…and this is a 
We miss something important when we just look at the genome as a string of nucleotides with scattered bits that will get translated into proteins — we miss the fact that the genome is a dynamically modified and expressed sequence, with patterns of activity in the living cell that are not readily discerned in a simple series of As, Ts, Gs, and Cs. What we can't see very well are gene regulatory networks (GRNs), the interlinked sets of genes that are regulated in a coordinated fashion in cells and tissues.
What this means is that if you look within a specific cell type at a specific gene, its state, whether off or on, will be correlated in a coherent way with a set of other genes. Look in a developing muscle cell, for instance, and you'll typically find a gene called MyoD is switched on, and also other genes, like Myf5 and myogenin. Look further, and you'll find others like C-jun and cyclin-dependent kinase 4, that also have their activity modulated in predictable ways. And when we start poking around experimentally, we discover that the relationships are often directly causal, with certain gene products binding to and modifying the expression of other genes.
Imagine that, instead of scanning a dead series of nucleotides to find genes, we were able to go fishing in the living cell and pull up a gene of interest, and we then also pull up all the genes to which it is linked by regulatory processes — catch one, and you'd pull up a whole collection of genes from scattered places in the genome, the gene regulatory network. GRNs are particularly interesting in studies of questions about phenotype, because they, not single genes, are actually the fundamental unit of the cell and tissue type. What makes a liver isn't one gene, but a whole suite of coordinated genes.
How do we go fishing for GRNs? It isn't trivial. One way is to focus on those single genes and do detailed studies of each, tracking levels of expression over time and space within the organism. Another is to use something like a microarray to sample a lot of genes in one tissue all at once, and ask which are up-regulated and which are down-regulated. Another is to look at epistasis directly, tinkering with one gene or its product genetically or biochemically, and asking what happens to the other genes in the genome. This is all a lot of work, and it's ongoing…but we don't have an automated shortcut to zip through a whole genome and identify all the connections between the genes.
There are some hints, though — conserved spots in the genome that are not part of the coding sequence of a gene, but are part of the regulatory control region. Here's an example of a plot of conserved sequences for one gene, SALL3. Each line is a comparison of the sequence between two species: H/F compares human to the fish, fugu; M/F compares mouse to fugu; and C/F compares chicken and fugu. The comparison starts 71,000 bases upstream of the SALL3 gene, and the vertical scale measures the degree of sequence conservation at each point; the red areas are non-coding regions, and blue is in the actual coding region of the SALL3 gene.
CNEs cluster in genomic regions surrounding developmental regulator y genes in ver tebrate and nematode genomes. Here, we show sequence conservation in the SALL3/sem-4 locus. This gene codes for a zinc finger protein that is involved in embryonic development in both vertebrates and invertebrates. The diagram shows sequence conservation (minimum 50% identity in 100 bp sliding windows) along the SALL3 gene and part of its upstream sequence in human, mouse, chicken, and pufferfish (Fugu) genomes. Conservation is shown with respect to the Fugu sequence in the region spanning from 71 k upstream of the SALL3 transcription start site to the end of the gene.
See all those pink peaks in the chart? Those ought to jump out at you. Those are highly conserved non-coding elements (CNEs), and the remarkable thing is that they are nearly identical in fish, mammals, and birds — these elements have been conserved for 450 million years. The evidence suggests that these CNEs have been under strong purifying selection, and that they are 300 times less likely to be lost than the nondescript junk in between them. These CNEs are all over the place, and are particularly strongly associated with regulatory genes, such as transcription factors.
Another interesting point: the figure above only shows comparisons within a single phylum, and we see CNEs all over. What if we look in other phyla? It turns out that CNEs are not unique to us chordates, and are found in invertebrates as well, but they are different. Compare homologous genes in a fugu and a fly, and there is little detectable conservation within these non-coding regions; compare a couple of different arthropods, or a couple of species of nematode, and there they are again…but they're different CNEs, a unique set for arthropods, and a different set for chordates.
So they're conserved within a broad group of organisms, and you might be wondering what they do. In the known cases, the CNEs seem to be transcriptional enhancers — they promote more consistent, robust expression of the associated gene in appropriate tissues. The mechanism isn't known for sure, but likely involves these regions having sequences that promote the binding of transcription factors that strengthen the regulation of the gene. We know of cases of mutations in the CNEs (not the gene itself, but just in these little patches of non-coding DNA) that can lead to birth defects in human beings. Certain kinds of polydactyly and syndactyly, and a rather obscure heritable disease called Pierre Robin syndrome seem to be the result of changes entirely in CNEs.
These observations are all very suggestive. It suggests that the CNEs are part of genetic circuits that set up patterns of gene expression — the patterns that regulate organismal form. We don't know the specific details of those interactions, but we see the evidence of their existence.
One way to think of it is in comparing it to the functioning of a circuit board in a computer. You know that what is essential for the appropriate activity in the computer is that everything is wired up correctly — these gene regulatory networks are analogous to the circuit networks in electronics. In this case, we don't know the details of the wiring — we've just begun to trace all the connections — but what we have identified are sets of printed circuit board connectors, small keyed blocks that hook up in a specific way to wires with matching plugs. We're at the point where we've cataloged some interesting order: these sets of circuits use a 15-pin connector, that one over there has 3 pins on the board, so we need to find a cable with a 3-socket plug, etc. CNEs mark the spot in the DNA where connections are made between living genes.
What this all implies, because we see similar arrangements of these CNEs within vertebrates, is that the broad patterns of connectivity have been conserved for a very long time — since shortly after the Cambrian, at the very least. That phyla that diverged before or during the Cambrian have different patterns of CNEs implies that at that time of divergence, either these regulatory elements were less significant or more fluid. Together, these observations provoke the idea that maybe one of the factors that led to the emergence and stabilization of different body plans was the gradual reinforcement of fixed patterns of gene activity by the addition of these elements over time; CNEs contributed to the canalization of development.
An early, relatively simple set of genes with a small number of regulatory elements connecting them expanded by gene duplication…which also, of course, expanded the number of possible connections between them. This expansion was followed by a consolidation, where the connections between genes were selectively whittled down, but different lineages stabilized on different, smaller subsets of that huge combinatorial space. The interesting idea here is that diversification would proceed hand-in-hand with increasing stabilization, locking in different lineages to different body plans.
A model for the evolution of cis-regulatory elements involved in animal development. According to this model, duplication and rewiring of the regulatory toolkit of the common animal ancestor gave rise to a diverse set of complex regulatory elements that formed the core developmental programs of the major animal phyla. Since then, animal body plans have been largely conserved. This conservation may be reflected in a set of highly conserved cis-regulatory elements controlling the expression of developmental genes.
This leads to the situation we see today, where we see the same parts, the same genes in animals as different as fruit flies and humans, but how those parts are deployed and regulated and used in relationship to other genes may be very different and produce very different morphological outcomes. CNEs are a subtle part of the regulatory landscape that played an important role in marshaling patterns of core gene expression.
Vavouri T, Lehner B (2009) Conserved noncoding elements and the evolution of animal body plans. BioEssays 31:727-735.
Life Science
Comments
Posted by: Brownian, OM
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August 4, 2009 5:03 PM
You liberals are so obsessed with the nanny cell, probably one of the reasons we have so much cancer (bloated, unproductive growth).
Clearly, the answer for maximum prosperity is an unregulated free cell, preferably one with a currency pegged to the ATP standard.
Posted by: Glen Davidson
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August 4, 2009 5:09 PM
Cornelius Hunter likes to use these highly conserved sequences as "proof against evolution." Which is odd, because by his "thinking," then, stasis is the miracle, while apparently evolution is to be expected as a natural process.
But wait, wasn't it change that was the miracle, as in the evolutionary dependence upon ancestral genes coupled with substantial change isn't something that can happen naturally, and miracles are needed to make everything come out as predicted by nonteleological evolution?
I'm so confused.
No, that wasn't me, it was Cornelius Hunter who couldn't think enough to realize that all he's saying is that anything we will ever see must be miracle. Come to think of it, that's all ID says as well.
Glen D
http://tinyurl.com/mxaa3p
Posted by: MK | August 4, 2009 5:09 PM
ATGCs remind me of this vadlo cartoon.
Posted by: barfy | August 4, 2009 5:13 PM
Although I read Pharyngula for all the other stuff, I love it when you blog on research.
As a Husky alum and biology major, who now does the foot doctor thing, I admit that my subscription to BioEssays has lapsed.
Thanks for keeping me informed.
Posted by: Knockgoats | August 4, 2009 5:16 PM
Very interesting! Has anyone yet looked at echinoderms or hemichordates, or at onychophorans, for example, to see if phyla believed to be (relatively) closely related have similar CNEs? Do coelenterates have them? Sponges? (None of the first few google results answer these questions.)
Posted by: Jon D. Moulton | August 4, 2009 7:05 PM
Morpholinos are sometimes used to perturb gene networks by knocking down expression of a single gene; one approach is to measure the difference in the expression of other genes after a single-gene knockdown in order to map the members of the network.
Wu SY, Yang YP, McClay DR. Twist is an essential regulator of the skeletogenic gene regulatory network in the sea urchin embryo. Dev Biol. 2008 Apr 15. [Epub ahead of print]
Su YH, Li E, Geiss GK, Longabaugh WJ, Krämer A, Davidson EH. A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. Dev Biol. 2009 Mar 4. [Epub ahead of print]
Löhr H, Ryu S, Driever W. Zebrafish diencephalic A11-related dopaminergic neurons share a conserved transcriptional network with neuroendocrine cell lineages. Development. 2009 Mar;136(6):1007-17.
Nikitina N, Sauka-Spengler T, Bronner-Fraser M. Dissecting early regulatory relationships in the lamprey neural crest gene network. Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20083-8. Epub 2008 Dec 22.
Liu F, Walmsley M, Rodaway A, Patient R. Fli1 Acts at the Top of the Transcriptional Network Driving Blood and Endothelial Development. Current Biology 2008 Aug 26;18:1234-1240.
Smith J, Davidson EH. Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo. Proc Natl Acad Sci U S A. 2008 Dec 22. [Epub ahead of print]
Smith J, Theodoris C, Davidson EH. A gene regulatory network subcircuit drives a dynamic pattern of gene expression. Science. 2007 Nov 2;318(5851):794-7.
Nam J, Su YH, Lee PY, Robertson AJ, Coffman JA, Davidson EH. Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network. Dev Biol. 2007 Jun 15;306(2):860-9. Epub 2007 Mar 28.
Livi CB, Davidson EH. Expression and function of blimp1/krox, an alternatively transcribed regulatory gene of the sea urchin endomesoderm network. Dev Biol. 2006 May 15;293(2):513-25
Sinner D, Kirilenko P, Rankin S, Wei E, Howard L, Kofron M, Heasman J, Woodland HR, Zorn AM. Global analysis of the transcriptional network controlling Xenopus endoderm formation. Development. 2006 May;133(10):1955-66.
Yuh CH, Dorman ER, Howard ML, Davidson EH. An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network. Dev Biol. 2004 May 15;269(2):536-51.
Posted by: spudbeach | August 4, 2009 7:19 PM
Thanks for the science post! It's nice to see that the more we look at genes and all of biology, the more it looks like a kludged together computer program -- this part gives us more of that, but this other thing tells this part to cool it. That is exactly like an evolved programming system, or a system maintained by too many programmers, each adding or removing a feature.
This is why I became a physicist -- biology is just too darned complex! Darn you, evolution, darn you all to heck!
Posted by: lose_the_woo
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August 4, 2009 7:28 PM
You must believe in Gosh.
Posted by: Nerd of Redhead, OM
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August 4, 2009 7:46 PM
Heavy science after dinner. You are a cruel man PZ.
As usual, I could follow along with your clear explanation. I feel biochemistry is going to tie together the tree of life so tight that the creobots won't even be able to find a pry point. Not that they won't try.
Brownian, thumbs up!
Posted by: St.B | August 4, 2009 7:55 PM
Re: #7, spudbeach…
Lol. Get out of my head! After reading this, though much is largely over my grey matter, all I could think was, “sounds like a comp., information storage, processing...”
If they could just find the genetic markers for idiocy, we could switch it off.
Posted by: 'Tis Himself, OM
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August 4, 2009 8:13 PM
Brownian #1
The ATP standard will result in excess ion transfer. We need to go to a neurotransmitter standard to provide alteration in the postsynaptic membrane of the receiving cell.
Posted by: Nerd of Redhead, OM
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August 4, 2009 8:20 PM
IIRC, they were next to the "god gene".Posted by: St.B | August 4, 2009 8:40 PM
Heh. Damn, “sky daddy” , infiltrating the genome. Perish the thought. We all know GOD resides in the Hadron Collider.
Posted by: John Harshman | August 4, 2009 9:07 PM
Is this true? And can you show it? What we see in this post is that the sites for a particular gene have been stable since some time in the Devonian (i.e. throughout Osteichthyes), and I'm willing to take the small species sample and single gene as representative of the entire genomes of all osteichthyans. But in order to push this back to the Cambrian you will need to show that lampreys and hagfish, at a minimum, have the same conserved sites. Do they?
Posted by: No BS | August 4, 2009 9:21 PM
PZ
I gotta tell you.
You're a good teacher.
Haven't been in a Bio class since '77.
And I still get the jist of what you say.
Thanks for taking the time to edumacate us!
Posted by: Sphere Coupler | August 4, 2009 9:37 PM
PZ Myers
"since shortly after the Cambrian, at the very least"
And this is the question that is really important...what were the gene modifying specifics of environmental conditions that seems to be unique to this span of geological history while the genome was in a highly susceptible progressive mode and will there be similar natural altering episodes in the future?
Are we in this mode now?
Can these points and conditions be repeated?
And would we be able to recognise this in such a short experimental period of a possibly long determinate process?
Surly the process is not blanketed over the whole taxonomy.
Posted by: Jadehawk, OM
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August 4, 2009 9:38 PM
neat. I have nothing clever to add; just neat.
Posted by: Sphere Coupler | August 4, 2009 9:56 PM
I meant:
Surely a specific process is not blanketed over the whole taxonomy.
Great post.
Posted by: Staphylococcus | August 4, 2009 10:00 PM
Another interesting thing to note in the comparisons of conserved CNEs in the figure is that whilst the sequences between them are not conserved, the length of the sequence is. This suggests that the physical folding and packaging of the genome will affect the degree to which these elements can be brought together to alter transcription initiation.
Posted by: NewEnglandBob
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August 4, 2009 10:23 PM
I have been reading books on Evo Devo by Sean B. Carroll lately and a lot of this comes up. His terminology is different but he covers the same topics, generally.
Posted by: foxfire | August 4, 2009 10:24 PM
Jadehawk @17. Ditto.
@ PZ
Thanks! I don't suppose it is possible to get your science blog postings in pdf format (or something else) so thousands of trees don't have to die because of wasted space. You have a way of explaining things that is really cool. Write a book, would ya PLEASE!!!
@ Everyone
Sorry, but this OT commercial is being brought to you because Donors Choose is having a B&M Gates foundation two-fer special.
Here is the page for Science & Math projects.
I dropped some change on this one because molecular biology/genetics is just *so* fucking cool
Sorry for the commercial...couldn't help it...two-fers!
Posted by: Kagato
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August 4, 2009 10:26 PM
Sorry for the off-topic, and feel free to shoot me down in flames if this is covered elsewhere...
I'm getting 404 errors on all articles between
Romania struggling against the forces of ignorance
and
Never trust a guy named 'Hayseed'.
I'm assuming given the error that this is not just me.
I saw a "testing" post from ScienceBlogs Admin on a random thread, so hopefully someone is working on it...
Posted by: Rorschach | August 4, 2009 10:32 PM
I can confirm that.
Posted by: molliebatmit | August 4, 2009 10:39 PM
Man, if we did, my entire life would be so much easier. And my whole lab could take a vacation.But given that it's really, really hard, we're having a lot of fun figuring out how to make different kinds of neurons using different programs of genes.
Posted by: Jim | August 4, 2009 10:40 PM
#23 I confirm that too. #3 Nice link.
Posted by: Nerd of Redhead, OM
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August 4, 2009 10:40 PM
I was seeing 404 errors earlier for this thread, right after PZ posted it. We seem to be having roving errors.
Posted by: tohellwithyourturtle | August 5, 2009 12:56 AM
I love the (extremely) well explained science posts. You explain science how it should be explained, easy to grasp the basic concept, but with research cues for those who are interested in furthering their grasp beyond the rudimentary to "I still don't know shit, but this is one more piece of the puzzle," (referring to myself, yeah, I'm stupid, but willing to learn) while still providing substance to specialists. Absolutely beautiful.
Cheers!
Posted by: TheVirginian | August 5, 2009 1:24 AM
Sorry, PZ, but you must post the long form birth certificate for these genes if you claim they were born and evolved here on the Earth. If you don't show us their original, authentic, long form birth certificate, that will prove they were not born on the Earth.
Which means, then, that God created them off the Earth and put them here.
SHOW US THE ORIGINAL, AUTHENTIC, LONG FORM BIRTH CERTIFICATE FOR THESE GENES OR ADMIT THEY WERE CREATED BY GOD, NOT BORN AND EVOLVED NATURALLY!
Posted by: Vasha | August 5, 2009 4:01 AM
Sphere Coupler (#16/17):
Exactly -- that's why it's significant that evolution is a historical process. The authors hypothesize that back in the early days of metazoa, none of the small diversity of metazoans had these CMEs strongly channeling their development, but instead a much sloppier regulatory network, which had a tendancy to develop into CMEs -- and they all shared this tendancy because of their common ancestry. So, if this hypothesis is right, modern animals have moved away from this loose ancestral condition, and therefore can't form new body plans now (it's possible, but not likely, that we might find a lineage that's kept the ancestral flexibility). The only thing that's "blanketed over the whole taxonomy" is whatever all those species have in common because they inherited it from the ancestor of all of them -- common possibilities, common constraints.
Posted by: Intelligent Designer, OP | August 5, 2009 4:20 AM
So a genome has somethings comparable to variables in software
PZ also said:
Posted by: Beelzebub | August 5, 2009 4:32 AM
Eventually we'll be able to simulate GRN's computationally and tell why CNE are so crucial that evolutionary selection have conserved them. In the mean time, I think the information age metaphors to cell function are probably more of a hindrance than useful. Gene regulation operates in a chemical environment, and is probably so alien to our experience that we haven't yet been able to conceive how to accurately simulate it, but the time will come, I think, when we will.
Posted by: Kel, OM | August 5, 2009 4:43 AM
Stimpy, how'd you go with the Schneider paper / program?
Posted by: Kazeldxh | August 5, 2009 4:47 AM
Hi webmaster! kej
Posted by: DrFrank | August 5, 2009 5:57 AM
@#30
Hey Randy look, the cell is a system with an internal state that changes over time depending on inputs and its current state - it's God's Turing machine! Prooof of Jeeeeebus!
Oh wait, any non-trivial system would need to have such properties and thus could have a program metaphor broadly mapped over it. As a result, pointing this out is evidence of bugger all.
Finally, if DNA is a computer program, then where the hell are all the comments? I could never believe in a Deity that would produce such sloppy and uncommented code. I demand to see the design document.
Posted by: Bill | August 5, 2009 7:58 AM
PZ,
More, way more of this kind of post, please!
Posted by: applescrapple | August 5, 2009 8:10 AM
Thanks for the article. It is informative and well written. You are a very good teacher.
Posted by: James Sweet | August 5, 2009 9:29 AM
How long before a Creationist blogger writes, "Atheist and evolutionist PZ Myers writes that 'junk DNA' are like Printed Circuit Board Connectors.. Well, I've never seen a Printed Circuit Board Connector without a designer, so even Myers is saying goddidit!"
Posted by: Rorschach | August 5, 2009 11:35 AM
Just a question,
is "conserved" a word in English? Shouldnt it be preserved or something?
Translation from German or Dutch maybe?
:-)
Posted by: John Farrell | August 5, 2009 11:46 AM
@#24Molliebatmit, do you have a lab website or email contact for followup on the subject?
:)
Posted by: dNorrisM | August 5, 2009 11:50 AM
I love my cousin fugu.
Mmmmmm fugu
Posted by: Blake Stacey | August 5, 2009 12:08 PM
conserved, v.tr. 2. To keep (a quantity) constant through physical or chemical reactions or evolutionary changes.
[Middle English conserven, from Old French conserver, from Latin conservare : com-, intensive pref.; see com- + servare, to preserve; see ser-1 in Indo-European roots.]
Posted by: Alan Kellogg | August 5, 2009 1:31 PM
Vasha, #29
It would be interesting to follow the future evolution of myxobacteria; for that group appears to be on the verge of evolving true multicellular life. Imagine a world where plants are the only surviving multi-eukaryotic life, and the animals are composed of bacteria. :)
Posted by: Intelligent Designer, OP | August 5, 2009 2:04 PM
But you are certain that the vast majority of DNA is junk?
Posted by: Intelligent Designer, OP | August 5, 2009 2:07 PM
Hi Kel,
I haven't done any work on the program since you last asked. I am just too busy. I can remember the Schneider paper. Are you sure I am the one you were talking to about it?
Posted by: Nerd of Redhead, OM
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August 5, 2009 2:11 PM
Randy, this is science, just at the being of the study of genomes. Someone used the phrase junk DNA, because it didn't obviously code for proteins. Now, they are finding some regulatory uses for the junk DNA. They will find more as time goes on. The true junk DNA will become less and less. There are some remnants of retroviruses that are part of the true junk. Still no place to hide your imaginary designer.Posted by: Intelligent Designer, OP | August 5, 2009 2:37 PM
Hi Nerd of Redhead,
I don't think intelligent design predicts no junk. I would expect any DNA not completely necessary for survival to be corruptable by entropy. This means that DNA supporting redundant systems or required for adaptation to a changing environment could become corrupted. I speculate that there may be 5-15% junk.
Posted by: Brazuzan | August 5, 2009 2:38 PM
There are two things I love to see when I open this blog: one is that "Blogging on Peer-Reviewed Research" thing, the other is a citation block in Comic Sans.
Posted by: Intelligent Designer, OP | August 5, 2009 4:10 PM
Dr Frank,
Just so you know, I am not a Christian, I do not think a genome is a computer program, and I am familiar with molecular and cell biology.
Becareful PZ. Someone might think that you think the genome is a microscopic circutboard.
Posted by: Nerd of Redhead, OM
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August 5, 2009 4:23 PM
Randy, I would make a SWAG of more like 30-40% pure junk DNA. The the error bar plus/minus 40%. But, as usual, science will eventually sort it all out.
Posted by: Malcolm | August 5, 2009 4:39 PM
Dr Frank,
Just so you know, when Randy claims to by familiar with molecular and cell biology, he doesn't mean that he understands any of it.
He's familiar with the terms because whenever he makes inane arguments for design, people tell him that he needs to study more molecular and cell biology.
Posted by: DrFrank | August 5, 2009 5:17 PM
Thanks for the heads up, Malcolm :)
So, if Randy is not a Creationist, then what is his position? Certainly, his Intelligent Designer tag seems to indicate that he's a Creationist, and I'm sure I've seen him positing some of the standard bullshit ID information arguments before. So is it panspermia? Xenu? Last Thursdayism?
Posted by: Staphylococcus | August 5, 2009 10:46 PM
"I don't think intelligent design predicts no junk."
Exactly. That's because ID predicts nothing whatsoever. Come back when you have a testable hypothesis.
Incidentally, the whole "genome is like a computer program" thing is a poor analogy. Attacking it proves nothing.
Posted by: Intelligent Designer, OP | August 6, 2009 12:40 AM
DrFrank,
Intelligent design is a form a creationism. I am a software developer so intelligent design (creating software) is my job. It's not magic, it's design by intelligence. From my perspective intelligent design could be an evolutionary process driven by intelligence (just like software development) from one being, several beings or something we don't comprehend at all.
I don't subscribe to a religion or any religious creation stories. I am a former Christian. You could say I am a diest.
Malcolm,
You don't know anything about me. I suspect you are projecting.
Posted by: Kel, OM | August 6, 2009 12:53 AM
Indeed. It was the last time you shows up around these parts and started talking Shannon Entropy. I wasn't sure if you got the link or not, seeing as science blogs went down for like 2 days before I could post it. I just assumed you'd actually check the thread for replies before starting up the same conversation in a new thread.Posted by: Marcus Ranum | August 6, 2009 5:21 PM
Finally, if DNA is a computer program, then where the hell are all the comments?
I once had to debug a massive program written by Greek programmers. Yep - the comments were all in Greek. I'm guessing that maybe the "junk DNA" is just comments written in goddish.
Joking aside, I never understood the creos' argument that there's no way for increased complexity to arise from something less complex. Anyone who has ever written software can answer that pretty easily: you take a fairly simple programming language specification (compiler) and give it to CS undergraduates and dot-com kids (10,000 monkeys) and you get the Internet - which, as a whole, is much more complicated than the source code for a browser, but relies heavily on it. :D
Posted by: amphiox | August 6, 2009 7:49 PM
Hmm, my recollection of the numbers may be off, but isn't it already established that the majority of the "junk" DNA (by number of base pairs) really are the remnants of retroviral jumping genes and other forms of self-replicating repeating sequences?
If so, then we already know that the majority of the "junk" DNA can be considered non-functional, because it arose from contingency, essentially a genome infection or genome cancer. Even if some few former retroviral sequences get recruited into some regulatory function later on, that doesn't change the fact that it's origin was non-functional.
(And if you look at the figure in the post, the CNEs (red peaks) and gene (blue peaks) are all tiny little blips rising from the very long grey line that is mostly flat - ie non-conserved, non-useful sequences make up the majority of this stretch of DNA. (Even if we don't know for sure that they have no function, the fact they are not conserved is pretty suggestive that they don't have any particularly important function.)
Posted by: John Harshman | August 6, 2009 8:27 PM
You can get a quick and dirty minimum estimate of the proportion of the human genome that's junk like this: the fugu genome is 1/10 the size of the human genome. Even if we suppose that the fugu genome is 100% functional, if we grant that humans don't need vastly more DNA to specify their phenotypes than fugu do (and I know of no argument to that effect), that's about 90% of the human genome that's junk.
Posted by: RBH | August 7, 2009 2:01 AM
Intelligent Designer wrote
Posted by: Renay | August 7, 2009 4:44 PM
It's all about linguistics, my friend.
Posted by: David Marjanović, OM | August 8, 2009 2:40 PM
Yes.
To start with, over 50 % of it consists of retrovirus corpses in various stages of decay – we have 18,000 to at most 25,000 genes of our own, and 34,000 retrovirus genes –, and much of the rest consists of vain repetitions, followed by pseudogenes (gene corpses in various stages of decay, not of viral origin this time). The parts of our genome that could in principle have a function amount to at most 20 %. I think the real number of functional DNA, including all genes for regulatory RNA that will still be discovered, will turn out to be at most 10 %, and half that is easily possible.
And why would there be "any DNA not completely necessary for survival"? How intelligent is that?
Yeah. How many fingers are formed seems to depend on how much space there is for them. Check out the Australian lungfish, which has lots of space indeed, and has lots of ("radials" homologous to) fingers per fin.
Posted by: Lynna | August 8, 2009 2:57 PM
David M. @ #60: Thanks for exegesis regarding the percentage of functional DNA. I read something vaguely like that before, but not so clearly presented. All those retrovirus corpses!
OT, but thanks for debunking in another thread the cave paintings and rock art that supposedly depict dinos and humans together at last.
Posted by: Kel, OM | August 9, 2009 3:42 AM
I remember coming across a creationist who got upset at me over junk DNA. When I brought it up, he produced a paper showing that there was a part of our non-coding DNA that actually had a function. When I said that one piece of non-coding DNA doesn't account for all of our DNA, he called me closed-minded for refusing to learn that junk is not junk - even though I could show plenty of examples of junk that really was such as ERV remnants or pseudogenes.
Now there's some bad inductive logic if I ever saw it. Scientists say X is junk, X is not junk there for all possible X it cannot be junk. gah!
Posted by: Owlmirror | August 9, 2009 5:32 AM
/* Είστε δεν αναμένεται να γίνει αυτό κατανοητό. */
Posted by: David Marjanović, OM | August 9, 2009 6:24 AM
Does that mean "this statement is self-contradicting"?
Posted by: Snowflake | August 9, 2009 5:42 PM
I love your terminology: "Gene regulatory networks and conserved noncoding elements." Is that what they call junk DNA?
Posted by: Owlmirror | August 9, 2009 6:59 PM
While the sentence is indeed self-referential, it's a bit more subtle than that, and has a tech nerd meta-context that is embedded with it.
As a tangental point, have you used translate.google.com? While it supports a surprising range of languages, it would appear that subtle points of grammar and syntax are lost in translation, as would hardly be unexpected with any machine translation. So it may well be that the phrase as I pasted it in is sufficiently garbled as to be even more self-referentially correct.
(And as an aside which I hope will stop being correct in that what it references will mysteriously vanish in the near future: "Holy suffering shit, that's a lot of spam!")
(PZ: Don't miss the two stray spam up above the current massive block.)
Posted by: 'Tis Himself | August 9, 2009 10:03 PM
The spammers are active today.
Posted by: Rev. BigDumbChimp | August 10, 2009 1:23 PM
holy shit
Posted by: David Marjanović, OM | August 10, 2009 4:30 PM
Thanks, Owlmirror... wow, what a long list of spam comments... <headshake>
No. I found "autó" in there, figured that the first word looks like a demonstrative pronoun and the third like a noun (...though, actually, I'm no longer sure about that), and noticed that "this statement is self-contradicting" would be a logical thing to say in this context. I can read the letters, but I hardly know more grammar than I can figure from Latin and hardly more vocabulary than I know from scientific names. :-)
Click in the sidebar of this site to see a major failure of translate.google.com. Scary that my Italian is better than Google's, even though I've never learned it (only French and Latin, and now the uttermost basics of Spanish).