Wikipedia:Peer review/Evolution/archive1

Evolution

One of the core topics of biology. All suggestions are welcome - copy-editing, suggestions for content, sources, corrections and simplification. NOTE - if you have not edited Wikipedia before, please just click the "Edit this page" tab above and add your comments at the bottom. Formatting will be added later. Thank you. TimVickers 22:28, 9 May 2007 (UTC)

User:Quadell

• Wow. To this lay-person, the article looks fantastic. Well-written and approachable, copiously referenced and well-illustrated. I'm afraid I don't have the biology background to say if it's missing any major facets, but what's there is very good. (I don't think the to-do list at the top of the talk page is up-to-date, is it?) – Quadell ^{(talk) (random)} 00:10, 10 May 2007 (UTC)

No, that list even refers to some sections that no longer exist! Thanks for the comments. TimVickers 01:02, 10 May 2007 (UTC)

User:Firsfron

• There's a problem with this passage: "These anatomical similarities between living and fossil organisms can provide evidence of the relationships between different groups of organisms. Important fossil evidence includes the connection of distinct classes of organisms by "transitional" species, such as the Archaeopteryx, which provided early evidence for intermediate species between dinosaurs and birds,[161] and the recently-discovered Tiktaalik, which clarifies the development from fish to animals with four limbs.[162]" Archaeopteryx isn't a species, it's a genus. You could substitute Archaeopteryx lithographica here, or change "species" to something else. However, since every species can be considered an example of a transitional species (because species are always evolving), this passage is an oversimplification, and it should be modified to address this issue. Firsfron of Ronchester 02:25, 10 May 2007 (UTC)

Good point. How about "Important fossil evidence includes the connection of distinct classes of organisms by "transitional fossils", such as Archaeopteryx specimens, which provided early evidence for the evolution of dinosaurs into birds," Is that more accurate? TimVickers 02:33, 10 May 2007 (UTC)

That works for me. :) Firsfron of Ronchester 02:54, 10 May 2007 (UTC)

Nope. "Classes" implies a distinct taxonomic level. How about "taxa"? Esseh 04:50, 10 May 2007 (UTC)

OK, how about - "Important fossil evidence includes the connection of distinct species by "transitional fossils" TimVickers 05:24, 10 May 2007 (UTC)

I don't like the reference here to "transitional fossils". Technically, every fossil in the record is an example of a transitional fossil because all populations of organisms are in transition. Firsfron of Ronchester 06:48, 10 May 2007 (UTC)

Also, "distinct species" is far too specific (no pun intended). That implies the fossil record is complete. It also implies that the transition is a quantum jump, rather than a gradual transition. Is "taxa" too much jargon, even with a link? How about "distinct groups of organisms"? Clumsy, but not jargon. Esseh 07:25, 10 May 2007 (UTC)

OK, "distinct groups of organisms" added. Thank you. TimVickers 16:52, 10 May 2007 (UTC)

User:Esseh

• I tinkered with the 1st two paragraphs. I found that the gradual nature of evolution was too implied. Similarly, be VERY careful with the use of the word "survive". We're talking degrees of fitness here, not an "all" (survive and reproduce) or "nothing" (die and do not reproduce) phenomenon. This is a common misconception, and we have to avoid it here. I tried to make it clearer in the intro that even a slight edge in reproductive fitness (and some luck) will cause an increase in the genes for some traits.

On further comments, I notice you start with a microevolutionary approach and lead into macroevolution. I prefer that approach myself, but notice that they're not headings. Perhaps the article would be better divided into those sections, with appropriate sub-sections? Might do to explain the distinction up front, too. Hope that helps. Esseh 05:14, 10 May 2007 (UTC)

Added a brief definition of these terms at the beginning of the "Outcomes of evolution" section. TimVickers 05:32, 10 May 2007 (UTC)

Tim. Well worded. Thanks. You may want to check the intro paragraph again. Apparently someone didn't like my changes - the inclarities remain, and I promise to keep my hands off from now on. Esseh 05:37, 10 May 2007 (UTC)

Tim, couldn't resist tinkering a bit with the genetics section. One bit bothers me still. This section:

"His research laid the foundation for the concept of discrete heritable traits, known today as genes.[20] Mendel's ideas replaced the notion of "blending inheritance" prevalent at the time Darwin wrote The Origin of Species, and solved the long-standing problem of the persistence of variation within populations."

My problems are:

1. Heritable traits are not genes; genes encode (carry information about) heritable traits.
2. Blending inheritance was more than a "notion", and there was more than one flavour. Though now discredited, they were widely accepted hypotheses (even theories) at the time. Might I suggest "...replaced various theories of "blending inheritance" prevalent..." Or "hypotheses", if you don't want to give them undue weight from a modern perspective. Esseh 18:12, 10 May 2007 (UTC)

Replaced with "Mendel's findings disproved the various ideas of "blending inheritance" prevalent at the time Darwin wrote The Origin of Species," and also "His research laid the foundation for the concept of discrete heritable traits, which are controlled by genes." Thanks for these corrections. TimVickers 18:36, 10 May 2007 (UTC)

Sounds good. Thanks. Esseh 19:03, 10 May 2007 (UTC)

User:Nowimnthing

• I don't think I like the outcomes of evolution section. I think we have avoided the macro-micro terms due to their conflation with the ID movement in the public/layman mind. I know that is not too valid of a reason, but if we are going to have this here we need to word it very clearly that there is not a qualitative difference between the terms just a quantitative one. Nowimnthing 05:49, 10 May 2007 (UTC)

Not all the references I found agree with that interpretation. Have a look at the citations and see what you think. TimVickers 05:53, 10 May 2007 (UTC)

I am not a biologist so I will take your word for it, but as someone who has battled the hords of creationist vandals I would just note that they try to exploit any crack in scientific knowledge. Sure there may be some scientists, working at the cutting edge of genetic and biology who have the knowledge to disgree about the exact definition of macro vs micro but if we word that incorrectly, the ID people will jump all over it as proof that they were right all along and that macro does not exist. They will point to wikipedia for proof that there is a fundamental difference between the two. In the past I have done some academic article database searches for the terms micro and macro and found very few peer reviewed articles using them. Maybe part of the problem is the poor shape the macro and micro pages here. We need some serious work to be done there, but most of us are not biologists and not competent enough to take a stab at it, maybe we need peer review on those pages as well. Nowimnthing 06:07, 10 May 2007 (UTC)

OK the latest edit seems to read a little better I think the technical aspect and references help, we do need something like this to clear up the confusion in laymen. Nowimnthing 06:13, 10 May 2007 (UTC)

User:Madprime

Intro

• this is minor. 1st paragraph, last sentence - natural selection and genetic drift are mentioned. Later in "Mechanisms of Evolution" these two are mentioned, but gene flow is also mentioned. Is this inconsistent? (I'm not an expert in these definitions, don't take this too seriously.)

Heredity section (and a little beyond)

• (minor) I don't think it should start with Mendel, although it should certainly mention him, but I'd rather the concept be mentioned first since this is really about the concept itself... For example I start Genetics#Discrete inheritance and Mendel's laws with: "At its most fundamental level, inheritance in organisms occurs by means of discrete traits, called "genes". This property was first observed by Gregor Mendel, who studied the segregation of heritable traits in pea plants."

Reworded.

Now completely re-written and Mendel removed to the History section. TimVickers 23:37, 12 May 2007 (UTC)

• I'm a bit uncomfortable with how much material is given to non-DNA inheritance. (This said as someone who is supposedly trying to study DNA methylation.) I think these are exceptional cases and it's very speculative that these might at all apply to evolution. If it's going to be in here, I think it should be done more succinctly. (I see this material was here before you got to the article. Well, my opinion is this is confusing trivia that, as far as we can tell, has very little to do with evolution. Maybe something will be found, but it's all very speculative. In my opinion, be bold and cut a lot of this out. Just because it's true doesn't mean it belongs.)

I cut about half of this.

• If you want to add more appropriate material to this section, maybe add more about the sequence nature of DNA? DNA as a polymer of four different nucleotides. I'd also change "genes re-defined as regions within this DNA" to instead say something more like "genes re-defined as sequences of DNA within the chromosome" since they're more really defined by sequence rather than location. Also, I don't think it should say DNA is "within chromosomes", that almost sounds like the DNA is buried within a non-DNA chromosome when really the chromosome most fundamentally defined as being that piece of DNA. :-)

I think a lot of the mass of a chromosome is protein, maybe about half, judging from the nucleosome structure. I've reworded this completely to try to work around this.

Yeah, I only meant "most fundamentally" -- chromosome generally also includes proteins, but always includes the DNA. That is, admittedly, a definition that was arrived at after time, as originally chromosomes were just those things that got stained ... I just reworded it again to my liking, hope that's ok. Madeleine 03:10, 11 May 2007 (UTC)

• If you add stuff about genes being sequences, maybe you can then you can say the sequence of genes determines the sequence of amino acids in proteins, which consequently determining protein structure and function? I wonder if maybe you're avoiding this level of detail. Later you can say point mutations sometimes change an amino acid in the protein sequence, causing a structural change that can affect the protein's function. (I notice now that the article mentions amino acids and codons in the context of frame shift mutation, given that it's mentioned there I think it'd be good to add this other stuff.)

Added, thanks.

Variation

• "The heritable portion of an individual's traits, their phenotype, results from the interaction of their specific genetic makeup, or genotype with the environment." This sentence is confusing, it appears to be saying "A phenotype is the heritable portion of an individual's traits".

I've defined genotype and phenotype earlier, makes this much easier.

Recombination

• The section starts with a statement on asexual = linked, then goes on to describe linkage in sexual organisms. It would be nice to have a little statement noting that between independent assortment and recombination, most genes are not linked to each other. Don't want the reader to walk away thinking linkage is the rule rather than the exception. :-)

Expanded, and added independent assortment (this is what comes from working on an (asexual diploid)!

• "Recombination in sexual organisms allows disadvantageous mutations to be purged and beneficial mutations to be retained more efficiently than in asexual organisms.[52] However, recombination can also lead to more individuals with new and advantageous gene combinations being produced." I would replace "However" with "In addition", I don't see these as contrasting statements.

Good point. I'm addicted to "however"! TimVickers 00:41, 11 May 2007 (UTC)

Okay I have to do some other stuff but that's probably the major material I would be commenting on anyway. Good luck with the editing. :-) Madeleine 21:17, 10 May 2007 (UTC)

• Please see automated peer review suggestions here. Thanks, APR _t 23:29, 10 May 2007 (UTC)

User:Verisimilus

Images

Images are laid out a bit haphazardly. Avoid sandwiching text between images on left and right, be wary of placing images on the left when they may offset section headings and make the article look messy.

Formatted left-aligned images. TimVickers 16:44, 13 May 2007 (UTC)

Adaptation

The last sentence of the first paragraph here would use rewording, it's a little messy.

Ugh! It was wasn't it. Reworded. TimVickers 16:44, 13 May 2007 (UTC)

mdashes

Should be consistent in the presence or absence of a space on either side. I can't remember what the MOS says here...

I'll get back to you on this one! :) TimVickers 16:44, 13 May 2007 (UTC)

All text em dashes spaced, all citation en dashes unspaced. Done. TimVickers 20:17, 13 May 2007 (UTC)

Co-evolution

The descriptions of the mechanisms could perhaps be expanded or clarified. At the moment it's a little opaque for the non specialist.

Reworded for clarity. TimVickers 20:36, 13 May 2007 (UTC)

Common descent

Perhaps a mention of molecular clocks would be fitting here?

Added link. TimVickers 20:36, 13 May 2007 (UTC)

Speciation

has also been observed in the natural world, which should perhaps be added to "under laboratory conditions". There's a dandelion-like grass whose name I can't remember (maybe a ragweed?), which evolved into a new species, "Norfolk ragweed", by polyploidy. (I've probably got the names very wrong!) :I've also heard that mosquitoes have evolved into separate sub-species on different lines of the London Underground, although this may be an urban myth...

Added, with ref for apple fruit-fly review. TimVickers 20:36, 13 May 2007 (UTC)

Evolution from monkeys

Monkeys is a paraphyletic group and thus the explanation may perhaps be more scientifically satisfactory if, say, Chimpanzees was used? Can't really use "apes" as we are apes...

I know, but this is the phrase you so often hear. Are we trapped by their inaccuracy? TimVickers 16:44, 13 May 2007 (UTC)

Permian-Triassic extinction event

I'm pretty sure it's more than 90% of marine species that went extinct. I've heard 95% and think that was with regards to genera, it may even have been 99% of species? I'm sure there's a lot of variation in the literature but a reference would be useful. It would also make sense to use species as a measure of the size of the K-T extinction, for consistency.

Cited review and changed everything to species terms. TimVickers 20:36, 13 May 2007 (UTC)

"Human activities are probably the cause of the ongoing extinction event"

{{fact}}

Ref added. TimVickers 16:44, 13 May 2007 (UTC)

Phylogenetic tree of life

An unrooted version of this image would be much more satisfactory.

True, do you have any examples to hand? TimVickers 16:44, 13 May 2007 (UTC)

Not in the public domain, alas...

Sigh. Welcome to the rat race that is Wikipedia. I replaced a previous rooted version with this upload of mine some time ago, but clearly, the dipsticks prevailed. There is an SVG version of this, too that I don't like particularly. Someone should probably do a more modern version from scratch and in SVG. Not me. Samsara (talk • contribs) 01:59, 1 June 2007 (UTC)

Abiogenesis / Origin of life

Both of these links lead to the same page. Should both be wikilinked in close proximity? (I think maybe it's okay to do so.)

Removed link and defined abiogenesis in first sentence. TimVickers 16:44, 13 May 2007 (UTC)

Last universal ancestor

Should this read last universal common ancestor?

The Wikipedia page is "last universal ancestor" but I've piped the link. TimVickers 16:44, 13 May 2007 (UTC)

All these multicellular forms of life were eukaryotes

It's simply not true that all multicellular forms of life are eukaryotes. All plants and animals are but that renders the eukaryote statement redundant.

Slime moulds are multicellular amoebae; Thiomargarita are multicellular sulfur-reducing bacteria that have been reported (unconvinceingly, see Bailey 2006, in Science) in the Precambrian, and acritarchs are still by definition unplaced in the tree of life. The Twitya Nimbia discs which are the first firm evidence of multicellularity are commonly assumed to be a microbial colony. I'd remove or dilute this probable overstatement.

Slime moulds are eukaryotes and Thiomargarita spp are unicellular, although macroscopic. Myxobacteria are the best example of multicellularity in prokaryotes, although this is just in part of their life cycle. Removed word "all" to blunt this statement slightly. TimVickers 16:27, 13 May 2007 (UTC)

I stand corrected... Some Thiomargarita (if I've understood correctly) become multicellular as a response to stress. However they're not complex multicellulars... I'd recently received a firm slap on the wrist for making a similar statement but perhaps I said eumetazoans... Verisimilus T 21:12, 13 May 2007 (UTC)

And repetition of 'Which' in the following sentence makes it read clumsily

Reworded. TimVickers 16:44, 13 May 2007 (UTC)

[The Cambrian Explosion] originated all the known body plans, or phyla, of modern animals ; Somebody's been reading too much Gould! Investigations into the Ediacaran biota have shown that not to be the case. It is in many cases the first instances of the phyla entering the fossil record, or becoming mineralised - not the same thing as their genesis at all. Hox genes certainly didn't cause the explosion, they evolved long before it (Rosa 1999?); Sex was almost certainly long before it too. Oxygenation of the atmosphere was produced by photosynthesis since around 3.5-2000Ma, depending on how sceptical you are - it was the accumulation that has been cited as a probable cause of the explosion. This may have been triggered by the completion of "rusting planet earth", i.e. the oxidation of all the metallic iron and rocks and minerals.

A favourite author, you've caught me! Replaced with "majority of body plans" I don't make any judgement on which explanation for the Cambrian diversification is correct, if that is the right word to use with HOX being a proximal explanation and oxygen an ultimate one. I've removed the un-cited example. TimVickers 17:13, 13 May 2007 (UTC)

I'm still uncomfortable about the inclusion of Hox genes. Just about everything imaginable has been cited somewhere as a possible cause, and whilst I'm surprised to find HOX genes being mentioned so recently - especially from Jim Valentine - I can't help but feel that something more understandable to the lay reader would be more appropriate, especially as there's pretty condemning evidence against the role of Hox, and indeed reasonably firm evidence for the splitting of phyla well before the Cambrian (e.g. Kimberella) which stand against the hypothesis. Maybe I'm bordering on POV here though... Other perhaps more easily understood triggers could include an influx of nutrients or Calcium into the oceans (See Squire et al 2006, Brennan 2005), the advent of biomineralisation, or the evolution of planktonic microherbivores (mentioned in pretty much anything by Butterfield from 2001-2007). All these have their weak points, and indeed attempting to pin the explosion on a single cause is probably doomed to failure (which makes me feel that it may be best to avoid it altogether, as any hint of wavering on the part of science will probably be seized upon by the ID types).

I think you are right, HOX genes will be meaningless to the general reader. I've retained the reference and just used O2 as an example. TimVickers 22:03, 13 May 2007 (UTC)

References

A large and tedious job, this one! Use a consistent reference style (e.g. spacing and type of dash in pages xxx-yyy, author initial punctuation); expand all journal names. Try and ensure that all references contain a link, either in the form of URL or DOI or equivalent. DOI is by far preferable to PMID; these should be replaced if possible.

I'll check through these again. However, journal names do not need to be expanded, and PMID or DOI are perfectly acceptable equivalents - this is left up to the author concerned, see WP:CITE for discussion of reference styles and Wikipedia:Featured article candidates/Proteasome for a discussion of this last time it came up during FAC. TimVickers 16:44, 13 May 2007 (UTC)

Fine. I prefer DOI as it actually takes you to the article but I suppose that's a personal preference.

A rule I try to follow is that if the article is free-full text I add a link and then the article name is hyperlinked. However, if a subscription is required I just add a PMID, which takes you to the abstract. I think this makes it easier for the normal reader with no library access at their IP address. TimVickers 21:57, 13 May 2007 (UTC)

That sounds fair enough... I assumed that DOIs took you to an abstract if you didn't have access rights, clearly not. The perils of being spoilt with access...

User:BirgitteSB

• History of evolutionary thought Great subtitle :)
  • I like everything here, but I feel it should not necessarily end at 1953.

Fixed by merge with "Modern research" section. TimVickers 16:54, 1 June 2007 (UTC)

• • It reads Lamark's idea were "seen in England as a threat to political and religious stability". By omitting this angle in the rest of the section it gives the impression later trains of thought were not seen as a threat. This is later dealt with; but I feel you should mention some thing like "evolutionary thought continued to evoke social and religious controversy throughout its history."

Added, thank you. TimVickers 16:55, 13 May 2007 (UTC)

• Mutation
  • When talking of germline vs somatic mutations, you might want to spend a little more time making it clear that somatic mutations have no effect on evolution.

Added. TimVickers 17:39, 13 May 2007 (UTC)

• • An example of chromosomal rearrangements is the fusion of two chromosomes in the Homo genus that produced human chromosome 2; this fusion did not occur in the chimpanzee lineage, and chimpanzees retain two separate chromosomes. However, in this case, chromosomal rearrangements do not appear to have driven the divergence of the human and chimpanzee lineages. It would be much better if you could replace this example with one that supports the idea of chromosomal rearrangment causing rapid speciation. It is too confusing to talk about that, give an example, and qualify it by saying that the example isn't actually and example of what was being talked about.

Looking at the literature more closely, I think chromosomal rearrangements are not really thought to be involvewd directly in speciation events. Have reworded the para to reflect this. TimVickers 22:19, 13 May 2007 (UTC)

• Gene flow
  • I think the discussion of hybridization needs to be reworked. The first mention is with mules which really should be just mentioned at the end as a counter-example. The introduction of mule is followed by Such hybrids are generally infertile, due to mispairings of chromosomes during meiosis. Which is really bad because many people will not read it as [Mules] are generally infertile; but instead may understand it as [Hybrids as a group] are generally infertile. I really think this paragraph should first discuss viable hybrids and their evolutionary consequences; importance of hybridization in plants, and then bring in non-viable hybrids.

But hybrids as a group generally are infertile! Verisimilus T 16:01, 13 May 2007 (UTC)

I have a bit of an agriculture background so I was mis-understanding hybrids there. Hybrid is primarily understood as "cross-bred variety" as opposed to "a product of different species" in my mind. Perhaps it is incorrect to call a cross-bred variety a "hybrid" but it is commonly done. If we are mainly talking about infertile hybrids here, I am even less certain how this is a relevent example for gene flow. It seems to be example of when gene flow doesn't happen and should be a less prominant part of the section.--BirgitteSB 17:27, 13 May 2007 (UTC)

The term hybrid does have two common meanings in biology, this section obviously needs re-working for clarity! TimVickers 17:32, 13 May 2007 (UTC)

Lead to this section re-written to (hopefully) make this clearer. TimVickers 22:34, 13 May 2007 (UTC)

• • The discussion of reinforcement should probably be moved to the natural selection section. It reads Selection against hybrids may result in reinforcement, this seems to be really about natural selection rather than gene flow.

Good point, removed. TimVickers 22:34, 13 May 2007 (UTC)

• Genetic drift
  • First I think the second paragraph about effective population size needs to be moved to the "Mechanisms of evolution" heading. Add some information about a population size having relevance or not to the importance of gene flow in evolution and it is a great introduction putting the various mechanisms in relation to one another.
  • After moving that out this section simply needs more content. One idea is to move "natural selection" to being the first of the three subheadings and then put the paragraph on current research prompted by the neutral theory of molecular evolution in this section. The new order would also help readers make sense of the phrase "In the absence of selection".

A very good idea, thank you. Rearranged as suggested. TimVickers 23:17, 13 May 2007 (UTC)

• Outcomes of evolution This little paragraph on macro-/micro-evolution fails to actually introduce what follows.
• Adaptation This section is the most problematic so far.
  • The intro says an adaptation is a specifically defined trait that not only enhances performance of some specific function, but also evolved under selection to perform that function . However the section quickly begins discussing common descent and then spends a lot of time on vestiges which do not actually enhance performance of some specific function. If the description of adaption given is correct; the section should stick closer to discussing things that fit that description and describing how they fit that description.
  • I can see the relevance of exaptations here but only if there much more content of adaption discussion vs exaptation discussion. Right now there is little discussion that's main focus is adaption.

Section re-written with new introduction. TimVickers 18:46, 20 May 2007 (UTC)

This is better, but I still feel you need more information on things which are adaptions rather than things which are not. Actually I find the difference between expaptation and adaption hard to identify. Exaptation is co-opting an existing struture for a new use. Adaption is gradual modification of an existing structure for a specific function. Surely penguin flippers have been modified through evolution since the ancesteral species flew just as the bat wings were modifed from the forelimbs of some ancestral species which did not fly. Why is one an adaption and the other not? Also reading that section again, I see "trait" occasionally used, but all examples given are about structures. Behaivour is also subject to adaption. In fact adaption of behaivour likely drives the adaption of structures. Especially sex-specific traits relating to courtship. I think some readers could leave that section thinking adaption only relates to structures and not behaivour or complex processes at all.--BirgitteSB 20:13, 20 May 2007 (UTC)

• Co-evolution and cooperation
  • Missing the discussion of coevolution of symbiotic relationships.

Added plant/fungus Mycorrhiza. TimVickers 16:35, 15 May 2007 (UTC)

• • The second paragraph is weak. Human cells not growing uncontrollably is either a poor example or insufficiently explained. Cooperation should be explained more in terms of evolutionary fitness and who's evolutionary fitness.

Tried to explain this better. TimVickers 16:35, 15 May 2007 (UTC)

• • The ubiquity of cooperation in the natural world reveals that cooperation is a common outcome of evolution and it is now recognised as the third fundamental principle in evolution, alongside variation and selection. If these are the thrre fundamental principles they are given no particular weight in this article.

Hyperbole removed. TimVickers 16:35, 15 May 2007 (UTC)

• Common descent I feel strangely about this section. It seems immature but I cannot say exactly what it should mature into.
  • It is misplaced. If, and I feel it is a big if, we are going to look at this as an "outcome of evolution" it should probably be placed last; possibly first.
  • I feel this is missing the necessary tie in to classification models.
• Speciation Strongest part of the article so far. I love the first paragraph.
  • Second paragraph mentions what method is most common in animals . It would be nice if the other three processes could be mentioned with the group most commonly using them.
  • I find the image slightly confusing compared to what terms are used in the text. Looking at it I am now unsure how peropatric involves isolation. I thought it did not reading the text, but then how is it different than parapatric. The illustration shows separation between populations as the only difference. After a few re-readings I understand the only difference between the two is parapatric involves a change in the fertility time-frame that makes inter-breeding highly unlikely while peropatric involves organisms fully capable of inter-breeding which do not. Can the illustration be made less confusing.

Do you mean the difference between peripatric and parapatric?

Yes.--BirgitteSB 10:48, 14 May 2007 (UTC)

Added discussion of difference between these two mechanisms.

• Extinction A good summary of extinction itself, but little discussion of what this means in terms of evolution.
  • Holocene extinction should mention the time frame. Readers will unlikely think "current" means prior to the agricultural revolution.

Added, with discussion of species selection. TimVickers 00:47, 16 May 2007 (UTC)

The Holocene extinction event is the current mass extinction, involving the rapid extinction of hundreds of thousands of species and the loss of up to 30% of all species by the mid 21st century. Human activities are probably the cause of the ongoing extinction event, and climate change may further accelerate it in the future It looks like you added the bit about the mid-21st century. My problem with the time frame is readers will not understand that this is an event that began at least 9,000 years ago. It is unlikely most readers will realize "human activities" could include the Clovis people's spear-hunting from reading the current wording.--BirgitteSB 16:29, 16 May 2007 (UTC)

Thanks, I'd mixed my edits up there. Added a broad time-frame "...associated with humanity's expansion across the globe over the last few thousand years..." TimVickers 19:03, 16 May 2007 (UTC)

• Major events in evolutionary history
  • No intro text
  • What follows is not really organized as the major events in evolutionary history.
  • I have a problems with covering "Common descent" separately from the topics in this section. Common descent info should be incorporated here.
• Evolution of life Worst section of the article
  • This sub heading has no intro. Right now it seems added in by breaking up of a pre-existing train of thought.
  • Most of this could be bullet form. Needs an explanation as to why these facts are notable or how they fit in to the bigger picture.--BirgitteSB 15:46, 13 May 2007 (UTC)

Both these sections re-ordered and re-written. TimVickers 19:59, 20 May 2007 (UTC)

User:Adam Cuerden

Right, let's see...

• Lead: Mentions "genetic drift", but does not explain what it is, and genetic drift's really just a difficult name for a simple process (if an important one in some circumstances). Worse, in Paragraph 3, you act as if genetic drift had been explained, bringing it up as if people knew what it was.

• History: Why is this first? It's hardly the most important thing about the subject.

It either goes first or last, I'm not fussed. TimVickers 04:43, 31 May 2007 (UTC)

• Heredity: Wanders far from the point, contains some things that are simply wrong, like "This simple correspondence between a mutation and a trait works in many cases". No, it does so for very few cases. The explanation of an allele never actually comes to the point of really explaining alleles. For that matter, very little it tries to explain is explained effectively.

Rewritten and greatly simplified, epigenetics removed entirely. TimVickers 03:35, 31 May 2007 (UTC)

• Mutation: There's a third important type of mutation: A duplication, usually from a crossing over error. The term "codon" is used as if you had explained it. Another mark against the Heredity section. The terms "germline" and "somatic" are carefully explained. They never appear in the article again. The description of the fusion event in human chromosome 2 fails horribly because there's no real explanation of chromosomes.

Chromosomes defined in hereditary section, cut codons, since this level of detail doesn't really help explain evolution. SImilarly cut "germline" and "somatic" definitions. TimVickers 03:35, 31 May 2007 (UTC)

• Recombination: "In these circumstances, the effective population size is reduced in the Hill-Robertson effect". Like anyone's going to understand that.

Cut and reworded. TimVickers 03:35, 31 May 2007 (UTC)

Thoughts so far: Some huge percentage of what I've reviewed so far has nothing to do with evolution, and more to do with teaching terms, mostly rather badly, and many of which are only brought up for the purpose of defining them. The least important gfacts get a lot of space, key concepts get a passing mention. Feels like the content was gutted, then re-expanded by adding trivia.

• Mechanisms: What's with listing the terms, then explaining them in reverse order? More importantly, why aren't these simple, easy-to-understand explanations in the lead, insstead of the awful explanations that are there? Only quibble is "founder effect" needs explained.

Rearranged, and founder effect defined. TimVickers 04:05, 31 May 2007 (UTC)

• Natural selection: Natural selection is not actually explained, except in the diagram. Only things relating to it are. The last paragraph, "An active area of current research is the level of selection, with natural selection being proposed to work at the level of genes, cells, individual organisms, groups of organisms and even species.[68] None of these models are mutually-exclusive and selection may act on multiple levels simultaneously.[69] In the gene-centered view of evolution, which is the lowest level of selection, intragenomic conflict is caused by "replicators" such as transposons that can multiply within genomes,[70] while group selection may allow the evolution of co-operation, as discussed below." is non-essential information dealt with in huge numbers of new jargon terms.

Defined process in first sentence, reworded "gene-centric", clarified list and re-written sexual selection. TimVickers 17:20, 31 May 2007 (UTC)

• Genetic drift: Content is good, with the quibble that "most evolutionary changes are the result the fixation of neutral mutations that do not affect the fitness of an organism" should actually read "most evolutionary changes are the result the fixation of neutral mutations that do not affect the fitness of an organism at that time." Somewhat pedantic, could use a little copyediting.

Changed, also changed "affect" to "effect". Copy-edited. TimVickers 16:13, 31 May 2007 (UTC)

But it *is* affect in this case, isn't it? Adam Cuerden ^talk 16:51, 31 May 2007 (UTC)

I have to look this up every time! I think effect is better here see usage note as I think we mean no immediate changes, rather than no immediate influences. TimVickers 17:03, 31 May 2007 (UTC)

• Gene flow: "Horizontal gene transfer has also occurred within eukaryotes, from their chloroplast and mitochondrial genome to their nuclear genome.[90]" - I'm not sure that's actually HGT. "According to endosymbiotic theory, chloroplasts and mitochondria probably originated as bacterial endosymbionts of a progenitor to the eukaryotic cell." - That's the fusion theory of creation of Eukaryotes. Symbiosis is not normally considered HGT. "Horizontal gene transfer complicates phylogenetics, since it produces genetic connections between distantly-related species." Phylogentics has not actually been explained yet.

Good point, reworded to just "gene transfer", cut phylogeny sentence but kept "endosymbiotic theory" as this is the name of the Wikipedia page and is the most common term for this in Pubmed, are you meaning something else? TimVickers 17:50, 31 May 2007 (UTC)

• Outcomes: Who the hell uses macroevolution and microevolution any more? What's "Within the modern evolutionary synthesis, macroevolution is the compounded effects of microevolution." supposed to mean? Is there an "outside the modern evolutionary synthesis"? Cut the whole paragraph. And, for that matter, that paragraph on how evolution does not imply progress should come after the adaptations section, because you haven't explained adaptations yet, indeed, you don't define them until the first subsection, yet harp on about them throughout the progress paragraph. Write an introduction that actually introduces the content in the subsections, and doesn't presume you already read them!

Macro/microevolution added at request of Esseh, see above. As the terms are still in textbooks, I'm in two minds on if we should keep it. I've reworded it as a compromise. "Progress" paragraph was originally a section after adaptation, which probably explains why it presumes too much. TimVickers 04:43, 31 May 2007 (UTC)

Reworded complexity to replace adaptation with natural selection, simplified language a bit. Also added introductory paragraph. TimVickers 00:04, 1 June 2007 (UTC)

• Adaptations: Poorly-organised, introduces a lot of jargon, and keeps presuming you know the jargon. Typical for this article so far, I fear.

Re-written and condensed. TimVickers 18:52, 31 May 2007 (UTC)

• Co-evolution and cooperation Content selection and orginisation are good; writing abominable.

Orginisation kept, writing chaged. TimVickers 04:45, 31 May 2007 (UTC)

• Speciation: The explanations of the types of speciation fail to explain very well. For instance:

"In contrast, the second mode, sympatric speciation, is species divergence without geographic isolation, and its identification is typically controversial, since even a small amount of gene flow may be sufficient to homogenize a potentially diverging species.[137][138] Generally, models of sympatric speciation in animals require the evolution of stable polymorphisms associated with non-random assortative mating, in order for reproductive isolation to evolve.[139] However, a common mechanism of sympatric speciation in plants appears to the the formation of polyploid species and can involve either a single plant doubling its numbers of chromosomes (an autopolyploid such as cabbage),[140] or two related plants cross-breeding to form an allopolyploid such as wheat.[141][142]"

This article varies between baby-talk, pedantic term-definition, and journal article complexity. Do any of these terms actually matter at the level of competency this article is trying for? Save it for sub-articles.

Re-written and condensed. Unnecessary technical terms removed. TimVickers 18:52, 31 May 2007 (UTC)

• Extinction Pedanticism mixed with lists. Do not presume knowledge of the geologic column.

Re-written and condensed. TimVickers 18:52, 31 May 2007 (UTC)

• Origin of life: This is the most pedantic, content-free waffle I've seen. The point is "While the origin of life, or abiogenesis, is not strictly part of evolution, it of course had to happen before evolution could start. Abiogenesis is believed to have started once chemicals that could encourage (catalyse, in the language of chemistry) their own production emerged, followed by gradual increases in complexity that gradually produced something that could be called life. However, not much is yet certain about the process, though RNA, which is somewhat self-catalytic, may have had an important role.

Removed unnecessary technical terms and condensed. TimVickers 18:57, 31 May 2007 (UTC)

• Common descent: "All organisms on Earth are descended from a common ancestor or ancestral gene pool." I still don't understand how you're supposed to get a gene pool that can't reduce to a single ancestor if you back up far enough, given we surely don't presume that the genetic code originated multple times. Otherwise, it's pretty good.

• Evolution of life Another jargon-farm. "The engulfed bacteria then evolved into either mitochondria or hydrogenosomes, structures that are still found in all known eukaryotes." makes it sound like both exist in all eukaryotes, I'm pretty sure that's untrue.

Good point, split into 2 unambiguous sentences. Section re-written for clarity. TimVickers 19:07, 31 May 2007 (UTC)

• Modern research: Informative and well-written enough.

No references however. TimVickers 19:07, 31 May 2007 (UTC)

• Social and religious controversies: An awkward section to end the article on.

Moved history section to end. TimVickers 19:07, 31 May 2007 (UTC)

My recommendation: With the few exceptions I praised above, this article is awful. I think some parts used to be somewhat better - content wise, if not writing-wise - than this, there may be content in versions from six months to a year ago that can be used profitably. Adam Cuerden ^talk 02:46, 31 May 2007 (UTC)

Note: The section on mutation in this March version is probably stealable, you could probably use the HGT description as well, though cut Valich's POV-pushing about how HGT is why trees cannot be rooted and the last common ancestor is hypothetical. Adam Cuerden ^talk 03:16, 31 May 2007 (UTC)

Looking on this, I really should clarify: The "you" is plural, editors in general. Not meant to refer to any one editor. There's a mixture of old awfulness, a litle new awfulness, and some real improvements, and no one editor, as far as I'm aware, is responsible for all of them. Adam Cuerden ^talk 15:23, 31 May 2007 (UTC)

It's OK, I knew what "you" meant! TimVickers 15:51, 31 May 2007 (UTC)

Right. I'm going to be a bit nit-picky, but:

• Lead still doesn't explain genetic drift.

Added.

• Heredity section is still a bit misleading, though trying to explain the many-to-many mapping of genes to traits is very difficult in the first place. The description of alleles needs to be a little more explicit in connecting the variant genes with possible changes in function.

Re-defined in terms of alleles.

• "Variation also comes from exchanges of genes between different species, through horizontal gene transfer in bacteria, and hybridization in plants." - Too specific, ignores between-population gene flow.

I thought this was covered in the sentence preceding it. TimVickers 21:49, 31 May 2007 (UTC)

More in a bit. On a quick skim, it looks a lot better, but there are still probably some things to fix. Adam Cuerden ^talk 21:25, 31 May 2007 (UTC)

User:PhDP

First, Tim, thank you for your dedication.

Genetic drift

Some relatively minor modifications;

• Slightly deleterious alleles can easily reach fixation when the effective population size is low, I just added a line about this in the intro of the Mechanisms section, but it's not enough. The fate of mutations, and how the different forces of evolution act of them, is a central element of the theory of evolution and it’s worth more details.

• Nothing on the molecular clock ?

• The time for an allele to become fixed by genetic drift depends on the effective population size. The distinction is quite important.

• I think any discussion of genetic drift should contain an explanation of the concept of effective population size, it's fundamental to understand drift and the single sentence in the introduction of the Mechanisms introduction is simply not enough. In comparison, in Genetics of Population by Hedrick, more than half of the chapter on Genetic drift and effectice population size is devoted to the effective population size. Many discussion on effective population size are quite technical and I don't think they should be added to the article, but at least some explanation is necessary. I might do a simple graphic with Matlab to show how different sex ratios can reduce the effective population size.

• These investigations were prompted by the neutral theory of molecular evolution, which proposed that most evolutionary changes are the result the fixation of neutral mutations that do not have any immediate effects on the fitness of an organism. That's inaccurate. A mutation can be neutral and still have an immediate effect on fitness. It's just that, considering the effective population size, the effect is so small that natural selection won't affect the fate of the allele significantly, by definition, a mutation is neutral when its fate is determined by random genetic drift, it's not defined by its effect on phenotype.

History of evolutionary thought

In my opinion, this section is too short. There's nothing about the development in the past the 50s, nothing about our great discoveries and new problems we've encountered; the importance of gene duplication, the C value enigma, molecular clock, endosymbiosis, the important of random drift, the neutral and nearly neutral theory, the integration of game theory...