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CRISPR-Cas9 ("Mr. Sandman" Parody) | A Capella Science

eric3579 says...

CRISPR-Cas9
Bring me a gene
Encoding for a specific protein
Make a few snips at this coded locus
You work so well inside a streptococcus
Cas9
I'm so alone
Without your scissors in my chromosome
Cut me up and do it clean
CRISPR-Cas9 bring me a gene

CRISPR-Cas9
Keep me a gene
A viral sequence you've already seen
Chopped into bits and stored as genomic
With clustered repeats
That are palindromic
Cas9
Bind with this code
Use it to target infections of old
Immunized like a vaccine
CRISPR-Cas9 keep me a gene

CRISPR-Cas9
Cut me a gene
With a precision that I've never seen
Unzip a strand and interrogate it
Seek out your sequence until you locate it
Cas9
Lock into place
And do your job as endonuclease
Chop just like a guillotine
CRISPR-Cas9 cut me a gene

Snip snap!
CRISPR-Cas9
CRISPR-Cas9

CRISPR-Cas9
Bring me a gene
By commandeering my repair routine
A strand to match your severed location
For some homologous recombination
Cas9
Cheap and precise
Rewriting genomes from microbes to mice
And soon the humble human being
CRISPR-Cas9 bring me a gene

CRISPR-Cas9
Give us a gene
Give us a miracle like that one Nazarene
‘Cause giving the lame their legs and the blind their sight is
In view for dystrophy and retinitis
But CRISPR-Cas9
What if you fall
Outside our power and inside us all
That really could incite a scene

When this terrible wonderful power unsettling
Opens the door to unethically meddle
Is ev’ry congenital malady bettered
Sufficient to warrant genetics unfettered
To modify man in the manner of Gattaca
Raise up a mammoth or make a rattata
Dramatical medical means to eradicate aging
Or cancer or make a fanatic
A mass epidemic a weapon nefarious
Single mosquito to wipe out malaria
Send in a viral infection to ferry a
Cure to the cells of an HIV carrier
Freed of disease as we're free to uncover
What nature and accident failed to discover
And free to be other than
All that we ever have been

CRISPR-Cas9
CRISPR-Cas9

Oh CRISPR-Cas9
Bring us a gene
You wondrous ribonucleoprotein
You have the power to vanquish or save us
Who would have thought that the microbe that gave us
Cas9
S. pyogenes
The source of strep and flesh-eating disease
Housed this marvellous machine
Full of uses great and obscene
CRISPR-Cas9 bring us
Please don't sting us
Cas9 bring us a gene

With adenine
And thiamine
Incite a scene
Cas9 bring us a gene!

Native American Protesters Attacked with Dogs & Pepper Spray

bcglorf says...

@newtboy
I admit that perhaps invading Palestine slowly was their best viable option before the war ended.....I just think it's helpful to be perfectly honest that that's what happened and not play some game about it and pretend they hold the moral high ground on that part of the issue.

I guess I just don't agree on calling it an invasion from the outset. European Jews had the doors closed to them everywhere the world over, illegal immigration or staying in what would become Nazi occupied Europe were their only options. Palestine was hands down the most attractive option, despite a hostile Arab Palestinian population. The main reason being that the Jewish Palestinian minority were basically a state within a state. The Arab and Jewish populations had both sufficiently failed to integrate already that they were operating as largely segregated and autonomous regions. Thus, Jewish Palestine was both reasonably close to Europe, and very much welcoming to the people leaving. I don't believe that's fair to be marked as an invasion from the outset. I must insist that if we get to insist all actors conduct themselves in their own self interest, that the Jewish immigration from Europe to Palestine could have been entirely peaceful, and if the Arab population had taken a live and let live approach things could have gone swimmingly. Of course humans aren't ideal or moral very often, so both sides fought and tensions arose. By the time WW2 was over it was too late, the dice were cast and another Jewish exodus from Palestine back to Germany wasn't gonna work. Neither were the Jewish people promised a thing from Germany and it would all be on a hope and a prayer. They had a better shot making their own future by standing their ground in Jewish Palestine. Truth be told, I really can't blame the Jewish side for saying enough is enough and we're gonna stand and fight. Neither can I blame the Arab Palestinian's over much as their biggest fight was really just for independence from the British. With the British gone, both the Jewish and Arab residents fought it out over who would control what, which is sadly fairly natural.

The point I DO lay blame is when the civil war took a pause and Israel declared independence on the UN mandated borders. The Arab world(not the Arab Palestinians) jointly refused to accept any Jewish portion of Palestine and swore to drive them into the sea. Worse, they vehemently called for the retreat of all Arab palestinians from the region to make it easier to clear the country out. Of course, they failed to win that fight and it's been a source of great shame and horror ever since. They didn't fail for lack of strength in arms or numbers, but because each neighbouring Arab state cared not a whit for restoring Palestine to the Arab Palestinians but instead each sought to seize a portion of it for themselves, as invaders. Luckily for Israel they exploited those divisions to come out the other side.

There's plenty of atrocities to blame on the Palestinian response, but also empathy for a displaced and, today, a decimated people still suffering horrifically, mostly for 'sins' of their grandfather's, namely the sin of fighting invaders stubbornly.

But that is all the more the tragedy, as that is very clearly the way the Israeli's started out. They remained peaceful and fled as nation after nation tried to destroy them. The most open place to them in the time probably was Jewish Palestine. For all the atrocities to blame on Israel, I also have empathy for the plight they started from. Even their whole history through today is a tight rope walk were losing any single one of the wars from then till now would have seen the end of Israel as state.

As much blame as one can put on Israel for meeting homemade rockets with professional air strikes, they aren't the only ones to be blaming. Yes, more empathy is needed for the Palestinians than blame. But their are plenty of states, mostly Syria and Iran using the Palestinians as proxies and pawns. So many Arab entities WANT to see dead Palestinians in the news because it plays well for them. I really insist they get as much or more heat than Israel for the tragedy unfolding.

Are You Ready To Be Outpaced By Machines? Quantum Computing

moonsammy says...

I was hoping for more meat to his presentation, and was disappointed. I feel that he said absolutely nothing to help anyone in the audience understand what quantum computers actually DO or what sort of problems they'll help to solve. They'll absolutely not increase your FPS, as that's not what they're well-suited to do. What they are quite excellent at is taking a problem with many possible solutions and finding the correct (or best) one at an extremely high speed.

One example would be the Traveling Salesman problem. In brief, find the optimum route for traversing a number of points on a map. This is useful for things like scheduling package delivery routes, airline flights, etc. With a classic / current computer we write software that cleverly chugs through the possible solutions, throws out any that prove to be poor, and eventually gets to what appears to be the best or is at least a "good enough" solution. As the number of necessary points to be visited increases this problem scales in complexity quickly, so eventually a current computer would just choke on the problem and at best return an ok-ish solution in a reasonable period of time.

A quantum computer is a totally different beast. If it's "big" enough (IE, is comprised of a sufficient number of qubits), it takes the entire set of all possible solutions to the problem, and rather than iterate through them to find the best one, it checks them all simultaneously and immediately returns the optimum solution. It does this by using properties of quantum mechanics, and I think this is where the speaker was drawing his talk of parallel universes. If there are 3 qubits, they would exist as 000, 001, 010, 011, 100, 101, 110, and 111 simultaneously. The software would then define what the best answer would look like, and the computer returns the answer.

You can hopefully see how this totally breaks encryption. With a current computer and a long enough encryption key, an encoded message would take the fastest machines a huge number of years to decipher. With a quantum computer you hand it a gibberish encrypted message, it loads all possible transformations of that message simultaneously, and it then returns the transformation which looks most like a coherent message.

I'm excited to see what these machines can do for us, but they're going to necessitate some significant structural changes in how we handle sensitive data.

RetroReport - Nuclear Winter

RedSky says...

I agree it's fair to argue there is an incentive in science, fudge statistical methods so your findings are more significant and warrant publishing in a scientific journal. But this is an incentive across science, and it hasn't stopped scientific progress as by nature, the process is self correcting when contradictory studies come out especially in a busy area such as climate science. The cost of falsifying studies or having your study contradicted is also significant however.

If you want to talk incentives though, consider the benefits to spreading doubt about climate change by the fossil fuel industry. 7 out of 10 of the largest revenue generating companies in the world are in oil. The industry stands to lose some $30 trillion from climate change in the next 25 years. Paying a PR firm to promote an agenda, paying researchers to dummy up research with a pre-determined anti-climate change conclusion is chump change to them. The cost to them are negligible if they disguise the source of funding sufficiently (e.g. funnel it through a business lobby).

Meanwhile any impropriety on the part of some climate scientists has not shaken the 97% consensus on climate change.

http://climate.nasa.gov/scientific-consensus/

Buttle said:

It became obvious that the calculations supporting the idea of nuclear winter were fudged. Same with climate change -- I'm not saying that it does not exist, just that there is a strong and pervasive incentive to maximize hysteria without regard to science or facts, which leads, eventually, to climate fatigue.

Climate change will be remembered as one of the more striking popular delusions or madnesses of crowds.

Daily Show Extreme Vets Trump Supporters

Next leak will lead to arrest of Hillary Clinton – Assange

MilkmanDan says...

For a moment, assume for the sake of argument that Assange is right. Next round of emails gets released, there's damning evidence of criminal actions or other behavior that are sufficient to arrest or at least force Hillary to drop out of the race. What would happen if that does come to pass?

Would the Democrat party be able to name Bernie as their candidate, since he got the second highest number of delegates? He has already endorsed Clinton and officially returned to being an Independent instead of a Democrat (or at least says that he would return to the Senate as an Independent). In light of that, would they pass the torch to Tim Kaine as Hillary's VP pick?

It's all pretty weird and unprecedented. I can only think of the Nixon resignation as setting any sort of example; but maybe there have been Governor candidates disqualified due to criminal activity in the middle of a race before?

I must say, it seems to me that it would almost be a blessing for the Democrat party if it *does* come true and they revert to Sanders for the nominee. I tend to think he'd easily beat Trump in the general election (although having endorsed Hillary could be damaging), and we'd all have the benefit of having someone with actually positive favorability ratings on the ballot...

Probably all wishful thinking on my part as a Sanders fan. But still interesting to contemplate.

Racism in UK -- Rapper Akala

Barbar says...

I'm far enough away from these issues to admit that I don't have anything like concrete knowledge on the subject, but I feel like I should mention some of the more obvious counterpoints to some of the things he's said in this video. Otherwise I'd get that dirty echo chamber feeling, and no amount of showering seems to wash that away. Could be I'm just a masochist, though, who enjoys arguing.

I think there's racism in every culture. I think it's often much more subtle than described in the video, often even subconscious. I also think that modern western culture is among the least racist cultures to have ever existed, despite our many complaints.

I guess I'll talk about Libya first. The west (the white people he was talking about) is continuously demonized for supporting tyrants and the like. Yet when they participate in overthrowing a clear example of a extravagant super villain tyrant, they are demonized for that. I'm not saying they didn't have other motives, I'm just saying that it's an example of a tautology. No matter which choice they make they are labeled racist.

Now, when beleaguered folk make a desperate attempt to dangerously cross a sea, well knowing the risks they are incurring, it is again the fault of the Italians for not rescuing then with sufficient alacrity. Yes, many of them are coming from countries the west had a hand in destabilizing. But it would be pretty racist for you to demand that the Italian navy take full moral responsibility for the actions of other western nations, simply because they are white too. Also, if the only number you pay attention to is the number that drown, your bias is showing.

Next the issue of the Commonwealth. It seems absurd to expect the UK to treat former colonies populated by citizens that had moved there the same as former conquests that have since shrugged off the yoke of empire. The justifications for this discrimination would seem to be a combination of racism, cultural chauvinism and sober pragmatism. The latter two factors clearly scale with the gap between the culture of the colony in question and the home country, and probably ought to in some sense.

The incarceration thing is tougher to poke holes in, and clearly a much more touchy subject. Once could argue all sorts of justifications for why more members of ethnic minorities are apprehended, but it's nebulous and smells of bias and chauvinism, at best ending in a chicken vs egg conundrum. But once you're in police custody, I think can agree on demanding a higher level of equality of outcome. So I checked out a charity called Inquest who had compiled pretty comprehensive stats on police custody deaths since 1990. Here's a link: http://www.inquest.org.uk/statistics/bame-deaths-in-police-custody
To summarise, since 1990, ethnic minorities have made up a total of 153 out of 1557 deaths in police custody, or roughly 10%. Given that they currently make up 13% of the population, that seems to be well within an acceptable range of results, so I was confused at first. Then I thought maybe he had misspoken and had meant to say state custody, or inmate deaths. So again I looked for some numbers, and again Inquest had the most comprehensive data, broken down by year and ethnicity etc. Again here's a link: http://www.inquest.org.uk/statistics/deaths-in-prison
It shows 453 out of 3963 prison deaths are suffered by ethnic minorities. This seems almost perfectly in line with the 13% population of said minorities. So again, I'm a bit confused by the point he's making.

All of that said, I think I agree with the sentiment of his presentation, which perhaps confuses me even more.

John Oliver - The NRA

scheherazade says...

For obvious reasons. People that want something banned, don't want statistics showing that shows it doesn't kill. And people that don't want something banned, don't want statistics showing that it kills people.

Bed manufacturers wouldn't want the CDC studying beds - because 400+ people die each year by falling out of bed. Windows tint manufacturers would have no problem with the CDC studying the effects of window tint.
Combine that with sufficient political influence, and you get either a ban or a mandate.

Pretty much most things you encounter in the day have some lethality rate to them, just most don't have such an effective organization defending their use. Nor do most draw as much attention. Not much noise about the lethality of bad bread, or errors in GPS maps, or whatever else gets people killed each year. But if there was noise, and there was political strength behind it, you'd be seeing bans on CDC studying GPS map errors.

-scheherazade

SDGundamX said:

Man, CDC always seems to take it up the ass. Don't they also have some crazy restrictions on research into marijuana usage as well that prevents any meaningful research from getting done?

Islamophobia...Now there's a pill for that!

oritteropo says...

I'm impressed Unlike @newtboy, I don't automatically assume you're lying and feel compelled to do a bit more reading myself before discussing it further.

It's been a long time since I studied it at Uni, and even then we never studied the entire Koran (a one semester course would not have been sufficient for that).

There is, of course, some disagreement about what the hadiths say. The one that immediately springs to mind is "Seek knowledge even as far as China", and I'll quote the former prime minister of Malaysia here:{quote}A hadith says: “Seek knowledge even as far as China.” It was pointed out by detractors that this was just a saying of the Prophet and it was not a command from God. When they disagreed with a particular hadith, they were quick to discredit it and refused to acknowledge it as a source of Islamic teaching. But if they subscribed to it, then they would not cease to highlight it repeatedly, even if it’s authenticity is doubted. Surely seeking knowledge in China does not mean Islamic knowledge. During the Prophet’s period, China was also known to have deep knowledge in such fields as medicine, literature and paper, explosives and many others.{quote}

Certainly the early muslims were very keen on acquiring knowledge, and did indeed travel as far as China to do so (and brought the art of paper making back with them).

coolhund said:

Yes I did, it was very tedious because of the writing style. Its pure indoctrination, intended to. Even I felt like I have to think like that after a while.
I read every translation, there are nice sites that provide each translation side by side. But in essence they all say the same thing, and the translations only prove how Taqiyya is even used in some translations. For example, everyone knows what "hit them on their necks" means.

Elon Musk Explains Why We're Probably Living In A Video Game

spawnflagger says...

Any sufficiently lengthy simulation has a built-in checkpointing mechanism. So if there was a BSOD, we could just restart at the most recent checkpoint.

This also brings about the possibility of the universe being only 4000 years old, or only 0.001 seconds old - with all of reality and your memories implanted from that checkpoint.

Jinx said:

I think it is feasible that we could create a virtual world, which would make me quite terrified that our reality might suddenly BSOD.

Bill Maher: Dilbert Creator Scott Adams

ChaosEngine says...

None of those sound like support to me.

The first comment doesn't really state anything either way, other than he doesn't want to be associated with the circus of Trump.

The second still isn't an endorsement.
He says Trump isn't qualified to be President: patently obvious.
He says he thinks Trump can change that situation (people being scared of him): probably true, but again not an endorsement.
He predicts Trump will win in a landslide: it's certainly possible, but again, not an endorsement.

He says Trump doesn't scare him: This is the closest to an endorsement.

Basically, I agree with most of that statement (Trump doesn't scare me, but the thought of a Trump presidency is fucking terrifying).

That doesn't mean I support Trump, and no, it's not out of some fear of a social backlash, it's because I think he's a fucking pathetic excuse for what might charitably be called a human being.

Is it possible Adams supports Trump? Of course, but there isn't really sufficient evidence to make that claim.

Imagoamin said:

I'm getting it from the fact that whether he actually says it out right, he has great admiration for Trump, has done AMA's on the Donald Trump sub reddit (https://www.reddit.com/r/The_Donald/comments/4eglxx/) and routinely praises him to the point of endorsement.

In that AMA, he says:

"I don't want to be tarred with whatever ridiculousness gets spray-painted onto Trump's reputation. So it was a good way to document some distance. "

and

"In my view, Trump is not currently qualified to be president because he scares too many of my fellow citizens. (He doesn't scare me.) But I do think he can change that situation. That's why I predict he will win in a landslide."

His only reason for not outwardly supporting him is because its socially toxic, not that he doesn't actually support him.

Tesla Model S driver sleeping at the wheel on Autopilot

RedSky says...

@ChaosEngine

I'm not sure you understand what machine learning is. As I said, the trigger for your child.runsInFront() is based on numerical inputs from sensors that is fed into a formula with certain parameters and coefficients. This has been optimized from many hours of driving data but ultimately it's not able to predict novel events as it can only optimize off existing data. There is a base level of error from bias-variance tradeoff to this model that you cannot avoid. It's not simply a matter of logging enough hours of driving. If that base error level is not low enough, then autonomous cars may never be deemed reliable to be unsupervised.

See: https://en.wikipedia.org/wiki/Bias-variance_tradeoff
Or specifically: http://scott.fortmann-roe.com/docs/docs/BiasVariance/biasvariance.png

It's the same reason that a stock market simulator using the same method (but different inputs) is not accurate. The difference would be that while 55% correct for the stock market may be sufficiently accurate and useful to be profitable, a driving algorithm needs to be near perfect. It's true that a sensor reaction time to someone braking unexpectedly may be much better than a human's and prevent a crash, so yes in certain cases autonomous driving will be safer but because of exceptional cases, but it may never be truly hands-off and you may always need to be ready to intervene, just like how Tesla works today (and why on a regulatory level it passed muster).

The combination of Google hyping its project and poor understanding of math or machine learning is why news reports just parrot Google's reliability numbers. Tesla also, has managed to convince many people that it already offers autonomous driving, but the auto-steer / cruise and changing lanes tech has existed for around a decade. Volvo, Mercedes and Audi all have similar features. There is a tendency to treat this technology as magical or inevitable when there are some unavoidable limitations behind it that may never be surmounted.

Tesla Model S driver sleeping at the wheel on Autopilot

RedSky says...

Woah, woah, you're way overstating it. The tech is nowhere near ready for full hands-off driving in non-ideal driving scenarios. For basic navigation Google relies on maps and GPS, but the crux of autonomous navigation is machine learning algorithms. Through many hours of data logged driving, the algorithm will associate more and more accurately certain sensor inputs to certain hazards via equation selection and coefficients. The assumption is that at some point the algorithm would be able to accurately and reliably identify and react to pedestrians, pot holes, construction areas, temporary traffic lights police stops among an almost endless litany of possible hazards.

They're nowhere near there though and there's simply no guarantee that it will ever be sufficiently reliable to be truly hands-off. As mentioned, the algorithm is just an equation with certain coefficients. Our brains don't work that way when we drive. An algorithm may never have the necessary complexity or flexibility to capture the possibility of novel and unexpected events in all driving scenarios. The numbers Google quotes on reliability from its test driving are on well mapped, simple to navigate roads like highways with few of these types of challenges but real life is not like that. In practice, the algorithm may be safer than humans for something like 99% of scenarios (which I agree could in itself make driving safer) but those exceptional 1% of scenarios that our brains are uniquely able to process will still require us to be ready to take over.

As for Tesla, all it has is basically auto-cruise, auto-steer and lane changing on request. The first two is just the car keeping in lane based on lane marker input from sensors, and slowing down & speeding up based on the car follow length you give it. The most advanced part of it is the changing lanes if you indicate it to, which will effectively avoid other cars and merge. It doesn't navigate, it's basically just for highways, and even on those it won't make your exit for you (and apparently will sometimes dive into exits you didn't want based on lane marker confusion from what I've read). So basically this is either staged or this guy is an idiot.

ChaosEngine said:

*snip*

John Oliver: Primaries and Caucuses

bareboards2 says...

@newtboy

And yeah. I'll blame independents and moderate Republicans and Democrats who don't vote in November if Trump wins.

That will be on your heads. If you don't vote or vote for a third party and Trump wins.

Because Trump will be a disaster for the world and this country.

As one prominent solidly conservative R has said about his decision to vote for Hillary -- our republic will survive her presidency. It probably won't survive a Trump presidency.

And if moderate Rs vote Trump and Dems stay home and independents vote third party because they haven't been sufficient woo'd...

Yeah. I will blame all of you.

The Julie Ruin - Run Fast (Official Lyric Video)

chicchorea says...

What you think...is your problem. A mind can be a terrible, or banal thing.

It was an expression of the dislike or your insipid submission sufficient for me not to waste enough consciousness to finish watching it as is proper and mandatory for a downvoting which is what it deserved. I only gave it any attention as people that I like and respect gave you attention and thought to endeavor to give you a chance. No good deed goes....

You did provide the motivation to revisit the repulsive submission.

Your reactions, submission,...will not likely waste my consciousness again.

As to that individual being one sided in your view. You resemble your remark. He is intelligent, incisive, and predominately objective and even handed. Your perception to the contrary is as telling as, well,...doll.



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