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Jingjing decoded in part

The first species to have its genome decoded by ‘next-generation-sequencing’ (NGS) machines is the giant panda (Ailuropoda melanoleuca). The individual animal was known previously to the world as the mascot of the 2008 Beijing Olympic Games. Scientists have been excited by the report because the NGS approach is significantly cheaper and faster than other methods. [. . .]

The estimated size of the giant panda genome is said to be 2.40 Gb (compared with 2.45 Gb for the dog genome and 3.0 Gb for humans) making up about 21,000 genes (similar to humans). “Overall, we found that the quality of the predicted panda genes was comparable to that of other well-annotated mammalian genes.” Although the panda eats only bamboo leaves, genes associated with carnivory are present in the panda:

“Of interest, our analysis of genes potentially involved in the evolution of the panda’s reliance on bamboo in its diet showed that the panda seems to have maintained the genetic requirements for being purely carnivorous even though its diet is primarily herbivorous.”

There was no trace of genes that encode enzymes for digesting cellulose, raising questions about how the panda can possibly survive on bamboo. The hypothesis proposed is that the bamboo diet “may instead be more dependent on its gut microbiome”. Confirmation of this will require further work. A related dietary factor concerns the sense of taste. The authors refer to the five components of taste: sweetness, saltiness, sourness, bitterness and umami. The giant panda has lost the capability of sensing umami, which means that meat has become unappetizing.

“Umami is sensed through the T1R family. In the panda genome, T1R2 and T1R3 are in an intact form, but T1R1 has become a pseudogene – we found that [. . .] two panda T1R1 exons contain transcript errors.”
“Two frameshift mutations occurred in the third and sixth exons of the panda T1R1 gene. The third exon contained a 2-bp (‘GG’) insertion; the sixth exon contained a 4-bp (‘GTGT’) deletion.”

[. . .]

Some have considered whether the panda genome helps resolve the animal’s taxonomic status. Although most place the panda in the bear family (Ursidae), a case has been made that it belongs elsewhere – in the raccoon family (Ailuridae). Since we do not have the genomes for any of these possible relatives, there is little more that can be said on the matter. However, even if other genomes were sequenced, does the “genome” tell us much about what makes a bear differ from a raccoon or a dog or a human? The genome can be described as the repository of housekeeping genes; it provides the materials needed for the organism to function – but something much more than this is needed to inform taxonomy. The ENCODE project (along with many others) has revealed rich functionality in the non-coding DNA (alias ‘junk DNA’). Consequently, it is probable that the gene sequencers are just scratching at the surface of genetic information.

If the giant panda is correctly assigned to the Ursidae, the new research contributes significantly to the way we understand the speciation of this animal. Before genome sequencing, we could say that it has diversified significantly from ancestral Ursidae stock. It has a reduced number of chromosomes, 42, whereas most bears have 74. It has a wholly vegetarian diet and it has a modified sesamoid bone which it uses to strip bamboo leaves from stems. The panda genome findings provide the background for understanding herbivory: the panda still retains the genes for carnivory but mutations have destroyed the taste trigger for it to eat meat. Although the panda cannot make enzymes for digesting plant food, communities of gut microbes are the most likely explanation of its continuing survival. The reproduction problems experienced by giant pandas may also be linked to a mutation affecting follicle stimulation.

The overall picture is one of speciation/diversification linked to genetic degradation. Natural selection, which has often been portrayed as all-powerful and capable of building exquisitely complex structures, has failed to provide the giant panda with any enzymes for digesting plant food. We do not know whether the modified sesamoid bone is an evolutionary innovation, a part of the degradation story or information neutral. The News & Views essay that accompanies the research paper calls the panda China’s “national treasure” – and so it is. However, from the perspective of genetics, the giant panda is not in a healthy state. Whatever else may be relevant, this case has strong affinities with speciation by gene pool reduction. From the perspective of Darwinism, the giant panda genome testifies to the failure of Darwinian mechanisms to overcome problems caused by mutations. From the perspective of design, we have a story of how a superbly designed carnivore has managed to survive the effects of genetic degradation. From a conservation perspective, without human intervention, the chances of long-term survival are slender.

There is also the finding that Jingjing’s genome has a high degree of genetic diversity, but she is unlikely to be representative of the panda population taken as a whole. It is more prudent to assume that the relatively isolated panda enclaves harbour problems of inbreeding and that Jingjing is an example of the benefits of breeding across enclaves – further supporting the case for human intervention.

The research paper: is:
Li, R. et al., The sequence and de novo assembly of the giant panda genome, Nature 463, 311-317 (21 January 2010) | doi:10.1038/nature08696

For other references and additional comments, go here.

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18 Responses to Jingjing decoded in part

  1. Cool. Very interesting David thank you.

    Why am I not surprised about the lack of evolved herbivorous genes and the broken carnivorous ones? Because ID predicts this, and it’s a better theory.

  2. Your calculation for bytes is wrong.

    The human genome is 750 MB.

    http://www.tmsoft.com/article-genome.html

    http://www.nytimes.com/2007/06......html?_r=1

    Although I suppose they are converting it to binary for that calculation. If you did it using DNA’s four digit code it would just be 3 billion divided by eight, since there are eight bits per byte. That would be basically saying that instead of binary, we are using a four digit code where each nucleotide is equal to one bit. So in that case it would be 375 MB.

  3. I’m curious, if the panda is perfectly capable of digesting bamboo with its bacterial flora, why would you expect it to evolve plant digesting enzymes? Would you say termites are poorly adapted to their vegetarian lifestyle?

    Re #1: What would you think evolution would have predicted? And why would you think that ID would have predicted these results? And why didn’t it?

  4. The first species to have its genome decoded by ‘next-generation-sequencing’ (NGS) machines is the giant panda (Ailuropoda melanoleuca).

    I’ll be impressed when the develop the previous-generation-sequencing machine, as that is much more important to the evolutionism agenda.

  5. Some have considered whether the panda genome helps resolve the animal’s taxonomic status. Although most place the panda in the bear family (Ursidae), a case has been made that it belongs elsewhere – in the raccoon family (Ailuridae).

    What does evolutionary theory predict? Now that we can sequence entire genomes, isn’t it about time that we saw some testable predictions from the evolutionists?

    From the perspective of design, we have a story of how a superbly designed carnivore has managed to survive the effects of genetic degradation.

    How does that fit with a YEC view?

    The panda genome findings provide the background for understanding herbivory: the panda still retains the genes for carnivory but mutations have destroyed the taste trigger for it to eat meat.

    So it started out as an herbivore, evolved into a carnivore (by design) and then devolved back into an herbivore?

    …two panda T1R1 exons contain transcript errors.”
    “Two frameshift mutations occurred in the third and sixth exons of the panda T1R1 gene.

    When, if ever, will we be free of the teleological language in biology?

  6. tragic mishap @ 2
    I’ve followed the research paper’s format. They use Gb for “gigabases”

    hrun0815 @ 3
    I’m curious, if the panda is perfectly capable of digesting bamboo with its bacterial flora, why would you expect it to evolve plant digesting enzymes?
    When the mutations affected the ancestral giant panda, would it have a gut flora to digest bamboo? It is amazing the species is still with us – the fact that it is is no thanks to Darwinian mechanisms!

    Mung @ 5
    How does that fit with a YEC view?
    Maybe that’s a question for a YEC forum. There are distinct designs for herbivory and carnivory and anyone developing models of origins needs to address those design issues.

  7. David Tyler @ 6:

    “Maybe that’s a question for a YEC forum. There are distinct designs for herbivory and carnivory and anyone developing models of origins needs to address those design issues.”

    Can you determine for which of the two options (herbivory or carnivory) humans were designed?

  8. When the mutations affected the ancestral giant panda, would it have a gut flora to digest bamboo? It is amazing the species is still with us – the fact that it is is no thanks to Darwinian mechanisms!

    Why is it still with us then? Surely you don’t want to credit humans for keeping the panda alive. It’s humans that endangered the panda to begin with. Surely pandas were around well before humans hit the scene.

  9. #1 tragic mishap:

    Why am I not surprised about the lack of evolved herbivorous genes and the broken carnivorous ones? Because ID predicts this, and it’s a better theory.

    Did IDers actually predict this about the panda, or do you wish to take that back?

    I’m getting the sense that when you combine “there’s almost no junk DNA” with “some vague thing called genetic entropy is happening all the time”, you can postdict just about anything. Whereas, like it or not, the predictions of common descent are unequivocal. (The predictions of the rest of evolution are trickier creatures, I’ll grant that.)

  10. OP:

    From a conservation perspective, without human intervention, the chances of long-term survival are slender.

    Presumably, this is the case for all species, no? Unless the designer intervenes, genetic entropy, by virtue of accumulating deleterious mutations (but sometimes instead accumulating “junk”, somehow) will be the death of all life — or so I’ve been lead to believe in this blog.

  11. 11

    David:

    I’ve followed the research paper’s format. They use Gb for “gigabases”.

    Right sorry I thought you meant Gigabytes. My bad. I read a book recently referring to the size of genomes using bytes of information.

    Lenoxus:

    Did IDers actually predict this about the panda, or do you wish to take that back?

    I was using “predicts” in the sense it is often used in regards to scientific theories, not fortune tellers. I was not saying that somewhere some ID theorist made this specific prediction no. If you would like to continue being pedantic go right ahead. Pedantic can be fun.

    Something that would be surprising to me would be if say a panda had evolved enzymes for digesting cellulose within its own genome rather than relying on gut bacteria. If that drove speciation, rather than the loss of genetic information giving it a taste for meat, then yes that would be surprising. The prediction of ID is that all biological information was in one form or another there from the beginning, and that any real deviation from this will not be because of new information but loss of information or combining existing information. The panda genome provides interesting examples of both, but no examples of new information.

  12. 12

    Lenoxus:

    Presumably, this is the case for all species, no? Unless the designer intervenes, genetic entropy, by virtue of accumulating deleterious mutations (but sometimes instead accumulating “junk”, somehow) will be the death of all life — or so I’ve been lead to believe in this blog.

    Sure. Just as physicists talk about the “heat death” of the universe. Of course, we would probably hold that human beings are intelligent and in principle capable of supplying additional information to keep life going.

    http://en.wikipedia.org/wiki/H.....e_universe

  13. #11 tragic mishap:

    The prediction of ID is that all biological information was in one form or another there from the beginning, and that any real deviation from this will not be because of new information but loss of information or combining existing information.

    … except when the prediction is that the designer intervenes from time to time — for example, by means of saltation, a popular UD topic. The view you’ve just expressed there is in fact totally consistent with gradualism, and inconsistent with saltation. (It also sounds scarily like mainstream evolution, which does indeed hold that all changes must work with the existing DNA, not whole cloth.)

    “Information” is a concept with, as I understand it, mild rigor in mathematics. But not so much raw calculability when it comes to ID. The nature of evolution is such that any layperson can see any of its changes as “information loss” or “equal information” or whatever. Birds gaining wings? Only at the expense of forelimbs, ha! Even though, of course, a reptile with shoulder-wings instead would in fact contradict evolution by contradicting UCD.

    Any possible creature, no matter how laden with obvious evolutionary jetsam, just might be a designed one. In fact, the more vestigial features, the greater PROOF of “genetic entropy”, no? (If not, how not?)

    It’s 2010, and ID still doesn’t have a solid ground hypothesis. Even though you guys love to present evolution as never making up its mind (Oh look, someone critiquing Dawkins!) nothing matches ID for jello content. The designer might have done anything and everything and who are we to say? “Bad” design? That’s a presumptuous, theological question, don’t you know.

  14. hrun0815 @ 8
    Why is it still with us then? Surely you don’t want to credit humans for keeping the panda alive.
    You should be aware that extinction is a characteristic feature of the fossil record. Do we have coherent theories of extinction? Without reviewing the various ideas, I want to see genetic degradation associated with allopatric speciation as an option. That appears to me to be what has happened to the giant panda.

    Lenoxus @ 10
    Presumably, this is the case for all species, no?
    It would happen very quickly were it not for the elaborate (and designed) mechanisms for repairing genetic codes. You are obviously aware of the concept of genetic entropy – I think we should all be get familiar with this!

    Lenoxus @ 13
    It’s 2010, and ID still doesn’t have a solid ground hypothesis.
    I regard this as an unwarranted criticism. ID is still excluded from science by establishment gatekeepers and until this changes, ID’s main task is to press home the message that intelligent design is a legitimate conclusion that scientists can draw from empirical data. When we have a foundation to build on, that’s the time to get constructing.

  15. You should be aware that extinction is a characteristic feature of the fossil record. Do we have coherent theories of extinction? Without reviewing the various ideas, I want to see genetic degradation associated with allopatric speciation as an option. That appears to me to be what has happened to the giant panda.

    So first you say that genetic degradation is what made the panda into a panda (i.e. descent from flesh eating ursidae) and at the same time, the very same process that created the panda also leads to its extinction?

  16. hrun0815 @ 15
    So first you say that genetic degradation is what made the panda into a panda (i.e. descent from flesh eating ursidae) and at the same time, the very same process that created the panda also leads to its extinction?
    Yes. These ideas are by no means incompatible. I am not saying that extinction is inevitable, but that the impoverishment of genetic information makes the species more vulnerable to extinction. For more on the thinking behind this, go here.

  17. David, I still don’t understand: if the Panda, due to its genetic degradation is so poorly adapted that it is causing it to die out, how did it get established in the first place?

  18. hrun0815 @ 17
    I still don’t understand: if the Panda, due to its genetic degradation is so poorly adapted that it is causing it to die out, how did it get established in the first place?

    Genetic degradation is all around us. It does not make everything extinct in a generation, but it reduces fitness. That is what appears to have happened with the giant panda. Humans are affected too – although we are less afflicted than the panda. If others do not blog on it, I will post on this paper:

    Rate, molecular spectrum, and consequences of human mutation
    Michael Lynch
    PNAS, January 19, 2010, vol. 107 no. 3, 961-968 | doi:10.1073/pnas.0912629107

    Abstract: Although mutation provides the fuel for phenotypic evolution, it also imposes a substantial burden on fitness through the production of predominantly deleterious alleles, a matter of concern from a human-health perspective. [. . .]

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