Life under the microscope

[sp1214]

The fairly recent dicovery that within our DNA lies a book of instructions and text not disimilar from a work of literature. Statistical analysis of the non gene coding (junk dna) proves this. See this abstract:

Too uniform and patternedThe answers to the question of "junk" DNA have been coming in for years, and we now know that the "junk" is not really junk. Since "junk" DNA is not really junk, from now on I will call it "non-coding" DNA. Let's first look at some of the early studies which indicated that there was some design behind the non-coding DNA. Initial and subsequent studies showed there were long areas of non-coding DNA which contained palindromes, thus maintaining symmetry between complementary strands (2). Other studies, examining large regions of genomes, using statistical techniques borrowed from linguistics, have shown patterns in the non-coding DNA similar to that seen in human languages (3). For example, when you take human language texts and create a histogram plotting the log of the frequency of occurrence of words against the log of the rank, the resulting plot is always linear with a slope of -1 for every human language. Likewise, when you perform the same plot for coding and non-coding DNA, the plot for the non-coding DNA exhibits a nearly perfect linear relationship (much better than that seen for the coding regions of DNA). The purpose or function of this "DNA language" was not determined. Another study showed that DNA contains large areas with unexplained patterns (4). Such patterns could not be the result of random chance as stated by Dr. H. Eugene Stanley (Boston University), "it is almost incredible that the occupant of one site on a gene would somehow influence which nucleotide shows up even 100,000 bases away

Who are what is supposed to read this text?

[Clanad]

Proteins... for which DNA provides coding for assemblage ...

[123everton]

An interesting question.
I can't say I understand it entirely, but I think your alluding towards inteligent design (so it should be quite a lively thread) I believe in inteligent design, but I wonder if the techniques utilised in this examination are valid.
Linguistic sequencing deals in language not chemistry.
Scientists rarely agree on anything, a bit like some religionists...

[jake-the-peg]

Whoever wrote it really needs a course in writing readable English!

Where did you get it from?

The thing is large amounts of our DNA appear to have no purpose and are sometimes named Junk or Non-coding.

This is a bit of an issue for creationists in the same way that vestigal organs are ( those who've lost their purpose
through evolution).
Examples here:
http://en.wikipedia.org/wiki/Human_vestigialit y

I think someone ought to point out them that Dr H Eugene Stanley used the word almost and that that the universe is full of almost incredible things.

[Clanad]

Not wishing to be viewed as a Luddite on such a fine spring morning here in the U.S., it is important to understand that, whether one is a proponent of intelligent design or not should not dissuade one from understanding that current science clearly indiactes that there is very little if any "junk DNA". The article clearly relates to the understanding that DNA previously thought to have no purpose actually has an important purpose in coding proteins and RNA sequences...
Hence, "In a group paper published in the June 14 issue of Nature and in 28 companion papers published in the June issue of Genome Research, the ENCyclopedia Of DNA Elements (ENCODE) consortium, which is organized by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), reported results of its exhaustive, four-year effort to build a parts list of all biologically functional elements in 1 percent of the human genome. Carried out by 35 groups from 80 organizations around the world, the research served as a pilot to test the feasibility of a full-scale initiative to produce a comprehensive catalog of all components of the human genome crucial for biological function.

"...The ENCODE consortium�s major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active. )Source: NHGRI�s Genome Technology Branch)

The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. (Ibid)...

[jake-the-peg]

That makes it difficult of course to understand the "C-value paradox"
http://en.wikipedia.org/wiki/C-value_paradox

Why does it take 40 times as much DNA to code for a salamander as it does for a human if the salamander has no Junk DNA?

Mind you that reference only relates to human DNA anyway doesn't it Clanad?

[Clanad]

That's an astute observation, jake, but somewhat dated... In fact the term "C-Value paradox" is undergoing evolution (no pun intended) or more accurately a metamorphosis, in it's application, definition and even the term itself.
Richard Sternberg and James A. Shapiro wrote recently that "one day, we will think of what used to be called 'junk DNA' as a critical component of truly 'expert' cellular control regimes" ("How Repeated Retroelements format genome function," Cytogenetic and Genome Research 110:108�116 [2005]).
In article (actually a thesis) entitiled "Evolutionary Computation and the C-value Paradox", biologist Sean Luke, of George Mason University explains "...why do some �complex� organisms have few genes while
some �simple� organisms have many?" ... (from a footnote) "...As the C-value Paradox is not a �paradox� any more per se, Gregory has suggested using the term C-value Enigma instead.
Since then some junk DNA has been found to serve one
purpose or another in the genome, so at least part of it may
not be junk after all. At any rate, the term �junk� is falling
out of favor..."
Finally, from a thesis authored by Margaret Beaton and Thomas Cavalier-Smith, published by the Royal Society states "... Furthermore, the present lack of significant amounts of nucleomorph secondary DNA confirms that selection can readily eliminate functionless nuclear DNA, refuting 'selfish' and 'junk' theories of secondary DNA...", "...The skeletal DNA theory explains why nuclear genome size increases with cell volume and, using new evidence on nucleomorph gene functions, why nucleomorph genomes do not"...

[jake-the-peg]

Excuse the shallowness of my knowledge, I'm not a biologist.

Exactly how does that require 40 times as much DNA to make a salamander as a human?

Surely you're not arguing that it a larger cell is more complex?

A frog egg cell is enormous comared to a human egg cell

[sp1214]

Maybe the human DNA is much more efficient than a Salamanders. For instance the virus phage has IX174 has only 8 genes and a total of nearly 6000 letters but is able to code for the genes by altering the reading frame. ie there are genes coded within genes. As ATG starts the gene then ATG ... ... ... .AT G.. etc.

But putting this question into the realm of a creationist then its obvious the genetic code is designed as a human would specify a subject in literature. We are made in God's image so therefore you expect the similarity.

[Clanad]

Neither am I a biologist by training, jake... however, you are prime example of the fact that an intelligent layman can read the data, opinions and state-of-the-art revisiting of previously thought-to-be-true experimentation and thereby derive your own conclusions. I think you're selling yourself short concerning not being a biologist. In discussions of this nature, although we often disagree, you've adequately presented and defended your position(s) on a number of subjects that you have, obviously, well educated yourself..
I'm the first to agree that there's are tremendously large areas of genetics that are, even ow, not well understood. I submit only, that DNA previously thought to be "junk" by definition, is now known to have important function. I also submit that, in the future, additional information will probably further define DNA's tasks so as to eliminate, probably in total, the moniker of "junk" or "useless"... Thanks for the repartee...

[sp1214]

You are right Clanad, its no longer called Junk DNA and is found to have other yet unknown uses although stabs at it have been made. They say this is the future for any aspiring biologist. Gene study by comparison must be fairly dull as making proteins could be classed as engineering whereas deciphering, designing and the function must be more exciting and which will ultimately lead to the mind of god.

No intelligent person could ever believe that life was an accident. Its the work of a very supreme artist.

[sp1214]

Returning to my question about the distribution of 'junk dna' coding when this was plotted out on a histogram it obeyed the same laws in the distribution of words in any language whether it be English, German, French or any other and suggested by Zipf's Law.

http://en.wikipedia.org/wiki/Zipf's_law

In English the word 'the' will rank highly because it is used often whereas a word that is used less often in text will rank lower down the list.
The same applies to this 'junk dna' coding.