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.

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.

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.

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.

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.

because the parasite that causes malaria can't fully develop into the human pathogen outside of the mosquito (among other reasons).

Yes, I was incorrect. Please see the clarification I've since made. I'll accept the blame for having posted something for which I don't have sufficient justification or evidence. Feel free to mod down the original comment and the disinformation it contains.

From my original post:

and

And from my subsequent post

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.

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.

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.

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.

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.

That's a bit like what happened when I tried to get my brother to switch to Ubuntu. When I called him later and asked him how it was working for him, he informed me that he had switched back to Windows.

His reason? "I couldn't get the antivirus to install."

As I understand it, the "objectionable" was referring to the lyrics in the music rather than fear of infringement by the copyright holder.
Quoting from Engadget because I can't find the nin.com post:

The nin.com front page currently has a link to download the app for those of you who are interested in it.
Disclaimer: I'm not associated or affiliated with Engadget, the above quoting was simply convenient for posting purposes.

This VG Cats comic seemed pertinent to the topic. No I'm not affiliated in any way. http://www.vgcats.com/comics/