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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."
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...
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
For some reason your username makes me think of pron too.
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
I routinely make longer DNA sequences, and give the shorter ones away as gifts to women who I like.
--
make install -not war
there's gonna be a rude awakening for those who PLAY God without KNOWING God
Oh sh*t! We made a perfectly functional human heart that won't get rejected by the patient! The days of cutting open dead people and stealing their organs are over! What have we done?!?!
Damn you Science, damn you and your advances in medicine and technology that make life as we know it possible
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!"
...a rude awakening for those who PLAY God without KNOWING God.
Alright, I'll bite. Who are you to assume the scientists involved in these projects don't know God? Science, for many, is driven by the desire to better understand His creations (I'm talking studying evolution here, not non-science fundie jibberish). Experimenting and testing is a great way to learn things. I'm not saying that's the only reason to learn things, but you've made an unfair and pointed assumption and I just felt I had to call you on 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.
Oh come on.
"Playing God" is one of the more ridiculous accusations fired off by fundies. If you want to discuss the ethical concerns for toying about with DNA, that's fine, but by equating DNA manipulation with humans taking over a role of God you're either giving humans too much credit or God too little.
Show me where we are forbidden to explore these areas in the scripture of your religion and perhaps you'll have a foundation for your accusation. Otherwise, please let those of us who are willing to explore God's creation to the fullest extent do so in peace.
-f
Your brain is not a computer.
...will any of this science deliver me a pill that will make my penis bigger?
===========
All references to God, a deity or higher power, or any aspect of the so-called theory of evolution are not meant as an endorsement or denial of any particular religious belief, save Scientology. After all, I read L. Ron's other books and I didn't believe any of them either...
The last time I wrote code, it was Morse
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
>>> Who are you to assume the scientists involved in these projects don't know God?
h tenment.html
Who are YOU to assume that I assume that the scientists involved in these projects don't know God? I was referring to the ones who did not. You know, the sort that claims a 35,000 base pair sequence is the longest sequence ever made.
Well there is something you have failed to accound for. When things are OBSERVED they behave differently from when they are UNobserved. Scientists could account for that if they recognize FAITH in the equation. Faith can move mountains. Ask and you will receive. What is asked in Jesus' name will be granted. With God all things are possible. (or is that just a placebo effect? a statistical abberation. just refactor the equation. perform more experiments to coerce the equation to align with the hypothesis.) Meanwhile you extol the wisdom of Heisenberg saying things like "you just can't know where the particle is". Yes. Very wise.
Just remember, science is philosophy's bitch. Kant limited the role of science for good when he established that all the world of experience is phenomenal, meaning that it is all filtered through sensory input, and the origin of that input is always ASSUMED. Kant limited the role of life sciences in one fell stroke, and "levelled the intellectual playing field" for those who are willing to think fairly and objectively.
Quote:
"II. The Copernican Revolution in Theology
All three shifts left their mark on the day's theology. Emmanuel Kant's work proves most important. He taught that man is absolutely free and is the center of all things. Religious truth rests within man. For Kant, then, man's moral sense becomes his source of religious knowledge. Since reason can't prove God, He must be removed from reason and placed into another realm--an upper story realm called "faith."
Kant proceeded to develop a dualistic approach to knowledge. He conceived the phenomenal world, the world of sense experience. You can know this world through reason. Anything which does not come through the senses is unknowable. He also conceived of the noumenal world, a world which resides beyond sense experience and can be known only by faith. No one can prove or disprove this realm. He included here the "ding an sich" (things-in-themselves) but he denied a thing's real essence. Kant does say that given certain experiences it must follow that other things are true. "
source:
http://www.christianchronicler.com/history1/enlig
Therefore, from the perspective of a person who has no faith in God, but rather faith in science, logic and philosophy, the results of scientifically gathered data are, at best, just assumptions, since they are based on assumptions of the noumenal world, and are therefore no stronger than faith.
When self-proclaimed scientists claim that science, itself, is a bunker for atheism, and deny the role of faith in life, they essentially pluck out their own eyes to the truth, the way, and the life. What a person tries to achieve with prayer and humility, can be achieved with God's blessing.
On the other hand, when man takes on the essentially arrogant role of replacing God, and doesn't even give the LORD His credit, and does NOT give thanks, or ask for the LORD's blessing, and is irreverant... what did I say? There IS going to be a day of reckoning, a rude awakening, and I know because MY day of awakening already came and went.
Just remember, when the demons come knocking, that Jesus did save you.
"Forgive us our trespasses, as we forgive those who trespass against us." -Jesus Christ The Lord's Prayer
I'm not your average Christian; most of my ideas are the result of searching and asking the LORD, as well as scripture.
I never criticized the use of DNA. I criticized the fact that man had not given the LORD credit for the DNA they copied from his own creation. 35,000 base pairs is not the longest sequence, and that's a fact.
Have you ever seen a sunset in death valley? Every day the LORD paints a new one for you, if you'll go there. Have you ever seen an artists painting of a sunset in death valley? It's just a copy of the real thing, man. If the artist claims their painting is better than the one the LORD made... well... I must take issue with it. Nuff said.
"Forgive us our trespasses, as we forgive those who trespass against us." -Jesus Christ The Lord's Prayer
I did not condemn science anymore than I would condemn shoestrings. That was your own embelishment of my remark.
My argument is straightforward: When some hack steps in and claims that 35,000 base pairs is the most anyone has ever sequenced, I responded with the fact that God has sequenced more base pairs than they ever will, and to better effect.
Respect and trust the LORD, and ask for the LORD's help, put the LORD first in all things, and never forget the fact that the LORD is the reason you can take in a breath of air, with or without theoretical science, the scientific method or medicine.
"Forgive us our trespasses, as we forgive those who trespass against us." -Jesus Christ The Lord's Prayer
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.
You're mentally-ill.
Thanks.
Christ taught that we are to love our enemies, always forgive, never retaliate, return kindness and blessings in exchange for evil. Pray and ask the LORD to help our enemies.
As for your comment, I read it as an opportunity for rewards in Heaven:
Matthew 5:11 - 12
11Blessed are ye, when men shall revile you, and persecute you, and shall say all manner of evil against you falsely, for my sake.
12Rejoice, and be exceeding glad: for great is your reward in heaven: for so persecuted they the prophets which were before you.
God Bless You.
"Forgive us our trespasses, as we forgive those who trespass against us." -Jesus Christ The Lord's Prayer
There IS going to be a day of reckoning, a rude awakening, and I know because MY day of awakening already came and went.
Ironically enough, your day of awakening was based on your demonstrably flawed sense perception. And if we accept that even logic is faith-based, why does it make a bit of difference if you or Kant use said logic to posit the existence of a god?
Furthermore, Kant's supposition is that morality has Meaning with a capital M. He started with the premise that humans have some inherent sense of morality. I think morality has meaning in some sense, but it's born of a complicated mixture of sociological and biological influences. So complicated that we can never know if it's deterministic or a product of free-will. So the acceptance of even that supposition is faith-based.
Finally, even if I accept that morality has Meaning and that there's some higher power governing said meaning, why am I taken necessarily to the existence of a god in anything close to the christian sense, let alone Jesus? If you say that it's just something that you "feel" once you get there, then we might as well abandon all the arguments we've made, because we've just pinned them all on a highly contested, individual perception. Which is fine, as far as universal belief systems go, but sort of pointless to argue. In science we draw conclusions from collective sense perception, things that humanity as a whole can see and verify for themselves. There is a large consensus on things like "the Rocky Mountains exist" and "this sensor dial reads 91 degrees," but for every "I found Jesus" I can point you to a "praise Allah" or even a "hail satan."
It is a bit disquieting to abandon Truth with a capital T for some sort of evolving truth based on statistical sense perception, but if you look at it, disagreement on physical reality barely ever happens when you get a group of people together and ask them to focus their senses on something at the same time. In memory things are a bit more fluid, but the fact that there's so much agreement leads me to believe that physical reality exists for humans in every reasonable sense. If there is no physical reality, either I've conjured it all up in my head (and therefore all my observations are by default correct), or I'm describing another reality that's experienced in a hallucination en masse by humanity. Either way this reality might as well be physical reality, because it's indistinguishable from it in every way.
>>Ironically enough, your day of awakening was based on your demonstrably flawed sense perception.
Ad homein: "Attempting to discredit the debator rather than addressing the specific claims he has made."
First, I did not attempt to use logic to prove that God exists. I used logic to level the playing field and move science down to its rightful place.
Furthermore, A solipsist would tell you that consensus derived of corroberating empirical opinions is nothing more than phenomena corroberating other phenomena, and therefore empty. I am not a solipsist, but their argument does apply, in terms of [the negation of] your validating your own perceptions with those of other people.
When I point out that Kant's breakthrough (which was, in all fairness, Descarte's failure repackaged as Kant's success) levels the playing field between the fields of natural science and religion from the perspective of one who would default to the scientific and the empirical, I do so not in order to justify Kant's morality; Kant's morality is not all that interesting to me. Rather, my emphasis is on that levelling of the playing field, since that levelling of the field compells the intellectually honest person to reconsider religion and faith, and provides legitimate ground to disregard otherwise compelling things, such as arguments that Darwinian Speciation disproves creation.
I do not base my own definition of morality on Emmanuel Kant. But his achievement in the field of philosophy is unmistakable. He shattered the scientists "monopoly on truth," and levelled the playing field with religion.
Personally I don't think that "levelling the field" goes far enough. I've SEEN demons; I've seen miracles. I've seen signs. I pray and the LORD answers. I have a very good scientific mind, but there are things that can vex the most rational of minds until a person accepts the fact that the LORD is real, and is all powerful.
If you haven't seen it, I can understand that, but "atheist" is a negative faith, and it is intellectually dishonest, since it asserts that God does not exist, when God's existence is not a thing to be rationally proved or disproved. Agnostic is the default refuge for an intellectually honest (but spiritually lost) atheist. Go ahead, try agnostic and grow discontnent. Once you're sapped out, seek and ye shall find.
I warred AGAINST the LORD for years, before coming to terms with that.
Regarding the rest of your argument, fine, choose your own religion.
I recommend one that keeps the 10 Commandemnts.
Buddhism and hinduism both have karma, and believe me you don't want it on your tail. What's more, Tibetan Buddhusm and Hinduism are polytheistic. That means you can't abide them alongside the 10 Commandments, which are essential to Islam, Judaism and Christianity.
Regarding Islam. Mohammed spoke with an angel. Not God. That's from the verse itself. Satan is a [fallen] angel because he sought the worship of other angels, and tried to set his throne higher than God. So who cares if Mohammed spoke with an angel. As I see it, (being an infidel =) Mohammed doesn't have crudentials, since it is not up to angels to dictate faith to humans.
Christianity claims to offer salvation; I've seen days when it seemed unlikely, and other times when it seemed very likely. It also says keep the 10 Commandments, love your enemy, love your neighbor, love the LORD, help the poor, don't love money, always forgive, return kindness and blessings in exchange for evil.
As for me, I keep the sabbath on saturday, just as Jews and Muslims do. I don't believe Constantine or the Pope ever had the authority to change the sabbath day, and exodus 16 / exodus 20 make it clear that the LORD didn't want the sabbath changed.
And I believe the sistine chapel is painted with "God", who is in heaven, and therefore the catholic church maintains a sin on its chapel roof, and furthermore with the crucifixes, statues/drawings of angels and statues/drawin
"Forgive us our trespasses, as we forgive those who trespass against us." -Jesus Christ The Lord's Prayer