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Gene flow suggested text

Here is a start, originally based on breaking up the existing text. It will eventually matter whether variation or mechanisms comes first. Meantime, for variation,

Gene flow is the exchange of genes between populations, and between species. It can therefore be a source of variation that is new to a population or to a species.

Gene flow can be caused by the movement of individuals between separate populations of organisms, as might be caused by caused by the movement of mice between inland and coastal populations, or the movement of pollen between heavy metal tolerant and heavy metal sensitive populations of grasses.

Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer. Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring; this is most common among bacteria. In medicine, this contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance genes it can rapidly transfer them to other species. Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle Callosobruchus chinensis has occurred. An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which have received a range of genes from bacteria, fungi, and plants. Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains.

Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells and bacteria, during the acquisition of chloroplasts and mitochondria. It is possible that eukaryotes themselves originated from horizontal gene transfers between bacteria and archaea

For mechanisms,

The presence or absence of gene flow fundamentally changes the course of evolution. Because of the complexity of organisms, any two completely isolated populations will eventually evolve genetic incompatibilities through neutral processes, as in the Bateson-Dobzhansky-Muller model, even if both populations remain essentially identical in terms of their adaptation to the environment.

If genetic differentiation between populations develops, gene flow between populations can introduce traits or alleles which are disadvantageous in the local population, and this may lead to organism within these populations to evolve mechanisms that prevent mating with genetically distant populations, eventually resulting in the creation of new species. Thus, exchange of genetic information between individuals is fundamentally important for creating the biological concept of Species.

During the development of the modern synthesis, Sewall Wright's developed his shifting balance theory that gene flow between partially isolated populations was an important aspect of adaptive evolution. However, recently there has been substantial critisism of the importance of the shifting balance theory.

Let's take edits from here. BTW, after some investigation (I wanted to reprint in a Trends article), there appears to be no copyright applying to Wright's 1932 paper, so if anyone wants to scan and upload either for this or many other evolutionary pages, they should feel free. Joannamasel (talk) 16:25, 2 June 2011 (UTC)

Consolidated edits. Matthew Ackerman (talk) 13:28, 3 June 2011 (UTC)

Are these edits good to go? If so, I will insert them. mezzaninelounge (talk) 15:07, 3 June 2011 (UTC)

As far as I am concerned, yes. Refs would be good for the mouse and grass examples, but they can be inserted after this is on the main page. Joannamasel (talk) 15:42, 3 June 2011 (UTC)

OK, but before I do that, I think we should removed the population genetics text from the variation section, reedit it as follows, and reinsert it as part of first paragraph of the mechanisms section.

From a Neo-Darwinian perspective, evolution is a generation-to-generation change in the frequencies of alleles within a population that shares a common gene pool. According to the Hardy-Weinberg principle, the frequencies of alleles in a gene pool within a sufficiently large population will remain constant if the only forces acting on that population are the random reshuffling of alleles during the formation of the sperm or egg and the random combination of the alleles in these sex cells during fertilisation. Evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms, For example, the allele for black colour in a population of moths becoming more common. Mechanisms that can lead to changes in allele frequencies include natural selection, genetic drift, gene flow and mutation.

Thoughts? mezzaninelounge (talk) 16:43, 3 June 2011 (UTC)

I'd like to edit the gene flow section a little more, particularly I feel that examples of HGT could be cleaned up, and I'll grab those references. Matthew Ackerman (talk) 20:18, 3 June 2011 (UTC)

Population genetics suggested text

I'm not too keen on gene pools. While they appear in introductory textbooks, their usefulness is disputed by some, like Provine and Mayr, because they neglect both linkage and population structure. Generality is lost, and on the flip side, I don't see what is gained by referring to them. And are you positive that is the right ref for that first sentence? Ironic that it was part of the old text, given the recent discussion on mutation as mechanism. I put the Ewens monograph in instead, cited twice so it should get a name so they link together. Also, I support H-W under variation for reasons I have discussed earlier, but I don't think it adds much to mechanisms of evolution as a reason for absence-of-evolution. I would cut the text down to the following even shorter lead-within-mechanisms.

From a Neo-Darwinian perspective, evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms. For example, the allele for black colour in a population of moths becoming more common. Mechanisms that can lead to changes in allele frequencies include natural selection, genetic drift, gene flow and mutation.

But then I would retain a brief H-W section under mechanisms, as below, taken from the current article.

Natural selection will only cause evolution if there is enough genetic variation in a population. Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variance would be rapidly lost, making evolution by natural selection implausible. The Hardy-Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. According to this principle, the frequencies of alleles (variations in a gene) in a sufficiently large population will remain constant if the only forces acting on that population are the random reshuffling of alleles during the formation of the sperm or egg, and the random combination of the alleles in these sex cells during fertilisation.

More edit before insertion? Joannamasel (talk) 17:14, 3 June 2011 (UTC)

Joanna, if you would like to edit more, feel free. I didn't tinker with the references, so whatever you saw was in the original text. I just shortened the entire description. I just think that this section needs to be removed as its own standalone subsection within the variation section. We can insert it as part of the first paragraph in the variation section. The reason why I would prefer that it goes into the mechanism section is that H-W has been used as a null hypothesis to see if evolution has occurred. The violation of the assumptions of H-W are essentially the listed mechanisms in the mechanism section. I think readers might find that aspect/utility of H-W most interesting/informative. But I'm not opposed to other suggestions as well. I just don't like seeing it as a subsection of variation only because such an organization might mislead or confuse naive readers to think that population genetics is a major source of variation, which it is not. mezzaninelounge (talk) 17:25, 3 June 2011 (UTC)

BTW, I am not sure if I understood you correctly, are you suggesting we replaced the entire first paragraph under mechanisms with your suggested edits from above or do we put that before the first paragraph? If it is the latter, then we would also have to reedit the second paragraph so that it transitions from the first.

Before the current first paragraph, yes transition needs an edit.Joannamasel (talk) 17:42, 3 June 2011 (UTC)

I'm done editing. In research, H-W is not used as a null hypothesis to see if evolution has occurred, although sometimes undergraduate courses can give that false impression. The problem is that it takes only a single generation of random mating to reach H-W genotype ratios. H-W is used in research as a null hypothesis to detect assortative mating / population structure. Which makes the use of H-W as null hypothesis a little peripheral in a general article on evolution. Anyway, I agree with no longer using population genetics as a subheading, and using it in the intro part of variation instead. Joannamasel (talk) 17:39, 3 June 2011 (UTC)

Is that right (H-W not used as null hypo in research)? OK, if we put it in as the first paragraph of the variation section, then this is what it would look like:

From a Neo-Darwinian perspective, evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms. For example, the allele for black colour in a population of moths becoming more common. Mechanisms that can lead to changes in allele frequencies include natural selection, genetic drift, gene flow and mutation. Natural selection will only cause evolution if there is enough genetic variation in a population. Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variance would be rapidly lost, making evolution by natural selection implausible. The Hardy-Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. According to this principle, the frequencies of alleles (variations in a gene) in a sufficiently large population will remain constant if the only forces acting on that population are the random reshuffling of alleles during the formation of the sperm or egg, and the random combination of the alleles in these sex cells during fertilisation.

An individual organism's phenotype results from both its genotype and the influence from the environment it has lived in. A substantial part of the variation in phenotypes in a population is caused by the differences between their genotypes. The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will fluctuate, becoming more or less prevalent relative to other forms of that gene. Evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when a new allele reaches the point of fixation — when it either disappears from the population or replaces the ancestral allele entirely.

Variation comes from mutations in genetic material, migration between populations (gene flow), and the reshuffling of genes through sexual reproduction. Variation also comes from exchanges of genes between different species; for example, through horizontal gene transfer in bacteria, and hybridisation in plants. Despite the constant introduction of variation through these processes, most of the genome of a species is identical in all individuals of that species. However, even relatively small changes in genotype can lead to dramatic changes in phenotype: for example, chimpanzees and humans differ in only about 5% of their genomes.

Is this what you had in mind? mezzaninelounge (talk) 18:11, 3 June 2011 (UTC)

I would have the first 3 sentences as intro to mechanisms, not intro to variation. I would reorder 2 paragraphs in variation. So for mechanisms we have

From a Neo-Darwinian perspective, evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms. For example, the allele for black colour in a population of moths becoming more common. Mechanisms that can lead to changes in allele frequencies include natural selection, genetic drift, gene flow and mutation.

And for variation, where I have also removed a bit of redundancy and mechanism material to shorten it, and changed "changes" to "differences" at the end, how about

An individual organism's phenotype results from both its genotype and the influence from the environment it has lived in. A substantial part of the variation in phenotypes in a population is caused by the differences between their genotypes. The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will become more or less prevalent relative to other forms of that gene. Variation disappears when a new allele reaches the point of fixation — when it either disappears from the population or replaces the ancestral allele entirely.

Natural selection will only cause evolution if there is enough genetic variation in a population. Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variance would be rapidly lost, making evolution by natural selection implausible. The Hardy-Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. According to this principle, the frequencies of alleles (variations in a gene) in a sufficiently large population will remain constant if the only forces acting on that population are the random reshuffling of alleles during the formation of the sperm or egg, and the random combination of the alleles in these sex cells during fertilisation.

Variation comes from mutations in genetic material, migration between populations (gene flow), and the reshuffling of genes through sexual reproduction. Variation also comes from exchanges of genes between different species; for example, through horizontal gene transfer in bacteria, and hybridisation in plants. Despite the constant introduction of variation through these processes, most of the genome of a species is identical in all individuals of that species. However, even relatively small differences in genotype can lead to dramatic differences in phenotype: for example, chimpanzees and humans differ in only about 5% of their genomes.

Joannamasel (talk) 18:38, 3 June 2011 (UTC)

Those look good to me. If nothing else, I think we can now insert the gene flow texts into the gene flow sections as well as modify the lead paragraphs under the mechanism and variation sections. After that, we should finish off with the mutation bits and then move on to see how this entire article can be updated. mezzaninelounge (talk) 18:46, 3 June 2011 (UTC)

Let's do it

Seems a good critical mass of editors with good proposals has reached some grounds of agreement. Why not address these issues. Graft and numerous other editors that is too long to mention have written older versions and their input is valuable. But we need to make the changes and all recruit good editors we respect who are naive about evolution. What good is a great article that novices can't understand. I'm more of cell biologist and anatomist, and study evolution because you can't escape it's influence. But I think now, more than ever, we can write something we can all be proud of. GetAgrippa (talk) 12:19, 3 June 2011 (UTC)

Agree. I really think there is just too much detail in many of the descriptions that are best left to spin-off articles. If we are to embrace and include all the news ideas in this article, then I think we must strive for concision. mezzaninelounge (talk) 12:43, 3 June 2011 (UTC)

I think Thompsma is right on center about morphology. Phenotype is exactly what Mendel and Darwin were addressing, and much of the early advances (to the present)are morpological. I remember how logical and obvious evolution became from taking comparative anatomy decades ago, then evo-devo logically follows course extending the same ideas to development. The three-spine stickle back fish supermodel examines phenotypes, genetcs, organismic interactions, and environmental influences. None by themselves is explanatory but all together tell a story. I think this is key to Thompsma's suggestions. I always liked Gould's notion of a bauplan. We need a bauplan to glue everything together. GetAgrippa (talk) 23:03, 3 June 2011 (UTC)

Agreed GetAgrippa - this is exactly what is needed. This article has gotten outta hand and stagnant. Perhaps it might be best to start a scratch page and go from there? It will be a huge amount of work and a lot of hurdles to get the editors in here to agree. However, I think this could be accomplished. If you would like to start this up - I would be willing to poke in and assist. With a lot of work - I think a much improved article could be put together.Thompsma (talk) 23:20, 3 June 2011 (UTC)

Should the draft page be made on a user's page or can it be a subsection of this talk page? e.g., Talk:Evolution:New Draft. mezzaninelounge (talk) 21:53, 13 June 2011 (UTC)

Evolution of mutation rates: delete or move?

Since many seem to think the article is too long, I looked through it for things that look too specialised and out of place. Paragraph 2 under variation - mutation stands out to me. It summarises theories regarding the evolution of mutation rates. This is fairly arcane for a general reader, and there is no scientific consensus anyway. I suggest spinning it off as a stub for a new article on Evolution of mutation rate. Alternatively, the material can probably be merged into evolvability. Either way, I support moving it off the main evolution page. What do others think? Joannamasel (talk) 21:53, 6 June 2011 (UTC)

Sounds fine to me. mezzaninelounge (talk) 22:13, 6 June 2011 (UTC)

I moved it to mutation rate. --Ettrig (talk) 16:52, 7 June 2011 (UTC)

sounds fine to me. fwiw, in compsci this is called "meta-evolution". Kevin Baas^talk 19:54, 7 June 2011 (UTC)

There is an interesting article called Genetic Architecture related to genotype-phenoypte maps. It also includes evovability and also mutational robustness. I never realized the article existed. The idea of mutational robustness is interesting-phenotype persistence despite mutations so it counters evolvability. GetAgrippa (talk) 19:24, 8 June 2011 (UTC)

Intelligent Design in the see also section

I have added Intelligent Design in the see also section. This does not create system where the page gives undo weight to Intelligent Design. It is included because both topics explain the concept of how life was created and came to be the way it is today. The see also section of Intelligent Design contains links to Evolution (added by me) and Flying Spaghetti Monster. Ryan Vesey (talk) 14:53, 11 June 2011 (UTC)

I'm deleting it again, because ID is of only marginal significance to the topic of this article. Obviously, you never even took the time to read this article because it has NOTHING whatsoever to do with "how life was created". Sorry, you addition does indeed violate WP:DUE WP:POV. Dominus Vobisdu (talk) 14:58, 11 June 2011 (UTC)

(EC):I disagree with the inclusion as the two topics are not actually related. Evolution is a scientific explanation for the changes in living organisms after the appearance of life on Earth. ID is a mess of politico-religious nonsense attempting to describe how life on Earth began, which is a completely different subject. The two only appear related because ID was developed in the USA as an attempt to end-run around the U.S. Constitution and teach religion in public schools. There is no rational reason to conflate the two here. Doc Tropics 15:03, 11 June 2011 (UTC)

Would creationism be a more applicable term? Ryan Vesey (talk) 15:08, 11 June 2011 (UTC)

No, it wouldn't. For the exact same reasons that ID is not applicable. This is a science article. Religious topics are only of marginal significance here, as explained in the text of the article. ID, creationism and Creation Science are religious views without anything of scientific merit to say on the topic of evolution. Mentioning them in this section would violate WP:DUE and WP:NPOV. Dominus Vobisdu (talk) 15:26, 11 June 2011 (UTC)

Whatever Ryan Vesey (talk) 15:27, 11 June 2011 (UTC)

And your response is telling, isn't it? OrangeMarlin ^{Talk• Contributions} 16:52, 11 June 2011 (UTC)

And your response is useful, isn't it? Ryan Vesey (talk) 16:57, 11 June 2011 (UTC)

My above response of "whatever" was, in essence, a shorter way of stating that I realize that the page, as it exists right now, is what will remain. Rather than continue to argue for my personal beliefs, I am backing away from the discussion. Other editor can please consider this discussion closed. Ryan Vesey (talk) 17:11, 11 June 2011 (UTC)

I notice that both intelligent design and creationism are included in the social and cultural responses section; does this solve the problem? Abtract (talk) 16:16, 11 June 2011 (UTC)

With some reluctance, but out of a respect for logic, I guess I have to point out that intelligent design is by its own account supposed to explain patterns in nature which look "designed", so not only the origin or initiation of life, but also the origin of the diversity of species. Part of the problem here is that compared to normal biology, if we take ID seriously it basically equates the origin of diversity with the origin of life, thus ignoring an important distinction which biology needs to make, and which we on WP need to make. (Yes I know, sometimes it allows for "micro evolution" but this does not remove the problem.) Anyway, coming to practical advice, I think there are reasons to mention ID as a kind of adjunct to creationism, and these relate to a movement or movements opposed to the concept of evolution (and I'd say say science). That there is such opposition to evolution is mentioned, and should be mentioned, because it is notable. But discussing it at length seems problematic, partly simply because this article is already very long, and secondly because pop culture can no doubt invent an almost infinite number of variations on the basic theme of not being comfortable with the theory of evolution, and we can't fill this article with too much about them all.--Andrew Lancaster (talk) 16:40, 11 June 2011 (UTC)

So just to make it clear, yes, I think Abtract has the solution.--Andrew Lancaster (talk) 16:41, 11 June 2011 (UTC)

Recent debate on this: [[1]]

PART X IS THERE A PLACE FOR INTELLIGENT DESIGN IN THE PHILOSOPHY OF BIOLOGY?

• 19 There Is a Place for Intelligent Design in the Philosophy of Biology: Intelligent Design in (Philosophy of) Biology: Some Legitimate Roles. by Del Ratzsch
• 20 There Is No Place for Intelligent Design in the Philosophy of Biology: Intelligent Design Is Not Science Francisco. by J. Ayala 364

The first author has an interesting point: "The question then may not be, “Is there a place for intelligent design in biology?” but, rather, “Exactly what and how essential is that place?”" In terms of the SETI program looking at cosmic phenomena - scientists should remain agnostic and there are some interesting thoughts that could go into this, but let's all be honest here. If there was an honest discourse on intelligent design in scientific terms - there wouldn't be any problem with this as an idea worthy of consideration. However, we all know that it is a ruse - creationism masquerading as science. It is hardly worth mention, definitely not worth a see also link, and I agree with Andrew Lancaster. Once again, however, this article needs to be gutted and re-written. In my opinion it does not deserve featured article status. The length of the article is not a problem - the content is. If the presentation wasn't so prescriptive it could better serve to counteract the intelligent design movement. In many respects the content of this article does a great disservice to the science because it is so narrowly focused on genes as the ultimate case for evolution while ignoring the tomes of science that have described evolution otherwise.Thompsma (talk) 21:07, 13 June 2011 (UTC)

While the philosophical discussion supplied is indeed interesting it is important to remember Intelligent Design was specifically fabricated for one purpose...

• Evading the First Amendment for the purpose of teaching religion in public schools and excecuted with malice aforethought. Just sayin...sorry for the mini-rant ArtifexMayhem (talk) 21:36, 13 June 2011 (UTC)

Shorten the history section?

I still think the article is too long, and want to find ways to cut it, so that the really important information is more readily accessible. How about a radical reduction in the length of the history of evolutionary thought section? After all, there is a link to the full article on this topic. Most readers who want to know about the history will click on that, the rest probably skip the whole history section anyway. They may be less likely to skip it if it is much shorter and more accessible. To make this section really short, how about starting with the statement that modern understanding of evolution started with Darwin, cutting out the earlier stuff? Then briefly going forward from there, in particular to the eventual acceptance of Darwin's ideas via the modern synthesis? Joannamasel (talk) 22:14, 13 June 2011 (UTC)

I agree. However, I think we should still have just one to two sentences on the history of evolutionary thought before Darwin. Like before, I recommend that we post the entire history text here in this talk page and apply strikethroughs to the sentences that we would like to see removed from the current text. mezzaninelounge (talk) 22:22, 13 June 2011 (UTC)

Finalizing mutation edits for two sections

Joanna, I am following your suggestions as you seem to be most familiar with this particular topic. Feel free to make appropriate edits whenever necessary. I am trying to finalize the texts before reinserting them into appropriate sections of this article.

Here is the proposed text for the variation section.

Random mutations constantly occur in the genomes of organisms, which produces genetic variation in a population. Mutations are changes in the DNA sequence of a cell's genome, which can be caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication. When mutations occur, they can either have no effect, alter the product of a gene, or prevent the gene from functioning. Based on studies in the fly Drosophila melanogaster, it has been suggested that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70% of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.

There are three theories on what determines the mutation rate of organisms. The optimal mutation rate of organisms may be determined by a trade-off between costs of a high mutation rate, such as deleterious mutations, and the metabolic costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes. Additionally, higher mutation rates increase the rate of beneficial mutations, and evolution may prevent a lowering of the mutation rate in order to maintain optimal rates of adaptation. Finally, natural selection may fail to optimize the mutation rate because of the relatively minor benefits of lowering the mutation rate, and thus the observed mutation rate is the product of genetic drift. Viruses that use RNA as their genetic material have rapid mutation rates, which can be an advantage since these viruses will evolve constantly and rapidly, and thus evade the defensive responses of e.g. the human immune system.

Mutations can involve large sections of a chromosome becoming duplicated (usually by genetic recombination), which can introduce extra copies of a gene into a genome. Extra copies of genes are a major source of the raw material needed for new genes to evolve. This is important because most new genes evolve within gene families from pre-existing genes that share common ancestors. For example, the human eye uses four genes to make structures that sense light: three for colour vision and one for night vision; all four are descended from a single ancestral gene.

New genes can be created from an ancestral gene when a duplicate copy mutates and acquires a new function. This process is easier once a gene has been duplicated because it increases the redundancy of the system; one gene in the pair can acquire a new function while the other copy continues to perform its original function. Other types of mutations can even create entirely new genes from previously noncoding DNA.

The creation of new genes can also involve small parts of several genes being duplicated, with these fragments then recombining to form new combinations with new functions. When new genes are assembled from shuffling pre-existing parts, domains act as modules with simple independent functions, which can be mixed together creating new combinations with new and complex functions. For example, polyketide synthases are large enzymes that make antibiotics; they contain up to one hundred independent domains that each catalyze one step in the overall process, like a step in an assembly line.

And here is the proposed text for the mechanism section.

Mutation

In addition to being a major source of variation, mutation may also function as a mechanism of evolution when there are different probabilities at the molecular level for different mutations to occur, a process known as mutation bias. If two genotypes, for example one with the nucleotide G and another with the nucleotide A in the same position, have the same fitness, but mutation from G to A happens more often than mutation from A to G, then genotypes with A will tend to evolve. Mutation biases of different strength in different taxa can lead to the evolution of different genome sizes. Developmental or mutational biases have also been observed in morphological evolution.

Mutation bias effects are superimposed on other processes. If selection would favor either one out of two mutations, but there is no extra advantage to having both, then the mutation that occurs the most frequently is the one that is most likely to become fixed in a population. Mutations leading to the loss of function of a gene are much more common than mutations creating a new, fully-functional gene. Most loss of function mutations are selected against. But when selection is weak, mutation bias towards loss of function can affect evolution. For example, pigments are no longer useful when animals live in the darkness of caves, and tend to be lost. This kind of loss of function can occur because of mutation bias, and/or because the function had a cost, and once the benefit of the function disappeared, natural selection leads to the loss. Loss of sporulation ability in a bacterium during laboratory evolution appears to have been caused by mutation bias, rather than natural selection against the cost of maintaining sporulation ability. When there is no selection for loss of function, the speed at which loss evolves depends more on the mutation rate than it does on the effective population size, indicating that it is driven more by mutation bias than by genetic drift.

Thoughts? mezzaninelounge (talk) 18:14, 30 May 2011 (UTC)

Looks good to me! I just added a paragraph break to mechanisms.Joannamasel (talk) 18:44, 30 May 2011 (UTC)

Great! I will wait till tomorrow to apply the changes. Give other editors who may be on holiday a chance to look before proceeding. :D mezzaninelounge (talk) 18:49, 30 May 2011 (UTC)

• Opposed to change Sorry, but you're describing natural selection and genetic drift. Once again, please give us a strong and reliable source that makes the claim that mutation is a mechanism of evolution. If you can, then we have to rewrite the whole article from top to bottom, especially the lead. Once again, in lieu of any evidence to the contrary, mutation itself is not an evolutionary process or mechanism, it is merely a biochemical event upon which natural selection and genetic drift rest. It doesn't drive the evolutionary process. And Mezzanine, I hate being this critical, especially to one of the good guys around here, but your paragraph has a lot of synthesis to make a point with which I'm unconvinced even you support. OrangeMarlin ^{Talk• Contributions} 19:10, 30 May 2011 (UTC)

Orangemarlin, If we have to rewrite parts of this article, then that's fine but this issue needs to be resolved. With respect to my last paragraph, I've already given clear references. Have you had a chance to look at each and every one of them? The references (peer reviewed articles, course syllabus, and information website) themselves say very clearly that mutation is a mechanism of evolution. I don't see how I'm engaging in WP:synthesis here. Perhaps you could clarify as to how I'm synthesizing or engaging in original research. Moreover, instead of just opposing, perhaps you could provide references that clearly say otherwise. In the end, it is not a question of what I or you personally believe or accept, it is question of WP:verifiability and level of WP:consensus. So far both appear to be on the side of these changes regardless of what I personally believe or accept. mezzaninelounge (talk) 19:36, 30 May 2011 (UTC)

Mezzanine, it's your responsibility to prove the assertion, not for me to prove the negative. Your references certainly don't convince me, and I have more than a bit of expertise in the area. For example, I also know there's not a wizard in the sky that guides evolution, but I cannot prove that. Using the old canard, "extraordinary claims require extraordinary evidence", you haven't provided in my opinion. The fact is that everything that Joanna is pushing, and pushing hard, is that mutation is a mechanism of evolution. Without natural selection or genetic drift, mutation does nothing. Natural selection pushes the population (or subpopulation) that has a specific beneficial mutation to include the mutation in the population after a few generations. I know that this mutation as a mechanism arises from a lot of Creationist evolution denialism, so I have a gut negative reaction right up front. The whole epigenesis theory of evolution seems to get legs every 10 years or so, without gaining traction, so maybe I'm wrong. But I'm going to stand by my strongest possible objections against joanna's constant POV editing until a lot more editors join in, and form a consensus that we all can accept. Maybe I'm wrong. Maybe you're completely right and I'm full of shit. But right now, I'm not seeing it. There used to be dozens of Ph.D. level scholars editing this article. Where are they? Right now we have three stubborn editors who think each other's edits are all fucked up. This isn't going well. OrangeMarlin ^{Talk• Contributions} 20:15, 30 May 2011 (UTC)

I do not understand this argument and would be pleased if someone could describe it to me in terms accessible to a lay-person. It seems clear to me that both Darwin and neo-Darwinian/Modern Synthesis theories of evolution assume a certain degree of dynamic variation. I understand the importance of this - some of you may remember that some time ago I argued (to considerable opposition) that even though Darwin may not have formulated his argumnt in statistical terms, Darwin's key innovation was to reconceive of species as statistical phenomena, that the difference between specias is best understood statistically rather than categorically, and it is precisely because of the importance of variation (which can be described statistically). And mutation is one of the most important sources of variation, or of the dynamism of variation. Buuuut .... does this make mutation a "mechanism?" I was thinking of it as a "necessary precondition" or something like that. Are we arguing over how best to characterize "mutation?" Or are we arguing over the definition of "mechanism?" Slrubenstein | Talk 20:40, 30 May 2011 (UTC)

I'm in basic agreement. I like to use the word "foundation." Mutation cannot be the mechanism for evolution, because it's mostly a miserable failure (I can't remember the article I recently read, but it was like 90-99% of mutations were deleterious). Without mutation, there is no natural selection or genetic drift. But without natural selection or genetic drift, mutation cannot drive evolution. Oh, and being met with considerable opposition is a regular achievement on this article. A couple of editors need to understand that, it's nothing personal. OrangeMarlin ^{Talk• Contributions} 20:58, 30 May 2011 (UTC)

Slurbenstein, nice to have you join us. :)

The key point of contention here is whether mutation is a mechanism of evolution. To Neo-Darwinian ears (I'm assuming that is most of us), we have learned that it is not. We understand it to be just a major source of variation by which processes such as selection and drift can work on. However...., like many ideas (group selection, macroevolution) that I have across on this talk page, there are peer-reviewed articles that describe it as such, by stating that a series of mutations could potentially bias the evolution of organisms (e.g., see [2]). I especially recommend this review article in the Proceedings from the National Academy of Sciences [3]. The issue is whether mutation is described by the scientific community via peer-reviewed articles as a mechanism. The answer is yes. The next question is whether this is a WP:fringe view, which I really don't know. I suspect it is not.

In any event, the lead and parts of this article are at variance with its organization. This has to be resolved one way or another. Plus, I am getting tired of this. I have leeches to dissect. mezzaninelounge (talk) 21:00, 30 May 2011 (UTC)

OrangeMarlin, calm down. Nothing has been done yet, we are still in discussion. As you know, I value your input as well. Nothing personal. mezzaninelounge (talk) 21:06, 30 May 2011 (UTC)

Do not EVER tell me to calm down, that's fucking insulting. I'm perfectly fine, but since you obviously have a Psychiatry license, you should know that making a diagnosis over the internet is unethical. Joanna, a non-notable individual, thinks that she can make constant changes to fit her POV. That's all. OrangeMarlin ^{Talk• Contributions} 21:09, 30 May 2011 (UTC)

Calm down, calm down. It's not a diagnosis. Should I repeat? Calm down. Want a candy? :D mezzaninelounge (talk) 21:12, 30 May 2011 (UTC)

To clarify, this has nothing whatsoever to do with creationism, or with the pre-modern-synthesis concept of "mutationism". Genes are lost during neutral evolution (forming pseudogenes), but not gained during neutral evolution. This directional lack of symmetry cannot be explained by drift, nor by selection (which is excluded). It can be explained by mutation bias.

The text in question is well referenced. If you have any questions, please please read the Yampolsky and Stoltzfus papers. The earlier of these is in 2001. I think the fact that this is fairly recent explains why textbook coverage of mutation bias is sometimes spotty.

The question here is indeed whether the view is fringe. The 2001 paper has been cited 25 times, neither huge nor tiny. The citations are by varied authors, as far as I can tell all positive takes, including many notable authors writing in high impact journals. Eg, Lynch 2007 PNAS (an author not known for tolerance of fringe views, in an article that is largely a diatribe against them) cites these papers in the positive context "The notion that mutation pressure can be a driving force in evolution is not new (6, 24–31), and the conditions that must be fulfilled if mutation is to alter the direction of evolution relative to adaptive expectations are readily derived..."

If someone wants to write this up as something about which there is a dispute within the scientific community, please go ahead, but you may need to find someone willing to deny, rather than merely ignore, the peer-reviewed arguments of Yampolsky and Stoltzfus and others. I am not sure that you will find this. Maybe if you don't like it, but can't find a suitable reference arguing against the position, you can add something like "Some textbooks do not list..." with citations of those that don't. But one way or another, we need to stick to the references, and there are plenty peer-reviewed at this point supporting mutation bias as a cause of evolution. The position may need to be countered, but based on the current peer-reviewed literature, it should not be ignored. Meantime, I will work on finding and adding more refs.Joannamasel (talk) 21:28, 30 May 2011 (UTC)

I reread, verified, and added the Lynch PNAS ref, and may keep working on adding more to the draft text above.Joannamasel (talk) 22:05, 30 May 2011 (UTC)

As one of the authors (Stoltzfus) of the ideas in question, I'm fascinated by this discussion. I hope that I can offer some clarifying comments. The claim in Yampolsky & Stoltzfus is NOT that mutation is "a mechanism of evolution". This inadequate way of talking about about mechanisms and forces is based on the Modern Synthesis (not Darwin). The Modern Synthesis defined "evolution" as "shifting gene frequencies", i.e., the process of shifing from one complex multi-locus distribution of alleles in the "gene pool" to another. They defined "forces" accordingly, as processes that shift allele frequencies. Selection, mutation, drift and migration are "forces" becuase each can change an allele frequency from f to f + d. If evolution can be reduced to shifting gene frequencies, then the forces or mechanisms of evolution are the processes that shift gene frequencies.

Under various conditions, selection and drift can cause fixations, i.e., shift an allele from a very low frequency to a very high frequency, ~ 1. By contrast, mutation rates are so small that it would take billions of generations for an allele fixation to occur by repeated mutation. This is where the "mechanism of evolution" language comes from, and why Orangemarlin and many others tend to say that selection and drift are "mechanisms of evolution" but other processes are not. This conventional way of thinking equates "mechanism of evolution" with "process that causes fixation". When scientists, particular molecular evolutionists, asks "what is the mechanism of evolution?" in a particular case, they are often asking whether it is selection or drift.

Yampolsky & Stoltzfus expose a flaw in this view, which is that it fails to address correctly the dependence of evolutionary change on the kinetics of the allele origination process. The architects of the Modern Synthesis did not ignore this issue entirely, they just got it wrong. They knew that mutations "ultimately" are necessary to keep the "gene pool" full of variation, but they saw this as a very insignificant thing. They said that selection always found all the variation it needs in the "gene pool", without new mutations. They said that we could reduce "evolution" to "shifting gene frequencies" and everything would be ok.

With different implications, evolution can be understood as a process of the introduction and sorting of variants in a reproductive hierarchy. Yampolsky & Stoltzfus show (using simulations, with some mathematical arguments) that bias in the introduction of variants is a cause of orientation or direction in evolution, and that this kind of causation does not require neutral evolution; they explain that this way of thinking is unfamiliar due to the way that the Modern Synthesis defines "evolution" as "shifting gene frequencies" in the "gene pool", e.g., the "forces" view fails to account for this behavior. Mutation, as origination process, changes an allele frequency from 0 to 1/N. Selection and drift cannot do that. Thus, as Joannamasel suggests, we can see mutation in 2 roles. As a "pressure" or "force" that shifts non-zero allele frequencies, mutation is a weak force and is not a "mechanism of evolution" in the MS sense. As the introduction process, mutation is necessary for evolution, and biases in mutation can impose biases on evolution.

The lesson from this is *not* that mutation should now be counted as a "mechanism of evolution". The lesson is that, in order to understand the facts of evolution, we need to recognize that biases in the introduction process are a true cause of orientation. Such biases are not a feature of selection or drift-- to suggest that would be to make a category error. Biases in the introduction process act at a different step in a two-step process of introduction and fixation. I think Joannamasel understands this, although her understanding would be clearer if she were to use different language.

Is any of this mainstream science? Absolutely not! I said very clearly above that the conventional view of Orangemarlin is based on a wrong theory, namely the Modern Synthesis. Saying that the Modern Synthesis is fundamentally wrong about issues of population-genetic causation clearly is not mainstream. Of course, Wikipedia:Fringe_science is an absurd and insulting category that does not do justice to the way science actually works. But if you want to follow WP rules, you can't say anything that goes against the "forces" theory, even if someone prominent says it. The Fringe_science article says clearly that prominent scientists sometimes support fringe theories. Dabs (talk) 15:11, 9 June 2011 (UTC)

Dabs, I agree with you that "forces" and "mechanisms" are philosophically flawed ways of looking at evolution. I also agree with you that this probably still counts as fringe within professional evolutionary biology today (but interesting, probably not in the field of the PHILOSOPHY OF evolutionary biology). In any case, this is why I did not challenge the current organization of the article around "mechanisms", but instead tried to make-do within that category, defined loosely in practice. For example, it is possible to define evolution in terms of genotype or even allele frequencies without going as far as subscribing to the notion of a gene pool.

That said, while what you say is true about your work, there are also other examples under the new Biased mutation as mechanism text too. Dmitri Petrov's work on the evolution of genome size, driven by insertion vs. deletion biases, stands out. My own work shows that while mutation rates towards loss of function are low, they can still be high enough both to be seen during experimental evolution, and to be much higher than rates associated with genetic drift. See Masel et al. 2007: it does not take billions of generations, Maughan et al. 2007 saw it in 6000 generations. For this reason, one should talk about "loss due to mutational degradation under relaxed selection" rather than "loss due to genetic drift under relaxed selection". These other examples do fit the modern synthesis definition of an evolutionary force. Mutation rates are not lower than the sort of selection coefficients that Fisher believed were important. Joannamasel (talk) 18:36, 9 June 2011 (UTC)

On second thoughts, I think fringe is overstating things. I would call it a minority view within evolutionary biology, there is enough peer-reviewed stuff on it, from a diversity of authors, to exclude it from the definition of fringe. But what I really mean is that the minority is too small, and the material too inaccessible, to warrant hashing out on this very general page. Joannamasel (talk) 18:54, 9 June 2011 (UTC)

Joannamasel, thanks for the references to your work. I agree that some effects of mutation are effects of mutation qua "force". Such effects are included in the MS, e.g., classic deleterious mutation "pressure" (there is a long tradition in population genetics of working on mutational effects, almost entirely concerned with deleterious mutation). But I'm not sure I would agree with how you are describing what is happening in your system. Of course drift cannot be eliminated from any real system, but in an artificial deterministic system based on continuous allele frequencies, we can consider what it means for loss to occur by mutation alone, without drift. If the rate of mutation from A1 (present) to A2 (absent) is m, then the effect of mutation is to increase freq(A2) by m*freq(A1) every generation. Meanwhile, freq(A1) decreases. The kinetics of loss are first-order, so freq(A1) = exp(-mg) after g generations, treating mutation as a mass-action force. If we declare the allele fixation (loss of A1) finished when A1 is down to 1%, this will happen when g = ln(1%)/(-m) ~ 4.6/m generations, e.g., 4.6 million generations if m = 1/million. I said "billions of generations" on the assumption that m ~ 1/billion, but of course some mutation rates are higher. If m ~ 1/1000 then it would be "thousands of generations". What do you mean by "higher than rates associated with genetic drift"? The expected change due to drift is sqrt(pq/N), right? At intermediate frequencies, this will be close to sqrt(1/N). I'm thinking this often will be a considerable effect relative to m. Unless m > sqrt(1/N) in your experimental system, effects of drift are going to be important, aren't they? Probably we should be having this discussion somewhere else. Feel free to contact me by email. — Preceding unsigned comment added by Dabs (talk • contribs) 15:04, 16 June 2011 (UTC)

We probably should take this to email, but anyway, checking with Barton's textbook (p417), the variance after t generations of neutral drift depends on 1-exp(-t/(2N)). I just added that equation to the genetic drift page. In any case, drift becomes incredibly unimportant for moderately large N and intermediate allele frequencies. The strong stochastic contribution comes in with the branching process at low allele frequencies, which depends much less on N. In Masel et al. 2007, we had drift, selection and biased mutation altogether, with drift captured by the Moran model. Eq. 3 based on equation A3 in that paper are the relevant ones for this discussion, with s set to zero in order to look at just mutation plus drift. The important question is whether mN<1. If so, you have the classic neutral drift dynamics taking time N after the mutation destined for drift has happened BUT the waiting time 1/m for this to happen is larger and dominates. If mN>1, then N does enter the equation, but only as logN. Otherwise, you are right, the dynamics do depend on 1/m, and are therefore slow for low mutation rates. But in this mN>1 case, drift would be even slower. So I'm not saying that mutation bias is always a strong force, just that the equations regarding are more descriptive of the process than those concerning neutral drift. Joannamasel (talk) 16:32, 16 June 2011 (UTC)

Dabs, thank you for that comment. It definitely cleared up a lot of questions. mezzaninelounge (talk) 22:01, 13 June 2011 (UTC)

Draft text

The roots of naturalistic thinking in biology can be dated to at least the 6th century BCE, with the Greek philosopher Anaximander.

Early Christian Church Fathers and Medieval European scholars treated the Genesis creation narrative as allegory and believed that natural organisms were unstable and capricious, but the Protestant Reformation inspired Biblical literalism and a natural theology in which the concept of species was essentialist, static and fixed. All entities within a species were seen as sharing a common essence.

As emerging science explored mechanical philosophy in the 18th century, proto-evolutionary ideas were set out by a few natural philosophers such as Pierre Maupertuis in 1745 and Erasmus Darwin in 1796.

The word evolution was first used in relation to development of species in 1762, when Charles Bonnet used it for his concept of "pre-formation", in which females carried a miniature form of all future generations. The term gradually gained a more general meaning of growth or progressive development. The first published modern use of the word has been attributed to the Edinburgh New Philosophical Journal in 1826, edited by Robert Jameson but arguably authored by Robert Edmond Grant.

The Bible-based Ussher chronology of the 1650s had calculated creation at 4004 BC, but by the 1780s geologists assumed a much older world. Wernerians thought strata were deposits from shrinking seas, but James Hutton proposed a self-maintaining infinite cycle. Georges Cuvier's paleontological work in the 1790s established the reality of extinction, which he explained by local catastrophes, followed by repopulation of the affected areas by other species. He held that species were fixed and marginalised the ideas of the biologist Jean-Baptiste Lamarck about transmutation of species which were only taken up by radicals.

Geologists such as Adam Sedgwick adapted Cuvier's catastrophism to show repeated worldwide annihilation and creation of new fixed species adapted to a changed environment, identifying the most recent catastrophe as the biblical flood. In opposition to this view, Charles Lyell adapted Hutton's concept into a stricter uniformitarianism which strongly influenced the young geologist Charles Darwin during the Beagle expedition. Initially Darwin followed Lyell's idea of repeated "centres of creation" of fixed species, but questioned Lyell's views and in 1836, near the end of the voyage, he expressed doubts that species were fixed.

Prior to the work of Charles Darwin, the study of evolution was not scientific. At this time, most natural historians conceived of "species" in terms of essences or ideals; actual individuals were either good or bad examples of the ideal. But natural scientists began to view regular patterns in nature statistically (that is, in terms of probabilities rather than determinism). Thomas Robert Malthus took this approach to human populations in An Essay on the Principle of Population that influenced Darwin. Beginning with Darwin, "species" were conceived in statistical terms; actual individuals were expected to be different, with most diverging from the average form and species were viewed as variable and intergrading units.

Around 1854 Charles Darwin began writing out what became On the Origin of Species.

Darwin formulated his idea of natural selection in 1838 and was still developing his theory in 1858 when Alfred Russel Wallace sent him a similar theory and both were presented to the Linnean Society of London in separate papers. At the end of 1859, Darwin's publication of On the Origin of Species explained natural selection in detail and presented evidence leading to increasingly wide acceptance of the occurrence of evolution. Thomas Henry Huxley applied Darwin's ideas to humans, using paleontology and comparative anatomy to provide strong evidence that humans and apes shared a common ancestry. This caused an uproar around the world since it implied that the creation myth in the Christian Bible was false and humans did not have a special place in the universe.

Debate about the mechanisms of evolution continued and Darwin could not explain the source of the heritable variations which would be acted on by natural selection. Like Jean-Baptiste LamarckLamarck, he still thought that parents passed on adaptations acquired during their lifetimes, a theory which was subsequently dubbed Lamarckism. In the 1880s, August Weismann's experiments indicated that changes from use and disuse were not heritable and Lamarckism gradually fell from favour. More significantly, Darwin could not account for how traits were passed down from generation to generation. In 1865 Gregor Mendel found that traits were inherited in a predictable manner. When Mendel's work was rediscovered in the 1900s, disagreements over the rate of evolution predicted by early geneticists and biometricians led to a rift between the Mendelian and Darwinian models of evolution.

Hugo Marie de Vries was unaware of Gregor Mendel's work and rediscovered the laws of heredity in the 1890s. De Vries suggestedWhile the concept of genes as was originally part of his an alternative mutation theory of evolution. The rediscovery of Gregor Mendel's work provided a better understanding of how variation occurs in plant and animal traits. That , the gene theory ultimately described variation , which is the main fuel used by natural selection to shape the wide variety of adaptive traits observed in organic life. Even though Hugo de Vries and other early geneticists rejected gradual natural selection, their rediscovery of and subsequent work on genetics eventually provided a solid basis on which the theory of evolution stood even more convincingly than when it was originally proposed. At the beginning of the 20th century, Thomas Hunt Morgan was able to demonstrate that genes are carried on chromosomes and are the mechanical basis of heredity. These discoveries formed the basis of the modern science of genetics.

The apparent contradiction between Darwin's theory of evolution by natural selection and Mendel's work was reconciled in the 1920s and 1930s by evolutionary biologists such as J.B.S. Haldane, Sewall Wright and particularly Ronald Fisher, who set the foundations for the establishment of the field of population genetics. The end result was a combination of evolution by natural selection and Mendelian inheritance, the modern evolutionary synthesis. In the 1940s, the identification of DNA as the genetic material by Oswald Avery and colleagues and the subsequentThe publication of the structure of DNA by James Watson and Francis Crick in 1953, demonstrated the physical basis for inheritance. Since then, genetics and molecular biology have become core parts of evolutionary biology and have revolutionised the field of phylogenetics.

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 are used in even more distant disciplines such as psychology, medicine, philosophy and computer science.

In the 1960s, scientists such as W. D. Hamilton and George C. Williams pioneered a extended the gene-centered view of evolution pioneered by the founders of theoretical population genetics, to explain co-operation using, with concepts such as kin selection.

In 1975, E. O. Wilson's book Sociobiology established a significant place for evolutionary theory in psychology, giving rise to the field of evolutionary psychology. Critics argue that the hypotheses of evolutionary psychology are difficult or impossible to test, for example because many current traits probably evolved to serve different functions than they do now. While testing the hypotheses of evolutionary psychology is difficult, it is not impossible. Evolutionary Psychologists say that good evolutionary hypotheses can be corroborated or contradicted by data. The presence that evolutionary theory holds in psychology has been steadily increasing.

In the 21st century, evolutionary biology remains an active field of scientific research.current research in evolutionary biology deals with several areas where the modern evolutionary synthesis may need modification or extension, such as assessing the relative importance of various ideas on the unit of selection and evolvability and how to fully incorporate the findings of evolutionary developmental biology.

Draft text is above, I'm using strikethrough on the old text to mark it for deletion, and bold for new text to summarise it and take its place. Thoughts? Joannamasel (talk) 02:59, 14 June 2011 (UTC)

Joanna, it looks good. But I wonder if we can summarize it even further. I wonder if we need that bit about Thomas Hunt Morgan and how genes are found on chromosomes. Just for clarification, I understand the gene-centered or Neo-Darwinian view started with the modern synthesis even though it was pioneered by Hamiltion, etc. I wonder if we could just mention that the view started with the modern synthesis. Finally, Gould seems to be a major figure and his name is conspicuously absent. A brief mention perhaps? mezzaninelounge (talk) 15:52, 14 June 2011 (UTC)

Agreed, I made the changes for the first two suggestions. As for Gould, if we single out paleontology by mentioning him, we also need to mention George Gaylord Simpson, at which point we may get bogged down by mentioning every other major player in the modern synthesis.Joannamasel (talk) 16:12, 14 June 2011 (UTC)

I don't mean to be pedantic but I had always thought that it was the Hershey-Chase blender experiment that was the key experiment that led to the major conclusion that DNA is the carrier of hereditary information and not the work by Avery. Of course, I could very well be misinformed. In any event, I think the mention of Watson and Crick is more than sufficient, and we could strikeout Avery's name. Finally, I like the edits but I'm left dissatisfied with the last sentence of the entire text. It feels anticlimactic, leaving me with a "so what?". I feel like something more notable needs to be said such as "evolutionary biology remains an active field of scientific research, which has helped explain...." mezzaninelounge (talk) 16:58, 14 June 2011 (UTC)

I don't know the answer to that, but I agree that Watson and Crick are more than sufficient, and struck out Avery. As for the final sentence, there was a move to merge evolutionary biology into evolution, which would obviously solve the problem you mention, but would make the article longer. Otherwise, I think evolutionary biology is hard to sum up accurately in a single sentence. Joannamasel (talk) 17:29, 14 June 2011 (UTC)

Looks good. Give it a couple of days for the peanut gallery. I'm still a little dissatisfied with the last three sentences. They just seem to state facts without finishing off with insights. For example, evolutionary psychology has emerged, but what has it contributed or explained that has given it such staying power? Ditto for the sentence on kin selection. If they don't serve to be informative, then we may as well just delete them. But overall, I think this version is much more concise and on point. What's the consensus (if any) on merging evolution with evolutionary biology? mezzaninelounge (talk) 17:36, 14 June 2011 (UTC)

As a high ranking member of the peanut gallery with extensive credentials, all of dubious merit, in nothing remotely related to the topic (my mother was a microbiologist at the lunar receiving lab so I know what microbiology is....sorta)....The first sentence feels rather abrupt. Maybe it would work better as the tag line of the first paragraph ? Tease the reader a bit and then smack them with it? Regardless it is a really awesome edit. ArtifexMayhem (talk) 01:02, 15 June 2011 (UTC)

Nope, it looks like good writing practice to me, and the superfluous credentials in my pocket agree. Even with the valiant trimming seen so far, this chunk is pretty long, and that paragraph benefits from an executive summary right up front. Give it to them in a form that gets the essential parts of the message across, even when they don't have time to read the whole thing. __ Just plain Bill (talk) 12:43, 15 June 2011 (UTC)

I think the first and third sentences on Hugo De Vries in the fourth paragraph of the proposed draft can be deleted. The second sentence should then be merged with the paragraph that follows. The main focus should be on how Mendel's work complements our understanding of Darwinian evolution. All that information about the rediscovery of his work are unnecessary and distracting. mezzaninelounge (talk) 14:46, 15 June 2011 (UTC)

Attempted, with a few other minor tweaks too. Joannamasel (talk) 16:27, 15 June 2011 (UTC)

Lead Sentence

This discussion has been closed. Please do not modify it.
The following discussion has been closed. Please do not modify it.
I think we should change the lead sentence to include the fact that Evolution is a theory, as it is, it influences the reader to conclude that it is a scientific fact. I changed it to " is the theory that inherited traits found in in one or more populations of organisms change over time. " and was met with comments like "POV" and, "it is the biological phenomenon that the theory describes". This is the page for Evolution, let's not split hairs. The lead sentence is definitely not correct as it stands as it is absolutely necessary to include that it is a theory and I would appreciate it if these unfounded re-edits would ceased.--Jacksoncw (talk) 04:11, 1 July 2011 (UTC) Scientific theories are named after the phenomena they describe: if we wanted to discuss the theory of Evolution, then the page would be titled as such. Ergo, rewriting the lead to say that the article is about the theory and not the biological phenomenon is actually misleading.--Mr Fink (talk) 04:18, 1 July 2011 (UTC) Please see also question 3 of the FAQ at the top of this page and Evolution as theory and fact. --McSly (talk) 04:20, 1 July 2011 (UTC) Furthermore, if we are to talk and rewrite the lead sentence about the "theory" of Evolution, and not the phenomenon of Evolution, (why do you not consider that, itself, to be splitting hairs?) why would we then have the next sentence jump right into describing the very phenomena of Evolution?--Mr Fink (talk) 04:25, 1 July 2011 (UTC) Fink....good job. I haven't run across the "theory" issue in a long time around these parts. Evolution is a scientific fact. PERIOD. OrangeMarlin Talk• Contributions 04:54, 1 July 2011 (UTC) I'm glad you are so confident about your faith in Evolution, orange, but your arrogance doesn't change the fact that Evolution is a theory. That is a fact. PERIOD. This is the page for Evolution, this isn't the page for Evolution the Phenomenon or Evolution in Action or wahetever you would like to call it, this is the page for Evolution, and Evolution is a theory, and as I stated before, it is absolutely necessary to include that in the lead sentence. Apokryltaros, to answer your question, because that is how it works on almost every other page concerning scientific theories and such.--Jacksoncw (talk) 14:36, 1 July 2011 (UTC) Which other pages? I don't see it used in the lead sentence on the theory of gravitation? Joannamasel (talk) 14:45, 1 July 2011 (UTC) Just read some of the FAQ's and it is utter nonsense. How is anyone who didn't read that supposed to understand the colloquial difference or whatever it says. I would love to see the citation for the "observations" that supposedly happened. I don't believe there is any way to adequately warrant not calling this a theory. Those FAQ's just sound like a jumble of wordplay and partly coherent mentions of Wikipedia policies. P.S. Is gravity a theory?-Jacksoncw (talk) 14:50, 1 July 2011 (UTC) What is your position exactly? Are you stating that evolution is not a fact? Are you suggesting that it is a hypothesis instead? mezzaninelounge (talk) 15:02, 1 July 2011 (UTC) Here's an ongoing experiment that has, among other things, directly observed the evolution of new traits in e. coli bacteria (such as being able to "eat" citrate), simply by changing environmental parameters. Mildly MadTC 15:14, 1 July 2011 (UTC) Jacksoncw, it's blatantly obvious that you're trying to push a Creationist-friendly POV by wanting the lead sentence rewritten into a camouflaged version of the old canard of "It's a theory, not a fact." As such, please reread the Boiler Plate at the top of the talkpage, and please remember that the talkpage is for discussing how to improve the article, not a soapbox with which to redefine terms as per your own personal whims.--Mr Fink (talk) 15:30, 1 July 2011 (UTC)

Interwiki ia

Please add ia:Evolution to the list of interwiki links. Almafeta (talk) 09:58, 7 July 2011 (UTC)

• Nevermind, I thought it was protected for administrators only. Almafeta (talk) 10:24, 7 July 2011 (UTC)

Integrative beyond population allele frequencies

I'm lodging my formal complaint against the lead sentence (again!). At some point this article needs to broaden the horizon beyond the prescriptive mode of evolution that made its way into popular media (i.e., Dawkin's selfish gene). Is there a way to present on evolution as it really exists in peer-reviewed journals? The lead sentence is the most narrow definition of evolution that one could derive: Evolution "is the change over time in one or more inherited traits found in populations of organisms." Perhaps, but that is such a small part of it that it really only serves as a useful definition of population genetics. According to that definition there is a fleet of evolutionary biologists in history (e.g., August Weismann) that must have done some other kind of research - because this definition does not cut it. Here is a quote from a recent text on evolution[4]:

"When I was a student, I bought a book that defined evolution as 'a change in the gene frequency of a population'. While evolution does indeed involve change at the population level, it involves changes at other levels too- most importantly at the level of the individual organism, like you and me....The overly population-based approach to evolution is now giving way to a more integrative approach - one in which the process of development that turns fertilized eggs into adults is seen as being important to the evolutionary process in a variety of ways."

Why do the editors of this article insist on the narrow focus? Integrative evolution was pretty much the focus of Stephen J. Gould's career - one of the great evolutionary biologists of all time. Yet this article concentrates on the population genetic level with minor reference to the integrative aspect, which is a biassed distortion of evolution proper.Thompsma (talk) 20:42, 18 July 2011 (UTC)

Here are two articles that talk about the integrative concepts and how they apply: 1. A classic and highly cited paper, Novikoff, A. B. The concept of integrative levels and biology. Science 101, 209–215 (1945) doi:10.1126/science.101.2618.209[5], 2. A modern summary from Nature Scitables, Lobo, I. (2008) Biological complexity and integrative levels of organization. Nature Education 1(1)[6]

Here is what Gould had to say in the Structure of Evolutionary Theory (p. 32):

"Thus, for Darwin's near exclusivity of organismic selection, we now propose a hierarchical theory with selection acting simultaneously on a rising set of levels, each characterized by distinctive, but equally well-defined, Darwinian individuals within a genealogical hierarchy of gene, cell-lineage, organism, deme, species, and clade. The results of evolution then emerge from complex, but eminently knowable, interactions among these potent levels, and do not simply flow out and up from a unique causal locus of organismal selection.

Is Gould wrong? Here is a quote from a recent publication in Evolution[7]:

"Our results demonstrate multilevel selection in nature and stress the importance of considering social selection whenever conspecific interactions occur nonrandomly."

I've stated as much in this discussion forum many times over. Each time a debate ensues and the lead remains narrowly focused. I'm not willing to come in here to debate this issue over and over - I'm waiting for the editors to wake up and see the writing on the wall. Evolution as defined in the lead is narrow and as such - it is incorrect empirically, theoretically, quantitatively, and qualitatively. It isn't even close to how Darwin defined evolution who somehow managed to come up with the theory without single reference to nor knowledge of genes, whereas this article would indicate that genetics is all you need to know.Thompsma (talk) 23:17, 18 July 2011 (UTC)

Here's a great book [8] that outlines this aspect to evolution in simple terms. This article does have it wrong - because life is hierarchical:

"The abstract character of the principal of natural selection, combined with the hierarchical nature of the biological world, implies that selection can operate at levels other than that of the individual organism; and the existence of phenomena that defy interpretation in terms of organismic advantage suggest that this has actually happened...Weisman (1902) wrote that the 'extension of the principle of natural selection to all grades of vital units is the characteristic of my theories...this idea will endure even if everything else in the book should prove transient, (quoted in Gould (2002, p. 223)." - Whole quote from Okasha[9]

Okasha provides a very up-to-date chronicle of evolution as it has been presented in the scientific literature. This article would suggest that the only causal entities responsible for evolution are genes, which is a debilitating view of evolution and misses the richest history that has given rise to a better understanding of what evolution is. Darwin, Weisman, Maynard-Smith, Richard Lewontin, Edward Wilson and many other evolutionary biologists have written extensively on the hierarchical aspect to evolution that is nearly ignored in this article.70.77.232.44 (talk) 00:54, 24 July 2011 (UTC)

Proposed change to lead:

"Evolution (also known as biological or organic evolution) is the change over time in one or more inherited traits found in populations of individuals. Each organism is composed of organs and tissues, which are composed of cells with organelles and at the molecular scale genes reside in a nucleus. This is known as the hierarchy of life with smaller components nested into larger structures. Principles of evolution apply to different levels in the hierarchy of life. For example, individual genes form populations that give rise to new populations of genes just as individual organisms aggregate into populations, reproduce, and then give rise to new generations of organisms. The multi-level aspect to evolution means that conflicts can arise across levels. What is beneficial at one level, such as selfishness, may not benefit a larger group, which can give rise to altruistic behaviours that seems to go against ones sense of self-preservation."

This could be shortened and I'm sure not everyone will like it. However, I am hoping that it could at least get the discussion started on how we can integrate the evolutionary concepts properly.70.77.232.44 (talk) 01:21, 24 July 2011 (UTC)

I'm fine with the content, but I don't think it belongs in the lead of this article. For example, before one can understand a conflict in selection between levels, one has to know what selection is. Exposition of this is clearest at a single level, with across-level complexities arising later. Other topics need to be explained first, before this material can be covered. Also, I would avoid mentioning a "sense" of self-preservation, since this applies independently of whether an organism can be described as having such senses. Joannamasel (talk) 15:59, 24 July 2011 (UTC)

Thanks Joannamasel...I agree entirely with what you've said. I didn't realize yesterday that I hadn't signed in - those were my posts. The goal was to give a general overview of the larger viewpoint that is missing and so I hope that we can make is clear from the onset that the hierarchical view has a strong scientific legacy and role in evolution. Genic selection is a causal process, whereas a genes eye view - what this article presents - is a perspective on evolution. The point of paragraph was just to get the discussion started on the expanded synthesis. This article mainly presents on one theory of evolution, but it is actually different from what Darwin originally presented and from where evolution has been making its greatest advances in the past 30 years or so. It is biased toward a Dawkin's perspective - where he has even stated that 'selfish' wasn't the best choice of words, the 'eternal' gene would have been better. He makes an error stating that genes are the only survival machines - all other complexes have been lost only the genes have survived. I disagree - and so do others. If this where true - why would I have a notochord in the same way that amphioxus has a notochord? It seems to me that notochords are surviving just as well. This is where the concept of burden comes into play - which is a rejection of the gene's eye perspective and genic selection as the sole causal explanation.Thompsma (talk) 18:51, 24 July 2011 (UTC)

In case people are unfamiliar with the concept of Rupert Riedl's burden in evolution, here are a few papers that can assist: [10], [11], [12]. In Okasha's (2010) words, here is where I see fault with this article:

"Usually when we think about selection, we think of it acting at the level of the individual organism, favouring the fittest individuals over the less fit and thus leading to evolutionary change. But individual-level selection is only one possibility among many. For the key requirements of evolution by natural selection — variation, associated differences in fitness and heritability — can in principle be met by entities at many levels, above and below that of the individual organism."

This article mainly presents the singular evolutionary theory - genetic-level selection. In its emphasis on the gene - the article misses the organism-level principles of evolution that Darwin's book was about and the way that evolution was primarily exposed prior to the advances in allozyme electrophoresis and (more recently) Sanger molecular sequencing technology. I particularly like how Okasha highlights the faulty logic of the Dawkin's genetic only model[13]:

Consider for example Richard Dawkins’ brief discussion of how independently replicating units may originally have become grouped into compartments. Dawkins says that it is ‘easily understood’ why independent replicators might have gained an advantage by ‘ganging up together’ into cell-like compartments, because their biochemical effects might have complemented each other (1982, 252). This is a plausible idea, but what Dawkins fails to realize is that it in effect invokes group selection.

As much as I admire Dawkins - it is apparent that he is out of touch with modern evolutionary theory - as is noted in his 2010 article in Science where he wrote about George Williams:

"It is only the meiotically dissociated fragments of the genotype that are transmitted in sexual reproduction, and these fragments are further fragmented by meiosis in the next generation. If there is an ultimate indivisible fragment it is, by definition, ‘the gene’ that is treated in the abstract discussions of population genetics.” (<-This is Williams quoted by Dawkins.) Quite so. Williams efficiently disposed of “group selection,” which never recovered (except as a muddled version of kin selection)."

Dawkins is wrong on two counts - the first is that he supports Williams notion that the indivisibility of the gene is what makes it the eternal unit of evolution. As we well know - there are other major evolutionary transitions and burdened complexes that have persisted in like fashion to the indivisible gene; multi-cellularity, for example has persisted for quite some time like an indivisible unit (see Maynard Smith and Eors Szathmary for other examples of major evolutionary transitions). His second critical error is that Williams did not dispose of group selection - because it is still alive and an active area of research. It is astonishing that Dawkins would dismiss this - even if he disagrees with the idea, it is an active area of investigation in peer-reviewed literature where many scientists have concluded in favor of group selection.

I've gone through this in detail - because this article gives the Dawkins perspective of evolution. The second paragraph explains the mechanism of evolution in four parts. The first allows for traits (but it is still a genic view). The second mechanism is 'genetic drift'...the third mechanism is 'mutation, which is a permanent change in a DNA sequence...the fourth mechanism is 'gene flow'. It is all genetic!!! That is a narrow perspective on evolution and it disregards the expanded synthesis that has stated (experimentally, empirically, quantitatively, and qualitatively) that not all causal explanations extend from the genetic mechanisms as outlined herein. I think what is going on here is an extension of techno-hype in favor of the gene - because it looks fancy, technical, and very new - the latest showing how science can 'see' things even at the molecular level!! Bah...who needs to look at the antiquated morphologists when we have this new and fancy genetic technology that can tell us about the wonders of the world. The problem with this viewpoint is that it is inaccurate and wrong.Thompsma (talk) 04:31, 25 July 2011 (UTC)

Last picture

"As evolution became widely accepted in the 1870s, caricatures of Charles Darwin with an ape or monkey body symbolised evolution." I could not find a better alternative but calling the caricature (which is really a satire or a ridicule of Darwin by those who did not evolve with his scientific reasoning) a symbol of evolution? Is there perhaps a way to ameliorate this sentence because frankly it feels a bit disrespectful and inaccurate. This sentence more reflects an anti-evolutionary perspective and so shouldnt the caption capture the sentiment? Cheers Dr. Persi (talk) 23:11, 21 July 2011 (UTC)

It's a good picture. Brings to mind things like the Scopes Monkey Trial. I don't see it as insulting or showing a bias. I think the caption should say something like "Darwin and monkeys became symbols of evolutionary theory as the ideas were popularized." Modinyr (talk) 07:23, 23 July 2011 (UTC)

What the picture shows is that ordinary people care about the theory of evolution for reasons quite different from most evolutionary biologists. Most evolutionary biologists (and I am happy to be corrected) want to understand the diversity of life on the planet and the modern synthethis provides a great paradigm for making sense of this diversity and generating new research proposals (baldly: proposals for external funding). Ordinary people recognize that the theory has profound implications for how one views humanity (a step below the angels no more ... now a step above the apes). This seems to bug an awful lot of people in ways that the average scientist finds hard to understand (how many evolutionary biologists think that the proposal to prohibit the teaching of evolution is "understandable?") Without taking sides, I think the article should acknowledge this particular divide. Slrubenstein | Talk 18:24, 24 July 2011 (UTC)

You make a good point. There is a big divide between people's understanding of evolution and what scientists in the field actually do. I still like the picture. I think it is hitting that concept of people's misunderstanding of Darwin and his ideas. So to get back to the caption, I think it works.Modinyr (talk) 22:46, 26 July 2011 (UTC)

Fixing the error in the lead

To save people time, I am posting my proposal at the top of this thread. After thinking this through, I realized that the entire lead needed a re-write to properly present the integrated view of evolution. Feel free to disregard the remainder of this thread, because it outlines my development of thought as I tried to enlist feedback, but received none.Thompsma (talk) 05:17, 27 July 2011 (UTC)

I propose the following fix:

Evolution (also known as biological or organic evolution) is the change over time in one or more inherited traits found in populations of individuals. All of life exhibits the properties of reproduction, heritability, and variation in traits among individuals and this embodies the core principals of evolution by means of natural selection. Inherited traits are particular distinguishing characteristics, including anatomical, biochemical or behavioural characteristics, that are passed on from one generation to the next. Evolution may occur when there is variation of inherited traits within and among populations. Evolutionary science explains natural patterns, such as adaptations or seemingly random events. Traits that enhance an individuals chances of survival become adapted to the environmental pressures shaping the character, appearance, or phenotype of individuals over time. The extensive mechanics of evolution applies not just to organisms, as it is generally introduced, but to nested and integrated units of genes, cells, organs, species, or any kind of individual that fits into the biological hierarchy. Populations of individuals aggregate and nest into a larger collective and become the units of evolution that form the subjects of scientific inquiry. Evolution has led to the diversification of all living beings from a common ancestor, which are described by Charles Darwin as "endless forms most beautiful and most wonderful".[6]

There are four common mechanisms of evolution at the genetic level that helps to explain how evolution operates generally across the biological hierarchy. The first mechanism is natural selection, a process that leads to differential survival in the multiplication or reproduction of functional genes that differ in one or more heritable traits. In the case of genes, the heritable traits are the templates of DNA sequences that replicate near exact copies through the simple mechanics of biochemical bonds (Watson-Crick base pairing) that ensure a match between newly replicated DNA strands and the original template. Natural selection describes the processes in nature that determine what DNA copies survive and preserved into subsequent generations. A second mechanism is genetic drift, a process in which there are random changes to the proportions of two or more inherited traits within a population.[7][8] A third mechanism is mutation, which is a permanent change in a DNA sequence. Finally, the fourth mechanism is gene flow, which is the incorporation of genes from one population into another.

This gives a more correct explanation of evolution by placing genetic evolution in context of the more extensive hierarchy.Thompsma (talk) 16:59, 25 July 2011 (UTC)

I'm not a fan of the third sentence as it is currently written: "Inherited traits are particular distinguishing characteristics, including anatomical, biochemical or behavioural characteristics, that are passed on from one generation to the next." - I think a definition of phenotype would be better. For example: "Inherited traits (e.g., eye color) may have variable states (e.g., blue vs. brown eyes) that define the observable phenotype of an individual (e.g., one individual has blue eyes while another has brown eyes). Traits are the elements that distinguish individuals from each other and can include anatomical, biochemical or behavioural characteristics." If we can define phenotype early on in this article - it will help to fix the confusion that has resulted toward the prime emphasis on genic evolution.Thompsma (talk) 18:02, 25 July 2011 (UTC)

The second paragraph still has a few kinks - the sentence on natural selection is cumbersome, so I offer the following:

There are four common mechanisms of evolution at the genetic level that helps to explain how evolution operates generally across the biological hierarchy. The first mechanism is natural selection, a process that leads to differential survival in the multiplication or reproduction of functional genes that differ in one or more heritable traits. In the case of genes, the heritable traits are the templates of DNA sequences that are arranged in an orderly pattern or string of nucleotides (A, G, C, T). The sequence of nucleotides is replicated into near exact copies through the simple mechanics of biochemical bonds. This ensures a match between newly replicated DNA strands and the original template. Natural selection describes the processes in nature that determine what DNA copies survive and are preserved into subsequent generations. Hence, the conditions for natural selection are satisfied, namely: variation in a population of genes, differences in reproductive output where some genes replicate more readily than others (i.e., fitness differences), and heritability through the mechanics of Watson-Crick base pairing. A second mechanism is genetic drift, a process in which there are random changes to the proportions of two or more inherited genetic traits within a population. Genetic drift refers to neutral genes that exhibit an equal chance of replicating into subsequent generations when there is no clear relationship between the fitness of a genetic trait and its performance. A third mechanism is mutation, which is a change in a DNA sequence either by single nucleotide substitution (e.g., A to C, or G to T) or by wholesale duplication of an entire gene within a genome. Finally, the fourth mechanism is gene flow, which is the migration of genes from one population into another. This last mechanism (gene flow) exhibits the multi-levelled aspect to evolution. At one level, genes code the information of traits that develop within an organism and at another level these genes are exchanged amongst populations. Evolutionary biologists may query the mechanics of genetic evolution in a developmental context of individual fitness, such as what genes and mutations lead to different developmental outcomes. Alternatively, they may query the mechanics of genetic evolution in a larger population context, such as what genes spread more readily or are extinguished from one population to another.

I hope this helps.Thompsma (talk) 18:28, 25 July 2011 (UTC)

In an effort to summarize, make this very clear, and to organize the structure of the paragraphs, here is the proposed change to the lead in total:

Evolution (also known as biological or organic evolution) is the change over time in one or more inherited traits found in populations of individuals. All of life exhibits the properties of reproduction, heritability, and variation in traits among individuals and this embodies the core principals of evolution by means of natural selection. Inherited traits (e.g., eye color) may have variable states (e.g., blue vs. brown eyes) that define the observable phenotype of an individual (e.g., one individual has blue eyes while another has brown eyes). Traits are the elements that distinguish individuals from each other and can include anatomical, biochemical or behavioural characteristics. Evolution may occur when there is variation of inherited traits within and among populations. Evolutionary science explains natural patterns, such as adaptations or seemingly random events. Traits that enhance an individuals chances of survival become adapted to the environmental pressures shaping the character, appearance, or phenotype of individuals over time. The extensive mechanics of evolution applies not just to organisms, as it is generally introduced, but to nested and integrated units of genes, cells, organs, species, or any kind of individual that fits into the biological hierarchy. Populations of individuals aggregate and nest into a larger collective and become the units of evolution that form the subjects of scientific inquiry. Evolution has led to the diversification of all living beings from a common ancestor, which are described by Charles Darwin as "endless forms most beautiful and most wonderful".[6]

There are four common mechanisms of evolution at the genetic level that helps to explain how evolution operates generally across the biological hierarchy:

• The first mechanism is natural selection, a process that leads to differential survival in the multiplication or reproduction of functional genes that differ in one or more heritable traits. In the case of genes, the heritable traits are the templates of DNA sequences that are arranged in an orderly pattern or string of nucleotides (A, G, C, T). The sequence of nucleotides is replicated into near exact copies through the mechanics of biochemical bonds and replication enzymes. This ensures a match between newly replicated DNA strands and the original template. Natural selection describes the processes in nature that determine what DNA copies survive and are preserved into subsequent generations. Hence, the conditions for natural selection are satisfied at the genetic level, namely: variation in a population of genes, differences in reproductive output where some genes replicate more readily than others (i.e., fitness differences), and heritability through the mechanics of Watson-Crick base pairing.
• A second mechanism is genetic drift, a process in which there are random changes to the proportions of two or more inherited genetic traits within a population. Genetic drift refers to neutral genes that exhibit an equal chance of replicating into subsequent generations when there is no clear relationship between the fitness of a genetic trait and its performance.
• A third mechanism is mutation, which is a change in a DNA sequence either by single nucleotide substitution (e.g., A to C, or G to T) or by wholesale duplication of an entire gene within a genome.
• Finally, the fourth mechanism is gene flow, which is the migration of genes from one population into another.

The last mechanism (gene flow) is a prelude to the multi-levelled aspect to evolution. At one level, genes code the information for traits that develop within an organism. At another level, however, these genes are exchanged and selected amongst populations. Hence, evolutionary biologists may query the mechanics of genetic evolution in a developmental context of an organisms fitness, such as what genes and mutations lead to different developmental outcomes. Alternatively, an evolutionary biologist may query the mechanics of genetic evolution in a larger population context, such as what genes are extinguished or spread more readily from one population to another. This hierarchy of life is itself the product of evolution. The principals of evolution that were detailed in Charles Darwin's Origin of Species explain and apply generally to any level in the hierarchy produces offspring in like manner, such that genes give rise to genes, cells give rise to other cells, colonies give rise to other colonies, and so on through the hierarchy.

Thompsma (talk) 21:02, 25 July 2011 (UTC)

Realizing that the suggested changes are way too long - I wanted to stimulate the discussion - I have been whittling this down in size in my sandbox. My primary goal here is to fix the error in the lead that would suggest that genetic evolution explains the entire theory. Please feel free to comment. Now that it has been brought down to a manageable size - I will next be adding wikilinks and citations.Thompsma (talk) 20:54, 26 July 2011 (UTC)

Citations and wikilinks have now been added in my proposal for a new lead to fix the mistake of a genetic only viewpoint. I'm looking forward to comments and feedback. I borrowed some of the citations from this article - but noticed that the formatting is a bit chaotic. This article is in need of a serious clean-up.Thompsma (talk) 22:53, 26 July 2011 (UTC)

Claim made re) Huxley

Hello. Just passing by. Read this splendid article and came across this passage: "Thomas Henry Huxley applied Darwin's ideas to humans, using paleontology and comparative anatomy to provide strong evidence that humans and apes shared a common ancestry. This caused an uproar around the world since it implied that the creation myth in the Christian Bible was false and humans did not have a special place in the universe.[24]" Is this precisely true? In her two-volume biography of Darwin, and in her recent "biography" of Origin of Species, Janet Browne states that most Victorians had long since ceased to believe in the literal truth of the creation myth in Genesis by the time Darwin wrote Origin. Rather, the problem, as so many of Darwin's contemporaries saw it, was that evolution by natural selection would, as the second part of the quotation above states, deny that humans had a special place in the universe and, moreover, deny that there was a necessary role for an interventionist creator in the origin of modern species. As Browne put it, "We have a fundamentalist problem - they did not." (Not an exact quotation - my copy of her book is in my office.) I can provide citations if you like. --99.249.6.237 (talk) 21:59, 10 July 2011 (UTC)

I fail to see support in the Britannica article that the public reaction to Huxley was due to his stance on human evolution. This may be true, but I don't see where the article says it. Matthew Ackerman (talk) 15:51, 21 July 2011 (UTC)

Just to follow up on the comment I made above on 10 July, the reference to which I referred was on page 86 of Janet Browne's Darwin's Origin of Species: A Biography and is elaborated on in her two-volume biography. Surely some regular editor of this article would like to improve it by adjusting that claim made re) Huxley? --Ggbroad (talk) 12:06, 8 August 2011 (UTC)

Well, I'm something of a highly irregular editor, but I'll go ahead and cut the sentence out since there hasn't been any objection to your comment. Matthew Ackerman (talk) 02:53, 9 August 2011 (UTC)

Looks like the change has already been made. Matthew Ackerman (talk) 02:55, 9 August 2011 (UTC)

Ready to change the lead

I have now sufficiently revised a new version of the lead to fix some of the mistakes that exist in the current version. My version is a bit more lengthy, but with some help I hope that it can be truncated. With the new lead I hope that this article will take a turn toward a more integrative approach. Many of the sections in this article are superfluous and miss the main thesis of the topic. Without a proper lead giving an introduction to the hierarchical perspective it has been very difficult to develop and/or discuss any of the modern evolutionary ideas that follow. For example, there is no section on homology (a major gaping hole), phylogenetics (cladistics, systematics, parsimony), paleontology, or even a developmental section on growth and form (explaining heterochrony). Once a hierarchical perspective is put into place we can disregard the gene reductionist perspective that has biased the content herein and start anew to set off on a more current view that will explain what evolution is really about. I will leave this open for discussion - but I am hoping that we can get this done soon, because this has been debated to death and it is glaringly apparent that the lead as it stands is erroneous, disjointed, and hardly worthy of featured article status.Thompsma (talk) 22:58, 28 July 2011 (UTC)

The following sentence is misleading: Genetic drift refers to lineages of neutral genes that exhibit an equal chance of replicating into subsequent generations when there is no clear relationship between the fitness of a genetic trait and its performance. The magnitude of genetic drift is not affected by fitness. Sometimes a favorable allele is lost because of drift. It is also repetitive, neutral and no clear relationship between fitness and performance. It is using the word performance in an obscure way. Fitness IS expected reproductive success. If performance is not reproductive success, what is it? Suggested replacement: Genetic drift is significant for gene variants that have small effects on reproductive success. --Ettrig (talk) 08:26, 29 July 2011 (UTC)

Thanks for the feedback Ettrig. Some of the confusion here may be related to the term fitness - I was expressing it in the way that it is commonly applied in population genetics - reproductive output or expected number of offspring. Or, as John Endler put it (which is the source I turned too when writing that statement): "a consistent relationship between that trait and mating ability, fertilizing ability, fertility, fecundity, and, or, survivorship: fitness differences" -(see: [14] - read pages 4-5). Endler follows on his excellent definition of natural selection with an explanation of genetic drift. My statement is repetitive, because I thought it was prudent to follow-up with a definition of 'neutral' in case new readers didn't know what that meant and to re-enforce its meaning. My statement is actually saying that the magnitude of genetic drift is not affected by its performance - there is no covariance between performance and fitness. In other words - the reproductive output has nothing to do with how the trait performs, because it is blind to the forces of natural selection and drifts stochastically. "If performance is not reproductive success, what is it?" - I was thinking of it in terms of how an adapted trait would perform its functional utility - you can think of it in how a tool might perform in its task. In my attempt to make this a short statement - I think the meaning must have been lost?? Actually, when I read it again it makes perfect sense to me, but that is not always a good guide. I don't understand your suggested replacement - it doesn't define what genetic drift is. Can we find an alternative? I suggest using Endler's simple example as a source. Daniel Hartl usually has simple definitions for this kind of stuff as well - I'll see what I can come up with.Thompsma (talk) 16:34, 29 July 2011 (UTC)

Perhaps: "Genetic drift refers to lineages of neutral genes that exhibit an equal chance of replicating into subsequent generations when there is no clear relationship between the fitness of a genetic trait and its performance. In other words, the reproductive output (i.e., fitness) is random and not related to the way a trait functions or performs its task (if it even has one) in a population." - it is a bit convoluted perhaps - but you can appreciate the difficult in summarizing or explaining fitness in so few words. Fitness has several meanings - such as the way that a trait is fitted to its purpose, or the way that we use it colloquially as I am very fit because I run, and then the way it is used in population genetics as in reproductive output spanning generations. Some people get confused with neutral genes and think that they only refer to genes that have no functional purpose such as 'junk DNA'. While non-utility, such as the wobble position in the third position of a codon is a good place to find neutrality, it is also true that functional genes can be neutral with respect to each other - they may have equal capabilities and so they are effectively neutral with respect to each other, one is no more superior to the other and this is especially true in larger populations.Thompsma (talk) 16:50, 29 July 2011 (UTC)

Daniel Hartl defines neutrality like so[15]: "Suppose that some new mutations are selectively neutral, which means that they have no effects on the ability of the organisms to survive and reproduce..." - replace ability with performance: "Suppose that some new mutations are selectively neutral, which means that they have no effects on the performance of the organisms to survive and reproduce..." and you can appreciate the semantics here.Thompsma (talk) 16:59, 29 July 2011 (UTC)

The problem with using ability vs. performance is that ability implies that they have a functional utility - that they are adapted for some purpose. In contrast, performance is more generic: "manner or quality of functioning: a machine's performance" or "any accomplishment"[16]. I changed the sentence in the sandbox - perhaps I have fixed the problem?

This is actual a complex and subtle matter, so requires a lot of thought. I did a bit of research and thought this through. I think I can explain. If you were to watch a play you would see a performance. At the end of a show the audience could say that the performance went well, poorly, or neutral. You can imagine the performers (genes) acted in all sorts of ways and the audience was neutral in opinion. This is what I mean - covariance between trait fitness and performance = selection, if there is no correlation between the two, then you have random genetic drift. It made no difference how the genes performed.Thompsma (talk) 02:09, 30 July 2011 (UTC)

First, to address the genetic drift question. Genetic drift is not consistently defined in the primary literature. The most common explicit definition is random sampling of gametes. One common implicit definition, which was explicit for Wright himself as well as for a few others, is any stochastic rather than directional change in allele frequency, for any cause (including selection, eg at linked sites). Another common but hard to defend implicit definition is every change in allele frequency not due to selection. If you use the first definition, you need to be careful not to claim that genetic drift is important, since this has never been proven. The second definition is the one used in the current lead, with the article subsection on drift being a bit of a fudge between the first two definitions.

Second, about the changes in general. I am sympathetic to the hierarchical POV, but I still think it is a POV, and probably a minority one in the professional field at large. I agree that that the hierarchical POV should be addressed. I think the best way to do this is to add a short, balanced section somewhere other than the lead, and also to make minor edits throughout the article so that those sentences that apply across multiple levels do not contain gratuitous reference to one particular level. That short balanced section, once written, could then be appropriately summarised in a single sentence in the lead. The lead should be a summary of the article, and if the article is deficient, this should be addressed before the lead is changed. I prefer the existing lead to the proposed new one, and I think we should proceed through smaller modifications to the existing one.Joannamasel (talk) 16:17, 30 July 2011 (UTC)

Unfortunately you are incorrect on a couple of points Joannamasel. Foremost, you will note that the new lead is cited using extensive peer-reviewed literature on the hierarchical context. You could argue that Darwin's evolutionary theory is a POV using your same logic and it would be equally as unconvincing. I'll leave it up to the scientific peers to determine if it is a working scientific theory and indeed it is. Moreover, we are not in here to report on majority of opinion - even though you are incorrect that the hierarchical view is a minority. It is part of the extended synthesis and it is being reported in Nature, Science, Evolution, and pretty much every journal on evolutionary theory. The current lead cannot stay - because it is incorrect. It is not giving the correct view on evolution - it isn't that we need a small section explaining the hierarchical view. The hierarchical view began with Darwin and stayed throughout the history of evolutionary theory - it is integrated with it. The current lead suggests that genic evolution explains the entire theory - and this is incorrect. I suggest that you read through some of the literature I cited. Here are some notable ones that will give you insight in this direction:

• Gould, S.J. (2002). The Structure of Evolutionary Theory. Cambridge: Belknap Press. ISBN 0-674-00613-5.
• Okasha, S. (2007). Evolution and the Levels of Selection. Oxford University Press. ISBN 0-19-926797-9.
• Hall, B. K. Evolution: Principles and processes. Jones & Bartlett Learning. p. 400. ISBN 0763760390.
• Pigliucci, M. "Do we need an extended evolutionary synthesis?" (PDF). Evolution. 61 (12): 2743–2749. doi:10.1111/j.1558-5646.2007.00246.x.
• Pigliucci, M.; Müller, G. B., eds. (2010). Evolution—the Extended Synthesis. MIT Press. p. 504. ISBN 0-262-51367-6.

I'm actually finished making this argument. I'm tired of going over and over this. Either read the literature, understand it, and return here to help reduce the size of the text of the lead - or drop the erroneous idea that multi-level selection is not true. I'm a scientist and I trust my peers. Read the literature. Correct the erroneous presentation in this article.Thompsma (talk) 18:46, 30 July 2011 (UTC)

I never said that multi-level selection is not true or a POV. What I am saying is that the centrality of multi-level selection to evolutionary thought as a whole is a POV. Saying something is true and saying something is central are not the same things. Even a proponent such as Pigliucci phrased his title as the question "Do we need...?" in a speculative piece whose subject was the likely direction of future research. In other words, he openly acknowledges that this is a POV. There is no dispute that multi-level selection is true. I support discussing it in this article. I do not support discussing it only in the lead of this article, and not in the body. If you think the current lead is incorrect, please point to which sentence is incorrect. The same applies to the body of the article. Your criticism seems to be about the balance of the lead, rather than its components. An unbalanced lead is not the same thing as an incorrect lead.Joannamasel (talk) 19:12, 30 July 2011 (UTC)

Thompsma, with respect to your new lead, I have just two suggestions:

1. The proposed new definition of natural selection is more gene or molecular centric than the current one (which I find a little ironic). I prefer it if it refers to differential survival of "individuals" that differ in one or more inherited traits. I think we can leave the details on gene sequence and replication enzymes in the main body of the text. Plus, I'm not familiar with traits being defined as DNA sequences. At least, that it how it appears to me.
2. As a matter of style, I don't think it's necessary to say "The last mechanism (gene flow) is a prelude to the multi-leveled aspect to evolution." If it is, then just state it as "gene flow may result in selection at multiple levels.... and thus selection is therefore hierarchical" or something like that. I think if the writing style was changed in a way that introduces the concept of multilevel selection in a "not a big deal" sort of way, it won't appear awkward or attract attention of POV. My two cents. mezzaninelounge (talk) 19:16, 30 July 2011 (UTC)

In response to Joannamasel - it isn't that the lead is just unbalanced, it is incorrect and I've tried picking it apart piece by piece in the past - it was a complete waste of my time. Hence, I've given a re-write. It is incorrect because it suggests that evolution is just a genetic phenomenon - when it isn't. Charles Darwin gave us the hierarchical view of evolution and saw the generality of the principals and even extended his discussion into macroevolutionary theory.[17] Following Darwin, we had Weismann (1902) who wrote (as I stated above): "extension of the principle of natural selection to all grades of vital units is the characteristic feature of my theories...this idea will endure even if everything else in the book should prove transient.."[18] He was not alone in this way of thinking and so the multilevel perspective has been in the literature all along - Sewall Wright even wrote about this stuff. You could argue that Gould was just giving us his POV and that he wasn't a central figure in evolutionary biology - but then you would be wrong. He devoted his entire career on the hierarchical nature of evolutionary principals. More than a perspective - multilevel selection is a causal process; there are peer-reviewed publications demonstrating this, several recent and historical examples of this exist - here's one in Evolution[19]. Hence, it is not a POV - it is a causal process and I can provide you with the literature showing the evidence to support my claim. In contrast - your posts are just POVs - please provide citations to support your 'feeling' that it is 'just a theory' (sound reminiscent?). Don't just refer to the title of one article I provided - lame - once again - read deep into the literature and then return to discuss the matter when you are properly informed and prepared to do so. It is apparent that you are ill informed. Here's an intro to a POV - think of the way that Dawkin's talk's about his "gene's-eye view" - think about that metaphor for a moment. A view is a perspective. However, genic selection is both a perspective and a causal process in its own right - it is a distinct level of selection of its own. Species level selection is also important - and you should read up on the history of the founder-flush and genetic revolution models of speciation - where there is experimental evidence for this[20] - and if you can access this article[21], Alan Templeton does a great job discussing the importance of these events - even if they are rare. Once again, reading this lead and having an understanding of these models for speciation - you couldn't account for them, because the lead gives an incorrect description of what evolution is. Niche construction, eco-evo-devo modularity, Vrba's emergent characters, and punctuated equilibrium are other areas that have had central roles in evolutionary literature - all multilevel evolution. If you read the lead to this article - the authors working and publishing in these evolutionary fields (by the definition in this lead) are not doing evolutionary research. Here is a link to a well-written book on evo-devo [22] - read it and then read the lead to this article; or, if you don't have time, turn to page 169 and read chapter 7. Why are these important contributions being excluded?

In response to mezzaninelounge - I have no idea why you would find it ironic that I would provide a cogent explanation of genic evolution? First I work full-time as a geneticist. Second, genes are potent replicators and I am an admirer of Dawkin's and George Williams work in this regard. I enjoyed reading selfish gene many years ago precisely because it gave such a simple introduction to the mechanics of evolution that could be easily understood at the genic level. This is one reason why I think people are favoring this approach - it is much simpler to understand from the gene's-eye view. Multilevel evolution requires a great depth and insight into the subtleties of evolutionary science - reading through Maynard Smiths ESS's through the multilevel lens and Lewontin's distinction between selection for fitness vs. a trait is a mind twister. I appreciate the difficulty, but it has been a persistent component of evolution and it makes it very difficult in other parts of this article to explain certain things without this introduced in the lead. I'm not sure what you mean about referring to "individuals" - because that's what I have done in lieu of "organisms". I've worked as a geneticist for the past eight years at a university - so I hope I am qualified enough to define a genetic trait, but that would be an ad hominem argument and I frown on that approach. However, a trait is a difficult thing to define in precise scientific terms and it would take a while for me to go through the history of this - it is a job for a long-winded philosopher. I worked in a paleontology lab for many years where we debated the meaning of trait, state, character, in context of morophology vs. DNA in phylogenetics, cladistics, and homology at great length. Interestingly, you will find that few papers actually define the term trait - it is more of a colloquial term, character is what you will find in most instances. However, if you are dealing with a DNA sequence you have a four multi-character state table (AGCT) - simple morphological characters are binary (present/absent). In a DNA sequence - the character is the position in the alignment and the state is the nucleotide that occupies that position - because you must assume homology based on nucleotide position - if you are dealing with introns of different size, you have to use more complex alignment software to determine positional homology. The sequence itself is the trait. For example, a unique allele is a trait (e.g., search "allelic trait"). What is an allele? Answer: it is a unique DNA sequence. Hence, "heritable traits in genes are the orderly templates of DNA sequence that are preserved through copied lineages that stem from an original template."

In response to the second part of mezzaninelounge's comments - perhaps you missed the big <<CUT>> that I had included at the end? Perhaps I should have made it more clear that it was <<CUT>> from the proposal? You are commenting on the part that I had <<CUT>> from the proposal. Those are my notes as I was going through and revising the work - so I will just disregard that part of your comments. Please don't waste your time reading the stuff below that - I wrote the rest of that stuff on a 3am blitz from the top of my head.

It is very important that we get this correct - it should be clear to everyone in here how important evolution is from the way that we look at our society to medical research (I am of the opinion that you can really only understand cancer or immune response apoptosis through a proper multilevel perspective). I will state it again to be clear - THE CURRENT LEAD IS INCORRECT, it fails, it is wrong - it does not give an introduction to what evolution is - it is a very narrow introduction to genetic evolution (not a good one either) and that is it. Call me crazy - but I read about evolution every single day until I fall asleep - it is my passion; I have thousands of books in my personal library devoted to this subject. Unfortunately, this knowledge is only useful for wikipedia stuff - it doesn't employ me very well beyond the few undergrad courses I teach. I have a very deep insight into this area - and when I read this article it falls flat. Moreover, I'm not trying to present on my own insight in the points I am trying to get across in here - I keep providing links to citations. I try to find citations that are freely accessible, because I have a lot of other historical books and stuff that you can't find online. I can keep giving link after link in here to the extended synthesis - but that doesn't seem to be working based on the comments that keep coming back - people are not reading the literature and just post their opinions without linking to the literature. All I'm asking - is that people accept that I am using reliable sources and it is my understanding that generally this qualifies for the addition of material into wikipedia. Hence, there is a sufficient mass of literature and expertise on the multilevel evolutionary perspective, published evidence on it as a causal process, and an explosion in the past 20 years of literature that is dealing with this very matter. It seems very strange to come across an article on evolution that just gives one view - a genetic view and implies (actually it does more than imply) that this is what evolution is. Fail. Fix it. If you don't like my lead - fine, but drop the idea that multilevel evolution doesn't belong in the lead. If it isn't integrated throughout the article - it makes it impossible to intelligently present on evolution proper.Thompsma (talk) 07:47, 31 July 2011 (UTC)

Thompsma, No need to remind us of your credentials or your passion of evolution. We accept that you know what you're talking about so let's assume good faith here. We know what happened the last time when communication fell apart. And we don't want to go there again. So let's focus on making this work.

The reason why I brought up the gene-centric definition of natural selection in the new lead is precisely because of multi-level selection. If for example we define selection with respect to entities (I admit individual organism may be inadequate, not my first choice) as Futuyma does, then we can we have a wide range of things that can be refer to such as selection of molecules, viruses, cells, organisms, clades, etc. But to define in terms of just genes may potentially be limiting. I know you are big about multi-levelselection, that is what I mean when I say ironic, because I see it as consolidating the gene-centric or Neo-Darwinian view of this articles which you correctly pointed out is not adequate.

The issue as always is not about content as much as writing style and detail. This article needs to be accessible to Grade 12 students. The new proposed lead is a bit difficult to follow. I know, I have taught non-science college students, and I can tell you they wouldn't get it. Again, I and perhaps several others have seen and read the literature, so we are not disputing the validity of multi-level selection. It is just how do we communicate this in such a way that is accessible and balanced. That is why I brought the issue of defining traits as DNA. It is not a question of whether it is defined that way in the literature as much as keeping the vocabulary in this article as consistent as possible, particularly with secondary sources. Cheers. mezzaninelounge (talk) 18:34, 31 July 2011 (UTC)

Thanks mezzaninelounge for your helpful feedback. I can agree that the new lead proposal may be too confusing to some and this is where I am hoping that we can work together; there is also the introduction to evolution article for that purpose. I agree that not every evolutionary biologist has joined in extending the synthesis to embrace multilevel selection. We can either ignore it and give the gene only view, but that would exclude a lot of the important work that is going on in this direction. Here is an important section of text from an article in evolution, published 11 years ago[23]:

"(1) Gene interactions play a much more important role in ‘‘ordinary’’ adaptive evolution than presently believed, and our understanding of epistasis with respect to evolution is only in the beginning stages; (2) Multilevel selection is far more common in nature than previously believed, and ‘‘pure’’ individual selection is far less common; and (3) Theories of evolution and speciation that incorporate multilevel selection and epistatic interactions as central to adaptation within populations as well as genetic divergence among them will provide the means for connecting microevolutionary processes with macroevolutionary patterns. Models that minimize their joint importance will not."

The problem is that there is so much going on - that it is difficult to talk about these aspects of evolution unless they are integrated. Niche construction, for example, is an experimental approach to multilevel selection and this has a huge history in evolutionary research: (see [24]). If multilevel selection is far more common that previously thought - as Darwin originally proposes - I think that is a big deal and somehow that idea needs to be threaded into the article.Thompsma (talk) 19:03, 31 July 2011 (UTC)

It is difficult. Which is why, the broader a definition is, the more inclusive it becomes. The only thing we have to worry about is not making them so broad as to make them vacuous. You will have to forgive me if I am not as heavily involved in accumulating sources or in the writing as much as I would like to, as I have a few other things (lab work) to finish. Now, with respect to your proposed lead (the last yellow block), here is where I think we can work on:

1. first paragraph is fine
2. again, the definition of natural selection should be broadened. I am not personally in disagreement with the gene-centric definition. But I see it as being potentially confusing, especially when we describe selection at multiple levels.
3. No problems with the genetic drift definition. But I suspect other editors may have a different opinion.
4. No problem with the mutation definition BUT..... by specifying DNA, wouldn't that exclude retroviruses that carry only RNA?
5. Gene flow definition is OK
6. This one needs more fixing. Mainly in terms of style and word order. Here are my suggestions. Words in bold are suggested additions. Again, nothing is final but a work in progress. I hope my edits will allow you to see what I was getting at.

The last mechanism (gene flow) is a prelude to the multi-levelled aspect to evolution. As a result of these four mechanisms, the evolution of life occurs at multiple levels and is therefore hierarchical. At one level, genes code the information for traits that develop within an organism. At another level, however, these genes are exchanged and selected amongst populations. Hence, evolutionary biologists may for example query determine the mechanics process of genetic evolution in a developmental context of an organisms fitness, such as what genes and mutations lead to different developmental outcomes, and may in turn constrain evolutionary change. Alternatively, an evolutionary biologist may query identify the mechanics process of genetic evolution in a larger population context, such as what genes are extinguished or spread more readily from one population to another. This The hierarchy of life is itself a product of evolution as molecules over time form cells, which in turn gave rise to organisms and diverse populations. The principals of evolution that were detailed in Charles Darwin's Origin of Species explain and apply applies generally to any level in the hierarchy produces offspring in like manner, such that genes give rise to genes, cells give rise to other cells, colonies give rise to other colonies, and so on through the hierarchy. <perhaps a finishing statement here. Maybe Darwin's quote could be moved down here?>

Alternative lead solution

Instead of rewriting the lead from scratch, and grappling with all sorts of other issues that the current lead has solved, how about making the following changes to the existing lead?

Evolution (also known as biological or organic evolution) is the change over time in one or more inherited traits found in populations of organisms. Inherited traits are particular distinguishing characteristics, including for example anatomical, biochemical or behavioural characteristics, that are passed on from one generation to the next. Evolution may occurs when there is variation of inherited traits within a population. The major sources of such inherited variants variation are mutation, genetic recombination and gene flow. Evolution has led to the diversification of all living organisms from a common ancestor, which are described by Charles Darwin as "endless forms most beautiful and most wonderful".

There are four common mechanisms of evolution. The first mechanism is natural selection, a process in which there is differential survival and/or reproduction of entitiesorganisms that differ in one or more inherited traits. Selection can act at multiple levels of organization, for example differential survival and/or reproduction of organisms, populations, or gene variants. A second mechanism is genetic drift, a process in which there are random changes to the proportions of two or more inherited traits within a population. A third mechanism is mutation, which is a permanent change in a DNA sequence can affect phenotypes expressed across multiple levels of organisation. Finally, the fourth mechanism is gene flow, which is the incorporation of genes from one population into another.

Evolution may in the long term lead to speciation, whereby a single ancestral species splits into two or more different species. Speciation is visible in anatomical, genetic and other similarities similarities between groups of organisms, geographical distribution of related species, the fossil record and the recorded genetic changes in living organisms over many generations. Speciation Common descent stretches back over 3.5 billion years during which life has existed on earth. It is Both evolution within populations and speciation between them are thought to occur in multiple ways such as slowly, steadily and gradually over time or rapidly from one long static state to another.

The scientific study of evolution began in the mid-nineteenth century, when research into the fossil record and the diversity of living organisms convinced most scientists that species evolve. The mechanisms driving these changes remained unclear until the theory of natural selection was independently proposed by Charles Darwin and Alfred Wallace in 1858. In the early 20th century, Darwinian theories of evolution were combined with genetics, palaeontology and systematics, which culminated into a union of ideas known as the modern evolutionary synthesis. The synthesis became a major principle of biology as it provided a coherent and unifying explanation for the history and diversity of life on Earth.

Evolution is currently applied and studied in various areas within biology such as conservation biology, developmental biology, ecology, physiology, paleontology and medicine. Moreover, it has also made an impact on traditionally non-biological disciplines such as agriculture, anthropology, philosophy and psychology.

Do these changes address what you were looking for? If not, why not? Which sentences remain a problem?Joannamasel (talk) 20:16, 31 July 2011 (UTC)

Yes, make this change. --Ettrig (talk) 07:50, 1 August 2011 (UTC)

Most of it is an improvement (when I wrote this - I had only read the changes & missed that this was the same as the current lead). The last sentence is kinda weird - how are any of those fields non-biological, traditional or otherwise? I'm not a fan of lists: "There are four common mechanisms of evolution." This always strikes me as odd - especially in light of the parallel development that occurred in developmental biology.[25] Developmental plasticity and epistatic genetic networks seem important here - just to name some other mechanisms. This is why I have suggested introducing the biological hierarchy - this get's rid of the listing idea and you can refer to levels in the organization. I can understand your reason for thinking that it makes it too complicated, but we can't dumb it down so far that it becomes inaccurate. This article has a habit of producing lists as a compromise - I'm not a fan of it - not trying to be stubborn, but I find the prescriptive nature of it irksome. I'll return with some feedback on the 'mechanisms of evolution'.Thompsma (talk) 19:02, 1 August 2011 (UTC)

The closer I look at this, the more I dislike the direction we are heading back into. The changes you have made are more of platitude than substance. You've added a single sentence in an effort to appease my concerns: Selection can act at multiple levels of organization, for example differential survival and/or reproduction of organisms, populations, or gene variants. This is one of the problems with this article - people find controversy, someone sticks in a sentence and expects that the story will take form. Effective writing doesn't work that way - the words, paragraphs, and meaning has to take form - it has to be integrated. We need to do better than this - we need to integrate the ideas, otherwise it becomes piecemeal and prescriptive. You could list a million mechanisms for evolution: sexual selection, artificial selection, isolation, time, small population size, epistasis, contingency, and so on...the list could go on. Evolution should not be presented in a prescriptive manner - it goes against the tradition of this discipline. Also, as I read through the proposal you have put together - I can see that you've removed almost every citation that I included in the revised version. Why? I spent a lot of time sorting through a great many citations and picked ones that were of importance for historical significance. Moreover, now that you've arbitrarily stuck or left Futuyama in there - it doesn't makes sense, because his text isn't the correct resource for that material. Futuyama's text gives a different kind of perspective. I really don't understand why people are so bent on holding onto the much of the current lead - I don't think it reads well. I'm not saying we necessarily go with my proposal. However, picking a sentence or two out of the current lead isn't going to fix the problem. Some parts stick out like a sore thumb. I actually don't agree with this proposal. It will take me a long time to go through this piece by piece...but the more I look at it, I can see lots of problems with it. The section on speciation is terrible. The historical part is so simplified that it reads worse than a Fox News report on evolution - plus the bit about Wallace and Darwin gives an inaccurate picture of how things really happened. If you want to keep the current lead - go ahead. It will take too much work to make headway in here. I was hoping to go through other sections of this article - but I can't deal with this. The rest of this article needs a major clean-up, it goes all over the place. It's easier to get published in real scientific journals than to contribute to this article.Thompsma (talk) 23:14, 1 August 2011 (UTC)

Let's go through this sentence by sentence. I'll start with the second and will work my way through painstakingly to get this finished:

"Inherited traits are particular distinguishing characteristics, including anatomical, biochemical or behavioural characteristics, that are passed on from one generation to the next."

How is this simple? It is a very contrived sentence and it is vacuous in meaning. Characteristics is superfluously repeated twice and why is 'particular' stuck in there; it would read the same without it? A trait is a phenotype - the two are synonymous (see [26]). Further down in the article in the section on heredity - trait is defined (incorrectly, I might add): "The complete set of observable traits that make up the structure and behaviour of an organism is called its phenotype." It is incorrect, because once again this article flip flops and ambles its way around the biological hierarchy. Any trait is a phenotype - eye color can be a phenotype - not the complete set that make up an organism as this article wrongly suggests. The other part to that sentence that is complex is that it uses 'characteristic' as though it is a simple term to toss around. If anyone in here knows anything about systematic zoology, character is anything but a simple term in evolutionary science (see [27], for example). A character in evolutionary science has a very specific meaning and it has a long philosophical history - as in a taxonomic character. The character concept relates back to homology - which is not even discussed in this article (Amazingly!!). I think this is what this sentence is trying to accomplish (but fails) through reference to particular distinguishing characteristics is that traits serve as diagnostics or as taxonomic defining features? In my version I tried to keep it simple and started with the colloquial term for 'phenotype' (i.e., trait) and used this to introduce the concepts in a gradual way and using terminology that you regularly encounter in published literature on the topic:

"Traits are measurable features that distinguish individuals from each other and include anatomical, biochemical and behavioural characteristics."

Note how I wikilink 'characteristics'. I think it is important to mention that features are measurable and that they serve some taxonomic purpose - they distinguish individuals as group defining features in the biological hierarchy; this is what puts the meat into the sentence. This sentence is an introduction to something that is missing in this article - namely phylogenetics, where we find the systematic and logical evidence for evolution. Evolutionists are busy doing things - they are measuring (at the basic level any experiment is measurement). This is the science of evolution, whereas the sentence in the current lead gives no direction in this context. Since this article lacks a proper section or introduction to phylogenetics or homology - it is no wonder that people are confused. Moreover, why does it have to be inherited trait? Take inherited out of the sentence and it says the same thing. Non-heritable traits have a role to play as well - as in phenotypic plasticity and the way that the environment has a role in the expressed phenotype. This brings us back to the first sentence, which ignores the neglected process in evolution (niche construction). Richard Lewontin drew our attention to this problem back in 1983 [28], that environmental change (traditionally viewed as the non-heritable component) is also dependent on the evolution or organisms. So, I have no idea why you would want to confuse the reader further by placing a caveat of heritable vs. non-heritable traits. This can only be understood once you have a clear understanding of the biological hierarchy[29]:

"Although natural selection and niche construction are reciprocal interacting processes, they are logically distinct. Niche-constructing traits need not be products of earlier selection."

Third sentence (I'll lump with the fourth): "Evolution may occur when there is variation of inherited traits within a population. The major sources of such variation are mutation, genetic recombination and gene flow." Barf!! It is overly prescriptive and what is this 'may'? Why are genes (yet again) the only sources of variation? Can't you have developmental variation? Species variation? As Sober stated in his paper:

"This is the lesson we learn from other vague concepts – from rich and poor, hairy and bald, tall and short; a vague boundary does not entail that no one is rich, or hairy, or tall. Even so, ‘‘species’’ is not the central concept in Darwin’s theory. True, the process he describes produces species, but it produces traits and taxa at all levels of organization. For these reasons, Darwin’s theory is better described as ‘‘the origin of diversity by means of natural selection.’’"[30]

Traits are produced at all levels of organization, so why would the major sources of variation point directly at genes? Why does variation link to genetic diversity? Is this article about genetic evolution? Once again it moves away from the multilevel evolutionary synthesis. The traits are inherited yet again - can this term sit on its own or must it always be qualified by inheritance? I disagree completely with the second sentence - it reads like a recipe book and once again, these are not the major sources of variation in a multilevel perspective. On a side-note and for those who continue to berate against multilevel selection, there was a recent article in the journal Evolution that has information of reviewers to take note of group selection and the misconceptions surrounding this issue (I raise this point, because the misconceptions apply to multilevel selection concepts as well).[31] You can read the abstract and get the main point, if you want a pdf - ask and I'll e-mail it.

I can go on, sentence by sentence. The lead was written by someone who does not understand evolution. It is riddled with little mistakes and contrivances that goes all over the place. Does anyone seriously read this lead and think it is well written? The citations also make no sense - some things are cited in weird places that say nothing about the sentence they are referencing. This is what I was trying to clean up in my revised proposal. I think the citations become contrived from the sort of thing that took place here - someone tries to tweak a sentence, they keep the citation, but then the meaning changes from the original source. This lead is a mess - the article is a mess without synthesis and proper integration of the biological hierarchy.Thompsma (talk) 04:12, 2 August 2011 (UTC)

I want to revisit the third sentence - that evolution 'may' occur. Whoever wrote that sentence must not have received the memo about common ancestry. You can look it up in The Origin; it is absurd to suggest that evolution 'may' occur, because the second part to Darwin's theory (namely - ancestry) clearly tells us that evolution 'has' occurred. Subsequent authors have mainly discussed this under the topic of evolution - a topic that gets missed in here. The last sentence in the first paragraph is the only one I like, because it quotes Darwin. I don't want to go into the second paragraph, because it is complete garbage - and I'm being kind. First sentence, third paragraph: "Evolution may in the long term lead to speciation, whereby a single ancestral species splits into two or more different species." There is that may stuff again. This is dumbed down to a level that my five year old could understand it - one splits into two. It is another vacuous statement. The next sentence is an attempt to give evidence for speciation, but it is hardly convincing. Here we see the first vestiges of homology through reference to 'similarities'. However, without any knowledge on how similarities relate to common ancestry the novice reader is just left with an impression that they have to buy into this idea.

Next sentence: "Speciation stretches back over 3.5 billion years during which life has existed on earth." Really? Read that sentence again please and think deeply for a moment - because there is nothing kind I can say about it. Speciation stretches back that far? Who's speciation? Does this mean the process of speciation goes back to the origins? What respectable author ever gave this idea? It sounds like make-up again - an interesting idea, perhaps, but it would require some original research considering the phyletic origins of speciation in a hierarhcical context from genetic species to prokaryotic species concepts in the early days of evolution. What on Earth does that weird sentence even mean? Peculiar how I introduced a real theory in my proposal on the symbiogenic origin of eukaryotic cells and this nonsensical sentence is favoured? Next sentence: "It is thought to occur in multiple ways such as slowly, steadily and gradually over time or rapidly from one long static state to another." That isn't multiple - two is a couple, by definition. Plus, it is a terrible lead to gradualism v. punctuated equilibrium - you would have to be a genius to make the connections. It is like playing mystery - we wont tell you what the evolutionary terms are, you will have to guess. Why not just come out and say what it is and say it correctly.

Fourth paragraph, first sentence - okay. Second sentence, mechanism should be mechanisms. Darwin not only proposed natural selection, but common descent was an important part of the theory. I suggest that someone read the first paragraphs in this paper[32] - it explains the independent origins of the idea much more clearly. The way it is presented in the current lead - the reader is just supposed to make the leap that the independent origins of the theory suggests that Darwin didn't just pull the idea out of the air, that it was somehow fundamental to nature that could be independently derived and verified. For a lead that is supposed to be simple - this expects much of a novice reader. Plus - Darwin didn't keep his evolutionary ideas a secret - they were well known and shared after he distributed his notes in 1938.[33] The next sentence - okay, it is a very broad stroke and I would remove paleontology, because Darwin himself worked on paleontology so I don't think that this is an apt descriptor. I suggest that Ernst Mayr's take on the modern synthesis[34] (since he was a part of it) be read for a proper definition to be derived. I follow this with the question - if the 'modern' synthesis gained ground in the late 1930's - then is it still modern?? The answer is no - so why no mention of truly modern evolutionary theory?? Many in Evo-Devo had noted how developmental biology was left out - yet in the modern context there has been a huge interest in this area. Why leave the reader hanging - as though nothing has happened since?Thompsma (talk) 08:30, 2 August 2011 (UTC)

The current lead refers only to genetic means for variation. I will give an example to the contrary - published herein[35]. This relates back to the idea that Gould put forward, known as 'spandrels'. Here we have the secondary palate of mammals drawing a bridge in evolutionary history. Prior to contact there was no net increase in torsional strength. Once the palate comes into contact - the physical forces come into effect. The mechanical advantage is not related to the action of genes, but it is due to the physics of form. Here is how Darwin refers to this:

"Let an architect be compelled to build an edifice with uncut stones, fallen from a precipice. The shape of each fragment may be called accidental; yet the shape of each has been determined by the force of gravity, the nature of the rock, and the slope of the precipice,—events and circumstances all of which depend on natural laws; but there is no relation between these laws and the purpose for which each fragment is used by the builder. In the same manner the variations of each creature are determined by fixed and immutable laws; but these bear no relation to the living structure which is slowly built up through the power of natural selection, whether this be natural or artificial selection." (Darwin C (1868) The Variation of Animals and Plants under Domestication (D. Appleton, New York), 2nd Ed.)

This is why I disagree with the sentence: "The major sources of such variation are mutation, genetic recombination and gene flow." - It runs counter to the physics of morphology, pleiotrophy, epistasis, and our modern understanding of genetic to phentoypic effects. Epigenetics also has a role to play in this as well.Thompsma (talk) 17:06, 2 August 2011 (UTC)

If you would like to understand the previous context on the bridge of the secondary palate, you can turn to Brian Hall who has done extensive work on the evolution of variability from a evo-devo context. He has written several textbooks on evolution and is highly qualified in this respect:

"At the cellular level, condensations (as modules) are fundamental developmental and selectable units of morphology (morphogenetic units) that mediate interactions between genotype and phenotype via evolutionary developmental mechanisms. Both intrinsic and extrinsic developmental processes affect condensations to modulate morphological change during ontogeny and phylogeny. In a hierarchy of emergent processes (Figure 8), gene networks and gene cascades (genetic modules) link the genotype with morphogenetic units such as condensations, while epigenetic processes such as embryonic inductions, tissue interactions and functional integration, link morphogenetic units to the phenotype."

Hall explains how you can understand the evolution of phenotypic novelty through the evolution of morphogenetic units (multilevel selection) that involves emergent processes - not just changes via genetic mutation. This is where this article suffers (starting with the lead) - it misses the integrative levels of evolution with narrow focus on genes missing epigenetic effects on phenotypic plasticity, emergent characters, and interlevel causation (see [36]). Hence, my attempt to restructure the lead is a prelude to a larger shake-up that this article needs. It goes off in tangents and does not in its current form provide the proper synthesis or description of what evolution is about.Thompsma (talk) 19:28, 2 August 2011 (UTC)

You make some good points, I'll try to address them, but within the current lead. I am not addressing criticisms of the rest of the article for now. I started by adding one of your refs, to Okasha in support of multi-level selection. "Traits" already wikilinks to the same page as you did. I fixed other wording and other issues you brought up both here and in other places. Evolution works whether a trait is measurable by us or not: our taxonomic purposes do not determine evolution. Traits must only be visible to selection. Requiring evolving traits to be heritable is standard. Theories such as Mary Jane West-Eberhard's, which emphasise phenotypic plasticity, state that genes are followers rather than leaders. But even such a strong proponent for phenotypic plasticity requires stable inheritance via genes to come along in the end in order to meet the definition of evolution.

I agree with you regarding the tendency for citations to be orphaned, but it would help if you would be specific about which ones no longer support the statement they are next to. I disagree that Mayr is the best source for the modern synthesis: as somebody who was part of it, he had a distinct agenda regarding how he would like its history to be written. Professional historians such as Will Provine are better sources for historical matters.

The modern synthesis is standard terminology, even if it happened a long time ago, and the word modern applies to art etc. of the same period. As for including more recent developments, right now the page for that is evolutionary biology. I would be sympathetic to a merger between this page and that, as has been discussed before.Joannamasel (talk) 22:12, 2 August 2011 (UTC)

Thanks for your insightful assistance Joannamasel! Your changes are helpful and it is good to see some headway here - you are addressing the issues in an effective way. To the subject of traits. I agree with everything you just posted. Question: "Evolution works whether a trait is measurable by us or not: our taxonomic purposes do not determine evolution." - I can see why you were confused with my sentence. The point I was getting at was the practical science of evolution - working at a bench with calipers in hand, scoring characters, or pipette in hand, sequencing DNA. It might be helpful to give the reader a tangible perspective on what a character is and how this relates to phenotype (synonymous with trait). This is lacking in the body of text - tree building methodology linking to phenotypes that people can envision as character states in context of homology would be a key way to bridge the ideas - tree thinking in evolution. We could stick Darwin's only image from the Origin in here - copyright has expired.

The hierarchical view makes the tracking of heritable vs. non-heritable trait a little more difficult to conceptualize (selection for vs. selection of) for attributable causation through the extension of extrinsic traits (heritable or non-heritable) in niche construction or Lamarkian fashion as in Margulis' symbiogenesis of acquiring genomes: "Acquired traits can be inherited not as traits, but as genomes."[37] "Symbiosis is a neo-Lamarckian mechanism of evolution: we assert that the genome evolution required for organism evolution is not only a consequence of the accumulation of mulations."[38] Suppose West-Eberhard's example[39] description of non-heritable variation - such as nutrition contributing to size in social dynamics is applied to niche construction theory. In niche construction theory, available nutrition within the environment is a product of the actions of the animals themselves - trophic dynamics adding to ecological productivity. Some traits may be transient and apparently non-heritable, but in multi-level context entities may manifest emergent traits evolved by bottom up, or top down causation. Okasha would say that you partition according to level - cells give rise to cells and emergent traits are attributed to that level. "But even such a strong proponent for phenotypic plasticity requires stable inheritance via genes to come along in the end in order to meet the definition of evolution." I agree - but would change genes to emergent characters or evolutionary units (not just genes). Putting the complexity of this issue aside - my basic point was that trait was always followed by the term heritable and I was questioning why it was worded this way, trait (or phenotype) can stand alone. Non-heritable traits at one level may be heritable at another (shifting from extrinsic to intrinsic in a nested hierarchy).

"Traits must only be visible to selection. Requiring evolving traits to be heritable is standard." So if red is a phenotypic trait of blood, must the color be visible to selection, or is that a by product (spandrel) of the physics of the heme group carrying an oxygen molecule? Its adapted as an oxygen carrying molecule, the functional trait is the structure of the protein folding pattern holding the heme group but its aesthetic trait is red. Redness is heritable, but not because it is red, but because it so happens that hemoglobin carrying oxygen is red. Red may become exapted - as in blushing, but prior to the adaptive transition the color trait red was invisible to selection yet heritable. Specific behavioural traits may not be heritable due to their transient nature, but at another level the emergent behavioural tendencies may be heritable as an expected kind of behaviour that a group of organisms may exhibit. There are many examples of community level traits:

"The traditional phenotype is the sum of direct genetic and environmental influences on individual trait expression. By contrast, community and ecosystem phenotypes arise from interactions with other species that comprise the community. Whether particular species contribute to community phenotypes depends on how genetically based traits within species interact to influence the fitness of other species. Recent findings suggest that the variation in community and ecosystem phenotypes that is associated with a foundation species can indeed have a genetic basis and result from indirect genetic effects (IGEs), in which the phenotype of one organism is part of the environment of another." [40]

I should have written Mayr & Provine (1980) - the link will take you to a paper that was written by both - part I Mayr, part II Provine - they explain the modern synthesis in the linked paper. I disagree about the 'modern synthesis' still applying to today - which is why some have called for an extended synthesis. The reality is that this is such an amorphous topic that it is difficult to say what happened? Was it a scientific paradigm shift - sensu Kuhn?? There was a consilience in the 1930's on Darwinian evolution as central to biology. Has multilevel selection created an extended synthesis? Some have suggested that this has occurred - so I think that there should be an updated beyond the synthesis saying something to the effect that evolutionary perspectives went from a rejection of Darwin's notions of group selection via George Williams, popularized by Richard Dawkins, but in this new genomic era where the complexity of phenomena operating above the gene have become more macro- or hierarchically orientated. Douglass Futuyama has a section on "Evolutionary biology since the synthesis" in his textbook (2nd Ed) - for example - and refers to neutral theory, evo-devo, and evolutionary genomics..

To the question of orphaned citations. There are a lot of citations after the following sentence: "The major sources of such inherited variants variation are mutation, genetic recombination and gene flow." - are they all necessary and why is Margulis stuck in there? It seems odd. The first sentence should refer to individuals not organisms - but Futuyma refers to individual organisms in his definition - although he does a very thorough job of explaining macroevolutionary principals later on. If this change is made - Gould should be cited instead of Futuyma. Your addition of fixes one of the orphaned citation problems I identified earlier.Thompsma (talk) 03:50, 3 August 2011 (UTC)

I leave town for 3 weeks shortly, and have limited time before then. Margulis is cited there because endosymbiosis is an important mechanism of gene flow. I will go ahead and move the revisions so far into the lead of the main article. As for future changes, whether to lead or body, I'll state my position/vote upfront since I won't continue this conversation for a while. I support incremental changes to existing text, but not deletions, including of evolutionary biology, nor in general do I support starting from scratch. If your concerns are not met in the current evolutionary biology article, I suggest making incremental changes to that article as a prelude to any merge. Even post-merge, evolution (what is known) and evolutionary biology (the science, past and present, of discovering it) should be identified as distinct concepts. Joannamasel (talk) 23:35, 3 August 2011 (UTC)

I do not support major retention of the structure of material in this article and evolutionary biology in their current state. They are over bloated, disorganized, and off the mark. We need leadership in here to bring order to the confusion on this important topic. In my expert opinion - this article and evolutionary biology are a complete mess and incremental changes are not going to cut it. I'm going to start working on the improvements - because, as I state below on impediments to progress, the topic of evolution suffers from editors that are resistant to change, from people making changes that do not understand the topic, and this leaves us in this quagmire. At present, this article and evolutionary biology do not make sense in light of what is known evolution. Your statement: "evolution (what is known) and evolutionary biology (the science, past and present, of discovering it)" does not make sense to me. It is the scientific philosophy that tells us what is known - hence, "the science, past and present, of discovering it" =(is the same as)= "what is known". You will have to make a stronger argument than this - at present it is nothing more than a weak pedantic argument. Let's work together to put a strong article together. There is strong support in the evolutionary biology talk pages for a merger and so I foresee this going forward.

The first sentence in that lead still needs to be changed to individuals - not organisms. The reason can be understood through reference to David Hull's papers on individuality and selection[41],[42],[43] (which spurred on several books / chapters - e.g., [44], [45]), Michael Ghiselin's radical solution to the species problem[46], Gould & Lloyd's paper on the generalization of Darwin individuality[47], plus the work of Vrba, Eldredge, and many others who have written how individuality explains evolution through the biological hierarchy[48], [49]. The expanded context of individuality encompasses organisms, whereas organisms are a subset of nested individuality. There has been too much work in evolutionary literature to ignore this. Hence, the current lead sentence cannot accommodate the theory broadly enough. The last 'paragraph' - by definition a paragraph must have at least three sentences - is still a problem through its perverse statement that those areas are traditionally 'non-biological'. The sentence is absurd.Thompsma (talk) 19:02, 4 August 2011 (UTC)

Impediments to progress

This article has over 300 references to genetic evolution - not a single mention of phenotypic plasticity comes into play!!! If that isn't enough of a glaring and shocking omission - then let's look at what else is missing: Scant mention of homology (none in reference to morphological traits), no explanation of tree building methods (character state systematics, cladistics, parsimony, continuous/discrete characters), no mention of heterchrony, only one mention of niche construction that I added last year (no reference to ecosystem engineering), no mention of ring species, no mention of phylogeography, no mention of gene regulation networks (Hox genes absent), no mention of quantitative trait loci, no mention of evolutionary radiations, no mention about rates of evolution ('Temp & Mode of evolution, plus I think it important to reference Emile Zuckerkandl I'd think!) only a single link to molecular clock, no mention about biogeography, no discussion on palaeontology with scant disjointed referencing to fossils an lack of integration to geology, no mention of the major evolutionary transitions, no reference to evo-devo, no mention about ontogeny recapitulates phylogeny, no mention of orthogenesis, no mention of Lamark in context of Lynn Margulis', Marion Lamb, Eva Jablonka's neo-Lamarkianism concepts, evolution by symbiosis is completely missed, and I'm sure I've missed some key topics in evolution. People may feel bothered by my comments in here - they are extensive - but I seriously question the featured article status in here and if this article even discusses evolution. Perhaps I need to take a new approach? I've tried linking to hundreds (if not thousands) of external sources - but meet a wall and barrier each time. How can an article about evolution miss each and every one of these MAJOR themes in evolution? For the past couple of years I have come in here and rambled on just to get a few tweaks into the lead - it has been a gargantuan task and I even left for a while out of frustration. I've decided that it is better that I stick in here and do the right thing - because I know that I am bringing attention to some major flaws in this article. Editors in here are resistant to the point of being obstinate. Something needs to change in here. I think people are reading this article and seeing what they want to see, the way they think evolution is, but based on my expert opinion - this article fails to give even the most introductory overview of this important topic. I'm going to ask that editors take a second look at the way that they have been handling proposed changes in here and coveting their pet ideas instead of opening this article to inclusion of some of the ideas stemming from reliable published sources. If you are rejecting material from reliable sources - you are impeding progress.Thompsma (talk) 21:23, 2 August 2011 (UTC)

Thompsma, I wish to remind you that the editors are not resistant to your suggestions. Again, please assume WP:good faith. For example, I myself have looked at your proposed lede and would like to help you make it work. I think Joanna is working hard to see what can be done to address your concerns. It is just that you have posted a lot of information/criticisms and it is really daunting, especially for people who have not kept up, to go through all of it, let alone respond to any of them. Making many changes to this article can be done but it requires tremendous amount of work. Moreover, to incorporate many of the suggestions you gave would require for example, a merger of this article with the evolutionary biology article. That also requires time. So given the size of this article, the slow wiki process, limitations on time (many of editors are graduate students and/faculty) and the complexity of this article and subject, it is going to take a little time. So patience is key. I know it is not as fast as you like, but progress is being made. At this point, it is probably a good idea to continue to focus on making specific cleanups first by providing specific examples of what needs work. Your list of specific criticisms above were most helpful and I think more of those would help move things along. Alternatively, if you want to continue to work on your proposed lede above, I and other editors would be happy to give you feedback on it. Once it is ready, we can post it, have an RfC and be done with it. mezzaninelounge (talk) 15:51, 3 August 2011 (UTC)

I agree mezzaninelounge - progress has been made recently. In past, however, I have encountered resistance in here. In particular, the notion is floating about that multilevel selection is not held by the majority of evolutionary biologists. The idea of a majority in science is irksome to begin with and philosophically bereft. What matters is that the concept appears in reliable sources and as such it is a serious contender. If I found an obscure paper with a novel idea and wanted to put it at the forefront, I would question the validity of that approach. Obviously, multilevel selection is not obscure and I'm pleased to see that some are now helping to integrate the concepts. My post was aimed directly at some of the editors who disregard concepts even though they are backed by reliable sources. Moreover, it was a call to whip this article into shape - to help people see that this article is in need of improvement to live up to its FA status.

Instead of a merger with the evolutionary biology article - that article should just be deleted. I wasn't even aware of it until recently. Perhaps my list of major themes in evolution that are absent from this article could serve as a scaffold for a new index? I would like to propose the following scaffold:

• History
  • Pre-Darwin
  • Turn of 19th century
  • Darwin's Origin
  • Early 20th century
  • Modern synthesis
  • After the synthesis

• Introductory terms
  • Life cycle
  • Heredity
    • Character
    • Phenotype
    • Genotype
  • Organisms
  • Individuals
  • Populations
  • Microevolution
  • Macroevolution

• Common descent
  • Homology
    • Morphology
    • Genes
  • Taxonomy, systematics, and phylogenetics
    • Biological hierarchy
    • Lineages and trees
      • Parsimony
      • Cladistics
      • Maximum likelihood and Bayesian
  • Biogeography
    • Speciation
    • Phylogeography

• Natural selection
  • Definitions
    • Artificial
    • Sexual
  • Adaptation
  • Levels of selection
  • Experimental studies
    • Paleontology and extinction
      • Tempo and mode
    • Eco-evo-devo
      • Developmental biology
      • Niche construction
    • Coevolution

• Genetical evolution
  • Population genetics
  • Genetic drift
    • Neutral theory
    • Molecular clock
  • Genomic research

• History of evolutionary transitions
  • Chemical origins
  • RNA to DNA
  • Origins of sex
  • Symbiogenesis
  • Group selection
  • Cultural evolution

• Societal and philosophical implications
  • Evolution as science
  • Health and education
  • Conservation biology
  • Social sciences
  • Human evolution
    • Cultural transmission
    • Society and religion

The section on introductory terms can kept minimal. I suggest a restriction to each sub-heading must be less than 250 words and third sub-headings less than 100 words. We can adopt text from the current article, but this scaffold could serve as a means to better organize the body of this article and to synthesize the topic. I took a similar approach when I wrote ecology - it is at good article status, hoping to get it featured soon. However, if you compare to ecology, you can see how the size of each section is manageable and easier on the eyes. With this change in mind - I propose that remove evolution from its current featured article status until we get some of the mess cleaned up.Thompsma (talk) 20:13, 3 August 2011 (UTC)

Thompsma. I like it. I don't think we need to worry ourselves about the featured article aspect. That's just a bureaucratic distraction. I wholeheartedly support the newly proposed reorganization of this article. mezzaninelounge (talk) 23:55, 3 August 2011 (UTC)

Great! I will start working on this in my sandbox. I made one last change to societal and philosophical implications "Social sciences" - to include aspects of evolution in art and literature (for example, [50], [51], [52]). I will repost my efforts in here after I have made headway.Thompsma (talk) 17:03, 4 August 2011 (UTC)

Errors for brevity

If one reads this article at a glance, it reads like a nice story. However, as someone who is familiar with the history of evolution and its intricate details I am appalled by the glossy tales that have weaved their way into this article. I'm concerned that wikipedia may be incapable of handling such a topic. For example:

• "Prior to the work of Charles Darwin, the study of evolution was not scientific."

Complete rubbish! Michael Ruse never makes this claim. This wreaks of entrenched evolutionary fears - a fortress mentality - or as Faber[53] describes it: "Stake out a claim, build an intellectual fortress of evidence to defend against all oncomers, and pour boiling oil over the ramparts on the barbarians who attack." The negative consequences of this approach - which is common in the American educational system - brings a negative backlash against evolution and a misunderstanding of what it is truly about. This is the kind of stuff that has crept into this article for brevity. You cannot sacrifice the validity of content for the sake of brevity. Here is another example:

• In the 1960s, scientists such as W. D. Hamilton and George C. Williams extended the gene-centered view of evolution pioneered by the founders of theoretical population genetics, to explain co-operation using concepts such as kin selection. In 1975, E. O. Wilson's book Sociobiology established a significant place for evolutionary theory in psychology, giving rise to the field of evolutionary psychology. In the 21st century, evolutionary biology remains an active field of scientific research.

I've read most of the works by Hamilton, Williams, and Wilson. Reading the preceding 'paragraph' gives me a migraine - it's garbage. First, it isn't even a paragraph - you need at least 3 sentences to have a paragraph. Second, it is uninformative in the way it glosses over detail for the sake of brevity. We would be better dropping the names of these people with wikilinks and saying absolutely nothing about them. This problem continues throughout the article - not just in the section on history, every paragraph is riddled with mistakes. I really want to improve this article, but I have seen this before in wikipedia - deterioration in meaning for the sake of brevity and simplicity. How can this problem be rectified? I'm working on a re-write, but I'm concerned that it will be a waste of time.Thompsma (talk) 17:03, 8 August 2011 (UTC)

This is a tough one. We are writing and editing an article for a very naive audience. In doing so, we have to oversimplify and yes, tell a little lie here and there. Most people just do not have enough background information or the expertise to get all the important nuances. If they did, they wouldn't be reading this article.

With respect to the two sentences/parageraphs you mentioned, do you have a couple of proposed statements that you would like to see instead? We could just do a quick edit and replace. danielkueh (talk) 17:14, 8 August 2011 (UTC)

You've captured the very essence of the problem with this article - "we have to oversimplify and yes, tell a little lie here and there." - that's a terrible philosophy and it seems to be common in here. Are you really suggesting that we MUST tell lies (i.e., give misinformation) because 1) the audience is naive and 2) we are forced into an oversimplification? I reject that and this should be placed at the forefront of the editorial section of this article. This is an encyclopedia and as such we must strive to reveal factual information and resist the temptation to tell lies in our attempt at simplifying for a naive audience. Sounds condescending and this kind of reasoning would be cause for dismissal on any reputable editorial board. We can do better and (with all due respect) I suggest you rethink your philosophy if you want to contribute in here.

I see that the paragraph is three sentences - got lost in all the mark-up. I am working on alternatives. I would just delete the reference to Ruse suggesting that prior to Darwin everything was 'unscientific' - but this would again bring us back to two sentences. Such a shame, because Ruse wrote such a wonderful book and to have it distilled down to a lie is insulting. The work by Williams actually entrenched the gene-centred view of evolution. Moreover, Hamilton and Williams did not extend the theory beyond the gene - that was already accomplished by Darwin himself and others prior to their work. The suggestion or implication that Wilson's book only impacted evolutionary theory in psychology should also be removed. No doubt that his work had an effect in this field, but I would hardly stick to the claim that this is the only development that came out of his text. Another sentence: "The apparent contradiction between Darwin's theory of evolution by natural selection and Mendel's work was reconciled in the 1920s and 1930s..." - is this a prelude to the modern synthesis? If so - it's incorrect. Mendel's work was reconciled with Darwin's theory immediately after de Vries rediscovery - Sewall Wright gives a great overview of this history in his one of his classic books on evolution[54]. For example:

"De Vries carried out breeding experiments with many species of plants other than O. Lamarckiana. In the course of these he rediscovered (in 1900) Mendel's forgotten principles of the inheritance of simple character differences. These were also rediscovered in the same year by Correns and by Tschermak, with verification soon after by Bateson and others who were engaged in breedin experiments. It was immediately recognized that Mendelian heredity was a phenomenon that should throw new light on the theory of evolution."

If you read some of the work at that time (which I have) it is very clear that Mendel's work was not reconciled in the 1920s and 1930s, but just after its rediscovery.Thompsma (talk) 18:26, 8 August 2011 (UTC)

Before you get overexcited, I used the term "lies" to describe the euphimism "oversimplification." The tendency to "lie" is a consequence of a particular writing style/genre, its purpose, and the level of the target readership. It is more prevalent than you think. I challenge you to find anyone (yourself included) who doesn't practice it, be they professors, journalists, economists, scientists, parents, etc. Let me give you several examples. First, take Dawkins's book, The Selfish Gene. In the second chapter of that book, he used the analogy of a wire to describe the axon of a neuron. To a neurobiologist such as myself, I would be horrified if a fellow scientist used such an analogy in a scientific conference or journal. But it is just a popular science book and Dawkins was just trying to make a point that neurons send signals. I could have quibbled or dismissed the entire book based on that one sentence alone. But then again, I would have missed the point of the entire book. For another example, think back to your early days of learning science in elementary and high school. Unless you started out working as a tech in a major science lab, I'm assuming it is nothing like the science that you do now. Your teachers and the system that you were in oversimplified or "lied" to you by giving an impression of science that bears little to no relation to the day to day real thing. Is that wrong? I would say no, they had to start somewhere. Besides, they were more interested in stimulating your interest or curiosity in science rather than training you as a scientist. Finally, one last example. Look at the descriptions of a specific topic such as muscle contractions in an introductory biology textbook, in an undergraduate physiology book, in a graduate level medical textbook, and in a journal article. The amount of detail, sophistication, and assumption of prerequisite knowledge increases exponentially as we move up the chain. Science reading can be dense and it requires practice and experience. Which is why, it is no accident that it takes several years to accumulate Ph.D. level knowledge in the natural sciences or any other scholarly field. Thus, my statement was not meant to be condescending but to emphasize the point that we are here to write and edit an encyclopedia article that should be accessible to anyone with up to a twelve grade education from any part of the world. We cannot shove in every single detail or specify or overemphasize every single nuance. We have to brief and learn to pick and choose what is important and what to leave out. So for a naive audience (I make no apologies using this description), we should not intentionally try to give misinformation. Rather, we try our best to emphasize the bare essentials that we hope they would take away from an encyclopedia article such as this. If we can even accomplish that and at the same time, stimulate some interest, we would have succeeded. What more do you want? danielkueh (talk) 19:12, 8 August 2011 (UTC)

It is amazing that you have written a paragraph of contrivance trying to defend your position. Rhetoric, logic, and metaphor in language have a long history in the arts of creative and scientific writing - on this, perhaps we can agree. However, your synopsis is lacking in any depth and it is a contrivance to justify an ends to a means. I wouldn't try to defend your position talk - you are on shaky ground here. I suggest you take a step back and rethink your position. There is a vast difference between analogy for the purposes of forwarding an argument and the purposeful distortion of facts for the purposes of trying to get a point across. In the metaphor of language we can distinguish between epiphor (colourful content - poetic elicitation of meaning open to interpretation) and diaphor (a hypothesis of sorts, interrelating concepts for explanatory relations with explicit links for interpretation). Selfish gene, black hole, natural selection, and mechanisms of life are examples of diaphoric metaphors. They are not intended to be read as literal translations - but they do present an explicit hypothesis of relation. Genes are acting in a 'selfish way', not literally, but there is an explicit theory here that they act as if they had selfish motives. Dawkin's analogy of wire to axon is a clear and upfront analogy. What I am identifying is something very different - a complete distortion of truth such that the reader cannot leave with a correct understanding. "What more do you want?" - facts, honesty, and diligence in reporting on this topic. I keep hearing the idea repeated that this has to be written for someone with grade 12, but that is a ruse in defence of the sort of nonsense that you are trying to put forward here. There are nonsensical statements throughout that are likely symptomatic of the kind of 'philosophy' that you are trying to support here - and I'm not buying it. Here is a sentence from variation:

• "Natural selection will only cause evolution if there is enough genetic variation in a population."

Delete. Who ever made such an outlandish claim?? This is a notice to editors in here - stop the distortion of truth for the sake of brevity. Use correct writing style, argumentation, and reporting.Thompsma (talk) 19:55, 8 August 2011 (UTC)

Thompsma, Correction, I never claimed that we should distort facts. If so, I would not for example have asked you for suggested corrections. That is a clear misreading of what I wrote. Anyone who has read what I wrote would clearly understand this. I have nothing more to add. danielkueh (talk) 20:08, 8 August 2011 (UTC)

Not being au fait with the particulars being hashed out here, I will just say this and step aside: Map-makers do something similar, which they call generalization, the aim being to "emphasize the most important map elements while still representing the world in the most faithful and recognizable way." Calls for skill and experience to get it right for any particular use (i.e. audience.) __ Just plain Bill (talk) 20:04, 8 August 2011 (UTC)

Bill, if only I was just as eloquent. You summarized the point that I was trying to make in just a couple of sentences. danielkueh (talk) 20:23, 8 August 2011 (UTC)

"In doing so, we have to oversimplify and yes, tell a little lie here and there." - "I used the term "lies" to describe the euphimism "oversimplification."" I apologise, I glanced over the part where you redefined 'lie' to suit your argument, but you can forgive me for being a bit confused on that one. Next time I'm caught in a lie, I'll redefine it as an oversimplification of the truth. I have no problem with talk's statement. It is odd how arguments go astray. I was pointing out 'deliberate' (or unconscious - but still evident) distortions for the sake of brevity. Somehow this got contrived to suggest that I was putting forward that we need to report on every last detail. Stick to rational discourse here. The point I have made remains valid - and by valid I don't mean "undersimplification", I mean valid.Thompsma (talk) 20:52, 8 August 2011 (UTC'

Clarification. In this context, I used the word "lie" as defined by the second sense definition in Webster [55]. Thus, I consider all oversimplifications to qualify as lies based on this definition. I never "redefined" lies to "suit my argument." If anything, I just defined it once.

And no, I was not suggesting that you were trying to report on every single detail. I was just making a general comment about writing a general article such as this. Hence, I started my first comment with "This is a tough one. We are..." Anyway, this is getting off topic and I agree that problems may from time to time arise from brevity. danielkueh (talk) 21:11, 8 August 2011 (UTC)

I respect intellectual honesty and expect it in this article. Lie (verb):

1. to make an untrue statement with intent to deceive
2. to create a false or misleading impression

I ask that no editor lie to get a point across - either one of these meanings will suffice, neither of which means to oversimplify. An oversimplification means that the original meaning or complexity of meaning is changed by using simple alternate terms as in common vernacular. I also ask that no editor oversimplify the text either. Please add honest, coherent, and terse statements about the topic using effective prose.Thompsma (talk) 03:23, 9 August 2011 (UTC)

I find that oversimplification often, but not always, leads to an impression that is false or misleading (second sense definition) (also see[56]). I'm not going to quibble over this. I am just explaining why I used the term, "lie" in the way I did, which I admit, in hindsight was not effective and was perhaps a little confusing. Anyway, point taken. danielkueh (talk) 14:49, 9 August 2011 (UTC)

Darwin's heritability

The following sentence in the history section: "Like Jean-Baptiste Lamarck, he still thought that parents passed on adaptations acquired during their lifetimes,[31] a theory which was subsequently dubbed Lamarckism." - is another oversimplification that is misleading. Darwin's theory was more complicated than this and he didn't think very kindly of Lamarck's theories. Darwin developed his theory of pangenesis and gemmules (which were Lamarckian) and his ideas about inheritance (dismissive of Lamarckian modes) are actually more in tune with our modern understanding of multilevel inheritance via phenotypic plasticity; moreso than most have appreciated.[57] Once again, this requires a nuanced and in depth understanding of what Darwin wrote and what a character is. Elizabeth Vrba and Niles Eldredge (1984)[58] provide an excellent description of character in the emergent context:

"For instance, at the organism level relevant characters include ecophenotypes (usually defined as "nongenetic modifications of the phenotype in response to an environmental condition" [Mayr 1963)). The latent epigenetic variability which allows the range of expression of different ecophenotypes in response to environmental stimuli is hereditary. Although an individually acquired ecophenotype is transient and purely environment-dependent, it may become assimilated, via selection, as a hereditary character (Waddington 1956; Williams 1966; Riedl 1978)...But we argue that only emergent characters can be selected, and thus be aptations, at the focal level. (We use "aptation" as an inclusive term for any character currently subject to selection, irrespective of how it evolved, sensu Gould and Vrba (1982), in contrast to the narrower term "adaptation" for a character shaped by selection for current function, sensu Williams (1966). Gould and Vrba (1982) suggest the term "exaptation" for an aptation whose origin is not ascribable to selection for current function."

With this quote in mind, revisit Darwin's concepts of heritability and you will discover that "Much of Darwin's discussion of "direct and definite action of the external conditions of life" and on "use and disuse" refers not to Lamarckian inheritance but to what we would now call "phenotypic plasticity."[59] - Darwin had an appreciation for the assimilation of characters - causal relation from higher level selection imparting downward effects. Darwin always cautioned that his ideas on inheritance via pangenesis was provisional and that the answer to this problem was the most pressing issue for biology at his time.Thompsma (talk) 20:37, 10 August 2011 (UTC)

Here are some links to papers on Darwin's pangenesis theory that are relevant to this topic: "It is now apparent that Darwin’s Pangenesis contains a great truth and needs to be reconsidered; whether it can serve as the basis for a new comprehensive genetic theory is another question."[60] - In Darwin's own words: [61], [62]Thompsma (talk) 22:18, 10 August 2011 (UTC)

Moreover, "Prepotency (Mendelian inheritance)...Many people thought that Darwin did not read Mendel’s paper, thus he did not know Mendelian inheritance. This is not the case. Segregation in the Mendelian sense was well known to Darwin...Of course, in Darwin’s work it was just one of many examples, not the crucial mechanism, as it was in Mendel’s research...Darwin’s gemmules: the embryonic form of our modern genes...The word gene, which was coined in 1909 by Johannsen, was derived from de Vries’s term pangen (pangene), itself a substitute of gemmules – genetic elements in Darwin’s Pangenesis."[63]

Understanding that Darwin used prepostency to refer to Mendelian inheritance we can see how he saw it as one of many explanations for inheritance:

"When two species are crossed, one has sometimes a prepotent power of impressing its likeness on the hybrid; and so I believe it to be with varieties of plants. With animals, one variety certainly often has this prepotent power over another variety" (Darwin 1872).

It is "prepotent" because it was inherited from its parents from birth in a classical Mendelian sense.Thompsma (talk) 22:31, 10 August 2011 (UTC)

There are interesting concepts there, including stuff that is well over my head, and in most cases I only have access to the abstract. However, there's an inherent confusion about Lamarck's theory as opposed to the "Lamarckism" of inherited acquired characteristics, which in his theory was a secondary mechanism, "the influence of circumstances". This explained diversity and branching, but the main thrust of Lamarck's transmutation was linear development, "a force that tends incessantly to complicate organisation". It was this linear "force" that Darwin rejected. Gould covers this in his essay "A Tree Grows in Paris" in The Lying Stones of Marrakech, which seems to be online. Darwin clearly went along with inheritance through "use and disuse" which seems later to have been dismissed as "Lamarckism", but it will be interesting to find how much of his ideas or indeed Lamarck's can be related to modern findings. . . dave souza, talk 23:06, 10 August 2011 (UTC)

If found a linked copy to the paper on "Darwin’s contributions to genetics" here[64]. Yes..the concept of heritability is more complex than most people appreciate. The basic idea in the quote above from Vrba and Eldredge (1984) stems from the Gould and Vrba (1982) paper[65] on exaptation. They suggest that most usage of the term adaptation should be aptation instead. There are ad-aptations and ex-aptations. In older lingo the term for exaptation was pre-adaptation, but linguistically this does not make sense - how can something be pre-adapted? Instead, an exaptation is a character (a physical trait) that serves no current functional utility (e.g., redness in blood in an early reptile that did not blush) that is later co-opted for a new functional utility (e.g., the redness is used for blushing in mammalian descendants); Gould and Vrba use a hypothetical example of proto-feathers first used for warmth exapted for flight function. In William's classical book[66] he refers to characters in the sense of an adaptation - current utility only. Whereas, Gould, Vrba, Eldredge and other multi-level selectionists extend the notion of character to include all aptations (ex and ad). The cooption phase of an exaptation to an adaptation (see figure 1 here[67] and more expansive description here [68]) is where Darwin's use and disuse comes into play. An emergent character from phenotypic plasticity can become exapted for a new functional utility and later assimilated. The cause for selection for emergent heritable characters does not stem directly from a gene, but can stem from a higher level of organization. "In sum, Darwin explained the increased inheritance of acquired traits with a kind of "genetic assimilation", erroneously ascribed to local effects on the particles of inheritance under natural selection."[69]Thompsma (talk) 23:34, 10 August 2011 (UTC)

I made some revisions in an effort to clarify pangenesis. It is not a simple task and I hope that some editors will assist in truncating and simplifying the text I added. There is a lot of history here. Importantly, it should be noted that genes are not what most people think they are. Strands of nucleic acids are not genes - information coded in the pattern are. Genetics is the study of inheritance and does not necessarily involve genes. Epigenetics is the process or the activity of the gene in development that translates the genotype into its phenotype. Darwin's theory of pangenesis was about genetics in the sense that it set out to explain the mechanisms of inheritance. de Vries devoted his book to Darwin's pangenesis theory as he was the first to describe the induction of pangenes in the nuclei of cells being expressed to migrate out of the nucleus and affect the morphogenesis of phenotypes. Darwin's gemmules are very much reminiscent of DNA acting through horizontal transmission, methylation of chromatin, and other epigenetic phenomena that are most recently being discovered. It also gets more complicated when you start to take niche construction into account. I hope I simplified it well enough in the text.Thompsma (talk) 23:31, 11 August 2011 (UTC)

Off topic? (paragraph removed)

The article discusses the Scopes Trial, and then we see 'Social Darwinism takes ideas about "survival of the fittest" out of their biological context and applies them to commerce and human societies as a whole, misusing them . . .'. At a minimum we need a transition, and I think this just plain off topic. Why not a parenthesis near the top that says essentially "so-called social Darwinism (which see) is a whole different thing"? -- Jo3sampl (talk) 03:07, 11 August 2011 (UTC)

I'm a total newcomer to this article but I agree entirely. If social darwinism is going to be discussed, it should be presented in a way that clarifies that it really has nothing to do with the theory of evolution, and especially that slapping Darwin's name on it does not imply that he would have supported it, which he didn't. --Grapplequip (formerly LAR) (talk) 06:50, 11 August 2011 (UTC)

The more I researched the right way to do it, the more I became convinced it shouldn't be done. Paragraph removed. -- Jo3sampl (talk) 22:47, 11 August 2011 (UTC)

An error about genetic drift

There is still a minor error in the drift section (it looks like the previous error regarding drift has been corrected [Joannamasel is correct]) in that the drift section claims that "The effective population is always smaller than the total population since it takes into account factors such as the level of inbreeding, the stage of the lifecycle in which the population is the smallest, and the fact that some neutral genes are genetically linked to others that are under selection." I went ahead and check the Charlesworth reference, since Brain Charlesworth is pretty good at this stuff, and indeed he list several factors that increase Ne.

• "Genetic structure: the long-term maintenance of two or more alleles by balancing selection results in an elevation in Ne at sites that are closely linked to the target of selection. In contrast, directional selection causes a reduction in Ne at linked sites (the Hill–Robertson effect)."

• "Conversely, if there is less than random variation [in offspring number], Ne can be greater than N; it equals 2N in the extreme case when all individuals have equal reproductive success." (I'm just going to change it, forgot I wasn't logged in) Matthew Ackerman (talk) 20:03, 24 May 2011 (UTC)

Change to mutation

I went ahead and chopped out a sentence saying that the observed mutation rate in a species represents a balance between the metabolic cost of repairing mutations and the deleterious consequences of mutations on offspring. This is an active area of research, and many authors would disagree with the sentence (i.g. Allen Orr or Mike Lynch). For what it is worth, I don't think the authors of the article cite would agree with this sentiment, their main point being that the mutation rate in rapidly adapting asexuals does not increase because of the benefits of increasing the mutation rate. I don't really see a need for the main article to get into this aspect of evolution, even though many people find it very interesting (myself included). Matthew Ackerman (talk) 17:41, 25 May 2011 (UTC)

Since Orangemarlin reverted my edit, I assume he/she feels that we must talk about this issue. Again, I don't believe that it really adds much to the article, but there is very clearly no consensus in the literature that metabolic cost are the major determinants of mutation rates, as can be gleened from the abstract of the Sniegowski et al. paper. In fact, the Sniegowski paper presents all three possible mechanisms for determining the equilibrium mutation rate in their paper, and I don't see why we should only mention the single mechanisms that Sneigowski et al. give a very tentative statement of support. Matthew Ackerman (talk) 20:42, 25 May 2011 (UTC)

Death rates exceed the replacements

The following passage must be wrong, cannot see what is intended: limits to population growth to explain the way death rates exceed the number of replacements by births during the struggle for existence. It is an obscure formulation, but I think it says that deaths exceed births. This is not necessarily what happens even when limits to growth are reached. It is certainly not the general pattern in evolution. In average in the long run, births and deaths are approximately equal in number. The observation by Malthus and Darwin was that the births have the potential to produce exponential population growth. Darwin shows that when this surplus is culled there can be a tendency in which forms prevail. --Ettrig (talk) 07:31, 12 August 2011 (UTC)

It was probably just a typo - I changed it.Thompsma (talk) 20:56, 12 August 2011 (UTC)

Cuvier and antiquity of Earth

A recent addition stated:

"Equally important for the development of a scientific theory of evolution was the recognition of the age of the Earth: independently, in 1811, Georges Cuvier and Alexandre Brongniart published an influential study of the geologic history of the region around Paris, based on the stratigraphic succession of rock layers. These works helped establish the antiquity of the Earth."

This is incorrect and I changed it. Foremost, Bowler (2003) says no such thing on page 113. Second, the age of the earth was a problem for Darwin and Cuvier pre-dates Darwin. During Darwin's time there was a huge debate between Lord Kelvin's estimated 100 million years held until radioactive decay research by Rutherford and Arthur Holmes showed the true antiquity of the Earth. James Croll was one of Darwin's fiercest critics stating that the age of the earth was too young for things to have evolved. Darwin provided his own calculations at 306,662,400 years by calculating the amount of rock that had been eroded at the Weald - a large valley that stretches between North and South Downs in the south of England. Please read your sources properly and place the correct information in the body of the text.Thompsma (talk) 03:19, 13 August 2011 (UTC)

Is this information necessary? It was not there to begin with. If we are going to talk about the age of the planet, I would prefer that we stick with antecedents that directly influenced Darwin such as Charles Lyell's Principles of Geology. danielkueh (talk) 03:26, 13 August 2011 (UTC)

Re text currently in article "Georges Cuvier is known as the father of paleontology": Can we please not use "father of" which is not very helpful and is a phrase that POV warriors have dropped into many articles to suggest that their favored person or group is particularly wonderful. However appropriate in some cases, such descriptions are ultimately just someone's opinion and should be attributed, if it were necessary to use such language. Johnuniq (talk) 04:27, 13 August 2011 (UTC)

Yes...on both accounts. I'll spend some time this weekend going through and picking through this to shorten it. It was expanded by me (guilty) mainly because I saw a lot of factual errors. Now that a correct story line has been put together I think a shorter summary can be distilled out of this. The history of evolution article is featured - but it doesn't include some of the info in here - so I'll try to integrate and transfer.Thompsma (talk) 05:15, 13 August 2011 (UTC)

I put the father aspect in there - because he is actually called the father of paleontology often in the literature[70] and in this case, he really is the founder. But I agree that we could take it out.Thompsma (talk) 05:17, 13 August 2011 (UTC)

On the age of the Earth, Darwin started with a very ancient Earth as put forward by Sedgwick, and before becoming an evolutionist was convinced by Lyell's concepts of an infinitely old Earth. While Darwin's calculations on the Weald were disputed and dropped by him in later editions, this related to the rate of evolution and wasn't insurmountable, let alone a return to the Ussher chronology. If anything, the need for speed contributed to the popularity of other mechanisms in the eclipse of Darwinism. Note also that Kelvin's estimates changed over time, becoming increasingly out of line with geology. It's very debatable whether this detail belongs in this overview. . . dave souza, talk 09:02, 13 August 2011 (UTC)

The question is not when the actual age of the earth was established. The question is, when did enough people realize that the earth was considerably older than the 6,000 years preached by many clergy? Realizing that the earth was considerably older (even if people had not yet realized it was four billion plus years old, or did not even have a specific idea) was essential to the success of Darwin's ideas, and belongs in the history section. It is not enough to say that the age of the earth was determined after Darwin. We ned to say that before Darwin published his books natural historians were already arguing that the Earth is much older than 6,000 years. Slrubenstein | Talk 10:41, 13 August 2011 (UTC)

This is something we covered in On the Origin of Species#Developments before Darwin's theory which may be useful more generally for referenced info:
The Ussher chronology of the 1650s had calculated creation at 4004 BC, but by the 1780s geologists assumed a much older world. Wernerians thought strata were deposits from shrinking seas, but James Hutton proposed a self-maintaining infinite cycle, anticipating uniformitarianism. .....
And on Cuvier:
Geoffroy contended that embryonic development recapitulated transformations of organisms in past eras when the environment acted on embryos, and that animal structures were determined by a constant plan as demonstrated by homologies. Georges Cuvier strongly disputed such ideas, holding that unrelated, fixed species showed similarities that reflected a design for functional needs. His palæontological work in the 1790s had established the reality of extinction, which he explained by local catastrophes, followed by repopulation of the affected areas by other species.
As for Kelvin, the Challenges to natural selection section notes that Darwin's estimate that the age of the Earth allowed gradual evolution was disputed by William Thomson (later awarded the title Lord Kelvin), who calculated that it had cooled in less than 100 million years. Not as significant as the earlier shift from 6,000 years. . . dave souza, talk 11:09, 13 August 2011 (UTC)

The article is already extremely big and has many good side articles to go to for specialized side issues? Do we have to include every possible digression?--Andrew Lancaster (talk) 11:41, 13 August 2011 (UTC)

Agree, which is why concise mention that by the 1780s geologists assumed a much older world is appropriate as a main precondition for modern concepts of gradual evolution. Later disputes over 100 million or 4.5 billion aren't significant enough here. I'm rather reluctantly thinking about a considerable streamlining of the section on the history. . dave souza, talk 12:53, 13 August 2011 (UTC)

I think Danielkueh's suggestion to mention Lyell is constructive. I agree that the section as a whole can be streamlined a great deal. There is no need at all to go into detail about debates over the age of the Earth. What is important is that Darwin believed he had good reason to think the Earth is very old, and a great many of his readers had reached the same conclusion (even if they differed or were wrong about the details), and two hundred, even a hundred, years earlier, far fewer Europeans would have found this believable. I do not see why this can't be communicated in two sentences, three at the most. Details – up to Lord Kelven &c. – can go in the linked daughter article. Slrubenstein | Talk 17:50, 13 August 2011 (UTC)

Recent changes to History of evolutionary thought section

As changed, the structure is incoherent, starting with Darwin and wandering backwards. This section should summarise the more coherent account in History of evolutionary thought, and not get bogged down in new details. No objections to clarifications about Pangenesis being added to the main article and concisely reflected here, but other changes have been for the worse. . dave souza, talk 09:02, 13 August 2011 (UTC)

I disagree with your assessment. When I started to re-work the history section it was filled with misinformation. If you want me to go back and present sentence by sentence the mistakes I found - I can do this. I think it is most important to give a reliable account - even at the expense of going into too much detail to begin with. I agree that it is too lengthy at this point, but I disagree that it is incoherent. It is well sourced and it does not gloss over the details to an extent that it gives the wrong idea of what happened. It just needs a bit of tweaking.Thompsma (talk) 18:22, 13 August 2011 (UTC)

You are each talking about two different things. Dave is talking about the level of detail, and Thom is talking about accuracy. Obviously it is the actual article on the history of evolutionary thought that should have all of this detail, and this article should contain a summary of that one.

I do wonder about the coherence of some parts. For example, the quote about Paley's natural theology - I am sure it is accurate but why is it here? Why does it matter? The quote is accompanied by three citations, one is an article on why Darwin abandoned intelligent design — does this article explain the significance of the quotation? If so, we need to add more information. Added context would make the section longer, but would also make it more coherent. I also wonder why we include the details about "atomic sized gemmules." I have no question about its accuracy, but is it necessary in this article? Slrubenstein | Talk 18:47, 13 August 2011 (UTC)

Slrubenstein based on the misinformation that you keep adding and your abuse of privilege as discussed above - you are not in position to discuss this. It is clear to me that you don't have a grasp of the history. I think that User:Dave souza may have read the history section with some of your recent posts on Menand - which was a diversion - and this is why he felt is was incoherent. You also inserted the incorrect information about Cuvier and the antiquity of the earth.Thompsma (talk) 19:35, 13 August 2011 (UTC)

This kind of argument is NOT ACCEPTED BEHAVIOUR in Wikipedia! --Ettrig (talk) 17:36, 14 August 2011 (UTC)

"one is an article on why Darwin abandoned intelligent design" - I'm starting to see a pattern in your work Slrubenstein - you read the titles of work, but you don't go into their depth. Why don't you read the literature like I did and understand why Paley's work was so important in the historical narrative. Obviously Paley was important to Darwin - as Darwin himself noted. Paley's work was required reading at Cambridge for nearly 200 years - influenced a lot of intellectuals and it was an explanation of design (adaptations).Thompsma (talk) 19:40, 13 August 2011 (UTC)

A technical point, Paley's Natural Theology was not required reading at Cambridge in Darwin's time there, Darwin read it out of interest. The required reading, Evidences of Christianity, was to do with miracles and entirely off topic. Paley's natural theology placed great emphasis on adaptation, and this influenced Darwin but the present mention of Paley is excessive and a diversion from the main thrust of the history of evolutionary ideas.

I'm not comfortable with this issue of the shift from typological idealism to population statistics, and have been looking through sources about this but don't have a firm conclusion as yet.

The incoherence I see is exemplified by the first paragraph, starting with "Prior to the published works of Darwin, a theoretical synthesis threading what seemed at the time to be disjointed facts forestalled advancement in the life sciences." This appears to be disjointed nonsense, and should be replaced by a brief statement of ideas of the Ancient Greeks, the medieval great chain of being, and the introduction by Ray and Linnaeus of the concept of fixed generative species, as well as the natural theology of Ray and Paley seeing adaptation as evidence of divine design. We don't need a long ramble about how Paley had a great working knowledge of biology or Darwin learnt his writing by heart. . dave souza, talk 20:05, 13 August 2011 (UTC)

By the way, William Paley's "published works on natural theology were required reading at Cambridge University from 1787 to 1920" is frankly nonsense, as Natural Theology; or, Evidences of the Existence and Attributes of the Deity wasn't published until 1802. You seem to be getting it mixed up with Paley's oher books. Note that Dawkins isn't a historian, and it would be helpful if you could cite the online correspondence of Charles Darwin – or was it a commentary from the book? Either way, it's longwinded and largely if not entirely offtopic. . . dave souza, talk 20:25, 13 August 2011 (UTC)

Hi Dave:

• "Paley’s works were mandatory reading at Cambridge University from 1787 to 1920. During Darwin’s undergraduate years (1829-1831), Paley’s influence on the university’s curriculum was second only to that of Isaac Newton (Crimmins 2004)." Copied from: Sulloway, F. J. (2009). "Why Darwin rejected intelligent design". Journal of Biosciences 34 (2): 173-183. doi:10.1007/s12038-009-0020-8, p. 174

The Crimmins (2004) reference is: Crimmins J E 2004 William Paley; Oxford Dictionary of National Biography 42 445–45 - I checked and it states this correct. Paley was required reading during that time.Thompsma (talk) 20:37, 13 August 2011 (UTC)

"From 1787 into the early nineteenth century the Principles was mandatory for Cambridge examinations, and from 1822 to 1920 the Evidences of Christianity was on the required list for the Previous, or Little-go, examination for all second-year undergraduates."[71]

I'm looking into this further - to see what other citations say about this.Thompsma (talk) 20:53, 13 August 2011 (UTC)

I see what you are saying, however, about his natural theology text.

"His 1794 book A View of the Evidence of Christianity was required reading at Cambridge University until the 20th century. His most influential contribution to biological thought, however, was his book Natural Theology: or, Evidences of the Existence and Attributes of the Deity, Collected from the Appearances of Nature, first published in 1802."[72]

This reference[73] also contradicts the statement that it was required reading. I will fix the mistake. Paley's work is still quite relevant to the historical tale - he influenced many who studied evolution and was the source behind Dawkin's book 'The blind watchmaker'. Hence, I think there is enough notable reason to mention Paley's natural theology.Thompsma (talk) 21:05, 13 August 2011 (UTC)

Thom, ditch the bitchy attitude and just read what I wrote. The article as written does not make clear why Paley is important. Now, reread what I wrote before you get bitchy again. I am not saying that Paley is not important, I am just saying that our article is not clear about it. I thought that one of the three references provided might explain the importance and based on the scant information provided in the references, I posed a question. It is a question that one can politely answer with a "yes" or a "no" but you opt for "snotty" instead. Well, that's just you being you, I guess. The fact remains that the article does not make this clear, and if it did maybe it would be more coherent. You seem pretty smug that you have the secret knowledge that explains why reference to Paley is so important to this article, perhaps you will actually edit the article and you know improve it. That is my only interest here. If you cannot accept constructive feedback, well, good luck with your writing career in the real world!!! Slrubenstein | Talk 20:28, 13 August 2011 (UTC)

Slrubenstein - I am not getting snooty, I respect diligent and accurate scholarship - your posts don't cut it.20:37, 13 August 2011 (UTC)

In response to some of your other comments dave souza - please feel free to modify the text as you see fit. Paley not only influenced Darwin, but many others of his time and prior. It seems quite relevant in the history of evolution - enough so that Dawkin's wrote a book about Paley's natural theology through his reference to the 'Blind Watchmaker'. Moreover, it also has relevance in contemporary history in light of the intelligent design movement. Darwin wasn't threatened by natural theology - he had great admiration for Paley's work. Gould (2002) provides a section on Paley's influence on Darwin in his book[74] on page 116 (page 117 is cut, so I'll relay info from my copy):

"The main lineage of this national tradition for "natural theology" based on the "argument from design" runs from Robert Boyle...John Ray...in Newton's generation that promulgated what historians call "the scientific revolution"; to a grand culmination in William Paley's Natural Theology (1802), one of the most influential books of the 19th century...Darwin's essential argument begins with a definition of the dominant philosophy for natural history in his day--natural theology in the Paleyan mode."

Gould (2002) writes about the parallel between Paley's Natural Theology and Darwin's work and how Paley was an influence to Darwin through his life. It seems important to include this. I cited Dawkins, because "The Blind Watchmaker" comes straight out of reference to Paley, it is a popular book on evolution, and it also discusses these issues at length. I agree that we can shorten the text - and will work on this with you.Thompsma (talk) 21:26, 13 August 2011 (UTC)

Sorry to interrupt, but a lengthy and comprehensive discussion of Paley and Darwin is contained in the chapter "Darwin and Victorian Christianity" by John Hedley Brooke (a distinguished historian of science) in the Cambridge Companion to Darwin. Amongst other things it contains this statement by Darwin himself, "the old argument by design in nature, as given in Paley, which formerly seemed to me so conclusive, fails, now that the law of natural selection has been discovered." There are other sources, but this seems to be an excellent start. Similarly for Darwin's concept of "species", there is the CUNY book "Darwin and the nature of species" by David N. Stamos, another historian of science. I agree with dave souza's remarks above, particularly concerning the first paragraph in the section under discussion. Mathsci (talk) 23:50, 13 August 2011 (UTC)

Thanks for the info Mathsci. dave souza - I went to remove the quote and to fix the information on Paley, but there was a protection put on the article just as I went to do this. As for the first sentence: "Prior to the published works of Darwin, a theoretical synthesis threading what seemed at the time to be disjointed facts forestalled advancement in the life sciences." I'm fine with a re-write, but "disjointed nonsense" is a little unfair. The paragraph needs an opening sentence. I took the lead from Paul Farber's book "Finding Order in Nature" [75], linked this to Gould's essay on Evolution as fact and theory[76], combined this idea with theory: "By contrast, a theory in science, again following the definition given by the NAS, is “a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences, and tested hypotheses."[77] Hence, it is evolutionary theory defined - it is true that Darwin's theory synthesized the facts of nature and his ideas have lead to many advancements in the life sciences. Here is how Farber (in another paper[78]) gives a similar sentence:

"Evolution theory, which was a synthetic theory that united all the many disciplines of the life sciences, grew out of the attempts of naturalists to solve problems posed during the early decades of the nineteenth century."

In many instances you can read sentences that evolution is the central organizing principle in the life sciences. Many educators refer to the alternative way that biology is taught without evolution (as in a creationist setting) as a "disjointed list of facts".(e.g., [79]). Hence, I surveyed a broad cross-section of the literature to put that sentence together. But - if you have a problem with it - feel free to change once the editorial ban is lifted. If you want to discuss the older version - I am willing to go back to it, but I will tear apart the misinformation that was contained in it.Thompsma (talk) 02:17, 14 August 2011 (UTC)

This used to be a featured article. My suspicion is that the changes to the section on the history of evolutionary thought, which used to look this [80], would prevent it from even being a good article. What is striking at the beginning of the section is the anachronistic language, with the liberal use of words like "intelligent design" and "life sciences". The section as written lacks coherence and now looks more like an entry in a blog than part of an authoritative encyclopedia article. When writing about an area well covered in the history and philosophy of science, it would be normal to expect the secondary sources to be written by experts in that area. That does not seems to be the case at the moment. My suggestion is that the previous stable version be restored and that discussion becomes calm with no inflammatory language. Each small proposed change can then be discussed here more carefully without personalizing the discussion as appears to have happened so far. The proper use of secondary sources is essential when writing about the history of science; and this section should not depart in any radical way from what can be found in the main article, History of evolutionary thought, of which this section should essentially be a summary. Mathsci (talk) 07:50, 14 August 2011 (UTC)

I am not in a position to contribute much until Aug 26 or later, but I want to second the proposal of Mathsci. We should go back to the previous stable version, take one small change at a time, and reach consensus on a draft text in each case before changing the main article. I believe consensus is possible, but the process must be incremental.Joannamasel (talk) 11:53, 14 August 2011 (UTC)

Exactly. "Incremental" is exactly how I would put it. Mathsci (talk) 12:32, 14 August 2011 (UTC)

This also sounds reasonable to me. Another problem this would help avoid is the accretion of digressions that can happen for quite understandable reasons in many Wikipedia articles.--Andrew Lancaster (talk) 13:33, 14 August 2011 (UTC)

I agree that changes need to be done carefully and with thought and planning. Nevertheless, I do not think the version that Matchsci suggest that we start from is a good place to start either. That version contains more errors than the current version. One of the errors that was just recently resolved was most acrimonious (see Statistical species thread). The current version needs to be adjusted, particularly its language, which I wholeheartedly agree needs to be less personalized. I urge other editors to take one more look at it and see if we can bring in line with secondary sources as MathSci suggested, which I also wholeheartedly agree. danielkueh (talk) 18:08, 14 August 2011 (UTC)

Sorry, the current version is hopeless: the writing and sourcing is exceedingly poor. The article should be restored to a previous stable state, before danielkueh and Thompsma started making large-scale modifications. Please see WP:OWN. Mathsci (talk) 18:29, 14 August 2011 (UTC)

Mathsci, If you looked at my recent edits of this article, it was done primarily to condense and clarify the content of this article rather than adding information to it. I have taken a back seat to determining its content and I was trying to help whenever I can. So for you to suggest that I made "large scale modifications" or that I somehow claim ownership of this article is rather outlandish. I suggest you take a look at WP:good faith first before making such insinuations.

The current version is long and lacks focus. That I agree. But it is certainly not "hopeless" and the sources are certainly not "exceedingly poor". In fact, majority of the sources are largely the same and many of them are peer-reviewed (See WP:sources). Perhaps you could identify specific sources that we should remove or replace rather than making such sweeping comments. danielkueh (talk) 18:45, 14 August 2011 (UTC)

Sorry. This will not happen. We will move back to an earlier version, not written by either of you. The present version is incoherent and ungrammatical; indeed for such a high level article, the most some of the most poorly sourced, ungrammatical writing I have seen on wikipedia so far. It seems best to revert to an earlier stable version, open to discussion; the present version is only suitable for deletion. Mathsci (talk) 20:24, 14 August 2011 (UTC)

If that is the case, then you would have to go much further back. Because I also had "a hand" in the version that you suggested. If you are not going to respond to my comments and continue to make sweeping generalizations such as "poorly sourced" and "ungrammatical writing" and that I somehow am responsible for this, it will definitely make further collaborations very difficult. This is most odd considering that I agree with your previous statement "that discussion becomes calm with no inflammatory language." danielkueh (talk) 20:30, 14 August 2011 (UTC)

I am completely open to discussing which previous stable version of this section is restored. I don't see any point in continuing a discussion of the current version. Mathsci (talk) 20:46, 14 August 2011 (UTC)

Well, I'm glad you are able to back track a little bit. Also, thank you for your POV about the current version. The point I'm making is that we should not rush, either forward or backwards. We should consider every option carefully. Editors of this article deserve to be presented with different choices as to how best to proceed. Since this article is locked until August 20, we have plenty of time and no decision needs to be made now. Now if you don't mind, I would like to get the views from the rest of the peanut gallery so that an overwhelming consensus is reached. danielkueh (talk) 20:54, 14 August 2011 (UTC)

Sorry, to me the current version of this section is unacceptable and not a suitable starting point for discussion. Please be patient and wait for input from other editors. There is no point in jumping the gun to preempt discussion. Thanks, Mathsci (talk) 21:04, 14 August 2011 (UTC)

Mathsci, I think you need to follow your own advice by "not jumping the gun" or "preempting discussion." I am not saying we should not go back to a previous version nor am I saying that we must use the present version as well. I'm simply saying that let's wait for the responses of all the editors. Maybe they have other solutions. You are not the in the position to decide which is the best "starting point" of discussion. Especially since you are late and are not fully informed of all the details of the last two days. danielkueh (talk) 21:09, 14 August 2011 (UTC)

By the way, be original. It was I who suggested that we "be patient and wait for input from other editors." danielkueh (talk) 21:11, 14 August 2011 (UTC)