The Science of Jurassic Park. Part One.

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

3. Background At the heart of the tremendously successful movie and best selling novel Jurassic Park. is a simple but provocative proposition: If 65 million years ago, an insect that had bitten a dinosaur had then been preserved in amber, could modern scientists extract dinosaur DNA from the insect and use it to clone a new dinosaur? To answer this question, I will attempt to summarize the book that was written by Rob Desalle and David Lindley and then take you on a “fun Romp” into the far reaches of modern science to explore the world of dinosaurs and DNA, where you can learn: Its all in the code. Can we Crack or Hack it?

4. Topics of Discussion • Where to search for Amber from the dinosaur age • How to identify DNA • Why the hardest part of the process would be to find an egg that ”knows” everything a dinosaur embryo needs to develop and survive. Part Two • Whether a dinosaur could learn how to behave like a dinosaur if there were no other dinosaurs around to teach it. Its all in the code. Can we Crack or Hack it?

5. The DNA Animation The main idea of the novel and movie is to build a dinosaur from ancient blood trapped in the abdomen of a mosquito trapped in amber. Play DNA Cartoon Video From Jurassic Park: https://youtu.be/qUaFYzFFbBU Its all in the code. Can we Crack or Hack it?

6. A few mistakes in the movie. • One big error is the location of the amber mine. It is in the Dominican Republic, but while the rock and amber there are old, but only about 25 million years old. The amber there is also found in the highlands here, not in caves in the lowland swamp regions. Its all in the code. Can we Crack or Hack it?

7. Where do we find DNA of the right age In the same place where dinosaurs are found. Such as: (see next slide): Its all in the code. Can we Crack or Hack it?

8. New Jersey Its all in the code. Can we Crack or Hack it?

9. Or Canada… Its all in the code. Can we Crack or Hack it?

10. But we lost out to the “Exotic Dominican Republic”. • Hollywood. • Go figure eh. Its all in the code. Can we Crack or Hack it?

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

12. Logical isn’t it? Its all in the code. Can we Crack or Hack it?

13. 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?

14. 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 unique to you, and gives you your characteristics. Its all in the code. Can we Crack or Hack it?

15. Now this is neat! The Rule of Bases Its all in the code. Can we Crack or Hack it?

16. Can we get Dino Blood from a Mosquito in Amber? • Many things have to go right for this to happen. • The main problem even if the insect is perfectly preserved is how much of the blood was digested in the stomach of the insect before it became entombed in the amber. • This natural “Ambalming” takes time and perhaps the DNA has already been destroyed inside the insect before natural process have stopped. How much DINO DNA will be left over??? Its all in the code. Can we Crack or Hack it?

17. But First things First. • Can we get DNA from the insect itself that has been trapped in amber. • Take a look at this video About Extracting DNA from Amber: https://youtu.be/kRTBhGGEk8g Its all in the code. Can we Crack or Hack it?

18. DNA Detection methods • First remove contamination BEFORE you open the Amber. • This is done by Placing the amber in a closed glove box to separate it from the outside world. DNA from many sources is floating on tiny dust particles and this can cause contamination and false results. Its all in the code. Can we Crack or Hack it?

19. Glove Box Its all in the code. Can we Crack or Hack it?

20. Sterilize Amber inside Glove Box. • Inside the clear Plexiglas glove box there is an Ultraviolet Light. This light kills any foreign DNA on the outside of the amber and keeps the Insect DNA and Dino Blood inside the Amber safe. (That is why UV light is bad for your skin as it can alter DNA structure and cause things like cancer). • All of your tools, instruments, chemicals and devices are also placed in the box to be sterilized along with the amber. • Box also has positive airflow to reduce contamination when box is opened Its all in the code. Can we Crack or Hack it?

21. Drill, or Crack the Amber? • Drilling through the Amber will mean passing through material that could contain DNA from other plants and animals. • Therefore, cracking the Amber is better since you can go directly to the insect. • In fact, the whole lab room is kept as cleans as possible and separate from experiments other rooms. • Then you plunge the Amber into super cold liquid Nitrogen and crack open the Amber. Its all in the code. Can we Crack or Hack it?

22. Next Dissect the insect. • This procedure will take practice as you learn how to remove different parts of the insect and separate out what you need to proceed to the next stage. Its all in the code. Can we Crack or Hack it?

23. The DNA Lab • To prevent contamination the DNA lab has plenty of UV lights on to disrupt DNA, and they are kept on all the time except when we are working on our DNA samples. • We don’t want to zap our samples or blind ourselves do we? • We also wear clean clothing, such as overalls and a mask with a respirator. • The authors suggest following the same protocol as used in the Human Genome project. Its all in the code. Can we Crack or Hack it?

24. Getting the DNA • We use a portion of the insect since we may need to do multiple experiments to find what we are looking for. • Insect is placed in a soap like solution that will disrupt the lipids, which are the fatty molecules that make up the cell membranes. • An enzyme is added that degrades proteins that can harm the DNA Its all in the code. Can we Crack or Hack it?

25. Shake it Baby! • To extract as much DNA as possible from the sample you shake the test tube for a few minutes, so that the contents are mixed thoroughly. • Then place the test tube in centrifuge for a while, which makes the water and the phenol separate like oil and vinegar salad that’s been left to stand. It would separate on its own given time, but this is nice short cut. Its all in the code. Can we Crack or Hack it?

26. Add Phenol • This separates the DNA from the other material. • The DNA will float in the soapy solution while the Phenol will dissolve the most of the fatty molecules from the cell structure. • Proteins and proteins fragments that do not dissolve will form a cloudy layer between the two. Its all in the code. Can we Crack or Hack it?

27. Separation process. • Use a pipette to suck water from the top of the test tube. • Since DNA falls apart in water, you don’t want to wait too long to do this procedure. • When scientists want to store DNA for later work, they generally freeze them. • This is an efficient method, but NOT perfect. Some cell membrane will still be present. Its all in the code. Can we Crack or Hack it?

28. One more purification step • In the movie a scientist has just performed this same operation and is showing the result to the visitors. • He is holding a test tube that has weirdly glowing red florescent ring. • The test tube contains a thick slurry of Cesium Chloride (similar to ordinary table salt, but much heavier and denser). • Again it is spun in a centrifuge as fast as 100,000 times a second. Its all in the code. Can we Crack or Hack it?

29. Dye added to solution • You add a dye that will chemically attach to the molecules of DNA. • After centrifuging you briefly as possible, shine a low intensity light (because UV light is damaging) so that you can mark the DNA layer. • Then you stick a fine needle through the side of the test tube… • Ah, you remembered to use a plastic test tube didn’t you?! A glass one would have shattered during the centrifuge process anyway. Its all in the code. Can we Crack or Hack it?

30. Those test Tubes… Its all in the code. Can we Crack or Hack it?

31. This method is very tedious and outdated… • You need a LOT of DNA to get a test tube ring that was shown in the Jurassic Park. • And historically, the technology of Ultra-Centrifuging test tubes was on its way out when Michael Crichton wrote Jurassic Park. • There is a much better, more sensitive, and easier way to extract DNA. Its all in the code. Can we Crack or Hack it?

32. Go back to where we separated the layer of water containing the DNA from the phenol layer. • Now, add ethanol along with a little salt. • DNA molecules will precipitate out in a mixture of water and ethanol, so when you add ethanol the liquid will take on a cloudy, white appearance. That white precipitate is DNA. • Next place the test tube is a standard (not ultra high speed) centrifuge and spin it to force the DNA to the bottom Its all in the code. Can we Crack or Hack it?

33. Pour off most of the water and leave the rest to evaporate. • If there was a lot of DNA in our sample then it would be visible as a quantity of white material at the bottom of the test tube. • However, if there is only a small amount of DNA it will not be visible. • The test tube will look empty, but we proceed to the next step assuming that there is some DNA present. • You add a drop of distilled water to the test tube, swish it around briefly and then go to the next almost MAGICAL step. Its all in the code. Can we Crack or Hack it?

34. Place the drop of distilled water into another test tube containing a special brew of chemicals and stick the test tube into a slot in a hotplate controlled by a timer that raises and lowers the temperature every couple of minutes. • Then go away and watch a movie, or walk your dog and when you come back two or three hours later there should be plenty of DNA in the test tube. • Millions of times more than there was a few hours ago. • Neat trick, huh? Its all in the code. Can we Crack or Hack it?

35. The secret lies in the chemicals we added before we put the test tube into the automated heater. • BUT! • The ancient DNA will have broken into small fragments. What we have are bits of ancient insect DNA in very small fragments. Its all in the code. Can we Crack or Hack it?

36. Those double helices. • The machine that multiples these fragments do so by heating the test tube to almost the boiling point. This causes the two strands of the helix to fall apart. • But the individual strands stay together. • Then the temperature is lowered and the chemicals we added does their work. These include a plentiful supply of the individual bases; A’s, C’s, T’s, and G’s floating freely about. Its all in the code. Can we Crack or Hack it?

37. 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. • 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?

38. Five repetitions multiply the quantity of DNA 32 times; another Five give you 32 squared, which is just over 1000-1,024, to be precise. Twenty cycles give you a million, and 30 cycles, which the machine can complete in a matter of hours will multiply the original amount of DNA a Billion times. • Doctor Evil would be pleased… • This procedure is called Polymerase Chain Reaction or PCR for short. • Show PCR Video: https://youtu.be/Nl6eLez3CNI Its all in the code. Can we Crack or Hack it?

39. 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?

40. 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?

41. The Polymerase first has to latch onto the single strands, so it can can start ratcheting along. And to attach itself it needs help. • 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?

42. 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?

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

44. 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?

45. 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?

46. 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?

47. 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. • Play Video 4: Dino Tail in Amber • https://youtu.be/piYOPzMZ8Oc Its all in the code. Can we Crack or Hack it?

48. 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. • Video Dino Soft Tissue: https://youtu.be/bS6TXh_bx8Q Its all in the code. Can we Crack or Hack it?

49. 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?

50. 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?