Human genome further unravelled ('Junk' DNA not so junky after all).

BBC ^ | Thursday, June 14, 2007

[Jedi Master Pikachu]

The researchers hope to scale the work up to the whole of the genome

A close-up view of the human genome has revealed its innermost workings to be far more complex than first thought.

The study, which was carried out on just 1% of our DNA code, challenges the view that genes are the main players in driving our biochemistry.

Instead, it suggests genes, so called junk DNA and other elements, together weave an intricate control network.

The work, published in the journals Nature and Genome Research, is to be scaled up to the rest of the genome.

Views transformed

The Encyclopaedia of DNA Elements (Encode) study was a collaborative effort between 80 organisations from around the world.

It has been described as the next step on from the Human Genome Project, which provided the sequence for all of the DNA that makes up the human species' biochemical "book of life".

We are now seeing the majority of the rest of the genome is active to some extent Tim Hubbard, Sanger Institute

Ewan Birney, from the European Molecular Biology Laboratory's European Bioinformatics Institute, led Encode's analysis effort. He told the BBC: "The Human Genome Project gave us the letters of the genome, but not a great deal of understanding. The Encode project tries to understand the genome."

The researchers focussed on 1% of the human genome sequence, carrying out 80 different types of experiments that generated more than 600 million data points.

The surprising results, explained Tim Hubbard from the Wellcome Trust Sanger Institute, "transform our view of the genome fabric".

THE DNA MOLECULE The double-stranded DNA molecule - wound in a helix - is held together by four chemical components called bases Adenine (A) bonds with thymine (T); cytosine(C) bonds with guanine (G) Groupings of these "letters" form the "code of life"; a code that is very nearly universal to all Earth's organisms Written in the DNA are genes which cells use as starting templates to make proteins; these sophisticated molecules build and maintain our bodies

Previously, genome activity was thought of in terms of the 22,000 genes that make proteins - the functional building blocks in our cells - along with patches of DNA that control, or regulate, the genes.

The other 97% or so of the genome was said to be made up of "junk" DNA - so called because it had no known biological function.

However, junk DNA may soon need a new moniker.

Dr Hubbard said: "We are now seeing the majority of the rest of the genome is active to some extent."

He explained that the study had found junk DNA was being transcribed, or copied, into RNA - an active molecule that relays information from DNA to the cellular machinery.

He added: "This is a remarkable finding, since most prior research suggested only a fraction of the genome was transcribed."

'Complex picture'

Dr Birney added that many of the RNA molecules were copying overlapping sequences of DNA.

He said: "The genome looks like it is far more of a network of RNA transcripts that are all collaborating together. Some go off and make proteins; [and] quite a few, although we know they are there, we really do not have a good understanding of what they do.

"This leads to a much more complex picture."

The researchers now hope to scale up their efforts to look at the other 99% of the genome.

By finding out more about its workings, scientists hope to have a better understanding of the mechanics of certain diseases.

Dr Birney said that in the future, they would hope to combine their findings with some of the larger studies that are currently investigating genes known to be associated with particular conditions.

He added: "As we understand these things better, we get better insight into disease, and when we get better insight into disease, we get better insight into diagnosis and the chances to create new drugs."

[<1/1,000,000th%]

It applies liberally in the sciences.

[onedoug]

ping

Francis S Collins, The Language Of God. He is/was head of the Human Genome Project.

[AFreeBird]

Yea, that analogy works too. But since I’m not a programmer per se, I didn’t think of it.

[El Cid]

Re: 12

He’s accusing science of being unreliable because results can change in the light of new evidence,

I read that 'even if one is a Macroevolutionist (i.e., one who rejects the notion that life was created by The Creator), it is the height of arrogance to presume that just because you don't understand the function of an organ, or gene, it must be junk'... A sensible statement - which you twist into the claim that an accusation has been made that 'science is unreliable'.

...as opposed to received religion, which never changes... unless you count that flat earth and geocentricity and all those other things.

Care to quote, from Scripture ('received' religion), the references to flat earth and geocentricity... and 'all those other things'?
I thought the geocentric model was derived from the work of the Ptolemy and Hipparchus.
If I'm not mistaken, they were not renown churchmen...But don't let that stop you...

[El Cid]

Re 13:

The way you put it, you're making it sound like the scientists and the theologists are sitting on either side of an imaginary aisle, while some mysterious force passes the answers along the central pathway.

This is similar to post #12, and my complaint/response will be similar.

All I read from the post was the statement that 'even if one was a Macroevolutionist (i.e., someone who rejects the premise that life was created by The Creator) it is still the height of arrogance to presume just because we do not understand the purpose of an organ or gene to claim that it is junk -- or a vestigial remnant'. Seems to me that you are forcing an extrapolation to some another fight...

What you're seeing here is science refining itself. That's exactly the self-correcting feedback loop that religious dogma lacks.

I don't have a big argument with this statement. Again, I don't think the post disputes this point -- the original post focused on the starting point position of the 'experts' being a bit 'skewed' (i.e, 'if I don't understand some thing's function -- it must be junk').
But I agree with your general premise: true science allows for observations to modify previous held conclusions, whereas true religion is going to be fixed upon some unchanging set of principles (be they Scriptures, 'holy books', divine revelations, Darwin's Origin of Species, Al Gore's An Iconvenient Truth, creeds, etc...).

[Ultra Sonic 007]

Consider the time is relative to the speed of light.

Consider also that time has been slowing down since the beginning of the universe.

Thus, time was faster back then.

What might have seemed to be a day back then, might be something far longer to us now, with a slower ‘c’.

Also consider that a day to God might have been something else entirely.

[CarrotAndStick]

"...just because we do not understand the purpose of an organ or gene to claim that it is junk -- or a vestigial remnant'

No argument against that from me. I hate it when people say things like the appendix is a vestigal organ, the foreskin is unnecessary, etc. Who knows what tiny function those things perform, that may affect the functioning of the body in a way that might not be immediately apparent?

Another extension would be how people pop vitamin pills in preference to foods that naturally contain them. Who knows what vitamin may have what kind of carcinogenic effect, simply because it is presented to the body in a highly unnatural, ultra-pure form, unlike how it would have been present in a natural food source? Our bodies have been adapted to take nutrients in the form it is available in nature, not in the form of pills. Recently there was some news on an association between taking vitamin pills and prostate cancer.

When things are complicated to understand, assumptions must not be made. This goes to both scientists, and theologists.

[CarrotAndStick]

Also consider that a day to God might have been something else entirely.

Duration of Brahma’s Day

One day of Brahma is of duration equivalent to 1000 mahayugas. His night is equally long. At the beginning of every day creation starts. At the end of the day all that was created merge in the Absolute and Brahma ‘sleeps’ as it were. 360 such days and nights make one year of Brahma. According to the Puranas, He has spent 50 years like this and this day is the first day in his fifty-first year!

One day of Brahma = 14 manvantaras + 15 manvantara twilights
(because there is an extra manvantara - twilight at the end of all the 14 manvantaras)

= 14 x 71 mahayugas + 15 x 4 l
= 994 mahayugas + 60 l
= 994 mahayugas + 6 mahayugas
= 1000 mahayugas
= 1000 x10 l = 4,320,000,000 human years.

Note: 1 mahayuga = 43.2 ‘seconds’ for Brahma.

THE HINDU CONCEPT OF TIME

According to Hindu religion and cosmology the flow of Time is eternal. Creation and Dissolution are only two events in a long cyclic succession of Cosmic events. There is no beginning in the past and there is no end to the future. Creation is a manifestation in concrete terms of the Absolute. Dissolution is when all the created universe merges in the Absolute. And that is when the period of non-manifestation begins. The periods of manifestation and of non-manifestation alternate. These are the days and nights of Brahma.

Brahma Himself is a manifestation of the Absolute. He has a life of 100 years in His time.

Between one kalpa (technical name for Brahma’s day) and the next, the only thing that survive are, Brahma himself (who has to be ‘brought back to memory’, by the Absolute, after his ‘sleep’ !), the vedas in their latent form and the collected aggregate of vaasanaas (imprints of actions and thoughts) of all individual souls. Just as each kalpa is followed by another kalpa with an intervening Cosmic Night, so also one Brahma is followed by another Brahma.

You see where that can lead? :^)

The 'Word of God' was supposedly presented to man in a way in which he can comprehend. Why would God want to add to the confusion by mixing His units with ours?

[r9etb]

To review the bidding, I labeled as "strawman" the following comment:

Your original comment was: "That's exactly the self-correcting feedback loop that religious dogma lacks."

To which you replied:

So once the statement that the earth is about 5000 years only, is declared, you’re implying it can be revised? If not, the statement you made declaring mine a strawman, is in fact, a strawman in its own standing.

You seem to be saying that "the Earth is about 5000 years old" is an example of an unchangeable point of religious dogma. The problem being that it's not an unchangeable point of religious dogma. If it ever was a universal point of dogma (which I doubt), it certainly isn't one now.

The strawman you erected was simply this: that religious dogma cannot change. You should perhaps read a bit of theology to understand how very wrong you are.

[neverdem]

Thanks for the link. Here's a link to the Nature article. It's free but you may have to register.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot...

[lepton]

Donald Rumsfeld was too maligned for that one—personal opinion. It actually made sense, even if oddly phrased

No offense, but that Rumsfeld comment was perfectly clear - both in the specific, and in context. The mediots (apparently including some English professors at Oxford) were simply too unacquainted with logic to understand it. Their ignorance was appalling.

[CarrotAndStick]

The strawman you erected was simply this: that religious dogma cannot change.

dog·ma(dôgm, dg-)

n. pl. dog·mas or dog·ma·ta (-m-t)

An authoritative principle, belief, or statement of ideas or opinion, especially one considered to be absolutely true.

[Dustbunny]

Very interesting.

[r9etb]

An authoritative principle, belief, or statement of ideas or opinion, especially one considered to be absolutely true.

And? If something really is absolutely true, common sense should dictate that it would be best not to change your viewpoint on it....

That said, it's simply untrue that what religion treats as "dogma" doesn't change, because it does. Seriously, pal -- go read some theology so you won't speak out of ignorance.

[mad_as_he$$]

Ok so you are the guy that puts that crap in for me to try and figure out!!!

[r9etb]

Ok so you are the guy that puts that crap in for me to try and figure out!!!

Heck no ... I don't do "elegant" code! And I use comments!

[mad_as_he$$]

lol.. comments are good!

[El Cid]

RE: 27

Agreed with your post 27.
Good comment about vitamins -- there are a lot of 'assumptions' built into the benefits of these supplements.
On the other hand, it is also difficult to get fresh food/vegetables in the cities -- so I can relate to the desire to take vitamin additives.
But you are absolutely correct that this requires one to make unproven assumptions that these additives are actually beneficial and not a detriment.

[SunkenCiv]

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