Talk:Human genome

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Former good article Human genome was one of the Natural sciences good articles, but it has been removed from the list. There are suggestions below for improving the article to meet the good article criteria. Once these issues have been addressed, the article can be renominated. Editors may also seek a reassessment of the decision if they believe there was a mistake.
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Concept → limitations[edit]

One possible way to resolve the above controversy over the "concept of the human genome" is to instead focus on the limitations on how we define the human genome and the practical consequences of those limitations. While Ken Weiss in The Scientist opinion piece did write about the genome as a "Platonic ideal", he also illustrated how the genome deviates from that ideal with specific examples. The advantage of focusing examples and limitations is that it is (1) closer to the sources, (2) it will be easier to understand by a general audience, and (3) is more relevant to the main topic of this article.

From Agricolae's analysis above, which I agree with, the following sentence is noncontroversial:

  • Some find the phrase of "the human genome" represents a Platonic ideal, arguing that "'the human genome' that we have labeled as such doesn't actually exist".
  • Source: Weiss K (2012-08-17). "What Is the Human Genome?". Opinion. The Scientist. 

To which we could add:

Thoughts? Boghog (talk) 08:54, 25 July 2013 (UTC)

Boghog: Thanks for considering my ideas further. As for me, I am done with editing on this page. The most antagonistic departmental discussions are preferable to the way dialogue tends (not) to occur on Wikipedia. However, I will make one very tiny note, given your extensive and valuable commentary: Ken Weiss did not illustrate how "the genome" deviates from that ideal. He said that genomes deviate from the ideal. While I started out by fixating, then continued to fixate, on the odd obsession on this page with the monolithic generic use of "the", a linguistic construction which favors absolute objectivist truths, it is a broader point--that using simplifications obscures good science and creates bad science-that I am largely concerned with. Nobody has been able to defend the value of the phrase "the human genome" beyond the value of simplicity. My goal wasn't a grand debate about abstractions or even normality, but some editors dig their teeth into *the oddest thing*. With more suggestions like yours above, perhaps the article editors will collectively reach a point I would be happy with, even in my absence. I'm sure some clarification of the kind you provide would be helpful to non-technical readers, who might be currently wondering, if there is only one human genome, how can everyone have it and be different from it. Best wishes and good luck. Dylan Hunt (talk) 18:55, 25 July 2013 (UTC)

==Supplementary talk of genetic filaments---the physical function test and findings == 1, To bring back life with health by their direct relatives saw this and felt sad and cried.

      Around 2-3 yrs ago, I read in a newspaper in US, a patient with cardiac problem was declared death by the hospital, but he came back to life afterwards.  There are around 22-23% cardiac patients coming back to life after the death declaration, and this phenomenon is yet not well explained.
  My explanation for this: when these patients were resuscitated, their direct relatives saw this and felt sad and cried. These sad cries came into the patients’ brains and resonated their double spiral filaments of the DNA. The same thing happened in the cardiac cells as well. And this led to the resurgence of the patients.  During the resuscitation, the electric defibrillator must have been used, but this is only a single extrinsic factor. If we compare the defibrillator with the genetic filament resonance; first of all, they differ in being the intrinsic and extrinsic factors, second, the cries of the relative should provide the same frequency as the patients’ genetic filaments, and so the filaments are easier to resonate. Thus the resonance would have better effect and make resurgence easier.  We declare death at the stop of the respiration and heart beat, but when the body temperature is still higher than 35 degree, the cells in the heart an brain are still alive, so the genetic filaments can still sense and resonate with the microwave from the external world, and the resurgence is still possible. But it requires their own children as it requires the same frequency and amplitude of the wave. If they are wife, daughter-in-law, son-in-law or brothers and sisters, the frequency and amplitude would vary and the resonance would be less effective, and the resurgence rate would only be 25% in those who can be resurged.
      In June 2013 in yahoo news, “three professors in Oxford University were frozen to wait for resurgence”. Two of them had their heads cut and the third one was frozen as a whole.
       In my opinion, the first two cannot be resurged while the third holds some possibilities, but it should be validated by multiple experiments with the mouse. Of course, if they were already dead due to severe disease, that would be another story.
        Four to 5 decades ago when I was living in the north, I saw goldfish frozen in the glass bottle.  After 1 day or two, when the ice melted, the goldfish could come back to life again. I also picked up one frozen fish in the lake in a winter, and when I put it back to water at home, it came back to life and swam again.  The low cold blood animals could be resurged in this way, but if we cut their head when they were frozen, would they come back to life and swim again?
       Human are higher animals, when they are sick, before they were really dead in all cells, if we finish all the process of preparation of resurgence, and when later they need to be resurged, it requires the blood circulation back gain, thus the cells could function and the genetic filaments would open and resonate with the wave exactly of the same frequency and amplitude from the external world. The hormone effect should be added as well. However, the electric field varies from one person to another, so the start and maintenance of the resonance would be a challenging task which needs at least 30 years of effort, lets wait and see.

2, The association of genetic filaments in plants with the external world;

         A hundred year ago, we learned heredity secret lying in DNA from the bean experiment, but we never elaborated the close association between the DNA and the genetic filaments interaction.
         In the Epoch Times on Jan 11th 2013, there was a piece of news titled “plants are like humans”, also in the newspaper of Kanzhongguo (www.kanzhonguo.com) in June 28th 2013, there was a paper titled “Thirsty! The first time that human heard the ‘scream’ of trees.”
        In “plants are like humans”, it mentioned the extraordinary experiment done by lie detective Baxter in the sixties of the last century, that the plants could sense, and could have emotions as humans detected by lie detectors.
      The happiness: when we watered the tongue orchid, the detector sensed a decrease wave as in humans
       The terror: when we twitched the leaf and put it into hot coffee, it didn't change obviously, but if we tried to burn the leaf with the fire, even just with the thinking in mind would make a great shake in the wave and it surged to the peak. So we could know “my god, it knows what we are thinking!”
     The super-sense: (here is extracted from the original article)“Baxter carried out an experiment like this: he threw several shrimps into hot water alive, and the plants were immediately irritated. The same response was recorded after several times. To exclude the man-made interference and to confirm the accuracy of the experiment, he used a newly designed machine and threw the shrimp into hot water in random time, and used a very delicate recorder to record the result. Baxter locked the 3 plants in 3 rooms and connected them with electrode, and no one was allowed to enter the rooms.”                                                                                                                    

The next day, when he went in to check the result, he found the waves were soaring 6-7 seconds after every throw of the shrimps into the water. All the 3 plants showed response, so Baxter said; we could almost affirm that plants have communications among them. In Yale University, Baxter put a spider and a plant into the same room, and the spider climbed onto the plant. But the recorder recorded a miracle--- before the spider came onto the plant, the plant had already showed some response. Obviously, the plant could super-sense the intention of the spider. The ones who ever doubted the experiments became the supporters: the experiment of Baxter surprised the world. The Doctor of Chemistry Mike in California thought the result was ridiculous. In order to challenge the result, he also did some experiments, but then his attitude changed absolutely. Mike also demonstrated that plant could sense human’s mind, which is to say, the plant can think as well, and feel the emotions of humans. So the plant is like human? Then where are their eyes? Why they could communicate their feelings? why they would feel the happiness, the terror or even super-sense? The experiments proved that they do have emotions, independently, and emotions don’t exist only in human or animals. The ancient Chinese people also always believed that “everything has spirit”, and they had fairy tales of the god of flower, the god of tree, telling that they have spirit like humans. In the article of “Thirsty! The first time that human heard the ‘scream’ of trees”: Just as human being are breathing desperately for air in dry season, the trees in draught, they would take as much the humidity as they could and give out the sound of “pah pah”. This sound is of a frequency 100 times more than the higher limit of frequency that human being could perceive. In my opinion: bean, tongue orchid and the trees are all plants, they have their own genes, so they would definitely have their DNA and double spiral filaments. All the connection between higher or lower mammals, birds, insects, fish, turtles, and plants, are based on resonance between double spiral filaments. They exchange information via it: happiness, sadness or terrors, or even the approach to death. All the species, as long as they have genes, they could send out and receive information with the double spiral filaments. The experiment of Baxter done 50 years ago, has supplemented my article of “genotype” published in Wikipedia between Dec 2009 and 2012. It proved the physical function of the double spiral filaments---they exchange information by waves, it can go across the wall and communicate between plants, it can go across oceans, go across half of the planet, it can go between the animals, or the animals with plants. The basic knowledge explained in the article in 2009 will not be explained here again. (Talker: Q. Y. Zhang; 香港 張其澐; --119.237.48.70 (talk) 00:27, 9 October 2013 (UTC))

Detail analysis of double spiral filaments in DNA beside function[edit]

One inspiration came over to my mind in one morning. Why DNA would contain two flat spiral filaments besides the 4 types of bases and thus form a “spring”in this way? And why they are hinging interlocked with the base groups, what do they serve for? And why there are also line style interlocks between C-G and A-T? I have designed great many machines including variant forms of the hinging spirals spring, so I am very familiar with the interlock theory. The dual long spirals spring could resonate in 3 dimensions, so the resonance could pass on in all directions. With the hinging interlock between base groups, the resonance could be achieved in the narrow intercellular space without affecting the functions of their own.  Generally, even only with the cells along the sulci in the temporal lobes, the resonance could be started. It would be enough if each cell could open 4-5 base groups. ( possibility there are 3-5 Nos. cells death.) Not only for animals, they could also send out the microwave telepathy between human beings. The trumpet shape of the cerebral sulci enhances the force of sending and receiving the resonance, which further enables reception and communication between species and genus. ( Talker : Q. Y. Zhang; 香港 張其澐;--96.237.238.212 (talk) 21:04, 10 February 2014 (UTC))

==Natural selection---“random” and “non-random”

The biological field always pays great interest to new species emerged from “natural selection”. But when it comes to the analysis of gender rules, the human intelligence reaction, or the intelligence difference between siblings, they only conclude roughly with the word of “random”.

For example, if we ask a agriculturist, whether we would get a female or male baby in a pregnant horse or cow (the animal which always gives only one child at a time), he would say as the book tells “it’s random”. If we ask a doctor of the baby gender in a pregnant woman, he would say “It’s random” as well, (of course, they would not know the love and pursue process between this couple, and how this couple thought and reacted to the environment during the pregnancy). “Random” is the applied-to-all word to everything before we could find any rules our of it.    

  In “origins of species”, Darwin admitted that the species are always evolving; generation after generation, and he also advocated that the main propelling power the evolvement is the “natural selection”. The natural selection means that, when an individual gains some minimal physiological changes, and if thesis changes could benefit it more than its parents in survival and reproduction, this change would pass on and makes the following generations always on the direction of “better adapting to the environment and survival competition”. This theory includes: the gender of the species, the balance of the sex, and the principle of selecting a partner, and some trivial adjustment. Also it includes the balance and supplement to the hetero-gender, intelligence, characteristics and appearance.
The “rule of balance” persists for thousands of years of evolution. We now discuss only the “random and non-random” things in the biological filed.
         
  The plants, including flowers, grass and trees, if they grow up, they need the sunshine, the rain and the soil. This is the rule of plant growing----the animals, they grow strong, they react fast and they run quickly, these are also the rules of “natural selection”. They could survive, and follow the rule of the biological food chain.The human beings could survive for thousands of years, there must also be some reproductive rules.
 The animals and human beings would not go into distinction due to the single gender; this is the effect of reproductive rule. I have been studying on this for over 30 years, and finally make out a reasonable hypothesis. The hypothesis includes the rule of gender, and also how you could get a reactive and intelligent child with genetic advantages since fetus.* And the “random” rule in general ideas for determining the intelligence among siblings, now becomes a “non-random” concept
         

Before we could dig deeper for some rules, “random” is always a good word to explain all.But our species exist on this earth for thousands of years, and there must be many rules regulating them. Let us work together to better find out these thousands of rules.

  • To see: www.gwencorp.com.hk/index.

(Talker: Q. Y. Zhang; 香港 張其澐--173.76.134.54 (talk) 16:48, 6 March 2014 (UTC))

Human, ape genome difference[edit]

Its not 4% its 1%. Please correct mistake. "Ever since researchers sequenced the chimp genome in 2005, they have known that humans share about 99% of our DNA with chimpanzees, making them our closest living relatives."

http://news.sciencemag.org/plants-animals/2012/06/bonobos-join-chimps-closest-human-relatives --109.23.159.201 (talk) 06:23, 21 May 2014 (UTC)

The above source appears to be in error. It appears to refer to earlier outdated estimates "which were made using shorter alignable sequence fragments" (see PMID: 16339373). Boghog (talk) 06:50, 21 May 2014 (UTC)
Most of the articles talk about 1-2% of difference.

http://www.livescience.com/20940-unraveling-bonobo-genome-secrets.html http://en.wikipedia.org/wiki/Bonobo--109.23.159.201 (talk) 08:05, 21 May 2014 (UTC)

It depends on how the difference was measured. Many of the analyses are restricted to protein coding genes where the conservation is much higher (on the order of 99%). The variations in sequence in between genes (the so called junk DNA) is much lower (on the order of 95%). "Non-coding" DNA has a large influence on when and how genes are expressed, hence these differences are important to include in any between genome comparisons. The following analysis is particularly relevant:

  • Larry Moran. "What's the Difference Between a Human and Chimpanzee?". Sandwalk. This value of 1.5%, rounded up to 2%, gave rise to the widely quoted statement that humans and chimps are 98% identical. Britton (2002) challenged that number by pointing out that humans and chimp genomes differed by a large number of insertions and deletions (indels) that could not have been detected in hybridization studies. He claimed that there was an addition 3.4% of the genome that differed due to indels. That means the the real difference between humans and chimps is closer to 5% and we are only 95% identical!  Boghog (talk) 19:45, 21 May 2014 (UTC)

β-globin[edit]

The β-globin is on chromosome 11 and I think β-globin is too short a description.--Mark v1.0 (talk) 20:46, 5 November 2014 (UTC)

Hi Mark v1.0. I'm afraid I don't understand where you're coming from. You're referring to this edit, in which you added "on chromosome 11" to the cell containing "β-globin" in the table at Human_genome#Human_genetic_disorders. The title of that column is "Chromosome or gene involved". Other cells in that column contain the name of a single gene, eg "APC", "Huntingtin", "CFTR". Do you think those cells should also include what chromosome the gene is on? Or do you think β-globin should be presented differently? Adrian J. Hunter(talkcontribs) 10:30, 7 November 2014 (UTC)
Human_β-globin_locus says it is five genes, so you can not call it a single gene. What is your problem with having (chromosome 11) next to it?--Mark v1.0 (talk) 14:58, 9 November 2014 (UTC)

quality[edit]

according to the url below, a paper from top experts in a top journal (ie highly authoritative) says that there are many many gaps (unsequenced) regions in the human genome imo, the lack of attention paid to these gaps is somewhat misleading for the general public; eg when scientists use the word "complete" it means, per the dictionary, that we have no gap, no missign sequence genome yet this is empirically false http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13907.html