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  1. #11
    no clinkz 'til brooklyn Nocapszy's Avatar
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    No one said anything about strange. It's cool though.

    Also, eyes are pretty complex. For them to be as similar as it sounds, without being an influence on one another is pretty phenomenal.

    Maybe it implies that what they have in common are the only ways (or one of them) carbon life can use light energy for information.

    Either that or, the groundwork was already mostly laid down, and eyes were inevitable (using the term loosely) thanks to what evolutionary steps came before them, but the two incarnations being shaped differently and such were the responses to the environment.
    we fukin won boys

  2. #12

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    For the biology majors here (and other knowledgeable individuals), I have a lot of questions about biological evolution in general. I think, it is still on-topic.

    What is a "gene?" I have never quite gotten it's definition from it's usage. Is it a protien? Is it a small sequence of half a DNA-molecule that is known to be responsible for a certain function in an organism? What is it really? In specific/concrete terms?

    What does it mean for a gene to be "expressed?" Is it that the through RNA (or whatever comparable mechanism there is in the organism), the identified "gene" creates the phenotype (or rather the little section of it) from the genotype (or rather the little section of it)?

    Are there quantitative measures of "selection pressure"? IOW, are there somethings analogous to a "fitness functions" used by computer scientists in synthetic (computerized) genetic algorithms? If so how does one determine such functions?

    Accept the past. Live for the present. Look forward to the future.
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    "As our island of knowledge grows, so does the shore of our ignorance." John Wheeler
    "[A] scientist looking at nonscientific problems is just as dumb as the next guy." Richard Feynman
    "[P]etabytes of [] data is not the same thing as understanding emergent mechanisms and structures." Jim Crutchfield

  3. #13
    no clinkz 'til brooklyn Nocapszy's Avatar
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    Quote Originally Posted by ygolo View Post
    For the biology majors here (and other knowledgeable individuals), I have a lot of questions about biological evolution in general. I think, it is still on-topic.

    What is a "gene?" I have never quite gotten it's definition from it's usage. Is it a protien? Is it a small sequence of half a DNA-molecule that is known to be responsible for a certain function in an organism? What is it really? In specific/concrete terms?
    I'm not entirely sure (so someone who is should piggyback / correct me) but I think you're kind of right.

    It's any combination of the segments of one's DNA that decides a characteristic. That is, the order of the chemistry provides groundwork for growth, which turns into distinctive attributes.

    Again, I'm unsure if that's the full exact definition. I basically pieced that together from parts beginning physical anthropology class, so I could have easily left something out.
    we fukin won boys

  4. #14
    insert random title here Randomnity's Avatar
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    A gene is the DNA sequence that codes for a protein (or sometimes multiple proteins, or parts of proteins...but that's not important here). It is a blueprint, basically. Proteins are really what cause the eventual effects of the gene, for the most part.

    A gene is said to be expressed when its protein is being produced...in other words, the gene is actually doing something.

    I'm pretty sure there are quantitative measures of selection pressure, at least in models, but it's really not my area so I can't speculate.

    HTH

  5. #15
    ish red no longer *sad* nightning's Avatar
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    Quote Originally Posted by elfinchilde View Post
    And yes. Mutations by themselves are never good or bad per se. It is what nature dictates for survival, that says if it is a good or bad mutation.

    Using HIV again as the example (since it's quoted already), there are some people around who are naturally more resistant to the virus than others, due to some genes which they possess. In effect, this can be considered a good mutation, handed down from generations, and showing itself only when HIV surfaced in the human population.

    H5N1 (bird flu) is the other example. There are some people, as well as birds, and other animal reservoirs, which have evolved/possessed immunity to this deadly disease. This is again due to genetic mutation--or more precisely, genetic variation. Sometimes it's rapid, sometimes it's not. All depends on the species, and the rate of the disease spreading.

    note: because of the DNA/RNA thing---genetic mutation tends to occur much, much more slowly in animals, including humans, than in bacteria and viruses. In that sense, the microbes have one-up on us. Plus, one generation in humans is about 25 years, whilst for bacteria/viruses, it may be as short as a few hours. So generational mutation occurs much more swiftly in a same time frame for bugs than for us.
    Much agreed!

    Stickle cell anemia can be deadly... so why do some many African Americans carry the gene? Because it's a beneficial mutation... For the heterogeneous carrier, 1 normal allele (copy of the gene) & 1 mutant allele, they are less susceptible of catching malaria. It's only when you have 2 copies of the mutant allele that you get the disease.

    Mutation is just mutation... random changes. If you have a working system... there are more chances that random changes will impair the system rather than improve it. Perhaps that is why people associate mutation as being a bad thing. It really isn't... it's just RANDOM! Randomly good or bad.

    Convergent evolution and evolution in general is always an interesting thing to see... The eye wiring is neat.

    Another example would be the opposable "thumb" on the giant panda. They have 6 "fingers"... The ancestorial bears have evolved forward facing digits for running on the ground. The panda developed an appendage to help grip bamboo. Instead of relocating the first digit, the thumb is actually modified bone from their wrist. That's the power of random mutations for you.

    There's always more than one way of solving a problem... convergent evolution nicely demonstrates that.

    Quote Originally Posted by ygolo View Post
    What is a "gene?" I have never quite gotten it's definition from it's usage. Is it a protien? Is it a small sequence of half a DNA-molecule that is known to be responsible for a certain function in an organism? What is it really? In specific/concrete terms?
    A gene is a sequence of DNA. With the exception of viruses (they're technically not living) and bacteria, gene sequences are stored together in chromosomes, which are long long strands of DNA all coiled up together. Chromosomes are found within the nucleus (center) of every cell. As it's been said before, it's not a protein. It's the sequence of the DNA that allows for creating specific proteins. And it is the expression of these proteins that forms the phenotype of the individual (phenotype = what the individual looks like, eg hair color, eye color, height etc).

    Technically one gene codes for one protein. This is known as the one gene/one enzyme hypothesis. Although multiple genes can produce multiple proteins that can influence a single attribute. Take hair color for example. Textbooks usually tell you that blond hair is recessive (needing 2 copies of blond) and dark color hair is dominant (1 copy of dark is sufficient). But what about the multitude of shades of blond or brunette... what about red heads? Hair color is controlled by multiple genes... However there's a main one that gives you the overall color. The interaction with the rest of them gives you the exact shade.

    What does it mean for a gene to be "expressed?" Is it that the through RNA (or whatever comparable mechanism there is in the organism), the identified "gene" creates the phenotype (or rather the little section of it) from the genotype (or rather the little section of it)?
    Gene is "expressed" into proteins (mostly enzymes). The exact process is like this:

    DNA sequence (gene)-> translated (copied) to messanger RNA -> messanger RNA is processed and sent out of the nucleus -> mRNA is transcribed into (directs synthesis) proteins

    Proteins are what makes up cells or acts as enzymes to influence parts of the cell.

    Genotype = what gene alleles (copies) you have in your DNA
    Phenotype = what is actually expressed... you can see it visibly

    Are there quantitative measures of "selection pressure"? IOW, are there somethings analogous to a "fitness functions" used by computer scientists in synthetic (computerized) genetic algorithms? If so how does one determine such functions?
    I skimmed the wiki articles...
    Genetic algorithm appears to be a computer model of evolution... taking factors like selection, chromosome crossover rate, mutation rate etc. The fitness function just tries to describe the selection forces. What might be beneficial for survival.

    These parameters are difficult to pin point.

    Take the rate of mutation... The rate is affected by the rate of cell division. Every time a cell divides into two, its genomic DNA needs to be replicated (copied). Mistake in the copying gives raise to mutations. So a fast dividing (in the case of bacteria) or fast reproducing (sexual reproduction) organism will have a higher rate of mutation than a slower dividing/reproducing one. Also the error rate of replication is not constant. A cell under stress will mutate faster (hence the use of UV radiation for mutation studies... or UV causing skin cancer). Different species also have different enzymes to copy DNA. Some enzymes have less "proof-reading" abilities than others. RNA retro viruses have an enzyme to copy RNA into DNA for insertion into the host. That enzyme is notoriously error prone and probably have been evolutionary selected to be that way. Afterall, the more mutations it makes... the more difficult it is for humans to come up with vaccines and drugs to stop them.

    Selection forces... it's something to keep in mind. Evolution happens far too slowly to be looked at much in real life (with the exception on bacteria, viruses, yeast). So evolutionary studies are based mostly on fossil records and on genomic and protein data we can extract from species that are still alive today. You can't say definitively what the environment thousands of years ago look like. Therefore there's no way to determine what factors are important for survival... Even for current times, you can only guess.

    So they can't tell what exactly the selection forces are... but they can tell whether there are sudden changes in selection forces. Sudden change will be indicated in the fossil (DNA) record. With more changes in the DNA genome in the descendant species. (Age can be determined by carbon dating). It's also important to note that much of our genome (90 odd %) consists of non-coding DNA (what's known as junk DNA). Some sections might be necessary... but the sequence of these are not. The amount of random mutation arising in these segments can also be used to track time.

    Uhhhh please excuse my rambliness.

  6. #16
    a white iris elfinchilde's Avatar
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    Quote Originally Posted by ygolo View Post
    For the biology majors here (and other knowledgeable individuals), I have a lot of questions about biological evolution in general. I think, it is still on-topic.

    What is a "gene?" I have never quite gotten it's definition from it's usage. Is it a protien? Is it a small sequence of half a DNA-molecule that is known to be responsible for a certain function in an organism? What is it really? In specific/concrete terms?

    What does it mean for a gene to be "expressed?" Is it that the through RNA (or whatever comparable mechanism there is in the organism), the identified "gene" creates the phenotype (or rather the little section of it) from the genotype (or rather the little section of it)?

    Are there quantitative measures of "selection pressure"? IOW, are there somethings analogous to a "fitness functions" used by computer scientists in synthetic (computerized) genetic algorithms? If so how does one determine such functions?
    *applause for the mousie*

    i was going to answer your questions, ygolo, but then nightning and randomnity have said it all already. espcially nightning. hey, i perceive i have other bio people here!

    was going to raise sickle cell anemia as an example, but thought better leave it out as it was late, and i didn't want to go into the details of sickle-cell shaped red blood cells vs regular shaped ones, and malaria. mousie.

    just to give the poetic answer though, since what is life if it is only prose:

    genes: from latin, genesis, meaning: creation.

    that is why the standard defintion of DNA is "the blueprint of life". Because genes are essentially bases (A, T, C, G.) which code for all the functions of life.

    In that sense, a singular gene can be defined as that particular sequence of DNA which codes for a sense function. i.e., a function that has utility and can potentially be expressed. (as opposed to non-sense DNA, which are bits of DNA that are all about a genome, which do not code for any function.)

    note that a DNA 'molecule' is a complex structure. It is made of hundreds of thousands of bases linked together, then twisted together into a double-helix formation, which is THEN wound around what are known as histones. This is to compact the structure to save space in cells.

    to get an idea of its complexity, here's a double helix image:



    2) when a gene is expressed, it means it produces a protein (via the DNA->RNA->protein process described by nightning) that is phenotypically seen in the person. Eg, if you talk about eye colour, then all people possess the alleles (different forms of the same gene) for every eye colour. But what is EXPRESSED, depends on which allele is dominant. (refer to mendelian genetics if you're interested in this). Hence an expressed gene is one whose function is seen in the person/animal. Be it for behaviour, or skin colour, hair colour, eye colour, etcetc. Even height, voice and all things.

    3) quantitative measures of selection pressure. biostatistics. You use the chi-squared test, mainly.

    hope this helps!
    You gave me hyacinths first a year ago;
    They called me the hyacinth girl.
    Yet when we came back, late, from the Hyacinth garden,
    Your arms full, and your hair wet, I could not
    Speak, and my eyes failed, I was neither
    Living nor dead, and I knew nothing,
    Looking into the heart of light, the silence.

    --T.S Eliot, The Wasteland

  7. #17

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    I think it is clearer now what a gene and and what it means for it to be expressed. I don't think I was far off in my own conception.

    However,...

    Quote Originally Posted by elfinchilde View Post

    3) quantitative measures of selection pressure. biostatistics. You use the chi-squared test, mainly.
    Do you basically use chi-squared statistic to see if the relative frequecies of certain features/genes deviate significantly from expected (thereby indicating selection pressure for/against that feature/gene)?

    Accept the past. Live for the present. Look forward to the future.
    Robot Fusion
    "As our island of knowledge grows, so does the shore of our ignorance." John Wheeler
    "[A] scientist looking at nonscientific problems is just as dumb as the next guy." Richard Feynman
    "[P]etabytes of [] data is not the same thing as understanding emergent mechanisms and structures." Jim Crutchfield

  8. #18
    a white iris elfinchilde's Avatar
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    Quote Originally Posted by ygolo View Post


    Do you basically use chi-squared statistic to see if the relative frequecies of certain features/genes deviate significantly from expected (thereby indicating selection pressure for/against that feature/gene)?
    Chi-squared is just an example. THere are others you can use, as well. It depends a lot on your sample size, and all the other parameters that have to be fulfilled before hte results can be considered significant.

    But yes, you use it to see for deviations as you said.

    You can also use it to prove the links between genes and expressed phenotypes.

    So versus a standard population, say testing to see if NPC (nasopharyngeal carcinoma, otherwise know as ear/nose cancer) and the EBV (epstein barr virus) are linked, you'd take populations with NPC+EBV, NPC alone, EBV alone, and another group without both.

    Then apply whichever stats test is applicable, to see if there is significant deviation. the use of null hypothesis applies. So it all depends on the definition of hte criteria at the start.

    need to note that for microbes, it's a lot easier to use biostats, as their lifespans are shorter, so you can get generations of information in a day/month. whereas for humans, it becomes pretty much an extrapolation process, since we've in essence not changed for at least 5,000 years. (the span of civilisation as we know it).
    You gave me hyacinths first a year ago;
    They called me the hyacinth girl.
    Yet when we came back, late, from the Hyacinth garden,
    Your arms full, and your hair wet, I could not
    Speak, and my eyes failed, I was neither
    Living nor dead, and I knew nothing,
    Looking into the heart of light, the silence.

    --T.S Eliot, The Wasteland

  9. #19

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    Comming back to convergent evolution, doesn't convergent evolution indicate strong selection pressure (almost by definition--as defined by a chi-square comparisons using expected frequencies of all options)?

    Accept the past. Live for the present. Look forward to the future.
    Robot Fusion
    "As our island of knowledge grows, so does the shore of our ignorance." John Wheeler
    "[A] scientist looking at nonscientific problems is just as dumb as the next guy." Richard Feynman
    "[P]etabytes of [] data is not the same thing as understanding emergent mechanisms and structures." Jim Crutchfield

  10. #20
    a white iris elfinchilde's Avatar
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    Quote Originally Posted by ygolo View Post
    Comming back to convergent evolution, doesn't convergent evolution indicate strong selection pressure (almost by definition--as defined by a chi-square comparisons using expected frequencies of all options)?

    Yes. Athenian pointed out rightly. It shouldn't be a surprise at all. Life selects for the best; so the selection pressure will always be on the genes that confer survivability, across all species.

    Hence convergent evolution.

    Where you get divergent evolution, would be in a scenario of chaos. eg, different bugs specifically targetting different species, so that each species targetted needs to evolve different mechanisms for survival.

    It's what is known as immunology: host-pathogen interactions. one of the most interesting of the bio-fields to study, because it is dynamic interactions we're talkign about; a constant process of evolution, as the bugs try to outsmart us, and we try to outsmart them in return. Cat and mouse game.

    Alternatively, if there are more than one ways of beating the microbe, such that different paths evolve in different species (ie, different genes expressed, but all for the same function of beating the microbe, just in different ways). However, the end is the same: continued survival of the species. Selection pressure will always be for the best possible combination that best confers the ability to survive.
    You gave me hyacinths first a year ago;
    They called me the hyacinth girl.
    Yet when we came back, late, from the Hyacinth garden,
    Your arms full, and your hair wet, I could not
    Speak, and my eyes failed, I was neither
    Living nor dead, and I knew nothing,
    Looking into the heart of light, the silence.

    --T.S Eliot, The Wasteland

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