Extracting strawberry DNA

Following the instructions in Double Helix Issue 24 2018 to extract DNA from strawberries using common kitchen items and chemicals, plus methylated spirits, while keeping an eye on their blog to ensure it doesn't crash under load!

Mixing salt, detergent and water

Mashing up the strawberry with the detergent mix

After adding the chilled meths the DNA separates at the top

Sticky DNA!

Alex's awesome holidays

The last day of school holidays for the middle of 2016 and I think it's worth jotting down all the activities over the past two weeks. Left to his own devices, Alex would spend far too much time with his devices, so the idea was to get him out and about in a way to stimulate his body and mind with the kind of experiences he doesn't normally get while still having time to "chillax" as he so likes to say. Meanwhile, when he wasn't in vacation care I worked from home.

Thursday June 30

Second last day of school, but we had some expiring movie tickets so went to watch Steven Spielberg's version of The BFG at Miranda. We all enjoyed it, well acted and visually spectacular.

Friday July 1

Alex wrote his first Android apps using MIT App Inventor 2 and following their video tutorials. It''s very simple, much like Scratch, and you can do cool stuff using a device's built in sensors. He worked out how to customise the examples and we put one of the apps on my phone.

Later I had a play with an Arduino set I had recently purchased. Wish that mucking around with digital hardware was that simple when I was at university!

Saturday July 2

Bike riding at Centennial Park, B and I on hired bikes, Alex furiously pedalling his too-small kid's bike.

Sunday July 3

After the previous day's experience we decided to get Alex a new bike. Purchased an adult one so that we can ride with him.

Monday July 4

Vacation care with clowns for Alex after the 4-D cinema cancelled on them. 

Tuesday July 5

Bikes arrived! While I worked from home, Alex relaxed and did his own thing.

Wednesday July 6

Second day of vacation care. Alex went to indoor rock climbing and laser tag.

Thursday July 7

A full day Thinkspace workshop on Scratch programming at Sydney Observatory for Alex. He really enjoyed writing the three games and was very proud to show them off to me. A long way from writing text games in BASIC when I was his age!

Friday July 8

Took Alex for his first ride on the new bike - needed more practice!

Saturday July 9

Riding his new bike in the park, Alex saw his school principal.

  

Sunday July 10

Alex left us alone to go go karting at a friends birthday. Apparently he was a bit nervous at the speed of them.

Monday July 11

Sadly the holidays were not without some homework and Alex had to write a persuasive speech. Persuading him to write it was the real test. 

Tuesday July 12

I had a day off, or tried (forgot to undivert my phone). We built some of the plastic houses and shops for Alex's Japanese N-scale model railway layout. Wish the bath house was real!

We both went for a ride around the suburb on our bikes, but Alex found the hills a bit tricky. 

Wednesday July 13

While Kita was at the vet having his teeth cleaned I took Alex down to the ANSTO nuclear reactor at Lucas Heights for an hour and a half session of Atomic Kids. This fantastic session introduced kids to the periodic table, atoms and chemical bonds. Alex really enjoyed it.

Thursday July 14

Another full day workshop, this time learning about the circulatory and respiratory system at the Junior Science Academy at Macquarie University while I was over at work at North Ryde. They looked at dissected sheep hearts and lungs and made blood from Cheerios, marshmallows and food dye. He was pretty exhausted by the end of it but eager to tell me everything he'd learned.

Friday July 15

A chance for B to spend some time with Alex before going over to his best friend's house.

Saturday July 16

Alex came into our bedroom at 4 AM bawling his eyes out, having just fallen out of his bed. We then discovered a gash to the side of his head. Who knew sleep could be that dangerous? So off to the emergency department we drove. A couple of hours later, no stitches or glue, just plasters holding the skin together. Barely any rest then off to the first karate of the term.

As the head sensei is off recovering from an operation we had Sensei Leighton, the exercise fanatic.

Went off to eat Chinese at Hurstville and had an afternoon tea of chocolate pudding at Brighton. I could feel a headache building and by the time we were driving back home it was ferocious.

Chocolate flavoured vomit.

I was a write off for the rest of the night.

Sunday July 17

Another birthday party for Alex, this one at 10 pin bowling. I came second last amongst the adults. I would have been last but one of them let his toddler bowl. At least I got one strike! Alex won, thereby cementing what was a pretty awesome holidays for him.

A balance between exercise, education and relaxation. Hopefully he's starting next term in a good frame of mind. I think I need another holiday!

Gravitational waves observed!

So gravitational waves have been detected at last! The waves were observed from coalescing black holes 1.3 billion light years away. Rating the quotes from the linked Article's taken back to the more recent, though personally distant past, as an undergraduate at the Australian National University about 20 years ago.

Professor Dave McClelland was my optics lecturer. He and his team were heavily involved with designing a Laser Interferometry Gravitational Observatory (LIGO) in outback Australia away from human induced vibrations. Unfortunately the Australian observatory was never built, otherwise it would probably have participated in this observation and enabled observers to triangulate the source.

Despite the lack of an Australian observatory, the ANU team, and CSIRO, have contributed to the design and manufacture of the technology used in the gravity wave detection.

It just goes to show the kind of lead times involved with groundbreaking scientific research, something that certain science administrators would be wise to remember.

Communicating science

I recently read an article somewhere how versions of Pythagoras' Theorem were independently "discovered" in Egypt, India and China prior to its namesake. Why then do we associate it with a single Greek?

It is not uncommon for scientific and mathematical discoveries to occur multiple times. So who chooses the credit?

Communication plays no small part in this. The more widely a discovery is communicated, the more awareness there is of a result, the less chance that it will be repeated as if new. That means researchers can put their efforts into something new rather than wasting time on reinvention of the old.

Science communication shouldn't just be about promoting ideas for money and prestige, it should also be for ensuring that knowledge is accessible, not hidden away in some dark corner.

Time and Relative Dimensions in Cake: Baking a TARDIS (and a Dalek)

"People assume that time is a strict progression of cause to effect, but *actually* from a non-linear, non-subjective viewpoint - it's more like a big ball of wibbly wobbly... time-y wimey... stuff." The Doctor, Blink

There was an incident fifty years ago this month. Another that happened a tenth of that time ago at almost the same time of year. The two events are not connected by cause and effect, except they were today and by a big ball of squeezy wheezy blue stuff.

On November 23 this year we celebrate fifty years of Doctor Who. I'm not that old (though my Mum shares a name of one of his original companions), but I grew up watching the British series. I've been fortunate enough too my son Alex has similarly developed an enjoyment of the program and asked for a Doctor Who cake to celebrate his birthday this year.

What better way to celebrate five and fifty years with a cake of the Doctor's time machine, a blue policebox called the TARDIS? After all, it's rectangular, which hopefully meant it would be relatively easy to bake and decorate. We may have been "forced" to outsource the party to a play centre this year, but at least can put some effort into a decent cake.

Cake decorating seems to have expanded into more general society, judging by the number of cake decorating shops and shows on the topic on Pay TV. I have a couple of colleagues at work who are obsessed by the subject. Neither my wife B nor I are professional, semi-professional or even vaguely professional cake decorators. However, articles on the Internet and various YouTube videos make it seem a lot easier than it actually is.

Armed with a YouTube video and a few blog posts we set about making the TARDIS. Whilst the TV version may be bigger on the inside than the outside ours was just cake on the inside covered with icing.

Baking the actual cakes was the easy bit. B did the orange cake and I the chocolate mud cake (sans coffee). Both recipes are delicious. That night we also made the chocolate modelling paste to construct the outer shell of the TARDIS cake. We used melted white chocolate, corn derived glucose syrup and blue gel dye. This formed a thick blue dough which we rolled up and left overnight and into the next day.

I printed out a picture of the TARDIS as a template, but it was too large. How large should the template be? This is where relative dimensions come in, along with a bit of math. Yes, mathematics is useful!

Volume (V) = height (H) x width (W) x depth (D)

First find the maximum volume of cake available for use (Vc) by using the above equation (Vc = Hc x Wc x Dc) and the dimensions of the cake. Also we need to calculate the relative scale of the TARDIS (t) by using the dimensions of the template (m) where the dimensions can be written as a ratio with one side = 1. Despite the template being only two dimensional we know the depth = width as the base of the TARDIS is square. We need

Vt = Ht x Wt x Dt = (Hm x Wm x Dm)/Dm . Because of the square base this simplifies to Vt = Hm/Dm (neglecting units here).

For your information, Hm/Dm comes out to be about 1.6. So the TARDIS dimensions are of the ration 1:1:1.6.

If we let H, W, D be the dimensions that we'll use for our cake and taking advantage of the fact that the base is square then we get:

D = (Vc * Dm / Hm) ^ 1/3
W = D
H = Hm/Dm * D

And those are the dimensions that you need to make the cake. This meant carving the cake into blocks and pasting together with butter cream. The whole lot was covered with butter cream. We then cut out the four vertical sides of the TARDIS from the blue chocolate modelling paste with white icing for the windows and black writing icing for details. I printed the signs on ordinary paper and cut them out - they stuck easily enough to the chocolate.

And there you have it!

Alex gets a second birthday party at childcare, where he has a Doctor Who obsessed teacher. So we made a simpler Dalek cake using leftover red fondant from the previous year's birthday cake (briefly microwaved to soften), liquorice strips and chocolate coated marshmallows.

Now I've educated you about some mathematics, maybe you would like to read Andy Connelly's article in the Guardian about the Science of Cake.

Acrophylla titan - the titan stick insect

Look what I found on our garden fence tonight: Australia's longest insect Acrophylla titan. Earlier in the night we also spotted my first gekko in Sydney standing on our front doorstep.

The Australian Museum has some interesting information about looking after stick insects. Their life cycle is amazing, relying on ants to protect their young.

More photos

The crazy weather

Yesterday, in the middle of October, the area around Sydney experienced catastrophic bushfire conditions of heat and wind, leading to the destruction of hundreds of home. Last week there was apparently temperatures of 39 degrees in the city.

I didn't know at the time because we were on holiday in Asia. But even in Japan the weather was unseasonably hot (it's always hot in the other countries we visited) and we felt the turbulent effects of Typhoon Fitow on the way up, dodged Typhoon Danas on the way down. A few days after we left Da Nang and Hoi An at least five people in the region died due to Typhoon Nari and Typhoon Wipha was headed for Japan.

I asked my colleagues, some of who are climate and atmospheric scientists, if this was something we had to look forward. One replied that this was the hottest year on record, but they expected stronger typhoons in future, not more frequent.

He also pointed out the Madden-Julian Oscillation (MJO), which currently points to greater typhoon activity in the Pacific.

Good luck to all the emergency workers across the world.

Edit: This article in the Japan Times says that the country is on track for a 30 typhoons this season.

Partial annular eclipse

While checking my Twitter feed on the train this morning I discovered that Sydney was to be treated to a partial solar eclipse... right now! Fortunately, you can safely view an eclipse with nothing more than a sheet of card and a pin - enough to make a pinhole camera. I had to share this with the kids at Alex's childcare.

As soon as we arrived we got out a sheet of card, punched a tiny hole in it with a pin, held it out towards the sun and projected the image on a sheet of white paper. You could certainly see where a chunk of the Sun had been taken out by the Moon.

Back at the office I made a more "sophisticated" version by cutting out one side of an old tissue box, punching a tiny hole in one end and sticking some white paper at the other. Then I went outside an photographed the results. Unfortunately , the lens protector on my camera didn't fully retract, but, hey, at least I got something for surprisingly little effort.

When I returned to my desk I discovered that the education group had been running an eclipse viewing session outside an adjacent building, but it's kind of nice to have done something yourself.

ABC Science has more information about the eclipse.

Make it so!

A presentation from NASA's Dr Harold White about how an Alcubierre Warp Drive might work [pdf] and how they are testing for it. See the Discovery article for a less technical explanation.

Smooth skies and storms

Aircraft should stay well clear of storms according to research released by the ARC Centre of Excellence for Climate System Science.  A storm cell is an air mass containing a convective loop of updrafts and downdrafts. As the mass of air is sucked up, gravity exerts a force pulling it downwards and oscillatory motion is generated. These are called gravity waves (see undular bores for more information).

Being caught in an actual storm cell is an extremely hazardous situation for aircraft, but what this research is saying is that the turbulent effects of storm cells can be felt as far as 100 kilometres away. 

I've flown through a few regions of storm activity in my time and any research that makes for a smoother flying experience gets my vote!

Tentacle porn is painful

Opposite Hakodate station is the fish market, around which you can find small restaurants with tanks of squid in the window, ready for eating. We watched one customer use a barbed line to fish out her own meal of squid from a pool. It was then taken by the stall keeper, chopped up and served raw and still wriggling, along with a dash of soy sauce.

Perhaps I was right to feel squeamish. There have been a number of published cases of eaters of raw or undercooked squid experiencing severe pain as packets of squid sperm explode in their mouths. If this sounds disgusting enough, just wait until you find out how squids reproduce.

Rather than the (hopefully) gentle penetration of the male penis into the female vagina, followed by the individual sperm swimming up towards the egg, as happens in humans, the squid process is far more brutal.

The male stabs large sperm packets (spermatangia), each containing thousands or millions of sperm, into the female's arms like a hypodermic syringe. These long thin packets cement themselves to the arms and burrow into the flesh by using enzymes to dissolve it. They then remain there until such time as the female releases her big jelly ball of eggs, which she shapes into a ball with her arms. Sensing this, the sperm are released from their packets and burrow out and into the eggs, fertilising them.

There's a great video of the process on Inside Nature's Giants, recently screened on SBS in Australia.

In many species of squid the female's arms may be implanted with the spermatangia of multiple males.

So there you go, the pain felt by those unfortunately squid eaters was the sensation of the sperm packets adhering and burrowing into their tongue and mouth cavity.

Gross!

References

1. Park GM, Kim JY, Kim JH, Huh JK. Penetration of the oral mucosa by parasite-like sperm bags of squid: a case report in a Korean woman. J Parasitol. 2012 Feb;98(1):222-3. Epub 2011 Aug 11. PubMed PMID: 21834723.
2. Shiraki Y, Kawai K, Kojima S, Suzuki Y, Ono K. Stinging in the oral cavity caused by ingestion of the sperm bags of a squid: a case report. Pathol Int. 2011 Dec;61(12):749-51. doi: 10.1111/j.1440-1827.2011.02722.x. Epub 2011 Sep 1. PubMed PMID: 22126383.
3. Nagakura K, Nakano M, Kanamaru M. Two cases of oral-stings by sperm bag of squid. Tokai J Exp Clin Med. 1992 Dec;17(5-6):195-7. PubMed PMID: 1343427.
4. Nakashima H, Akagi M, Miyabe S, Iwasawa H. Two unusual cases of a foreign body in the oral cavity caused by eating raw squid. Acta Otolaryngol Suppl. 1996;522:104-7. PubMed PMID: 8740821.
5. Hoving H J T, Laptikhovsky V. Getting Under the Skin: Autonomous Implantation of Squid Spermatophores. Biol. Bull. June 2007;212 no. 3:177-179
6. O'Shea S. Architeuthis (Giant Squid) reproduction, with notes on basic anatomy and behavior. Mar 2003
7. Myers PK. Machines of aggressively loving grace. Dec 2008
8. Inside Nature's Giants - Giant Squid, SBS, 2012

Thanks for the memories Space Shuttle

I remember watching the very first NASA Space Shuttle launch on television back in April 1981. I was almost seven years old. Today marked the final flight of the shuttles. It's sad to see this magnificent, but flawed, vehicle retire, especially when the US has no replacement.

It felt funny visiting the Powerhouse Museum last Sunday and seeing the mock Shuttle cockpit standing over the other displays of space paraphernalia, knowing that Atlantis was up above the Earth on its final mission.

I hope we never stop gazing upwards.

The launch of Columbia on the very first shuttle mission © NASA

Atlantis lands on the last mission © NASA

Atlantis on its final mission as seen from the
CSIRO Parkes Radiotelescope
© John Sarkissian/CSIRO

The blonde gets blonder

Instead of taking 500 mg of chloroquine phosphate per week to prevent malaria, a 16 year old blonde took the dosage daily during a holiday in Costa Rica. One week after her holiday her hair turned even paler.

I wonder if any brain cells died in the process.

Reported in the New England Journal of Medicine.

A great excuse to go outdoors

Feeling a bit brain dead after a week in the office? Then it's time for a trip outdoors to ingest some bacteria!

According to research recently presented at the 110th General Meeting of the American Society for Microbiology, exposure of mice to Mycobacterium vaccae, a soil bacteria commonly ingested outdoors, stimulated neuron growth and improved their ability to navigate mazes.

Pity that it's raining outside right now.

Via ScienceDaily.

Links between Alzheimer's disease, Down syndrome and atherosclerosis

Apparently all Alzheimer's disease patients have some cells with three copies of chromosome 21 rather than the normal two. People born with Downs syndrome share in the trait, except that they are born with "trisomy 21" in all cells. In the case of Alzheimer's the trisomy 21 is probably due to damage inflicted in the cell microtubules by the amyloid protein, disrupting chromosomal replication. It is also suspected of causing the diabetes, strokes and atherosclerosis that is seen in many Alzheimer's patients. ScienceDaily has more details about the research.

Multitasking minds

An interesting article in Scientific American about the abilities of individuals to multitask media (eg blogs, television, music) and their ability to focus only certain information. The results were basically that heavy media multitaskers had difficulty focusing.

More sad news

I learned today that George Dobson passed away after an accident in India.

I knew George when he was the convenor of the CSIRO Double Helix Science Club's Rockhampton Chapter. He organised a number of events, including a wonderful bush trek and a talk I gave at the Rockhampton Airport terminal about human travel to Mars. As a high school student I had been agitating a number of years for a chapter to be set up in the local area and was delighted when George took up the role.

George was trekking in India when he fell down a mountainside, sustaining injuries that left him a quadriplegic. Hospitalised in India, while his family in Australia struggled to raise funds for his treatment and to bring him home, he eventually succumbed to complications.

You can read more about George Dobson on the Bring George Back website. And please learn from this tragedy. If you are travelling overseas, buy medical insurance because the Australian government can't bail you out.

Mock Nobody - Television Star

You can catch my (probable) Logie award winning performance as Mock Nobody on ABC television's Catalyst science program or watch the video online. It may not be a speaking part, but my lugging around of an ancient Toshiba laptop computer was crucial to the portrayal of the whole wifi patent case. I'm sure that a movie deal is just around the corner!

If you fall out of an aircraft

Imagine being blown out of an airfraft high above the land. What would you do?

• How to survive a long fall (Wikihow)
• The more humorous how to survive falling out of a plane (h2g2)
  

Mormon crickets

It's not sport, nor a religion. And they don't like rock music.