User talk:Plumbago/Sandbox 2

Comments 1
Intro
 * Intro image might be faintly confusing because as well as colour frequency changing, colours are drifting towards the red (i.e. selection and mutation). Is this what's intended?
 * Everybody dislikes the lead image. :(


 * Intro mention of genetic drift isn't qualified by pointing out that it's usually neutral
 * Genetic drift might be very important for evolution, see Neutral theory of molecular evolution.


 * Intro again, "A species is a group of animals"? Animals???
 * Problem is that this definition doesn't apply to asexuals, changed to organisms, since this is less inaccurate.


 * Intro again, might be an idea to qualify "The similarities between organisms ..." to note that the similarities range from the molecular up to the macroscopic; also, might be better as "Similarities between all organisms on Earth ..." or something to broaden it to include all life.
 * When we say "organisms" this at present means the same as "all organisms on earth" as we haven't yet discovered any non-earth organisms.

Heredity
 * Heredity focuses entirely on genes; after being a combatant in the recent epigenetics wars, surely a single remark indicating them might be worth adding?
 * This was in the article, but I removed it as we couldn't say if they were actually important or not.


 * Passing comment, "phenotype" includes organism behaviour and effects on other organisms; implied here that it's simply an organism's body.
 * That's how I understand the term. I'll do some checking.
 * Ah, of course behavior is included, added to definition.


 * Change "and a suntan is not hereditary" to "and a suntan itself is not inherited"
 * I actually prefer the simpler wording.


 * Change "four types of molecules" to "four types of molecular subunits"
 * Cut entirely.


 * "This simple correspondence between an allele and a trait works in some cases ..." - hmmmm, would it be fairer to say that the "simple correspondence" is unusual, and that it's normal for genes to be connected to phenotype via a complex set of interactions? Or something ...
 * I haven't been able to find any solid numbers on this, do you have any data? What kind of percentage are we talking about?
 * I've adjusted it a bit myself. Vanished user talk 11:37, 4 June 2007 (UTC)

Variation
 * Bit of repetition with immediate section above (genotype and phenotype)
 * Reworded to flow better.

Comments 2
Mutation
 * Change "interferes with the reading of the genetic code" to "interferes with the reading frame of the genetic code"?
 * This was cut as being too technical as we didn't explain translation above. In fact, all mention of proteins was removed and everything discussed in terms of genes.


 * Might be worth mentioning polyploidy in the context of gene duplication; and noting that it's a major mechanism in plants; and possibly noting that it's the main reason that phenotypic complexity is not correlated to genome size.
 * Added polyploids as a piped link, genome size is only peripheral to evolution, so doesn't really belong here.
 * It's dealt with a bit more in speciation. Vanished user talk 11:37, 4 June 2007 (UTC)


 * Clarify "three for colour vision" to "three for colour vision (red, green, blue)"
 * But then it would read to a naive reader that the genes were red, green or blue! Added links instead.


 * Change "... accelerate the divergence of a population into new species by increasing genetic differences" to "accelerate the divergence of a population into new species by increasing genetic differences that hamper sexual reproduction"
 * The role of chromosomal rearrangements in speciation appears to be doubtful from my more recent reading. People can't see how such a rearrangement could spread through the population.
 * I've seen discussion of this. The basic idea is that they can reproduce, because passing on a double chromosome is just as good as passing on both. But the offspring have more trouble mating. It's probably out of the scope of this article to go into more detail than we have, though. Vanished user talk 11:37, 4 June 2007 (UTC)


 * Although this section introduces the idea of virus effects, it doesn't go on to explain them; I can imagine viruses either causing errors by their activities, or even inserting "new" code like transposons; I've no idea which of these mechanisms is the correct one, but a sentence would help here.
 * We don't explain how any of the mutation mechanisms work, this would be a bit of a side-track.

Recombination Mechanisms
 * Fine by me
 * Change "The relative importance of natural selection and genetic drift ..." to "Within a population, the relative importance of natural selection and genetic drift ..." to make it clear why these two processes are being discussed separate from gene flow
 * Done.

Natural selection
 * I like the diagram here (for once!)
 * Now I'll have to go and change it. ;)


 * Change "previously neutral and harmful traits" to "previously neutral or harmful traits"
 * Good catch! Done.


 * Directional selection, etc., could do with a diagram; I can have a go if you think this would be a good idea; very easy in Matlab.
 * 103kb, 14 images! However, this might be a good addition for the natural selection article.


 * Change "hard to fake" to something less unencyclopedic; explicitly reference the handicap principle?
 * I think simplicity outweighs this one. Vanished user talk 11:37, 4 June 2007 (UTC)


 * "Selection at a level above the individual ..." - no mention made here of insect societies, where the concept of an individual is itself eroded.
 * Group selection is covered in the cooperation section.
 * This, by necessity, a very trivial discussion of levels of selection, insects are beyond its scope. Anyway, kin selection is dealt with in Co-evolution and cooperation, and there's a bit more on levels in my latest edit to Outcomes Vanished user talk 11:37, 4 June 2007 (UTC)

Genetic drift
 * This section could do with a remark to the effect that genetic drift is liable to be limited where an allele is strongly selected for/against; admittedly, in small populations it might still win out, but I thought in most cases it required fairly weak/absent selection; might just be my ignorance.
 * As I understand it, and tried to explain in the lead above, there are a couple of factors that interact to determine this.
 * Actually, more importantly we were saying it applied only when there was no selection. I fixed this.

Gene flow
 * Good section; I might be inclined to change "Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring" so that it's clearer that inter-species transfer is significant here; I know it goes on to say this, but the inter-species thing is crucial here.
 * That's in the first paragraph as a generalised statement, but this isn't true in all cases, eg E coli conjugation.

Outcomes
 * I'd be inclined to alter this sentence "Organisms can also respond to selection by co-operating with each other, usually by aiding their relatives or engaging in mutually-beneficial partnerships" to focus slightly less on behaviour per se and more on symbioses; perhaps "Organisms can also respond to selection by engaging in mutually-beneficial coevolutionary relationships with other species (e.g. flowering plants and insects), or through cooperation with conspecifics (e.g. insect societies)"
 * I got a lot of criticism about this section being inaccessible previously, this is why the writing here has been made as clear and non-technical as possible.


 * I'd definitely be inclined to ditch or minimise anything on micro-/macro-evolution; beyond the issue of the timeframe involved, there is no distinction as far as I'm concerned; the only significant "macroevolution" is speciation; and that can occur as a result of "microevolution"; I'm afraid of feathering the creationist bed here.
 * A much discussed point (see FAC discussion with Adam). However, as the reference is quite explicit, I can't really ignore it. TimVickers 14:39, 3 June 2007 (UTC)
 * I was able to use it to bring in some points from Gould and Vrba on species selection that I think justify the inclusion.

Adaptation
 * I like the bit about complexity; good
 * Change "An example that shows both types of change is bacterial adaptation" to "An easily observable example that shows both types of change is bacterial adaptation"
 * The squirrel example of exaptations is a bit lame; the pressure sensors of fish becoming our ears, or the front legs of land mammals becoming the front paddles of whales seem better to me.
 * I had the wing-flipper chnage in penguins as the example previously. There was debate over if the anatomical adaptations involved in changing a wing to a flipper made this an adaptation or not. I finally found an example that was unquestionably an exaptation!


 * Actually, the adaptation/exaptation distinction itself seems a bit blurry to me now.
 * It is to me as well, not a clear term at all.
 * It's not so bad. It's basically anything that evolved for onre function, then got co-opted to another. The hammer stirrup and anvil used to be part of the connection of the jaw, they went through a phase of being used both as a connection and for hearing, then emerged purely for hearing. It evolved for one thing, it then got adapted for use in a different thing by way of a dual use. exadaptaion! Feathers evolved for warmth, later became used in flight. Exaptation! I've added one listed by Gould. Vanished user talk 11:37, 4 June 2007 (UTC)
 * I was thinking glycolytic enzymes acting as lens crystallins was another good example, but we have one now. TimVickers 19:50, 4 June 2007 (UTC)

Comments 3
Co-evolution and co-operation
 * Nothing much to add here; given the degree of uncertainty in the main article on the topic, I'd suggest rewording "Other forces driving cooperation include group selection" to "Other forces driving cooperation may include group selection"
 * Done.

Speciation
 * Ugly grammar: change "... into two descendant species, and has been observed multiple times ..." to "... into two descendant species. It has been observed multiple times ..."
 * Done


 * This section introduces sexual reproduction early, but doesn't address speciation in asexual species; is this just to avoid confusing things too much for a general evolution article? I realise from the replies above that many of my suggestions to "improve" the article have already been extensively discussed
 * The problem is defining "species" in asexual organisms, this is a very knotty problem and probably out of the scope of the article.


 * In discussing the four types of speciation, it might help if the diagram (a good one I should quickly add) matched the order in which they're introduced (e.g. sympatric speciation is discussed second, but appears fourth on the diagram)
 * Excellent point. Done.
 * Let me guess, you rearranged the text just as I rearranged the diagram? Vanished user talk 15:08, 4 June 2007 (UTC)


 * I'd suggest rewording the punk-eek paragraph to: "Speciation events are important in the theory of punctuated equilibrium, which accounts for apparently short "bursts" of evolution interspersed with relatively long periods of stasis during which very little evolution appears to occur. In this theory, the majority of the fossil record will correspond to the parental population, with the organisms undergoing speciation and evolution being found mostly in small populations or geographically-restricted habitats, and therefore rarely being preserved as fossils.  Subsequently, when the daughter population invades and displaces the parental population, the fossil record records apparently rapid evolution."
 * Reworded. TimVickers 15:07, 4 June 2007 (UTC)

Comments 4
Introductory reading
 * I've not skipped to this section - this is a quick point on something I just noticed; I'd be inclined to replace The Selfish Gene with The Blind Watchmaker - the former is probably too technical and focused on animal behaviour to provide a good source for evolution; the latter is, to my mind, a first-rate popular science intro to evolution, undimmed by the 21 years since its first publication; that said, I can't believe no-one's said this before, so this probably isn't a helpful suggestion
 * I think most people don't get past the reference list! Replaced. TimVickers 19:47, 4 June 2007 (UTC)

Comments 5
Extinction
 * Tweak "The Permian-Triassic extinction event was the Earth's most severe extinction event, rendering extinct 96% of species" to "Because it extinguished the dinosaurs, the Cretaceous-Tertiary extinction event is the most well-known of these events, but the earlier Permian-Triassic extinction event was the most severe, with approximately 96% of species driven to extinction"
 * Tweaked.


 * Tweak "The Holocene extinction event is the mass extinction associated with humanity's expansion across the globe over the last few thousand years and involves the rapid extinction of hundreds of thousands of species and the loss of up to 30% of species by the mid 21st century" to "The Holocene extinction event is an ongoing mass extinction associated with humanity's expansion across the globe over the last few thousand years. Present-day extinction rates are currently 100-1000 times greater than the background rate, it is predicted that up to 30% Earth's species will be driven extinct by the mid 21st century"
 * Tweaked.

Origin of Life
 * Trim "Life must exist before it starts diversifying, and so the origin of life is a necessary precursor for biological evolution. However ..." to "The origin of life is a necessary precursor for biological evolution.  However ..."
 * Condensed


 * Would it be an idea to add RNA world hypothesis to the "For more details on this topic, see" note at the top?
 * Added

Common descent
 * Capitalise Earth in "The current set of species on Earth"
 * Condensed to "Current species are..."


 * I'd be tempted to bullet-point the four strands of evidence for the universal descent; this is a very important point, so making it stand out (while not increasing the length of the article) seems important.
 * I didn't want to emphasis evidence too much, this is covered in the Evidence of common descent article.


 * Tweak last paragraph to "More recently, evidence for common descent is derived from the biochemical similarities between organisms"
 * Reworded.

Evolution of life
 * The part about eukaryotes evolving is rather coy about the nature of the organisms that engulfed the bacteria; presumably these were just a different type of bacteria? anyway, perhaps we don't need to say anything specific here; actually, I can't think of anything better than what we've got here
 * If we're looking to shorten the article, I'd suggest deleting the unnecessary clause "which allowed the evolution of cooperation between the bacteria and the host cell"; the remaining sentence fragments fit nicely together
 * Cut


 * Later, drop the "second" from "... an independent second engulfment ..."; this implies only two stages, while in reality it's liable to have been a longer chain of successive fusions of bacterial cells
 * Cut


 * There's a bit of a jump from the ediacarans to "Soon after the emergence of the first animals"; we sound a bit definite on the edicarans all being animals; also, we omit to mention that it's believed that the ediacaran fauna were largely driven extinct before the Cambrian explosion; perhaps rewrite the start of the final paragraph to: "Although the Ediacaran fauna were the first multicellular organisms, they persisted for only a relatively short period of time. However, the demise of their ecosystems was followed by a period of remarkable biological diversification known as the Cambrian Explosion.  In around only 10 million years the majority of types of modern animals evolved ..."
 * Reworded to "Soon after the emergence of the first multicellular organisms.." As the actual fate of the Ediacaran fauna and its relationship to later organisms is mysterious. TimVickers 23:02, 4 June 2007 (UTC)

Comments 6
History of evolutionary thought
 * I don't like this "The first convincing exposition of a mechanism for evolutionary change was made in 1858"; it is really only true from a historical perspective; at the time I don't think it was viewed as a convincing theory; looking back from now we're bound to say that it's the first convincing exposition; the following might be better:


 * "Evolutionary ideas such as common descent and the transmutation of species have existed since at least the 6th century BC, when they were expounded by the Greek philosopher Anaximander. As biological knowledge grew in the 18th century, a variety of such ideas developed, beginning with Pierre Maupertuis in 1745, and with contributions from natural philosophers such as Erasmus Darwin and Jean-Baptiste Lamarck. In 1858, Charles Darwin and Alfred Russel Wallace jointly proposed the theory of evolution by natural selection to the Linnean Society of London in separate papers. Shortly after, Darwin's publication of The Origin of Species provided detailed support for the theory and led to increasingly wide acceptance of the occurrence of evolution.


 * Nonetheless, Darwin's specific ideas about evolution, such as gradualism and the mechanisms of natural selection, were strongly contested at first. Lamarckists argued that transmutation of species occurred as parents passed on adaptations acquired during their lifetimes. Eventually, when experiments failed to support it, this idea was abandoned in favor of Darwinism. More significantly, Darwin could not account for how traits were passed down from generation to generation. However, unbeknownst to Darwin, a mechanism was provided in 1865 by Gregor Mendel, who found that traits were inherited in a predictable manner. When Mendel's work was rediscovered in 1900 ..."
 * Added.


 * As some old enough to be schooled primarily in classical genetics, I'd suggest rewording this "Since then, genetics has become a core part of evolutionary biology" to "Since then, molecular genetics has become a core part of evolutionary biology"
 * Added both.


 * The last paragraph here is a bit unfocused, and misses a trick I think; I think it's important to emphasise just how broad evolutionary biology has become, and mention its percolation into fields traditional outside the so-called natural sciences; how about the following:


 * "In its early history, evolutionary biology primarily drew in scientists from traditional taxonomically-oriented disciplines, whose specialist training in particular organisms addressed general questions in evolution. As evolutionary biology expanded as an academic discipline, particularly after the development of the modern evolutionary synthesis, it began to draw more widely from the biological sciences. Currently the study of evolutionary biology involves scientists from fields as diverse as biochemistry, ecology, genetics and physiology, and evolutionary concepts even inform more distant disciplines such as psychology, medicine, philosophy and computer science."
 * Added.


 * Regarding the edit above, I could probably rake up some appropriate references for the "distant disciplines"; Steven Pinker for psychology; Randolph M. Nesse for medicine; Michael Ruse/Daniel Dennett for philosophy; erm, there must be someone obvious for computer science ... [actually, Alex Fraser might suit]
 * It's 99.4kb at the moment, I'm trying desperately to keep it below 100!

Social and religious controversies
 * This text "As Darwin recognized early on, perhaps the most controversial aspect of evolutionary thought is its application to human beings. Specifically, some people object to the idea that all diversity in life, including human beings, arose through natural processes without supernatural intervention" is a little confusing as the first sentence draws attention to humans, the second then starts by "specifically" identifying the diversity of life and humans; I'd suggest simply rewording to:


 * "As Darwin recognized early on, perhaps the most controversial aspect of evolutionary thought is its application to human beings. Specifically, some people object to the idea human beings arose through natural processes without supernatural intervention"
 * Done.


 * Tweak "... the ongoing creation-evolution controversy, a social and religious conflict ..." to "... the ongoing creation-evolution controversy, a religious conflict ..."; creationism is almost always borne out of religious conflict, not social
 * Done


 * Wow, I wrote this "While other scientific fields such as cosmology and earth science also conflict with literal interpretations of many religious texts, evolutionary biology has borne the brunt of these debates" yonks ago - and it's still here; clearly it has "survivor" stamped all over it ;-)
 * A living fossil?


 * The final paragraph is a bit messy, and would benefit (my POV) with a summary sentence that distances these movements from evolutionary biology; how about ...


 * "Evolution has also attracted controversy because it has been used to support philosophical and ethical positions that promote discrimination within or between social groups. For example, in the early 20th century the eugenic ideas of Francis Galton were developed into arguments that the human gene pool should be improved by selective breeding policies, including incentives for reproduction for those of "good stock" and the compulsory sterilization, prenatal testing, birth control, and even killing, of those of "bad stock". Similarly, "Social Darwinism", a term given to the 19th century Whig Malthusian theory of Herbert Spencer, was developed into ideas about the application of the "survival of the fittest" to commerce and human societies as a whole. However, these developments are frequently claimed to promote social inequality, racism, and imperialism, and contemporary scientists and philosophers consider them to be neither mandated by evolution nor supported by data.
 * Done

Uses in technology
 * The first paragraph here is fine; the second rather short and somewhat flimsy; I can't think how best to beef it up for now
 * Expanded with an example.

References
 * Any chance of arranging for these to be hidden unless the reader opens a tab?
 * I think that'd mess up the "click on a footnote number and jump to it" functionality. Vanished user talk 15:18, 5 June 2007 (UTC)

Further reading
 * Wikilink Almost Like a Whale, The Blind Watchmaker, Wonderful Life (book), The Structure of Evolutionary Theory, The Major Transitions in Evolution; most of the authors could also be linked
 * Wikilinked everything I could find. Vanished user talk 15:09, 5 June 2007 (UTC)


 * Whew - done. --Plumbago 12:17, 5 June 2007 (UTC)