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    Gene Regulation And The Difference Between Human Beings And Chimpanzees
    By Gunnar De Winter | October 26th 2011 07:44 AM | 14 comments | Print | E-mail | Track Comments
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    When the DNA sequences of Homo sapiens and Pan troglodytes were sequenced, the difference between the sequences of coding genes was smaller than expected based on the phenotypic differences between both species. If not the coding genes, then what is responsible for these dissimilarities?

       

    (Source: godlessgeeks.com)

       

    In the words of the authors of a new study that took a look at this question:

    Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six to eight million years ago, their genomes are more than 98.5% identical at protein-coding loci. Since this modest degree of nucleotide divergence does not seem sufficient to explain the extensive phenotypic differences that exist between the two species, it has been hypothesized that the genetic basis of the differences lies at the level of gene regulation and is associated with the extensive insertion and deletion (INDEL) variation between the two species. 

    So, it might not be the genes, but the genomic ‘gaps’ between them. Junk DNA, or stretches of the genome without any known function, does not code for any protein, and turns out to be quite different between human beings and chimpanzees. A lot of the difference between the two evolutionary cousins is due to the insertion or deletion of retrotransposons, genetic elements that amplify themselves and constitute about half the genome in both species.

    These gaps between the genes in both genomes can affect the extent to which genes are 'turned on or off'. The research team has found that the gaps in both genomes are significantly correlated with differences in gene expression. This suggests that the difference between chimpanzees and human beings might not be mostly due to changes in genes, but rather in changes of gene regulation.

    The researchers conclude:

    The results presented herein are consistent with the hypothesis that large INDELs, particularly those associated with retrotransposons, have played a significant role in human-chimpanzee regulatory evolution.

        

    Not so different after all?

    (Source: Scientific American, What makes us human?)

      

    Reference

    Polavarapu, N.; Arora, G.; Mittal, V.K. and McDonald, J.F. (2011). Characterization and potential functional significance of human-chimpanzee large INDEL variation. Mobile DNA. doi:10.1186/1759-8753-2-13. (Click here for a provisional version of the article.)

    Comments

    I want to do a chimpanzee. I bet they are great lovers.

    Gerhard Adam
    I'm always impressed by how dumb some comments can get. 
    Mundus vult decipi
    The thing of genes being turned on or off to get specific results is fascinating. Would it be possible to turn on the genes for human intellect in the chimpanzee and create an animal with human sentience?

    Gerhard Adam
    No, since that would require that human intelligence already exists in the chimpanzee, but it is simply "turned off".  Since that isn't the case, you couldn't do what you're proposing.
    Mundus vult decipi
    These "gaps" or "junk DNA" are hardly non-functional; the key is that the decrease in length across generations. They thus act as probabilistic "loop counter" which control turning on or off various portions of the genes as the cells multiply. It is the key to cell differentiation in multicellular organisms.

    DNA represents an approximate (since the loop counters are not absolute, but rather depend on an average number of reproduction cycles to terminate) Finite State Machine.

    Genetic researchers do themselves a great disservice by failing to incorporate theoretical Computer Science and Infomation Theory into their work.

    Error in previous; the phrase "that the decrease in length" should read "that these 'gaps' decrease in length".

    Prior work has suggested that there was a genetic bottleneck in human evolution, where the total world population of humans may have dropped to as few as 16,000 distinct individuals due to either disease or catastrophe - like a prolonged ice age.

    Also, geneticists have noted that to maintain survivable human genetic diversity - you need a minimum of 160 distinct individuals - which makes for an easily tracked laboratory population.

    This work suggests something interesting: The difference between humans and chimps may be as little as the difference between the wolf and the domestic dog.

    From Russian experiments in selective breeding for recessive traits with foxes, it is known that in a very few number of generations with selective breeding - a wide difference in body types and behaviors can be generated, from extremely aggressive animals with long snouts, to extremely social animals with short pug faces suitable for pets.

    Local environment can enhance selective breeding by isolating populations with specific advantages and disadvantages: Humans, for instance, deliver infants, who can instinctively swim - but not walk. Chimps deliver infants who can instinctively cling - but not swim. Most of the apes do not adapt well to environments that require swimming and are not known to develop marine diets that include fish, kelp, crustaceans, or easily harvested bivalves, such as mussels and oysters.

    We do know that a local diet that includes fish also includes a higher percentage of omega-3 oils which is essential to building brain tissue.

    Also, humans sweat - like sea mammals - to get rid of excess heat, while chimps pant. Humans, like sea mammals, have subcutaneous fat layers instead of fur to maintain body temperature in water environments without introducing excessive swim drag from body fur.

    Humans are naturally bipedal - which is easy to attain by adapting to shallow water environments for food gathering. Chimps use their arms and knuckles to brace themselves while crossing open ground because their geometry is adapted for rapid tree climbing.

    These observations suggest that a warm, shallow water, coastal environment may have provided the opportunity for selective breeding to reinforce the recessive characteristics that became the human body and behavior plan - as opposed to open savannah plains - as suggested by a number of anthropology text books.

    This suggests a multi-generational experiment: Can the chimpanzee be selectively bred by humans into a human-like social animal in a very small number of generations - in like less than 10 - in less than 30 years?

    If this can be achieved, could it confirm that selective breeding can be used to "design" humans - and could this lead to a "selective" breeding program for humans? Could that lead to an informed eugenics cultural movement with more deterministic certainty than the current reproductive donation programs?

    Most importantly, what traits would society want to develop in designed humans? Should we breed out all inherited genetic diseases - purifying the human genome - and amplifying traits essential to a technological society's survival, like strength, stamina, long life, sociability, histo-compatibility, and brains?

    Or, should the human genome be regressed to a more chimpanzee state which might be better adapted to a planet made "greener" thru major re-forestation campaigns to reverse global warming?

    These are some of the questions suggested by reading this research paper.

    Saying that the coding (or non-coding) genes determine traits has no meaning.

    Pick a difference and show HOW the DNA results in a trait..

    Speech would be a good place to start. Humans and birds have it but chimps don't.

    The reason is ?????????????????????????

    Gerhard Adam
    Your statement is incorrect since it presumes that specific DNA has a direct causal link to the trait represented.  This is NOT true.  The same DNA sequence may be expressed in vastly different ways so there is no way to be that specific.  This is despite the erroneous analogies that try to portray DNA as a type of program in a biological computer.

    Animals can have EXACTLY the same DNA sequences and still result in different trait expressions based on other factors, so it isn't a one-for-one relationship at all.  A perfect example is examining the individual cells of your body, so that despite the differences between a neuron and a heart muscle, they share exactly the same DNA sequences.

    You also can't argue that this is something unique that occurs during the development of the fetus, since it occurs throughout your life.  Heart cells NEVER become neurons, just as neurons never become liver cells, etc.  Despite each carrying identical copies of DNA, each reproduces only the specific traits for the environment in which it exists.
    Mundus vult decipi
    Though I am a little off topic, chimpanzees do have primitive speech. An experiment which introduced a type of food (grapes for this example) and recorded the vocal reactions of the "chimps" was combined with many others. A chimp was placed in a room with a touch screen computer with several images on the screen. as each recorded sound was plyed, the chimp touch the corresponding item on the computer, thus proving a basic language (at a minimum within the testing group) I personally do not know if they used the same sound recordings with chimps who where not part of the original social group (external control specimen)

    Gerhard Adam
    I think we tend to be a bit infatuated with this kind of stuff, despite having no evidence that it would ever really lead anywhere.  Certainly the chimpanzee lacks the vocal apparatus to have speech like humans, but even symbolic languages are quite restricted.  I personally suspect that the problem relates more to the chimpanzee's limited ability to abstract thoughts in the same way as humans, and consequently it isn't a matter of re-producing sound.  Rather it is that they don't have a mental process that is "verbal" in any sense that would make them want to translate it.

    This doesn't mean that chimpanzees or other animals don't communicate, because they certainly do.  However, much of human speech is far more nuanced than merely "communicating", so it is that aspect of it which prevents full speech for occurring in such animals, even given alternative methods of communicating.
    Mundus vult decipi
    The graphic caption "Not so different after all?" is a non-sequitur.

    The result of this study is not that humans and chimps are any less different than we thought. The authors still affirm "the extensive phenotypic differences that exist between the two species."

    What this study does support is the notion that non-coding ('junk') DNA, contrary to predictions of evolutionary theory, is not accidental junk but has important functions (http://www.evolutionnews.org/2011/10/post_32051651.html).

    The extensive differences that we can observe between chimps and humans are not diminished. What is diminished is the role of protein-coding DNA in producing those differences; and the role of non-coding DNA is increased.

    Gerhard Adam
    What this study does support is the notion that non-coding ('junk') DNA, contrary to predictions of evolutionary theory...
    There is no such prediction from evolutionary theory.  It was an assumption that some made because they became enthralled with the protein coding role of DNA and questioned why there were such many large segments that played no apparent role (consequently referred to as "junk").  That's complete nonsense and evolutionary theory strongly suggested that this was NOT the correct interpretation because it would make no sense to continue carrying forward information that was not used.
    The graphic caption "Not so different after all?" is a non-sequitur.
    What's your basis for claiming that it is a fallacy?  The point is the commonality of DNA which is where humans and chimpanzees are quite similar, and yet are also quite different because of the regulatory mechanisms.  However, if you want to argue against common ancestry then it's a non-starter.  Such arguments are hopelessly flawed, because instead of accepting the idea that there is a common set of DNA which diverges, they would have us believe that we've had parallel sets of segregated DNA all arrive at the same results with minor differences.  That truly would be a remarkable development for which absolutely no evidence exists.

    Please don't link to creationist or ID web sites, since the information is neither helpful nor informative.
    Mundus vult decipi
    This work suggests something interesting: The difference between humans and chimps may be as little as the difference between the wolf and the domestic dog.

    If that be true the research must be wrong because obviously there are the behaviors are vastly different. Dogs and wolves engage in many like behaviors but humans engage in a range of behaviors that is well and truly beyond the range of any chimp.

    What the research does demonstrate is that clearly the differences are not simply contingent on the genetic code as we know it. The genotype - phenotype bridge is a bridge too far. Until such time as we can cross that bridge we cannot meaningfully talk about the "genetic differences" between animals.