From Chuck D to Chuck D: Evolution, Synthetic Biology and the History of Hip Hop

Editor's Notes

• #3: The two things I am introducing tonight, origin of life and synthetic biology are immensely complex and both very unsettled science. These are two very current fields, both unsettled and immature, but that is what makes them interesting. These are extraordinary times for biology. It's now 153 years since Darwin published the Origin of Species in which he outlines the theory of evolution by natural selection. There is an overwhelming body of work that supports the idea that via the mechanism of genetic mutation over generational time, has resulted in the diversity of species on Earth. Our great understanding of the mechanics of living things has lead us to the point where we can consider what came before evolution   Unlike in physics, where the question 'what came before the big bang' is meaningless, what came before the first life form is a very interesting question. And now that we have a good understanding of how life works, the question of what we do with it is equally important. 
• #5: Here’s one of the classic stories of human genetics from the past This is Charles the second of Spain. He was the last member of the Hapsberg dynasty, which ruled much of Europe for 200 years, providing every holy roman emperor during that time. Charles was the last because he was severely disabled, he did not walk until he was 5, did not talk until much later, and was beset by many illnesses. He was also sterile, and despite many attempts by his family, The Hapsbergs died with him. Spanish war of succession
• #6: He was known as
• #7: The entire family had this characteristic jaw and chin, prognathus in medical terms, but known as the Hapsberg lip, passed down as a badge of royalty. Charles’ disability was a result of this family, and the staggering amount of in breeding that they indulged in.
• #8: Charles II had an F-value of 0.254. This figure is even twice as high as the expected value for the child of an uncle-niece marriage. It also means that Charles II genome was 25% homozygous  
• #10: that species would change over time according to the desirability of their characteristics. This lead him to sketch this, the tree of life. scribbled in his notebook in 1837, showing how species diverge from common ancestors. Darwin was reluctant to publish, but Wallace’s correspondence prompted him to go public Which he later went on to formalise in The Origin of Species.
• #11: This is what that PICTURE looks like today, though this is a representative as we have described around 2 million species and there are likely to be many more. And we also estimate that more than 9 out of ten species that have ever lived are already extinct.  However, if there's one thing we know about biology, it's that it is messy. If you thought that things were going to get simpler after sussing natural selection and genetics, think again. There are two domains of simple life that preceded complex organisms on earth by a couple of billion years, one of which is archaea and the other bacteria, both single celled organisms.
• #12: Just so you know where humankind fits onto this PICTURE: Now, Darwin didn’t know HOW inheritance worked, and had no idea about what we now call genes.
• #13: DNA
• #14: DNA does two clever things. The first is that it contains a code, held within the rungs of the double helix. The rungs are made up of 4 chemical letters A, T C and G, but they always pair up in the same way, A with T, C with G.   And that gives DNA its second clever trick: if you split the two strand you have all the information to replace the missing strand. You have a system of replication. This reproductive system, a coded alphabet forms the third cornerstone of biology, the third grand unifying idea because it appears that every living thing on the tree of life has used exactly this system. 4 letters of code, spelling 20 amino acids, assembled into an uncountable number of proteins, that make up the entire diversity of life on earth for almost 4 billion years.
• #15: 3000 per minute 30,000 in bacteria
• #16: This is what that PICTURE looks like today, though this is a representative as we have described around 2 million species and there are likely to be many more. And we also estimate that more than 9 out of ten species that have ever lived are already extinct.  However, if there's one thing we know about biology, it's that it is messy. If you thought that things were going to get simpler after sussing natural selection and genetics, think again. There are two domains of simple life that preceded complex organisms on earth by a couple of billion years, one of which is archaea and the other bacteria, both single celled organisms.
• #17: Here’s an example: this is a type of cress that has been modified to go purple if it grows in the presence of buried landmines. The seeds can by scattered, and the position of the landmines can be determined.  
• #18: Here are some striking examples: This is Freckles, a goat I recently met on a farm in Utah, who has been genetically engineered to produce spider silk in her milk. I milked Freckles, processed the milk to remove the fats, and then extracted a thread of spider silk and wound it onto a spool. Spider silk has physical properties akin to steel, but we cannot manufacture it, nor farm spiders as they are cannibalistic.
• #19: I apologise for showing a picture with me in it in my own talk, but the Observer used this photo in an article I wrote recently about spider goats, and they felt the need to caption it "Adam Rutherford, left". 
• #20: This is aequaro a jelly fish that glows in the deep ocean. In the 1990s researchers found the gene that makes the protein that glows green, GFP They extracetd it, and started using it as a tool to see where experimental genes were on and off.
• #21: These animals aren't just for fun, this system allows us to see exactly where experimental genetic manipulation is occurring, which might otherwise by subtle or cryptic.   That cat was designed by AIDS researchers as a means of identifying and tracking a protein that attacks HIV. 
• #23: When we talk about this as engineering, many of the principles are derived from electronic engineering. The field of synthetic biology really began in 2000 with a paper that described a genetic circuit called a represilator. The components are made of DNA, genes, but the way they are arranged means that it has a controlable input and output. The repressilator is a three way negative feedback loop which means that the output, in this case green fluorescant protein, will pulse on and off in the bacteria that this circuit is put into. That sounds quite complex, but here today, we are going to demonstrate the world’s first human represilator. This process of remixing DNA requires skill as pieces don’t always fit together easily.
• #25: What that means is that, the logic boards made of DNA have become much more sophisticated. Perhaps the biggest success in this area has been a paper last year in which a team from MIT put together a biological circuit that would identify a cancer cell using a 5-point logic checklist, and if that cell satisfied those criteria, it would release a toxin that kills the cell. This works in vitro, has not yet been tested in animals. But it is the obverse of blunderbuss cancer therapies like chemotherapy. The sophistication of this genetic circuit is such that it is in effect a biological computer.
• #26: The third was this, written on the physicist Richard Feymann’s blackboard at the time of his death:   Any geneticist will tell you that accuracy in genetic code is incredibly important. The actual quotation is:    
• #27: Here’s a fun story about ancestry
• #29: This is what that PICTURE looks like today, though this is a representative as we have described around 2 million species and there are likely to be many more. And we also estimate that more than 9 out of ten species that have ever lived are already extinct.  However, if there's one thing we know about biology, it's that it is messy. If you thought that things were going to get simpler after sussing natural selection and genetics, think again. There are two domains of simple life that preceded complex organisms on earth by a couple of billion years, one of which is archaea and the other bacteria, both single celled organisms.
• #38: Nas samples Amen break Come with me, 1998 Jake Holmes 1967 LZ 1969 uncredited
• #39: 99 samples, none authorized
• #40: White 68 Black 2001 Grey 2004 Encore, Glass Onion and Savoy Truffle Happy birthday Men at work
• #41: Creative commons founder The legality of this is a total mess. I find it sad that