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Mouse gene expression reveals “widespread differences” from humans

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Back in 2002, one could read in the New York Times,

An analysis of the mouse genome by an international consortium of scientists, a landmark event in biology, shows it is so similar to that of people that it should speed efforts to understand the human genome and the genetic roots of disease.

This is the first time that the reasonably complete genomes of two mammals, mouse and man, have become available for comparison. While the genome of a mammal even closer to the human, like the chimpanzee, may someday be decoded, the mouse is both genetically close and also an ideal laboratory animal.

Man and mouse are cousins, each descended from a small mammal that split into two species toward the end of the dinosaur era. Despite 75 million years of separate evolution, only about 300 genes — 1 percent of the 30,000 possessed by the mouse — have no obvious counterpart in the human genome, according to the new analysis published in today’s issue of Nature.

A friend writes to clarify,

99% of mouse genes have a homologue does not mean that they are 99% similar. It means for 99% of human proteins, the mouse has the same protein but with a slightly different sequence.

Meanwhile, chimp lab research ended in 2011, due to lack of necessity.

And now this. From ScienceDaily:

Looking across evolutionary time and the genomic landscapes of humans and mice, an international group of researchers has found powerful clues to why certain processes and systems in the mouse — such as the immune system, metabolism and stress response — are so different from those in people. Building on years of mouse and gene regulation studies, they have developed a resource that can help scientists better understand how similarities and differences between mice and humans are written in their genomes.

Their findings — reported by the mouse ENCODE Consortium online Nov. 19, 2014 (and in print Nov. 20) in four papers in Nature and in several other publications — examine the genetic and biochemical programs involved in regulating mouse and human genomes. The scientists found that, in general, the systems that are used to control gene activity have many similarities in mice and humans, and have been conserved, or continued, through evolutionary time.

The results may offer insights into gene regulation and other systems important to mammalian biology. They also provide new information to determine when the mouse is an appropriate model to study human biology and disease, and may help to explain some of its limitations.

Limitations? So the genome is not a Lego set?

From The Scientist’s take:

Mice are widely used to model human metabolism, disease, and drug response. But results published today (November 17) in PNAS reveal widespread differences between human and mouse gene expression, both in protein-coding and noncoding genes, suggesting that understanding these disparities could help explain fundamental differences in the two species’ physiology.

Mice are widely used to model human metabolism, disease, and drug response. But results published today (November 17) in PNAS reveal widespread differences between human and mouse gene expression, both in protein-coding and noncoding genes, suggesting that understanding these disparities could help explain fundamental differences in the two species’ physiology.

Michael Snyder of Stanford University and his colleagues compared how genes are expressed in 15 different human and mouse tissues, including brain, heart, liver, and kidney. They found that gene expression patterns clustered by species rather than tissues. For example, gene expression in a mouse liver more closely resembled the patterns observed in a mouse heart than those observed in a human liver. Using data from the ENCODE and modENCODE projects, among other sources, the analysis spanned “the most tissue-diverse RNA-seq dataset to date,” the authors wrote in their paper.

Advancing knowledge is always a good thing.

But it is fair to say that the purpose of lab work with mice was not to elucidate disparities between their genome and ours. That is a subject in which taxpaying stakeholders have no more intrinsic interest than they would in the disparities between the genomes of pigs and humans. Some things we just take for granted for free.

This must impact the perceived usefulness of mouse models, as The Scientist acknowledges:

These data “guide us as to where a mouse model might be useful and where to be more cautious,” said Snyder. “A mouse and human have almost the same genes. But how we express those genes differs quite a bit.”

We will watch developments with interest.

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12 Replies to “Mouse gene expression reveals “widespread differences” from humans

  1. 1
    bornagain77 says:

    Podcast: Richard Sternberg – ” On Human Origins: Is Our Genome Full of Junk DNA? Part 3″
    http://intelligentdesign.podom.....4_33-08_00

    here is part 1 of the podcast:
    http://www.discovery.org/multi.....-junk-dna/

    Richard Sternberg PhD – podcast – On Human Origins: Is Our Genome Full of Junk DNA? Part 2. (Major Differences in higher level chromosome spatial organization)
    5:30 minute mark: “Basically the dolphin genome is almost wholly identical to the human genome,, yet no one would argue that bottle-nose dolphins are our sister species”
    http://www.discovery.org/multi.....-dna-pt-2/

  2. 2
    humbled says:

    “Man and mouse are cousins, each descended from a small mammal that split into two species toward the end of the dinosaur era. Despite 75 million years of separate evolution”

    Oh man. What a load of bollocks.

  3. 3
    ppolish says:

    Common Creator makes more sense than Common Descent. Common Descent makes some sense, but Common Creator nails it all.

  4. 4
    Me_Think says:

    ppolish @ 3
    Yes. ID should clearly state that the ID agent is omnipotent. I don’t know why IDer are afraid to go beyond ‘ID just detects design and does nothing else’ stance.
    As it stands now, ID offers no mechanism, no sense of ID agent (if omnipotent) or thousands of non-omnipotent ID agents.No alternate mechanisms is being debated. How is ID theory any different from just CSI ?

  5. 5
    bornagain77 says:

    Of note: The mouse is not enough – February 2011
    Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.”
    http://www.the-scientist.com/news/display/57986/

    What scientific idea is ready for retirement? – Mouse Models
    Excerpt: A recent scientific paper showed that all 150 drugs tested at the cost of billions of dollars in human trials of sepsis failed because the drugs had been developed using mice. Unfortunately, what looks like sepsis in mice turned out to be very different than what sepsis is in humans. Coverage of this study by Gina Kolata in the New York Times incited a heated response from within the biomedical research community.
    AZRA RAZA – Professor of medicine and director of the MDS Centre, Columbia University, New York
    http://www.theguardian.com/sci.....t-edge-org

    Animal Testing Is Bad Science: Point/Counterpoint
    Excerpt: The only reason people are under the misconception that animal experiments help humans is because the media, experimenters, universities and lobbying groups exaggerate the potential of animal experiments to lead to new cures and the role they have played in past medical advances.,,,
    The Food and Drug Administration (FDA) has noted that 92 percent of all drugs that are shown to be safe and effective in animal tests fail in human trials because they don’t work or are dangerous.,,,
    Physiological reactions to drugs vary enormously from species to species. Penicillin kills guinea pigs but is inactive in rabbits; aspirin kills cats and causes birth defects in rats, mice, guinea pigs, dogs, and monkeys; and morphine, a depressant in humans, stimulates goats, cats, and horses.
    http://www.peta.org/issues/ani.....ience.aspx

  6. 6
    Andre says:

    This is a lie ask Keith S the people that wrote these papers are creationists. … ON is a fact and a trillion times better explanation for unguided evolution. Ask him

  7. 7
    Joe says:

    Me_Think- You are confused, as usual, as ID is about the detection AND STUDY of intelligent design in nature. And guess what? That is the only possible way to scientifically address those other questions. Had you any knowledge of how science operates you would have known that.

  8. 8
    Me_Think says:

    Joe @ 7

    You are confused, as usual, as ID is about the detection AND STUDY of intelligent design in nature.

    No Joe, you are confused – ID only detects design using CSI or whatever – dFSCI etc) Period. No design agent. No mechanism. Nothing.Nada. Just.if.design.is.above.certain.bits.that’s.it.

  9. 9
    Silver Asiatic says:

    Me_Think @ 4

    I don’t know why IDer are afraid to go beyond ‘ID just detects design and does nothing else’ stance.

    It’s not a question of being afraid. There are limits to what empirical science can detect. Agreed, right?

    When the ID inference is the best explanation of the obervation, then the conclusion is that there is a designer.

    Do you accept that natural laws, for example, could have been designed by an intelligent agent?

  10. 10
    Mung says:

    Me_Think:

    How is ID theory any different from just CSI?

    How is communications theory any different from just SMI?

    How is information theory any different from just SMI?

  11. 11
    Silver Asiatic says:

    How is forensics any different than evidence?

    How is decryption any different than code?

    There’s also a thread on non-probabilistic evidence in support of ID.

    I believe cosmological fine-tuning arguments do not rely on CSI either.

  12. 12
    lifepsy says:

    More evidence of cherry-picking and special pleading from the evolutionary “homology” argument.

    They find one level of similarity and tout it as “homology” and evidence of common ancestry, then when substantial differences abound on other levels of the same trait, such as developmental pathways, they ignore the implications… or more generally they are completely oblivious to them.

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