms, into which whole genera or families might be inserted, are seen to separate the nearest portions of the series."

Discussion Points
So was Lamarck a crank or a deep and subtle thinker whose main errors were simply due to not having all the appropriate information, such as an accurate mechanism for heredity, and a willingness to rely on Natural Theology (or, occult metaphysics) to do some of the explaining. (spontaneous generation, interior force for complexification)
Inheritance of acquired characters? Nearly everyone believed in this because they needed a mechanism to explain the general phenomenon that like generates like? If a new variety produces a novel structure, then if bred true it will pass it on to the next generation- an acquired character has been inherited. Also, experiments like cutting off the tails of mice, or observations regarding circumcision, do little to address the mechanism envisioned by Lamarck. In neither case does an internal volition, or want, have any part of their new circumstances.
Overall, Lamarck does a service by advocating forcefully an evolutionary picture: a mechanism of replacement of forms over time, that bears some relation to selection and fitness (e.g., giraffes with shorter verses longer necks and their ability to survive). His peers and subsequent authors criticized him primarily for invoking occult explanations for the transmutation.

Wallace, 1858. On the Tendency of Varieties to Depart Indefinitely From the Original Type.
argument to show that the belief in the fixity of species is erroneous, and that there is a general principle that assures that varieties can in fact replace the parent form, and that this principle over time leads to a divergence of characters from the original type sufficiently large that the varieties formed would now be a new species. Which varieties survive is due to a struggle for existence
P1, 2: Call into question the stability of species based on observations of varieties, in particular their tendency to revert to the original type, which Wallace argues applies to domestic productions only
-BUT, 'permanent or true varieties' arise in nature and frequently there is an inability to determine whether something is the variety or the parent species (persisient problem of sibling, cryptic species, etc.)
Obviously these points are in conflict, which is resolved by assuming that there are strict limits to the variability.
P3- Thesis of the paper: the belief that varieties in nature are analagous to those of domestic productions is false, because there is a general principle assuring that in some cases the variety will outlive the parent species, which will then continue to depart ever more from the type.
P4- "Struggle for existence", primarily due to food constraint and predation. (In part, this is the thesis of Malthus)
Enters upon a discussion of population ecology
General conclusion is that fecundity not the issue for population limitation. Example of passenger pigeon (not overly fecund, small brood size):
"..that the procuring a constant supply of wholesome food is almost the sole condition requisite for ensuring the rapid increase of a given species, since neither limited fecundity, nor the unrestrained attacks of birds of prey and of man are here insufficient to check it.
So, Who survives and Who dies?
"..the individual existence of each animal depends upon itself, those that die must be weakest—the very young, the aged, and the diseased, —while those that prolong their existence can only be the most perfect in health and vigor—those who are best able to obtain food regularly, and avoid their numerous enemies."
Sounds a lot like "survival of the fittest" (coined by Herbert Spencer), Wallace uses "struggle for existence".
P5,6- Extension of thesis, from intraspecific to interspecific struggle, and recapitulation. That is, there is a struggle for existence for whole species, just as individuals of a species struggle for existence.
Establish two points: 1) checks to increase and 2) actual abundance of a species is due its 'merits'.
P7- Variation, Fitness and Selection.
"Most or perhaps all the variations from the typical form of a species must have some definite effect, however slight, on the habits or capacities of the individual."
"It is also evident that most changes (i.e., variations) would affect, either favorably or adversely, the powers of prolonging existence."
"...any species should produce a variety having slightly increased powers of preserving existence, that variety must inevitably in time acquire superiority in numbers."
"Now, let some alteration of physical conditions occur in the district...those (individuals) forming the least numerous and most feebly organized variety would suffer first, and... soon become extinct."
"The superior variety would then alone remain, and...occupy the place of the extinct species and variety."
P18 "The variety would now have replaced the species..." & moreover, "...could not return to the original form." (Variation in a gene pool, selection, and statistical effects of 'sampling' alleles from the gene pool)
If this repeats, then there is a principle of "... progression and continues divergence." (Not an inevitable outcome in any particular case, because another change in circumstances may make the new variety less suitable)
Introduce the notion of 'deep time', that in nature there is almost unlimited time available for this process (Lyell).  "Now the scale on which nature works is so vast--the numbers of individuals and periods of time..."
P19: Return to arguments about domestic animals, and why the evidence of the fixity of type, by reversion of varieties to the type, is not a good analogy to what occurs in nature.
In general, there is lessened selection, except for that produced by humans, on domestic animals.
Among domestic animals "the healthy condition of all their senses and physical powers...are only partially exercised, and ins some cases are absolutely unused."
P10: variation in domestic animals, as long as in conformity with human selection, may in many cases be effectively 'unscrutinized' by nature, whereas "In the wild animal, all its faculties and powers" are being evaluated, and any increase (variation beneficial for the animal) will affect the "...whole economy of the race."
and thereby, "It (variation) creates as it were a new animal, one of superior powers..."
P11: In short, domestic productions would be a short lived joke is expected to survive in the wild. OR, they must rapidly "...return to something near the type of the original wild stock, or become altogether extinct."
P12: therefore, domestic animals offer no positive argument for the fixity of species.
P13: Lamarck's reasoning refuted and Wallace's reasoning employed in examples.
E.g. Giraffe. Lamarck would say that the giraffe acquired its long neck because its wants drove it to search out new food sources, and it then stretched its neck; Wallace would argue that
"...because any varieties which occurred among its antitypes with a longer neck than usual at once secured a fresh range of pasture over the same ground as their shorter-necked companion, and on the scarcity of food were thereby enabled to outlive them." [variation and selection]
Very Important:
"An origin such as here advocated will also agree with the peculiar character of the modifications of form and structure which obtain in organized beings..."
"...reason for that 'more specialized structure' which Professor Owen states to be characteristic of recent compared with extinct forms, and which would evidently be the result of the progressive modification of any organ applied to a special purpose in the animal economy."  This is esentially a reference to our concept of HOMOLOGY
P14. Recapitulation.
"...the continued progression of certain classes of varieties further and further from the original type—a progression to which there appears no reason to assign any definite limits..."

So, is anyone interested?

[Requia ☣]

I am, though this is a massive TL; DR atm, will have to read it all later.

[Kai]

I am, though this is a massive TL; DR atm, will have to read it all later.

Yeah, I figured it would be


Think of it as a resource, if nothing else.

[Quercus]

Thank you for the post!

My evolution class was a POS and I'm looking for true resources on the subject.

[Kai]

Thank you for the post!

My evolution class was a POS and I'm looking for true resources on the subject.

Its my impression that the best resources are the original sources, and that of my professor. We're more or less reading On the Origin chapter by chapter. Its not so much a seminar about evolution, but rather a seminar about a seminal text, the history surrouding it and the ideas in it. Lots of what Darwin said seems very, well, quaint I guess when you compare it to what we know today, but this was pre mendel, he had a mechanism but not a vehicle. Very little of the book is devoted to mechanism, most is supporting evidence. The third chapter is On Natural Selection, I think, which is more or less the major hypothesis.

[Quercus]

Thank you for the post!

My evolution class was a POS and I'm looking for true resources on the subject.

Its my impression that the best resources are the original sources, and that of my professor. We're more or less reading On the Origin chapter by chapter. Its not so much a seminar about evolution, but rather a seminar about a seminal text, the history surrouding it and the ideas in it. Lots of what Darwin said seems very, well, quaint I guess when you compare it to what we know today, but this was pre mendel, he had a mechanism but not a vehicle. Very little of the book is devoted to mechanism, most is supporting evidence. The third chapter is On Natural Selection, I think, which is more or less the major hypothesis.

Yes, I had hoped to have a good experience in my evolution class, but it appears the undergrads are not expected to know much on it and/or the bio department has a shamefully poor expectation of the class. We spent a third of the semester discussing ID vs Evolution and this was supposed to be the better professor    The book was terrible as well.

[Kai]

Thank you for the post!

My evolution class was a POS and I'm looking for true resources on the subject.

Its my impression that the best resources are the original sources, and that of my professor. We're more or less reading On the Origin chapter by chapter. Its not so much a seminar about evolution, but rather a seminar about a seminal text, the history surrouding it and the ideas in it. Lots of what Darwin said seems very, well, quaint I guess when you compare it to what we know today, but this was pre mendel, he had a mechanism but not a vehicle. Very little of the book is devoted to mechanism, most is supporting evidence. The third chapter is On Natural Selection, I think, which is more or less the major hypothesis.

Yes, I had hoped to have a good experience in my evolution class, but it appears the undergrads are not expected to know much on it and/or the bio department has a shamefully poor expectation of the class. We spent a third of the semester discussing ID vs Evolution and this was supposed to be the better professor    The book was terrible as well.

[willem]

Evolution is such a beautiful feature of life, making use of the very forces that are trying to wring it's neck.

Giving ol' entropy the finger like that... pure awesomeness.

[Vene]

Thank you for the post!

My evolution class was a POS and I'm looking for true resources on the subject.

Its my impression that the best resources are the original sources, and that of my professor. We're more or less reading On the Origin chapter by chapter. Its not so much a seminar about evolution, but rather a seminar about a seminal text, the history surrouding it and the ideas in it. Lots of what Darwin said seems very, well, quaint I guess when you compare it to what we know today, but this was pre mendel, he had a mechanism but not a vehicle. Very little of the book is devoted to mechanism, most is supporting evidence. The third chapter is On Natural Selection, I think, which is more or less the major hypothesis.

Yes, I had hoped to have a good experience in my evolution class, but it appears the undergrads are not expected to know much on it and/or the bio department has a shamefully poor expectation of the class. We spent a third of the semester discussing ID vs Evolution and this was supposed to be the better professor    The book was terrible as well.

Make that a double.  My biology profs typically say from the first day that they don't even want to hear about ID/creationist nonsense.

Evolution is such a beautiful feature of life, making use of the very forces that are trying to wring it's neck.

Giving ol' entropy the finger like that... pure awesomeness.

'Splain please.  Evolution and entropy are not at odds with each other.

[Kai]

yeah.

When people use the arguement of entropy, I say "you know, thats great and all, but theres one very big problem with your hypothesis..."

When they ask what I mean, I dramatically point towards the bright stellar object in the sky.

[LMNO]

[Iason Ouabache]

yeah.

When people use the arguement of entropy, I say "you know, thats great and all, but theres one very big problem with your hypothesis..."

When they ask what I mean, I dramatically point towards the bright stellar object in the sky.

http://www.fstdt.com/fundies/comments.aspx?q=8255

"One of the most basic laws in the universe is the Second Law of Thermodynamics. This states that as time goes by, entropy in an environment will increase. Evolution argues differently against a law that is accepted EVERYWHERE BY EVERYONE. Evolution says that we started out simple, and over time became more complex. That just isn't possible: UNLESS there is a giant outside source of energy supplying the Earth with huge amounts of energy. If there were such a source, scientists would certainly know about it." 

[willem]

'Splain please.  Evolution and entropy are not at odds with each other.

Life not only offsets entropy by using solar energy, it also makes it work to its advantage. Organisms allow for a sort of 'controlled' or tempered randomness. One of the most important mechanisms that are assisted by such random disturbances is mutation, which ultimately leads to genetic diversification, which in turn is one of the basic drivers for evolution.

[Vene]

'Splain please.  Evolution and entropy are not at odds with each other.

Life not only offsets entropy by using solar energy, it also makes it work to its advantage. Organisms allow for a sort of 'controlled' or tempered randomness. One of the most important mechanisms that are assisted by such random disturbances is mutation, which ultimately leads to genetic diversification, which in turn is one of the basic drivers for evolution.

At the time I asked that I didn't realize that you were a professional, especially since the vast majority of the time I hear about entropy with respect to evolution is from creationists I was a bit worried.  Not that I expect a creationist on this site, but maybe that some of their bullshit has entered somebody's head.

[Precious Moments Zalgo]

Here is a full fascimile of the First edition, in PDF: http://darwin-online.org.uk/pdf/1859_Origin_F373.pdf

Thanks for that.  I hadn't read it yet.  I have read Dawkins' The Anscestors' Tale and thought it was well written, engaging, and easy to understand.

Evolution is such a beautiful feature of life, making use of the very forces that are trying to wring it's neck.

Giving ol' entropy the finger like that... pure awesomeness.

The 2nd law of thermodynamics says that energy transfers can't be 100% efficient.  Entropy is the loss from those transfers.  It explains why perpetual motion machines are impossible, but what's this got to do with evolution?