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The Biggest Piece Of DNA Ever Made
An anonymous reader writes "Forbes has a story on 'the biggest piece of artificial DNA ever made'. The real story is that companies are racing to produce longer and longer DNA fragments to serve the growing science of synthetic biology." From the article: "On a piece of DNA as long as the one made for Microbia, ten or more genes may be present. By studying more than one gene at once, researchers hope to get a better picture of how they work in concert to produce an organism. Another advantage: These stretches can also be made to contain all the DNA letters that occur between genes. Scientists once thought of that stuff as junk, but many now believe it may regulate how the genes work or provide some other function."
cue the penis and poop jokes.. now!
How about "bases" or "base pairs"? Are they creating a string, or DNA? Granted, Forbes ain't a science rag, but still...let's show our readers we took some high school biology.
Slashdot Burying Stories About Slashdot Media Owned
Ah, "junk" in biology.
There was a piece of the brain that was once thought of as "junk", or "filler", until it was removed by a zealous neurosurgeon during an operation in that region of the brain of his patient. The patient unexpectedly lost the ability to learn new things (as in Memento)... Now we know.
The pancreas was once though to serve simply as a support structure for the more obvious organs...
Beware the tendency of the very litterate to dismiss that which they do not understand, it's simple hubris.
My not-supported-by-resasearch-of-any-kind take on "junk" DNA?
I think it's stored evolution.
DNA that isn't expressed, but stored in a way that it can mutate for generations and generations before being randomly reactivated, cueing natural selection. That would result in a simple mutation (only the reactivation of a chunk of stored DNA) with not-so-simple results from generations of stored changes.
You can't take the sky from me...
Maybe because everything makes me think of porn...
A friend once got told size doesn't matter, it's what you do with your DNA. Yeah..it was a friend...nothing to do with me. I'm lucky if I don't trip over my DNA.
!sig
Compels me to make this stupid joke about the biggest piece of dna once belonging to a Brontosaurus. Why oh why do I listen to my inner class clown?
My humor is probably your flamebait
You know, I bet if we unravelled that sucker,
It'd roll all the way down to Fargo, North Dakota
'Cause it's the biggest DNA in Minnesota
I'm talkin' 'bout the biggest DNA in Minnesota
- with apologies to Weird Al Yankovic, Biggest Ball of Twine in Minnesota
>Scientists once thought of that stuff as junk, but many now believe it may regulate how the genes work or provide some other function.
To clarify: a stretch of DNA that actually gets turned into RNA and thence into proteins is an exon, and the DNA that lives between exons is called an intron. It's been known for a long time that there are sequences before an exon that control it: regulators, promotors, and repressors, that are activated or deactivated by proteins binding to them during DNA reading, and in some cases there are sections of DNA that are processed into RNA, that help stabilize the RNA and are then clipped out before the RNA becomes protein, so they also have a function. (This is part of the reason that making insulin artificially has been tricky: you can't just stick the DNA into a bacterium and have it crank out insulin because the DNA is in a couple sections and requires post-processing.)
Also, many of the introns contain echoes of old sequences that used to be useful way back when, and aren't anymore, or bits of viruses that integrated into the genome hundreds or thousands of generations ago and are now widely spread in the population, and some intron bits are designed to facilitate shuffling of chunks of DNA into different orders for proteins that come in a wide variety of flavors with the same start and end sequences. Antibodies, for instance, have long, consistent, identical start and end chunks with wildly variable center chunks. (Think of a key, with differing teeth to fit various locks, but the same end piece, to fit your hand. Likewise an antibody has a hypervariable section that, for each antibody, can adhere to precisely one antigen, and a nonvariable section that signals passing cells that it has/hasn't found any of that antigen.)
Getting to go play around and make any set of repressor/promoter sequences and change the distances between them is a really nice tool, and being able to make massive sequences like this, helps play with gene interactions and with massive proteins like antibodies. Think of this as the beginnings of the transition from transistors to integrated chips, or maybe it'd be more apt to say from single computers to the beginnings of networks.
Nostalgia's not what it used to be.
Huh.
I figured this was some sort of bukkake story.
thank you folks, I'll be here all night. Tip your waiters!
It's a strange world -- let's keep it that way
The longest piece of DNA was made by God, and I believe there's gonna be a rude awakening for those who PLAY God without KNOWING God.
"Forgive us our trespasses, as we forgive those who trespass against us." -Jesus Christ The Lord's Prayer
I routinely make longer DNA sequences, and give the shorter ones away as gifts to women who I like.
--
make install -not war
Then mod Funny so we can MOD HIM DOWN AGAIN!!!
I've created customized a string of DNA and put it on a bumper sticker. The genetic sequencing of letters spells out: If you can read this you are too close
"You'll get nothing, and you'll like it!"
Isn't it time to stop talking about "junk DNA" as being junk? The idea that it might not be junk has been popular in the popular science press for decades now. Presumably the idea that it's useful has been around for much longer in academia. Every single article I have ever read in the last decade that mentions the stuff points out that it might serve a purpose. So isn't it time to stop saying "Scientists once thought of that stuff as junk" just like you no longer have to preface every discussion about relativity with the statement "people used to think there was an absolute zero velocity with respect to which the aether was at rest". It's kind of insulting, don't you think?
Doesn't it make you feel good to know that our freedoms are protected by politicans, lawyers and journalists.
...will any of this science deliver me a pill that will make my penis bigger?
Here's some DNA that's 6" big:
http://www.bathsheba.com/crystal/dna/big.html
If that's too big for you, they also have:
http://www.bathsheba.com/crystal/dna/
I've heard the argument made that one of its purposes is an evolved defense against viruses. The real genetic data (the exons) are scattered amongst garbage data (the introns), and when it's needed the exons are extracted and spliced together, with the introns just being thrown away.
The use of splicing is a defence against viral attack because the virus would need to be sure to insert its DNA into an exon. If it inserts its DNA into an intron, it will just get thrown away. If it inserts it half into an exon, half into an intron, it will get snipped in half, so the assembled mRNA becomes garbage and doesn't get translated into an active protein. Furthermore, by keeping the size of the exons down, you put a hard upper limit on the size of viral DNA that can be inserted.
I think the influence the war against the viruses has had on our genetic evolution is perhaps underappreciated.
At least some of this non-transcribing DNA is strongly conserved across evolution, e.g. virtually identical in mouse and human.
It is very likely the biological equivalent of the tables for state machines.
I haven't looked at this research for about 5 years, but there were the beginnings of understandings of some of these, and lots of analysis of "regulatory sequences", the DNA sequences that can promote or inhibit transcription of a gene.
To put this in context, a PhD student at the lab I'm working at this summer spent a year and a half constructing a ~7,000 base pair gene for her research using normal cloning methods. I've personally been struggling to clone and express a very small gene construct (~250 bp) for the past month. The ability to synthesize any DNA sequence would be every bit as significant as the recent genomics and bioinformatics revolution. Researchers could study entirely novel and specific variations of natural genes by simply sending the sequence off to be synthesized.
To me a more logical explanation of the filler DNA is to act as a buffer against flaws.
/* and */ "comment delimiters" are subject to conditionals, so that splicing is not performed at those points and the intron actually makes it into the finished protein. A number of regulatory mechanisms work this way- the intron changes the function of the protein product to either make it functional or non-functional or different somehow. The finished protein might suppress a "conditional" elsewhere or land on a promoter region to encourage expression of the next gene in some cascade. (Biology is full of needlessly complicated "cascades" with useless steps that can't be gotten rid of for legacy reasons.) It's as if "run time" and "compile time" are both all the time with an infinite number of threads running on code that constantly rewrites itself and controls its own compilation and execution.
Nothing in biology has a "purpose". It isn't like a car where every part serves a well thought out function. You can find some organs with single well-defined functions, like the heart, but most serve a range of ill-defined roles. Bones, for example, are making white blood cells. The liver does all sorts of stuff. Everything happens because it happened before in a way that it can happen again. Everything is needlessly complex, full of awful unstable hacks. Absolutely no consideration was made during the process to make anything easy to understand.
In fact, evolution bears a large resemblance to dysfunctional software development by a team of beginner developers who don't talk to each other and who like to create code with legacy issues. One guy will code something because he doesn't know some other guy already wrote something to handle it- creating redundant systems that compete with each other. The body is full of stuff like that. An example would be the anterolateral system (evolved earlier) and the posterior dorsal column system (evolved later), two competing systems in your spinal cord. You need two, because just one would make medical school too easy I guess. There is a lot of cut and paste coding going on (introns are full of commented out goodies). And just like bad software that "evolves", there are buried broken features in you that don't work anymore- but even evolution can't "refactor" them out of your body. Hiccups, for example, served a function in the gills of the Devonian fish we evolved from, but they just annoy us. There is zero selective pressure for us to retain hiccups- in fact there is negative pressure, since a tiger might hear you hiccup and eat you before you reproduce. And yet hiccups haven't gone away after hundreds of millions of years.
As for garbage DNA- while there are advantages conferred by noncoding DNA (in high radiation environments, exposure to mutagens, viruses, transposons, and other genetic parasites, etc.) strictly speaking the DNA has no purpose since it is part of an evolved system, not an engineered one. Introns are a side effect of most evolutionary algorithms that rely on crossover and exchange of homologous sequences. In the field of genetic programming, they are a nuisance- the profusion of introns quickly becomes a problem as they consume computational resources- but you can't just get rid of them, because they contain most of your genetic diversity and some of them have really good ideas in them.
Junk DNA contains many versions of (parts of) genes that are disabled; you can think of some of them as commented out code that gets cut and pasted around occasionally. There are "sunken ships", recognizable genes in noncoding regions that have been accumulating mutations for thousands of years. We use them to measure mutation rates. The most common gene in the genome is reverse transcriptase- a gene used only by viruses- there are several hundred "sunken ship" versions of reverse transcriptase in your genome that probably wouldn't work anymore if a virus tried to use them. Within introns, there are also "if statements", where the
the vast majority of Business ppl (including the reporter) have not covered base pairs within DNA. So keep it simple so that they do not have to be taxed.
I prefer the "u" in honour as it seems to be missing these days.