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[94ssd]

No it isn't.

According to a listing by the U.S. Geological Survey, Rugby is actually approximately 15 miles (24 km) from the geographic center of North America (6 miles (9.7 km) west of Balta), and even this designation carries no official status.

"A random cornfield in the general area of Rugby, North Dakota" doesn't work as well as saying "Rugby, North Dakota."

[pwhodges]

Windows XP requires more storage than the human genome: http://www.tmsoft.com/article-genome.html.

Actually, I don't know where that article got the 750MB for the human genome - I'm just working on pricing up a computer system based on a requirement of 250GB per genome (we're looking at 10,000 genomes, so 2.5 Exabytes).

[Barmymoo]

I'm utterly at a loss to work out why you would need a computer system with storage based on the human genome, but that's almost certainly due to my near-complete ignorance of what you do and what is being done with DNA. Please elaborate if you can!

[pwhodges]

Not storage based on the genome, but storage of the genomes.

We are working on the effects of drugs in the human body (cancer treatment, mainly, in my department).  When comparing the effects in different people, a comparison of their genomes may be one thing that leads to a better understanding of the mechanisms that the drug invokes.  Or maybe a feature of the genome can be identified that would enable prediction of the effectiveness of the drug in certain individuals (or even of their susceptibility to specific cancers).  I can't go much further, not actually being a bioscientist myself!

[LTK]

Windows XP requires more storage than the human genome: http://www.tmsoft.com/article-genome.html.

Actually, I don't know where that article got the 750MB for the human genome - I'm just working on pricing up a computer system based on a requirement of 250GB per genome (we're looking at 10,000 genomes, so 2.5 Exabytes).

I assume you're not writing the genetic code as a string of 1s and 0s directly onto a storage device, which is what the article is describing. Presumably that would require much less bits than storing it as an actual file that programs can read and write to. Even writing the genetic code as a string of ATCGs in a text document would require much more than 750MB.

[Barmymoo]

Paul, that does make more sense, but now I realise that I don't really understand what a genome is and how you can store one. Are you storing descriptions of them, as data on a computer? Presumably you're not somehow stuffing little tubs of DNA samples into a computer shell.

[pwhodges]

@LTK:
Much computer storage is in binary, though, especially with huge datasets; if the code were stored in ASCII, then it would compress dramatically using common algorithms, but I know from an article on the subject I've just read that gzip compresses a conventionally stored genome by only about 35%.

@May:
The genome is the actual sequence of bases (A, T, C, G) in all the DNA of the individual; i.e. the definition of all the genes on all the chromosomes (I don't know if mitochondrial DNA is included).  Essentially it is the complete chemical formula of the whole lot.  The term "sequencing" DNA is used, because the process is determining that sequence.

[LTK]

The article compares the genome to Windows XP when it is configured and installed, but a better comparison would be with the installation CD for Windows XP.

[Barmymoo]

Right, I think I understand up to my capacity for understanding stuff like this! I struggle with molecular biology and really any form of science I can't see, because I don't have the tools for thinking about it. But we briefly covered DNA at university in a single one hour lecture, so I at least recognise the words...

[Aimless]

Actually, I don't know where that article got the 750MB for the human genome - I'm just working on pricing up a computer system based on a requirement of 250GB per genome (we're looking at 10,000 genomes, so 2.5 Exabytes).

While the size of the average human genome may indeed in some way somewhere sometimes be ca. 750MB, the hardware will be used to handle extremely large datasets required for sequencing, analysing, aligning and backing up millions of overlapping snippets of DNA that, taken as a whole, account for many copies of several (in the case of pharmaceutival research, perhaps hundreds?) variants (rather than single straightforward genomes).

Hardware-gobblers:

http://en.wikipedia.org/wiki/Shotgun_sequencing#Coverage

http://en.wikipedia.org/wiki/Sequence_assembly

Data requirements:

http://www.avadis-ngs.com/support/ngs-data-storage-requirements

Overview of one method:

http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/De_novo_assembly#Comparing_datasets

Horrible gargantuan files:

http://en.wikipedia.org/wiki/SAMtools

[pwhodges]

The last computer system I installed for work on genomes has two 250TB storage arrays, and a processing cluster with 256 cores and 16GB of main memory available for each (i.e. 4TB of main memory).  When running flat out it draws 39A from the 240V mains; we had to have an extra air conditioning unit installed in the computer room before we could turn it on!

[LTK]

The article compares the genome to Windows XP when it is configured and installed, but a better comparison would be with the installation CD for Windows XP.

To sate my own curiosity, I've discovered that an original Windows XP disk contains considerably less than 750MB; no more than 600, in fact. The comparison will fall down anyway, because if you follow that analogy then inserting the installation disk in the drive would prompt it to start replicating the entire system, disk included, and it would install a different set of programs on each individual system and network the whole bunch into a massive machine whose primary function is to produce half of an installation disk that is then combined with another half a disk of another network of systems.

If Windows XP did that, tech support would be a nightmare.

[LookingIn]

No it isn't.

According to a listing by the U.S. Geological Survey, Rugby is actually approximately 15 miles (24 km) from the geographic center of North America (6 miles (9.7 km) west of Balta), and even this designation carries no official status.

Most of the other sources I encountered said the same thing: Rugby is the center. Why? Batla is too small(56 or so residents) and being the county seat of the county both towns are in it gets the default title...

[LookingIn]

The last computer system I installed for work on genomes has two 250TB storage arrays, and a processing cluster with 256 cores and 16GB of main memory available for each (i.e. 4TB of main memory).  When running flat out it draws 39A from the 240V mains; we had to have an extra air conditioning unit installed in the computer room before we could turn it on!

Liquid or gaseous cooling is out of the question with that hardware I take it...

[Is it cold in here?]

Three billion base pairs, each with four possible states (two bits). Before compression, six billion bits or 750MB. There are so many repeats that it should be highly compressible.

Today I heard a good example of talking down an upset person in a customer service situation, using a soothing tone of voice and empathizing with the other person's problems. Today I learned that sometimes the customer needs to talk down a weeping "customer service" employee.

[94ssd]

There has actually been a Supreme Court case where the decision was based on the Third Amendment, although it didn't have anything to do with quartering soldiers. In Youngstown Sheet & Tube Co. v. Sawyer, the court ruled that the Third Amendment shows that it was the Framer's Intent for executive powers to be limited even during wartime. The Federal Government had seized steel plants to assist in the Korean War.

Engblom v. Carey, which was decided by the Second Circuit Court of Appeals, is the biggest case that directly involve the Third Amendment. In that case, New York state prison guards went on strike and were evicted from their on-site housing. National Guardsmen were brought in to guard the prisons and lived in those homes.

[LookingIn]

I learned that no matter how many times you try to tell someone an idiosyncrasy of something that only a local would know they just won't listen to it. They ask a question, the don't like the answer, the ignore the answer and ask the same question again at another time 

[LookingIn]

There has actually been a Supreme Court case where the decision was based on the Third Amendment, although it didn't have anything to do with quartering soldiers. In Youngstown Sheet & Tube Co. v. Sawyer, the court ruled that the Third Amendment shows that it was the Framer's Intent for executive powers to be limited even during wartime. The Federal Government had seized steel plants to assist in the Korean War.

The wording of that ruling is more telling: not without congressional approval. It could be done, but requires help from Congress.

Engblom v. Carey, which was decided by the Second Circuit Court of Appeals, is the biggest case that directly involve the Third Amendment. In that case, New York state prison guards went on strike and were evicted from their on-site housing. National Guardsmen were brought in to guard the prisons and lived in those homes.

Ruling was one way, but the outcome went another way...it still went against the guards at the lower levels after the ruling, reason being the state officials would not have been aware of the interpretation.

[Method of Madness]

I'm just working on pricing up a computer system based on a requirement of 250GB per genome (we're looking at 10,000 genomes, so 2.5 Exabytes).

Wouldn't that be "only" 2.5 Petabytes?

[pwhodges]

Oops!  Yes...

[Is it cold in here?]

I don't have to trim my own ear hair!

[celticgeek]

Bill Cosby defines "old age" as "when hair stops growing out of your head, and starts growing out of your ears".

[Method of Madness]

Oops!  Yes...

That's ok, Paul! Learning has occurred!

[Carl-E]

I don't have to trim my own ear hair!

Not sure I want to know the answer to this, but...

who's doing it, then? 

[Aimless]

Babylonian medical texts are really cool. Today, while discussing epilepsy and its association with psychosis, we were reminded of this.

http://www.ncbi.nlm.nih.gov/pubmed/18479392

The lines read in transcription:

ˇsumma amŻelu antaˇsubbˆub Ż el Żuri...qŻat etimmi qŻat mŻamˆıti... eli-ˇsu ibaˇ sˇsi alˆu lemnu ireddi-ˇ s´ u...

and may be literally translated:

“If a man has been suffering from antaˇsubbˆu, bŻ el Żuri, qŻat etimmi or qŻat mŻamˆıti, and an al ˆ u lemnu then begins to in- flict him with ideas of persecution...”

Of the terms mentioned, the first antaˇsubbˆ u, is a Sume- rian loanword and has long been understood to mean “the falling disease,” that is, epilepsy characterized by major seizures. The term bŻ el Żuri which follows means literally “the lord of the roof,” and was evidently the ancient term for an absence attack, the common rolling up of the eyes being caused, supposedly, by a demon lurking in such a position as the roof of a house. qŻat etimmi means “the hand (power or influence) of a ghost,” and although it may have had a wider significance, we have suggested (Kinnier Wilson & Reynolds, 1990) that it refers to nocturnal epilepsy. The word mŻamˆıti in qŻat mŻamˆıti literally means “oath,” but was used medically to denote conditions in- volving obsession or repeated action, as if the patient had sworn an oath to perform a certain action and could not be dissuaded from doing it. In the context of epilepsy, the term may readily be understood as referring to the au- tomatisms of epilepsy or postictal confusion. The words alˆu lemnu translate, nonspecifically, to “evil demon.”

I sometimes feel like we don't learn nearly enough Babylonian medicine

[94ssd]

In addition to counterfeiting, the Secret Service also investigates identity theft. I learned this via a news story about the Target incident.

I have also just learned of the giant statue of George M. Cohan in New York City. I am a theatre major who has been to NYC three times. It is sad that I had to learn this via my musical theatre history class.

Although I also learned from the same class that Cohan was strongly anti-Union. In 1919, Cohan said that if Actor's Equity won the labor dispute they were in, he would quit show-business and run an elevator. A journalist retorted that to run an elevator Mr. Cohan would have to join a union.

[LookingIn]

I have also just learned of the giant statue of George M. Cohan in New York City. I am a theatre major who has been to NYC three times. It is sad that I had to learn this via my musical theatre history class.

Although I also learned from the same class that Cohan was strongly anti-Union. In 1919, Cohan said that if Actor's Equity won the labor dispute they were in, he would quit show-business and run an elevator. A journalist retorted that to run an elevator Mr. Cohan would have to join a union.

Have you seen the Miller Building in Times Square and it's famous statues dedicated to the first ladies of theatre?

[Carl-E]

I have also just learned of the giant statue of George M. Cohan in New York City.

Had my picture taken with it the only time I've been to a broadway show. 

There's a reason...

The Cohans (George, his parents and his sister) were residents of my great-grandmother's boarding house when they were performing in New York.  George got along famously with my grandmother, though she was about a decade younger.  Nevertheless, jokes were made of a "betrothal" (often in exchange for room and board when things were thin for the Cohans). 

George met Mary, so he never wrote a song called "Martha" (My grandmother's name), and my Gramma married a nice first generation German Engineer instead.  But had it gone a little differently...

Well, my last name would be Cohan.  Of course, it wouldn't be me, but... you get the idea. 

[94ssd]

I have also just learned of the giant statue of George M. Cohan in New York City.

Had my picture taken with it the only time I've been to a broadway show.

Our professor said when he got to New York to start his acting career, he got off the subway in Times Square, dropped his bags at the base of the statue, and said "I'm here, George!"

But had it gone a little differently...

Well, my last name would be Cohan.  Of course, it wouldn't be me, but... you get the idea.

Still, it's awesome that you have such a close connection to Broadway's first leading man.

[94ssd]

More news learning - it is against the law to leave your vehicle running and unoccupied, punishable by a $50 fine. Although I have violated this a couple times, I definitely understand how it can be a safety concern as well as an environmental one.

This was mentioned because car thefts increase in the winter

[Method of Madness]

Yeah, I never understand why people do that. You're basically asking for your car to be stolen.

[cesium133]

Today I learned that Jesse Eisenberg and Michael Cera are not the same person. They look very similar, though.

[Method of Madness]

Jesse Eisenberg is definitely the better actor.

[Patrick]

The barrels in which wines are aged matter so much and in such concrete and sciency ways, I had no idea

Things like the pore-size of the oak

whoa

Wine Chemist is an actual no shit career field.

Lemme tell you bout the shit I gotta convince rich white people about every day, dogg

[Carl-E]

So I was at a ukelele event (took my daughter, she learned in the hospital), and recognized a few people.  We were talking, and suddenly realized all three of us had part time jobs related to alcohol.  I sell beer, one of the others sells wines, and the third is a bartender. 


We all depend on alcoholics for our livelihood.  Because face it, the recreational drinkers just don't buy enough.  It's the daily customers that pay the bills...

[bainidhe_dub]

According to NPR, there are only three licensed midwives in the entire state of Maryland!

I found some more info - apparently Maryland doesn't allow CPMs to oversee home births, only midwives who are also certified nurses and work with an OB/GYN. Several groups are trying to get the more restrictive laws changed.

[Grognard]

one of my wife's friends is a CNM.
she's trying to get my wife to get trained.

[Barmymoo]

The difficulty of practising as a midwife is one of the (admittedly numerous) reasons I won't be moving to the USA to live permanently. Are you looking into having a midwife? Can out-of-state midwives come in?

[bainidhe_dub]

I have no idea, it was just mentioned in the radio news this morning that somebody had brought up reforms in the state house, but apparently they tried it last year too and that one never made it out of council.

[Aimless]

The past few weeks have been chock full o' learnin' among other things, I've learned a new structured way to discuss functional seizures with patients, learned a few "new" tricks for dealing with tricky migraine in combination with other chronic headache, learned about some really cool changes to the field of parkinsons wrt disease course as well as a few mysterious phenomena r/t a specific treatment regime, learned that there are DBS-systems that can use feedback mechanisms in order to activate and modulate themselves based on activity rather than just being go go go all the time, learned about some cool research into neurological aspects of space-travel... and that's just the tip of the iceberg. It's been a cavalcade of interesting facts and observations.

The two highlights:

- apparently the annual number of people in northern Sweden who ask to undergo some sort of gender-/sex-change procedure has nearly doubled in the last few years.

- S.A.D. follows V.D.

[Pilchard123]

Grandi's series is fun!

[GarandMarine]

I leveled up my engineering skill a lot this week, with focus on the computer and electrical sub-skills. I've done wiring and stuff before but setting up this cable rig to do my own car audio is a first for me in my personal life, and also marks freedom from the tryanny of the high prices of the car audio install guys. I also diagnosed, and repaired my computer from a catastrophic failure in under 24 hours pausing only to sleep/wait for the shop to open and confirm my diagnosis with my old man, who's been coding since Jesus was private, and "writing code" meant getting out a hole puncher.

So GM leveled up!

[GarandMarine]

Update: Install complete, I didn't mess up the wiring harness, the sound quality is vastly improved over the OME radio. I think I will want to upgrade the speakers at some point to a barebones quality kit, but that's about it. Oh and I confirmed I need an new Audio Aux cable.

[Aimless]

We've started to take the kitchen apart and my heart has been filled with equal parts hatred and admiration for the carpenter who put it together 5-6 decades ago. Everything is in great shape and so ridiculously sturdy, with all cabinets fitted perfectly... and stuck fast to one another so tight it's like the entire kitchen is just one single many-doored multidimensional indestructible cabinet.

In taking it apart (aka wrecking it) I've learned a little about cabinet-making, but, more importantly, I've come to the realisation that the crowbar is one of my favourite tools. So simple and elegant, yet so versatile. Two lever classes, a makeshift chisel, a hammer, a nail-puller... it's just beautiful. I have also learned that they used to be called "iron crows".

[Pilchard123]

Is it bigger on the inside?

[Aimless]

It's just... heavy

Also, the plural of anecdote is data:

http://evidence-based-science.blogspot.se/2009/11/plural-of-anecdote-is-data.html

mind = blown

[Pilchard123]

S₁  =  1 - 1 + 1 - 1 + 1 - 1 + 1 ...
1 - S₁  =  1 - [1 - 1 + 1 - 1 + 1 - 1 + 1 ...]  =  1 - 1 + 1 - 1 + 1 - 1 + 1 ...  =  S₁
1 - S₁  = S₁
S₁  =  ¹/₂


S₂  =  1 - 2 + 3 - 4 + 5 - 6 + 7 ...
2S₂  =  1 - 2 + 3 - 4 + 5 - 6 + 7 ... +
                  1 - 2 + 3 - 4 + 5 - 6 + 7 ...
2S₂  =  1 - 1 + 1 - 1 + 1 - 1 + 1 ...
2S₂  =  S₁
S₂  =  ¹/₄


S₃  =  1 + 2 + 3 +4 + 5 + 6 ...
S₃ - S₂  =  1 + 2 + 3 +4 + 5 + 6 ... -
                   1 - 2 + 3 - 4 + 5 - 6
S₃ - S₂  =  0 + 4 + 0 + 8 + 0 + 12 ...  =  4 + 8 + 12 ...
S₃ - S₂  =  4 [1 + 2 + 3 ...]  =  4S₃
S₃ - S₂  =  4S₃
- S₂  =  3S₃
^-1/₄  =  3S₃
^-1/₁₂  =  S₃
^-1/₁₂  =  1 + 2 + 3 + 4 + 5 + 6 ...

[Grognard]

stop that.

you're reinforcing my perception that I'm dumb as a box of rocks.

[Barmymoo]

It's just... heavy

Also, the plural of anecdote is data:

http://evidence-based-science.blogspot.se/2009/11/plural-of-anecdote-is-data.html

mind = blown

It's a clever quote, because of course it's true - if enough people say that something has happened to them, then collectively their answers are labelled "research data" - but also it is not true - saying something multiple times doesn't increase its validity.

[LTK]

Though not very good data. For starters, aggregating anecdotes is just going to lead to a massive confirmation bias. Think of what happens when you compare the number of anecdotes about Jews being greedy to the number of anecdotes about them not being greedy.