The Splicing Code
by BilboA couple of contributors have suggested that we have a thread on this article: The Splicing Code
In a paper published on May 6 in the journal Nature entitled "Deciphering the Splicing Code," a research team led by Professors Brendan Frey and Benjamin Blencowe of the University of Toronto describes how a hidden code within DNA explains one of the central mysteries of genetic research — namely how a limited number of human genes can produce a vastly greater number of genetic messages. The discovery bridges a decade-old gap between our understanding of the genome and the activity of complex processes within cells….
To figure out how living cells generate vast diversity in their genetic information, Frey and postdoctoral fellow Yoseph Barash developed a new computer-assisted biological analysis method that finds 'codewords' hidden within the genome that constitute what is referred to as a 'splicing code'. This code contains the biological rules that are used to govern how separate parts of a genetic message copied from a gene can be spliced together in different ways to produce different genetic messages (messenger RNAs). "For example, three neurexin genes can generate over 3,000 genetic messages that help control the wiring of the brain," says Frey.
"Previously, researchers couldn't predict how the genetic messages would be rearranged, or spliced, within a living cell," Frey said. "The splicing code that we discovered has been successfully used to predict how thousands of genetic messages are rearranged differently in many different tissues." Blencowe's group, including graduate student John Calarco, generated experimental data used to derive and test predictions from the code. "That the splicing code can make accurate predictions on such a large scale is a major step forward for the field," says Blencowe.
It's not clear from the article how much of this code is part of the "junk" DNA. I'm curious.
I'm adding this part of the article for later use:
"Understanding a complex biological system is like understanding a complex electronic circuit. Our team 'reverse-engineered' the splicing code using large-scale experimental data generated by the group," Frey said.
Prof. Frey has appointments to the Canadian Institute for Advanced Research and the U of T's Department of Electrical and Computer Engineering, the Banting & Best Department of Medical Research (BBDMR) and the Department of Computer Science.
May 10th, 2010 at 7:21 pm
This is the second time in my lifetime that I've witnessed the discovery of a "code within a code" in DNA. First overlapping genes, and now this. Isn't God amazing!!!
So what are the practical and theological implications of this finding?
What does this discovery tell us about the mind and methods of God?
How can we apply that knowledge to our world?
(These are the questions believing scientists should be trying to answer rather than just exclaiming – "Look… this is designed for sure!")
Comment by Daniel Smith — May 10, 2010 @ 7:21 pm
May 10th, 2010 at 8:00 pm
Hey Daniel,
I completely agree.
This newfound code in DNA reminds me of deep and intricate meaning filed prose found in great literature like Shakespeare and especially the Bible. Such a meaning intensive artifact is clearly the work of genius not just "intelligence".
One of the best books I’ve read from an ID perspective is A Meaningful World by Benjamin Wiker. It explores the characteristics of genius and how nature drips with it.
Like great literature the first level of meaning we see is elegant and easily accessible for those willing to put in the effort and also like with great literature the deeper we look at the world the deeper the meaning we find.
I fully expect to see humanity uncovering ever deeper levels of meaning for as long as we continue to look. Feel free to call that yet another distinguishing prediction of ID.
Anyway I highly recommend the book.
peace
Comment by fifth monarchy man — May 10, 2010 @ 8:00 pm
May 10th, 2010 at 9:53 pm
IMO, a code (such as described in the Nature paper) that is derived from biochemical principles is not very good news for ID. But it is consistent with the likelihood that all such "codes" in biology (such as the genetic code) have nothing more than chemistry at their cores.
Comment by Art — May 10, 2010 @ 9:53 pm
May 11th, 2010 at 6:31 am
Hi
This is my first post here. Very interesting and informative site by the way.
fifth monarchy man said:
"I fully expect to see humanity uncovering ever deeper levels of meaning for as long as we continue to look. Feel free to call that yet another distinguishing prediction of ID."
Charlie M:
I was going to reply to some comments on one of the UK's Guardian newspaper blogs but it closed before I could reply.
Then I came here and read the above comment which is in a similar vein.
Here is the gist of what I was going to say.
Every time our technology advances we have either copied from nature, as in powered flight or making paper, or we discover that nature has beaten us to it as with motors driving propulsion through a universal joint or devising a multi-layered code.
My prediction is that any new, useful technology we develop that has not been consciously inspired by nature will already have been utilized by nature. Why would unguided evolution always appear to be ahead of us in technological achievements?
This has only just come to me so if anyone has examples that they think can falsify this claim I'd be grateful if they would share them.
PS: I tried using the quick blockquotes but my post wouldn't send. I'm new to this so I've probably done something wrong.
Comment by CharlieM — May 11, 2010 @ 6:31 am
May 11th, 2010 at 9:09 am
Thanks for the link fmm.
I agree completely with this statement of yours:
I am awestruck at the depths of the mind of God whenever I learn of the intricacies of biology. We are clearly talking about an infinite mind here – one that can quite literally think of everything.
Comment by Daniel Smith — May 11, 2010 @ 9:09 am
May 11th, 2010 at 1:14 pm
[...] The splicing code In a paper published on May 6 in the journal Nature entitled "Deciphering the Splicing Code," a research team led by Professors Brendan Frey and Benjamin Blencowe of the University of Toronto describes how a hidden code within DNA explains one of the central mysteries of genetic research — namely how a limited number of human genes can produce a vastly greater number of genetic messages. The discovery bridges a decade-old gap between our understanding of the genome and the activity of complex processes within cells…. [...]
Pingback by Darwiniana » “The splicing code” — May 11, 2010 @ 1:14 pm
May 11th, 2010 at 3:14 pm
I think I'll add this part of the article to the OP, for later use:
Comment by Bilbo — May 11, 2010 @ 3:14 pm
May 11th, 2010 at 11:40 pm
Another "code" with a firm foundation in stereochemical molecular associations.
Is there any "code" in biology that is otherwise?
Comment by Arthur Hunt — May 11, 2010 @ 11:40 pm
May 12th, 2010 at 11:13 pm
Art you should read Koonin's paper on the matter, he thinks it's a weak case.
Comment by Guts — May 12, 2010 @ 11:13 pm
May 13th, 2010 at 6:46 am
Guts:
Art you should read Koonin's paper on the matter, he thinks it's a weak case.
Which paper is that?
Comment by KC — May 13, 2010 @ 6:46 am
May 13th, 2010 at 7:09 am
Unfortunately for you the alternative splicing code is not derived from biochemical principles anymore than a computer codse is dervived from electrical principles.
Do you really believe that blind molecules contain knowledge of what to splice and how to splice it?
If so you will believe anything and as such are not good at objectively assessing the data.
Comment by ID guy — May 13, 2010 @ 7:09 am
May 13th, 2010 at 11:33 am
KC,
Comment by Guts — May 13, 2010 @ 11:33 am
May 13th, 2010 at 1:12 pm
Guts,
Comment by KC — May 13, 2010 @ 1:12 pm
May 13th, 2010 at 2:19 pm
Art:
There is more to a code than chemistry or mechanics or electronics or whatever is involved in the mediation of a particular one. Illuminated letters are more than neon are they not? It's about the message folks. The theme of that message centers around biological function.
Comment by Bradford — May 13, 2010 @ 2:19 pm
May 13th, 2010 at 6:41 pm
Hey Charlie M,
Good to see you here. Your prediction reminds me of the characterization of science as “Thinking God’s thoughts after him”.
Providently today I ran across yet another example of the sort of code within a code that one often sees as the result of human genius.
In this case seemingly random unimportant details in the writings Of CS Lewis are discovered to be the result of a hidden code. Greatly enhancing the depth of meaning in the books.
I can think of no reason to expect this sort of thing to result from Darwinian process yet we see it over and over again in nature as well.
It’s not proof of design but it does make much more sense from a design perspective.
peace
Comment by fifth monarchy man — May 13, 2010 @ 6:41 pm
May 13th, 2010 at 7:26 pm
Another hidden code is discovered to be lurking in what was considered to be random noise.
My prediction is confirmed again.
Like I said nature is dripping with this stuff.
peace
Comment by fifth monarchy man — May 13, 2010 @ 7:26 pm
May 13th, 2010 at 7:49 pm
Here's a prediction I made back in 2007 while arguing with the atheists over at After the Bar Closes:
This prediction was not made because I had the science background (having only a high school level education in biology). No, it was made rather from a healthy respect for God and his ways. Sometimes having the correct philosophical view will lead you down the correct scientific pathway.
It's all connected boys! (and girls.)
Comment by Daniel Smith — May 13, 2010 @ 7:49 pm
May 13th, 2010 at 8:50 pm
You've now single-handedly bested the number of correct, illuminating predictions made by the I.D.-denialists at A.t.B.C. — a whopping zero.
Nicely done!
Comment by Jared Jammer — May 13, 2010 @ 8:50 pm
May 13th, 2010 at 9:53 pm
Way back in 2007. That's probably where these researchers picked up the idea.
Blencowe, Alternative Splicing: New Insights from Global Analyses, Cell 2006.
Modrek & Lee, A genomic view of alternative splicing, Nature Genetics 2002.
Smith, Patton & Nadal-Ginard, Alternative Splicing in the Control of Gene Expression, Annual Review of Genetics 1989.
Chow et al., An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA, Cell 1977.
Comment by Zachriel — May 13, 2010 @ 9:53 pm
May 14th, 2010 at 7:20 am
The point is Daniel was unaware of enbedded and overlaping codes at this time. His knowledge of the designer led him to expect such things.
The questions I have is
Does an acceptance of Darwinism lead one to expect such things in nature?
I can't see how it would. However I’m willing to be convinced, the floor is yours.
Why would RM filtered by NS necessarily lead to hidden codes within codes?
peace
Comment by fifth monarchy man — May 14, 2010 @ 7:20 am
May 14th, 2010 at 9:43 am
fmm writes:
This 'code' is no more 'hidden' than the chemical signature (i.e., structual 'code') that identifies retroviral insertions into the genome. Both had to wait until technology developed enough to enable us to recognize the associations. Both are simply tell-tale sequences that enable us to make certain inferences, that is, a viral insertion has occurred, or that an alternately spliced variant of a gene is likely. Both kinds of sequences are consequences of the physical structural chemistry involved, as Art pointed out.
Comment by KC — May 14, 2010 @ 9:43 am
May 14th, 2010 at 9:50 am
Art may have pointed that out but Art has not supported his claim.
IOW there isn't any evidence that any of the biological codes are reducible to matter, energy, chance and necessity.
Comment by ID guy — May 14, 2010 @ 9:50 am
May 14th, 2010 at 9:57 am
There are several responses to your question: It has been evolutionary biologists who have led the way on understanding alternative splicing. Alternative splicing lends flexibility to the evolutionary process as the original protein is unaffected. 'Codes within codes' is consistent with modern concepts of network evolution.
Comment by Zachriel — May 14, 2010 @ 9:57 am
May 14th, 2010 at 10:15 am
And not one has been able to show that blind, undirected chemical processes can produce such a thing.
But inconsistent with blind, undirected chemical processes.
Comment by ID guy — May 14, 2010 @ 10:15 am
May 14th, 2010 at 12:12 pm
Reading the atheist's delusional "explanations" of the splicing code reminds me of the saying:
"They strain out a gnat and swallow a camel."
Or this one:
"They can't see the forest for the trees."
Or perhaps:
"If it was a snake, it would've bit them."
You get the idea (though they, most likely, won't.)
Comment by Daniel Smith — May 14, 2010 @ 12:12 pm
May 14th, 2010 at 12:41 pm
Thanks KC, I had not seen that recent one. I still think the aptamer data are inconsistent (although it appears to be non-random), I will revisit whether the data in general is negative.
Comment by Guts — May 14, 2010 @ 12:41 pm
May 14th, 2010 at 6:39 pm
KC
Actually the reason we did not discover this code before is because we were not looking for it. We assumed the direct gene to protein code was all there was it was not until we discovered that often more complex organisms had fewer genes that the thought ever crossed our minds.
If on the other had we were working from a design perspective we would expect to be surprised by codes on top of codes as Daniel’s prediction proves.
Zach
That is irrelevant to my point. It was often cosmologists who believed in an eternal universe who lead the way on the big bang. The evidence lead them down that path kicking and screaming.
Is this a prediction? Do you expect to see yet more undiscovered codes?
Would you expect alien genomes to have multiple inbedded codes? If it only had one code would you conclude it did not evolve by Darwinian means?
Inquiring minds want to know.
I predict no clear answer will be forthcoming.
peace
Comment by fifth monarchy man — May 14, 2010 @ 6:39 pm
May 14th, 2010 at 8:24 pm
KC
I think a little elaboration is in order.
The Narinia Chronicles were thought to contain various elements that were more or less random and amateurish. Michael Ward’s knowledge of the designer led him to disagree. He expected to find that these elements were placed in the books for a purpose and would if understood correctly serve to point to the genius of the author.
Low and behold he discovered a hidden code that explained the supposed faulty design and to turn it into a monument to the meticulousness and superior abilities of the author.
By the same token
The Genome was thought to contain various elements that were more or less random and amateurish. Daniel Smith’s knowledge of the designer led him to disagree. He expected to find that these elements were placed in the Genome for a purpose and would if understood correctly serve to point to the genius of is author.
Low and behold a hidden code was discovered that explained the supposed faulty design and to turn it into a monument to the meticulousness and superior abilities of it‘s author.
On the other hand
The Genome was thought to contain various elements that were more or less random and amateurish. Darwinism's rejection of the designer led it to celebrate this idea (often on this forum) . It expected to find that these elements were the result of errors and inefficiencies in the evolutionary process.
Luckily contrary to the reigning paradigm a group of scientists decided to look at life as if it was designed and
Low and behold………
Quote:
"Understanding a complex biological system is like understanding a complex electronic circuit. Our team 'reverse-engineered' the splicing code using large-scale experimental data generated by the group," Frey said.
End quote:
peace
Comment by fifth monarchy man — May 14, 2010 @ 8:24 pm
May 15th, 2010 at 8:11 am
The results are consistent with and guided by evolutionary theory. Small mutational changes lead to novelty while maintaining proteomic integrity.
Xing & Lee, Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences, PNAS 2005.
Boue, Letunic & Bork, Alternative splicing and evolution, Bioessays 2003.
Kondrashov & Koonin, Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences, Trends Genetics 2003.
Andreadis, Gallego & Nadal-Ginard, Generation of Protein Isoform Diversity by Alternative Splicing: Mechanistic and Biological Implications, Annual Review of Cell Biology 1987.
And so on.
It's more properly called a model. The first-order prediction is a power-law distribution of relationships.
There is almost certainly more underlying complexity than is known at present.
As we expect alien genomes to be based on much the same chemistry, we would expect similar network evolution.
Comment by Zachriel — May 15, 2010 @ 8:11 am
May 15th, 2010 at 12:51 pm
me before:
Zach
I rest my case
Comment by fifth monarchy man — May 15, 2010 @ 12:51 pm
May 15th, 2010 at 6:40 pm
The answer was quite specific. Which aspect do you find unclear?
Comment by Zachriel — May 15, 2010 @ 6:40 pm
May 15th, 2010 at 6:51 pm
Hey an ID prediction from "The Privileged Planet".
Thanks Zach!
Comment by ID guy — May 15, 2010 @ 6:51 pm
May 15th, 2010 at 7:26 pm
A person concerned with clarity tends to answer yes or no questions with yes or no.
I asked three questions each of which could easily be answered with yes or no.That's three words.
You used just less than 50 and I'm still not sure what you would expect to find in alien life
Comment by fifth monarchy man — May 15, 2010 @ 7:26 pm
May 15th, 2010 at 7:40 pm
I'm also unsure if you expect to find more codes in the genome.
For you Zach it's par for the course
Comment by fifth monarchy man — May 15, 2010 @ 7:40 pm
May 15th, 2010 at 9:42 pm
A code is normally construed as a correspondence between sets. If that was your intended meaning, then the given answers were appropriate. You might try to understand those answers, or ask for clarification if you are still confused.
Alien life is posited to resemble terrestrial life, especially with regards to network evolution.
Comment by Zachriel — May 15, 2010 @ 9:42 pm
May 15th, 2010 at 10:36 pm
Zach is it that hard to just say yes or no?
you might try and give a clear answers instead of always playing word games. Try something like this this.
see how easy that was
peace
Alien life is posited to resemble terrestrial life, especially with regards to network evolution.
Do you expect at least two codes? multiple codes within codes? No expectations one way or the other?
Comment by fifth monarchy man — May 15, 2010 @ 10:36 pm
May 16th, 2010 at 7:11 am
When you use imprecise terms, answers may require elaboration. In the context of the paper, Deciphering the splicing code, a 'code' is assembled by extracting RNA features resulting in a more predictive set of relationships than previous, simpler splicing codes.
We expect a hierarchy of relationships, similar to terrestrial life. It is doubtful that the depths of those complex relationships has been fully plumbed in terrestrial life.
Comment by Zachriel — May 16, 2010 @ 7:11 am
May 16th, 2010 at 9:32 am
Fine, give a clear answer and then elaborate on it. Instead you gave your usual response which is all elaboration and no answer.
Even after you are shown what a clear answer looks like still can't bring yourself to give one. It happens like that here over and over.
That is why I can make the prediction I did and why I can rest my case.
peace
Comment by fifth monarchy man — May 16, 2010 @ 9:32 am
May 16th, 2010 at 9:33 am
Zachriel,
There isn't any evidence that blind, undirected chemical processes can produce a communicating code.
Fifth Monarchy Man- Zachriel is a poseur whose only purpose is to muddy the waters.
He is a confused individual with too much time on his hands.
Comment by ID guy — May 16, 2010 @ 9:33 am
May 17th, 2010 at 11:33 am
Deciphering the splicing code required studying and understanding complex interactions. A computer algorithm and a high-throughput sensing of mRNA expression were used to understand them. It has been demonstrated that a higher number of introns per gene is connected with a higher level of AS, in vertebrates. It was also demonstrated that AS is a link to phenotypic complexity. Evolution is much more sophisticated than we can imagine.
Comment by Guts — May 17, 2010 @ 11:33 am