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Comment Re:Central Dogma? (Score 4, Interesting) 196

Actually, as I was taught it (which, I will readily admit, could be wrong), Central Dogma is in fact the proper term, though the definition has been tweaked over time.
Originally it stated something along the lines of, One DNA gene is transcribed into one RNA transcript, which is then translated into one protein.
The discovery of antibodies threw that concept out the window. Variability in intron splicing and recombination means that a small handful of genes can yield a huge variety of protein products (See VDJ recombination).
Yet another twist was added with the discovery of retroviruses which reverse the direction of transcription, turning RNA into DNA. Previously we had thought the central dogma to be unidirectional.
The more we learn about life's mechanisms, the less surprised we are when exceptions to the rules are discovered. Evolution really is the ultimate hacker; constantly expanding the usefulness of very simple resources.

Also, kudos on the evangelion reference.

Comment Re:What? (Score 1) 414

Sounds nice in theory, but it's not as easy as you make it appear. First of all, modifying a plant is far more difficult (due primarily to the cell wall) than modifying a bacteria or animal cell. Viral vectors are limited by transgene size and target species, and gene guns are somewhat of a crap shoot. Add in plants' very high tolerance for polyploidy and polysomy, and it becomes quite difficult to add in an effective kill switch.

So, major structural changes that would prevent cross-breeding are out because
1: the knockout/knockin transgenes are simply too large for available vectors.
2: pollination efficiency would likely drop through the floor, making it ultimately unsustainable.
3: assuming you used the structures of some existing species, you now have to worry about your other transgenes spreading to those species as well (admittedly, this is unlikely, but still needs to be considered).
Artificial Chromosomes are out because plants will happily tolerate most all of the mismatch errors which would kill animal cells.
Making a gene metabolically expensive so that it confers no evolutionary advantage (and thus would not be preserved in wild populations) is essentially asking your crops to fail. You could compensate with more fertilizer, pesticide and water, but the extra maintenance required would defeat the purpose of growing GM crops in the first place.
Killswitch genes perhaps? They have plenty of their own problems too.

So, what mechanism would you propose?

TL;DR Breeding incompatibility with wild crops sounds nice in theory, but it's problematic to implement. Also, sorry if my rant is illogical/incoherent, It's the weekend, and my brain's on break as well.

Comment agreed! (Score 3, Interesting) 71

First, I agree completely. I can't tell you how much time a program like that would save.

I'd just like to add in a quick feature request. It would be very nice if it could take the .ab1 files from sequenced clones and quickly align and compare them to the theoretical construct, and then indicate what needed to be done differently. For example, "your inserts are forming concatemers: adjust their concentration relative to the vector during the ligation step, or treat them with CAP (alkaline phosphatase)." or "this particular sequence has internal cut sites: use this restriction endonuclease instead."

The software that I'm using now does allow you to figure out situations like the above, but all it does is alignments; Analyzing the reasons why something didn't work out takes guesswork, and the comparisons prettymuch have to be done manually. For the concatomers example, I'd have to back to my original insert sequence, make a text document of the DNA sequence, import multiple copies into the program, reverse a couple of them (sense/anti-sense), and then manually align the second and third copies. It's very time consuming when it really shouldn't be.

Comment Plasmids kinda do this already. (Score 2, Interesting) 71

'I'm interested in transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.'"

To some extent, this is already done with common bacterial strains, and the plasmid vectors we already use. Most of the plasmids we use in the industry have specific sets of features such as multiple cloning sites, inducible repressors, ORIs, antibiotic resistance sites etc... You need a plasmid that has a kanamycin resistance gene, high copy number, will add a His tag to your product, and lacks cut sites for a particular restriction enzyme? It's likely in the catalogues already. And if what you're trying to assemble is already in the catalogues, it's a target that may not be worth pursing anyway, since you're unlikely to get a publication or a patent off of it.

The approach he seems to be pushing here seems to be analogous to buying a car piece by piece rather than as a pre-assembled package. The difference is that while average joe has no idea how to fabricate a synchro for his transmission, your average molecular biologist is already quite adept at designing primers and cloning fragments out of a cDNA library. The hard part for the scientists is then characterizing, validating and optimizing the expression of their target; and then later demonstrating the functionality of the product. To continue the analogy, it would be showing that the car ran, was reliable, and was safe for the passengers. Having readily available gene circuits (the famous lac operon for instance) may help with the planning and initial development, but it really won't speed up the bulk of the work we do.

I'll readily admit that many of the expression/knockout constructs are somewhat ad hoc in nature, but interoperability isn't typically a concern. The thing is that evolution is a pretty laissez faire system where "duct tape and bailing wire" construction is more often the rule than the exception. Nature cares about what works, not about what conforms to standards (codon-amino acid translation being the biggest exception that comes to mind). As a result, expression systems have to be tailored to the organism that they'll be expressed in. For instance, bacteria cannot express functional mammalian genes unless the introns are removed from the sequence first. Sufficiently large yeast proteins will cause an immune reaction because the glycosylation patterns are recognized as foreign. Many genes won't be expressed very well at all unless the regulatory elements in the flanking sequences are also included. Once you start looking at things like inducible expression and tissue-specific expression, things get even more complicated, and more varied between species. In short, it's complicated, and the idea of instituting standards to achieve interoperability between expression systems is pretty much a pipe dream.

In short, I have my doubts about the plausibility of this plan, and I'll be mighty impressed if he pulls it off.

Comment Re:"Junk" DNA (Score 1) 360

I'm of the opinion that the person who coined the term "Junk DNA" did the field a disservice.

Much of the 'junk' DNA did serve a purpose at one point; deactivated genes for instance. Much of it still serves a purpose now, such as coding elements and transcription factors (see the work of Sean Carroll for more info on this point). Some of it is there for epigenetic and structural modifications such as the methylation of cysteine residues, (and similarly the acetylation of histones) which actually changes the shape of the DNA helix itself (and this affects transcription). And some of it is there simply to take up space. Intron splicing, for example, requires a minimum distance between the exons to function properly; longer is okay, but too short and you'll start skipping out on pieces of genes that *should* be there. And, following one of the older theories about the purpose of the 'junk' DNA, it acts as a buffer space to limit the damage caused by mutations that *will* happen.

So yes, the "junk DNA" isn't necessarily useless; but in many cases its sequence isn't necessarily meaningful either.

To use a car analogy: Sometimes it's like analyzing the composition of your engine block, where changes in the trace elements can have an affect of the performance of the vehicle as a whole. And sometimes it's analyzing samples of the air residing in your door panel (between the exterior sheet metal and plasticky interior) It's there to take up space and its composition really doesn't matter overall.

Comment Re:A bit unclear to me... (Score 1) 360

I'm guessing that it's a one time treatment.

As I understand it, no. Since the change this produces is in the transcription/translation machinery of the cell, rather than in the DNA itself, the treatment is not permanent. Different substances are recycled in the cell at different rates (and nearly everything gets recycled at some point), with the cell rebuilding the parts that are in its genetic blueprints. Parts that aren't in the blueprints (i.e. the molecule that allows the gene to produce a protein product) do not get rebuilt. So the change is _not_ permanent.

Otherwise they would use an engineered virus to deliver the mutation to your entire body.

This is very unlikely to be used as a treatment any time in the near future. When gene therapy using viral vectors was introduced, there were several cases where it was quite successful. There were also deaths. Those deaths and the fear mongering that accompanied have created a social climate where very few people would acknowledge gene therapy as a valid treatment option.

Comment Re: the islands (Score 1) 259

From my original post:

Obviously this is all unconfirmed at best. and I still have some serious doubts about the story,

and

Again, this is all just rumors and lies at this point

And from my subsequent post

Okay, I need to get my facts straight. After doing some reading up on the topic (too late obviously) it is not clear to me that this guy's story was crap.

Now, what part of all that indicated that I "believe anything someone tells [me]?" I apologize if my post came across as if I were preaching doctrine from the mouth of God Himself, but I thought I was pretty clear that this was all speculation.

Comment Re: the islands (Score 1) 259

Okay, I need to get my facts straight. After doing some reading up on the topic (too late obviously) it is not clear to me that this guy's story was crap. The GM island *does* in fact exist as confirmed by WoWwiki. The islands are in fact, closed zones; Tel Abim and Zandalar specifically. The exploit to get these islands (here I go with the crazy theories again) is covered in a Thottbot post on the Levitate spell.

[...] I mounted, and as I lept off into the horizon, I casted levitate. I came to a point where the map disappeared, but the water continued to stretch out into the distance.
Some theorize that this is where GM Island is located.
Okay, so we all know that GM Island is in an instance now. But like any instance, there's a non-instance version of it. Like when you set old world instances to "Heroic" and walk behind the portals. GM Island wasn't always an instance, and programmers just don't delete environment from the game. Case in point, Old Ironforge and Ironforge Airport.
Granted, you'd have to walk pretty far, assuming GM Island IS in that direction...
Moving on, it's unreachable alone...attempted it. However, multiple priests together could do this easy. Have 5 or so in a group together so they can heal off of each other with renew and circle of healing. Another tip, wear +healing gear that has no stamina. Fatigue hits for 20% of your max health every 1-3 seconds. Low health means low damage, high healing means you can heal over it. 5 priests means you can have a few of them sit back and relax while the others cast, so not everyone wastes mana.
If you are really interested in doing this, make it 4 priests and a warlock.
"Harmonex wishes to summon you to GM Island." [...] Of course, this is all under the assumption that GM Island even exists on the main map...

Comment Re: the islands (Score 2, Interesting) 259

There are also indications that early design work included some of the islands in this area,

It's true that a couple of islands appear on the map near the vortex. I heard a rumor about them once indicating that they were at one point accessible to players. Swimming there wasn't possible due to the fatigue that resulted from the deep water. However, if you had a couple stacks of elixirs of water walking, you wouldn't be affected by the fatigue since you weren't swimming. According to the one player I knew who had claimed to have been there, it took about 45 minutes of wandering around with nothing but waves in sight. Once he got to the island, he looted a chest that contained a full tier set of paladin gear. 20 minutes later his account had received a 72 hour ban, and all his recent loot had been removed from his inventory. His theory was that the island was a place where GMs could perform in-game testing of items and whatnot. Obviously this is all unconfirmed at best. and I still have some serious doubts about the story, but anyway, that's the only thing I've ever heard about the islands.

And just so that this post isn't entirely off topic, here's a link to some of the current speculation on the lore which will be experienced with the expansion. As an added note, it's doubtful that this will be the final expansion of the game. Most are speculating that there will be a 5th chapter in which players will get to enter the emerald dream. Again, this is all just rumors and lies at this point.

Comment Measure of a Byte (Score 1) 495

So which Petabyte are we talking about? The functional petabyte (i.e. 1,125,899,906,842,624 bytes), or the hard drive manufacturer's version( i.e. 1,000,000,000,000,000 bytes)?

Actually, a quick wikipedia search tells me that 10^15 is indeed the petabyte, while 1024^5 is the pebibyte. But according to Wikipedia I've been using the wrong terms this whole time anyway. kibibytes, mebibytes, gibibytes, tebibytes. etc... Somehow it all feels wrong now, and I want to blame Western Digital, or maybe Maxtor.

Comment And this is how this happened... (Score 4, Funny) 844

from Drs. Erick Janssen and Stephanie Sanders, both of the Kinsey Institute.

Erick: Hey Steph, I'll give you $100,000.00 if you sleep with me a few times.
Stephanie: How many times is a few?
Erick: Until we reach statistical significance.
Steph: Cash?
Erick: Sure.

Two weeks later, Erick pockets the other 300 Grand.

It's funny.  Laugh.

Submission + - Favorite Fallacy? (poll suggestion)

mauthbaux writes: Favorite Fallacy?

non Sequitur
cum hoc ergo propter hoc
ad hominem... you insensitive clod!
plurium interrogationum
Circular reasoning
false dichotomy
Loki's Wager
the Chewbacca defense
Cowboyneal said so!

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