Talk:Evolution/Archive 19

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Hoyle's Fallacy

I think that Hoyle's fallacy should be adressed in the section on evolution because it is an argument often cited by Creationists. It is important to adress questions someone may have had on the subject; elsewise they will think that something is being kept secret from the Creationists, or we don't address it because there is a fault in our reasoning.

The problem with Hoyle's fallacy is that it ignores an important property of biology: deep - or geologic - time. Many small changes happen but a lot of information stays the same. Deep time is the idea that life has been on Earth for billions of years. Basically, if you have enough time, even the very unlikely will almost certainly occur.

Misconception

Appending to the thread below, let me explain something.

Evolution and Theory of Evolution are principally NOT the same. If one speaks of evolution one does automatically refer to the state of the art in an scientific evolutionary context. If one speaks of the theory of evolution one rather means the theory of natural selection. These two are absolutely NOT the same. The one refers to darwin who borrowed more or less the idea, the crux if you so will,filling one book gradually another. Nowadays Evolution spans from physics especially quantum mechanics to quantum chemistry, medicine over virtually the whole biological field. In fact Richard Dawkins put it this way: When one speaks of biology nowadays one esentially speaks of evolutionary biology because biology only makes sense in an evolutionary context". Something that is correct.

No. The theory of evolution goes beyond natural selection. True, in it's original conception by Darwin, the thoery was heavily focused on natural selection, but 150 years of work within biology, genetics, immunology, embryology have expended the thoery to such a degree that saying it is just a theory of natural selection is a gross oversimplification. The biological theory of evolution has absolutly nothing to do with quantum mechanics (provide a source for this grand assertion).

There are several but few facts (=scientific concensus) in all of science which are general relativity, quantum mechanics, evolution,... If we speak of the modern models we do not usually use the term theory, unless due to contextual circumstances (e.g. chronology = history). In principal all of these theories once sprung from a few papers to tons of pages with accumulated experimentation that potentially verified those experiments ten, twentyfold or more. Once can then deduce, this really is how nature is and even if a new experiment doesn`t fit it doesn`t automatically nullifies the scientific fact but rather only modifies it. Slicky 18:39, 2 September 2006 (UTC)

A scientific theory can never become a fact. Please understand the epistemological nature behind fact and theory. Gould said it best (From this article): "...evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome.... In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms."--Roland Deschain 18:58, 2 September 2006 (UTC)

Youre a braver man than I am, Roland, for signing with your name to what you just said. The object of a "theory" is to enduce debate, which in turn stimulates research and which in return bears fruit in the form of a "fact", creativity is more important that knowledge ("Einstein"). I believe that aptitude would go further in real life, this write fest has certainly "evolved" into a one hell of a discussion, Fact idiot 15:15, 28 September 2006 (UTC)

"The object of a "theory" is to enduce debate...." This is the common misconception of confusing "theory" with "hypothesis" in the technical sense that scientists use them. A hypothesis is a proposal that should induce debate, whereas theory refers to a broad interpretive framework. See [1]. In science, "theory" corresponds to meanings 1, 3, or 5, whereas most people understand "theory" to correspond to meanings 2, 4, or 6. [RD, notice how I make no allusions to creationists or the validity of evolution. ;-) ] Gnixon 16:10, 28 September 2006 (UTC)

Well Roland i am glad about your contribution, given the FACT that i defined what i meant with scientific fact, and what its definition is, namely "facts (=scientific concensus)" i think you merely contributed in an additive fashion by reciting the definition of what scientific concensus means. I fail to see how you lectured me in any way other than expanding on what i summed up by by two words in a bracket. :)Slicky 09:57, 3 September 2006 (UTC)

Oh and BTW: yeas scientific fact exists as a term, i didn`t make this up if that`s what bothered you. Virtually any significant word nowadays has a two digit number of various meanings and definitions in the various scientific disciplines.Slicky 09:59, 3 September 2006 (UTC)

The reason for this apparent dispute is that Slicky is not using English very precisely. Yes, facts are constituted through scientific consensus (see Latour and Woolgar´s superb ethnography, Laboratory Life). But this is an inadequate (necessary but insufficient) definition of "fact" as it is true of paradigms as well. Moreover, Slicky muddied the waters by naming General Relativity and Quantum Mechanics as facts. they are not. They are theories or paradigms which themselves depend on certain facts. Roland was quite right to point out that facts and theories are different. That both depend on scientific consensus does not make them the same, it only means they have (at least) one point of congruity. I am one of many editors - not just Roland - who believe that this article must distinguish clearly between evolution as fact (e.g. measurable changes in the the descendents of hawthorne flies) versus evolution as theory (a set of concepts for understanding how and why these changes are occuring, and why they are important). I see no grounds for arguing against this view unless one has poor command of the English language (or is a creationist). Slrubenstein | Talk 15:34, 3 September 2006 (UTC)

The use of word theory, where inaproppriate (as i pointed out, that is in situations where a scientific concensus has been reached) is IMHO detrimental to the scientific world as a whole. It invites every guy from the street to make of his own theory about the involvent of god mixed in with some demented ideas about how the world works and proclaim this with a notion of festivity to the world. Quantum mechanics etc, are considered facts even though at some point of view (a scientific one that is - with the scientific dogma at heart) they an theory. But that is rather a curious result from the scientific dogma itself. I will refrain saying they are theories unless i am talking within a well educated group. Even though new experiments could contradict quantum theory it will not be replaced nor will the theory be proven wrong, albeit for a new theory which has yet to proove itself, such a sudden change in perspective regarding the validity of a theory can occur within weeks or even days. Science is not a totalitarian regime, it promotes an open process and thought fullness, i invite you do to whatever the heck you find fitting. You certainly are altering as little my reality as i can make an impact in yours. We both confide apparently in strict terminology, a prerequisite to good science - but be aware that such can be a hindrancewhen talking to the populace, especially when they associate with their everyday use of the word theory something that is on par with god and the scientists crazed notion of knowing virtually nothing except their own keen striving to get their mugshot in the press so the messages about new religious revelations is underminded - and be it so much as to not make the front page. Slicky 09:14, 4 September 2006 (UTC)

Well, actually the post of yours SIrubenstein "Let us be precise. Darwin and the modern synthesis do not rule out the existence of a supernatural power (on this they are agnostic). They simply demonstrate that the existence of any supernatural force is unnecessary for and irrelevant to any understanding of the evolution of species. Let´s be specific and we may avoid misunderstandings." explains a lot. PS: ...meaning our attitude towards the world is too different as to be inclined in furthering the discussion. Call it ignorance or whatever you want.Slicky 09:17, 4 September 2006 (UTC)

If anyone can decode what slikcy is saying to me, I would be grateful. Slrubenstein | Talk 23:48, 4 September 2006 (UTC)

I'll give it a go for ya Benstein: (assuming you want me to decode what he claims you said as well) "Your post, which reads "Let us be precise. Darwin and the modern synthesis of evolutionary theory do not rule out the existance of any supernatural powers. (both Darwin and the modern synthesis are agnostic). They demonstrate that the existance of any supernatural power is not something one has to acknowladge in order to understand the evolution of various species. Let us be specific, and then we will not mis-understand each other" Explains a lot of things. Furthermore, our various perspectives on how the world works are too different from each other, and we would not be able to continue this discussion productively. Call this observation ignorance if you want." I think that's more or less the gist of it, Slicky seems to be quoting you from some post I can't see in this section, and then trying to demonstrate that due to your supposed exclusion of, well, God from your understanding of how evolution occured, that therefore your ideas on how the earth works are opposed to Slicky's a great deal. However, his assertion that this would make it difficult for you two to talk to each other remains to be proven. Homestarmy 21:00, 5 September 2006 (UTC)

"absolutly nothing to do with quantum mechanics"

Quantum mechanics supports chemistry which supports biology. David R. Ingham 07:21, 2 October 2006 (UTC)

"Just a Theory"

Something that bothers me greatly is when people say, "It's just a theory." Well, fellow Wikipedians, "just a theory" is in fact an oxymoron in the scientific field. Why? Because a theory holds an incredible amount of weight. Like contributor Astrobayes said before, many accepted facts in our everyday lives are "just theories." As a matter of fact, if "theories" really are "just theories", then I suppose gravity does not exist. For something to officially become a theory, it must meet the following guidelines-1)be an organized model 2)be tested repeatedly through extensive research 3)No opposable data 4)can possibly predict future events and 5) always be open to new data and change.

Now, I agree that Wikipedia should be neutral. But the fact of the matter is that Wikipedia is an online encyclopedia created and edited by people who obviously feel at least a little bit of passion for what they are writing about.Try as they might, some bias is bound to slip in at one time or another. Not trying to be offensive or anything, but I am pretty sure that the creationism article contains some words that would make the page appear biased-words that accept creationism as the truth. Honestly, when it comes down to the basics, everyone has a little bit of hypocrisy in them.

Which brings me to my next point. People say that evolutionists are "bullheaded" or "narrow-minded". However, this begs to differ. Whenever I hear debates in the classroom, creationists are adamant and constantly saying "It's just a theory," or "That's impossible," without even listening to the arguments of others. I do try to stay open-minded, but I cannot honestly say that I have not wanted to counter things before listening.

Evolution is NOT a theory, it has been promoted to scientific fact (see scientific concensus) for decades. The understanding and studying of evolution requires nowadays an understanding of quantum mechanics in a less physical context (that is you don`t have to study as much as the physical sciences do)called molecular chemistry, the understanding of molecular genetics (e.g. the genome is only a small relevant part given all the mamalia are essentially built from the same informational concept [genes] but rather epigentics, gene expression = histone modification et al, makes up the individual species), and many more disciplines.

How can evolution be a theory? I will not argue whether it happened or not, but it is not a theory. Since it cannot be tested, it could not have even entered the hypothesis stage. Evolution is actually a "model" for the origins, a possibility with some scientific evidence behind it. I would advise that we slightly change the name of the page, as well as some of the information inside of it based on this. I would do it, but I'm not extraordinary at editing. 70.238.161.164

The major life science journal database [2] has 182,026 articles when the keyword evolution is used ;). That's a lot of research for only a hypothesis. Keep in mind that it's a life science database, so no hits are returned that deal with non-biology uses of the term evolution.--Roland Deschain 03:07, 14 September 2006 (UTC)

Roland I agree with what you are saying, but referring to a database is not an argument. If you read all 182,026 articles (I can't believe there aren't more?) the you find an agreement on the concept of evolution, however the literature is filled with disagreements, hypotheses, and varying notions of the details. That does not belittle the fact of the concept of evolution, but does indicate that the theory is still evolving through the Modern Synthesis and beyond. I find it reasonable to critique the theory to some degree, however arguments to discredit the concept of evolution as fact are ill founded.GetAgrippa 13:35, 14 September 2006 (UTC)

It was a weak reply to an even weaker argument. However, my reply still makes the point that the theory of evolution is a very viable theory which inspires much cutting-edge research to expand the theory (and all the arguments and criticisms that are inherent in an expending scientific field).--Roland Deschain 13:57, 14 September 2006 (UTC)

When ones speaks of the theory of evolution one usually speaks of the darwinistic concept, whose relevance isn`t all that important anymore, because todays technology and science has made this an ubiquitious fact. And plating of a mutated bacteria on a drop out media is already a evolution 1:1 and the whole spectacle takes `bout one hour - if you are fast. And fast is all what the economy is about. Religious dogma are about the techning of ignoring other information e.g. science = leading to ignorance. Neurologically this ultimately leads to stupdiity in some sense, because what esentially is exploited in religion, or totalism or education, adversitment etc, are esential neurological development stages of the early human which will.....k sorry i lack the time, each one is invited to study all those fields on his own. BTW: It is no secret that even "higher evolution" has been studies over the course of several decades within a certain bird. ALSO please don`t waste your time trying to explain a person who is already satstfied with his theory of how the world works how evolution or whatnot works, once that person has passed a certain neurological stage. This NEVER works and is just a waste of time. You cannot hypnotize a person who forcibly focuses elsewhere. This does work however with children.Slicky 18:56, 2 September 2006 (UTC)

Also, evolution is a theory, which means it is always open to new data and change. Ergo, if contradicting evidence does appear, I think I will listen. I do think there is a higher power, but as far as the progression of life, no contradicting evidence has appeared. In fact, they are constantly finding new supporting evidence. A recent prehistoric species between fish and land animals was discovered, the ''Tiktaalik roseae''. Nonetheless, if you have contradicting info, I would be glad to hear it.-ERgO22 17:13, 18 August 2006 (UTC)

You're right. You may be surprised to larn though that this comment is useless, as this issue has been discussed before. This is the Talk page of the article on evolution, and it is used to discuss the article. At times, we wander into discussions on the nature of evolution and faith, but please, don't elicit such discussions. -- Ec5618 21:03, 18 August 2006 (UTC)

You are correct ERgO22. In the world of natural science, where mathematics and physics are the foundations of models of the natural world - a model stands or falls on its own merit, and not upon the pejorative of the day. It's best to not get frustrated with individuals using "theory" as a negative, because by that usage they clearly do not understand science. It will take them time. So rather, focus your energy on improving the great articles on science here at Wikipedia and detach yourself from these meaningless debates. Have fun editing! Cheers, Astrobayes 01:06, 19 August 2006 (UTC)

I know precisely what happened. One of you dogmatists didn't like my post and removed it. Well, get over it; not everyone agrees with your silly ideas! 66.52.217.19 16:21, 21 August 2006 (UTC)

For the record, this conversation was moved to the user's Talk page, as he well knows. User talk:66.52.222.96. He had responded there, before he posted the above. -- Ec5618 16:31, 21 August 2006 (UTC)

Thank you for trolling, remember to close the door on your way out. Joelito (talk) 16:23, 21 August 2006 (UTC)

Would it be of any help for the article of Evolution, to add on what Evolution isn't, and more clearly what it actually means, to all Sciences. If this will be accepted I'll propose some things Evolution isn't and some of what it is. Otherwise disregard this comment, if not usefull to you, but don't erase. GeorgeFThomson 17:04, 26 August 2006 (UTC)

We already have a misunderstandings section. Jefffire 17:08, 26 August 2006 (UTC)

Where would that be, as no textbooks have 'misunderstanding section'. GeorgeFThomson 21:13, 26 August 2006 (UTC)

That is one of the problems when a text book has no misunderstanding section of evolution, is that it opens up school class discussions with out clear facts from the scientific community, and wrong things are said about evolution as if it were true, and correct things are failed to be said also. -- GeorgeFThomson 21:52, 26 August 2006 (UTC)

GeorgeFThomson, please stop. Wikipedia is not a text book, it is a encyclopedia. If you have trouble with the current textbook standards in your country (I assume US), please write a letter to your representative. If this article has "wrong things are said about evolution as if it were true" please point them out; if "correct things are failed to be said also", point these out as well. But, for the love of God, please stop being so vague in your posts. Your philosophical writing and vagueness is very bothersome and just wastes space rather than improve this article. Quote specific sections of the article that you want changed or write specific sections that you want included.--Roland Deschain 22:15, 26 August 2006 (UTC)

The misunderstandings section is right here. Please do me a favor and read the article before you start a discussion on it.--Roland Deschain 22:20, 26 August 2006 (UTC)

Sorry I only barely glanced at 'religious and social controversies', as I saw Darwin's primate 'head', oh no sorry primate 'body', and this distracted my accurate reading. But in 'misunderstandings', there is not a clear mention that "Evolution" clearly does have as a definition, that 'natural causes' are un-intelligent, although other terminology is used, like 'un-guided', 'chance', 'blind' process, etc... 'Intelliegnt Design' thought proponents deserve to be clearly mentioned, as to what 'Evolution' isn't: a intelligent process of design. -- GeorgeFThomson 22:44, 26 August 2006 (UTC)

I am a declared probably one of the first 'Atheist of the God of the Bible and probably of any other God(s) as such', of the 21st century educations standards, that is trying to develop theoretically, valid scientific arguments and hypothesis, differing and/or refuting "Evolution". -- GeorgeFThomson 23:01, 26 August 2006 (UTC)

No. Nobody knows if evolution is unguided. For all we know, gravity is simply God pulling on the planets. Same thing as evolution: all the evolution we have observed may be due to the mutations selected by God. If you want to discuss the agnostic nature of science go over to Philosophy Of Science.

I already discussed why ID is not included here. ID is not science and therefore should not be mentioned as a critique of a scientific topic.

Again, look up Wikipedia:No original research. Come back once you verifiable sources.--Roland Deschain 23:17, 26 August 2006 (UTC)

Actually "unguided evolution" is called genetic drift; "guided evolution" is stuff like evolution by natural selection, evolution by sexual selection, etc. "Unguided" seems to mean "random" (if you look at Snoke and Behe, who used a non-selectionist model in their paper). Guettarda 23:53, 26 August 2006 (UTC)

Yes this is the other 'guided' 'unguided' use of these words definitons, as also a bigger 'guidance' 'unguidance' is beyond "evolution", as Roland Deschain, clearly states, as this would be religion/philosophy like 'intelligent design'. GeorgeFThomson 18:04, 31 August 2006 (UTC)

Using the section misunderstandings/distinctions between theory and fact, would the fact that artificial intelligence robots designed by humans use humans design functions as of other beings for their functioning, permit a hypothesis like: Humans are a advanced organic robot. All this data can be experimented on and observed by comparison with available 'robots'. I plan on using numerous small hypothesis for my proposed study that would be base to differ and/or refute "evolution". -- GeorgeFThomson 23:19, 26 August 2006 (UTC)

Nothing I can say to that, as it doesn't concern the theory of evolution. You will find much better ground for discussion at Philosophy of A.I.

Great. That means that paralel or other theories can be proposed and mentioned in text books, that amplify, Science knowledge, but that won't affect 'Evolution', as you have clearly defined 'evolution' previously and bellow. But other hypothesis could qualify for Science, as 'intelligent design' semantics doesn't. -- 24.86.45.243 16:59, 27 August 2006 (UTC)

Yea.Well I'm sinning with the rule of 'no original research'. But I'm looking with controversy and disccusion for it. Can I share information via email with you or what site that you may know of. -- GeorgeFThomson 23:30, 26 August 2006 (UTC)

Talk.Origins is a good discussion forum run from a scientific point of view. True.Origin is the creationist counterpart.--Roland Deschain 23:59, 26 August 2006 (UTC)

Roland Deschain, I'm in full agreement with what you say about the terminology and definition of "guided or un-guided" forces behind evolution, now "Evolution" is more clearly defined to me. ----- GeorgeFThomson 23:49, 26 August 2006 (UTC)

Roland, natural selection may not be unguided in the sense that drift is, but I think the clear point (one George Gaylord Simpson argued elegantly some time ago) is that it is not teleological, which i think is the crucial point. As to George Thomson, please do not abuse Wikipedia. Just create your own blog, and blog on there. Slrubenstein | Talk 18:31, 31 August 2006 (UTC)

We need an article on Unguided evolution clarifying what various parties mean by this term. Supporters of the Theory of Evolution mean one thing, opponents mean another. So they wind up talking at cross purposes - and sometimes even cluttering up Wikipedia talk pages. I tried to create it last year, but it was deleted without merging. Is it time for re-creation? --Uncle Ed 19:58, 31 August 2006 (UTC)

I don't see how this article would differ from evolution, and I am concerned it would become a POV fork. Jefffire 20:10, 31 August 2006 (UTC)

I agree with Jefffire. Evolution proponent will agree that evolution is unguided (as there is no such thing as devolution only optimisation to current situation); opponents will agree as in their view this show improvement needs guidance. So I don't see the add value. Arnoutf 20:14, 31 August 2006 (UTC)

Agreed. Ed is suggesting a POV fork. At the most, there is a semantic issue here that can easily be cleared up The word choice is theoretically irelevant among scientists. Slrubenstein | Talk 20:28, 31 August 2006 (UTC)

Much like Evolution is a fact the concept of guidence does not require it's own topic. Most of the philosophical issues of evolution are dealt with in Creation-evolution controversy. I deeply oppose creating seperate topics for minority views that are not just ignorant of evolution, but of general science as well (is gravity guided?).--Roland Deschain 21:00, 31 August 2006 (UTC)

Actually, no I'm not suggesting a Wikipedia:POV fork: that would be by definition disruptive. I'm suggesting the use of Wikipedia:Summary style to turn a difficult aspect of the topic into a page of its own.

To do this, I suggest we:

1. Create a sub-topic article on Unguided evolution (and make sure it's neutral).
2. Write a short summary of this spin-off article for the main article (and make sure this is neutral, too).

Doing this in no way violates NPOV. --Uncle Ed 15:01, 1 September 2006 (UTC)

I don't like it for two reasons:

1. Unguided evolution is simply evolution with an unprovable variable (absence of supernatural direction), there is no other variable. So this can be dealt with in a couple of sentances in this article. A quick google search shows that the term is rarely used and top hits are creationists sites.
2. A search of all major scientific and philosophical peer-reviewed journals produced no hits for the term unguided evolution (as it relates to the biological theory of evolution). So no research is done on that term (see reason #1).--Roland Deschain 15:41, 1 September 2006 (UTC)

It also assumes bias where there is none. Evolution does not rule out anything supernatural to create a subpage that does rule out the supernatural is misrepresenting evolutionary theory. I think Theistic evolution goes enough into beliefs about what a guided evolution may be (notwithstanding the semantic distinction between that and 'guided by unguided forces' as discussed above.) Evolution itself is agnostic on the subject. Let's say a tornado flattens an entire town but leaves the curch standing. Some may see the hand of god others may see random chance, neither of those view affect the facts and science of the tornado. Nowimnthing 15:58, 1 September 2006 (UTC)

This is false. Evolution does rule out the supernatural, as do all scientific theories, insofar as the domain of the theory is concerned. To do otherwise invalidates the entire scientific process and does not allow further inquiry. Graft 17:26, 1 September 2006 (UTC)

Let us be precise. Darwin and the modern synthesis do not rule out the existence of a supernatural power (on this they are agnostic). They simply demonstrate that the existence of any supernatural force is unnecessary for and irrelevant to any understanding of the evolution of species. Let´s be specific and we may avoid misunderstandings. Slrubenstein | Talk 17:38, 1 September 2006 (UTC)

Well stated. I might go a bit further that evolution does not rule out supernatural actions. Again it is agnostic because supernatural is beyond its purview. Many of us may use the explanatory power of evolution to bolster our athiesm (and I think that is what frightens the religious the most, that there is no need for a supernatural agent when natural agents can be found.) But just because there are natural agents (fact) does not mean that supernatural agents do not exist, though to some of us and apparently to some worried religious people, it makes the supernatural agents redundant and therefore in trouble with Occams razor. Nowimnthing 18:25, 1 September 2006 (UTC)

I'd say that Graft and Steve are both right. Evolution as an experimental science does rule out the supernatural because it's outside the range of what it can consider. So yes, if you are doing science you rule out the supernatural or else you can't do science (how do you disprove the hypothesis "a miracle happened"). On the other hand, evolution as a fact is agnostic to the supernatural. Evolution as a descriptive science (or as the assumption that underlies all aspects of modern biology) is agnostic as to how the changes occurred. IMO, anyway. Guettarda 18:41, 1 September 2006 (UTC)

Indeed. There are theories that attempt to explain how the small changes occur, but exactly how mutations occur is still a bit mysterious. (Yes, I know about radiation and replication errors - but what causes those?) I would imagine that an omnipotent, omniscient creator would find it equally easy to use extremely obvious methods or extremely subtle methods in its work. If you are omnipotent, there is nothing preventing you from using the most ridiculously difficult, roundabout way of getting something done - if, say, you happen to have a good reason for wanting to hide from your inquisitive creations. Therefore, once again, there is still no necessary ideological conflict between deism and science. Kasreyn 23:58, 1 September 2006 (UTC)

We know what causes them; we know why radiation causes mutation (it damages the DNA itself by breaking bonds and changing conformation of molecules) and we know what causes replication errors (rarely, the wrong molecule will get enough affinity, get put in the wrong spot, and the error checker skips it). Titanium Dragon 03:26, 15 September 2006 (UTC)

My point was to put it a little differently that science "rules it out" in a very specific, precise way - and we would do well to emmulate the precision of science when we talk about science. Slrubenstein | Talk 19:58, 1 September 2006 (UTC)

Isn't intellegent deisign a theory also?

No, intelligent design is not a theory, it is a religious belief. Theories, as I know them, are scientifically based

I don't go so far as to say a theory must be proven to be called a theory, but the things I am surest about like Maxwell's equations and quantum mechanics are theories. I could be crazy or dreaming, but I know I am not ignorant. David R. Ingham 07:35, 2 October 2006 (UTC)

All organisms -> all known organisms

All known contemporary organisms would IMO improve the article: I am a firm believer of evolution and do believe, nay, accept the fact that most - if not all - species on planet Earth share a common ancestry. However, statement that's currently in the page all contemporary organisms is not limited to species that have been found and studied but is a ridiculous carpet statement about *all* species including, but not limited to, (possible) extraterrestrial species and some uncertain classifications (see eg. nanobes and nanobacteria, Red rain in Kerala, ALH84001). What the statement implies is a single unified origin for all life - Something that's more a religious standpoint than a viewpoint based on *available* evidence or even the hypotheses about the origin of life. I'll end my proposition with a quote from wikipedia itself: ''Nanobes are 20 nm in length which biological conventional wisdom assumes is too small to contain the basic elements for an organism to exist (DNA, plasmids, etc.) - G3, 03:48, 21 August 2006 (UTC)

For that matter, if you're afraid of it sounding too WP:Weasely then let's add All known organisms are without a doubt related to each other... - G3, 03:53, 21 August 2006 (UTC)

My objection is two fold. First, provide scientific research that shows at least one organism that does not support common descent. If you do that, then this article can neither use "all" or "all known". That's the easiest way to change it. The second objection is, if we allow this change, it would require huge amounts of rewriting in all scientific topics on Wikipedia. We would have to go to the gravitation page and write "All known astrological bodies support gravity" or in chemistry "All known atoms support the atimic theory". Do you see the problem. You are implying that there might one day be a discovery that shows common ancestry to be wrong and you are absolutly right. But this philosophy is so deeply ingrained in science that it does not need constant reaffirmation. If you believe that, you'll have to go through every single scientific topic and change it to reflect what you want to see in this article: that one day the entire thoery might be proven falls. I don't like it because creationist use it so often, since they can claim that their theory will be true for all time. --Roland Deschain 04:05, 21 August 2006 (UTC)

Addition: I did a quick search of major science databases and found nothing on Nanobes. Can you provide some scientific research on them, please. I'll go read the wikiarticle and see what it's all about.

Addition #2: Concerning ALH84001: that hypothesis is pretty much dead. It was just a big media hype and then nothing more. Concerning Nanobes or nanobacteria: I actually found some nice research on them, but nothing that indicates that they are a challange to common descent. I'll go back into the wikipedia article and make that point quite clear.

Addition #3: Red Rain. Again, nice example of organisms in weird places, but nobody said anything about these organisms refuting common descent. Mostly it was a big media hype due to biblical references. Hopefully these detailed responses show that no suggestions are thrown out by dogmatic wikieditors. If there is evidence there, I'll gladly put it in.

It's in no way about refuting the theoretical foundation of common descent (similarities of known & well studied contemporary species are staggeringly for it) - It's about possible, admittedly unverified, poorly studied or not yet found but still possible, exceptions to the carpet statement that *all* Earthly species share a single ancestor.

Though, I - personally (WP:OR) - could go a long way in hypothesizing how the common ancestor of organism A (eg. animal) could be different from the common ancestor of organism B (eg. bacteria) based on the endosymbiosis of other original species or maybe even that the fine structure of life as we see it now is the optimal (probability/complexity/efficiency -wise) evolution driven solution for the environment - solar input, mineralwise - of Earth thus rendering micro level similarities as more or less coincidental. Heck, there's even the possibility that in the primordial soup where life - as we know it - originated (assuming it did as opposed to eg. panspermia) there were two or more distinct self replicating molecules that were similar because of the similar origin but not the same ie. of different 'species'.

Regardless of this debate, if we accept abiogenesis then we must also accept that it's something that has most likely occurred multiple times during the history of Earth. - G3, 05:24, 25 August 2006 (UTC)

Leave it as it is. However I'd like to see the last words of the paragraph changed to "on Earth". There are many "worlds" but only one Earth. --Michael Johnson 09:08, 21 August 2006 (UTC)

That's better. However, I'd add the on Earth after the contemporary organisms (ie. All contemporary organisms on Earth). Secondly, the more I thought about the sentence the more brilliant the word contemporary seems: For the organism to qualify as contemporary it must be first shown that it exists in the modern world - Thus making it a known species... ;) - G3, 05:24, 25 August 2006 (UTC)

embryology

would sympathtic editors consider a positive vote here? [3]Slrubenstein | Talk 15:17, 23 August 2006 (UTC)

• (Deleted offensive and pointless post by User:Barry White. Moved it to User talk:Barry White)

Sentence order

This is mostly to Roland - I'd like to put the sentence order you reversed some ten days back in the intro the way I had it before. I think this makes more sense - common descent is what produces biodiversity, and so it makes sense to mention biodiversity first and then common descent second; plus I think the sentences read better the other way. Graft 16:58, 24 August 2006 (UTC)

Nope, common descent does not produce biodiversity. There are many mechanisms that do, but common descent in not one of them. Common descent actually does the opposite, keeping absolutly vital features of life the same in all this biodiversity. I changed it so the most far reaching sentance is at the end, as should be done. However, feel free to change it and I won't revert it, but our of courtesy wait for somebody to break the stale mate.--Roland Deschain 17:16, 24 August 2006 (UTC)

Erm, I think we're thinking of the tree in opposite directions - moving forward in time, descent means divergence, which is the production of diversity. I.e., common descent means I produce many from one. Anywho, yeah, I'll wait. Graft 18:21, 24 August 2006 (UTC)

But the concept of common descent doesn't cause biodiversity. The biodiversity is despite common descent. The important word here is 'common', surely? Descent itself could arguably be blamed for a lot of things! But 'common descent' narrows things down at the beginning. This may be rather confused, but basically I agree with Roland. Skittle 09:45, 26 August 2006 (UTC)

Again, you're thinking backwards in time. Move forward and the tree diverges, it doesn't converge. But, if this isn't obvious I guess it shouldn't be stated like that in the intro. Graft 16:21, 29 August 2006 (UTC)

You are confounding common descent (using evidence to argue that all life came from one ancestor, ie: going backwards) with mechanisms for biodiversity (natural selection, genetic drift or going forwards once that common acestor has been established). They are two fundamenally different parts of the theory of evolution and should not be confused. I agree that going forwards the tree diverges, but that does not indicate a universal common descent, but rather indicates a mechanisms of evolution. Rather, going backwards, looking at the tree converge one finds that it all (with high probability) comes back to one ancestor. So there is a difference and this topic should not confuse the two. These are two theories which complement each other: common descent (the theory that all life arose from one common ancestor) and origin of biodiversity (due to evolution as explained by the theory of evolution). They do complement each other, but they are not the same thing. --Roland Deschain 19:42, 29 August 2006 (UTC)

Drift and selection can only eliminate diversity; mutation is the only process that produces divergence. Anyway, I take by 'biodiversity' to mean "the tree of life", which we say is produced by common descent, i.e., it is a tree precisely because of common descent and for no other reason. Stating that there is common descent implies that over time, biodiversity will increase due to the divergence of species. No? Graft 18:19, 30 August 2006 (UTC)

You are very confused about evolution. Drift and selection are mechanisms that act on mutations to produce diversity. Mutations, by themselves, will never produce diversity without a mechanism to retain the beneficial ones. So mutation is the raw material for these two mechanisms to produce diversity. Saying that drift and selection do not produce diversity is therefore a very wrong statement. You have to differentiate biodiversity from common ancestor. The current trees produced go back to approx 550 million years back (based on Cambrian explosion), that is our tree of biodiversity based on fossils, molecular similarity, etc etc. The fact that the tree converges to a common ancestor is based on evidence quite different from the evidence used to justify our current tree for biodiversity. That's why biodiversity and common ancestor are two different theories that complement each other. They depend on different lines of evidence, but the conclusion for either theory complements perfectly the other one. Biodiversity does not have to increase. Certain species have remained static for millions of years. Furthermore, very frequent mass extinctions counterbalance any directional increase in biodiversity.--Roland Deschain 20:04, 30 August 2006 (UTC)

I suppose I am confused, then - could you specify what these different lines of evidence are, one supporting common descent and the other supporting biodiversity? I'm unclear on what you mean. Also, I'm unclear on how you're using 'diversity' - if you mean strictly speciation, then I'll agree that drift and selection are important forces that are required to produce speciation, since one couldn't have fixation/divergence without them by definition. If you just mean 'variation', e.g. the diversity evident within the human population, then you are wrong. Drift and selection in that context act AGAINST the existing diversity, produced by mutations, and can only result in eventual fixation - that is, the elimination of variation. Anyway, that's obviously a semantic argument that's not worth having. Let's assume we mean 'speciation' when we talk about 'diversity'.

That said, I still fail to see what you're positing as the source of diversity. Could you clarify? Graft 20:41, 30

August 2006 (UTC)

The source of diversity is explained by evolution: natural selection and genetic drift in the broadest possible sense. The thoery of common ancestor does not rely on the concept of natural selection or genetic drift. Rather it relies on the fact that all organisms have commonalities to them which are best explained by a common ancestor (such as nucleotides, cell membrane, chirality of amino acids, genetic code); notice that none of these can be used to create a phyloenetic tree of biodiversity as they are present in 'all organisms in the exact same state (there are exeptions of course, but they are minor). So different lines of evidence are used to attack each question. However, notice that both theories complement each other. If there was a universal common ancestor, then evolution would produce all current biodiversity we see today from this organisms. Again, notice that argueing for biodiversity we use evolutionary forces. Arguing for common ancestor we use common characteristics of all organisms. Two different lines of evidence that fit rather nicely into the theory of evolution.--Roland Deschain 21:01, 30 August 2006 (UTC)

Hardy-Weinberg equilibrium and other oversights

There are a number of problems I have with this. First, it is from the perspective of NeoDarwinism with little reference to Kimura and neutral evolution (I see now it is mentioned, my error), nor any mention of evodevo approaches and evidence (studies of ossicle development would be a good one). There is no mention of Hardy-Weinberg equilibrium. In the mutation section is doesn’t mention evidence from genomic sequencing that mutation appear to be restricted to hot spots, and there are sequences (500 long sequence and 1500 short sequence noncoding regions) that are 100% conserved in most chordates. No mention of examples of genomic alterations that have been associated with speciation (stickleback example and ecdysone) It doesn’t mention the excitement over small RNA’s interference RNA’s, etc. There is no mention of Gould’s ideas of punctuate equilibrium, and exaptations and spandrels. No mention of transposons (I think).A good transposon example: 80% of the world wide populations of drosophila melanogaster possess and transposon associated with cytochrome P450 and insecticide resistance. The transposon is I believe 90,000 years old, but it has only gained reproductive success the last 50-250 years. I would call this a Gouldian spandrel at the molecular level. It was already present in the genome, but it only recently acquired a function and reproductive success. I don't like the term "survival of the fittest" when it is generally a compromise of cost benefit interaction. A recent trend in garter snakes evolving resistance to tetrodotoxin in a newt within their diet is a good example. They can eat the newts with less detrimental effects, but the change in sodium channels is at the cost of slower reaction times (hence more prone to predators). Evolution only produces adequate strutures and changes for survival. I wouldn't say fittness is an appropriate term.

A good definition for evolution by my reckoning would be :A genomic (it is not just gene allele changes) alteration (change can be a transposon or small RNA so no mutation per se is necessary) within a population that proteogenomic, ecological, and behavioral interactions culminate in the reproductive success of the change within the population through time. I have a bunch more critiques, but this is a start. GetAgrippa 15:28, 29 August 2006 (UTC)

That's a lot of stuff to put in. Feel free to start adding that to the appropriate sections. If possible, add sources for your info. I am familiar with most of your assertions, but a couple are a little bit more specialized and require a source.--Roland Deschain 16:12, 29 August 2006 (UTC)

I don't agree with most of that - there IS mention of Kimura and neutral theory, where appropriate - in what context do you think more needs to be put in? Mutation hotspots exist, but mutations are by no means restricted to hotspots, they're just more frequent there. I'm not sure why Hardy-Weinberg would be relevant; it's an idiosyncratic population genetics point, really, and only true of ideal populations that are not evolving. Sequence conservation is fine, but again I think this is too detailed for a general overview article; ditto for transposons, though this might deserve a single-word mention in mutation section. Fitness is absolutely the correct term to use, it's practically tautological. "Allele" does not just refer to point mutations, it can include many other kinds of segregating polymorphisms.

I agree that spandrels are interesting and deserve a brief mention, as do specific examples of speciation events. Graft 16:29, 29 August 2006 (UTC)

I think Hardy-Weinberg should be mentioned first (gives reason why things don't change), and then mutation, natural selection, gene flow, gene drift, and nonrandom mating as what causes evolution. This could be useful to address the living fossils issue, that may have invisibly evolved. However it may be they just haven't. I didn't see the brief mention of neutral evolution (my mistake). There is a growing body of evidence of nongene mutations associated with evolution, that is why I like genomic change rather than concentrating just on genes, also at this point one could introduce small RNA's as a potential source of evolutionary change. I agree there as SNP's but it terms of gross evoluton I think the hotspots are associated with traits that are subject to change. I think evodevo is a great way to introduce the change in mindset in evolution. In the 70's when I was first introduced to evoluton it was from a comparative anatomy perspective-jaw elements becoming ossicles in middle ear. Now we see that the developmental process (molecular approach) within the pharygeal arch is altered to generate two of the ossicles, one is generated de novo. The jaw bones do not become ossicles rather the developmental sequence is altered to create something new. It demonstrates evoluton generally creates by altering what is has rather than creating something new, i.e. new genes from part of old, etc; The sequence consevation is critical to demonstrate that some processes are hard wired, hence we can study zebra fish and chick embryos to study embryology. I also think from that view you can introduce gene loss and gene gain as building blocks to alter a fundamental plan to generate diversity. View evolution in terms of genomes-struture,gene loss , gene gain , significance of nongene elements, transposons, small RNA's, methylation, etc.GetAgrippa 12:12, 30 August 2006 (UTC)

Oh yeah, I don't life suvival of the fittest, it should be survival of the sufficient or adequate. It gives people the wrong idea that evoluton is producing better or superior or perfect. I see it as humanistic bias. Why is a giraffe's neck so long? It could be from behavioral choice (like a lion's mane)and nonrandom mating, or the genetic network associated with long necks is linked with another genetic change that actually increase survival-gene linkage, or competitive for reaching food in the tree tops. Populations can respond by alterations in behavior and alterations in structural features,alterations in physiology or metabolism, but the change just has to be sufficient for survival (I guess it is semantics in how fittness is viewed the more I think about it).GetAgrippa 12:31, 30 August 2006 (UTC)

If you want to fit Hardy-Weinberg in there, go ahead, but I really don't think it belongs here. It just says allele frequencies stay the same despite dominance; that was all it was meant to demonstrate. It says nothing about evolution since it assumes absence of any evolutionary forces explicitly.

WRT fitness, you're maybe thinking of 'absolute' as opposed to 'relative' fitness. Evolution can only deal with the latter, which is what 'survival of the fittest' means. See fitness (biology). Graft 18:12, 30 August 2006 (UTC)

I hadn't seen the fitness biology link, that is good. Given that link then the fittest perspective seems reasonable. My only caveat is that laypeople often confuse fittest with moving towards some idealized perfection. I tend to agree with the gene analysis, but I also like to add macroevolution of gene and genome duplications events, gene loss, and regulatory non-gene regions (discovered gene-genome duplications are mentioned so forget this). I think that gene changes should not exclude the altering of existing gene networks via transposons and small RNA,etc. People tend to think only of point mutations rather than other changes. I agree with what you are saying about Hardy-Weinberg, but for laypersons it often seems like a logical starting point. I don't feel so strongly about it that is worth any changes. I'll give the whole section a closer re-read as probably many of my concerns have been addressed. ++These three suggestions maybe worthwhile.I think it would be worth while to have gene changes associated with speciation, because laypeople can see mechanistically evolution in a visible way with the alteration of a gene or gene network. Some of the archaic DNA studies like the cave bears and artic penquins is good continutity from a fossil record perspective to a molecular biology perspective (a good blend). Mention of Gould's idea of spandrels. Some of my comments may have been premature from failing to closely read the section. My apologies. For the length, it does an excellent job after closer scrutiny. GetAgrippa 20:47, 30 August 2006 (UTC)

Still harping on Theory vs. Fact ;)

There are two well written sections about this misunderstanding of theory and fact regarding evolution: Creationism versus evolution and in our article. As both sections deal with the exact same concept, I think the two can be combined as each has some information the other doesn't. If I don't get any strong objections, I'll get to it tomorrow. The only caution to be taken is that the Creationism article deals with creationist's misunderstanding, whereas out article misunderstaning section is more towards the general person.--Roland Deschain 05:20, 2 September 2006 (UTC)

I do not think there is anything at all wrong with two articles having some identical content. In fact, I think it is a good thing since many readers will go to one article but not the other. I think repitition is only a serious problem within the same article. Slrubenstein | Talk 15:26, 2 September 2006 (UTC)

Agree with Rubenstein, no reason to merge the two sections as they are in different articles.JPotter 19:12, 2 September 2006 (UTC)

Yeah... no need to merge. Some ppl read one & not the other. And given the immense amount of trouble it saves us when pov ips come in (just point them to the section), I say it should stay. Mikker ^(...) 20:19, 2 September 2006 (UTC)

Unlike a book, repetition in wikipedia is important. It is seems unlikely that both articles will be read by the same reader. David D. (Talk) 20:39, 2 September 2006 (UTC)

Spanish flu and Flu research both transclude Spanish flu research; which is one way to have the same content at two places. Usually it is good for the text to be seperate so they can evolve seperately; but not always. WAS 4.250 04:14, 4 September 2006 (UTC)

User:60.48.200.124's edits...

FUI... 60.48.200.124 made edits that were reverted first by Guettarda and then by me. I posted this on the ip's talk, who then responded on my talk with:

"You wrote: I have reverted your edits on the evolution article, I don't think they are accurate. The section you are editing has emerged out of a long process of consensus formation, so please justify why you think the changes you want are justified on the aticle's talk page.

1. You haven't said why the changes are not 'accurate'.

2. To explain: I made the adjustment because I regarded the old text as biased. To cite 3 Jewish groups as regarding evolution as coherent with their belief may be 'true' but it is unbalanced. For example, I am aware of Orthodox Jews who are not in agreement with evolution. I would also regard it as unbalanced to just cite this viewpoint.

3. You didn't say why you regarded the reference to Hinduism as inaccurate.

4. I liked the link [4] as more balanced overall.

I'm not going to remake the changes or add anything on the talk page. Your choice about what you do about it."

I think the ip might have a point about including Hinduism, but we need to find a better source than the link he/she provided - altough it is from an "edu" domain, the article in question is mainly a collation of web sources; not exactly reputable stuff. Mikker ^(...) 09:01, 3 September 2006 (UTC)

Location of 'Founder effect'

I was a bit surprised to find the Founder effect as an example under gene flow. Usually it is considered as a form of drift, because it changes allele frequencies as a consequence of sampling error in the (initially) small population and because it is a loss of alleles from the local population, rather than gain of alleles as happens with allele/gene flow. Isn't it better under drift? Satyrium 18:07, 3 September 2006 (UTC)

The Founder effect is from the small sample size so it under the heading of population structure, but it is also a bottleneck of mutations and it would also fit in mutations.GetAgrippa 19:33, 3 September 2006 (UTC)

• err, by that, just about everything would go under mutations -- gene flow, flow of mutations; natural selection, loss of mutations, etc. Satyrium 17:39, 4 September 2006 (UTC)

Yeah, that is a confusing statement I should have stated a bottleneck in population size. Oops, my mistake! I think the Founder effect is often classified as genetic drift the more I think about it, but I'll do a search and find out. GetAgrippa 21:24, 4 September 2006 (UTC)

In Structure and Function of Evolution by Gould he discusses the Founder effect as a subcategory of Genetic Drift (in terms of Mayr's definition). Other papers also appear to have adopted the same nomeclature.GetAgrippa 22:22, 4 September 2006 (UTC) Now someone has the Founder effect under both drift and flow? There is also the term founder drift. This needs to be addressed! It will confuse readers. This section is getting too complex and needs some simplification.GetAgrippa 22:29, 4 September 2006 (UTC)

Mobile elements and Micro RNA's

I added a section with transposons in the mutations section, and Micro RNA's because of their growing interest. I can add examples and references if needed.GetAgrippa 19:37, 3 September 2006 (UTC)

I appreciate that micro RNAs are interesting, but their relevance to evolution is unclear, especially from the text, which says almost nothing about their direct relevance; in an overview article, it seems highly out of place to include this section. Graft 18:15, 6 September 2006 (UTC)

Well it is pretty new, but it brings in epigenetic mechanisms of evolution and a link to evodevo. You cannot deny that natural selection has driven the success of the Micro RNA and the three references link them to evolution, so NPOV should drive some mention.GetAgrippa 00:14, 7 September 2006 (UTC)

Micro RNA should be mentioned, but the topic does not deserve its own section in the article. I'll put it in the current research header (it basically serves as a repository for all those topics that should be included once the research has accumulated enough research and novel/stable theories.)--Roland Deschain 00:30, 7 September 2006 (UTC)

Roland that sounds very reasonable as nongene alterations are growing in interest as being major evolutionary mechanisms.GetAgrippa 02:41, 7 September 2006 (UTC)

Merge of Hoyle's fallacy discussion

It seems that the Hoyle's fallacy article stub should best fit within this article at the discussion of self-organization. I did not check very far back in the talk archive (mea culpa) but it would seem that this sort of information/formal naming of the fallacy would best fit as a piece of this article and does not stand well (or well-sourced/backgrounded) on its own. Discuss. ju66l3r 06:32, 4 September 2006 (UTC)

What interests me about the article on Hoyle's Fallacy is that it explains what the formulation is, and that it has been rebutted, but it doesn't relate what that rebuttal was. So it's really not very helpful. It just says "here's something someone said, which a lot of people have copied, which turned out to be wrong. If you want to know why it's wrong, go read these books." That's not how WP is supposed to be. Kasreyn 08:52, 10 September 2006 (UTC)

Good idea to fix the Hoyle's fallacy article, bad idea to merge even more detail into this article which is rather long already. The TO article looks worth summarising. ..dave souza, talk 13:14, 21 September 2006 (UTC)

I'm with dave souza - Hoyle's fallacy could do with being expanded, but shouldn't be merged here because we're already waaaaay too long. If it's not already referenced in this article, perhaps mention it, but we don't need to bring it all here (and certainly not as it needs expanding along the lines Kasreyn has identified). Cheers, --Plumbago 13:21, 21 September 2006 (UTC)

History Section

The sentence about a consensus of the origin of Bacteria, Archae, Eukarya is not completely true. There does seem a consensus that whatever the Last Common Ancestor was that it was already fairly complex. I can provide references. I believe most feel the bacteria and Archae evolved through a process of gene loss. GetAgrippa 09:17, 8 September 2006 (UTC)

A fair few people do suspect that, but there is little evidnce and I would not call it a consensus. Jefffire 09:23, 8 September 2006 (UTC)

A recent Science article was speaking about a evolution meeting that debated the issue and a consensus was reached that whatever the last common ancestor was it was already a complex organism. I'll find that reference, but here are a few older ones that support the contention: Bioessays. 1999 Oct;21(10):871-9. Science 5 February 1999:Vol. 283. no. 5403, p. 791. Science 13 June 2003: Vol. 300. no. 5626, pp. 1703 - 1706.Science 19 May 2006:Vol. 312. no. 5776, pp. 1011 - 1014. GetAgrippa 13:03, 8 September 2006 (UTC)

Insertions and Deletions statment in Mutations section

While I agree that deletions and insertions are associated with gene dysfunction as in Fragile X syndrome, Huntington’s, and Cystic fibrosis, CATCH-22 syndrome, it also appears to serve positive effects in evolution. Gene insertions in the dog genome associate with the length of the dog snout, MHC polymorphisms and deletions and insertions, gene loss and deletions is significant in yeast evolution for example. 45% of the human genome is transposons I recollect. Here are a few other references beside what I just mentioned: Herrera RJ, Lowery RK, Alfonso A, McDonald JF, Luis JR. Ancient retroviral insertions among human populations. J Hum Genet. 2006;51(4):353-62. Hagemann S, Hammer SE. The implications of DNA transposons in the evolution of P elements in zebrafish (Danio rerio).Genomics. 2006 Jul 27; [Epub ahead of print]. Xie X, Kamal M, Lander ES. A family of conserved noncoding elements derived from an ancient transposable element.Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11659-64. Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, Devine SE. Recently mobilized transposons in the human and chimpanzee genomes.Am J Hum Genet. 2006 Apr;78(4):671-9. Epub 2006 Feb 2.It would seem that the addition I made to the end of sentence about insertions and deletions needs to be updated from the old reference and introduce transposon and significance of insertions and deletions in evolution. It is warranted to return some positive influence in evolution.GetAgrippa 13:39, 8 September 2006 (UTC)

First Sentence

The definition of evolution just including allele frequency is narrow and should mention genomic change as non-gene areas are also positively selected and regulates genes and gene networks and genomic change would also refer to duplication events of genome, chromosome, and gene. A Science article highlight my point: "A study of two species of fruit flies found that 40% to 70% of noncoding DNA evolves more slowly than the genes themselves. That implies that these regions are so important for the organism that their DNA sequences are maintained by positive selection. These noncoding bases, which include regulatory regions, were static within a species but varied between the two species, suggesting that noncoding regions can be key to speciation." "The genome data confirm our close kinship with chimps: We differ by only about 1% in the nucleotide bases that can be aligned between our two species, and the average protein differs by less than two amino acids. But a surprisingly large chunk of noncoding material is either inserted or deleted in the chimp as compared to the human, bringing the total difference in DNA between our two species to about 4%."Science 23 December 2005: Vol. 310. no. 5756, pp. 1878 - 1879.GetAgrippa 04:11, 9 September 2006 (UTC)

I understand your point, but the defenition of an allele is: "...any one of a number of viable DNA codings occupying a given locus (position) on a chromosome. Usually alleles are DNA sequences that code for a gene, but sometimes the term is used to refer to a non-gene sequence". So the term allele does not always refer to genes. Alleles, due to the steady rate of non-gene variation you describe, have been redefined to encompass a larger range of variability (not just genes anymore).--Roland Deschain 05:37, 9 September 2006 (UTC)

Excellent Roland I was unaware that the definition had been altered. I am Old School. I am glad that the definition has been expanded to meet current thinking. I have developed the habit of saying genomic elements, but now feel free to use the term alleles again. Thanks. Often current thinking lags in incorporation into introductory text or definitions.GetAgrippa 12:30, 9 September 2006 (UTC) Upon further reflection I find the Wikipedia definition of an allele including non-coding sequence is illogical and I wouldn't believe a geneticist would agree with that analysis. Polymorphisms are in gene alleles not non-coding regions. They are non-coding regions and are mostly regulators. The end product proteins manifiest the polymorphisms of gene alleles. I think it would be a huge mistake to include non-coding regions as parts of alleles. You can say there are polymorphisms in insertions that add to gene to create new genes and alleles, but they are coding sequence. You can mechanistically say they are important in the formation of the end product messenger RNA as regulators but not a part of an allele. I think genomic element is more accurate and I would hope it would be changed on the allele definition. I can find no reference of calling non-coding regions alleles. Further many non-coding regions are highly conserved with 98-100% homology across a variety of species in mammals, insects, and plants. Hence there no evidence of polymorphisms in these non-coding regions. I would also add the insertions and deletions should be changed from just inactivating genes in my argument before this one in the mutation section, since insertions and deletions are one of the main differences in human - chimp genomes and are obviously positively significant in our differences. GetAgrippa 15:42, 9 September 2006 (UTC)

This is a tricky topic, trying to get defenitions for such huge concepts. It all rests on how a gene is defined (as an alleles are simply varations in genes). In the classical sense, it was simply a protein coding region. Then discoveries were made and it was redefined to protein coding region + regulatory sequences. Since my second year of university genes have been defined thus: "The basic functional unit of inheritance". It's a horrible defenition, but that's why it is all encompassing. More discoveries will be made in the future to further expand the meaning of a gene, and this defenition will still hold. As long as a DNA/RNA sequence has a function (which can be selected upon) it can be called a gene. First it was protein, then protein+regulator sequences, now it's simply anything that has a function.

There is a Nature paper (2003 Oct 2;425(6957):457) that discusses the gene. It starts of "From the start, there was a tension between the concept of the gene as a ‘unit of inheritance’ — which was defined in purely operational terms as an autonomous unit that transmits specific traits through multiple generations — and the gene as a physical entity — whose position could be mapped in relation to other genes on the chromosome." And here is the final defenition that the author comes up with: "Instead, the gene has become a flexible entity with borders that are defined by a combination of spatial organization and location, the ability to respond specifically to a particular set of cellular signals, and the relationship between expression patterns and the final phenotypic effect." Like my defention, this is a very broad defenition.

So in the end I think the intro is fine. An allele is a alternative version of a gene (which is defenined in a functional sense, rather then in a protein encoding sense).--Roland Deschain 17:53, 9 September 2006 (UTC)

Roland, thanks for the explanation. I'll read the Nature paper. I guess it is in such transition a new definition is forthcoming, especially with all the genomes being sequenced. It is an exciting time to be a scientist. Good luck in your education. I was old school B.S., Master's and then Ph.D. I have met lot's of young folk going for the M.D./Ph.D. I would encourage you continuing on for your Ph.D.. Being a scientist is a great occupation, especially research. You are never too young or too old to learn. I learned something new today. I have always had a passion for science. I see you do too. Subscribe to Nature or Science as they are a good way to keep abreast of areas not in your expertise, and being a member of AAAS looks good on your c.v.. Many ideas from other fields have been useful in my pursuits. There pricey but well worth it. I think both will give you a student discount. GetAgrippa 19:07, 9 September 2006 (UTC)

Um, as someone who works with SNPs regularly, especially non-coding SNPs, I can assure you that allele frequency is regularly used to describe non-coding variation. 'Allele' does not mean an alternate version of a gene in most usages any longer; in the modern day we have a much finer-grained view of variation, and alleles usually refer to variation at any point in the genome. Graft 01:47, 10 September 2006 (UTC)

Yeah I gather. Apparently protein-coding and noncoding genomic regions are based on intron-exon structure. Noncoding genomic regions (98-99% of the human genome) consisting of introns found within protein-coding transcripts and intergenic regions between them that are transcribed into polyA stable RNA during development. The ENCODE consortium suggest calling them “Transcripts of Unknown Function”. A gene is described as "a complete chromosomal segment responsible for making a functional product." This definition includes the expression of a gene product, the requirement that it be functional, and the inclusion of both coding and regulatory regions. I realized all the changes, but was unfamiliar with the change in nomenclature. My apologizes for the lack of familiarization. Is this incorporated into modern genetic text books or is this just accepted by geneticist?GetAgrippa 02:33, 10 September 2006 (UTC)

I went to the NIH Human Genome Project ENCODE site for their definition. Their education resource defines an allele: One of the variant forms of a gene at a particular locus, or location, on a chromosome. Different alleles produce variation in inherited characteristics such as hair color or blood type. In an individual, one form of the allele (the dominant one) may be expressed more than another form (the recessive one). It defined a gene as: The functional and physical unit of heredity passed from parent to offspring. Genes are pieces of DNA, and most genes contain the information for making a specific protein. Perhaps we should just adopt a simple definition as these. I realize SNP polymorphisms are referred to as alleles, but since they are randomly scattered through the genome it would seem confusing to mention that as it maybe a part of a TUF. Are polymorphisms of indels-insertions and deletions also called alleles?GetAgrippa 04:11, 10 September 2006 (UTC)

I still think the first sentence should say genomic changes as genome, chromosome, and gene duplication events are responsible for evolution and transposons jump around and alter existing genes and gene networks. Saying allele frequencies is just too limited in my opinion. This is especially true in plants. GetAgrippa 02:18, 11 September 2006 (UTC)

The first section needs improvement

"In biology, evolution is the change in the heritable traits of a population over successive generations, as determined by shifts in the allele frequencies of genes." I suggest "In biology, evolution is the change in the heritable traits of a population over successive generations, as determined by genetic change." The mention of alleles seems to ignore larger macroevolutionary contributions of genome,chromosome, gene duplications, mutations of indels and transposons altering genes and gene networks. Secondly the next paragrapsh introduces Natural selection first, which seems to defy NPOV because more and more neutral evolution is becoming a prominent fact, such as most of the differences in human and chimp genomes are neutral. Further,two primary nonadaptive forces produce genetic change: mutations that define the excess susceptibility of genes with complex structural features, and random genetic drift that defines the degree of stochasticity in the evolutionary process. M. Lynch, Mol. Biol. Evol. 23, 450 (2006). It seems natural selection is given a significant mention over the other possibilities of genetic drift, gene flow, nonrandom mating, and mutations. Pushing natural selection is very much a NeoDarwinist perspective. GetAgrippa 12:24, 11 September 2006 (UTC)

Neutral evolution as the primary souce of genetic change is very much an accepted part of neo-darwinism. I think you may have your definitions confused. Jefffire 12:33, 11 September 2006 (UTC)

GetAgrippa may have a point about alleles though. That said, whether expanding the text to mention larger-scale genetic changes is necessary at the very head of the article is up for grabs. It's not clear to me that this is a major evolutionary process, so including it prominently may wind-up just confusing non-specialist readers. On the closing point however, I entirely agree with Jefffire. The modern synthesis explicitly includes "genetic drift, gene flow, nonrandom mating, and mutations" - and processes such as mutation and non-random mating are key to natural selection in the first place. Cheers, --Plumbago 12:46, 11 September 2006 (UTC)

The other points were entirely valid. Arrangement of genes for example is very important in the expression of some developemental genes, and possibly many more, so thanks to GetAgrippa for catching this point. Jefffire 12:55, 11 September 2006 (UTC)

I disagree that NeoDarwinist accept neutral evolution. I have witnessed huge arguments and the debate has almost evolved into two different camps. However, that is anectdotal to my perspective. Why not mention mutation, genetic drift, gene flow, nonrandom mating, and natural selection with equal weight and then interweave them. I guess my concern is that many people relate natural selection upon purely Darwinistic terms as in positive selection rather than reproductive success. The average person doesn't even know what you mean by Modern Synthesis, which is a continuing process that I personally believe that comparative genomics and evodevo will enhance greatly. Although evodevo is still a controversial field and some NeoDarwinist have argued its merits. Anyways, I wanted to put in my two cents and I won't change anything as this article has obviously been contentious.GetAgrippa 13:07, 11 September 2006 (UTC)

I'm surprised you see the field as having devolved into two camps. That's certainly not my experience, although I'm no longer a mainstream biologist. Regarding your point to tease out "mutation, genetic drift, gene flow, nonrandom mating", again, mutation and non-random mating are part and parcel with natural selection. I can't see why you'd want to separate them out this way. On your other point about how people see natural selection, the bottom line is that reproductive success is all that matters, and the article doesn't seem to be too far off on making this point clear. Whether people understand what's meant by the modern synthesis is by-the-by since they can look it up here directly (not least since it'd be wikilinked here). On a broader point, neutral evolution isn't evolution in an interesting sense - it's not constructive. When it does create something that constitutes an improvement (or an unimprovement for that matter), it's not neutral evolution any more, as it'll just be naturally selected. Cheers, --Plumbago 13:33, 11 September 2006 (UTC)

I said the two camps was anectdotal to a specific event. I agree with much of what you are saying, especially about reproductive success. However, natural selection has somewhat hardened around adaptation, and mutations are nonadaptive forces. Neutral evolution is obviously constructive and it has reproductive success that is neither positively or negatively selected upon. It exists and natural selection being the black box of ecological, behavioral, etc. interactions doesn't address why it has reproductive success. It doesn't have to be an improvement or constructive, nor could you eliminate an improvement as a purely stochastic event. I agree that peoples presuppositions are not important, but quoting Wikipedia is not widely accepted as authoritative. I have many friends in academia who will not accept Wikipedia as a valid resource. I personally like the idea of Wiki's that is why I bother to contribute. GetAgrippa 14:31, 11 September 2006 (UTC)

Ernst Mayr's at the age of 100 still would barely recognize Kimura's neutral theory, in fact in a recent review he did not mention it once. So my comments about NeoDarwinism and Neutral evolution is a real debate. GetAgrippa 00:44, 19 September 2006 (UTC)

As I said before, the usage of 'allele' that GA is making is NOT the modern usage. See, for example, this recent, well-received paper about a functional non-coding polymorphism, which regularly uses the term 'allele' to describe non-genic variation, including non-SNP variation. Use of 'allele frequency' in the first sentence is wholly appropriate. As to the 'two camps', no one would suggest that neutral evolution does not occur; people who study flies might suggest that there is very little fly junk DNA, but that's not to say that people disbelieve in neutrality. Graft 14:54, 11 September 2006 (UTC)

(Edit conflict) Whoa! Neutral evolution is constructive? The whole point about it is that it moves the genotype around without having any effect on the phenotype (since any effect on this is liable to affect fitness). To this end, it can't be constructive (unless you're using constructive in a very odd sense). It may take the genotype to areas that are ultimately more productive for constructive evolution, but this can only be by accident, and as soon as it affects the phenotype we're back in the land of selection.

I'm not sure where you're getting the idea that natural selection's connection to reproductive success is not addressed. That's the mode by which it operates. Organisms which have fewer than average offspring (whether that's down to survivability or mating success) are selected against. Period. Regarding mutation, it's the raw material upon which natural selection (ultimately) operates. While it can create neutral changes in the genotype (e.g. in cases where a change in base pairs doesn't change amino acid sequence), it's the source of genetic variability that natural selection relies upon. Finally, my point about people's perceptions wasn't that WP is not authoritative, merely that they can look stuff up if they don't understand particular terms (so we shouldn't always worry about using technical language). Anyway, hope this helps. Cheers, --Plumbago 14:57, 11 September 2006 (UTC)

Here is an introduction from a paper relating my concerns of Neutral evolution and Darwinian evolution: Advances in microarray technology have made the systematic study of expression levels of thousands of transcripts possible. This has been heralded as a major step forward in understanding the function of genomes, since transcript expression levels are expected to correlate with biological functions. Although this is clearly the case for many genes that change their expression in response to environmental stimuli (e.g., Spellman et al. 1998; Hughes et al. 2000; Miki et al. 2001), it is not known whether evolutionary changes in gene expression are determined primarily by Darwinian selection or by stochastic processes. Indeed, the extent to which natural selection has shaped the properties of organisms has been hotly debated ever since Charles Darwin proposed that organisms are adapted to their environment as a result of natural selection. At the molecular level, the view that most changes are due to Darwinian selection was challenged by Kimura's neutral theory of molecular evolution (Kimura 1983). This theory states that the vast majority of differences seen in nucleotide and amino acid sequences within and between species have no or only minor selective effects. Consequently, their occurrence within a species and the fixation of differences between species are primarily the result of stochastic processes. Thus, it is believed today that the evolution of the overwhelming majority of synonymous nucleotide changes within protein-coding exons, as well as changes in noncoding parts of genomes, are determined by mutational processes and random genetic drift (Li 1997). In fact, even at the level of morphology, it has been argued that many features are not adaptive, but instead result from physical constraints or historical accidents (Gould and Lewontin 1979). However, since selection acts at the level of the phenotype while variation is generated at the level of the genotype, the proportion of changes caused by selection can be expected to be largest at the phenotypic level and smallest at the DNA sequence level. As a corollary, we may expect the proportion of selected changes to gradually decrease at the proteome and the transcriptome levels, since these are located progressively further from the phenotype. Consequently, a large proportion of transcriptome changes might be explained by historical accidents rather than by selective events. We show that a neutral model of evolution can predict the main features of transcriptome evolution in the brains of primates and mice. A neutral model is also in agreement with published observations in Drosophila (Rifkin et al. 2003) and fish (Oleksiak et al. 2002). Although selective scenarios that explain some or even most of these observations can be found, the combined evidence presented leads us to conclude that a neutral model is the most adequate null model for transcriptome evolution. This suggests that the majority of gene expression differences within and between species are not functional adaptations, but selectively neutral or nearly neutral. The main challenge now is to develop a mathematical model of transcriptome evolution that allows quantitative predictions of transcriptome changes. Such a model, combined with experimental data estimating the normal variation of gene expression within a species and the relative contributions of genetic and environmental factors to this variation, should allow adaptive gene expression changes to be identified. Further work is also needed to reveal whether proteome evolution is also dominated by changes that are largely selectively neutral. I guess this best explains my concerns, and I apologize if I wasn't communicating my concerns concisely.GetAgrippa 15:21, 11 September 2006 (UTC)

Ah - it's different to say that people argue about how MUCH neutral evolution is occurring as opposed to WHETHER neutral evolution is occurring. The latter is not in debate, I think. This probably deserves one-line mention in the article; I think there's already discussion of it in the neutral theory of molecular evolution article. Graft 15:49, 11 September 2006 (UTC)

That helps somewhat (nice work by the way!), but as Graft notes it still seems to be a question of the quantity of neutral change rather than any black-and-white distinction in neo-Darwinism. And I'm still not sure what you're getting at regarding constructive evolution and neutralism. I can well believe (and do) that the majority of change is driven by neutral drift, but it's harder to swallow the idea that change in complexity (however that slippery quantity is defined) is driven in the most part by neutral drift. It's difficult to see how that sort of change won't set up selection gradients. Anyway, my interjections on constructive evolution seem to have driven us away from the article improvements you were initially suggesting. Oops.  :-) Cheers, --Plumbago 16:02, 11 September 2006 (UTC)

Maybe constructive evolution was a poor word usage. I mean neutral evolution like certain facial features in the human population are due to genetic drift and no selective advantages. GetAgrippa 17:51, 13 September 2006 (UTC)

Yep, We arguing perspective to some degree. My objections are: 1)Use genetic or genomic change instead of alleles as it is all encompassing with indels, duplications, etc. 2) Emphasis for NPOV. While I agree that for real constructive change then natural selection dominates, however genetic drift and gene flow can produce heritable changes in populations and species (another definition of evolution). I guess I want a little more expansion on neutral theory, but I guess a link to it as an article is sufficient. I haven't read the neurtal article. I would be nice to mention Gould's notion of spandrels. Sorry if I have meandered in my concerns and not communicated them well. GetAgrippa 17:10, 11 September 2006 (UTC) I guess I don't feel strongly enough about my concerns to warrant any change. I just wanted to put in my two cents. GetAgrippa 17:13, 11 September 2006 (UTC) Hey, at least I'm not egomanical enough to just start adding my changes Helter Skelter as many do. I see this has been contentious and a huge debate. We could right an article on the debate itself, or has someone done that?GetAgrippa 17:16, 11 September 2006 (UTC)

I still have a problem with "shifts in allele frequency". I think it boils down to my perspective. I agree with the significance of genes, however I see life at another level of using a conserved or limited toolkit of domains, motifs, signatures, structures, etc. This tool kit is used to varying degrees and varying complexity to generate genes in archaea, bacteria, and eukarya. Emphasizing alleles is a gene perspective (which is significant and should be addressed in the article like ectodysplasin alleles in stickleback speciation), whereas genomic or genetic change is all encompassing that will include genomic elements (motifs, domains,etc.), duplications, indels, gene alleles, micro RNA's, TUF's, etc. This recent Science article supports my contention of the significance of domains and gene duplications in genomes. It is about the duplication and expansion of a specific domain in humans compared with chimps and other mammals. Popesco MC, Maclaren EJ, Hopkins J, Dumas L, Cox M, Meltesen L, McGavran L, Wyckoff GJ, Sikela JM. Human lineage-specific amplification, selection, and neuronal expression of DUF1220 domains.Science. 2006 Sep 1;313(5791):1304-7. Since there is a debate of the level that natural selection acts- genes, organism, populations, etc. then we should go from the simplest genomic element and build from there. Molecular economy should be emphasized in the evolution of genomes. Comparative genomics looks at everything i.e. genes (presence or absence), TUF's, indels, transpositions, micro RNA's, etc. The orchestration of gene expression in development, maturation, and senescence and the influence of environment emphasizes the genome (and interactions) rather than the gene per se. Insecticide resistance in 80% of the worlds populations of drosophila melanogaster is because of the reproductive success of a transposon altering an existing gene. So the transposon truncated an cytochrome p450 gene allele and then rapid amino acid evolution generated the novel protein responsible for resistance. So the allele frequency was not altered so much as the allele was deviated to a new path.GetAgrippa 13:02, 13 September 2006 (UTC)

The first sentence needs to have a really strong reference behind it. The current definition is found in many textbooks (including my advanced biology textbooks). So those who want this sentence changed should go into the literature and find a sentence to replace our current one (stating the source, so that people can check up on the validity on the paper/book).--Roland Deschain 14:11, 13 September 2006 (UTC)

I haven't read a textbook in a number of years. I generally read journals (and books), as most textbooks are out of date to some degree. Perhaps that is my problem, and I should follow the adage "keep it simple stupid". My apologizes for being too anal. I just have a penchant for being current. It has been an occupational necessity. A single sentence would not suffice, because it an argument built from a body of literature. I will acquiesce and drop it. GetAgrippa 17:51, 13 September 2006 (UTC)

I'm sorry to but in here, but GetAgrippa, you seem to be taking roland's comment personally. I do not mean to speak for him, but in his comment he is not asking you to "drop it," he is just asking that a source be provided. That is a reasonable request. Moreover, if you can provide a reliable and verifiable source, you shouldn't drop the definition you propose. Now, Roland may argue that the textbook definition should be prefered over your proposed definition in the sense that it should go in the first paragraph. I leave it to roland to argue that. At the very least, though, if there are verifiable and reliable sources for both definitions, then the article can and should include both, somewhere, with enough explanation so that any reader can understand who would prefer one definition and who prefers the other and why. Slrubenstein | Talk 15:29, 19 September 2006 (UTC)

I am not offended nor take anything personal. I have listed a number of references in this section, the first sentence section, and insertions and deletions section. A recent article on human-chimp differences emphasized a gene and domain duplication event difference in chimp and human evolution, also the transposon example with drosophila insecticide resistance. I just think that genomic or genetic change without mention of alleles is less confusing and more all encompassing. Since molecular evolution is resoliving differences in genomes, emphasizing genome changes fits well with comparative genomics (it not just gene changes). I also quoted the ENCODE consortium and NIH website simple definition of allele. I am frustrated that I can't impart my reasoning, even with references. Indel polymorphisms are not referred to as alleles or are they? Also TUF's and small RNA's (miRNA, piRNA,etc )also regulate gene expression and are an evolutionary construct and they are not alleles. Evolution is not just changes in gene allele frequencies, but changes in genomic elements that are non-gene elements and TUF's are of unknown function. Here is a quote from an article emphasizing genomic changes "The evolution of eukaryotes, and subsequently of multicellularity, was accompanied by dramatic changes in the nuclear genome, including expansions in sizes and numbers of introns, proliferation of mobile elements, and increases in lengths of intergenic regions." Here is a Science review article on the significance of insertional elements in evolution. Science 12 March 2004:Vol. 303. no. 5664, pp. 1626 - 1632 Mobile Elements: Drivers of Genome Evolution by Haig H. Kazazian, Jr.. A large number of papers support that HGT and gene loss has dominated prokaryotic evolution. GetAgrippa 01:39, 20 September 2006 (UTC)

It is indeed a challenge for anyone to explain this stuff so that anyone would understand (and the point is not for me or roland to understand your point, the point is for non-specialists who read this articule to understand it. That sai, if you can explain it to non-specialists and provide the citation, I am sure no one would object to your adding it to the actual article. Slrubenstein | Talk 15:45, 20 September 2006 (UTC)

Three articles from Science really help explain my perspective. The first emphasizes how gene number does not correlate with complexity in evolution and that the gene per se does not mechanistically dominate evolution but brings in the significance of transcription factors and gene networks. Science. 2001. Vol 292(5520) pp.1315-1316. Molecular Biology and Evolution: Can Genes Explain Biological Complexity? The other article is about gene duplication significance as a evolutionary mechanism. Science. 2002. Vol 297(5583). pp 945-947. Gene Duplication and Evolution. Another article discusses the evolution of genomes and chromosomes and the significance of transposons and hot spots prone to genetic change.Science. 2003. Vol. 301. no. 5634, pp. 793 - 797. Structural Dynamics of Eukaryotic Chromosome Evolution. The statement about gene frequency of alleles should be changed to genomic or genetic change, which would encompass duplications, indels, transposons, and transcription factors. GetAgrippa 14:48, 21 September 2006 (UTC)

Then go ahead and incorporate these ideas in the article. Do your best to express them in layman's language. Provide any necessary context. Be clear about the status of these findings with regard to other points of view (e.g. contested facts; accepted facts the significance of which for evolutionary theory is still debated; accepted facts that have been fully incorporated into evolutionary theory), and provide the proper citations! Gor for it! Slrubenstein | Talk 10:33, 22 September 2006 (UTC)

I'm opposed to this change. What GetAgrippa is discussing is primarily divergence; the definition of evolution we currently have is much more specific than that, since it discusses processes that affect allele frequencies - including fluctuations within current populations. Since this is where selection and drift are really active, this is a much more appropriate decision - and, furthermore, since as I said earlier "allele" these days can be taken to include just about any kind of variation, I don't see the need to alter anything. Graft 14:17, 22 September 2006 (UTC)

If allele means epigenetic heritable changes like silencing RNA's, includes transposon insertion polymorphisms, and imprinting then leave it. GetAgrippa 14:39, 22 September 2006 (UTC)

Come on... what does epigenetic inheritance have to do with evolution? Insertion polymorphism is definitely covered in the meaning of 'allele', I think. Graft 15:38, 22 September 2006 (UTC)

Here is a useful book.Epigenetic Inheritance and Evolution: The Lamarckian Dimensionby Eva Jablonka, Marion Lamb Here are some excerpts from artilces: "Genomic imprinting confers a developmental asymmetry on the parental genomes, through epigenetic modifications in the germ line and embryo. These heritable modifications regulate the monoallelic activity of parental alleles resulting in their functional differences during development. Specific cis-acting regulatory elements associated with imprinted genes carry modifications involving chromatin structural changes and DNA methylation. Some of these modifications are initiated in the germ line. Comparative genomic analysis at imprinted domains is emerging as a powerful tool for the identification of conserved elements amenable to more detailed functional analysis, and for providing insight into the emergence of imprinting during the evolution of mammalian species." "The X chromosomes of mammals and fruit flies exhibit unusual properties that have evolved to deal with the different dosages of X-linked genes in males (XY) and females (XX). The X chromosome dosage-compensation mechanisms discovered in these species are evolutionarily unrelated, but exhibit surprising parallels in their regulatory strategies. These features include the importance of noncoding RNAs, and epigenetic spreading of chromatin-modifying activities." More excerpts from articles to help:…..”it is important to study the mechanisms of gene family interaction for understanding phenotypic evolution. Because gene duplication occurs more or less at random, phenotypic evolution contains some fortuitous elements, though the environmental factors also play an important role. The randomness of phenotypic evolution is qualitatively different from allele frequency changes by random genetic drift. However, there is some similarity between phenotypic and molecular evolution with respect to functional or environmental constraints and evolutionary rate. It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels.” Hybrid sterility has been well studied for more than a century by many prominent scientists, including Darwin, but the molecular underpinnings have remained unidentified. Masly et al. have identified a gene involved in sperm motility, JYAlpha, responsible for F2 hybrid sterility resulting from crosses of Drosophila melanogaster and D. simulans. During speciation gene translocation had placed the gene on two different chromosomes, leading to sterile F2 males lacking any copies of the gene. Thus, reproductive isolation can occur without sequence evolution. Hope these abstracts and articles help.GetAgrippa 16:27, 22 September 2006 (UTC)

Okay, this is great, but this is NOT about epigenetic mechanisms of evolution - it's about how epigenetics influences genetic evolution. Graft 18:49, 22 September 2006 (UTC)

"We discuss the role of cell memory in heredity and evolution. We describe the properties of the epigenetic inheritance systems (EISs) that underlie cell memory and enable environmentally and developmentally induced cell phenotypes to be transmitted in cell lineages, and argue that transgenerational epigenetic inheritance is an important and neglected part of heredity. By looking at the part EISs have played in the evolution of multicellularity, ontogeny, chromosome organization, and the origin of some post-mating isolating mechanisms, we show how considering the role of epigenetic inheritance can sometimes shed light on major evolutionary processes."Tsitologiia. 2003;45(11):1057-72. "Epigenetic heredity in evolution.

"We argue that modern epigenetics is important not only because it has practical significance for medicine, agriculture, and species conservation, but also because it has implications for the way in which we should view heredity and evolution. In particular, recognizing that there are epigenetic inheritance systems through which non-DNA variations can be transmitted in cell and organismal lineages broadens the concept of heredity and challenges the widely accepted gene-centered neo-Darwinian version of Darwinism." Ann N Y Acad Sci. 2002 Dec;981:82-96.The changing concept of epigenetics.So molecular neoLamarckism is a viable evolutonary mechanism, and epigenetics has an impact on evodevo mechanistically. It just challenges the gene focus. Micro RNA's are positively selected upon and by gene silencing (similar to gene loss which in bacteria HGT and gene loss are considered the major evolutionary changes that mold bacterial genomes) they influence evolution.GetAgrippa 19:22, 22 September 2006 (UTC)

Upon reflection just leave it as is. GetAgrippa 19:26, 22 September 2006 (UTC)

It's a bullshit argument - evolution requires inheritance and modification. I've yet to see any demonstration that epigenetic modifications are heritable AND themselves subject to modification without some governing genetic system changing. That is, if some methylase mutates so that some particular gene is now hypermethylated and the epigenetics alters, this is not epigenetic evolution, and I don't believe anyone has shown that novel epigenetic modifications can arise independently of genetics. Possibly I'm just ignorant, but I'd love to see a ref if you have one. Graft 19:43, 22 September 2006 (UTC)

Transgenerational epigenetic inheritance was first reported in plants. It has been reported in drosophila and yeast also, but in yeast it doesn't use methylation. Here are some mammalian references.Trends Genet. 2002 Jul;18(7):348-51.Metastable epialleles in mammals.Rakyan VK, Blewitt ME, Druker R, Preis JI, Whitelaw E. FASEB J. 1998 Aug;12(11):949-57.Maternal epigenetics and methyl supplements affect agouti gene expression in Avy/a mice.Wolff GL, Kodell RL, Moore SR, Cooney CA. Imprinting is also epigenetic and heritable. Admittedly the epigenetic reports are controverial.GetAgrippa 21:05, 22 September 2006 (UTC)

Well I read the definition of a gene on Wikipedia and it includes micro RNA's (TUF's would also be included), and obviously transposons (jumping genes) too as noncoding DNA besides promoters are included. Apparently this is a new controversial trend to include RNA as gene. Anything that affects the classical gene expression is now gene, which pretty much includes most of the genome. This ,of course , is not the definition used in comparative genomics, the human genome project, cancer research and numerous other fields, but it is the definition here. Also I found the term epialleles and that addresses alleles covering other epigenetic mechanisms. So apparently all my concerns are covered in this terminology. I presume trait includes behaviors as evolution is changes in characteristic, physiology-metabolism, and behavior. I would also assume that just because the next sentence is about speciation that does not preclude that evolution occurs without speciation or that evolution is synonymous with speciation. Given that I have wasted my time. Weird terminology and not in general use. GetAgrippa 12:43, 23 September 2006 (UTC)

"In biology, evolution is the change in the heritable traits of a population over successive generations, as determined by shifts in the allele frequencies of genes. Over time, this process can result in speciation, the development of new species from existing ones." I changed it slightly by adding can, because you have changes in allele frequency over time without speciation, as changes in allozymes,etc. It needs to made clear that evolution is not synonymous with speciation, because changes can be physiologic-metabolic, and behavioral like bird song. GetAgrippa 16:44, 23 September 2006 (UTC)

Well, Graft, do you see an appropriate place within the body of the article to discuss "divergence?" GetAgrippa, do you see a place in the article to discuss "divergence" vis a vis the current article definition of evolution? Graft, are you saying divergence is unrelated to evolution? If not, surely it should be discussed somewhere in the article. GetAgrippa, are you discussing an aspect of evolution, or a competing definition of evolution? Or are you saying that the definition of "allele" is what is at issue? If we have an important point of view that comes from reliavble and verifiable sources, surely there is room for this view in the article. Slrubenstein | Talk 14:46, 22 September 2006 (UTC)

"overwhelmingly believed"

Removed this addition, as it is not possible to prove how many in the world believe this concept over others and, as it is not necessary to the article and may antagonise some readers, I removed it pending discussion. - Ballista 05:20, 15 September 2006 (UTC)

The same anon had added "concept of" in front of change. The two alterations together implied that evolution is a "concept" and "belief" rather than a set of observable facts which need explanation. Which suits those opposed to the scientific explanation and in denial about the facts. Both additions have now been removed. ..dave souza, talk 06:36, 15 September 2006 (UTC)

The article states that Catholic adherents overwhelmingly believe in Evolution. However, that is apparently not the belief of the Pope. See http://ansa.it/main/notizie/awnplus/english/news/2006-09-12_1128196.html. I don't know if it is worth mentioning that point in the article.[[unsigned2|18:35, 15 September 2006|66.170.53.111}}

Where does the article say that? The bit I've read says " Judaism and Catholicism are notable as major faith traditions whose adherents generally see no conflict between evolutionary theory and religious belief.", and cites sources. The linked article is open to interpretation and is certainly not a definitive statement of what would be a major change in doctrine. It does however appear to be sadly misinformed about the extent to which ID is taught in US state schools. Doesn't appear to be a reliable source for a topic wich is more relevant to the Evolution and the Roman Catholic Church article than this one. ..dave souza, talk 18:56, 15 September 2006 (UTC)

This article does a very poor job to relate what Benedict said during his trip. Read a couple of the European articles that do not immediatly fall into evolution vs. creationism rut everytime science is mentioned and you'll see that Benedict talked mostly about science and religion (and not evolution and religion) and when he did mention evolution, he still professed the idea of theistic evolution and not creationism.--Roland Deschain 22:19, 15 September 2006 (UTC)

The article should simply discuss evolution without a defense of evolution. All this seems POV. Religious beliefs, majority beliefs, etc, are still POV, and NPOV should warrant avoiding this kind of language. The issue is evolution and not who believes what. Social and religious issues belong in another article. GetAgrippa 16:30, 21 September 2006 (UTC)

Disambiguation

The link pointing to the Evolution (disambiguation) is dead. I'm going to delete it. I'd like to either create a disambiguation page or have someone else do it. I'll start it in a few days if no one volunteers.

--Mooselover801 00:34, 18 September 2006 (UTC)

What do you mean dead? I see it just fine. Evolution (disambiguation). Joelito (talk) 00:37, 18 September 2006 (UTC)

It pointed to a page stating that there wasn't a disambiguation. --Mooselover801 00:40, 18 September 2006 (UTC)

Something weird is going on - if you click on "Edit this page" the whole page is there. Guettarda 00:45, 18 September 2006 (UTC)

It is a bug, it's mentioned somewhere in the village pump (technical). The page is there for some users. Joelito (talk) 00:50, 18 September 2006 (UTC)

"Misunderstandings" NPOV problems

I think this section, including its title, reads like a defense of evolution against creationism instead of an explanation of common misunderstandings. If so, it violates NPOV policy. Can someone take a shot at improving it? By the way, the following section seems like it could be merged with this section. Gnixon 16:50, 19 September 2006 (UTC)

(Patience, please, joelr31.  ;-) ) Gnixon 16:56, 19 September 2006 (UTC)

Before we edit, it might be worth trying to list common misunderstandings here. I'm suggesting this because I'm hard-pressed to think of any that aren't motivated (or, at least, usually motivated) by some flavour of creationism. In broad outline the evidence for evolution, and for natural selection as its majority driver, is fairly straightforward - it surely must qualify as one of the simplest of major scientific theories (although I do say this from the perspective of a semi-biologist). Anyway, if we can create a list of misunderstandings and creationist "misunderstandings" (they're rarely genuine misunderstandings in my experience), we can perhaps sort out the problem Gnixon describes. My suspicion is that this will be harder to do than it first seems, and that we'll have a majority list of the latter. Still, that's worth knowing as we could then relabel the section and perhaps fuse with the "social and religious controversies" (why social just out of interest?). Cheers, --Plumbago 17:12, 19 September 2006 (UTC)

"They're rarely genuine misunderstandings in my experience." See, I think this is the issue. The section is rebutting (admittedly weak) creationist attacks against evolution in the guise of explaining common misunderstandings. But such a rebuttal is not NPOV. The same issues could be discussed in an NPOV tone by explaining these objections to evolution and how scientists answer them. Better yet would be to first separate common misunderstandings from objections to the theory. Gnixon 17:38, 19 September 2006 (UTC)

Each of these misunderstandings is a major creationists talking point. I really don't know of any prominant misunderstandings about evolution that have not been exploited by creationists. They are the major output of those misunderstandings (in the form of books, lectures, debates, etc etc). Furthermore, the basic premise of this section is to explain the misunderstanding and then show why it is indeed a misunderstanding. Be happy that we don't call this section "Lies spread by creationists to support their religious agenda". I can provide more than enough sources to support this viewpoint ;).--Roland Deschain 17:33, 19 September 2006 (UTC)

Thanks, Roland, for making my point better than I did.  ;-) A more appropriate title for the section, given the tone it currently takes, would indeed be "Lies spread by creationists to support their religious agenda," but such a section is clearly not NPOV! In no way am I trying to lend support to the creationists' arguments here, but it's important that the article maintains NPOV. Gnixon 17:38, 19 September 2006 (UTC)

"Untruths" would be more NPOV than lies, since "lies" implies a level of intention which is difficult to prove. "Misconceptions" may be better than "misunderstandings" for many people. While some of the people behind these statements are intentionally spreading falsehoods, many people have simply been deceived by people they trust, and believe these falsehoods to be true. So it is correct to call them misunderstandings or misconceptions. Obviously it doesn't violate NPOV - these are things that people genuinely believe about evolutionary biology. They are demonstrably false. So what's the problem? Guettarda 17:46, 19 September 2006 (UTC)

The problem is in the tone. Please see my above comments and WP:NPOV#Fairness_of_tone. Gnixon 18:07, 19 September 2006 (UTC)

Can you provide direct quotes and examples about the tone that implies NPOV. It's hard to judge tone, as it is very subjective.--Roland Deschain 19:06, 19 September 2006 (UTC)

I agree tone is a subtle issue. Here are the first few things I notice:

• "Misunderstandings" in the title of a section about "controversy," which is the title of the "main article," takes the POV that creationists' objections can be dismissed as misunderstandings.

  Is "misconception" a better word? There is absolutely no controversy within the scientific community about evolution (which is what this section deals with). Each of these arguments is indeed a misunderstanding if viewed through the current scientific literature; they are not valid objections . . . they are scientifically and philosophically flawed and can be rejected easily. Of course, it can be claimed that creationists objections are a different kind of science and are equally valid as modern science in which case they could be termed valid objections. However, there is no support for the validity of their science. This is a science article and it falls within a science POV. As the current scientific understandings goes, every creationist point laid out in this article is a misunderstanding by the general populace or a lie used by creationists to further the misunderstanding.

  Even if there is no controversy among scientists, all scientists are aware of the public controversy over evolution. Wikipedia's main article on evolution has a duty to address this controversy from a neutral point of view. Gnixon 22:27, 19 September 2006 (UTC)

  And it is addressed in wikipedia. There is an entire article on that contraversy. However, this article is about the science of evolution and there is no contraversy there. Not one single scientific publication that supports any creationist claims.

• In the first paragraph, evolution is "almost universally accepted within the scientific community," whereas "people" find it goes against "their perceptions." Disagreement with evolution is presented as a failing of individual people, rather than a point of view held by many people (e.g., all creationists). Again, I don't argue with the veracity of either statement, just the appropriateness of the tone.

  The sentence is accurate in its content. Evolution is accepted and many people find it goes against their personal perceptions of the world. If you think you can change the tone without changing the content go ahead.

  I think it's clear that this sentence, as worded, exists to deliberately denigrate those people whose "perceptions" conflict with accepted scientific theory. Wouldn't such a sentence be personally offensive to those who disagree with evolution? Is that consistent with NPOV policy? Gnixon 22:27, 19 September 2006 (UTC)

  Wikipedia is not a politically correnct site (ie: you don't have to twist facts not to offend people). It is a fact that science contracicts people's believes. If that fact offends some people, then I'm sorry, but that's not what NPOV is about.

• "In the resulting controversy, publicity is given to creationist arguments..." (implying it shouldn't be) "...which generally involve misunderstandings...." (implying that all creationist arguments derive from misunderstandings of evolution, which may or may not be true, but is hardly NPOV).

  Publicity is given to creationists (that is a fact) with all that goes with it. The vast majority of creationist arguments are misunderstandings. There is no point beating around the bush. The objections are misunderstandings: conclusions based on false scientific premises. If we assume that the bible is correct then the objections would be completely valid. However, looking at the science, (for the third time) these are misunderstandings at best and ruthless lies meant to confuse at worst.

  Trust me, I'm not failing to follow your point that the scientific community gives no merit to creationism. As an aside, I personally and, as a non-biological scientist, professionally agree that creationist arguments are without merit. That's not at issue here. Evolution is not merely a scientific topic---it has great philosophical and social import, and those aspects must be addressed by Wikipedia in an NPOV manner. Gnixon 22:27, 19 September 2006 (UTC)

  Yep, and in my opinion they are. If this article offends some people, so be it. NPOV is not about being politically corrent. It's about showing all points of view and this article does that. If you think the wording is unfair, feel free to change it, but the content is very good in my opinion.

• "Some of the most common arguments are explored in this section." Here again, creationist arguments are being labelled as misunderstandings so they can be dismissed. NPOV discussions of such arguments and the scientific rebuttal to them belong in a section on "controversy", but not in a section on "misunderstandings," even if those two topics are related.

  No. There is NO scientific controversy about evolution. There is a controversy within the social effects of evolution as that is beyond science. These arguments are not scientific objections. They are thinly vialed and deeply flawed philosophical arguments. They are not scientific objections. They have no scientific validity in them at all (I'm trying to get the point across here ;) ). To apply the term "controversy" would be a vast NPOV as it implies that it exists when it does not.

  You seem to be trying to straw-man me here. Nowhere did I suggest there was a scientific controversy about evolution. However, there is great social controversy, as your vehement arguments against creationism suggest you appreciate. This is the main Wikipedia article on evolution, and social controversy must be addressed. Gnixon 22:27, 19 September 2006 (UTC)

  Social contraversy is found here here. You said "NPOV discussions of such arguments and the scientific rebuttal to them belong in a section on "controversy". That is what I don't want to happen. That for creationist arguments to be given such status as to assume that they cause a scientific contraversy. They don't. They do cause a social contraversy, but that's discussed here.

• Link to "An index of creationist claims." The title of the link, and the page it links to, are obviously not NPOV.

  All the claims are well known creationist claims. They make them openly.--Roland Deschain 20:13, 19 September 2006 (UTC)

  And the webpage openly exists to refute these "claims." Use of the word "claims" to characterize creationists' objections, as well as the webpage itself, is clearly not NPOV with respect to the social controversy over evolution. Furthermore, including this link makes it clear that the motivation behind this section is not to discuss common "misunderstandings" about evolution, but rather to refute creationist arguments. Such a section is more appropriately entitled "Controversy" and deserves a neutral point of view. Gnixon 22:27, 19 September 2006 (UTC)

This covers the introduction. I think the subsection on Theory vs. Fact, for example, takes a similar tone in terms of rebutting the implicit creationist argument that evolution is a theory, not a fact. If the section is to be about misunderstandings, this subsection could easily, for example, refer to a less controversial figure than Stephen J. Gould. If the section is to be about controversy, this subsection could, for example, attribute the quote to Gould as a rebuttal of the creationist argument (after presenting it) while explaining his prominent role as a defender of evolution against creationist attacks. Similar comments apply to the other subsections. Cheers, Gnixon 19:29, 19 September 2006 (UTC)

I must repeat this: this section is not about controversy as it applies to science. It links to Creation-evolution controversy but that largely deals with the social effect of evolution vs. creationism. The closest example I can give you is this: calling the creationist objections about evolution a controversy is like calling flat earth objections about the round earth theory a controversy. I'm more than open to finding another word for misunderstanding, but it should NOT be controversy.--Roland Deschain 20:21, 19 September 2006 (UTC)

For reasons given above and below here, I believe strongly that this section is about controversy, not about "misunderstandings," as it purports to be. The two issues should be separated, and the discussion of social controversy requires NPOV. Gnixon 22:27, 19 September 2006 (UTC)

If I may chime in, I think the last Flat Earther society sort of vanished just a year ago or two, so the reason there's no controversy there is pretty much because there isn't much of anyone left at this point. Homestarmy 21:00, 19 September 2006 (UTC)

Roland, thanks for responding. However, I think you misunderstand my objections. Of the several people who have chimed in here, I think we can all agree that evolution is a fundamental, well-established, and almost universally-accepted theory among scientists. We can also probably agree that creationists' objections to evolution are fully motivated by their religious preconceptions, are easily rebutted within the framework of science, and for good reason are almost universally dismissed within the scientific community. Furthermore, we can agree that proponents of creationism often base their attacks on popular misunderstandings of the theory of evolution (e.g., that it guarantees more highly evolved species are "better"), of other branches of science (e.g., that thermodynamics prohibits evolution), or of science itself (e.g., that "theory," as used by scientists, has the same meaning as its popular usage, which is in fact much closer to the scientific term "hypothesis"). Finally, we could discuss whether the presence of these misconceptions in creationists' attacks is due to honest misunderstanding, willful ignorance, or deliberate deception of the public.

But none of that is relevant here. My objection is twofold.

• First, the section conflates two issues: (a) common misunderstandings of evolution, and (b) creationist attacks upon evolution.

• Second, insofar as the section addresses (b) (which it decidedly does), it does so in an extremely POV-ish tone and structure.

The main article, Creation-evolution_controversy, addresses (b) in a way that is consistent with Wikipedia policy. The same reasons that justify the existence of that article (i.e., that evolution vs. creationism is a controversial issue, that creationism is a POV held by a significant and influential minority, and that evolution, although it belongs to the domain of science, is a subject of such philosophical importance that social controversy must be considered) demand that this section maintains a Neutral Point of View. Gnixon 21:05, 19 September 2006 (UTC)

We are not that far apart. I'm just trying to make the point that every single creationist scientific claim is a misunderstanding. Why. Because they make that claim based on assumptions that are scientifically false. They reach the wrong conclusion because they have a misunderstanding in their premises. It's a whole new world when it comes to the social effects. However, this article seperates the two. Scientific misunderstandings are here and social contraversies are here.--Roland Deschain 22:41, 19 September 2006 (UTC)

Good point. I agree we're not that far apart, and it's good that the controversy issues are addressed elsewhere. However, I still think it's a non-NPOV argument to say that all creationist objections are based on scientifically false misunderstandings (clearly creationists would disagree), regardless of whether or not I agree---many readers will be very interested in the social controversy, which can't be ignored here. Can't we just purge this section of any reference, explicit or implicit, to creationist attacks, and instead discuss misunderstandings of evolution as they are commonly held by people in general? On the other side, there's also good information in this section about scientific rebuttals to creationist attacks that I'd advocate moving to the next section. Gnixon 23:07, 19 September 2006 (UTC)

"I still think it's a non-NPOV argument to say that all creationist objections are based on scientifically false misunderstandings (clearly creationists would disagree)"

• This article does not state that all objections are misunderstandings (it is impossible to prove that). However, it gives examples of creationist's most common talking points and shows how they are misunderstandings. If you think the factual basis of the claims is wrong, bring it up. I think if you go through the Creation-evolution controversy talk page you'll find that I've already defended the factual basis that these creationist's claims are indeed misunderstandings about science.

"many readers will be very interested in the social controversy, which can't be ignored here."

• They are not. See here.

"Can't we just purge this section of any reference, explicit or implicit, to creationist attacks, and instead discuss misunderstandings of evolution as they are commonly held by people in general?"

• No. It is very hard to get verifiable data on what the general population thinks and believes (most polls are contested, are biased, etc etc). However, creationist publications speak for themselves. There are literally thousands of them in book, debate, radio, interview, movie format. --Roland Deschain 23:28, 19 September 2006 (UTC)

Roland, you continue to be more interested in proving the validity of evolution vs. creationism rather than discussing whether such proof is appropriate in this section of the article. If you'd like to continue that discussion, I suggest we move it to my talk page. Best regards, Gnixon 00:40, 20 September 2006 (UTC).

Gnixon, I appreciate your good efforts in trying to find the fairest way of covering the "controversy", but think it's important to appreciate Wikipedia:Neutral point of view/FAQ#Pseudoscience as well as the earlier section in that article which discusses Giving "equal validity". It's right that this article clarifies points which people commonly misunderstand, and that it gives a proportionate mention of non-scientific "viewpoints", but it should not represent these viewpoints as having equal scientific validity. Other articles cover social and faith aspects fully, this article is to explain the science. ..dave souza, talk 23:42, 19 September 2006 (UTC)

Dave, I'm fully cognizant of the NPOV FAQ, especially the pseudoscience part, since that's obviously an issue here, and I'm in no way advocating that creationism be given anything like equal weight here, or that the article should lend validity to creationism or intelligent design. Quite to the contrary, my point is that creationism should be ignored when discussing common misunderstandings about evolution. Instead, this section of the article is clearly motivated by the desire to refute certain creationist attacks against evolution. As such, much of the content of this section belongs in the next section, which discusses the social controversy concerning evolution (and which takes pains to maintain an NPOV stance). There are plenty of common misconceptions about evolution that have nothing to do with creationism, and I feel strongly that using this section dishonestly as an excuse to argue against creationist attacks without admitting to that objective greatly diminishes the credibility of the article.

"Quite to the contrary, my point is that creationism should be ignored when discussing common misunderstandings about evolution."

• As scientists cannot be ignored when talking about evolution, creationists cannot be ignored when talking about common misconeptions about evolution. Creationist publications are the main published source for these misunderstandings. ID is the most current example where all these misunderstandings are published in every format imaginable.

"Instead, this section of the article is clearly motivated by the desire to refute certain creationist attacks against evolution."

• Creationists make those scientific claims and scienists have refuted them using scientific evidence. This section simply reports this. If it comes of sounding bad for the creationists, too bad, but that's not what NPOV is about.

"There are plenty of common misconceptions about evolution that have nothing to do with creationism, . . ."

• This might be the case, but this article only states misconceptions that are clearly a part of the creationist movement. Every misunderstanding is consistantly a part of creationist publications, as is clearly seen in the newest creationist movement, ID.

On the other hand, I agree that it's entirely proper, and very useful, for this article to clarify points which people commonly misunderstand, but I believe that can be done without taking a stance on the creationism vs. evolution controversy, despite the relationship of those two topics. I also think it would be entirely appropriate to mention at some point in this section that, say, "many people believe that" these misunderstandings are the basis of many of the creationists' attacks on evolution. The issue isn't so much one of the relative weight we give to creationism relative to evolution, but rather just one of writing a professionally neutral article. Gnixon 00:40, 20 September 2006 (UTC)

I can live with that. All I want in the misunderstanding section intro is one sentance that states that creationsists have used these misunderstandings extensively in their arguements against evolution. This is easily verifable. I know it casts a bad light on creationists, but, one again, NPOV is not about being politically correct. It is a fact that creationists use these misunderstandings extensivly even today (for the most recent addition, see [5]).--Roland Deschain 14:18, 20 September 2006 (UTC)

It's been 8 hours since my original post, which has been more controversial than I expected. I've pretty much said my peace, and I'd like to give others an opportunity to weigh in, so I'll be quiet for at least 48 hours. Tomorrow, if it seems appropriate, and at 24 hours since the original post, I'll add the NPOV-section tag, which was itself controversial, in order to draw more people to the discussion in accord with my reading of the NPOV tag discussion, although that reading disagrees with comments on my talk page. I appreciate everyone's comments---I think the article on Evolution is extremely important for Wikipedia and its audience, and it's an important piece of the larger puzzle of how to reconcile science and religion in our society, on which subject I claim no special enlightenment. I hope we can reach a consensus on this page. Very best regards to all, Gnixon 01:08, 20 September 2006 (UTC)..

Personally I don't see how the section is POV. It examines some common misconceptions and explains them. It is very difficult to seperate these misconceptions from creationism, at it is creationists who promote them. Of course most people have a very crude idea about what evolution involves, but that could be said for most topics of human enquiry, and is not surprising. But once you get beyond this general ignorance, genuine misconceptions mostly stem from a creationist perspective. --Michael Johnson 01:46, 20 September 2006 (UTC)

There is a Dilbert book called "When Did Ignorance Become a Point of View?" - which hits this nail on the head.

Common misconceptions are an important part of the history of the the idea of evolution. By some weird coincidence, all creationists I ever read about or talked with (a few dozen, maybe a hundred) were people who held such misunderstandings. So clearing up the misunderstandings will necessarily step on lots of toes. Should that stop us from clearing them up? The article Monty Hall problem does not, as far as I could see, give the "ignorance POV" any leeway. The evolution situation is very similar. --Hob Gadling 10:30, 20 September 2006 (UTC)

Rather than just adding the POV tag, what about rewriting the section and see how people react.--Roland Deschain 14:18, 20 September 2006 (UTC)

Given the reaction so far to what I've said, I'm afraid that would just start an edit war. Let me add the tag to try and draw more people to this discussion, and if after a day or so I'm the only one that has a problem with the section, I'll drop it and remove the tag. Fair? Gnixon 17:12, 20 September 2006 (UTC)

Adding POV-section tag as discussed above. Comments appreciated. Gnixon 17:12, 20 September 2006 (UTC)

I disagree with virtually all the changes proposed. As such, I have rved the change. Also, since the version was established via consensus it would be best to discuss matters here before re-inserting pov tags. If you can convince a good number of editors that this is justified then you can obviously re-insert the tag (or changes) then. --Davril2020 17:20, 20 September 2006 (UTC)

I've re-added the tag. Please see WP:NPOVD. The tag says "the neutrality of this section is disputed," which it is, by me. I've added it to draw people to this discussion, given my reasons in some detail above, and explained my willingness to remove the tag if everyone disagrees with me after a period of time. Gnixon 17:25, 20 September 2006 (UTC)

• Proposed solution: Remove most of the references to creationists and teleological disputes and such from the "misunderstandings" section (since those views are beliefs, not misunderstandings, regardless of whether they're based on misconceptions or not), and transfer them to the "social controversies" section. I realize that creationists utilize these misconceptions in their publications, but that fact is relevant to the social effects of evolution (the section following "misunderstandings"), not to misunderstandings of the science of evolution. By reserving the "misunderstandings" section solely for clarifying various genuine errors people make about the nature of evolution and evolutionary theory, we will avoid the (indeed POVed in tone, even if that POV is the correct one) current characterization of all creationism as just "misunderstanding" science; clearly creationism is based more on religious dogma than on genuine misunderstandings of science, even if the latter play a large role too. This will also help keep the section from accumulating bloat or redundancies: we currently have "Main article: Creation-evolution controversy" at the top of the misunderstandings section even though clearly that link should only be at the top of the "social controversies" section (where it also is). There is no daughter article for "misunderstandings of evolution", and portraying a quasi-related article as being such a page is worsening the lack of focus and NPOV in the section in question. Save it for creation-evolution controversy, guys. -Silence 17:49, 20 September 2006 (UTC)

Having to rush a bit here, but what Silence says sounds good to me. The misunderstandings aren't confined to creationists: Evolution and devolution covers a common misconception that evolution's about progress. ..dave souza, talk 18:29, 20 September 2006 (UTC)

Exactly so. Most people I know don't understand evolution, and most people I know aren't creationists. :) -Silence 19:01, 20 September 2006 (UTC)

As I said somewhere in this lengthly discussion, I have no problem with most references to creationists removed from the misunderstanding section (there are people out there that do not understand evolution but are not creationists). However, one sentence must be set aside that these misunderstandings are, in part, propagated by the creationist movement. There is no POV in this. It's a statement of fact that has been recognized for a long time, especially with the very prominent US controversy about evolution where these misunderstandings are used as a way to convince the public about the inadequacy of evolution. These misunderstandings are not just a passive product of an uneducated society. It has been shown that the creationist movement actively propagates these misunderstandings in all their publications.--Roland Deschain 19:45, 20 September 2006 (UTC)

One sentence (properly cited, and perhaps even attributed, ideally) sounds perfectly fine to me. It needn't be the first sentence in the section, but I don't see any reason not to briefly mention the creationist movement's reliance on such misunderstandings in the course of our explaining them. What matters is that the overall thrust and focus of the section is explaining popular misconceptions regarding evolution, not rebutting creationistic arguments; we have dozens of other articles for that, and the evolution article is already exceedingly long (almost 100kb!). -Silence 20:24, 20 September 2006 (UTC)

Explaining the misunderstandings about evolution (and why they are misunderstanding) necessities rebutting most of creationistic arguements as those arguements are based on the premises that we, in this article, term misunderstandings. However, the concensus seems to be to briefly mention the creationist exploit of those misunderstandings and then to simply state the misunderstanding and then show why it is a misunderstanding. It is not necessary to constantly draw attention to the fact that creationist aruements are refuted.--Roland Deschain 20:42, 20 September 2006 (UTC)

No, it does not necessitate specifically rebutting creationist arguments, it necessitates rebutting common misconceptions upon which many different creationist arguments are based. We can point out that evolution is both a fact and a theory without then going on to say "therefore the creationists are wrong!"; again, this article is about evolution, not about the evolution-creationism dispute. It sounds like we agree, in essence; you are simply using "rebut creationist arguments" to mean "rebut premises upon which creationist arguments are based". But for the purposes of the evolution article, what should concern us is how common (to meet our notability standards) and well-attested (to meet our WP:NOR policy) these misunderstandings are, not how fond creationists are of them. -Silence 21:01, 20 September 2006 (UTC)

I agree that we can and should identify most if not all of these misconceptions as popular misconceptions without specifying creationists. What makes these misunderstandings notable and worthy of inclusion in the article is that they are common, not that they are held by people of a particular faith or set of faiths. Slrubenstein | Talk 09:58, 21 September 2006 (UTC)

I agree with Slrubenstein that it should just be misconceptions like speciation is not synonymous with evolution, evolution has no direction, Darwinism isn't synonymous with evolution, natural selection does not create perfect structures,etc. There could be a brief mention and reference to the creationist article debate, but it should be minor. I would leave out the fact and theory subject completely for NPOV (the subject is evolution and evolution theory).I would also add that it could also be presented in historical perspective to criticisms from Darwin's contemporaries, through the Modern Synthesis, to the present. Stephen Gould did an excellent job of historical perspective in Structure and Function of Evolution. Ernst Mayr's opposition to Kimura's Neutral theory and other scientist perspective pro and con for different hypotheses and ideas in evolution theory would fit nicely. It should be misdunderstandings and scientific debates in different aspects of evolution theory. I like the scientific debate aspect for NPOV. The illustration of the tree of life in the article is subject of debate for example. The more I think about it the subject should be an article because there are so many noted debates by anthropoloigist, molecular biologist, etc, and the historical perspective would make an article also. I don't know if there is a stub for these two subjects but they could easily make lengthy articles-History of Evolution and Scientific Debates in Evolution. GetAgrippa 11:52, 21 September 2006 (UTC)

There's History of evolutionary thought which includes scientific debates, and Evolutionism, so there's merit in severely pruning the history section here. A hazard of removing all discussion of misconceptions which are commonly used in creationist claims is that there are then extended talk page debates with those who think their favourite claim hasn't been covered or refuted. ...dave souza, talk 13:05, 21 September 2006 (UTC)

I would recommend changing this section without reference to creationism. First address the second law of thermodynamics issue and include self-assembly of molecules. Then I would address that evolution does not generate diversity or information by de novo synthesis of new DNA but molecular economy of using old parts to generate new and novel genes and gene networks (mention evodevo examples such as jaw evolution, ossicle evolution, parathyroid evolution). Then I would address that genetics is not synonymous with evolution, but emphasize genetic changes have to have reproductive success. State natural selection has nothing to do with creating perfect structures, purposeful structures, or more complex structures. Then mention speciation is not synonymous with evolution, but emphasize the significance of speciation and give examples of gene changes associated with speciation (BMP in Darwin’s finches, Ectodysplasin in stickleback fish, Gene alterations in parallel evolution of bird plumage, etc) Talk about how evolution does not have a direction, but in higher animals that trend does exists. Darwinism is not synonymous with evolution and mention neutral evolution, genetic drift, gene flow, and behavioral nonrandom mating. I am sure there are other issues to address, but I’m blanking right now. Forget about the fact and theory section, because it just aggravates creationist objections, nor is it needed. Statements about the overwhelming majority believe in evolution, etc are still POV, and NPOV should warrant dropping such statements. The religious and social issues are already covered in an article. The article should present evolution and not defend evolution. The misconceptions section should address common misconceptions.GetAgrippa 15:44, 21 September 2006 (UTC)

I am not sure if there have been any recent changes, I am just catching up on the talk page, but rereading the section I like it how it is now. It only mentions creationism in the intro and in the section about speciation (with a nice segue into created kinds.) All the other sections already focus just on the misconceptions without mention of ID or creationism. Nowimnthing 00:10, 22 September 2006 (UTC)

Returning from my self-imposed 48 hour hiatus, I'm happy to see how far the discussion has advanced. It sounds like we've reached at least a tentative consensus based on the Proposed Solution from Silence. Can we proceed with edits, attempting to restrict this section to common misunderstandings about evolution, and pushing material on the evolution/creationist controversy to the next section? I would advocate leaving out any reference to creationists exploiting these misunderstandings, at least until someone can find an attributable source for that statement. Onward! Gnixon 01:30, 22 September 2006 (UTC)

Modern Synthesis Separate Article

Why is the Modern Synthesis of evolution treated as a separate article when it is fundamentally what evolution theory is all about at present? You can't separate out the modern synthesis from evolution theory. If so just change the title of this article tp Darwinian evolution and change the whole article. The Modern evolution article is redundant to some of this article. GetAgrippa 18:29, 21 September 2006 (UTC)

This article, evolution, is about a biological process. Modern evolutionary synthesis is about the current most widely-accepted scientific theory which explains that process. The two overlap, but are distinct, just like evolution (again, a process) and evolutionary biology (a field of scientific research) are distinct. -Silence 18:38, 21 September 2006 (UTC)

Evolution is more about explaining a possible mechanism for earth's life history and the significance of biologic change. Evolution evolved into biology and was not accepted as a biological process till Darwin helped make it popular. Darwin's notions of speciation do not define evolution, because speciation is not synonymous with evolution. You can have evolution without speciation. An article on evolution should start with Darwin and evolve into the Modern Synthesis to the present. I think the history section should be a separate article addressing all to present. Your definition seems to indicate evolution is fact(like gravity) and the theory explains the fact. Evolution is not gravity. Evolution is inferred and deduced from observation, while I agree evolution is conceptually a fact. I think you can state the concept of evolution as biologic change and it provides a mechanism to explain earth's life history through the continutity of life and the reproductive success of inheritable traits and genomic change. Evolutionary biology is a distinct field but so is geology, developmental biology, etc that all have evolutionary significance. The process has to have a mechanism and so the theory is inherantly significant to the process. Changes in gene frequencies of alleles through time does not define evolution, but it also encompasses genomic change in duplications, indels, HGT, transposons, small RNA's, transcription factors, etc as significant to evolution as a process. Natural selection, mutations, genetic drift, gene flow, and nonradom mating all contribute to evolution as a process and are a part of evolution theory. I understand what you are saying but is seems a somewhat capricious distinction, because theory aspects like natural selection,mutations,etc. are entertained in the article. I think dividing the subject up is a mistake, except the history and religious and social implications deserve separate articles. I think there needs to be continuity on the subject as process and theory. GetAgrippa 19:22, 21 September 2006 (UTC)

In a perfect world there'd be no need to divide up the article. However, the term evolution (even when only considering the word as used in biology) has so many sides to it that putting them all into one page in Wikipedia would make for an unreadable article. Right now this article is very large. However, this page is pretty much about the Modern evolutionary synthesis: it states all the facts of evolution and then uses the theories from the synthesis to explain them. It is pretty clear that this page is not solely about the facts of evolution, such a page would be useless to any general reader. Rather, as Silence has said, evolution as fact and the theories that explain them overlap. I would argue with GetAgrippa that they do so to such a degree that talking exclusively about just one is utterly useless. What the editors of this article have to decide is how much of each side this article should have: how much facts about evolution and how many theories about the nature of these facts. This article, rightly so, only picks the major facts of evolution and also shows the major theories of evolution. The same applies to the Modern evolutionary synthesis article (it should be focused more on the theories within evolutionary biology). As in all of science, everything is interdependent. This article is the hub for the evolution field. Everything else should flow from here.--Roland Deschain 21:27, 21 September 2006 (UTC)

My point was that most of the modern synthesis article, except the history which is most of the Synthesis article is in this article. I think the history part would fit into the section of Evolution history already mentioning the Modern Synthesis. It just seems a weak article on its own, especially without the history section which I would fuse with Evolution history. I guess if the article develops then it would stand. I have not questioned it overlapping or the interdependence of fact and theory. I did not suggest talking exclusively about one or the other. I just noted the reference to the Modern Synthesis article and thought it was weak and mostly covered in this article and figured fuse part with this article and fuse part in Evolution history. It just seems a logical path and gives the reader more information in fewer articles. Silence stated the article is about process and that theory is distinct, but they overlap. It is obvious the article entertains both, which well it should as I elaborated. Now Roland starts talking about I suggested just talking about one, which is just opposite of my point that you can't separate them out because they overlap.Weird. As I stated, if the Modern Evolution Synthesis article is complete it should be divided and fused to this article and history article. That is it!GetAgrippa 22:10, 21 September 2006 (UTC) I do agree that detailed aspects of evolution can become separate articles, but the Modern Synthesis article at present seems redundant and mostly history.GetAgrippa 22:18, 21 September 2006 (UTC)

Addressing NPOV

I just rewrote most of the intro for the misunderstanding section. I've removed any direct reference to the reason for these misunderstandings (ie: religious believes). I have added the sentance that creationists use these misunderstandings. All these changes are, I believe, in line with the above discussion concensus. I'm not sure what else in this section requires a rewrite. Any suggestions.--Roland Deschain 01:00, 22 September 2006 (UTC)

I think that looks good. I didn't like the look of the one line paragraph, so have removed the return, but I think it still reads well. Hope that is ok. --Michael Johnson 01:05, 22 September 2006 (UTC)

I think you're on the right track, especially with including references. Thanks for starting the process! Gnixon 01:22, 22 September 2006 (UTC)

Two points...

• First, I read the Science article you referenced, but unfortunately, it doesn't address misunderstandings. The article is about the lack of acceptance of evolution in the U.S. relative to Europe due to religious fundamentalism in the U.S., which I think makes it more relevant to the controversy section and not appropriate in "misunderstandings."

• Second, part of the consensus in the above discussion was that if a sentence about creationists exploiting misunderstandings is to be included in this section, then for NPOV purposes it is critical that the statement be attributed to someone and referenced. Gnixon 01:22, 22 September 2006 (UTC)

  Ok, I've provided the reference. The book, by the way, in an excellent source to see the modern day creationist tactics, including using misunderstandings to sway both the public and the politicians.--Roland Deschain 01:46, 22 September 2006 (UTC)

  I think it would be much better to find something from, say, the NSF or the Department of Education, or something published in a major journal like Science or Nature. The book you reference (see synopsis) was written as an argument against creationism (not to mention that the author is a philosopher, not a scientist). We need a publication from some widely respected group with unbiased bona fides. Gnixon 02:06, 22 September 2006 (UTC)

  I have read the book and it spends very little time on the science of creationism (that's why the main author isn't a scientist). Rather, it gives clear examples of the fact that scientific misunderstandings are used against evolution. And the second author is actually a zoologist, so the credentials for the book are just fine. Furthermore, Fisher was in the Dover trial testifying under oath about the use of misunderstandings against evolution. The book is perfectly valid. It takes a stance agaist creationism but that does not invalidate their conclusions at all. Finding something in Nature would be even more against creationism than this book I'm afraid. If you want, I can cite the Dover trial. It's probably the best example where all these creationist tactics have come into the light.--Roland Deschain 02:23, 22 September 2006 (UTC)

The judge in the Dover trial ruled against I.D., but he did say it was the same tactic of contrived dulaism used by creationist as an 80's strategy. Further he did nor rule if favor of evolution. An excerpt "ID is at bottom premised upon a false dichotomy, namely, that to the extent evolutionary theory is discredited, ID is confirmed. This argument is not brought to this Court anew, and in fact the same argument, termed 'contrived dualism' in McLean, was employed by creationists in the 1980s to support 'creation science'. … However, we believe that arguments against evolution are not arguments for design. Expert testimony revealed that just because scientists cannot explain today how biological systems evolved does not mean that they cannot, and will not, be able to explain them tomorrow." The misunderstandings and straw man arguments are used by creationists, but not solely contrived by creationist. There are plenty of Christians who are evolutionist and plenty of atheist who have misconceptions concerning evolution. Because misunderstandings are used as a political ploy by a group does not give that group dominance over the misconceptions. I don't think creationism should be mentioned just address misconceptions, not all misconceptions are used by creationist. Why make it a political statement which is what a minority of politically active fundamentalist Christians have done. Lawsuits in Kansas and Pennsylvania don't make a nationwide trend. GetAgrippa 03:41, 22 September 2006 (UTC)

"Because misunderstandings are used ... by a group does not give that group [ownership of] the misunderstandings." Excellent comment. This is the point I've intended to make. There's plenty of room to address misunderstandings in this section without any hint of creationists. This section can then provide excellent support for a discussion in the next section of how creationists have exploited misunderstandings in their attacks. Gnixon 15:31, 22 September 2006 (UTC)

I think the religious fervor against evolution is more political than a widely accepted belief in the U.S. I have seen different polls indicating that 40-60% of christians believe in evolution. Given the population is something like 80% Christian then the majority of Americans believe in evolution. I don't think problems with evolution necessarily arise from religion but a lack of understanding and misconceptions. I don't think any reference to Creationism is warranted. Just make it about misconceptions. Otherwise POV issues arise. A one book reference seems a pitiful way to address NPOV. Further Science has a huge evolution lobby and I would not offer it as a neutral stance on relgious impact. It seems a blame game and fails to recognize that there is a huge gap independent of evolution between laypersons and scientist, which Science has wrtitten many articles on that subject of this gap.GetAgrippa 02:09, 22 September 2006 (UTC)

Am I going to have to cite creationist publications to drive the point home (see the most recent publication, it has all those misunderstandings [6]. There is no arguement that this section is indeed about misunderstandings. Furthermore, there is no arguement that major creationist groups use these arguments (ID being the most recent example. . . read the wiki page for more info). What's even more important, this phenomenon is large enough in the US to have a easily noticable impact (with many publications, of which I've put in the only one I have read). I really believe that it needs to be mentioned. Misunderstandings about evolution are not just passive entities in the society. There are reasons for them and leaving them out would be NPOV. Let's wait a couple of days and see what other people think. We'll leave in the sentance, but also leave the POV tag.--Roland Deschain 04:20, 22 September 2006 (UTC)

On further thought about this, I think I should let this go. I think my arguements are still valid, but this is the wrong place for them as nothing here has anything to do with the science of the thoery of evolution. So yeah, I'll cut that sentance and remove the POV tag.--Roland Deschain 04:38, 22 September 2006 (UTC)

I think the intro as it is looks very good, and I like that we've referenced articles quoting the National Academy of Sciences as saying that acceptance of evolution has been hindered by misunderstandings. Still, I think the subsections still need work, so we should leave the POV tag. Let me read through them again to refresh my memory and I'll add another comment here. Gnixon 15:23, 22 September 2006 (UTC)

How about if we tackle the subsections one at a time? In keeping with comments elsewhere on this page about the unwieldy length of the article, I think it would also be useful to trim these subsections as much as possible. Gnixon 16:00, 22 September 2006 (UTC)

Theory vs. Fact

I'd suggest the following:

• Remove link to "Theory vs. Fact" in the creation vs. evolution page.

  As argued above, let's move everything about the creationist attacks to the next section

• Remove Stephen J. Gould quote

  Primarily to save space, but if such a quote is neccessary, let's find someone who isn't so actively engaged in the creation/evolution debate.

• Reference citation 50 (or was it 49) from the intro, which does an excellent job explaining the issue in a neutral tone.
• Change title to something like "Scientific Theory" or "Theory vs. Hypothesis" or "Technical Meaning of 'Theory'"

  On second thought, maybe Theory vs. Fact is appropriate, but why don't we take our cue from the Theory#Science article?

• Make two separate points:

  • (1) The scientific usage of "theory" differs from the common usage.

    Here we can pull content from Theory#Science and refer to other well-established theories, like General Relativity (or better, something more commonly understood). We should contrast "hypothesis".

  • (2) Evolution is that kind of a theory---it is well-tested, long-established, and fundamental to virtually all areas of biology. Gnixon 16:00, 22 September 2006 (UTC)

Responses from Guettarda:

• Link to "theory vs fact" - what is the benefit on removing the link? It's a link to a more indepth discussion of the idea, which is normal for a "seemain" sort of link. In the absence of a stand-alone article, this is normal for Wikipedia. Wikipedia is hypertext, after all.
• "[M]ove everything about the creationist attacks to the next section" - why? When it comes to popular (mis)understanding of science, evolutionary biology is where "the rubber meets the road". Ordinary people don't claim to have opinions on cohesion-tension theory, so that sort of a section isn't necessary. But lots of people have been told "evolution is just a theory", and are surprised when it's presented as a fact. So it needs to be addressed. Many people who are not creationists have still been influenced by the debate. So it isn't a "creationist" issue, it's a issue about popular understanding (and misunderstanding) of science. It is needed as a section in this article.
• Remove the quote from Gould because he was "actively engaged in the creation/evolution debate"? That makes absolutely no sense. He was a populariser of science, one of the great ones, and he was an evolutionary biologist. I can't think of a better person to quote. Removing the quote because he was a populariser makes no sense - you quote the people who are best at communicating.

• We could add this Gould quote too, so he won't seem blatantly like a Darwinian sympathetizer and it would address evolution doesn't necessarily act at the level of the organism as Darwin proposed:"The essence of Darwinism lies in the claim that natural selection is a creative force, and in the reductionist assertion that selection upon individual organisms is the locus of evolutionary change. Critiques of adaptationism and gradualism call into doubt the traditional consequences of the argument for creativity, while a concept of hierarchy, with selection acting upon such higher-level "individuals" as demes and species, challenges the reductionist claim. An expanded hierarchical theory would not be Darwinism, has strictly defined, but it would capture, in abstract form, the fundamental feature of Darwin's vision--direction of evolution by selection at each level." Science, 1982. Oops, Forget about it. I was engaged in something else and started writing without focus, Sorry I am not good at multitasking. GetAgrippa 18:19, 22 September 2006 (UTC)

• "Primarily to save space" - I was unaware that space was a problem.
• "but if such a quote is neccessary, let's find someone who isn't so actively engaged in the creation/evolution debate." - as per above, no. Gould is a great choice. Quotes should be chosen based on quality, not on person like or dislike for the source.
• "Reference citation 50 (or was it 49)...does an excellent job explaining the issue in a neutral tone." And? Are you proposing the we outsource the entire article?
• "Evolution is that kind of a theory---it is well-tested, long-established, and fundamental to virtually all areas of biology". Evolution is a fact, it's an observation. Mechanisms of evolution, ie, the modern synthesis, are a family of well-supported (and less well-supported) theories. Guettarda 16:26, 22 September 2006 (UTC)

Guettarda, I think you'll find that your objections were addressed in the above discussion. (Which took place in this section and in Talk:Evolution#"Misunderstandings"_NPOV_Problems.) Gnixon 19:27, 22 September 2006 (UTC)

I've followed the discussion, re-read it before I posted. The concerns I raised have not been addresses. Guettarda 21:56, 22 September 2006 (UTC)

I agree with Guettarda, I don't see a problem with how it is now. I don't think we need to be politically correct here. People should be offended by things they read. Theory vs Fact is important becuase people do not understand how evolution can be a fact that is explained by the scientific theory of modern evolutionary synthesis. Gould is one of the biggest names in evolution, trying to remove him is almost like trying to remove Darwin. Your suggestions just feel way too watered-down for me. Evolution is a hard science. I think the changes to the misconception area were decent, but further redactions will either make readers think we are ignoring the social controversy (and fuel even more conspiracy see [7]) or that evolutionary theory cannot explain some of their points. Sure the controversy page is there for people to do more in depth research, but this page is where a lot of people will go first. It needs to remain a heavy portal for all evolution sub-pages. Like it or not, the social controversy, at least in the U.S. is bigger news than much of the science. Maybe we should look at how a social controversy is mixed into a science article like Race as an example.

I think you're missing that the next section after "Misunderstandings" is about the creation/evolution controversy. Gnixon 21:43, 22 September 2006 (UTC)

I also call for a show of hands on the neutrality tag. All references to creationists seems to have been removed from the section. If there are other non-neutral statements, they must be pretty vague if they don't have a specific object they are being non-neutral about. Does anyone besides Gnixon think we need the tag? Nowimnthing 20:18, 22 September 2006 (UTC)

There were at least 4 editors (Silence, Dave Souza, GetAgrippa, Slrubenstein) in the original discussion who seemed to agree that the section needed broad revisions to avoid NPOV issues, and our discussion wasn't limited to the introduction. I thought most people had come around to the Proposed Solution from Silence. Obviously I'll back off if I'm alone here, but I don't think that's the case. Gnixon 21:43, 22 September 2006 (UTC)

Removed the tag. I think the major NPOV issues have been resolved. The body of the article makes no strong and exclusive mention of any special group and simply reports misunderstandings. All objections above are not really about NPOV but rather about specific content of the section (ie: use a different tag). Gnixon, please let somebody else add the tag to see if there is support for your objection. Also Gnixon, start editing this article rather than spending this much time in the discussion alone. Will make this process go a lot faster and will make the article better (+ will make the section actually be what you want it to be).--Roland Deschain 00:18, 23 September 2006 (UTC)

Okay, I still think there are NPOV issues, but I'm willing to let it go if I'm the only one who feels this way (Anyone?). I think we've come a long way just by editing the intro (thanks, Roland). Roland, you're probably right that I'd do better to spend this time editing the actual article instead of the talk pages. It's just that I've been worried about starting an edit warn on such a sensitive subject. I'd particularly like to purge use of the word "claims." If nobody else thinks there are deep NPOV issues, I'll just proceed with edits and see how they're received. Thanks everyone working on this issue with me. Best regards to all. Gnixon 02:35, 23 September 2006 (UTC)

In the misunderstandings section maybe we should discuss distinctions between evolution and evolution theory, distinction betweeen species and cladistic species, molecular evolution-chromsome evolution-genome evolution,earth's life history-macroevolution, that evolution is not synonymous with speciation and mention physiologic-metabolic and behavioral evolutionary change? Is there an article discussing the mystery of the evolution of sex? GetAgrippa 17:16, 23 September 2006 (UTC)

"In the misunderstandings section maybe we should discuss distinctions between evolution and evolution theory". I think the Theory vs. Fact section already states the evolution is a fact and a thoery and why that is so. Here is the Evolution of sex article.--Roland Deschain 18:10, 23 September 2006 (UTC)

Roland the discussion seems more about the distinction between theory and fact conceptually. I am saying repeat the explicit definiton of changes in gene pools through generations and give examples in drosophila and yeast to demonstrate it is indeed an undenial fact. That would lead into theory and macroevolution (on a long time scale) as mechanisms to explain the life history of earth. I am glad there is a sex article thanks for pointing it out. I think we need to point out that evolution includes speciation, but evolution can produce behavioral and physiologic-metabolic changes also. Mention living fossils have not changed as in speciation but they have accrued genetic change that is evolution (at least I would presume some genetic drift)Also give more examples of speciation or at least mention plants.GetAgrippa 18:59, 23 September 2006 (UTC)

" And humans evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered"[52]. I think you'll lose people there because just because a large number of fossils, molecular biology,and other facts support the idea it is not a fact with impunity in itself like gravity (the analogy used). People have to build the argument. It is an inferred and deduced concept from facts. Gravity will exist without any humans to name it or explain it with a theory, thus apples don't suspend in air. That humans evolved from ape-like ancestors as an idea will not exists without us, it will be suspended. Without us no other animal will likely conceive it and even though we believe the evidence or facts overwhelmingly support it as fact it is still a belief. I'm being the devil's advocate as I believe it is fact, but the analogy of gravity to mans evolution aren't equivocal. GetAgrippa 21:07, 23 September 2006 (UTC)

• You are talking philosophy. The fact that humans evolved from ape-like ancestors is a scientific fact, just as much as it is a scientific fact that the earth revolves around the sun or that apples fall to the ground."That humans evolved from ape-like ancestors as an idea will not exists without us, it will be suspended." As a friend, you need to take a philosophy class ;). The fossils will remain when humans die out (ie: the fact) but the modern synthesis will vanish (ie: the theory). That is exactly what Gould states with the quote.
• "Without us no other animal will likely conceive it and even though we believe the evidence or facts overwhelmingly support it as fact it is still a belief.". Again, you are making a philosophical fallacy saying that no other aniaml will concieve of the idea. It's a strawman statement that cannot be proven right or false. You are counfounding believe and scientific fact.
• "but the analogy of gravity to mans evolution aren't equivocal." Yes they are. We observe an apple falling and we explain that by gravity. We observe progressive humanoid fossils and we explain it by the modern synthesis. Now of course a different explanation might be proposed to explain those facts (God pulls an apple down and God put the fossils there) but neither of those explanations invalidates the fact of progressive humanoid fossils and the fact of a falling apple.--Roland Deschain 21:25, 23 September 2006 (UTC)
• And lastly I don't think this will confuse people. It was written by one of the greatest and most respected science spokespeople. It is a clear statement about what the evidence tells us. I think you are more concerned that people will find this troublesome as this is a forcefull statement about an a very sensitive public (NOTE: NOT scientific) issue. And as I've just spend a good two days removing any consideration to public contraversy from this section, this statement fits perfectly. It is cited and can be found easily (via Google) at all major scientific websites.--Roland Deschain 21:39, 23 September 2006 (UTC)

I agree with Roland. GetAgrippa, you are confusing yourself with philosopy. A fact is a true proposition, it is a direct or indirect observation. Theories, on the other hand, though constructed out of facts, are different - because (1) they cannot be observed and (2) they explain. Consequently, that human beings "evolved from" apes is a fact. (BTW we didn't evolve from apes, we ARE apes. But that's another argument. Also, Newton didn't just "observe" gravity, he too had to "infer" and "deduce" it from other facts and present an argument. It's still not a theory though). Mikker ^(...) 21:53, 23 September 2006 (UTC)

I am not arguing philosophy and I agree that Gould was a brilliant man. I also agree that it is an direct and indirect fact from observable fossils and other facts as genomic comparison of relatives. As I said, I'm playing the devil's advocate from what I thought would be a laymans perspective or a high school student. This is an encyclopedia not a publication by peer reviewed scientist. The fossils remain but no one will be there to interpret them nor find new fossils to resolve issues within the story. I can see an apple fall, something pulled it down. I can see a room full of ape and humanoid fossils and I don't know if I would instantly see they are connected is my point. Wow! What a flurry. Playing the devils advocate shouldn't stir a personal rebuff. I don't think a stupid paragraph should qualify as a personal judgement. I don't particularly like a reprimand nor "I need a philosophy course", since I said I was playing the devils advocate.I thought there were rules against such childish nonsense. GetAgrippa 22:51, 23 September 2006 (UTC)

Nothing I said was meant to offend. If it did, I apologize.--Roland Deschain 03:50, 24 September 2006 (UTC)

Roland no need to apologize, I applaud your diligence in the edit war. I agree with what you are saying. I just am trying to step out of my skin to “see” as a student would see. I find it difficult not to get too technical or detailed for a general audience. People often confuse fact as truth (philosophical debate). I think the section addresses the issues in a concise and balanced manner. Excellent job! Perhaps end it with a strong statement that according to the definition of evolution as a change in ….. through successive generations that this is a undeniable fact that has been repeatedly validated. Sorry if I flew off, it was a bad day. Oh yeah, sorry for being redundant I hadn't read the whole section before I added the quote. I am trying to multitask again. Too much going on-sensory overload. Maybe I should just take a break.GetAgrippa 13:53, 25 September 2006 (UTC)

Help with change

User:Shlomi Hillel deleted the following sentence, "The Sun provides a large amount of energy to the Earth, and this flow of heat results in huge increases in entropy, when compared with decreases associated with decreasing the disorder of biological systems. ", with this edit summary, "The sun is in fact a source of NEGATIVE entropy, and the amount of energy absorbed by the sun is equal to the amount released... This sentence is just not in place". Since I have no idea if his statement is correct I post here to gather a discussion. Joelito (talk) 18:40, 24 September 2006 (UTC)

The sentance "The sun is in fact a source of NEGATIVE entropy, and the amount of energy absorbed by the sun is equal to the amount released... This sentence is just not in place" does not make any sense. The sun is indeed a source of negative entropy. But the sun does not absorb energy; it rather releases vasts amount of it. The sentance implies that the net energy output of the sun is zero ("the amount of energy absorbed by the sun is equal to the amount released") which is of course a ridiculous statement. Where is the energy that the sun is absorbing coming from? The sentance that was deleted was entirly vaid so I put it back it.--Roland Deschain 19:26, 24 September 2006 (UTC)

I'm sorry, I think I didn't explain it properly... The current sentence says "The Sun provides a large amount of energy to the Earth, and this flow of heat results in huge increases in entropy" - which is true but it ignores the fact that the earth is emitting all of this energy back into space. Roland Deschain: I did not mean that the net energy output of the sun is zero. Instead, I meant that the net energy gain of the earth is zero. All energy taken in from the sun is emitted back out into space. The net effect of this is a net increase of entropy in the system that includes the sun and the space, and that's what I meant by saying that the sun is a "source of negative energy"... The point of all of this is that since the net effect is an increase in entropy outside of the earth, the earth can "afford" to lose entropy without violating the second law. Therefore the "entropy argument" by the creationists is faulty. More can be found at http://physics.gmu.edu/~roerter/EvolutionEntropy.htm . As the current sentence does not reflect the whole truth in this reflect, I suggest to remove it or correct it. Shlomi Hillel 20:00, 24 September 2006 (UTC)

"but it ignores the fact that the earth is emitting all of this energy back into space."

• No. A part of the sun's energy is trapped on Earth (ie: by plants). This energy allows life to continue. If all the energy was lost back into space, no work could be done on earth (ie: no wind, no huricanes, no life, no waves, no warmth (except by Earth's own radioactivity), etc etc). As phenomena on Earth clearly do work (which requires energy), a part of the energy is not lost into space but rather does work on Earth. The most clear example that non all energy is lost into space is that we have warm weather. --Roland Deschain 20:08, 24 September 2006 (UTC)

On average, the temperature of the earth is not increasing, and that's a sure sign that the energy it takes in from the sun is eventually emitted into space (as radiation at longer wave-lengths). (Wind is coming from the fact that the suns shines on different parts of the earth unevenly, etc...) The temperature of a planet is roughly determined by equating its blackbody radiation output with how much it absorbs by the sun. If it absorbed more than it emitted, its temperature would increase... Moreover, the logic of the current sentence is flawed: If it were true that the sun causes an entropy increase on earth, it would be an argument in favor of creationism. The sun's energy would only increase disorder, and therefore, even with an energy source, evolution would still violate the second law. This is exactly the opposite of what the paragraph is trying to say. Shlomi Hillel 20:46, 24 September 2006 (UTC)

It's not quite correct to treat the Earth as a blackbody, since the atmosphere has a confounding effect - we might say that the Earth acts as a blackbody above the level of the atmosphere, but actually the amount of radiation emitted is inconsistent with the surface temperature of earth. Shlomi's right that the earth won't overheat so long as it can continue to radiate in infrared into space, but there are mechanisms for trapping heat on earth - the greenhouse effect is the major one, and in our case, the biosphere is another obvious one. Graft 19:00, 25 September 2006 (UTC)

You are right, the earth is not really a blackbody. Its temperature may well change because of a changing atmosphere and so forth. But it doesn't change the argumentation very much, as it's still true that the amount of energy absorbed is very nearly the amount radiated out, on average over long periods of time... (energy considerations, neglecting minor effects like "entrapment" of energy in fossil fuels; here is what Penrose says about this in his books, if it interests anyone). However, I'm not sure as to how much all of this relevant to the main topic. As I see it, the whole point of all of this is to debunk the creationist "2nd law" claim. For that, all you have to say is that the earth, or living material, is not a closed system and the second law says nothing about it. In an open system structure may form without violating any physical law. Shlomi Hillel 20:03, 25 September 2006 (UTC)

Shlomi is absolutely right that the old sentence was at least misleading, and the webpage he linked to gives a very nice explanation of why evolution doesn't violate the 2nd law. I changed the sentence, replacing it with a summary of the webpage and a link to it. Gnixon 14:22, 25 September 2006 (UTC)

While the link looks helpful, it starts out with the confusing description that "the second law says that things get more disordered over time". I've added clarifications and a reference for this particular point. ...dave souza, talk 18:04, 25 September 2006 (UTC)

By the way, the fact that it's obvious to everyone that this material exists to "debunk the creationist "2nd law" claim" is why I think it should be moved to the section on creation vs. evolution. (But no need to rehash that debate; I'm just sayin'....) Gnixon 17:31, 26 September 2006 (UTC)

But wasn't the point of cleaning up the misuderstandings section that the misunderstandings can be by anyone, even if some of them are promoted by creationists? Moving this to the evo vs creationism section implies that only creationists use this argument. I think that would be hard to prove. Really this is two misunderstandings mixed up together, one about the 2nd law in general and another about the application of the 2nd law to biological processes. Nowimnthing 13:33, 27 September 2006 (UTC)

Surely we all agree that it should be both accurate and accessible. I think the question of whether the misunderstandings are common among creationists is in and of itself irrelevant. For me the questions are, (1) are these widely held misconceptions and (2) will explaining them help people understand the scientific theory of evolution and why it is so powerful and widely accepted among scientists? If the answer to both questions is "yes," then I think we shoulod keep in the misconception, and explain it. The result will be an article that will educate a much wider circle of readers, and more effectively. In this case what is important is how the 2nd law does or does not relate to evolution, and I think this is indeed an important point. Let's distinguish between accuracy and detail. We do not need to provide en extensive, detailed account of the second law, that belongs in the linked article. We should explain just enough so that lay people can understand how it does or does not apply to evolution. But that "just enough" of course has to be accurate. I am certain we can explain it accurately, clearly and concisely. Slrubenstein | Talk 13:38, 27 September 2006 (UTC)

Idea, but possibly not a good one

As a biology student and lover of W. S. Gilbert, I'm aware of some rather good Victorian comments on the subject, e.g. "A lady fair of lineage high" from Princess Ida (final line: "But man, however well-behaved, / At best is only a monkey shaved!") and my favourite, though much more obscure:

That men were monkeys once—to that I bow;

(looking at Lord Margate) I know one who's less man than monkey, now,

That monkeys once were men, peers, statesmen, flunkies—

That's rather hard on unoffending monkeys!

-La Viviandre, W. S. Gilbert

But are these relevant enough even for a little side box (See W. S. Gilbert for an example of these sideboxes), let alone in-line text? Adam Cuerden ^talk 13:16, 27 September 2006 (UTC)

No. Quotations from leading biologists might be, but I don't see what informational value a quotation like the above would have for readers looking for information on the scientific process or theory of evolution. At best, such a quotation might be relevant enough to include in social effect of evolutionary theory, if given appropriate context and explanations (to avoid further propagating the exceedingly common misconception that evolution claims that "humans evolved from monkeys"). -Silence 14:02, 27 September 2006 (UTC)

Agree completely wish Silence, especially since we didn't evolve from monkeys. Slrubenstein | Talk 08:44, 28 September 2006 (UTC)

As a complete aside, while it's true that we didn't evolve from extant monkeys, this statement always strikes me as pedantic. We did evolve from something that, to the zoologically-untrained eye, almost certainly looked just like an extant primate. The discomfort of people who dislike the idea that we evolved from a "monkey" is unlikely to be assuaged by the knowledge that they evolved from something that "looked like a monkey". Factual accuracy is not really what this particular complaint against evolution is about. Then again, it's arguable that none of the common complaints are! Cheers, --Plumbago 09:32, 28 September 2006 (UTC)

Humans are an extant primate, so I'd be surprised if we didn't evolve from something that looks like an extant primate. While I agree that people's discomfort on an emotional or religious level would not likely be significantly affected by us pointing out that we have ancestors like proconsul rather than true monkey ancestors, that doesn't change the fact that it is just as incorrect to say "humans evolved from monkeys" as it is to say "horses evolved from rhinoceroses". To condone the former while pointing out the error in the latter would be hypocritical. Humans and monkeys share a common ancestor, just as horses and rhinoceroses do, but it makes more sense to point to a dramatically more closely-related species groups, such as zebras for horses or chimpanzees for humans. In any case, we certainly shouldn't propagate such misconceptions, regardless of whether we go out of our way to correct them; an encyclopedia's job is to inform, not to misinform. Also, I don't think that the above quotation is specifically a "complaint against evolution"; read it more carefully. I was simply pointing out that we shouldn't accidentally propagate an exceedingly common misconception about the evolutionary lineage of humankind; whether or not people will "still be offended" when we've corrected their error is irrelevant for our encyclopedic purposes. -Silence 13:05, 28 September 2006 (UTC)

I'll concur with Silence, but we should keep in mind that this is the main article, so it's appropriate to discuss all aspects of evolution, including its social consequences. The general public is at least as interested in the social/psychological/philosophical implications as it is in the scientific details. Gnixon 15:53, 28 September 2006 (UTC)

You are correct to some extent—this is the top-level article. But remember that the very top of evolution states "This article is about evolution in biology." Consequently, the social significance of evolution, though significant, is of secondary, not primary, importance. Furthermore, we don't have a daughter article called "Evolution in biology", where we could expand on the general topic of biological evolution; we do have exactly that kind of daughter article for "Evolution in society/culture", called Social effect of evolutionary theory. Consequently, simply as a matter of practicality, it makes a lot of sense to be dramatically more willing to include a quotation like the above in Social effect of evolutionary theory (where it is more specifically relevant to the topic) than in Evolution (which is already overstuffed with trivia and needs tightening up and summarizing, not further expansion—unless the expansion is truly of vital importance, which a funny joke by W.S. Gilbert is not). -Silence 16:09, 28 September 2006 (UTC)

"Evolution in biology", as opposed to, say, evolution of the solar system. That doesn't mean the ramifications of evolutionary biology for society, religion, etc. don't belong in the top-level article, or even that they're secondary to laying out the theory in technical detail (this article would be fine if it never used the word "allele"). There should certainly also be a daughter article on technical aspects of the theory, which would go a long way towards tightening up the main article. In any case, I definitely agree that this article needs to shrink much more than it needs to grow---we can do without the quote for now. Gnixon 15:06, 29 September 2006 (UTC)

Crystals and entropy

The article says "In fact, the flow of matter and energy through open systems allows self-organization enabling an increase in complexity without guidance or management. Examples include mineral crystals and snowflakes." No. Crystals are an example of self-organization occuring in a closed system and not violating the laws of thermodynamics. The following quote makes my point:

We observe lots of cases in this world where the natural course is increasing order. Here are just a few examples:

• Crystals: the natural state of most solids is crystal - the atoms line up in orderly fashions. For most materials it takes much deliberate effort to make it non-crystalline.
• Marbles: try this... take a bag of marbles and randomly drop them into a small bowl. They come to rest in orderly layers and form hexagonal patterns. Very natural order arising out of disorder.
• Rain: When it rains we have water molecules distributed over a huge area of sky become more ordered by forming into tiny droplets, then become more ordered still by falling to the ground and gathering into relatively small volumes.

BUT: If I throw a stack of papers into the air it starts ordered and ends up disordered. This is true, and it may even be cited in a statistical mechanics class in order to introduce entropy. The reason is that this is an example of how you can use Laplace's principle of insufficient reason to analyze likely outcomes in dynamic situations, and we are then going to proceed to do something similar for entropy. In other words, this is an analogy to help us understand something microscopic and it is not to be taken literally. When we say "entropy is disorder" after making this analogy, we have defined a very specific type of disorder. To apply this definition of disorder to the world around us will be like measuring the "power of an argument" in Watts. Most cases of what we perceive as "disorder" has little if anything to do with entropy, and hence little to do with the Second Law of Thermodynamics. [8] WAS 4.250 18:28, 27 September 2006 (UTC)

Good point and an interesting article which also links to a useful page about Entropy, God and Evolution giving more detail. One question: sure you mean a Closed system? The article doesn't mention that, but does relate the 2lot to an Isolated system as the links here do. ...dave souza, talk 19:14, 27 September 2006 (UTC)

Aye. Entropy is about the likelihood of a particular formation. Crystalisation, planet formation, and many other thing s that seem to increase order still increase entropy. Adam Cuerden ^talk 21:21, 27 September 2006 (UTC)

Viz. every single hydrophobic-core protein, cell membrane, etc., in the body. Graft 22:31, 27 September 2006 (UTC)

Self assembly is ubiquitous in biological systems and for nanostructures under equilibrium and some in non-equilibrium conditions. There are numerous examples of entropy driving order and self assembly. Here are some articles of interest concerning self assembly and entropy. Self assembly at all scales.Science. 2002. 295(5564)pp 2418-2421. Building Programmable Jigsaw Puzzles with RNA . Science.2004. 306(5704) pp 2068-2072. Entropically driven helix formation. Science. 2005. 307(5712)pp1067. Self-assembly: towards precision micelles. 1: Nature. 2004 Jul 29;430(6999):519-20. GetAgrippa 02:34, 28 September 2006 (UTC)

Well at its heart, all organization is driven by entropy; the trick is getting the entropy to work for organization, which biological organisms are very good at doing. Titanium Dragon 03:36, 29 September 2006 (UTC)

Have just come across this point expanded in an online excerpt from Into the Cool which is a book on the concept that energy flows and in particular the 2LoT underlie and support evolution rather than being a difficulty for it. This looks like a worthwhile link as a reference for the paragraph, which presumably should have "open systems" changed to "isolated systems". ...dave souza, talk 09:58, 29 September 2006 (UTC)

I think we should stick to peer-reviewed journal articles and material published by well-respected scientists at major universities. Gnixon 14:59, 29 September 2006 (UTC)

Might make a suitable external link, however. Adam Cuerden ^talk 16:27, 29 September 2006 (UTC)