An Open Letter to (some) Forensics People

Dear Forensics People,

When you send out DNA to be sequenced, please, please, please, pleeeeease make sure that the test requested is appropriate, and the DNA is actually useable before you ask to have very expensive and time-consuming tests done on it.

Case in point – the glowing band with the big fat red arrow pointing at it! That band of DNA, according to the size marker on the left-hand side is approximately 200-600 base pairs long. THAT IS NOT GOOD QUALITY DNA. NOOOOOO. BAD QUALITY DNA. BAAAAAAD. I would have to actively try to fragment the DNA to get a band this small when extracting DNA, even from days-old rotting cadavers.

Shitty forensics DNA

The majority of the other glowing bands on that picture are DNA fragments that are ~10,000 base pairs long, which is a good length and ideal for most DNA sequencing applications.

Being able to exctract DNA of this quality shows that you are actually halfway competent at handling various human body parts, and have the requisite three brain cells available to use a DNA extraction kit, which is the molecular biology equivalent of a shake-and-bake mix for paraplegic retards.

 

Actually, I don’t have the foggiest idea WHY any forensics-related human DNA would be sent to us for sequencing in the first place! Human DNA sequencing tests that my lab performs are RNA transcriptome, cancer-specific panel, whole-exome, whole-genome and targeted panel sequencing! More to the point – NONE OF THOSE TESTS HAVE ANY FORENSIC USE WHATSOEVER .

 

So, certain forensics people? (you know who you are) Learn to use a DNA extraction kit properly, educate yourselves on the tests you request, and maybe READ WHAT TESTS A LAB CAN DO BEFORE YOU START WASTING OUR TIME AND MONEY.

 

Kind regards,

EbolaBooze

lorekai: And so my faith in humanity has been whittled away a little more…

I’m assuming by now that many of you have seen, or at least heard about, the video of the woman walking around New York City, if not you can view it here.

But it’s not the unsolicited commentary, or the downright creepy behavior of some of the men in the video, or even how it demonstrates a fairly serious societal issue, that whittles away my faith. No, it’s the number of people who seem to think that that sort of behavior is completely alright, that a woman should expect to be harassed if she dresses up nicely and goes out in public. And if she doesn’t like it, she should move, she shouldn’t dress so provocatively, she should loosen up and learn to take a compliment. What helpful suggestions, except, it happens everywhere, regardless of what you are wearing, the sincerity of a compliment is obvious, and it most certainly is not a compliment if you are left fearing that the wrong response could be met with anger, or even violence.

It’s ridiculous, and I cannot comprehend how some people can think this way, that they cannot even try to think of what things are like from another person’s perspective. Surely it cannot be hard to understand that being hassled nearly every time you walk along a street is unpleasant, that being followed around by a complete stranger is at best uncomfortable, at worst terrifying. How can they be so closed off, that they think it’s it’s perfectly alright for anyone to face this on a regular basis. I thought people were better than this.

Sorry for the rant, thanks for reading.

lorekai: Things More Likely to Kill you than Sharks.

Coconuts.

Jellyfish.

Falling out of bed.

Falling in general.

Horses.

Dogs.

Snakes.

Ants. (nasty creepy things)

Bees.

The flu.

Food poisoning.

Other people.

Hippos.

Cows.

Vending Machines.

Driving.

Hot water.

Mosquitoes.

Christmas Trees.

Hang Gliders.

Spiders.

Fireworks.

Falling off a chair.

Canoes.

Sport.

Champagne Corks.

Choking on food.

Weather.

Auto-erotic Asphyxiation.

 

And yet do we propose coconut culls, or try to ban furniture? No, we don’t, because any one of these killing someone is a tragic accident, yet a shark doing anything is a vicious attack. How is that right? People who enter the situation do so knowing the risks, so why are sharks considered monsters for doing what comes naturally? It doesn’t make sense, and it angers me to no end that there are people out there who think that the mass slaughter of sharks would be a viable solution.

Sorry for the slight rant, came across a stupid on the internet (who’d of thought), so here is a picture of a happy shark. Thanks for reading.

happy-shark

 

wildfillysama: Friesian Horses, and how people have ruined my plans

Today I’d like to talk a little bit about one of my absolute favourite breeds of horses, and how dodgy breeders have managed to almost completely cancel them off my list of equines I’d like to one day own. Or at least, make my looking for a Friesian substantially more complicated.

UK_Friesen_APASSIONATA_01

Just look at that glorious beast. Friesians are stunning. Centuries of inbreeding have generated a horse that is nearly always black, with thick feathering and luxurious mane and tail, hawklike heads, and high-stepping front ends. However, as with all inbreeding stories, this causes problems. The front end of the Friesian is so heavily engineered, it almost looks as though the back end has been completely ignored in some individuals. However, this is the least of potential problems.

 

Kendall Park Friesian Stud openly acknowledges potential risks on their website, including dwarfism.

T2Maturationfriesians

“Dwarfism is relatively rare in Friesians, but is still a real possibility of happening, and there are known cases.  There are 2 types of Dwarfism – A chondrodystrophic, basically causes shorter legs, and Brachiocephalic, which results in more extreme disfigurements of bones, legs, face etc.  Both types are debilitating to the horse.

It is thought that the Preferent Stallion Ritske 202 has most likely had a large impact on Dwarfism, but also Wessel 237 and Oege 267 are thought to have been carriers of the gene as well.  At present it is estimated that there are 12 Studbook Stallions that are carriers of the Dwarfism gene.”(http://www.kendhallparkfriesians.com.au/Friesian%20Health%20History.html)

The fact that these stallions are still in the studbook at all is a huge worry. The fact that this stud is openly acknowledging the risk shows a good level of responsibility on their part, but the same transparency and name-dropping is not widespread. Kendall Park lists several other potential genetic issues with Friesians on their website, including water on the brain, which is well worth a look if you are interested in potentially purchasing a Friesian horse in the future.

In addition, there is also the risk that the Friesian’s iconic, massive crest can be subject to weakness, the causes of which have not yet been fully researched.

Friesian Health History_clip_image002That looks practical, doesn’t it? Frustratingly, the Friesian Studbook’s response has been to “grade” levels of crest degradation in its elite breeding horses, rather than remove affected horses from the gene pool. These crests will be noted, but are not grounds for elimination from Premium, Star, Crown, and Model ranks. Let the sagging continue! Here’s what it looks like in its more pronounced form.

Friesian Health History_clip_image002_0000

Kendall Park Friesians cites Waling Haytema, a veterinarian and associate of the ‘Dierenkliniek Wolvega’ (Animal clinic) and member of the KFPS Breeding Council, in their acknowledgement of this issue: “With the advance of age some horses develop an unstable, sometimes fallen or broken crest. Up to now this problem has not been researched, therefore we cannot define the obvious causes. It is generally believed that there are two possible factors that seem to be involved in the development of a fallen crest.

The first cause for a fallen crest may be the occurrence of inflammation of fat tissues, steatitis, in young horses. The crest has a fair amount of fat deposits. Inflammation in these fat deposits produces connective tissues. The tendency for a weak crest thereby is formed at a young age but will start to show at a later age when the connective tissues lose their elasticity. Fat disease is considered to be an expression of deficiencies in antioxidants, especially vitamin E and selenium deficiency. In this light it is crucial that young horses have a sufficient intake of vitamins and minerals.

Another contributing factor could be obesity in horses when too much fat tissue is stored in the crest. If the horse is subsequently put on a diet and the fat tissue is reduced, what remains is weak connective tissue.”

Equinews also lists several other conditions, including skin, heart, esophagus and immune system issues, that are overrepresented in Friesian horses. Even more excitingly, we don’t yet know why these issues keep occurring. For example,

“Many Friesians suffer from chronic dermatitis that causes thickened and ulcerated skin on the pasterns. The lesions are often unresponsive to treatment. Though other draft breeds also have this problem, Friesians are overrepresented, and a genetic cause is suspected but has not been proven.” (http://www.equinews.com/article/health-problems-friesian-horses)

Yay! Insufficiently researched painful conditions that don’t respond to treatment! Just what everyone wants for their horse.

612_blackEfriesianEhorses

All in all, this is a pretty poor turnout for such a treasured breed. Breeding Friesians has been a highly focused process for years. It seems ridiculous that so little research has gone in to understanding what causes these problems and limiting their spread. Plenty of equine breeds have their share of genetic quirks and predispositions, for better or worse, but Friesians seem to have collected a pretty nasty set, all in the name of long hair and a black coat. All that I can say is that if I end up looking at a Friesian horse in the future, I will be doing a much more thorough genetic history research than I had initially planned. Or looking at an out-cross.

 

 

300 Megapixels Worth of Heartache

So the DNA sequencing facility I work at moved to a different hospital campus a couple weeks back, and the boss finally got rid of a few deprecated sequencing machines that were taking up valuable storage space. Gave them a good clean-out so no nasty chemicals were left in them, and sent them off for disposal.

Two SOLiD 5500XLs, two SOLiD 5500s and a single SOLiD 4 sequencer. Five sequencers in total. These sequencers use fluorescently-tagged DNA fragments to sequence stands of DNA bound to microscopic beads immobilised on a glass plate; in short, they take pictures of glowing DNA, cleave off the glowy bit, attach a new, different glowy bit, rinse and repeat. Then, through the magic of SCIENCE and COMPUTING POWER, we get a DNA sequence.

Solid5500xl_SMALL_100410

 

That’s not important at the moment.

What’s important is, that to get the sorts of resolution needed to tell each of these microscopic beads apart, you need a pretty damn good camera and optics assembly. I don’t care about the optics assembly, I have narrower bandpass filters in my camera already. The camera sensor though….. There were five of these beasts that I could have acquired.

The sensors inside those machines were sixty, that’s right, six-zero, 60 megapixel CCD-type sensors. That’s not the biggest sensor in the world, but it’s certainly up there. As a comparison, the sensor I used for all of the astrophotos I’ve put up on this blog is a TrueSense Imaging KAF-8300, 22.5mm diagonal 8.3 megapixel sensor.

A little bit of searching brought up the model of sensor in the sequencing machines.

They were FTF9168M sensors from Teledyne DALSA, the glorious bastards that brought into the world the 111MP single-chip sensor for the Astrometry Department of the U.S. Naval Observatory (http://www.dpreview.com/articles/1319797632/dalsa100mp), and the 570MP FermiLab Dark Energy Survey camera (https://www.darkenergysurvey.org/DECam/DECam_add_tech.shtml).

dalsa100mp

 

Long whitepaper short: these imaging assemblies had larger sensors with a higher resolution than any commercially available CCD for astrophotography, quantum efficiency that puts a lot of other sensors to shame, and double the dynamic range of my current sensor.

I only learnt of this AFTER the machines had been disposed of.

 

No chance of salvage, no chance at making an array of sensors, no chance at selling three off and making obscene amounts of money. I was in physical pain when I heard that. The expression on my boss’s face when he realised what he had done was an amazing amount of shock and horror. I will be hurting about this to the end of my days.

 

300 megapixels worth of heartache.

 

Stay angry my friends, I certainly will.

lorekai: A noisy noise annoys…

…well in this case, a lorekai. Due to a lack of inspiration and another factor, here are the ten noises, I could think of, that annoy me the most.

 

10 – My cat’s “why are you doing that, pay attention to me instead” meow, it’s loud, incessant, and sounds almost exactly like a baby crying.

9 – Maracas, or any music involving maracas, they are pretty much a guaranteed  headache.

8 – An individual cricket chirping, multiple crickets don’t bother me at all, but one by itself is just infuriating.

7 – Aw Naw Crows, they like to crow loudly early in the morning and it’s difficult to chase them away.

6 – The sensors that make noise when you walk into a shop, it’s not so much the noise but that fact that it draws attention to me.

5 – The buzzing noise the filter on my fish tank makes when the light on top of the tank is in the wrong spot, it only ever seems to do this just when I’ve gone to bed.

4 – Sonic the Hedgehog drowning music, not so much annoying more of it frightens me every time I hear it.

3 – Babies crying, I don’t know why, they just fill me with rage.

2 – Alarms, any sort really, especially those I can’t do anything about.

1 – The stupid, high pitched, electrical noise coming from somewhere across the road, that’s been going on for ages and that I can’t even drown out by listening to music with my headphones on.

wildfillysama: Argh.

I’ve had a long and stupid morning trying to stop twenty-somethings from acting like infants via online bullying. OVER IT.

 

Going to spam funny pictures to cleanse my brain!

 

On the bright side, four of my recent poems have been accepted for publication (PAID PUBLICATION!!!) in three different places over the last week! Yay, possible career path!

 

Enjoy the pictures.

 

312707_10150278415749997_2070785797_n

 

10352781_717928754925866_2165258381637698244_n

 

students

 

-301

 

-297

 

Hope you have a good week with more poetry than bickering!

lorekai: How many updates does it take to access the Playstation Store?

The answer is three, plus two installation screens, and a very long privacy policy agreement to skim through. Twenty-five minutes of my life only to find out that game I was considering is almost five times the price on the Australian store when compared to it’s US counterpart. Very annoying, it was quite an interesting looking little game as well, slightly creepy and very atmospheric, but not at that price.

The price discrepancy of games  between regions is one of the things that bothers me most when it comes to gaming, especially when it comes to digital copies. It annoys me for physical copies as well, though not to the same extent, as they have things like shipping costs to factor in. Can it really be that much harder to make a game available for download in Australia that it needs to be five times the price? I don’t understand it, and I’d almost go as far as to say that it’s pricing based on the hopes of consumer ignorance or because they know that there is no easy alternative, neither of which eases my levels of irritation.

 

I’m going to stop myself here before I go in to a small tirade on everything that annoys me about digital copies of games. So in happier news my ikebana skills have progresses enough that I get to move on to the next type of arrangement, which is exactly the same as the one I was on, but to the right instead, exciting.

20140429_211455

My most recent arrangement, I much happier with this one than the previous one, though my photography skills still need some work. I also have my own kenzan, the spiked thing you use to hold the flowers, and a proper dish that is quite heavy, so I no longer have to worry, as much, about the cats knocking it down. That’s all this week, thanks for reading!