The Science of Jurassic Park. Part Two.

1. The Science of Jurassic Park. Part Two. Michael Kostiuk Its all in the code. Can we Crack or Hack it?

2. Introduction • Based on the books and movies of the same title, hopefully this will be an entertaining look at the viability of cloning as portrayed in Michael Crichton’s two Dinosaur novels, and by extension, Spielberg’s films. • Since the book that this presentation is based on was published in 1997, I will also attempt to bring the topic up to date on recent developments in this area of science and palaeontology. Part One was presented on June 14, 2017 Its all in the code. Can we Crack or Hack it?

3. Where we left off at Part One. Where we can find Amber of the right age Explaining DNA Where can we find Dinosaur DNA Why search for Red Blood cells? How to extract DNA Its all in the code. Can we Crack or Hack it?

4. How to clone DNA with the PCR machine Why primers are needed to start a Polymerase reaction. Soft Dinosaur Tissue Other Sources of DNA. E.G. Modern Birds. Its all in the code. Can we Crack or Hack it?

5. CDN Dino DNA • . Its all in the code. Can we Crack or Hack it?

6. Where Dino Age Amber is found Its all in the code. Can we Crack or Hack it?

7. So what exactly is DNA? • DNA stands for deoxyribonucleic acid. It’s the genetic code that determines all the characteristics of a living thing. • Deoxyribonucleic acid is a large molecule in the shape of a double helix. Its all in the code. Can we Crack or Hack it?

8. Nucleotides & Bases • Each nucleotide contains a sugar and a phosphate molecule, which make up the ‘backbone’ of DNA, and, one of four organic bases. • The bases are adenine (A), guanine (G), cytosine (C) and thymine (T). It’s the specific order of A, G, C and T within a DNA molecule that is DNA Polymerase • In addition, there’s an enzyme called DNA Polymerase, whose job is to ratchet along a single strand of DNA, reforming the double helix by fashioning the correct adjacent strand. Its all in the code. Can we Crack or Hack it?

9. For example, if the Polymerase is at a T, it will pick up one of the free floating A’s and attach it across from the T; if it’s at a C, then it will find a G and do the same. Its all in the code. Can we Crack or Hack it?

10. Its all in the code. Can we Crack or Hack it?

11. Want a PCR? • A few thousand dollars will get you a Plain Jane PCR. • For $12,000 you can get something a little fancier: Some machines even have robotic arms that pick up the test tubes and dunk them into tubs of hot and cool water; while others blow hot air and cool air over the test tubes. Its all in the code. Can we Crack or Hack it?

12. So, are we ready to clone a Dinosaur? • No and the reason is that Polymerase, the enzyme that attaches A’s, C’s, T’s and G’s to single DNA strand to make new double helices doesn’t work unless it’s given a head start. • If all you have in your test tube are DNA strands, Taq Polymerase, and free floating bases, NOTHING will happen. Its all in the code. Can we Crack or Hack it?

13. The Polymerase first has to latch onto the single strands, so it can can start ratcheting along. And to attach itself it needs help. • But, We need a PRIMER! • This is a single strand of DNA typically 15 or 20 bases long. • Once the PCR machine has broken the double helices down during the heating cycle, it cools the solution to 50 Celsius, which is cool enough to let the primers hook onto longer strands of DNA. • So, we need to add primers, what’s the big deal? Its all in the code. Can we Crack or Hack it?

14. Complementary Sequence is required • A primer will only attach itself to another single strand of DNA if it has the complementary sequence: that is if the primer sequence (to pick something completely at random) is ACTTGACCTGAAGTT, then the one and only sequence it can hook up to is TGAACTGGACTTCAA. Recall that there has to be a T opposite and A, A G opposite a C, and so on. Its all in the code. Can we Crack or Hack it?

15. So what is the primer for a Dinosaur? • Bird? • Crocodile? • Frog? Its all in the code. Can we Crack or Hack it?

16. Red Blood Cells • In Jurassic Park Henry Wu the chief geneticist explains that they get dinosaur DNA from the Red Blood cells found inside the insect that was trapped in Amber. • This IS significant since insects do NOT have Red Blood cells so if Red Blood cells are found that means they are not from the insect and MUST be from an animal that the insect fed on. Its all in the code. Can we Crack or Hack it?

17. Do Dinos carry their DNA in their Red Blood Cells? • Human Red Blood Cells do NOT carry a full complement of DNA. But the whole blood does since there are other cells such as White cells. • But birds do, and if birds are dinosaurs, then maybe their red blood Cells will carry the complete DNA. • Wu as a minimum wants Red DINO Blood Cells, but he would use White Cells , but Red are much more plentiful and more likely to be found. Its all in the code. Can we Crack or Hack it?

18. But can the DINO blood survive the chemistry inside the insect? • What if the DNA in the red blood cell cannot survive the digestive juices that act upon it immediately after the insect has fed? • Are there better sources for DINO DNA in amber? • What if a piece of flesh had been ripped off an dinosaur that was attacked. That would be MUCH better than trying to use DNO blood inside an insect Its all in the code. Can we Crack or Hack it?

19. Funny that Lindley and Desalle would say that! • Because we have found Dinosaur Flesh inside Amber. • Not perfectly preserved, but still it was found. • Maybe there are a better samples to be found. Its all in the code. Can we Crack or Hack it?

20. And! Soft Tissue from Dinosaurs! • The controversial discovery of 68-million-year-old soft tissue from the bones of a Tyrannosaurus rex finally has a physical explanation. According to new research, iron in the dinosaur's body preserved the tissue before it could decay. • The research, headed by Mary Schweitzer, a molecular paleontologist at North Carolina State University, explains how proteins — and possibly even DNA — can survive millennia. Schweitzer and her colleagues first raised this question in 2005, when they found the seemingly impossible: soft tissue preserved inside the leg of an adolescent T. rex unearthed in Montana. • Play Video 5: Dino Soft Tissue. Its all in the code. Can we Crack or Hack it?

21. Back to Primers • But what ever source we use we still need a primer to set the process moving. • So how can we do this? Desalle and Lindley suggested that we use a primer with a shorter length and that we use it from birds. • And how long is a Dinosaur DNA? • Lets say its about 1 Billion long letter specification. Its all in the code. Can we Crack or Hack it?

22. We could use random primers that have a good chance of appearing once or twice along the billion long DNA sequence • It turns out if you use random primers of 15 letters, there are a little more than than a Billion different possibilities (1,073,742,824 to be exact). Were you really counting? • This means that each one would have a good chance of occurring somewhere in your dinosaur DNA. • This would give fragments a few hundred bases long. This is as long as we should expect. Its all in the code. Can we Crack or Hack it?

23. And it is easier than you would think. • We just throw the all the Billion Plus 15 base primers into a single PCR test tube with our Dinosaur DNA and let the machine run. • We can make the billion 15 base primers in about an hour; a little machine costing a mere $25,000, if you want to keep track, will do the job for you. • Sounds like a lot, but it is not. We are talking molecules here. About a trillionth of a sugar cube in size. Its all in the code. Can we Crack or Hack it?

24. Now we have to organize the Dino Fragments. • The best way is to use a standard cloning technique. • Since the fragment are small we can use Bacteria to hold the fragments. Bacteria contain little circles of DNA called plasmids which perform various house keeping function for the bacteria. Its all in the code. Can we Crack or Hack it?

25. Scientists have learned how to incorporate a small fragment of foreign DNA into a plasmid and then to slip the modified plasmid back into the cell itself. • E. Coli is the bacterium of choice • The bacteria will multiply with the bits of extra DNA inside their plasmids, and easy to keep large colonies of the bacteria alive. Its all in the code. Can we Crack or Hack it?

26. Storage space is HUGE! • So we now have a means of storing and multiplying the individual bits of DINO DNA. • Each plasmid must pick up only one DINA fragment. And ALL fragments must be picked up by a bacteria. • To accomplish this you have to adjust the relative concentrations of DNA, plasmids, and bacteria in your mixing and control the amount of time they are allowed to mix. Its all in the code. Can we Crack or Hack it?

27. So many Dino Fragments! • If a billion-based DINO DNA genome is broken down to fragments of 500, that would create about several million fragments. • But the process would probably result in a larger set of fragments since the DNA would have broken up different along different sections. • So that could mean up to 100 million tiny fragments of DNA each one tucked inside a bacterium that you are going to grow into a colony Its all in the code. Can we Crack or Hack it?

28. If each little colony needs a square centimeter of space to grow in, you’re going to need 100 million square centimetres of goo-covered glass. • That is a space 100 metres by metres on a side – comparable to a couple of football fields placed side by side. • Of course you will have lots of little plates all stacked up – but still, you’re going to need a big lab. • Then you will scrape off into individual Test Tubes for the Next Step. Its all in the code. Can we Crack or Hack it?

29. A large building for each DINO DNA Storage • You can use little plastic tubes the size of a little finger, but the they will need to be stored in an automated warehouse with a robotic arm traveling along the rows. • This will require the space of a large department store. Think of the Bay on Rideau Street for example. • And then there is the required people to do the work. Its all in the code. Can we Crack or Hack it?

30. How many people are required? • Every time you have to perform a routine operation on you samples – some task that should take you no longer than scratching your nose – you’ve go to to it 100 million times. • A full year contains only 30 million seconds, so it would take three people a whole year just to do a 1-second operation on every test tube. • Oh well, we do need a man like John Hammond who has both the financial resources and patience to see this project through to completion. Its all in the code. Can we Crack or Hack it?

31. But what if we decide another Method? How about a Nebula-tibia Cornu-asaurus? Its all in the code. Can we Crack or Hack it?

32. Or Foghorn Leg Horn to be precise Its all in the code. Can we Crack or Hack it?

33. Use Birds to Bring Back Dinos • If birds are dinosaurs, could we just manipulate their DNA to change their appearance into something that looks like a dinosaur? Is that the best place for us to look for DINO DNA. Its all in the code. Can we Crack or Hack it?

34. More on Financing • To put together the Dino DNA fragments in the correct order we will need to put the DNA sample into a sequencing machine. • A good sequencing machine costs around $125,000 and can sequence as many as 64 strands of DNA at once (based on the book’s date of 1998). • 100 million test tubes divided by 64 equals two million sequencer runs. Its all in the code. Can we Crack or Hack it?

35. Each run takes an afternoon (allowing mornings for clean up and preparation), so you will need 2 million “Sequencer Days” – That’s 2000 sequencers (costing a total of $250 million) operating continuously for about three years. • Not to mention all the technical staff you’ll need: lab space, chemical supplies, clean-up crews, electricity bills. • The task seems tedious, but NOT infinite. • Expensive, but not prohibitively so. • If Hammond really wants a Dinosaur, we can supply it. One day… Its all in the code. Can we Crack or Hack it?

36. That will be covered in Part Two Next Season… Its all in the code. Can we Crack or Hack it?

37. The Humpty Dumpty Problem • What came first? • The Dinosaur • or the Egg… • or the Cloning Lab? Its all in the code. Can we Crack or Hack it?

38. But our Next Step is to assemble the DINO DNA in the correct order Its all in the code. Can we Crack or Hack it?

39. Now that we have all those DNA Framents that we ned a way of putign thme in the corect order. • We will have DNA fragments that are only a few hundred bases long at best and like Humpty Dumpty they will have to be put back together again. • To reassemble the Dinosaur DNA we will need some Really Big computers. • And Hammond in Jurassic Park has three of he largest Super Computers in the world to do this task. Its all in the code. Can we Crack or Hack it?

40. In the book and the Movie Henry Wu mentions in his demonstration in the Lab that there are missing pieces in the DNA sequence. • A little section of 5 bases is missing. • How we fill in these gaps is the BIG problem. • So how do/would we put DNA Strands together? • When we get DNA fragments from Amber there will be fragments from “DIFFERENT” cells that will have its own set of DNA instructions Its all in the code. Can we Crack or Hack it?

41. This does make it easier for use since the DNA fragments will have broken at different locations along the DNA strands. These overlapping strands make it easier for the Computer to connect the broken pieces of the DNA. • Wu uses restriction enzymes to help find common sequences. The restriction enzyme breaks the broken strands back to where there are identifiable sequences recognized by the restriction enzymes. • Page 61. Its all in the code. Can we Crack or Hack it?

42. Its all in the code. Can we Crack or Hack it?