Number 28: Homemade Magnetic Slime

Fancy making some magnetic putty? There have been a few videos of the stuff doing the rounds on Youtube and I thought it  would be cool to see if I could make some of this fabulous stuff from scratch. Mines a bit more like slimes so it slithers and slides towards magnets like this..

And it consumes magnets like this...

(3 minutes compressed into 8 seconds with the help of imotion app.)

You’ll need:

• A large bottle of PVA Glue
• Borax (some supermarkets or hardware stores stock this, or get it online)
• Black iron oxide (its used in cosmetics and tattoo inks so its harmless)
• Zip lock freezer bag
• Neodymium magnets
• Some plastic cups.

Safety: 

• Borax is toxic in large amounts, so don’t swallow it. And wash your hands after handling the slime.
• The neodymium magnets are VERY strong. They can shatter if they fly towards each other and will pinch if you trap your skin between them. They should only be handled by a responsible adult. Be very careful with them and follow the safety instructions on the packet. 
• AND unless you want to see an adult explode DON'T get the slime stuck in the carpet!

What to do:

1. Dissolve 1/2tsp of borax in 1/2 a cup of water (its not very soluble so don’t worry if some of it doesn’t dissolve)
   
   
   
2. Pour out 1/4 of a cup of PVA into a cup, add the same amount of water.
3. Add 4 teaspoons of iron oxide to the PVA/water and mix it all together. The iron oxide is quite a fine powder and can make quite a mess so be careful.
   
   
   
4. Pour the PVA/iron oxide mix into the zip lock bag.
   
   
   
5. Add the borax solution to the zip lock bag. Flatten the bag so there isn’t any air in it and then zip it up.
   
   
   
6. Massage the contents of the bag. The liquid mix will slowly turn to a black slime. After 5-10 minutes you should be able to take it out of the bag. If its still quite sticky then leave it in the bag for another 5-10 minutes.
   
   
   
7. Once the slime is ready put in on a plate and start experimenting with the magnet. You could try rolling a small bit of slime into a sausage shape and then putting the magnet near it or stick the magnet in the middle of the goo. Have fun!
8. If you want to try some of those time-lapse videos download imotion for Apple or Android. And why not upload it to Youtube and then post the link in the comments below.

What’s going on:

First how does the liquid mixture turn into slime? Well, the PVA glue is made of long thin molecules and together they make a thick liquid. The borax connects the PVA molecules together making a network of connected molecules, which resembles a 3D network, turning it from a pourable liquid in a putty. 

Meanwhile the iron oxide* particles have magnetic properties which makes them align  in the magnetic field of the nearby magnet. Then they are drawn to the magnet, dragging the slime with them.

If you are feeling lazy you can buy some ready made putty (but where’s the fun in that). And besides if you make it yourself you can muck around with the PVA to water ratio to make it more or less runny. More water makes it more slime-like, more PVA makes for a firmer putty.

And if you just want some classic slime then leave out the iron oxide and add some food colouring instead.

* The most common form of iron oxide is rust with a chemical formula of Fe₂O₃. Black iron oxide is Fe₃O₄.

Number 27: Genetic Code Jewellery

Right, lets make genetic code jewelry that spells out your name. Or if you don't fancy that use if for sending secret messages!

But first I need to explain what the genetic code is.

DNA is the code for life, right? But what does that really mean? Well DNA actually contains the instructions that tells cells how to make proteins. And proteins are nature's mini-machines that make all living things work. They are like tiny robots that are involved in just about everything that goes on in your body. There are proteins that digest food, others that fight diseases and some that help make other proteins. Not only that but they hold your body together; skin, hair, muscles, cartilage and ligaments are all made from protein.

So all the information on how to make proteins is contained in DNA. This information is written as a string of 4 bases called adenine, thymine, guanine, and cytosine which are abbreviated to A, T, G and C.

RNA vs DNA

Now proteins are made up of stings of 22 possible amino acids, which are also abbreviated to single letters codes.

Amino acids and their 3 letter and 1 letter codes

So how does the 4 letter code of DNA get translated into a 22 letter code of proteins?

First off the DNA gets transcribed into RNA (which is like DNA but it is sometimes single stranded instead of double stranded like DNA, and secondly it has uracil (U) instead of thymine (T)).

To work out what protein sequence the RNA codes for you need to read it in groups of three bases. For example the sequence AUGGGAGGG would get split up into AUG GGA GGG. Each of these groups of three bases are called codons and each codon represents an amino acid. You can work out which amino acids a sequence codes for using the genetic code in this table.

The Genetic Code (click for a bigger version)

So AUG codes for M, GGA codes for G and GGG also codes for G. 

In the genetic code table there are 25 letters (X is missing) so we can spell stuff out using codons instead of the full alphabet.

How we've got that sorted lets make the jewellery.

You'll need:

• Red, green, blue and yellow beads 
• Elastic Stretchy Beading Cord/String/Thread

What to do:

1) First decide what you want to spell out using the code. How about starting with your name?

2) Now figure out what codons you need to spell out your name.

So in my case I want to spell out 'Mark'. So I need the codons AUG GCG AGA AAA. 

3) Next select the coloured beads that represent the bases. So AUG is blue, red, yellow. The GCG is yellow, green, yellow.

4) Finally thread the beads onto the string in that order. Tie it off and hey presto a bracelet with your name spelt out in the genetic code.

FAQs.

Why are there more codons than amino acids?
There are 4 bases and codons consist of 3 bases. So that makes 64 possible codons. But there are only 22 amino acids (and in most organisms there are actually only 20). Which means that there are loads more codons than amino acids. This means that there are some spares, which turns out to be quite handy, because its suppresses the effects of mutations. For example, if ACC got mutated into ACG it wouldn't make any difference because they both code for the same amino acid.

Why do some codons say 'STOP'?
Genes always end in a STOP codon. It signals the end of a protein, its sort of like the full stop at the end of a sentence. If you fancy it put a STOP at the end of your sequence.

Why do some STOPs have have U or O after them?
U and O are the two rare amino acids. Most organisms don't use them. But when they do crop up they code for U and O instead of STOP.

How come some of the codons have two letters after them?
22 of the letters represent individual amino acids. Plus there's Z, B and J which are used for some of amino acids that are quite similar. So if a biochemist isn't sure if she's got a I or a L in her protein then she'll write down J.

I've got an X in my name what do I do?
You'll have to cheat, maybe use one of the stop codons instead.

Number 26: Jelly Baby DNA

A couple of weeks ago I showed you how to build a passable model of DNA with K'nex. Now for something tastier.

You'll need:

• 2 long sweets like Strawberry Lances or similar
• A few handfuls of soft sweets, like Jelly Babies
• About 10 cocktail sticks .

What to do:

1) Sort the jelly babies into colours. Keep four of the groups and eat the rest.

2) Pair up the jelly babies so that one colour always goes with another. e.g. red with green and yellow with purple.

3) Stick the pairs onto a cocktail stick like you are making mini-jelly baby kebabs.

4) The attach the jelly baby kebabs to the long sweets. Carry on doing this until you have something that looks a bit like a ladder.

5) Pick up your ladder and give it a twist.

Hey presto a model of DNA made from sweets!

So what does it all mean?

DNA contains the information needed to build a living thing. That info is recorded in the form of four bases called adenine, thymine, guanine and cytosine (usually abbreviated to A,T,G and C). In my  model each of the coloured jelly babies represent one of these bases. So lets say yellow is A, purple is T, green is G and red is C. In DNA the base T always pairs up opposite A, whilst C pairs with G. And to represent that I  paired yellow with purple and green with red. 

The DNA molecule then twists up to form a cork screw like (helical) shape, hence the twist I gave it at the end.

Our model of DNA represents just a tiny fragment of a real DNA molecule. In reality DNA could be billions of bases long (and I couldn't get hold of that many jelly babies).

The Pope resigns and lightning strikes, what are the chances of that!

The Pope retires and on the same day a lighting bolt stikes the Vatican! Amazing what are the chances of that,  pretty unlikely? Surely its a sign from God. Or is it? Lets just run through a quick back of an envelope calculation and see what we end up with.

So what do we need to know? 

Firstly, the Vatican is about 0.48km2. 

Secondly, lets take a look at the frequency of lightning strikes in Rome. The best data I could find (whilst eating my lunch) came from this image.

http://geology.com/articles/lightning-map.shtml

And if you zoom in on Italy is looks, to me, like that's about 5 flashes per year per km2.  So that works out at about 2.4 flashes per year above the Vatican. But not all of those flashes are going to result in stikes. According Wikipedia only 25% of flashes result in a strike. So 0.60 times a year lightning stikes the Vatican. 

Which means that there is 0.60/365 X 100 = 0.164% chance that lightning will strike the Vatican on the same day that a Pope resigns.

OK, so that's not exactly likely, but its hardly a rare occurrence (the lightning strike, that is). Its certainly a good coincidence but I'd hardly say it was a sign from God.

EDIT: A decimal point when missing in an early version of this post which resulted in a massive error in the area of the Vatican. Sorry, fixed now.

Number 25: 'DNA' diffraction with a spring and a laser pointer

Photo 51

Time for my second DNA post and I thought I'd take a look at the data that allowed Watson and Crick to work out the famous molecule's structure.

The crucial bit of information came from a photo taken by Rosalind Franklin and Raymond Gosling.  The image is now quite famous and is known as photo 51.

But photo 51 doesn't much look like a picture of DNA. And thats because it is in fact an X-ray diffraction image taken by shining X-rays at a crystal of DNA. Its a bit of a leap from the photo to the DNA structure but luckily there's a really easy way to demonstrate how an image like this comes from a helical structure.

You'll need:

- a laser pointer

- a retractable ball point pen

Safety:
Adult supervision required here. Be careful with the laser and don't shine it in anyone/anythings eyes.

What to do:

1) Unscrew the pen and remove the spring. The spring is of course a helix, so its going to act as our model for DNA.

2) Shine the laser through the spring, and then onto a white wall or card about 3 meters away. Best to do this at night with the lights dimmed.

You should see an image on the wall that looks a lot like this.

Which also happens to look a lot like photo 51. And that's because the same processe generates both images.

What's going on:

Both photo 51 and the cross you've just made on the wall are formed by a process known as diffraction. To explain what that is we need to remember that light is a wave.  Now imagine two waves meeting each other. If the waves overlap so that he peaks are in the same place then they combine and the result is a wave that is twice as high. But if the peak of one wave meets the trough of the other they cancel each other out, and in the case of light you get a dark spot (you can also see this happening if you shine the laser at a CD). So some of the laser light that diffracts off the spring interferes with other waves of light giving you a cross and the spots. And from the distance between the spots and the angles of the cross you can work out the shape of the spring (or DNA).

Exactly how its done is explained very nicely here.

And a hat tip to Suzie Sheehy who told me about this fab demo.

Spiderman's breakfast and the physics of spider silk

Electron micrograph of a spider spinneret producing spider dragline silk.
 (photo credit MicroAngela)

I've got the perfect excuse to sit down and watching a load of movies. I need to research a course I'm running called "Science on the screen". We're going to dissect the science in some movies and then reshoot scenes with the science 'fixed'. Its the brain child of some imaginative chaps in Scotland who call the project NonFiSci.

First up on my list is the 2002 version of Spiderman. It struck me that Peter Parker must have an enormously high protein diet to generate all that spider silk (which is made from protein) he goes through. So being the geek that I am I set about working out what his protein consumption must be and putting it in terms of eggs eaten/100m of spider silk.

Here goes (and feel free to pick me up on any mistakes).
I started with the assumption that Spidey produces spider's silk that has the same characteristics as dragline silk produced by the European garden spider Araneus diadematus i.e. it has a tensile strength ,about equal to piano wire, of 1.1 Giga pascals (Gpa) and a density of 1.3 g/cm³.¹

1.1 Gpa = 1.1x10⁹ Newtons per meter squared (N/m²)

Spiderman weighs 75kg (according to Marvel)²  so the force he exerts is 75 x the acceleration due to gravity which is 9.8 m/s/s  = 735 Newtons

Therefore cross sectional area of spider silk required to support Spiderman = 735N/1.1x10⁹N/m² = 6.68x10^-7 m² = 6.68x10^-3 cm². That works out to be a bit of silk with 0.046 cm radius. Pretty cool huh, you could hang from a piece of spider silk about 1mm thick!

A 1m long piece of silk has a volume of 0.668 cm³ which would weigh in (given a density of 1.3g/cm³) at just  0.87g. Therefore 100m weighs about 87g

There’s about 6g of protein in an egg.  So it looks like Spidey only needs about 15 eggs for breakfast if he plans to use 100m of silk. That’s not too bad.

But, spider silk consists predominantly of a protein call fibroin which is about 42% glycine.³ Whilst egg consists of just 10.7% glycine and serine (I’m counting serine because it is easily metabolised to glycine). So lets say Spidey needs 60 eggs for his 100m of silk.

The thing is I’m not quite happy with that,  I think he’d need a reasonable safety margin, I’m sure he doesn’t what to hang about on a thread just barely strong enough to hold his weight. Plus he’s busy swinging from tall buildings whilst carrying Mary-Jane Watson around. So lets go for a thread 5 times thicker than what’s barely adequate. So that gives us 300 eggs/100m of Spidey silk.

But that’s not really the end of it either. After all what happens if he leaps from a building to save a falling MJ and deploys his webslingers to save the day (like at 1hr 6 min into the movie). Hmm...I’m guessing he’s still using his drag silk (which stretches by 27%). He could got for the flag silk, its not as strong (tensile strength = 0.5 Gpa) buts its got amazing elastic properties; it can stretch to 2.7 times its original length! But that might be a bit too bouncy.

In the scene I’m talking about Spidey leaps from the  balcony and falls for 7 seconds before his silk starts to arrest his fall. He’s caught MJ so lets say their combined weight is 125kg. How much silk is he going to need here?

Spidey accelerates at 9.8m/s² for 7 seconds giving him a velocity of  68.6 m/s.  Given that velocity =√2.g.h we can work out Spidey fell for 240m (wow, that’s one high balcony).  So assuming the silk stretches to its maximum that gives us a stopping distance of 64.8m. The impact force on the silk rope as they slow down is F=1/2mv²/d = 4,538 N (where d is the stopping distance, m is mass and v is velocity)

That’s not too bad, just 6.17 times greater force than Spidey just hanging around by himself. But still he’ll need 1288g of silk (minimum) to catch his fall. So I reckon he must have had about 860 eggs from breakfast that morning. I think Aunt May might have noticed.

Anyone what to check my working?

p.s. As for the scene at the end of the movie where he catches a cable car full of kids, I draw the line there.

p.p.s I know, I know in the comic books he has some wrist mounted devices, but in the films he glads the silk out of his wrist, so that's what I'm working with here




1.Lin Römer and Thomas Scheiber, The elaborate structure of spider silk. Structure and function of a natural high performance fiber, 2008 Prion 2:4, 154-161
2. Marvel directory http://www.marveldirectory.com/individuals/s/spiderman.htm (accessed Jan 2012)
3. S.O. Anderson. Amino acid composition of spider silk. 1970. Comparative Biology and Physiology, 35, 705-711
4.http://en.wikipedia.org/wiki/Egg_(food) (accessed Jan 2012)

Number 24: K'nex DNA

60 years ago James Watson and Francis Crick were busy trying to figure out the structure of DNA.  So to celebrate the anniversary I thought I'd come up with a series of DNA related activities.

Watson and Crick eventually worked it out the structure by building models of the molecule and comparing them to X-ray pictures collected by Rosalind Franklin.

Watson and Crick built their model from bits of lab equipment and other odds and ends. You can see just how cobbled together it is if you visit  London's Science Museum. Which just goes to show that even Nobel prize winners use whatever they have to hand.

The model shows that DNA is made from two intertwined helices. Sort of like two corkscrew shapes wound around each other. Each helix is made from a backbone of sugar-like molecules bound to phosphates. Then each helix is zipped up to its partner via something called basepairs.

So what else could we use to build a model of DNA? How about K'Nex?


You'll need:

A load of these three K'nex peices (or similar)

These will represent the 3 main parts of DNA. The green pieces are going to be the sugars, the white bits are the phosphates and the blue ones are the base pairs.

To make 1 complete turn of K'nex DNA you'll need 14 green bits, 14 white and 7 blue bits.

What to do.

1) Connect up the 3 green pieces with the 3 white pieces and then 3 green pieces with 4 white pieces, so you have two sections that look like this.

2) Add the blue pieces onto the green pieces, like so.

3) Here's the tricky bit. Connect up the blue pieces to the other section like this.

You should end up with a twisted bit of k'nex model that is starting to resemble the double helix of DNA. 

4) Now just continue to build more of the same and link them together to form as long a strand of k'nex DNA as you can!

The model you've built isn't quite accurate but its still shows some of the important features of DNA. Most importantly it's a double helix  and you might notice that it's also got grooves running around the double helix. One of these is narrower than the other. These are known as the minor and major grooves , DNA has them as well.

If you want to do more DNA related stuff with K'nex you can buy the official model kit or have a look at this great site from Mount Sinai University.