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Oldest Human Genome Reveals When Our Ancestors Mixed With Neanderthals

kinko Re:Question for sequencing expert. (128 comments)

I don't know if ancient samples are processed differently, but for 'fresh' samples, the DNA gets broken up into small fragments (200-1000 base-pairs long), and then these fragments get sequenced. All bits of the genome have roughly even chance of getting sequenced, and with thousands or millions of copies of each fragment, you normally get reasonably even coverage over the whole genome.

The problem is when you map your sequences back onto a reference genome (ie the currently known chr1, chr2, chrX, etc). The aligning software will have trouble deciding where to place a fragment that is part of a highly repetitive sequence (like centromeres or telomeres) , or is duplicated several/many times (eg large gene families that have large sections of the genes in common, or pseudogenes that look like copies of other genes). In addition, we don't even know the exact sequence for some of these regions, so our reference human genome is contantly being updated (currently up to version 38).

For bioinformatics analysis, sometimes it is easier to sweep some of this under the rug. For example, some people use a reference genome that masks out the centromeres and telomeres (ie our reference sequence just has NNNNNNNNNNNN bases here, instead of As,Cs,Gs and Ts). Otherwise there are databases that list the regions containing repeated sequences or duplicated segments, so you can check any of your findings to make sure they aren't in a suspicious region.

about a month ago
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"Double Irish" Tax Loophole Used By US Companies To Be Closed

kinko Re:Why..... (259 comments)

That's generally what each country does to the companies operating inside it.

But here's the problem. Lets say an iPhone costs $400 to make, and sells retail for $1000. One Apple-related company pays $400 to get the phone made in china, and then sells the phone to Apple Ireland. Apple Ireland pays $450 to get the phone, then sells the phone for $995 to Apple Australia or Apple USA or whatever. Australia/USA can tax the profits of the local company, but the local company only made $5 per phone, and then used most of that for local expenses/advertising. Apple Ireland books most of the profit, and at a tax rate far less than other Western countries.

about a month ago
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Previously-Unseen Photos of Challenger Disaster Appear Online

kinko Re:PHB's strike again (207 comments)

from what i remember the worker bees warned against a launch due to ice and whatever but the bosses said to launch

what if I told you that every single launch has had some worker bees who thought their part of their module wasn't up to scratch, or might not work in the current conditions, and voiced this opinion to their manager? People with an engineering mind-set don't like uncertainty....

I don't have any evidence that this is actually the case, but it seems likely when so many people are involved in a project.

about 10 months ago
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Online Retailers Cruising Tor To Hunt For Fraudsters

kinko Re:Geo-fencing, nothing more. (188 comments)

Ever ask yourself why the merchant would spend money on this? I mean there's no risk to the merchant. If stuff is bought with a stolen credit card then the credit card company or the bank bears the risk.

No, it's the merchant who bears all the risk. If someone disputes a charge, the merchant's acquiring bank writes a friendly letter asking for proof of the card-holder's authorization, eg a signed receipt. If you can't offer evidence that it was authorized, then you get a chargeback (ie they deduct the purchase amount from your account) and you are out of the value of whatever you mailed out to the customer.

When we sold stuff online, obviously we don't get physical signatures, but normally we could convince the customer that they had made the purchase (normally they forgot, or didn't recognise our name on their credit card bill) and the customer cancelled the dispute.

Why would the bank voluntarily eat the loss for fraud/disputes? :)

1 year,28 days
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Industrious Dad Finds the Genetic Culprit To His Daughters Mysterious Disease

kinko Re:95% die, not survive (204 comments)

I understood that the high mortality is because most pancreatic cancers are not detected until the cancer has already spread. At which point it usually has already mutated enough to pick up a number of tricks that make it harder to kill, and thus less responsive to chemotherapy.

most solid tumours in organs are like that... they are asymptomatic until they get to an advanced stage.

But in this case, 95% of pancreatic cancers are in the tissue around the pancreatic duct. The other 5% are in a different type of pancreatic tissue and aren't as aggressive, so if they are detected and removed then most patients survive.

about a year ago
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Harvard Secretly Searched Deans' Email

kinko Re:"HP's Playbook" (113 comments)

That would seem to be the new HP tablet that looks like a BlackBerry PlayBook but with a worse display and camera. What has that got to do with Harvard seeming to have forgotten the difference between a university and a corporation?

Some years ago, HP's board of directors approved spying on some of their own top executives to try to find the source of a leak. "Playbook" was supposed to be a metaphor for "game plan", not a product name :)

about a year and a half ago
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Photo Tour of Google's Data Centers

kinko Re:Terrible inteface (88 comments)

The photo tour has one of the worst interfaces I've seen for viewing photos. Hiding half of the photo caption by default? Who comes up with this idiocy?

One small redeeming feature is that they haven't hijacked the right-click with a bloody Lightbox script.

it feels like the interface was designed to work on both big monitors and hand-held devices. Can't blame them for trying.

more than 2 years ago
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Photo Tour of Google's Data Centers

kinko Re:Storm Trooper (88 comments)

I presume that's related to this caption from the tape library photo:

    "Unlike a real library, you can't check out anything, but if you try, we have a security team standing by" :)

more than 2 years ago
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Last Available IPv4 Blocks Allocated

kinko Re:240/4 subnets (312 comments)

> Isn't it a bit idiotic to hard code refusal to route addresses reserved for "future use"?

they were reserved for multicast, back when everyone thought TV/movies would be distributed through the web. Multicast (1 server stream sending to lots of clients) never really took off though....

It's not so much a "refusal to route" to them as they are handled specially, and aren't designed to be routed as normal. Lots of home routers (eg my WRT54) will occasionally send out multicast broadcast packets onto the LAN, which you can see with a network capture tool.

more than 3 years ago
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Twitter Developing Technology To Thwart Censorship

kinko Re:How far should social responsibility reach? (144 comments)

just to pick nits, I think the Sea Shepard vessels are careful not to break any Australian or New Zealand laws when they are in Australian or New Zealand waters. All the "action" happens in the Southern Ocean near Antarctica.

They're definitely not following the established "rules" of the sea though, in terms of who has right-of-way...

more than 4 years ago
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NZ School Goes Open Source Amid Microsoft Mandate

kinko Re:Naming (305 comments)

"Koha" is a Maori word meaning gift/donation. The Maori are the indigenous people of New Zealand, so it's a pretty appropriate name for a FOSS library catalogue system written in NZ for anyone to use freely :)

PS Slashdot ate my "a macron" character - "Maori" should have a "-" over the "a".

more than 4 years ago
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Linux-Friendly Label Printer Recomendations?

kinko Re:Does Brother Make Any Label Printers? (188 comments)

Yes, we use the Brother P-Touch QL-550. It works fine with CUPS but we had to install a 3rd party (open source) driver for it that converts the postscript input from applications into the correct raster format for the printer.

Driver here: http://etc.nkadesign.com/Printers/QL550LabelPrinterCUPS. Brother also release a binary-only driver, but why use that when an open source one works....

more than 5 years ago
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Qantas Blames Wireless For Aircraft Incidents

kinko Re:The crash you mention (773 comments)

But he was flying below tree height - and the software could not see the trees. The pilot forgot that the engines take 10 seconds to spool up from the low power used in near-stall to enough power to climb above the trees. So when he ordered climb power and nose up, the software refused to try to climb until the engines were delivering enough power to do so safely. Unfortunately, by this time the aircraft had hit the trees.

[...]A classic case of software-induced complacency. The software performed exactly according to the spec.

there were several other factors iirc - one was that because the plane was under 200ft, the software was assumed he was trying to land and did a few things against the pilot (although I can't recall exactly what right now).

The other more important one is that the pilots did not have adequate training about what the software would or would not do in all situations, so it wasn't simply a case of the pilot "forgetting" things.

more than 6 years ago

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