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Eric H. Davidson (1937–2015), and the function of “junk DNA”

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From obit:

Inherent in the idea of gene regulatory networks was the concept that genome sequences that provided information about how genes should be expressed would be as important as the genome sequences that coded for the proteins themselves. Although non-protein-coding DNA was long considered to be “junk,” Davidson recognized that the key regulatory code resided in this genetic material. In 2006, Davidson co-led a group of 240 researchers from more than 70 institutions that sequenced the purple sea urchin’s genome. In 2008, a consortium of institutions led by Davidson’s lab characterized the 23,000 genes of that genome.

In parallel, the Davidson group systematically created a comprehensive functional testing strategy to detect all of the control connections between the genes involved in the key events in the earliest stages of sea urchin embryo development, and to determine how the activity of each gene affected the ability of every other gene in that part of the embryo to be expressed. The network model, first described in 2002 and elucidated and extended over the next 13 years, revealed that the regulatory networks governing high-level processes such as the formation of a specific type of cell are built from gene circuits that can have striking similarities even when the identities of the genes in the circuits are different. These circuits can be viewed as a few dozen types of modules that perform specific functions. Because similar modular systems appear to exist in flies, frogs, chicks, mice, and zebrafish, they may be a universal feature of higher organisms.More.

Requiescat in lucem pacis aeternitatis

See also: The Myth of Junk DNA

6 Replies to “Eric H. Davidson (1937–2015), and the function of “junk DNA”

  1. 1
    Larry Moran says:

    “Although non-protein-coding DNA was long considered to be “junk,” Davidson recognized that the key regulatory code resided in this genetic material.”

    It’s a shame that the person who wrote this didn’t understand the science and wasn’t aware of the possibility that people like Denyse O’Leary would be happy to misinterpret.

    For the record, no knowledgeable scientist ever believed that all noncoding DNA was junk DNA. We’ve known about the existence of regulatory noncoding DNA since the 1960s.

    It’s true that Roy Britten and Eric Davidson proposed in 1969 and 1971 that a large percentage of the DNA outside of genes would prove to be involved in regulation. They were aware of the fact that much of this excess DNA consists of repetitive sequences that don’t look like they are functional but they suggested that these repetitive sequences could be involved in the evolution of developmental regulation. They opposed the idea that most of our genome is junk.

    Subsequent work has not supported their idea. Most knowledgeable scientists now agree that about 50% of our genome consists of bits and pieces of broken transposons (repetitive DNA) and hardly any of this has a biological function. It’s almost all junk except for a few bits that have evolved a secondary function. The known functional bits account for less than 0.1% of the genome.

  2. 2
    Andre says:

    Translating Prof Moran’s soapbox above…

    “You don’t understand evolution but I do, trust me, I know better don’t question my authority!!!”

    Then he tells us that the once known figure of 90% junk is now only 50% junk but that the 50% is just about 100% junk.

    He also takes a stab at Denyse for hitting a nerve.

    Then he tells us it evolved, how he does not say, we must just trust his authority, that it is so because he knows better because we just don’t understand.

    How did I do Prof Moran?

  3. 3
    Virgil Cain says:

    Larry Moran:

    We’ve known about the existence of regulatory noncoding DNA since the 1960s.

    We’ve known that undirected evolution cannot account for regulatory non-coding DNA since the ’60s. Coincidence? I think not…

  4. 4
    Dr JDD says:

    If we are still on this earth in 50 year’s time people will be laughing about how wrong scientists were on transposons.

  5. 5
    bornagain77 says:

    Dr. Moran claims that “It’s almost all junk except for a few bits that have evolved a secondary function. The known functional bits account for less than 0.1% of the genome.”

    Here is a response, by a ENCODE scientist, to Dr. Moran’s neo-Darwinian claim that most of the genome must be junk :

    “That said, I can’t help but notice a trend: over time, “junk DNA” is disappearing. Good riddance: this is just a term for DNA that we don’t have any guesses about its function. The more we learn about the genome, the more functions we uncover, thus fewer unknowns and a more seemingly “useful” genome. Where will it end? I have no idea,,,”
    http://www.reddit.com/r/asksci.....of/c667vqi

    Dr. Sternberg also begs to differ from Dr. Moran

    Podcast: Richard Sternberg PhD – ” On Human Origins: Is Our Genome Full of Junk DNA? part 1
    http://www.discovery.org/multi.....-junk-dna/

    Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 2 (Major “Species Specific” Differences in higher level chromosome spatial organization)
    http://www.discovery.org/multi.....-dna-pt-2/

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

    Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 4
    http://www.discovery.org/multi.....-dna-pt-4/

    In the following podcast, Dr. Sternberg’s emphasis is on ENCODE research, and how that research overturned the ‘central’ importance of the gene as a unit of inheritance. As well he reflects on how that loss of the term ‘gene’ as an accurate description in biology completely undermines the modern synthesis, (i.e. neo-Darwinism) as a coherent explanation for biological life.

    Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 5
    http://www.discovery.org/multi.....-dna-pt-5/

    As to repetitive DNA in particular,

    Safeguarding genome integrity through extraordinary DNA repair – April, 2011
    Excerpt: Unlike euchromatin, where most of an organism’s genes reside and where most DNA consists of long, unrepetitive sequences of base pairs, DNA in heterochromatin consists mostly of short repeated sequences that don’t code for proteins; indeed, heterochromatin was long regarded as containing mostly “junk” DNA.
    Heterochromatin is now known to be anything but junk, playing a crucial role in organizing chromosomes and maintaining their integrity during cell division. It is concentrated near centromeres, where chromatids are in closest contact, which are required to transmit chromosomes from one generation to the next. Maintaining heterochromatin structure is necessary to the normal growth and functions of cells and organisms.
    http://phys.org/news/2011-04-s.....y-dna.html

    Sternberg, R. v. & J. A. Shapiro (2005). How repeated retroelements format genome function. Cytogenet. Genome Res. 110: 108-116.
    Excerpt: Employing an information science model, the “functionalist” perspective on repetitive DNA leads to new ways of thinking about the systemic organization of cellular genomes and provides several novel possibilities involving retroelements in evolutionarily significant genome reorganization.
    http://www.ncbi.nlm.nih.gov/pubmed/16093662

    Shapiro comments here:

    Bob Dylan, ENCODE and Evolutionary Theory: The Times They Are A-Changin’ – James Shapiro – Sept. 12, 2012
    Excerpt: In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled “Why repetitive DNA is essential to genome function.”
    These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for “guilt-by-association” claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written.
    The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful.
    http://www.huffingtonpost.com/.....73935.html

    “Most of the mammalian genome is transcribed. This generates a vast repertoire of transcripts that includes protein-coding messenger RNAs, long non-coding RNAs (lncRNAs) and repetitive sequences, such as SINEs (short interspersed nuclear elements). A large percentage of ncRNAs are nuclear-enriched with unknown function. Antisense lncRNAs may form sense-antisense pairs by pairing with a protein-coding gene on the opposite strand to regulate epigenetic silencing, transcription and mRNA stability.
    (Carrieri et al., “Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat,” Nature (2012), doi:10.1038/nature11508 )

  6. 6
    Mung says:

    For the record, no knowledgeable scientist ever believed that all noncoding DNA was junk DNA.

    So?

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