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Genes, phenotypes and populations

  1. Aug 7, 2004 #1

    Monique

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    There seems to be a lot of confusion about the influence of genes on phenotypes. I happen to have worked in the field, so I will just give my view on the matter.

    Geneticists are studying populations and try to find genes that cause the population to be at risk for certain phenotypes. Examples of populations: a family, a country, a race. Examples of phenotypes: severe combined immune deficiency (SCID), alzheimer, atherosclerosis, alcoholism.

    The best population for a geneticist to use for their studies are isolated populations. There are different kinds of isolated population:
    * geographic (Pacific island chains, Arabia, Inuits)
    * cultural (Indian castes, Amish)
    * historic (Quebec - Sanguenay Lac-Saint-Jean, S. Africans, native Americans)

    The reason you want to use isolates is that the following are likely: rare alleles are enriched, the population is homogeneous, environmental factors are homogenous and more detailed things I won't go into. It makes it easier to find a correlation.

    Even with such special population it is important to choose special sampling designs (unrelated case/control, parent/child, relative pairs, nuclear families, extended pedigrees). In isolated populations you have the most power to detect genetic effects when you sample from huge pedigrees, that is why they started the deCODE project in Iceland.

    The search of these scientists have been succesfull: look for instance at the Finnish disease heritage. There are 35 monogenetic disease that are more prevalent in Finland than in any other population. For more information, this is an excellent website http://www.findis.org/main.php?action=disease

    Does that mean the finns have a sick population? No, diseases that are frequent in other populations are rare in the finns (like cystic fibrosis), it's like a balance. Can you define the finns by those 35 diseases? No, the diseases are distributed regionally.

    Scientists are most succesfull in finding monogenetic diseases, since their inheritance pattern is easy to detect. Diseases that inherit in a dominant fasion, have a high penetrance and low age at onset are easiest to find. Most importantly they need a very good definition of the phenotype they are looking for.

    The case is, most genes that cause disease don't follow those rules. Disorders like alcoholism or psychiatric disorders are difficult to define and are heavily influenced by the environment someone grows up in. Only with good matched controls will a study succeed to find a correlation.

    That is an important point: matched controls, you cannot compare apples with pears. In recent threads I feel that has been the main obstacle.

    Another important point: the populations. In the discussion before, the populations were very carefully choosen and defined. Finding genes on a mixed genetic background is very difficult.

    I certainly do believe that certain populations can harbor different genes. The thing that pops to mind most clearly is milk intolerance. Milk tolerance is a mutation, Dr. Leena Peltonen discovered the genetic basis. The following is a nice article http://www.newscientist.com/news/news.jsp?id=ns99991787 but again, this is a very well defined disease and is not influenced by outside factors.

    I'd be very careful with extrapolating data on poorly defined phenotypes to poorly defined populations.
     
  2. jcsd
  3. Aug 8, 2004 #2
    With reference the motivation for starting this thread:
    "Let freedom reign. The sun never set on so glorious a human achievement."
    - Nelson Mandela
     
  4. Aug 8, 2004 #3

    marcus

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    Hello Monique, in the historic category when you say S.Africans do you mean the Bantu majority of the Union of South Africa, or the Boers, or does S. stand for Subsaharan? It wasn't clear what historically isolated population you meant.

    I commend you for openly and straightforwardly confronting the issue of
    :surprise: RACE :surprise:
    that we so often have difficulty coming to grips with in PF and elsewhere.

    there is a fearsome lot of baloney and mythologizing about race.
    I wish as Mentor you would zap people who just talk silly about it.
    But you probably wont so i will use the Ignore feature to tune them out if they show up.

    I see that you connect race with the technical idea of ISOLATE.
    That is, a group of people who only date within the group.
    (Indian castes are an example because social rules prevent marriage between caste.)
    An isolate, as you use the word (a noun not a verb) is a group of people that doesnt mix reproductively very much with the other people for whatever reason.
    If you wanted to destroy all races in the USA you could force people to marry randomly.

    Within an isolate, there can be genetic features or DNA aspects that are distinctive----I think you are telling us----and indeed, as you suggest, that is why geneticists like to study isolates. (an Indian caste, some people on a pacific island, Subsaharan Africans).

    I live near a large university campus and I notice the Han Chinese students keep pretty much to themselves. Han date Han, it looks to me.
    Maybe Asian students in general tend to mostly date other Asians. Maybe that is an Isolate too.

    OK, so Monique I recognize you are an expert, obviously, and I am trying to learn about Race from you.
    The first thing I think you are telling me is that it has to do with mating behavior (a group of people can choose to make themselves into an isolate, like the Amish, or in past times the Jews, simply by consistently mating within their group----or they can be made into an isolate by other people's treatment, and then if there is enough visible phenotypic difference then it gets to look like a race)

    The second thing I think you are saying is that once you have an isolate, then a geneticist can look for statistical differences in the DNA or in the phenotypic expression of the DNA or whatever----genetic differences between isolates.

    Have I got it right so far? (there is some monster question hiding in the wings and maybe BlackVision will show it to us----there must be some real scary issue or people wouldnt be walking around with their hot-buttons showing----but what is it? so far this seems pretty harmless)
     
  5. Aug 8, 2004 #4

    marcus

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    just for reference I want a link to a thread Nereid started called
    Is their a scientific basis for race?
    https://www.physicsforums.com/showthread.php?t=25340

    I havent read this thread beyond the first couple of posts but I want to
    quote the first thing I saw there from selfAdjoint because it shows that we have a fair amount of agreement already
    https://www.physicsforums.com/showthread.php?p=208729#post208729

    ----quote from sA---
    I am on record as saying the concept of human races is prescientific. And the way most people use it, it is. But it has been brought to my attention that biologists commonly use the term race for subpopulations of species other than human, and that this term seems to have a more or less well defined basis. So I suggest that we look into this concept of race in nonhuman species and see whether or not it can be meanignfully extended to human populations, and what populations it would than apply to.

    I would also suggest that the "box checking" type of self identification that has been so much discussed in connection with statistics may be meaningful in sociology but is much less so in biology. So we may have legitimate schools of interpretation.
    ----end quote---

    I think that what Monique is telling us is that the term "race" which biologists use does, in fact, apply to humans as to other species of animal. Race has a clear scientific basis and is a scientifically useful concept, as applied to humans---if I understand Monique correctly.
     
    Last edited: Aug 8, 2004
  6. Aug 8, 2004 #5

    selfAdjoint

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    Boy am I glad you noticed that, Marcus. I had the feeling I had dropped that post into a black hole.
     
  7. Aug 8, 2004 #6

    marcus

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    that was a crazy discussion back there at Feedback!

    but nereid linked me to "Scientific Basis" and
    your post was one of the clearest things I got out of what little
    of that I read.
     
  8. Aug 8, 2004 #7

    marcus

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    It seems to me that we humans may be "on the cusp" of
    getting for the first time a rational and constructive understanding
    of our races

    maybe this is overly optimistic.

    BTW I am interested by Black Vision----he may be an utterly reprehensible malefactor. but I dont know anything about that. The main thing is I didnt see (in the limited sample) anything un-objective-----which is already very singular as i am subjective all the time. And he always seems to get a whole lot of people mad at him. Quite enviable in a way.

    Another strange thing about Black Vision is his name. As if he was, like Korean, and didnt want anyone to know. So he puts Black on his name to suggest that he's black.

    The way NoahAfrican puts African on his name. Its a custom in internet handles. But in NoahAfrican case it is authentic for sure.

    However in Black Vision case it might be "flying false colors" on the handle.
    He says to me "I wont tell you my race because I dont want to be profiled---I want you to consider my words on their own merit." But here he is with a loud Black Vision handle. that does not compute. Either he wants the identification or not.

    Also english not first language, so could be Asian, e.g. korean. Anyway the guy is brilliant and i hope he sticks around. never a dull moment
     
  9. Aug 8, 2004 #8

    Monique

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    I meant the Boers in South Africa, I should've been more precise..

    Well, I wish I could zap people who are out to stigmatize..

    I don't necessarily connect race to an isolate, actually I don't like to think in races: I like to think in populations.
    It depends on the history of the isolate. Certain historical events like the plague or famine shrinks down a population to a small size, followed by expansion of the population (a bottleneck). Finland went through several bottlenecks. Another historical event that impact on a population is the founder effect: this means that the population was settled by few individuals, an example are the Mormons. Some social influence would be consanguious marriages: in some countries it is normal to marry cousins.

    There are a number of things that can happen to the DNA.. the explanation would be rather technical.. I'll try to keep it simple.
    * genetic drift causes rare alleles to become frequent (or frequent to become rare)
    * inbreeding causes recessive diseases to be more prevalent
    * markers on DNA are shared between families
    * fewer alleles are present of a gene

    O sure, they might be a mini-isolate. Remember: a family can be an isolate too, right now the main focus of researchers is to connect people in a population to one common ancestor. Analysis of data from such a micro-isolate could give extra power to detect effects. Unfortunately, we need biostaticians that can write us programs to handle large families like that. I've seen such a pedigree, it would span the four walls of a conference room.

    I don't necessarily think I am an expert. I did attend a conference on the genetics of isolated populations so I do have insights, it was the first conference of its kind.

    Again you mention race, I don't like that word since I don't know what it means. Are the Amish a seperate race? I guess a tree could be draw, where the Amish are a small branch off their ancestors. But truely, I don't know how to quantify race.

    I don't think anyone has ever analyzed the statistical differene in DNA of isolates compared to phenotypes. The major hype at the moment is to give as many people in an isolate medical evaluations and do whole genome scans of those individuals. The idea is that the isolate has some characteristic that makes it easier to find a gene.
     
  10. Aug 8, 2004 #9

    selfAdjoint

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  11. Aug 8, 2004 #10

    iansmith

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    http://www.wordiq.com/definition/Race

    This article I quoted does good job a discussing race in different aspects.
     
  12. Aug 9, 2004 #11
    Does knowing his race matter on an internet forum?
     
  13. Aug 9, 2004 #12
    Can't we just define race as the genes and culture of a population?
     
  14. Aug 9, 2004 #13

    Monique

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    Right, but how isolated are the human populations? How divergent are they? How different is one population from the other?

    With genes you can do homology mapping. If you have a single gene that over evolution duplicated into a number of other genes and those mutated, you can map the genes into a tree and see which one gave rise to another. It will give you a branched output.

    With humans you might be able to do the same thing, but we have ~30,000 genes. All these genes have a number of alleles. You might be able to come up with a gene that is characteristic for a certain branch: think for instance about lactose tolerance or aldehyde dehydrogenase deficiency.

    But the term Caucasian is very outdated, although it is still used in peer-reviewed biology papers.

    So the Japanese would be a race, the Saumi would be a race, the Inuits would be a race? I prefer to say these groups are all populations: you acknowledge they have different characteristics.

    Some families have a gene that cause them to be very small. That certainly does not make them a different race, although they do look very different. If these people would only mate among other small people, I think you may call them a sub-population.
     
  15. Aug 9, 2004 #14
    You would have to define a norm to measure this.

    How much difference is there between a jap and a korean genetically?

    Are you sure that it is only 1 gene? I always thought that it would be several genes controlling height.
     
  16. Aug 9, 2004 #15
    Do you finally admit that some families might have some combination of genes causing them to commit more crime, or to have lower IQ?
    If there were many of these families and they became isolated from the rest of humanity, would they still have genetic prevelence of high crime and low IQ? What if there were millions and millions of such people? And if they were like this due to evolution and not chance?
     
  17. Aug 9, 2004 #16

    Nereid

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    Between any two individuals, far more than between the two groups. "Evidence from the analysis of genetics (e.g., DNA) indicates that most physical variation, about 94%, lies within so-called racial groups. Conventional geographic "racial" groupings differ from one another only in about 6% of their genes." Source: American Anthropological Association
     
  18. Aug 9, 2004 #17

    Monique

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    Did I ever refute that? No.
     
  19. Aug 9, 2004 #18
    "Originally Posted by plus
    Do you finally admit that some families might have some combination of genes causing them to commit more crime, or to have lower IQ?"

    It's noteworthy that phenotypes like "high IQ" and, even more so, "predisposition to crime" are poorly defined. That plus the limited knowledge of the genome and proteome we have at this point make it hard to decide if they're actually genetically determined and if yes, what genotype corresponds to them.

    For now, we basically have to stick to crisply and clearly defined phenotypes that can be traced back to one or a very limited number of genes in the interpretation of genomic data. More complex questions are better left unanswered until we have the means to tackle them rather than being "answered" with unscientific speculation.
     
  20. Aug 9, 2004 #19

    Neo

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    Have you heard of Robert Plomin? I recently read about "high IQ" genes possibly on chromosome 6.

    Here is an article about it:
    http://www.wellesley.edu/Chemistry/chem227/nucleicfunction/transcription/sci-gene-intelligence.html
     
  21. Aug 9, 2004 #20

    Evo

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    That is an excellent article Neo, I had read that some time ago, but I haven't seen anything about any progress. Are there any updates? He seemed to be on the right track.

    Also, I agree with his concerns about the potential for misuse, but there is so much potential for helping people with learning disabilities and diseases like Alzheimer's.
     
    Last edited: Aug 9, 2004
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