Talk:Human genome/Archive 2

Archive 1

Archive 2

Archive 3

Response from Q.Y. Zhang

WP:FRINGE material

Answer some question: (For Mr. John Mackenzie Burke; and Mr. Agricolae; ) It is indeed hard enough to imagine that the fine double-spiral shaped DNA can pass messages via resonance to another animal or person. But if we take a look at the evolutional history, the double-spiral shaped DNA is the result of thousands of years evolution. The evolution never happens for no reason; it takes every possibility to improve. The pair of A-T and G-C, they never get into a mess during duplication; they help animals to call friend when looking for food, send alert when meeting with enemies, signal when they have missing children (e.g. the penguin can find their lost children). These are all relying on genetic resonance. The connection between A-T and G-C keeps the stability during resonance. The animal brains are not as complicated as that of the humans beings. But still, they have sulcus and gyrus. The sulcus is filled with fluid, which helps to keep a stable environment of resonance and leave space for the gene opening as the gene filaments inside the cells are usually not in their fully-extended mode.Four to six pair of A-T and G-C can sustain a 3D resonance, adding that the spiral construction can vary from tense to loose, thus change the protein shape, the signal they sending out are of various frequency.This is the result of evolution Around one hundred year ago, the genetic resonance was referred to as secondary voice. The secondary voice can be detected by machines, so as the genetic resonance. They are actually the same in nature being the frequency. The animal flee before earthquakes, the bat preying on the small insects, the pets welcoming the hosts, the telepathy for long-distance children, the hand or eye expression of masters of Qi Gong,all these frequency and energy can be explained as the genetic resonance, which transforms to be the heat or other energies for passing messages. If we take a try for about 10 days on the Zuo Chun Gong (standing still, wide-based legs as the distance of the shoulders, feet parallel and pointing to the front, gentle flexion of the knees, up-right trunk, gentle lifted hands, abducted fingers and tensed anus, this is the basic posture of Zuo Chun Gong. And then we breath slowly, imaging that the flow of air go through to the lung and then to under the umbilicus- Dan tian acupoint in traditional chinese medicine, then we hold it for a while and expire it slowly. The breath holding can be varied individually). We would feel the palm and fingers are tingling, this is caused by the genetic opening of the palm cells, (I would like that the master of Qi Gong or doctors can give some detailed explanations on this phenomenon). If we detect the palm of masters of Qi Gong, we might find the microwave and heat of their palms are higher than ordinary people. (However, as this is no my major, I cannot really tell the name of the detectors), According to a report dated 2 decades ago in Taiwan, there was indeed higher microwave and heat in the palm of masters of Qi Gong detected. I don’t know much about Qi Gong, nor did I believe in it at the very beginning, But one of my junior high school classmates is a master of it. Once I brought him to visit another friend, where there happened to be 3 patients. My classmate observed them, and then named exactly their diseases one by one. Another time, my sister suffered from lower back pain so much that she couldn’t get up. The doctors in hospital couldn’t fix it. My classmate visited me by accident and I told him about my sister, so he paid a visit to my sister with my brother. A moment later, my brother came back and told me what happened: My sister was lying there, and my classmate was sitting next to her with a cigarette in the hand, saying “keep still, I help you to straighten out the spines and tendons. You will be able to get up even before I finish my cigarette”. Surprisingly, before he finished his cigarette, my sister really got up, further more, walking, going up and down the stairs and working on the sewing machines were all out of question. Even the neighbors who was watching aside got astonished. My sister suffered from 3-5 recurrences of lower back pain before she saw my classmate, but after that time, this disease never came back again. That is why I say, for the real masters of Qi Gong, they can use their eye to stimulate the internal cell signaling and straighten out the “internal channels”. If they keep staring at the a body part, but detect no genetic resonance, it means the lesion is right there. (Talker: Q.Y. Zhang; 香港 張其澐 --119.236.56.235 (talk) 08:14, 3 February 2013 (UTC))

Human Genome is a Scientific Model

I have tried to edit the main section for Human Genome to indicate that genomes refer to individual organisms and that, therefore, the human genome is a scientific model. This was changed first using the rationale that the edit discussed sequences and not the human genome. After I amended the edit accordingly to focus on human genome, another user changed it using the rationale that there was a copyright violation. As far as I can see, neither rationale was valid. I can only guess there is some aversion to recognizing that the human genome is a model, not actual genetic material/information. Can someone please address why people are using erroneous justifications for "undo" actions. Thank you. — Preceding unsigned comment added by Dylan Hunt talk 15:50, 15 July 2013 (UTC)

First edit: The human (Homo sapiens) genome is a composite analysis of chromosomal sequences found among various samples of human individuals. When people say that the genome of a sexually reproducing species has been "sequenced", typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as a "genome sequence" may be a composite read from the chromosomes of various individuals. Therefore, "the human genome" is a colloquial simplification. In this sense, it refers to the ideal representation of the complete set of human genetic information, stored as DNA sequences within the 23 chromosome pairs of the cell nucleus and in a small DNA molecule within the mitochondrion.

Second edit: In modern molecular biology and genetics, a genome is the entirety of an organism's hereditary information, including both the genes and the non-coding sequences of the DNA/RNA.[1] The human genome is a model of the complete set of genetic information found in human (Homo sapiens) individuals, as a composite model of human genetic material that is stored as DNA sequences within the 23 chromosome pairs of individual cell nuclei and in a small DNA molecule within individual mitochondria. Dylan Hunt talk 16:32, 15 July 2013 (UTC)

Your initial attempt described the genome as a composite produced by genome sequencing. It is not. The genome is the DNA complement of a cell/organism. I get the distinction that you are trying to make, that the human genome sequence is a composite and not the actual sequence of any particular cell, but that is the sequence, not the genome itself. The concept of the human genome is not a composite of anything. It was just wrong, and that is a perfectly valid reason for reverting. The second edit copied a sentence verbatim from somewhere, and that is a COPYVIO. Copyright violations can be reverted with no further justification. Thus, both reversions were, in fact, based on valid rationale - accuracy and copyvio. Now, if you want to discuss the actual content you are trying to insert, I can't tell if this is just a question of semantics or a different viewpoint, but the human genome is not a model. It is formally defined as the actual genetic material. That it is a little bit different in everyone is worth pointing out, but does not change anything, any more than the fact that every zebra is a little bit different means that the term 'zebra' is a composite, a model. Agricolae (talk) 16:30, 15 July 2013 (UTC)

Thanks for the explanation. I can see how the difference in opinion caused the non-conservative edits (see below on the issue of "copying"). The term, "zebra", is much like a model, if we are talking about the concept. The concept, zebra, is not an actual zebra, but a generalization. All models are generalization, and many concepts are generalizations of actual tokens (instances) of those concepts (zebra-concept is a generalization of actual zebra organisms). I am not sure where your formal definition is coming from. I would be grateful if you could let me know what your source is for this formal definition.

Alternatively, please explain how "the human genome" can consist of "actual genetic material". Does this mean that the human genome consists of genetic material from all humans, all over the world, past, present, and future? I maintain that when people refer to the human genome they are using a generalization, and more specifically, a model. I would be surprised if you could find a biologist who would disagree, when pressed to speak carefully about the subject. Dylan Hunt talk 16:50, 15 July 2013 (UTC)

A generalization, yes, a model, no. When you get to saying that 'the concept zebra is not an actual zebra' all seems a bit like semantic gymnastics to me - we don't actually feel the need to draw the distinction between zebra, the generalized concept, and zebra, an individual that collectively contributes to that generalization. I would be surprised if you can find any scientist using the term 'model' to refer to the human genome. Agricolae (talk) 17:42, 15 July 2013 (UTC)

To continue: If you are thinking in terms of "model species" or even functional models, I can understand your cognitive dissonance, but there are many kinds of scientific models (sometimes, "model" is used in the sense of an instance that represents desired properties (e.g., a fashion model), but this is a prototype, not a model). This page, scientific model, might be helpful. There are only two options here, given the use of the human genome generalization: Either the human genome is the genetic material for all members of the species, Homo sapiens--in which case, "human genome" is not an abstraction--or it is an idealization that represents the human species as a single ideal representation of genetic material (i.e., a scientific model).

At any rate, you still have not provided any reference or authority for what you referred to as how "human genome" "is formally defined" (i.e., as "actual genetic material"). I can't find any such formal definition of "human genome" outside of this Wikipedia article. It applies to "genome" accurately, but you haven't backed up your claims regarding that definition of "human genome".Dylan Hunt (talk) 18:23, 15 July 2013 (UTC)

If it applies to 'genome' accurately, then putting the adjective 'human' in front of it doesn't 'break' the meaning, suddenly causing it to become all abstract and modelly. Agricolae (talk) 18:33, 15 July 2013 (UTC)

The issue isn't one of "breaking" meaning, but one of making meaning. There is an enormous difference between talking about a model of humanity or about the collection of all instances of humanity. Geneticists (though I am not one) clearly mean the former. Consider that congenital diseases do not occur in the human genome, but in individuals. Are you the administrator for this article (I can't imagine a scientist would use a phrase like "all abstract and modelly"). It is important that this article be factual. If you don't have a source to back up your claim, then I will provide a definition in the article that includes your view (as the perspective offered by journalists), as well as the concept applied by geneticists, with adequate sources.Dylan Hunt (talk) 18:45, 15 July 2013 (UTC)

Sorry, no. There is nothing 'made' by talking about a genome in a subgroup of organisms, whether it be a human, a dog or E. coli. The fact that all diseases, genetic and otherwise, occur in individuals does not mean that a genome is just a model, any more than that it implies that diseases aren't real but just a model. That person with the disease - they are a human and they have a genome, and it is thus a human genome, and it is real, and it has a precise sequence in every one of their cells and it isn't a model. (Who ever said that a genetic disease 'occurs in the human genome' anyhow?) This is not just a 'journalist's perspective'. I am not an administrator for this article - Wikipedia does not have article administrators. Here is the problem with those references you are demanding. Everyone knows what 'human' means, and everyone knows what 'genome' means. You want a reference that 'the human genome' is the 'genome' of 'humans' - it's right there in the phrase and it would be tautological and pointless for anyone to be that pedantic. (Oh, and by the way, scientists use whatever language they think will get the point across, that may be 'modelly', it may be 'tautological'. They also may be grammatically incorrect in their usage - just look how often real actual scientists say 'data shows'. If they were English majors, they likely wouldn't have become scientists.) The way forward here is not to give ultimata, but to work on a consensus here on the Talk page. Then once a consensus is achieved, move the text into the article space. Agricolae (talk) 19:28, 15 July 2013 (UTC)

I offered no ultimatum. I proposed a solution that would include both views, which is better than insisting on an incorrect view, or even than insisting on a correct view and continually blocking another person's view. Your view happens to be one that any molecular biology major at university/college would refute, as well as would any geneticist (with some thinking of individual genomes as versions of the ideal referent "human genome", rather than thinking that the ideal is an amalgam of individual genomes).

Calling something "human" (as an adjective) doesn't mean that it includes all humans (as "Bob's hair" would include all or some of the hair on Bob). It could mean, and in this case *does* mean, that the genome pertains to human beings *as opposed to* frogs or mice. It is only in a trivial sense that the genome of a human individual is a human genome. This is important when you consider the ethical, legal, and sociological (ELSi) implications of the human genome concept (e.g., ownership of genetic material used in refining the human genome model). It is also important when talking about diseases--the point being that congenital diseases (or symptoms) are real because they occur within individual genomes (not in a composite model), whatever theories and models accompany their treatment. *The* human genome--since there is no single genome (in a body) that consists of all human genetic material--is an abstract, ideal representation, as if there were a singular genome representing variable characters of the species--and this is widely acknowledged, common (expert) knowledge that should be conveyed to readers of this article. The human genome certainly does not contain genetic material itself.

Please do some research, as I'm not sure two opposing views can ever be called "consensus". What you are protecting on this article does not represent a Wikipedia consensus at present. Even more importantly, it is false.Dylan Hunt (talk) 12:32, 16 July 2013 (UTC)

This is all wrong on just so many levels, but I am not going to pick it apart sentence by sentence. If you want this to move forward, your approach is not productive. You alone are proposing that the consensus that has existed on this page for some time be changed. You continue to maintain that the human genome is a model, so do a Google search for the exact phrase "the human genome is a model". I mean, if that is a fundamental truth then someone should have said it. And how many matches do you get? it is not a very large number, is it? Perhaps, your absolute certainty about the understanding of university students aside, your viewpoint is exactly that - yours. Just repeatedly proclaiming that your view is the only legitimate one, and must be in the article, does not make it so. Agricolae (talk) 13:43, 16 July 2013 (UTC)

People do say it, but I don't think anyone has drawn your attention to the distinction between genetic material and models of genetic information before. There is a reason that people refer to "the human genome" (notice, not any genome of an individual of the human species) using metaphors like "autobiography" or "compendium" or even more obviously, "code". These are representations of objects (descriptions of a person's life, not the person), not the objects themselves.

The distinction is more common when people aren't comparing human to non-human animals, but are already focused on humans--because of rights issues. So, you might have to look in discussions where the applications of your perspective is known to have bad consequences (e.g., in the human genome diversity project). Here is one example by a geneticist, that literally spells it out for you:

http://www.the-scientist.com/?articles.view/articleNo/32446/title/Opinion--What-Is-the-Human-Genome--/#articleCommentsDylan Hunt (talk) 14:23, 16 July 2013 (UTC)

So, your Google search, how did that go? There is nothing special about the human genome. We could be having this discussion about the E. coli genome - not every E. coli has the same sequence either. Your attempt to make humans somehow special with regard to their molecular biology is misplaced. And your link - it is an opinion page in a popular science magazine and its main point is that the sequence arrived at is more a reference human genome and not the human genome per se. Anyone who uses "autobiography" as a metaphor doesn't know what they are talking about (or doesn't understand the concept of a metaphor). On the other hand, "code" is hardly a metaphor at all - the genome encodes the information necessary for cellular and hence organismic function. The correspondence is literally called the Genetic Code. Now you may choose to call the Genetic Code an abstract representation, but it is also a real biochemical phenomenon - the recognition of specific tRNAs by specific tRNA-amino-acyl-transferases, the specific Watson-Crick and Hoogsteen hydrogen bonding interactions between the anti-codons of those aa-tRNAs with the codons of the mRNA in the A site of the ribosome, so as to incorporate a specific amino acid into the growing peptide chain - that is real, not a just metaphor. Now, it is time you quit lecturing me like you are an expert and I am a tyro. Neither is actually the case. You just repeatedly telling me that I don't know what I am talking about does nothing to improve this page. Agricolae (talk) 15:21, 16 July 2013 (UTC)

I apologize if I appeared to be lecturing you. At the same time, since you do not recognize that "genetic code" is in fact a metaphor that has become routinized in scientific talk (and now appears as literal description), there wouldn't be any harm in looking at an introduction to the philosophy of science, or a history of the development of these concepts (e.g., Kay, L., 2000, Who Wrote the Book of Life? A History of the Genetic Code. Palo Alto: Stanford University Press). The exact sort of reactions you are talking about are physical interactions. To say transferases are using code is to speak loosely, almost as loosely as suggesting that a protein can write a play (theoretical physicists use this sort of poetic license). (Even though Shannon's information theory interprets information as correlations of state-changes...) Codes, as information that produces differences that humans are interested in, are intellectual representations of the mechanisms and operations of physical interactions. They are used by humans to describe, while those very descriptions, in shorthand, suggest that enzymes are manipulating "code"--because this is an infinitely easier way to say it. Unfortunately, people can become trapped by these shorthand expressions, as we are seeing in this discussion. Dylan Hunt talk 15:59, 16 July 2013 (UTC)

Right, you apologize for appearing to lecture and then launch into yet another lecture. I tried to be subtle about this, but no more. Wikipedia is not about editor expertise, but I can only be talked down to by a novice so much before it gets old. Unless you have done it in real life - actually cloned and sequenced genes, modified the genome of an organism, performed metabolic assays, or for that matter earned a PhD and lectured at a university in molecular biology, genetics and biochemistry, then stop playing 'Gulliver among the Lilliputians'. If you want to talk about the disputed content of the page, do so (you can start by reporting how many times Google reports the phrase "the human genome is a model", which one would expect to be a large number were that the predominant viewpoint), but these meta discussions are getting us nowhere. Agricolae (talk) 17:15, 16 July 2013 (UTC)

Based on your criterion, I guess I qualify as a Gulliver among Gullivers. However, I don't think the issue should be about my PhD, but about clear communication. Technical expertise in biochemistry is not equivalent to understanding these concepts for the purpose of communicating them to the Wikipedia audience. If you don't like my change, which excludes the idea of models that you rejected, and only includes what you have admitted yourself, please point out where it is in error, rather than making a knee-jerk "undo' action.Dylan Hunt (talk) 17:45, 16 July 2013 (UTC)

It's not how you structure an article, and it's not how you resolve a dispute, just just by incorporating the conflicting viewpoints into the first sentence of the lede - a true synthesis is what is needed, not a false dichotomy between 'human' 'genome' and 'the human genome'. Further, once you initiate a discussion to resolve a dispute on the Talk page, it is disingenuous to then decide you can institute the 'perfect' solution unilaterally. We need to work this out here - hash through the disputed text here, not in the article. WP:BRD - it's OK to be bold, but when it is reverted, you discuss it. It is incumbent on the person desiring a change to gain consensus on the Talk page. You might be surprised: there could be a way to describe this that satisfies both of us (I suspect we aren't as far apart as you make it seem when you condemn the current content of the article as false), but we are unlikely to get there by edit warring in the article space. Agricolae (talk) 18:24, 16 July 2013 (UTC)

I wouldn't be surprised by a mutually satisfying solution. However, I am waiting for you to explain why the dichotomy is false, since you have already agreed with these changes. I am likely to be more surprised by your explanation of what you see as the false dichotomy; also, why the sources I provided are wrong; and why the other minor edits do not improve the lead. Perhaps you can even go further than explaining the false dichotomy, and propose a resolution. I can't solve the false dichotomy problem if you don't state it. As things stand, your reaction can only appear as a knee-jerk reaction.Dylan Hunt (talk) 18:31, 16 July 2013 (UTC)

We don't start an article on zebras by saying that 'zebra', the name used to refer to an individual animal, is distinct from 'zebra' a scientific abstraction that is a model representing the average of all individual zebras. That 'human' 'genome' is distinct from 'the human genome' is similar semantic wrangling that ossifies as completely different two ways of looking at the same overall concept. The phenomenon encompassed by the term 'human genome' is not best defined by saying that it is two different concepts, just because we can't agree on how best to express it. Plus it's just bad form to start an article with such a dichotomy - if they are really distinct there should be two articles, one about each concept, rather than one article about two different concepts. If it is to be a single article (as it should be), then the first sentence of an article needs to unify - to express it in its totality, and not immediately divide into (falsely) mutually exclusive concepts. Agricolae (talk) 18:52, 16 July 2013 (UTC)

The article is called, "Human genome". This involves a singular kind of genome (that of individual humans) and a species kind (abstraction). "The human genome" is not a description of my genome or yours. I have offered three references that indicate there is an important difference between "a" and "the" genome of humans. If you looked at those sources, I would hope you would see that this is more than "semantic wrangling". If you are not aware of the enormous challenges that arise as a result of not distinguishing the two, I am not sure what to say (Perhaps: take a break from the lab). People are spending millions of dollars in legal challenges because of the difference between "my" genome and the ideal representation of of human genomes.

I get that you are trying to bring an ethical/legal perspective to this issue, but the fact that lawyers make millions of dollars by fighting over petty distinctions does not (must not) take precedence over a scientific viewpoint where the same word can and is used to encompass different aspects of a unity, just like the zebra analogy (which fortunately very few lawyers argue about). It is important that when you talk about a single zebra, you know you are talking about one specific critter, and that when you talk about 'the zebra' you are speaking in generalities, but the scientific understanding of 'zebra' encompasses both, not as two completely distinct and mutually exclusive concepts that the same word is used to describe and that must be distinguished in the first sentence of the Wikipedia article, but as two different aspects of the same concept. This is the way of many words - they encompass a plurality of understandings and we don't feel the need to lay out in the first sentence that it could mean this or it could mean that or it could mean the other thing when these meanings are all part of a whole. (And for all of the supposed enormity of these supposed challenges, this has nothing to do with how much time one spends in a lab.) Agricolae (talk) 20:02, 16 July 2013 (UTC)

It is not an ethical/legal perspective. It is a scientific perspective, which happens to be of social (and not merely semantic) importance. Would you want a blind surgeon to operate on your body just because he had expert knowledge of "the human body"?Dylan Hunt (talk) 20:23, 16 July 2013 (UTC)

Nobody is blind here. Let's go look at Human body, then, since you think this makes for a good analogy. Does it start by saying that A 'human' 'body' is different from 'the human body', an abstraction that represents no actual body but rather is an abstraction across all humans? No, it does not. It says, "The human body is the entire structure of a human organism" without bothering to differentiate an individual human body from the collective generalization, just as this article described the human genome four days ago. Agricolae (talk) 20:44, 16 July 2013 (UTC)

Amusing :) and helpful, too. I agree that zoologists and surgeons don't have a problem with conflating the particular and the general patients/zebras, as the case may be. This is because zebra (particular animal/token) to zebra species (general/type) is only one abstraction, while "the human genome" involves about two or three orders of abstractions (token-organism : species-type; genetic material of organism : common features of genetic material of members of species-type). If a surgeon is asked to operate on the human body, she would most definitely want to know whose particular body, even if drawing on theoretical knowledge about human bodies in general--a distinction I hope any surgeon would make while operating on me.

However, people discussing genetics and genomics frequently conflate the general with the particular as the previous version of the article did. When it is a general category ("the human body" or "the human genome"), it is clear that the subject is a theoretical object (like the human body). Yet, you refuse to include this point in the article. I cannot understand why. There are two ways of doing this, as you suggested: 1) Make the article unequivocally an article about *the* human genome (rather than a confusion of the two), or 2) make the distinction and then model most of the article on "the human body" article. Either way, since it is not obvious that the article is referring to an abstraction, it seems like the solution would be to make clear from the start that "the human genome" is an abstraction, especially as a later section of the article refers to "personal genomes" (which are still theoretical abstractions in reference to particular bodies, but one level of abstraction removed from "the human genome").Dylan Hunt (talk) 21:34, 16 July 2013 (UTC)

This 'two or three orders of abstraction' is just your personal POV. There is no difference in kind between the levels of abstraction involved in 'the human body' and that in 'the human genome'. Look at Human body. Where does it mention that everyone has a different body? It doesn't even specify that it comes it two basic flavors, male and female. Does it ever call the human body a theoretical object? no. It is perfectly comfortable with the whole concept without specifying all of the implications. It particularly doesn't specify that body and body mean different things, depending on your perspective. What I am opposed to here is not pointing out somewhere in the article that every genome is different. That is a notable if pedantic point, and perhaps it would be good in the lead to the personal genomics section. What I am opposed to is the need to make it more complex than it needs to be, by immediately, in the first sentence of the article, launching into the semantic distinction. We don't start zebra by saying that every zebra is different from the collective concept, we don't start horse genome by distinguishing the genome of one horse for the general genome of horses (although that article lacks a true lede, so it is not the best model), nor bovine genome, nor jute genome, nor adenovirus genome. There is no reason to do so here. The most important concept is not that every human genome is different but the general concept, just as human body begins with and focuses on the general concept. That is what goes in the lede, at its start, not fine distinctions. Agricolae (talk) 22:12, 16 July 2013 (UTC)

It is a fact and not merely my personal POV that the references I provided corroborate my POV about orders of abstraction--in fact, that is why I provided them. If you want to ignore the references I provided, that is your prerogative, but don't be surprised if you continue to miss the point. It is also your prerogative to undo productive and informative references within limits, but I don't think you should use Wikipedia to block other people from becoming better informed about complex issues.

I can go into more detail as needed, but the complexity of the issues is better stated by those references, and my elaborations will simply make the point seem even more like it is merely my personal POV. Your best move is to read the references. A substantive response will repeat some of the same points that your latest response rode roughshod over, but repetition can sometimes be helpful... "The human body" is a generalization (many:one) of something (i.e., actual body), whereas "the human genome" generalizes (many:one) an abstraction (i.e., genetic code) of something (i.e., biochemical material associated with an actual body). As a result, the generalization in genomics/genetics is correspondingly more complex than that of 'the human body' because 'the human genome' is not simply a quantitative generalization (all or some, from one), but involves an abstraction from complex information associated with individual specimens. One might argue that 'the human body' is no different--not every human body has two arms and two legs--but this means that 'the human body' concept (a theoretical object) is a prototypical concept. By contrast, there are technical methods of abstracting a reference genome (also a theoretical object) from sampled specimens and these techniques are not comparable to the non-technical "method" by which prototypical concepts are produced (i.e., common-sense (non-stochastic) sorts of induction).Dylan Hunt (talk) 04:21, 17 July 2013 (UTC)

That no two individuals have the same genome is not your POV. That the fact that no two individuals have the same genome is the most important thing to say about a genome, more important than saying that a genome is made up of actual genetic information in the form of biochemicals, and that this fact has uniquely importance in humans, is your personal POV. There is nothing abstract about an individual genome. It is a collection of specific biochemicals, and those biochemicals exist in the real world, just as an individual human body exists in the real world. The concept that a every genome is inherently abstract is just plain wrong. You already have admitted that the biochemical description is perfectly valid for genomes in general, but then for the human gene this is somehow invalid - it makes no sense. An E. coli cell has a genome. It is a circular piece of double stranded DNA, and it has a specific sequence of nucleotides around that ring in a specific E. coli. Going from an E. coli to a human genome is a difference in scale, not of kind. The start of articles on any other organism genomes - cattle, horses, adenoviruses (not really an organism, but you get the point) - don't lead with the whole 'every genome is an abstraction' canard. What makes humans so different? That they hire lawyers? Sorry, that changes nothing about the biochemistry or its importance in describing what a genome is. Agricolae (talk) 19:53, 17 July 2013 (UTC)

Let me add that I am not saying there is no role for ethical or legal perspectives. We can have a whole section of the article on the ethical considerations and another one on the legal considerations if there are the references to support it. We just don't want to lead the article by drawing flawed distinctions based on which grammatical article appears before the word human, and where one places mini-quotes, while missing the big picture entirely.Agricolae (talk) 21:18, 17 July 2013 (UTC)

My point is not an ethical or legal one, as I have noted before. It is about the basic concept.Dylan Hunt (talk) 14:44, 18 July 2013 (UTC)

I will add that there is a difference between a source making the point that the human genome (at least as they are referring to it) is an abstraction, and defining the human genome as an abstraction. I have returned the text to how it was before this edit war, then changed the wording to better incorporate your 'abstraction' concept without obliterating what a lead is supposed to do and without deviating from the pattern established on every other page in Wikipedia that deals with similar ambiguity. Agricolae (talk) 21:18, 17 July 2013 (UTC)

I actually find this to be a more or less satisfactory resolution, in the sense that it is progress. However, in continuing your edit-war (returning to a previous version) before making edits, it does gut some of the useful information I provided (e.g., references). While your first constructive contribution does signify some progress in the process toward consensus, it came only after a series of attempt to police this article and after receiving a caution from Wikipedia admin. I have no confidence that you will react to more of my contributions with any more open-mindedness because you seem to have set yourself up as a gatekeeper, as others on your talk page have noted regarding your actions on other articles. As a result, I have asked for arbitration. I would suggest re-reading the wiki policy on consensus, which often does require gradual steps toward resolving differences of opinion.Dylan Hunt (talk) 14:44, 18 July 2013 (UTC)

(Didn't you recommend below that, "Wiki-editors should be more concerned about substance and content of the pages than with the tactics and maneuvers of edit-wars, don't you think?" I guess that just referred to other Wikipedia editors.) The reason I went to the earlier version is that there was no salvaging the flawed distinction between a human genome and the human genome, and no article should start with such a distinction, flawed or otherwise. The reason I removed the references is that they did not document the sentence that ended up being used there - references are used to document statements in the article, not just placed in the article for their own sake. You want to make progress, so here - on the Talk page - suggest how you would improve the text, or we could discuss where, other than in the first sentence of the lede, we could get into the semantic gymnastics. In all of this, you have yet to come up with a valid justification for why we should treat the human genome any different than any other concept in science, where we don't start pages by drawing distinctions between the individual and the collective applications of the term. Agricolae (talk) 15:18, 18 July 2013 (UTC)

I see that you filed a report. You said that you offered a "warning", but there was none when I made the revision.Dylan Hunt (talk) 19:30, 16 July 2013 (UTC)

There was - you even referred to it in your edit summary so you can't say you didn't see it. Anyhow, this is not the place to discuss that. Agricolae (talk) 20:02, 16 July 2013 (UTC)

I don't know why you prefer to be so adversarial. I referred to *your unedit explanation* in my edit summary, not to *the warning you put on my Talk page*. Wiki-editors should be more concerned about substance and content of the pages than with the tactics and maneuvers of edit-wars, don't you think?Dylan Hunt (talk) 20:23, 16 July 2013 (UTC)

That is why I said this in not the place to discuss this. Agricolae (talk) 20:44, 16 July 2013 (UTC)

COPYVIO

"In modern molecular biology and genetics, a genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of viruses, in RNA" is found all over the place on the web. They may all be Wikipedia mirrors, I didn't take time to check, but it is clearly copied from somewhere. (Note - you aren't allowed to copy text verbatim, ever, even from one Wikipedia page to another.) Agricolae (talk) 16:14, 15 July 2013 (UTC)

If you check the revision history, Agricolae, you will notice that I changed the verbatim text prior to your undo action for COPYVIO reasons. I copied the first sentence from the Wikipedia article called Genome, saved the change, and then returned to the editing box and edited the verbatim Wikipedia text prior to your unedit.

Further, the undo action you made affected more than the sentence(s) you claimed to be verbatim. As a result, I am undoing and editing to change the sentences that have nothing to do with any alleged COPYVIO. Please restrict your admin edits to applicable text.

I don't think there is any reason to be offensive in your response: "Don't play dumb. The first sentence is a verbatim copy of material found elsewhere. You may have copied it from the web, you may have copied it from elsewhere in Wikipedia, but you obviously copied it. Agricolae (talk) 16:11, 15 July 2013 (UTC)" — Preceding unsigned comment added by 128.174.160.178 (talk)

You just, again, copied material from elsewhere in Wikipedia. Don't do that! (Oh, and you need to sign your posts - put four tildes (~) at the end of it when you are done.) Agricolae (talk) 16:36, 15 July 2013 (UTC)

I don't know what you mean by "copied from", unless you mean the mechanical act of copy (Ctrl-C/Ctrl-V). If the latter, then yes I copied from the previous version of the exact same section of the exact same Wikipedia article that I "copied" to. What is the issue that you are raising: Is mechanical copying not allowed because of artifacts (non-ASCII) elements that are carried with mechanical copies? Please explain. However, there is absolutely no copyright issue here if a previous version of the same section of the same article appears again.128.174.160.178 (talk) 16:40, 15 July 2013 (UTC)

The first time you copied from some other page and put it into this article. The second time, you copied text that I put on my personal Talk page (in response to your seemingly disingenuous query) to this Talk page. The Creative Commons license under which Wikipedia operates does not allow the copying of text from one page to another (without some very precise steps regarding attribution). If you wish to draw attention to an edit made elsewhere, you should do so by linking to the 'diff' (call up the page history and compare before and after the edit in question, grab the URL of that comparison page, and provide that as a link in the new discussion, flanked by single brackets []). Agricolae (talk) 16:55, 15 July 2013 (UTC)

Need for authority/reference regarding initial description of Human Genome

This Wikipedia article, Human Genome claims that The human (Homo sapiens) genome is the complete set of human genetic information. Can anyone provide a reference for the idea that "the human genome" is the genetic material/information found in actual human organisms (now and forever?). I believe it is widely acknowledged, if only tacitly, that "the human genome" is a generalization/model. It is only journalists and laypersons, and scientists using terms of convenience, rather than speaking carefully, who treat "the human genome" as if it is an actual thing in the world, as opposed to a very useful and important knowledge construct, like "humanity". There are important ethical, legal, and sociological implications to how we define this term. — Preceding unsigned comment added by Dylan Hunt talk 17:06, 15 July 2013 (UTC)

See reference genome, as this contrasts with "genome" when used for the genomes of individual organisms.Dylan Hunt (talk) 19:17, 15 July 2013 (UTC)

Not exactly. 'Reference genome' is not just any old genome from an individual, and back to our zebras, the presence of a reference specimen of a species does not mean that the species doesn't exist in the real world. Agricolae (talk) 19:31, 15 July 2013 (UTC)

See reference genome, as this *contrasts with* (i.e., is not the same as) "genome", which refers to the genomes of individual organisms.Dylan Hunt (talk) 12:33, 16 July 2013 (UTC)

Scope of article

I added the following in an attempt to define the scope of this article. I do understand that these estimates may be controversial. On the other hand, the lead should not get bogged down in details. In addition, the lead should also summarize the important points of the article, and I think this is important. I would appreciate comment on the following so that it hopefully be re-added to the lead. Thanks. Boghog (talk) 21:04, 19 July 2013 (UTC)

• While there are significant differences between the genomes of human individuals (on the order of 0.1%), these differences are considerably smaller than between humans and humans closest relatives, the chimpanzee (approximately 1%).

First a few grammatical notes: it should either be 'among the genomes of human individuals' or 'between the genomes of any two human individuals' (among - collective; between - two); there is a possessive problem with the second 'humans'; and it is best to avoid using humans twice within three words if it can be avoided. The other problem is that chimpanzees and bonobos are equally close, yet the commonly referenced data are specific to chimp, so that will need to be massaged somehow. I do think it is important to indicate that there is variability, and likewise in the body when we get to the lengths, to indicate that the numbers are of a representative genome and not 'the' genome. It actually wouldn't be bad to have a section discussing the nature of the variability found among human genomes. Elsewhere, in an AfD, an editor has suggested adding a section providing historical perspective - certainly even though its core meaning has remained the same, the view of the genome has changed since the 1980s, the push-back over ENCODE being just the latest turn of the wheel. Agricolae (talk) 22:15, 19 July 2013 (UTC)

Thanks for your suggestions which I have incorporated in the following revision:

• While there are significant differences among the genomes of human individuals (on the order of 0.1%), these are considerably smaller than the differences between humans and their closest living relatives, the bonobos and chimpanzees (approximately 1%).

Anything mentioned in the lead should be simple and short. The variability I think is covered by the adjective "approximately". We can mention in the body that the inter species differences are calculated from reference genomes. Boghog (talk) 10:16, 20 July 2013 (UTC)

'The' human genome

I can see no support for explicitly defining 'the human genome' as different from 'human genome'. The use of that grammatical article is not distinctive to the definition it is being given (for example, "On average, the human genome is 99.9% identical between any two individuals", Krawetz, Introduction to Bioinformatics, makes no sense if "the human genome" is defined as what all humans have in common. Further, the so-called 'abstraction' is not that which is common to all humans: it includes the Y chromosome, which is only found in half of all humans. I have given another try. Agricolae (talk) 15:51, 18 July 2013 (UTC)

I think you've answered your own question for why we need to indicate different ways of using "the human genome". If the human genome is 99.9% identical between any two individuals, we do not therefore say that the human genome is only 99.9% human. You are missing *why* it is important to say something substantive about there being an abstraction involved: When people refer to the human genome, they are referring to something that is variable. The variables are common to humanity, otherwise it wouldn't be intelligible at all to refer to *the* human genome. Dylan Hunt (talk) 20:31, 18 July 2013 (UTC)

I am not missing why it is important, I am rejecting the importance of it. All concepts in science are effectively simplifications of some sort, and we don't feel the need to explain all of the different individual but overlapping interpretations that are tied up in every scientific concept. We have been over this before. The human body is variable, but we don't distinguish between 'human body' and 'the human body' and harp on about all of the different things people have in mind when they see the words 'the human body'. Zebras are variable, but we don't distinguish between 'zebra' and 'the zebra'. The color red is variable. But we don't distinguish "the color red" from just plain 'red'. All of these are abstractions, generalizations, because of that variability but we just explain what red is - that is the nature of the descriptive process, generalization among minor variability, else absolutely everything is unique. Further, there is no need to imbue the three-word phrase 'the human genome' with special meaning distinct from 'human genome', and not any support for such a distinction in actual usage. 'The' is just a grammatical article that doesn't change what we are talking about. Agricolae (talk) 21:41, 18 July 2013 (UTC)

If you are not interested in how words get applied, I'm not sure why you are so invested in editing. Wars have been fought over emphasis on the definite article and years of bad science have been done as a result of not recognizing variation. There is no reason to create an article in a monolithic fashion. Many other articles start out with the plurality (e.g., Human) and still manage to meet the goal of WP:MOSBEGIN. It is important to recognize that there isn't only one way to write a Wikipedia article.Dylan Hunt (talk) 21:46, 18 July 2013 (UTC)

OK, correct me if I'm wrong, but I don't think your reference says anything about the term 'the human genome' being "usefully ambiguous". We don't make things up as a way of resolving content disputes. And why????? must the phrase 'the human genome', in quotes, appear in this article as if it had some special distinct meaning? It doesn't. What you insist on calling 'the human genome' (in quotes) is just the human genome. Agricolae (talk) 22:16, 18 July 2013 (UTC)

I have reverted the latest edit for the following reasons: 1) the first sentence changes human genome from a specific entity into a descriptive term - it is more than that, hence human genome, not just a genome of a human; 2) the second sentence is just wrong - the genome includes structural material that is not 'read' as that term is generally understood either in molecular biology or in common speech; 3) it launches into the semantic quagmire, unnecessarily, - 'the term x can mean a lot of different things to a lot of different people' - a word that means a lot of different things to a lot of different people needs a disambiguation page, not an article. And a hypothetical future when humans become all-knowing about genetics? This is not how you right an article about a scientific concept. It just doesn't work because it is predicated on forcing an issue that doesn't need to be forced, and it unnecessarily confuses things rather than clarifying them. Agricolae (talk) 19:12, 18 July 2013 (UTC)

I agree that there is no such thing as the human genome since there are between individual variations of the genome. On the other hand, starting the article out with the phrase "genome of humans" or something similar is awkward. The first sentence should be dead simple and per WP:MOSBEGIN, should "establish the boundaries of the topic". Furthermore, per WP:BOLDTITLE, "Links should not be placed in the boldface reiteration of the title in the opening sentence of a lead". Hence I suggest the following for the first two sentences:

• The human genome is the complete set of genetic information for humans (Homo sapiens). There are significant differences between the genomes of human individuals (on the order of 0.1%), however these differences are considerably smaller than between humans and humans closest relatives, the chimpanzee (approximately 1%). ...

Or perhaps the second sentence above could be added to end of the first paragraph. Thoughts? Boghog (talk) 20:33, 18 July 2013 (UTC)

I think we want to define what is meant by 'information' first before we indicate that said information differs. Also, I am hesitant to use those 0.1% & 1% figures without clarification, as it all depends on how you count - those numbers are based primarily on SNPs (as determined by sequencing and earlier hybridization studies), while if you count the content of indels, humans themselves can differ by much more (I have seen numbers as high as 10% reported, although that must be taking into account what would be considered abnormal - Turners, Klinefelters or XXX). My biggest issues with the material so far has been the MOSBEGIN issue (thanks for the policy reference there) and the intent to define "the human genome" as a term somehow distinct from "human genome". Doing the latter suggests there is some significance to having that three-letter word at the start, when there isn't. Agricolae (talk) 21:17, 18 July 2013 (UTC)

I agree that we should define the subject a little more before mentioning the boundaries and that is why I suggest the second sentence proposed above be added at the end of the first paragraph. We absolutely do not want to get bogged down with details like SNPs and indels in the lead. The details are discussed in the body of the article. At the same time, I think it is useful to give an order of magnitude estimate of the differences in the genome between individuals and between us and our closest relatives, the chimps. Finally debating whether to include "the" in the title is sematics. Not including "the" results in awkward language and hence I think we should include it. Boghog (talk) 21:46, 18 July 2013 (UTC)

Again, see other articles like Human or, interestingly, Article (grammar) for examples where not including "the" does not result in awkward language.

While I am sympathetic to the idea there is no "the human genome" in the universe, that isn't my point; neither is the between-species variation. "The human genome" is needlessly simplistic and suggests things that are false or misleading. Notice that people don't ordinarily notice nucleotides unless they are doing highly technical research. Being careless about monolithic concepts like "the human body" isn't significant (but try telling an amputee about the two legs and two arms of the human body), whereas a science founded on human variation should not take kindly to monolithic ways of speaking.Dylan Hunt (talk) 21:56, 18 July 2013 (UTC)

All science on humans takes variation into account - all science for that matter. Nobody sees that one person's liver is different from another, but it can have deadly effects when they take the wrong drug, and yet we still speak of 'the liver'. You are portraying 'the human genome' as somehow uniquely in need of excessive semantic falderal, when it is not. For all of your opposition to the phrase "the human genome" unless it appears in quotes, a look at Google Scholar shows 1.2 million hits for "the human genome" and only 6600 for "a human genome", and a quick scan shows none of the first several pages of results to be putting the phrase in quotes. You are arguing here for your personal preference over the predominant scholarly usage, so you had better have a better reason than that armies might march if we aren't careful. Agricolae (talk) 22:16, 18 July 2013 (UTC)

You make a good argument for calling the article "the Human genome" (were it not against wikipedia policy). If the goal is to describe what human genomes are, then it's not a compelling argument. A google search merely shows the typical way of representing human genomes as a linguistic construction (Did you eliminate critiques of "the human genome" as a phrase?). I concede that it is very convenient, not to mention seductive, to think or talk about "the human genome". It is also a matter of habit to use the term "mankind", a similarly flawed way of talking about humanity. It doesn't mean that it is a good idea; particularly not when you are trying to explain to people something they don't encounter in their everyday life (unlike "the apple tree[s]"); even less so when "the human genome" has been the object of enormous rhetorical positioning since the 1980s. Wikipedia articles should be neutral and should not be supporting the cause of "big science". If it is good science, it doesn't need the help of Wikipedia editors.Dylan Hunt (talk) 22:58, 18 July 2013 (UTC)

After all this, we learn that using the word 'the' in front of human genome is just a way of 'supporting the cause of "big science"'. This whole mess turns out just to be WP:SOAPBOX after all. It is more than just convenient and seductive to refer to "the human genome". That "A google search merely shows the typical way of representing human genomes as a linguistic construction" is precisely my point, only without the merely. Agricolae (talk) 23:15, 18 July 2013 (UTC)

I think you would have to put "merely" in front of my point about neutrality if you want to declare it a soapbox, but that would be a misrepresentation. Can you tell me what you gain in conceptual value by adding "the" to "human genome"? I have maintained it is convenience alone (but accompanied by the habit of thinking in monolithic terms, and all the rhetoric of projects related to "the human genome"). I am no enemy of "big science", having worked on the staff of subcommittee for a former Chair of a Congressional Committee on Science. However, I do think intellectual clarity is preferable to bias toward a specific cause.Dylan Hunt (talk) 23:23, 18 July 2013 (UTC)

The use of the word 'the' biases the article toward a specific cause (that of 'big science')? Umm, do you know how that sounds? It sounds like SOAPBOX. Wikipedia follows usage. Oh, and I'm still waiting for that reference calling 'the human genome' "usefully ambiguous". Agricolae (talk) 23:45, 18 July 2013 (UTC)

We are writing for a general audience and it is especially important that the lead be written in a clear, simple fashion. Using awkward language to cater to dubious grammatical distinctions is not helpful to the general reader. Also the overly abstract description "for collective mankind is an abstract representation of the genome of a generalized or representative human" does not belong in the lead or anywhere else in this article for that matter. Boghog (talk) 06:40, 19 July 2013 (UTC)

The version of this article that was promoted to Good article status used the "the" word in the first sentence. This was maintained in the vast majority of the versions since. Hence there is a clear community consensus that including "the" in the first sentence is appropriate. Why is this all of a sudden an issue? I am with Agricolae on this. This clearly is a SOAPBOX issue that has no place in the lead of a widely read Wikipedia article. Boghog (talk) 09:18, 19 July 2013 (UTC)

Boghog: 1) I agree that the sentence about "mankind" does not belong in the article, but it was Agricolae's constructive suggestion. 2) Please explain what is awkward about alternatives to "The [general concept] (see other Wikipedia pages that use the same construction, as mentioned above). 3) If the topic hasn't come up before, then you don't know what the consensus is regarding the topic. 4) Please state your criteria for clarity of seeing a "SOAPBOX" issue, given my points above. 5) There isn't anything dubious about the distinction between definite and indefinite articles, or even their use regarding technical categories as 'mass noun' and 'countables'.Dylan Hunt (talk) 13:06, 19 July 2013 (UTC)

Does your source actually accuse scientists of "camouflaging" their divergent issues? That's an attack on an entire field that at a minimum needs to be balanced, but better, not made to begin with. If Google Books is to be believed, the words 'camouflage' or 'camouflaging' do not appear in the entire cited source - that's your SOAPBOXING, and has no business being there. The whole paragraph is a mess. The sequenced human genome has not 'displaced the concept of the gene' and your source does not say it has. Next, you talk about "the phrase 'the human genome'", but the sources I can check make no statement about the meaning of 'the human genome' as a phrase except the last, and it doesn't say what you claim. Ref 7, Ann Rev Anthro, doesn't even refer to evolutionary biologists collectively using phrases, at least not that I could find (perhaps you could be more specific as to on which page and paragraph this supposedly appears). Ref 9 makes no reference to the phrase 'the human genome'. Ref 10 does not say that the connotation with Platonism is unavoidable (it also points out that 'dog' and 'chair' are Platonic ideals, but we don't have a paragraph on their pages to indicate their roles as philosophical constructs). It outright states that 'the human genome' represents a platonic ideal. The paragraphs is telling its own tale about the phrase, 'the human genome', not what the sources are saying about that phrase. That's not how it's supposed to work. Agricolae (talk) 14:57, 19 July 2013 (UTC)

What is awkward about discussing the general concept is there is no need to discuss it. Of course the genomes of individuals will slightly differ. If this were not true, the entire human race would be genetically identical. The general reader will immediately appreciate this. Hence there is no need to mention the obvious in the lead. Furthermore if we need to be worried about distinctions between definite and indefinite articles, then we have completely missed the point of the article. Boghog (talk) 21:24, 19 July 2013 (UTC)

I agree completely. The whole distinction seems to be a personal hobgoblin (a view reinforced by the accusation that the use of 'the' biases the article in favor of 'big science', a few I find unique and unsupportable). So far, I see one source that mentions the phrase, as a phrase, and then only to indicate the variability, and not concerning the phrase for its own sake, and hence the meander through all of the possible meanings of the phrase 'the human genome' seems WP:UNDUE, and is invariable WP:OR since there is no basis for it in the sources. Agricolae (talk) 22:03, 19 July 2013 (UTC)

Many people question the concept of "the human genome" not by challenging the actual construction, but drawing attention to issues of the scope or variability. Sometimes people merely emphasize/italicize the "the", without italicizing the whole phrase. You have to realize that discussions about "the human genome" take place among people who are not molecular biologists (who do not have exclusive rights to talk about a concept on which their paycheck depends; other researchers have to be kept off the streets too by getting paid to discuss these issues). In other words, you are not going to find people saying that there is a problem with the phrase because of a sequencing procedure like shotgunning. Sometimes they talk about The Human Genome concept in terms of the target of sequencing or genome projects, but that is because you are not going to "find" the human genome (something that is whole by definition) except by means of some strategy like sequencing or mapping. All of the quotations I cited are about the problem of essentializing, which is expressed by "*the* human genome". The following article in particular elaborates on precisely this issue. If you're not familiar with discussions outside of technical/textbook discussions, this will help precisely because these issues of definition are crucial to the project of definition. Perhaps you haven't located the relevant part of the online content, which is a large article and I couldn't specify the section very well:

"Early in the debates surrounding plans for the HGP, questions arose concerning what it means to map and sequence the human genome - “get the genome,” as Watson (1992) put it. About these concerns, McKusick (1989) wrote: “The question often asked, especially by journalists, is ‘Whose genome will be sequenced?’ The answer is that it need not, and surely will not, be the genome of any one person. Keeping track of the origin of the DNA that is studied will be important, but the DNA can come from different persons chosen for study for particular parts of the genome” (p. 913). The HGP and Celera reference sequences are indeed composites based on chromosomal segments that originate from different individuals: the sequence in any given region of the genome belongs to a single individual, but sequences in different regions of the genome belong to different individuals. However, in both cases, the majority of the sequence originates from just one person. As HGP sequencing efforts accelerated, concerns arose that only four genomes, a couple of which belonged to known laboratory personnel, were being used for physical mapping and sequencing (Marshall 1996b). The decision was made to construct 10 new clone libraries for sequencing with each library contributing about 10 percent of the total DNA. In the end, 74.3 percent of the total number of bases sequenced was derived from a single clone library—that of a male, presumably from the Buffalo area; seven other clone libraries contributed to an additional 17.3 percent of the sequence (International Human Genome Sequencing Consortium 2001, p. 866). A similar proportion—close to 71 percent—of the Celera sequence belongs to just one male even though five ethnically diverse donors were selected; incredibly enough, rumors have been confirmed that this individual is Venter himself (McKie 2002).

The deeper question, of course, is how we might understand a single human genome sequence, a composite that belongs to no actual individual in its entirety and only a handful of individuals in its parts, to be representative of the entire species. This seems to ignore the extensive genetic variability which exists. The functional equivalence of many DNA polymorphisms led two early critics of the HGP to argue that “there simply is no such entity as a ‘representative sequence’ or the human (or any) genome” making it “fallacious and even dangerous to call any one ‘normal’” (Sarkar and Tauber 1991, p. 691). Another critic pointed out that problems with the idea of a representative sequence persist even when consideration is limited to DNA differences that are not functionally equivalent but related to health and disease: the sequence will contain unknown defective genes (since no one, including donors, is free of these), there is a heterogeneity of mutations even in so-called single gene diseases, and it is impossible to identify the genetic basis of a disorder simply by comparing the sequences of sick and well people since there will be many differences between them (Lewontin 2000 [1992]). For Gilbert (1992), these criticisms of representativeness arise from a failure to appreciate the difference between the approaches of molecular biologists who attend to similarities and evolutionary biologists who attend to differences within the species: “The human genome project … is directed toward a molecular biologist's view of a species rather than a population biologist's view. The latter views a species as the envelope of all possible variants that can breed together; the importance of that envelope is that different aspects of a species population will be drawn forth if you change the environment. Molecular biologists generally view the species as a single entity, sharply defined by a set of genes and a set of functions that makes up that entity” (p. 84). Gilbert held that the two approaches are consistent with each other, but many evolutionist critics of the HGP—both scientists and philosophers—did not, deriding the aims of mapping and sequencing the human genome as a throwback to anti-evolutionary, preDarwinian, typological, and essentialist thinking.[17] The functional approach of molecular biologists alluded to by Gilbert is said to represent genetic variation in improperly normative ways, whereas “in evolutionary biology, variation is not the same as deviation” (Hull 1994, p. 208). When molecular geneticists view mutations as abnormal, not in the sense that they are rare or a change in form, but as “errors” in the genetic code or “damage” to the genome's proper structure, they impose an arbitrary a priori categorization: “it is genetic ‘errors’ that made us as a biological species: we humans are integrated aggregates of such ‘errors.’ Genetic variation is the source of evolution; it is the reason why there could be primates and not just protists or their precursors” (Limoges 1994, p. 124)."Dylan Hunt (talk) 01:36, 20 July 2013 (UTC)

So you have posted a whole lot of text that has no bearing on anything you have put in the article, all because the first sentence in the paragraph italicized the word the. By the way, it is also predicated on a lie, that the Celera project is not based on any one person's DNA, it was and that has been known for a long time. That means it is either terribly out of date, or badly researched. Much of the text is about the human genome project, rather than the human genome, and is asking whose genome was sequenced, not making any contribution about the phrase 'the human genome' - that is all you. You tell us that when they talk about "the target of sequencing" or "genome projects", they are really talking about "the human genome", then you valiantly slay the straw man about only molecular biologists being able to talk about it and follow that with a veiled ad hominem, that maybe I am unfamiliar with how it is talked about outside of textbooks and technical literature (a far cry from when you suggested I didn't have the knowledge of an undergraduate - which is it?). It is still just you, pursuing your personal hobgoblin and projecting this on all your supposed sources, none of which make comments justifying a whole section about the phrase "the human genome". Agricolae (talk)

You are still missing the point, Agricolae. Are you sure that you are not using this Wikipedia article as a soapbox? You've moved from trying to eliminate valuable content on the basis that the lede needs to be focused, to an argument (SOAPBOXING) that reveals your underlying purpose of supporting a single point of view. What you called a "veiled ad hominem" was a suggestion to look at the text differently than a Science/Nature research article and as a discussion of the meaning of the concept--it was not said to impugn your point of view or opinion, but as a comment on your rejection that the evidence is in front of you. You have been reading very narrowly (e.g., criticizing a minor point of a cited article), as it serves your purposes. Incidentally, to make an inclusive comment about less narrow ways of talking about scientific concepts is not a straw man argument. Actually, my contribution supports a number of viewpoints about this important concept, whereas your viewpoint is singular. You are also missing the point by arguing that the topic of the quoted text is the Human Genome Project, rather than 'the human genome' concept. I helped you out on this point by stating that Gannett and others talk about the Human Genome Project (when talking about the human genome) because it is one of the primary ways, and the most visible way, the scientific community (in the US) is "finding" the human genome (particular or generic reference). You are perfectly welcome to interpret more broadly of your own volition (e.g., to take it as encouragement rather than as an ad hominem). After all, as in the quoted text, discussions of concepts by researchers not doing sequencing are often developed over the course of more than one (rather verbose) paragraph (as opposed to within a single sentence or two). Writings on the essentializing image of "the human genome" form a literature (including work by those cited: Weiss, Hull, Gannett, among others) that is more than a cottage industry, and certainly larger than an individual's personal hobgoblin, as my representation of more than one point of view supports.Dylan Hunt (talk) 15:46, 20 July 2013 (UTC)

These are just more words pushing your personal interpretation that the phrase 'the human genome' has some greater fundamental importance than simply 'human genome'. This whole waste of time has been about this groundless semantic quibble, projected by you onto the sources rather than being supported by them, and it has no business in this article. Agricolae (talk) 16:15, 20 July 2013 (UTC)

You seem to have demonstrated that you support a single point of view (what Gilbert called the molecular biologist POV), which makes your revert-action into SOAPBOX, by your own criterion. For other people (not just me), the definite article in "the human genome" serves to essentialize, which takes different forms (neglect of variability, Platonism, etc.). It is not just a reference to the general concept of a human genome.Dylan Hunt (talk) 19:03, 20 July 2013 (UTC)

What I support most is that if an article is going to have text stating "some people say this" and citing a reference, that reference should actually be an instance of some people saying what is claimed. The text that keeps getting added does not live up to this standard. I support that if a sentence says "this group has this viewpoint on the use of that term", then the source cited should actually explicitly refer to the term in question. Again, fail. I also support the idea that text in an article should represent the weight given those concepts, rather than making the placement of quotation marks the most important thing to discuss about a scientific concept. My revert removed text that was not supported by the citations and I explained this in detail. You keep proclaiming that your viewpoint is widespread, and yet you keep failing to find sources that actually present it, without twisting them out of all recognition. And you just did it again: Gilbert, writing 20 years ago (a long time given that the human genome was only fully sequenced 10 years ago) was talking about the approaches of molecular and evolutionary biologists toward variability, and their view of the species. It is right there in the text you cited and yet you have decided that he was talking about a view of 'the human genome' instead. Agricolae (talk) 19:40, 20 July 2013 (UTC)

Certainly, some of the techniques used to sequence genomes came after Gilbert's chapter, but the idea of representativeness and identity goes back to the ancient Greeks, even if the relevant technology and science has changed. Gannett demonstrated that this issue has been a key one in the late 20th century and continues today, not only in basic science, but in scholarly commentaries on the concepts and implications, and in the actual applications of genomic research. The concept of "the human genome" clearly raises the issue of representativeness, which most of Gannett's article on The Human Genome Project is about.Dylan Hunt (talk) 20:45, 20 July 2013 (UTC)

Gilbert was referring to the species, and to the viewpoint of different fields on variation, so when he wrote about these other issues is largely irrelevant. I can't have Gilbert's molecular biologist POV about 'the human genome' because that's not what he was categorizing. And yes, representativeness is an old topic, neither unique to, nor particularly special to, the human genome. Let's go to Chair and start the body of that article with a discussion that some people think the term 'chair' raises the specter of platonism. No, better yet, let's get rid of the inaccurate material you keep insisting on putting in this one. Let's just focus on that rather than which POV of Gilbert you happen to think I hold, shall we? Agricolae (talk) 21:17, 20 July 2013 (UTC)

Gilbert wasn't talking about the human genome? The cited chapter is famous for Gilbert talking about having a genome on a CD. If you accept that representativeness is not a strictly 21st-century concept (or even if it were) clearly the authors cited are discussing the human genome. If you go to prototype theory you will find chairs and essentialism discussed. However, since the concept of "the human genome" is of vastly more interest to humans (many millions of US currency devoted to this concept and to the implications of it) than the concept of "the wooden chair", discussion is warranted and my contribution is very brief.Dylan Hunt (talk) 15:17, 21 July 2013 (UTC)

I am not going to argue about your inaccurate portrayal of Gilbert, as you have not (at least not yet) put your misquote into the article. However, your 'contribution' is inaccurate SYNTH, as detailed below. How about addressing that? Agricolae (talk) 15:56, 21 July 2013 (UTC)

Barring History and Philosophy of Science

I cannot find a Wikipedia policy that declares HPS off limits when writing about any subject. Even the quark article, which avoids the problem created by the present article (by not making generic reference to *the* quark in the first place), puts "the quark model" into historical context: "The quark model was independently proposed by physicists Murray Gell-Mann and George Zweig in 1964.[5] Quarks were introduced as parts of an ordering scheme for hadrons, and there was little evidence for their physical existence until deep inelastic scattering experiments at the Stanford Linear Accelerator Center in 1968.[6][7] All six flavors of quark have since been observed in accelerator experiments; the top quark, first observed at Fermilab in 1995, was the last to be discovered.[5]" Dylan Hunt (talk) 13:54, 22 July 2013 (UTC)

We are well beyond general policies and dubious analogies (dubious because this is talking about the history of the theory - not the history of what philosophers think is meant by the word 'quark' and how it represents a type without raising the specter of being a Platonic ideal). Your specific text is being disputed, its accuracy (whether the sources actually say what you are claiming or if it is OR by SYNTH) and whether its inclusion in the manner it is currently being inserted reflects UNDUE WEIGHT. Let's stick to that and not talk about generalities and quarks, shall we? Agricolae (talk) 15:19, 22 July 2013 (UTC)

Disputed discussion of phrase 'the human genome'

This material was added without consensus, and is not supported by the cited sources. Only one of the cited sources actually highlights the phrase itself, the rest are just interpreted as doing so, but do not:

"The Human Genome"[edit]

Following the successes of recombinant DNA technology, through which the concept of the (sequenced) genome has been said to have taken pride of place from the concept of the gene,[4] it has become common to see the phrase, "the human genome" (i.e., generic use of the definite article). This phrase connotes unity among humanity's genetic inheritance in the abstract, while glossing over the divergent interests of scientists from different fields.[5][6] Among molecular biologists "the human genome" is simply a general concept applicable to any genome from a member of the species;[7] while, among evolutionary biologists, variation at the molecular level means the term is best applied to a composite reference genome sequence.[8][9] Some find the phrase of "the human genome" misleading because it carries for them the specter of "Platonism", arguing that "'the human genome' that we have labeled as such doesn't actually exist".[10], For others, the phrase can suggest a "wild type" unaffected by medical intervention in the process of natural selection, which similarly conveys the connotation of a Platonic ideal.[11]

Ref 4: This reference says nothing about the "concept of the genome taking pride of place from the concept of the gene". The sentence makes a specific claim of what is said and supports it by a reference. Except the reference never says what is claimed. Further the article never mentions the human genome at all and so its relevance to a section about the phrase 'the human genome' is dubious at best. In fact, most of the critics of the traditional gene concept that it highlights predate the genomic age. This may be relevant to gene, but is not to human genome.

The statement, "it has become common to see the phrase, 'the human genome' (i.e., generic use of the definite article)" is a specific claim that is being presented without a source. This observation appears to be the editor's.

Ref 5: Makes no explicit reference to the phrase, and hence cannot be used to support a statement of what that "This phrase connotes".

Ref 6: can't find anything relevant, but I can't see enough of the source on Google Books to be certain - perhaps a relevant quote where it says what the phrase 'the human genome' connotes will demonstrate its propriety.

Ref 7: doesn't say what is being claimed - it does not discuss the use of the phrase by molecular biologists. The closest they come to defining it is the following "The human genome contains approximately 3 billion of these base pairs, which reside in the 23 pairs of chromosomes within the nucleus of all our cells. Each chromosome contains hundreds to thousands of genes, which carry the instructions for making proteins. Each of the estimated 30,000 genes in the human genome makes an average of three proteins." So, no such molecular biology-specific usage.

Refs 8 & 9: I won't even try to confirm them, because they are being used to support a statement not related to 'the human genome' - different interpretations of variation on a genetic level, not genomes at all.

Ref 10: does not say that 'the human genome' is misleading because it carries a specter of being a Platonic ideal - it says that it is one. That this is spectral, and that the spectral nature is the source of it being misleading, are the interpretations of the editor.

Ref 11: never mentions the phrase, so it cannot be used to say that, "For others, the phrase can suggest . . . " anything.

This leaves the following, which certainly doesn't merit the first section of the article:

Following the successes of recombinant DNA technology, through which the concept of the (sequenced) genome has been said to have taken pride of place from the concept of the gene,[4] it has become common to see the phrase, "the human genome" (i.e., generic use of the definite article). This phrase connotes unity among humanity's genetic inheritance in the abstract, while glossing over the divergent interests of scientists from different fields.[5][6] Among molecular biologists "the human genome" is simply a general concept applicable to any genome from a member of the species;[7] while, among evolutionary biologists, variation at the molecular level means the term is best applied to a composite reference genome sequence.[8][9] Some find the phrase of "the human genome" misleading because it carries for them the specter of "Platonism" represents a Platonic ideal, arguing that "'the human genome' that we have labeled as such doesn't actually exist".[10], For others, the phrase can suggest a "wild type" unaffected by medical intervention in the process of natural selection, which similarly conveys the connotation of a Platonic ideal.[11]

This paragraph is a personal essay that misquotes and misuses sources to make the editor's point, not that of the sources. Agricolae (talk) 16:58, 20 July 2013 (UTC)

The so-called personal essay is Gannet's, whom I am citing. The idea that there is an idea "the human genome" is also not my personal view, but is too ubiquitous to cite. According to the Wikipedia policy you cited, a personal essay "state[s] your particular feelings about a topic (rather than the opinion of experts)." However, I have cited opinions all related to the idea of essentializing human genomes, or the general concept of them, into an abstract object of scientific interest. You might question whether scientists have turned a general concept into an abstract object of scientific interest (because I sense that you think the phrase, "the human genome", is just a phrase that makes generic reference in the way that the article, Apple, mages generic reference to the "the apple". However, what I have done is cite sources that discuss the ways this general concept is used, typically by means of the linguistic construction, "the human genome" (but not necessarily), in order to advance a molecular view of the gene that displaces the classical concept (ref 4), to separate scientists into those who privilege variation (refs 8 and 9) from those who privilege species-unity (refs 5 and 6), reify a simplified concept into a Platonic object (ref 8), and to reify the "wild type" interpretation.Dylan Hunt (talk) 19:36, 20 July 2013 (UTC)

Too bad not a single one of your sources say what you claim they do in the text. Agricolae (talk) 19:44, 20 July 2013 (UTC)

To be clear, I went through the detailed sentence by sentence analysis above to show you precisely what is wrong with the text. The appropriate response here is for you to show exactly where, for example, Ref. 4 discusses 'pride of place'. The inappropriate response is to just speak in generalities, or reinsert the unsupported text back into the article as if it was accurate. Agricolae (talk) 19:52, 20 July 2013 (UTC)

And you are still making it up as you go. "For some gene skeptics, the concept of the (sequenced) genome . . . " is inaccurate. Neither cited source gives the opinions of gene skeptics on the concept of a sequenced genome. (And that doesn't even address the weight issues - why are the opinions of the 'gene skeptics' what we begin the body of a scientific article with?) Agricolae (talk) 20:05, 20 July 2013 (UTC)

Re the latest sentence, "differences of opinion regarding identity and variability across instances of a type of genome", isn't even coherent. Further, the cited source says nothing about a type of genome. It talks about type specimens, it talks about types of individuals, it talks about genotypes and phenotypes, but it says absolutely nothing about types of genomes. Agricolae (talk) 22:48, 21 July 2013 (UTC)

Should be obvious--take a look at the title (if you are referring to Gannett 2003). It is called "The normal genome". Once again, you need to read broadly: Gannett's entire article is about a type of genome (really it is about a type of genome set, since it is about the idea that "the human genome" is a type of genome for those members of the set, H. sapiens). Trees --> Forest.Dylan Hunt (talk) 01:12, 22 July 2013 (UTC)

That is absurd wordplay. Gannett's paper is about the view (or misconception, if you will) that the genome sequence being reported by the HGP is indicative of normality. It is not about different types of genomes. This is why your material is SYNTH - you write the conclusion you want to reach, and then decorate it with a citation where the general topic is being discussed but that does not reach the conclusion you indicate. When you attribute a specific position to a specific author or source, the source needs to have said exactly that, not just be about the general topic. This is not a failure to see a big picture - it is a failure to accept that it is OK to invent conclusions the author did not make. One of two things is happening here - either you don't understand the papers you are reading or you intentionally are misquoting them. Either way, there is almost nothing accurate in that paragraph, as I demonstrated above. (Oh, and any time you say, 'it should be obvious' and then suggest I put two and two together, you are as much as admitting that you are doing WP:SYNTH.) Agricolae (talk) 01:46, 22 July 2013 (UTC)

What is normality if not a type? If there is a claim that there is a normal genome (note that this claim does not say any individual's genome is the normal one), then it is a type. If you don't get this, I'm not sure how the article could make any sense to you. See for example p. 145: "It is suggested that these sequence maps represent a typical or average human being." Or p. 146: "This [that the view a single DNA sequence could represent all of humanity is criticized by evolutionists] is so whether the sequence is taken to represent a typical haploid human genome, a healthy haploid human genome, or the very essence of humanity. Writes biological anthropologist Kenneth Weiss: ‘The Human Genome Project, which will create a stereotype of human genetic structure, is in a sense history’s greatest exercise in platonic essentialism’ (1996, p. 1)." But really, almost any other page would give the same "clue". It is the motivation for talking about a *typ*ological viewpoint (defining/exemplifying representative) vs evolutionists' viewpoints (type specimen without defining/exemplifying).

Here's a solution to your problem of seeing the forest: Write to Gannett and ask her if this article makes any mention of a type of genome. I'm sure she would welcome attention to her work that does not require grading.Dylan Hunt (talk) 02:09, 22 July 2013 (UTC)

p.s., this should help (if not hurt) in decoding philosopher: talk:http://plato.stanford.edu/entries/types-tokens/#SciEveDisDylan Hunt (talk) 02:26, 22 July 2013 (UTC)

What a monumental waste of words. There is a difference between 'a normal genome is a type', and 'types of genomes'. This is a plain-language encyclopedia, and it uses a straightforward style of presenting real-world concepts. In our page on pins, we don't start with a discussion of how many angels can dance on the head of one. I am having no problem seeing the forest. I am seeing that the forest does not have the trees you say it does. I am struggling to AGF here. Agricolae (talk) 04:33, 22 July 2013 (UTC)

Mutual funds aside (AGF), I think your point above is why you think my small paragraph is original research, or personal essay. It is obvious that the concept of 'the genomes of humans' constitutes a type for scientists (whether they can make this distinction or not), and it is different from the type to which genomes of, say, E. coli individuals belong. It is also obvious that many people have published much on this subject with various conclusions *they* have drawn (which I do not try to represent at any length). The writings of Weiss, Hull, Gannett, Gilbert, etc. all differ in certain ways, while all writing on the issue of the human genome type. I cited those writings in pointing out that the concept of "the human genome" has different meanings (something Gannett adequately demonstrates). The concept of "the human genome" has been taken in ways other than your nominalist view of a phrase that makes merely generic reference using the definite article (though you clearly think the human genome type is more than grammatical). Notice that the definite article in "the human genome" has been taken in much more robust (more than grammatical) ways than you claim to take it, and the concept of the human genome speaks to the type at the center of these more robust ways of understanding our particular species' identity-at-the-genomic-level. Just because you think the distinction is a waste of time to make is not a reason to malign the published writings of others, whom I have cited. If you can't see the forest, at least you should be able to find the library.Dylan Hunt (talk) 04:58, 22 July 2013 (UTC)

In addition to containing original research, Concept of "The Human Genome" section fails WP:JARGON. It is clear that you are writing for yourself and not the general reader. The second sentence of this section starts with:

• The phrase connotes unity among humanity's genetic inheritance in the abstract, ...

At this point, the general readers eyes will have glazed over. If we are lucky, the reader will skip the remainder of this incredibly esoteric section and read the remainder of the article. If we are unlucky, the general reader will conclude that reading the rest of the article will be a waste of time and move on to something else. Even molecular or evolutionary biologists don't normally worry about such esoteric minutiae. This article is about science, not the philosophy of science. With or without WP:OR, this section does not belong in this article. Boghog (talk) 06:57, 22 July 2013 (UTC)

Boghog-You are welcome to improve language by constructive means, rather than destructive reverts. If you look up the professions of those cited, you will find that scientists do "worry" about such thing. Such things are an important part of scientific inquiry.Dylan Hunt (talk) 13:49, 22 July 2013 (UTC)

Agree with Boghog. It's totally both OR and synth, and completely out of place in this article. There's nothing worth saving. Dominus Vobisdu (talk) 13:51, 22 July 2013 (UTC)

The reverts are not destructive (the deleted section is still of course accessible from the article history). The point of the reverts is that there is currently no consensus to include a concept section in the article. The lead and initial sections of the article need to be written so that they are understood by a wide audience. The section in question is by its very nature refractory to clear explanation. Furthermore even if it could clearly be stated, it gives undue weight to a subject that is of minor importance relative to the main subject of this article. In analogy to history sections of articles which are normally placed at the end of an article, it would be much more appropriate to place this section (minus the original research) near the end rather than the beginning of the article. Finally I note that the Human Genome Project (HGP) is effectively the history section of this article. If the concept section could be rewritten to remove all original research, an alternative is to split out the concept section as a separate article analogous to the HGP article. Boghog (talk) 19:48, 22 July 2013 (UTC)