Introduction to Computer Science using Python part 1

I’m finally getting around to making another Introduction to Programming series on YouTube, this time for my Introduction to Python course. Here is the first video with more to follow over the next few days/weeks.

On Zombies

So I have been thinking about zombies recently and I think they are the next obvious evolutionary step in our progress as a race.

1) 100% peaceful to each other, no more war. They even share food.
2) No bigotry or prejudice, zombies don’t care if you are male/female, black/yellow/red/white, zombies don’t care about religion/non-religion.
3) They want to share the blessings of zombieism with everyone. No one should be left behind in the transition to zombiehood.
4) They live in peace with nature. No zombie destroys nature just to make a quick buck.
5) They are the ultimate practitioners of a Zen like state, no cares about the future or the past.

6) They don’t care if you are rich or poor, or what you are wearing or what you look like.

The life of a zombie is a peaceful one.

The results for I’m a Scientist

I made it to the final round where it was Thomas Clements and myself battling it out for the top spot.

Both Thomas and I got many questions from the students, but in the end Thomas won with his knowledge of fossils. I am the runner-up. I am quite please about lasting to the end and Thomas said he is going to use the prize money to build a portable fossil lab to take to schools and teach kids. How can I be upset about that?

All in all, this has been one of the best experiences of my life and I want to thank the students, my fellow scientists, and the #IASUK team for bringing so much joy into my life.

Science Questions from 10 year olds part 5 #IASUK

Question: whats the weirdest animal you have ever worked with

Unfortunately, I only work with humans. But some humans can be pretty weird.

Question: If you had to, would you go through with hurting an animal just to find out how the body works, or would you just leave it until it eventually falls to its death?

I would never hurt an animal if I could avoid it, thankfully my work only requires a blood test from my human volunteers. But there is more to this question than just that. The study of animals has helped us to understand ourselves and helped us to produce medicines. This is important and needs to continue. However, I think that all animals that are being studied must be treated very well, they must not suffer, and they must have the ability to run around and play. I certainly don’t think animals should be used by businesses to test their products (like make-up or hairspray) but I know that many humans would die if we stopped researching animals.

Fortunately, technology is advancing so that animal tests are becoming less and less necessary, instead of doing early “trials” in animals we can test new medicines against lab grown cells or simulate tests in a computer. This allows us to save many animals that in the past would have died to keep us healthy. I think that we need to continue to improve our technology so that we can absolutely minimise the number of animals that need to be studied and so that animals can lead the lives that they deserve, to be happy and free.

Question: how long will it take for all the resources in the world, such as coal to run out

Within your lifetime we will run out of energy. The question is what to do about it, now, while we still have a chance? We need to be really pushing towards renewable energy sources. If we stop using coal, gas, and oil (all the remnants of ancient life forms by the way) and replace it with energy generation from wind, wave, and solar we can power our civilization forever. The sun provides us with more energy than we can ever use and if we solidly invest in renewable energy now we won’t have a problem when we run out of oil, coal, and gas.

Question: how old were you when you started science

I started learning science in school, but I really liked airplanes and space rockets. So I build model rockets and launched them high into the sky to watch how force and flight work. I even made a shuttle like rocket which attached a rocket engine to an airplane like glider model! That was super fun, but if you are going to do it make sure there is an adult in the area, I burned myself on one of the rocket engines and I still have a scar.

As far as becoming a scientist, I did my first research project in 2010 which taught me that I love figuring out new knowledge and introduced me to the thrill of discovery!

Question: what got you into doing science?

I love computers, I have been using computers since I was about 6-7. At first I loved playing video games (I still do!), then I loved programming them, then building them, then making them talk to each other.

I worked as an IT administrator for many years (with a couple of years as a Video Game Tester) before returning to University to get my degree in Computer Science, I wanted to become a Games Programmer and Designer. But something interesting happened while I was at University, I learned that I love doing research. I got involved in a project that was helping people recover after brain damage and the act of creating new knowledge was so much fun that I figured that it would be a more fun job than making video games (it is, I have done both). When I graduated from University I started looking for a PhD (to become a scientist and researcher) and I looked at a number of different places. Oxford was at the top of my list because they were offering a program that allowed me to mix my love of computers, with my love of research, with my love of evolution (evolution is awesome). I could not believe my luck!

Now I spend my time using my computer to create new knowledge about evolution, best job in the world!

Question: what is the best thing you have discovered?

What I do is I look for mutations in humans that are beneficial to the human that has it. I have discovered a number of beneficial mutations (we are still trying to figure out what they do) but the best thing is that the method I have developed may turn out to be the most powerful method for detecting beneficial mutations yet built.

Question: What is the worst thing that has happened in your experiments?

Because I work with computers my stories aren’t as interesting as everyone elses. When my experiments go wrong I have to figure out why they went wrong and fix the program so it won’t make the same mistake.

The worst time was when I discovered a mistake after 3 months and had to redo it all :(

Question: do you harm any animals at you work

I don’t study animals, I study humans, and I do it with a computer. So no animals are harmed in my work.

The people that provided the DNA that I work on did have to collect blood from 1092 people around the world however, so some humans had to have a needle put into their arms to extract the blood, but that doesn’t hurt very much and only a little blood is needed :(

Science Questions from 10 year olds part 4 #IASUK

They keep coming

Question: Why does evolution occur?

When DNA copies itself it never does it perfectly, there are always new mutations being added to the population. So in each new generation there are a ton of new mutations all fighting for a place in the population, almost all of these mutations are what we call “neutral”, which means they don’t do anything. But occasionally, a mutation that is helpful enters the population and the individual that has it has a leg up on everyone else and will be more likely to live and have babies, who in turn will be better at surviving and having babies, etc.

So take for example humans. We all come from Eastern Africa (near Ethiopia) about 70,000 years ago and each baby born since then has added between 75-150 new mutations into the human population. Nearly all of these are neutral and most of them have disappeared, but occasionally something useful appears like the ability to drink milk as an adult. Now this is only useful if you have domestic animals to get milk from and other food sources are scare for part of the year.

Did you know it is a mutation that some adults can drink milk without farting? There is a sugar in milk called Lactose, babies have a special enzyme in their stomach that breaks lactose in half which allows it to be digested. All mammals are like this, babies drink their mother’s milk when they are born, however since mammals stop drinking milk after being babies the body shuts off the enzyme and the mammal can no longer digest lactose. This causes the lactose to be passed into the rest of the digestive track (the intestines) where bacteria eat the lactose and give off gas as a response giving the adult smelly farts.

But in Europe, one person 15,000 years ago or so mutated so that they continued to produce the enzyme as an adult and could digest lactose. This gave them an additional source of food during the winter which helped them to survive the cold winters of Europe before there were Tescos to buy food at. So from this one person now 95% of Northern and Western Europe all have this mutation. Pretty crazy, right? Everyone in Europe that can drink milk as an adult is descended from this one person!

Going into the future other features that help humans will continue to spread through the population just like the ability to drink milk did. I personally think that most of our future evolution will revolve around fighting diseases.

Question: is it true that the TREX evolved into the chicken

Unfortunately this isn’t true, but what is true is that the chicken is believed to be the closest living relative to the T-Rex! The cousins of the T-Rex are those that evolved into birds and then became chickens, but it is because the ancestors of the chickens were so closely related to the T-Rex that people believe this.

Question: why did you join this project, have you met any new people, what project are you planning to do next and when do you think natural resources will run out such as wood?

I joined this project because I love talking about what I do and I want to show everyone how awesome it is. When I was your age I had no idea about any of this stuff so I didn’t have any clue as to how awesome science is. I want to bring to you and the other students my love of science so that you can think about becoming a scientist or even if you don’t want to do that you will understand how much fun science can be.

I have met a few adults and many students so far! It has been great fun, I even got involved in another project exploring how science and religion can work together to help describe and understand the universe and reality. I am really enjoying that as well.

My next project for talking to students or for my work? My next project for talking to students is part of that project I just mentioned, I will be putting together a website to discuss the scientific history of the universe and evolution but also talking about religion at the same time. I want to provide a website that kids can go to when they have questions about what something means in the bigger sense than just here is science and here is religion and never the two shall meet.

My next work project is a long way away but once I am done working with humans I am going to look at the evolutionary past of Chimpanzees and Mice.

If we run out of natural resources it will be because we have wasted them and our ability to adapt to new situations. Wood can be farmed and if taken care of correctly it can even help to combat climate change. With other resources like gas, coal, and oil. These are finite, but we need to do everything we can now to stop using them and switch to renewable sources of energy. If instead we harness the wind, the waves, and the sun for our power then we will never run out of power. The sun gives us so much energy we could power the world just from a large enough solar array in Africa.

Question: is a komodo dragon a evolved form of a lizard dinosaur

Komodo Dragons are really neat aren’t they? I believe they are the largest lizard in the world and they have a type of poison bite!

So where did they come from? Komodo Dragons are a type of lizard, which is distinct from dinosaurs (I know that sucks) but they do share a common ancestor way back in the past millions and millions of years ago. So the Komodo Dragon is more closely related to the dinosaurs than we are.

If you want to see the last survivors of the dinosaurs you need to look no further than modern birds. Birds descend from a particular type of dinosaur and I always love thinking about that when I am eating chicken nuggets. Chicken nuggets are dinosaur nuggets.

Science Questions from 10 year olds part 3 #IASUK

Yet more

Question: what do you think the world will turn into in the future?

Plate Tectonics will continue to change the way the world looks and the climate will change over time turning jungles into deserts and deserts into jungles. I think that is pretty cool. As far as humans are concerned, I think we will continue to evolve as we travel forward in time and we will continue to learn a great many things about the universe. I am very excited to see what we figure out!

Question: what did fish evolve from

Originally there were only bacteria, little single cell organisms ruled the world! Eventually one became the ancestor of all plants and animals, but it was still a single cell organism. But it learned a trick! by clumping together these early cells learned that they could specialise and adapt to their world. Some of these became plants and some of them became the first animals, like sponges. Now as I understand it, these then started to learn how to control their movement and you started to see the first worm like creatures and those worm like creatures started to grow fins and gills and eventually they became the first fish!

Question: do you believe that if you wear glasses you a nerd

The simple answer is that no, wearing glasses doesn’t make you a nerd.

But what is a nerd? Someone that is really interested in learning things and is very passionate about the things they love! There is nothing wrong with that. You should be passionate about the things that you love and you should love learning things (whatever it is, if you love Pokemon then that is great, if you love Video Games that also great, if you love Football then you can be a football nerd).

I only recently started wearing glasses for when I read and there is nothing wrong with wearing glasses, it doesn’t make you less than anyone else. If anyone is calling you names then you should go to your parents or a teacher and let them know. You do not deserved to be bullied because your eyes need some help. Being called names hurts and no one should have to put up with it.

/edit

I just found a great quote from one of my favourite scientists, Carl Sagan.

Science is a delight, evolution has arranged that we take pleasure in understanding — those who understand are more likely to survive.

This means that people that like to learn and are passionate about things have an edge up on those that don’t. But that still doesn’t make you a nerd for wearing glasses.

Question: why cant penguins fly?

Penguins fly through the water instead of the air. Penguins have evolved to hunt in the water which is where they find their food, so instead of being able to fly from place to place they can swim faster than the fish that they want to eat. The way that a penguin swims is very similar to the way that other birds fly. Their wings guide them through the water and their feathers keep them safe and warm from the cold water and air. Because water is much thicker than air the penguins’ bodies have changed in ways that make the penguin stronger and heavier than other birds of the same size, they have also lost their flight feathers in exchange for the ability to swim even better than before. A penguins’ streamlined form is perfect for swimming through the water and catching fish!

Question: how many hairs do dogs have

According to Miller’s Anatomy, there are about 15,000 hairs per square inch on a dog, so it really depends on how big the dog is!

My chihuahua is tiny, but my german shepherd is huge. So they each would have a different number of hairs on them.

Question: Do all animals have life cycles

I certainly think so.

There is the bit that happens before they are born, either from a mother or an egg.

The bit when they are babies.

The bit when they are stroppy teenagers.

The bit when they are adults and having children of their own.

Then the bit when they get old and pass away.

Sadly, nothing lasts forever.

Question: Have you ever invented enny think

I invent programs all the time. As a computer based scientist I am constantly making new tools to do new things. Unfortunately most of them are only useful for a few days and aren’t of much interest to anyone but me.

The really cool thing about being a computer scientist is that you have the ability to create tools out of thin air to make things work. I’m not limited by the materials I have on hand to make a new hammer or spanner, but instead I have all of my imagination to create new tools and then use them to help me do my science.

The main project that I am working on is a brand new program to discover which mutations in humans are helpful. I invented the program! I love it!

Question: What is your favourite project that isn’t yours? do you like all of the scientists or no because there competition and have you ever been hurt when doing your work

My favourite project outside of my own is the Large Hadron Collider. It is a big physics experiment where they are trying to understand the very nature of the universe and reality. How cool is that? What they do is they take a part of an atom, speed it up to almost the speed of light, and then they smash it into another part of an atom that is also travelling at almost the speed of light. That seems pretty cool to me.

I love other scientists, there is just too much for any small group of people to do in science. So I work on my things and other scientists work on other things and then we have a great time telling each other about all the cool stuff we have discovered. Sometimes I worry about another scientist discovering what I am trying to find first, but I don’t worry about it too much. There is just so much to do that if that happens I can just move onto a new project to discover even more cool stuff.

The only thing that has even been hurt in my job is my pride when I have thought I have done something well but I have actually made a mistake and done it wrong. Like right now, I had an experiment that I was really proud of, but I messed it up so now I have to redo it and that is taking a ton of my time to do. But I have never been physically hurt doing science

Science Questions from 10 year olds part 2 #IASUK

More questions from 10 year olds! This is so much fun!

Question: what’s your favourite part of science

I love solving puzzles. The world is the biggest and best puzzle there is. So my favourite part of science is when I am solving a problem and learning something new. I love discovering things!

Question: If people came from monkeys what did monkeys come from

Humans didn’t really come from monkeys. Both monkeys and humans have what is called a common ancestor. Somewhere back millions of years ago there was a species that looked like a cross between a monkey and a squirrel that lived in the trees, this is what we both came from. Over time the ancestors of the monkeys and the ancestors of the humans moved into different areas of the Earth. Monkeys tended to stay in forests and jungles and the ancestors of humans moved into the plains of Africa. Because we lived in different environments, we evolved differently. We needed to stand up to see over the grass to see if any lions were going to eat us, where monkeys stayed in the trees so they evolved to become better tree dwellers. So both humans and monkeys both descend from another animal way back in time.

Question: wy do you be a scintits [sic]

I really like to know about stuff, I am constantly interested in new things, and figuring out how things work. That is what scientists do. We study things to figure out how they work, we solve problems, and we are constantly wondering “why”?

To me science is a big game and a huge puzzle and I get to spend my time playing the game and solving the puzzles. What is better than that?

Question: what was you ferst scinse experiment

I’m not sure if you mean when I was a student like you or after I became a scientist, so I will answer both.

When I was about your age I was really into flight and airplanes. So I build a model rocket and launched it. I was able to see the thrust of the rocket engine fly the rocket high into the air, I loved it. Though I have to warn you model rockets can be dangerous, I still have a scar from where I got burned by one, so make sure to have an adult around, just in case.

When I became a scientist one of the first things that I did was learn how to extract DNA. Since all my work is to do with looking at DNA, I figured that I should know how to pull it out of a cell. So I got some strawberries, mashed them up, added some chemicals to break down the cell wall, and then purified the DNA from the rest of the plant. When I did that I was really surprised how much there was and how much it looked like clear snot!

Question: will we evolve further

The short answer is yes, we will. Evolution just means that how many people have a particular mutation changes over time. Every time a human is born that baby introduces between 75-150 new mutations that have never been seen before. Most of these mutations are called “neutral” because they don’t benefit or harm the baby, but occasionally (very rarely) a new mutation is beneficial to the baby. This mutation, once the baby is grown up with their own babies, will spread through the rest of the population over time until everyone has it.

For example, did you know it is a mutation that some adults can drink milk without farting? There is a sugar in milk called Lactose, babies have a special enzyme in their stomach that breaks lactose in half which allows it to be digested. All mammals are like this, babies drink their mother’s milk when they are born, however since mammals stop drinking milk after being babies the body shuts off the enzyme and the mammal can no longer digest lactose. This causes the lactose to be passed into the rest of the digestive track (the intestines) where bacteria eat the lactose and give off gas as a response giving the adult smelly farts.

But in Europe, one person 15,000 years ago or so mutated so that they continued to produce the enzyme as an adult and could digest lactose. This gave them an additional source of food during the winter which helped them to survive the cold winters of Europe before there were Tescos to buy food at. So from this one person now 95% of Northern and Western Europe all have this mutation. Pretty crazy, right? Everyone in Europe that can drink milk as an adult is descended from this one person!

Going into the future other features that help humans will continue to spread through the population just like the ability to drink milk did. I personally think that most of our future evolution will revolve around fighting diseases.

Question: what is your most favourite job that you could have but it cant be yours and how fun is your job are you enthusiastic or would you want a different job

If I couldn’t be a scientist I would go back to making video games. I used to work for Sony PlayStation2 as a games tester and Nexon as a games designer but I have since learned to program so I would program video games for a living.

My job is tons of fun, admittedly I love playing with computers. So what I do is I have access to a bunch of people’s genomes (the DNA that tells your body what to do) and I break them up into countries. So for instance I have a group of people from Britain, I then look for particular mutations that are young but most people have them which tells me that they are beneficial as they have spread through the population. Science to me is a great game, the graphics are kind of poor but the gameplay is the best in the world. I get to solve puzzles and build tools and use those tools to discover new knowledge.

I am very enthusiastic about my job, I love it. I also love teaching and programming so I could also do those if I decide not to be a scientist anymore.

Science Questions from 10 year olds #IASUK

So I am involved in a science outreach programmed to get kids talking to scientists, it is pretty awesome. Here are some of their questions and my answers.

Question: have you always liked science?

I have always liked science, but I didn’t always want to be a scientist. I was an IT administrator (I took care of different companies’ computers) and for a while I was a video game tester for PlayStation2. I had originally returned to University to retrain as a programmer and I was going to get back into gaming as a programmer. BUT! While I was at university I got involved in a research project helping people recover from brain damage and I learned that I LOVE doing science and research. I love figuring things out and solving puzzles (what gamer doesn’t??). So with that knowledge I started to look for a PhD degree (the university course that teaches you to be a scientist). I found one that allowed me to combine my love of computers with my love of evolution and that is how I became a scientist.

It is kind of funny how things work out. I never intended to be a scientist (though I have always loved science) but sometimes opportunities happen and you need to be flexible in your life plan to take advantage of your life opportunities. I still have friends that make video games so I get to hear about all the stuff that is happening, but I think that doing science is more fun than making video games. I still get to play them all the time!

Question: why aren’t apes still evolving into humans now ???:)

Humans and apes share a common ancestor. This means that millions of years ago in the past there was a species that gave rise both to us and to the apes. For instance 6 million years ago we split from the Chimpanzees and Bonobos. So for the past 6 million years the Chimpanzees have taken a different evolutionary path than we have. So they have a bunch of different mutations than we do including we had two chromosomes join into one so we have less chromosomes than chimpanzees do. This is why chimpanzees cannot become humans, they don’t have the right mutations. However this also means that humans can’t evolve into chimpanzees because we don’t have the right number of chromosomes or the right mutations.

But did you know that chimpanzees can learn sign language? It is true! They are so closely related to us that they can learn how to communicate with us using sign language! Check out this chimpanzee, Washoe, for some awesome details:http://en.wikipedia.org/wiki/Washoe_%28chimpanzee%29

Washoe even taught another chimpanzee how to use sign language!

There is a less well known group of apes called the bonobos (who are very cool) who are an offshoot of chimpanzees (so they are just as related to us as chimpanzees are) and they have learned some amazing stuff. Kanzi the bonobo can make and use stone tools! Just like a cave man!
https://www.youtube.com/watch?v=PljsEwjGSn0

Kanzi can even use fire and roast marshmellows!
https://www.youtube.com/watch?v=EMbWDRzqNhc

Then there is another bonobo that can drive!
http://www.animalfactguide.com/animal-facts/bonobo/

Question: If all life came from a tiny spark millons of years agois everyone and everything related?

Yes! All life is related. 3.5 billion years ago the first life forms evolved in the oceans and over the past several billion years these life forms have evolved into every life form on the planet. So we are related to apes, and dogs, and fish, and lizards, and plants, and bacteria. Everything has a common ancestor!

Question: what do you believe in more science or Christianity

Well, I’m not a Christian so it isn’t too much of a problem for me. I am what is called a Humanist. I believe that morality and ethics (what we think are right and wrong) are best learned from human compassion and empathy. The world would be a much better place if everyone really worked at trying to get along and be better friends to each other.

On the question of Christianity and science. There isn’t any real trouble between science and Christianity if you think that God created the universe and science works to discover how God did it. Yes there can be some problems between the Bible and some parts of science, if you believe that the Bible is 100% fact instead of a story that describes man’s place in the world. But if you think that the Bible was written by people that loved God and were trying to understand their place in the universe and maybe they got some of it incorrect. But can there really be a problem between God and science? I don’t think so.

Science is the process of learning about how the universe works. If God made the universe then this is how he intended it to work. So by learning about science you are learning about the world that God made. By becoming a scientist you are increasing the understanding of God’s universe.

You don’t need to choose between Christianity and God if you think that science is just discovering things about God’s universe. The authors of the Bible didn’t know about dinosaurs or the Big Bang, but we do and we understand more about the world than the authors of the Bible did.

Hiding in the Trees: Positive Selection using Lineage

Last month I gave a talk on my research and it went so well that I decided to record a longer version of the talk for the public. Please have a watch and let me know what you think!

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