Listening to a genome…

The HIV-1 virus was the first genome to ever be tweeted (@GenomeTweetHIV). After that I also tweeted the genomes of E. coli, yeast, a nematode, and the fruit fly. If you want to know more about these projects (or why the hell I did them) you can read more here, hereherehere, and here.

Tonight I took the entire HIV-1 genome and transformed it into music. This is something I’ve wanted to do for quite a while. The four nucleotide base pairs are cytosine (C), thymine (T), adenine (A), and guanine (G). Every C in the sequence has become a C note. The A bases are A notes and G bases are G notes. A friend suggested making the thymine (T) a pause in the music, but I preferred the idea that every base has a note so T has become a D note.

Is it great music? No. This is just yet another way to observe the genome. This is the smallest genome I’ve worked with and the track is one hour long. Obviously it could be shortened by altering the tempo but I liked it like this.

Have a listen to HIV.

Here’s a shortened version with a different instrument. It’s only 33 minutes long.

Scotland end-to-end in 2 days and 6 hours

I’ve been so busy recently I forgot to post an update about my Scotland end-to-end charity cycle! Spoiler alert: I did it. As soon as I got home I moved to the Land of Eng and I’ve been settling in since and never got round to writing a blog post.

To raise funds for the Scottish Association for Mental Health (SAMH), and as a “goodbye for now” to Scotland as I move south of The Wall, I decided to cycle the length of Scotland over 3 days. I trained for it but probably not enough, which is the usual for endurance events. The journey would be just over 400 miles in 3 days. I wanted to do it solo (no other cyclists) and also unsupported (no support car to carry my food etc). I wanted it to be tough. On the 12th of September I got the train up to Thurso and cycled along to John O’Groats. It got dark quickly, became very misty, and a shortcut I thought was a paved road turned out to be off-road in a field (but I did it anyway, on my road bike). Eventually I got to my accommodation, got everything ready for the next day, and slept. It was a great little house hotel with the most wonderful hosts. I met an interesting couple of American ladies who stay there every year and they were kind enough to give me donations. Everyone was going to wake up during the night to see the northern lights but I knew I had my longest day of cycling ahead of me. I went to bed at about 11pm.

The cycling was over the 13th-15th of September. The first day would take me from John o’Groats to Loch Oich (a bit further south than Loch Ness), a good 150 miles. The second day would go from there, passing Fort William and Glencoe, through the Trossachs and along Loch Lomond (where I usually cycle during training), and into Glasgow to call it a day after about 130 miles.  The third day was a coastal cycle as far south as I could get in Scotland. This took me to the area of land south of Kirkmaiden and actually further south than places in England like Carlisle. If I could cycle on water, I wasn’t too far from Northern Ireland. I had to cycle another 20 miles north again to get to the nearest train station then slept in Glasgow another night before coming home on the 16th.

My route on day 1.

My route on day 1, tracked with GPS on Strava.

The most dangerous day was definitely the first. The sea mist was everywhere on the east coast when I was cycling and I couldn’t see more than a few metres in front of my face. If I did this again, I wouldn’t cycle along the coast. When I did see some beautiful scenery that was worth photographing, it was gone before I could get my phone ready. Every picture was mist.

This was how bad it looked when stopped. Imagine cycling nearly 30 mph.

This was how bad it looked when stopped. Imagine cycling nearly 30 mph.

Believe it or not there are mountains behind this wall.

Believe it or not there are mountains behind this wall.

It felt safer when I started to climb and get away from the mist, but the downhill sections were pretty crazy. I didn’t have any accidents on the entire journey but I came close twice and both occurred while flying downhill at nearly 40 mph. Both times I was able to get things under control and avoid an incident. It might not be the Alps, but Scotland has its impressive downhill sections. Ignoring the couple of times I nearly came off, I loved them. Especially after climbing a few thousand feet!

Climbing was the only way to avoid the sea mist.

Climbing was the only way to avoid the sea mist.

The weather improved dramatically as the day went on and I moved further inland. The mist vanished and the sun came out. Food and hydration became my main priority instead of visibility.

Improved weather away from the coast.

Improved weather away from the coast.

I must have passed about 20 whisky distilleries that I noticed. Sadly I didn’t have time to stop at any because I had to cover 150 miles in one day and I didn’t want to be cycling too late into the evening. Firstly, I wanted to avoid cycling in the dark for safety reasons. But I also wanted to be done as early as possible so my muscles could recover for the 130 miles I would be doing the next day.

I didn't have time to stop!

I didn’t have time to stop!

Day 2 started extremely well and I was in a good mood. I cycled strong, I stopped to take pictures where I could. It was exactly how I imagined the ride going when I visualised it during the planning stages. A fun ride through beautiful landscapes. That’s how it started at least.

Day 2 started beautifully.

Day 2 started beautifully.

I’ve been to Loch Ness so many times in my life, but my brain never really gets used to how big it is. This was the first time I had cycled it and it seemed to go on forever. I didn’t mind since the view was constantly beautiful and I was still in a good mood at that point. The only problem was the winding roads and tourist traffic. Many cyclists choose the south side of the loch because it is quieter, but I know the quality of the road is better on the north side and I knew I could cycle it quicker. It was much more dangerous, but I think I made the right decision in the end. The loch is so long that the climate seemed to change while cycling alongside it. At first it reminded me of being back on the coast. I could barely see the other side of the loch for mist. Eventually it cleared and it was a perfect summery day.

The mist on Loch Ness starting to clear.

The mist on Loch Ness starting to clear.

Urquhart Castle.

Urquhart Castle.

Still on Loch Ness, but now everything is crystal clear.

Still on Loch Ness, but now everything is crystal clear.

Everything went downhill after Loch Ness and I’m not talking about gradient. I’d started a little too strong and I was struggling. I cycled for as long as I could, eating small amounts every 15 minutes (while cycling). Eventually I passed a loch (I don’t even know which one) and stopped for a proper meal. On the first day I found it impossible to eat a proper meal because my stomach was in a really weird place having to cope with eating every 15 minutes for a whole day. But this time I ate the entire meal like it was a biscuit, despite my weird regular snacks. In hindsight this was a good idea just to make me feel a bit more normal, but it slowed me down considerably. Not just the stopping for the food, but the meal itself. I was desperately tired and eating a huge meal so quickly just made cycling seem like a really bad idea. I sat for 10 minutes then got back on the bike.

My first break since Loch Ness. Starting to get into trouble.

My first break since Loch Ness. Starting to get into trouble.

A welcome meal to keep me going through.

A welcome meal to keep me going though.

I didn’t stop again or take photos until I got to Spean Bridge. This was a bit of a milestone because at that point I realised I had really cycled from the east to the west of the country. I took another break here and it was the last time on day 2 that I felt good about the ride and the last time I stopped for photos and fun.

Taken from Spean Bridge in the Great Glen.

Taken from Spean Bridge in the Great Glen.

Of course I found time to stop for this one.

Of course I found time to stop for this one.

From here I struggled. I didn’t slow down, I didn’t need to keep taking breaks… actually it was the opposite. I realised that if I took too many breaks they would take their toll. I knew I needed to keep my head down and just keep things steady. Consistent pace, just keep the legs turning. I did take the odd break now and then but just for a few minutes to stretch a bit and write the odd text message. By the time I was getting to Glasgow it was getting really dark as I’d taken too long in the morning and set off a bit later than I meant to. In Glasgow I stayed with my brother and his girlfriend. Their sofa was the most welcome sight and I collapsed.

I’m not going to lie, day 3 was difficult too. Especially at the very end when it was just hills keeping me from my goal. But none of it compared to the day 2. Day 3 was more like the first day. My legs felt warmed up after the previous day cycling and a good long sleep, but I knew not to go too strong this time in the morning. I had over 100 miles to cover but nowhere near as far as the previous days. Most of the day would be navigating my way around motorways and busy roads out of Glasgow and then down the west coast. I tried to keep a good pace because I knew this day was the only one that mattered for my overall time. I was never doing this to set a record, but it has to be said that I couldn’t find a cycling record for this journey anywhere online so I’m happy to set one for people to beat. I knew I couldn’t cycle non-stop like some people have done on the LEJOG route. I needed to sleep at the end of each day, so I knew my ride would take over 2 days even if I was only cycling for less than 20 hours during those 2 days. But on day 3 I could stop the clock once I reached my destination. I wanted to get there asap. There was also the added pressure that I had to cycle another 20 miles back north again to the nearest train station to get back to Glasgow that night. I didn’t want to miss the last train.

Most of the day was a case of keeping my head down and just cycling. I forgot about texting people, I forgot about social media, I didn’t take many pictures except when I stopped to stretch. I just thought about my cadence, calorie intake, and hydration. Once I reached Stranraer I had good feeling for how far was left. I could estimate how quick I needed to be to make the train later. I was tired but suddenly I felt as happy and motivated as I did on the first day. I kept up the pace so I could get a decent time but the hills were constant between Stranraer and the coast south of Kirkmaiden. This was difficult after days of cycling but I enjoyed it. I could feel the end coming up. I had to dodge cows. Every downhill only lasted a moment before I was going uphill again. But it was all worth it as I could feel the entire ride coming to a close and it felt very rewarding. As I reached the last couple of hours of cycling, the clouds rolled in and I thought I was going to see my first rain of the entire journey. Amazingly I didn’t. The sun was gone, the atmosphere completely changed, but it didn’t rain on me once during the entire 3 days of cycling.

The clouds...

The clouds…

...were rolling in.

…were rolling in.

I didn't care if it rained because I knew the end was near.

I didn’t care if it rained because I knew the end was near.

Looking back at some of my cow friends. When I came back down they were all over the road! All of them.

Looking back at some of my cow friends. When I came back down they were all over the road! All of them.

When I finally reached the end of the journey, this was the view I was treated to:

The finish line.

The finish line.

And this is what the most southern point of Scotland looks like:

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Finished! I found a tiny old lady and she managed to take this picture after about 10 attempts. She must have been about 100 years old.

Finished! I found a tiny lady and she managed to take this picture after about 10 attempts. She must have been about 100 years old.

It took me 2 days and 6 hours to cycle mainland Scotland end-to-end. That’s like cycling from Edinburgh to London. It was very rewarding in an athletic sense because I’d never done endurance cycling before. But far more importantly, we managed to raise £1229.53 for the Scottish Association for Mental Health. It’s such a brilliant cause, a genuinely great charity, and I’m so grateful for everyone who donated. I’m also grateful to my friends who weren’t able to donate for whatever reason but gave me support and motivation during training and the ride itself.

1229.53

I’m sad to have left Scotland and I really do miss it. Sure, it’s only a train journey away, but it’s not quite the same. I’m so glad I was able to take in so much of the country in such a short space of time. It was the perfect way to say goodbye as I managed to see a bit of everything, even if I was struggling to take it all in during the darker moments (especially day 2). I’ve only been back once since I moved but I intend to visit whenever I can. In the meantime I’ll be sipping whisky and listening to Caledonia ;)

Cycling Scotland end-to-end over 3 days

On Saturday I’ll be starting the first of three days cycling the length of Scotland. It’s something I’ve always wanted to do and will serve as a “goodbye for now” as I move to the Land of Eng later in the month. The primary reason I’m doing this is to raise funds for a great charity, the Scottish Association for Mental Health (SAMH). They provide great support for those in need and also tackle the stigma of mental health. One in four people in the UK have to deal with mental health problems.

Various Scottish poems have mentioned the journey from John o’Groats to Kirkmaiden, which is generally considered to be the end-to-end journey for mainland Scotland. Robert Burns wrote of the journey “frae Maidenkirk tae Johnnie Groats” in his poem On the Late Captain Grose’s Peregrinations Through Scotland. Robert Louis Stevenson wrote:

But maistly thee, the bluid o’ Scots,
Frae Maidenkirk to John o’ Grots,
The king o’ drinks, as I conceive it,
Talisker, Isla, or Glenlivet!

The Maidenkirk they speak of is now Kirkmaiden. Although being in Scotland, it’s actually further south than Carlisle. Day 1: Leaving John o’Groats and cycling 160 miles through Inverness, along Loch Ness, and staying the night near Loch Oich. Day 2: Cycling through Fort William, through the Trossachs and Loch Lomond National Park, then on to Glasgow to stay the night. Day 3: Cycling as far south as I can get until I’m pretty close to Northern Ireland! I’ll post an update after the cycle with photos if possible.

If you would like to support SAMH you can donate on my Justgiving page for the ride. Thank you!

Best of “Not New Scientist”

I made a light-hearted Twitter bot to poke a bit of fun at New Scientist. @NS_headlines attempted to automatically create sensationalist and surreal headlines. The account has posted over 1000 tweets now, so I feel it’s a good time to switch it off. To the 845 followers who I know must be desperate for it to continue, I might improve the script in the future and restart it, but I’m more interested in other side-projects just now. I felt it might be worth making a short Best Of list to see some of what the account was able to come up with. The account was featured on Buzzfeed so there is a collection of favourites there, but here are a few more that were highlighted by Favstar as being popular.

GenomeTweet – Yeast is finished!

It’s done.

Finally, after 98345 tweets, the entire Saccharomyces cerevisiae genome is on Twitter.

S. cerevisiae is a yeast commonly used in brewing, wine-making, baking, and biological research in the lab. Now we have virus (HIV), prokaryote (Escherichia coli), and eukaryote (S. cerevisiae) genomes on Twitter.

HIV – 70 tweets

E. coli – 34767 tweets

Yeast – 98345 tweets

People who use Twitter can appreciate how much data can be stored in a tweet. A single tweet has a limit of 140 characters. When I see that tweeting the E. coli genome took  34767 tweets, I understand that it took me about 4 years to tweet that many times. I can visualise and appreciate this better than learning “a genome would fill a few squintillion books”. What books? How big are the books? How thick? How many pages? I can’t visualise it because I’ve never seen that many books at once. Actually, is squintillion a thing? But I can compare these genomes with my own Twitter output and appreciate the size a bit better. It’s not perfect, but hey I was just bored one evening and thought tweeting genomes could be interesting.

I’m now taking a break from tweeting genomes, at least for a while, so my Raspberry Pi is free to be used as a brain by Deckard The Robot. He’ll be coming to life over the next few months.