Largest Genome Ever Sequenced - and it's 82% Junk

by cofty 37 Replies latest social current

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  OUTLAW

  You're welcome, KW. Actually, the "we use only 10% of our brain" nonsense has been promoted by WT,

  but a JW will never verify that info. one way or the other. If it's in WT literature, it must be true.....ADCMS

  ......The WBT$ encourages JW`s to only use 10% of their brain..

  .

  .................That Way They Don`t Ask Questions..And.................

  ...........They Don`t Sh*t Their Pants In The Field Service...................

  ...................

  .

  ......I only use 5% of my Brain..

  .............I Just Sh*T My Pants...........So Did I LOL!!..

  ...................

  ................................................................................. ...OUTLAW
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  Vidqun

  Cofty, interesting articles. I personally don't like the term "junk" DNA. It's called "junk" because we don't know why it's there. Is this not a case of DNA cell memory? Trees have longer lifespans than humans, so it woud make sense that more information is stored in their genomes.
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  cofty

  The term "junk" DNA shold not be used without explanation. It isn't inaccurate and some top science writers and researchers still don't hesistate to use it. Nick Lane, Sean B. Carroll and PZ Myers for example.

  It is junk in as far as it got into the genome through accidental gene copying and other parasitic methods. It is code that is hitching a free ride and contributing nothing in return.

  Having said that, as explained above, some of it - but by no means all - can be pressed into service through later beneficial mutations.

  The VAST majority of it remains junk.

  Vidqun - We do know exactly how most of it got there. No information is added to a genome during the lifespan of an organism, there is no connection with longevity. I don't know what you mean by "DNA cell memory"?

  A large percentage of our own genome is "junk". LINES, SINES, ALU elements, pseudogenes etc.

  There is approx 40% still unkown which may turn out to have function or may be yet more junk. Of huge significance was the discovery of genetic switches - regulatory sequences - that control the activaton of particular genes in specific cells. The way the cascade of switches operate is fascinating. It also answers how mutation and natural selection can account for the huge variety of life.
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  Vidqun

  Quite a few studies have indicated that "memory" is retained by genes and is then passed on to their offspring. Here’s a few thoughts from an article published in the journal Science. They worked with genetic switches:

  Epigenetics concerns the inheritance of gene expression through the passing on of DNA. A chemical tag, known as an epigenetic mark, is attached to DNA that subsequently tells a cell to use or ignore a particular gene. The most common of these marks is known as a methyl group, an alkyl derived from methane. When it binds itself to DNA, by a process called methylation, it prevents protein from being added to the gene, and as a result, turns it off. Epigenetic marks are usually erased between each generation due to the way in which primordial gene cells (PGCs, precursors to sperm and eggs) restructure the genetic information ready for the next generation.

  The Cambridge study, led by Jamie Hackett, discovered how the methylation marks were erased by the PGCs, resetting them for the next generation. As the PGCs divided, they broke down the methylation marks and diluted them with each divide. The study claims that such an understanding of epigenetic resetting "could be exploited to deal with adult diseases linked with an accumulation of aberrant epigenetic marks, such as cancers, or in 'rejuvenating' aged cells."

  This is important because aberrant methylation could accumulate at genes during a lifetime in response to environmental factors, such as chemical exposure or nutrition, and can cause abnormal use of genes, leading to disease. If these marks are then inherited by offspring, their genes could also be affected.
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  cofty

  Yes epigenetics is a fascinating field. I am reading a book on the topic right now - "The Epigenetics Revolution" by Nesssa Carey.

  Its amazing how environmental factors during development can effect genetic switching.

  None of the epigentic effects add letters to the code however.
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  Vidqun

  Here's a Time-article on Junk DNA which is not junk at all:

  Junk DNA — Not So Useless After All

  Researchers report on a new revelation about the human genome: it’s full of active, functioning DNA, and it's a lot more complex than we ever thought

  Junk. Barren. Non-functioning. Dark matter. That’s how scientists had described the 98% of human genome that lies between our 21,000 genes, ever since our DNA was first sequenced about a decade ago. The disappointment in those descriptors was intentional and palpable.

  It had been believed that the human genome — the underpinnings of the blueprint for the talking, empire-building, socially evolved species that we are — would be stuffed with sophisticated genes, coding for critical proteins of unparalleled complexity. But when all was said and done, and the Human Genome Project finally determined the entire sequence of our DNA in 2001, researchers found that the 3 billion base pairs that comprised our mere 21,000 genes made up a paltry 2% of the entire genome. The rest, geneticists acknowledged with unconcealed embarrassment, was an apparent biological wasteland.

  But it turns out they were wrong. In an impressive series of more than 30 papers published in several journals, including Nature, Genome Research, Genome Biology, Science and Cell, scientists now report that these vast stretches of seeming “junk” DNA are actually the seat of crucial gene-controlling activity — changes that contribute to hundreds of common diseases. The new data come from the Encyclopaedia of DNA Elements project, or ENCODE, a $123 million endeavor begun by the National Human Genome Research Institute (NHGRI) in 2003, which includes 442 scientists in 32 labs around the world.
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  cofty

  That’s how scientists had described the 98% of human genome...

  Yes its a very long time since anybody thought 98% was junk. As I said above some of our non-coding DNA turned out to be genetic switches. Having said that a large part of our genome is "junk".

  If anybody doubts the reality of junk DNA they have to tell us why 82% of the pine tree's genome is repitition.

  Here is a lecture by developmental biologist PZ Myers on the topic...

  ...
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  Vidqun

  Transposons or “jumping genes”, earlier viewed as "junk":

  Later researchers have found similar results—that TEs can influence gene transcription—in other species, such as fruit flies, morning glory flowers, and (vindicating McClintock's suspicions) maize (Slotkin & Martienssen, 2007). Moreover, in primates, scientists have identified a SINE known as Alu that seems to play an important role in gene regulation and evolution. These new discoveries are prompting scientists to think twice about dismissing such a large portion of the genome as nothing but "junk."

  Recently scientists have established that the older the man, the greater the chance that his children will be born with abnormalities. So, some of his gene sequences are skipped, creating mutated strands. Contrary to de novo mutations which occur during cell division, inherited gene mutations are transferred at an equal rate by the father and mother, are more common and thus more commonly responsible for disease. Scientists believe that both inherited and new mutations are responsible for diseases like autism and schizophrenia, but have not worked out the ratio of blame. On the positive side, de novo gene mutations are a necessary element, allowing us to adapt to our changing environment.

  In some cases DNA sequences are duplicated, e.g. men with XYY chromosomes. So letters to the code are constantly being added or subtracted. Certainly, similar processes would be taking place in the DNA of trees and plants.

  Your arrogant (but very humorous and crude) scientist will obviously not benefit from above mentioned research, because he has made his mind up that all inactive DNA ("the white stuff") is junk. By the way, the coding of proteins by m-RNA is a separate process. Because m-RNA doesn't use the "white bits," (e.g., transposons or "jumping genes") does that mean it should all be classified as junk? I call it bad science.
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  cofty

  Vidqun - If you read what I wrote and what you wrote/quoted/paraphrased you will see that there is no contradiction whatsoever.

  The "arrogant scientist" you refer to is a developmental biologist who knows more about the role of regulatory DNA than you or I will ever know.

  You still have to explain why a tree needs 7 times as much DNA as a far more complex human and what you think that has to do with a tree's longevity.
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  snare&racket

  my goodness religious people are so fragile.....

  There is context to this terminology Vid, we mentioned the usefulness of the junk dna almost immediatly this thread started. You can recycle a used plastic coke bottle, but it is still 'junk'.

  It bothers you because you think this fact contributes to proving your perception of god to be wrong, the perfect designer. Tough shit. You can't go around telling people what parts of life offend you or you dislike because of its implication to you, grow up and move on. I have heard this junk dna nonsense several times by ignorant stubborn religious people and it is so annoying.

  We don't need our appendix, but of course it does something, it is living tissue, a part of the intestine...so religious people love to copy and paste uses for vistigial, useless organs, because the implication bothers them.

  It is time to grow up....... there is a region of junk dna, garbage....but it can become useful. A mutation is a mistake, an error, but it can become useful,mthat is evolution. But junk is still junk, an error is still an error and useless tissue is still useless.

  snare

  P.s......to be fair PZ myers is a bit of a dick....but his data is the data...his evidence the evidence. His personality is insignificant.