The Cambridge Engineer: Freshers' Edition 2018

Cambridge Engineering Society Freshers · Sep 2018

The World of Bioengineering

THE CAMBRIDGE ENGINEER CUES MAGAZINE W W W. C U E S . O R G . U K

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From the Editor

Hello new students and welcome back our old students! I’m Lettice Wei, a third-year engineer from Magdalene College, the new magazine Editor this year.

The Cambridge Engineer - CUES’s magazine - is written for students to cover a broad range of engineering-related topics. The articles are mainly provided by company interns and society leaders.

This year we will launch a series of article competitions to enrich the content of our magazine, along with the a “pick-me-up” during lunchtime - a puzzle page.

The theme of this issue is the world of bioengineering. This field is gaining popularity in recent years. A quarter of the article entries are related to biotech.

Also, you can look into the life of interns in other areas such as aero and civil engineering.

For Freshers, don’t forget to check out the new societies. Their articles on this issue may appeal to you.

The suggestion given by Akhil about university life is also worth a look. Hopefully, this magazine will inspire you for a better life as an engineer.

Magazine Editor Lettice Wei magazine@cues.org.uk 2

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Contents CUES Introduction by President 4 Understanding More About Aviation

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Cambridge Engineers in Dyson 13 P&G: Do Something that Matters From Day One

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Schlumberger Q&A 18 TTP: The Technology Partnership

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CUMIN 23 The Genetic Engineer’s Toolbox 24 Cambridge Development Initiative TTP Full Blue Racing

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A New Video Game 37 Biomimicry: A Short Introduction 40 My Introduction to Machine Learning Through the World of Biotech

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Approaching the Brain from an Engineering Perspective at Harvard

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One Small Step into the Department, One Giant Leap for Your Career

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Designing and Building a Winnig Card Board Boat 50

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CUES INTRODUCTION BY PRESIDENT

CUES Introductio C

ambridge University Engineering Society (CUES) has continued to serve its members faithfully and diligently since its inception in 1901. More recently, it has undergone immense transformation to adapt to the needs of the current times and has in the process realised its unique position in the Cambridge ecosystem. We believe however, that there is still huge opportunity for the society to grow and develop to fulfil all of its potential.

The CUES mission has been pivotal in guiding it along its transformative journey, and in establishing it as one of the most active and professional student societies in Cambridge. Several difficult decisions were made easier when looked at through this prism, and it is hoped that successive leaderships will continue to embrace and uphold the mission similarly. CUES exists to show students what an incredible world of opportunity awaits them when they leave Cambridge. CUES’ mission is to deliver technical enrichment and increase employability so that its members have the skills to seize those incredible opportunities. It achieves this by forging strong relationships with its sponsors, the department and several other partners, and by pursuing quality execution in everything that it does.

From the viewpoint of president for the coming year; the society currently stands on a rock-solid foundation as the most active society in Cambridge with an exceptional membership base and considerable links to industry.

There is no doubt CUES is continuing to thrive, with ample opportunities for growth.

The society can currently claim an impressive membership body of around 1300. In itself, this statistic is unsurprising given the broad nature of the society’s mission and the quantity of Cambridge undergraduates with an interest in engineering and technology. However, as part of the strategy analysis undertaken last year, it was estimated that only around 50% of the members would be considered ‘active’ (regularly engaging with CUES emails and/or events). While this nevertheless still represents a considerable number of involved members, it is recognised that there is still a significant amount of work to be done, not only (as always) to

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ion by President try and boost the society’s overall membership but also in engaging more with the current members.

A key focus for this year therefore, is creating a sense of ownership in CUES amongst the entire membership. The opportunities offered

by CUES are being extended to reach as wide a proportion of the members as is possible- making the society applicable and relevant for all of the engineering & technology community.

The current activities led by CUES are generally recognised across the university as well-run, successful events; a significant part of the work for next year will, of course, be maintaining and developing these to be as effective as possible. New initiatives will also be introduced to continue to grow the society and maximise the benefit of CUES to both the members and the sponsors. In terms of broad aggregates, the main initiatives for next year are outlined as follows; Venture Competition A constant concern expressed by employers and students is the lack of opportunity to undertake extra-curricular side projects in the engineering area of their passion. Some CUES initiatives already aim to encourage students to pursue these practical projects (such as the ARM hackathon or the grants scheme).

These are extremely popular events but due to the nature of the course, often the time available to students working on them during term is very limited. Furthermore, in turn this can limit the type of project as some, such as software can be much more flexible in time commitments relative comparable hardware projects (which require multiple rounds of iteration and re-ordering).

The Venture Competition event would occur over summer- the one main time window that students have away from intense course workload demands. The event would be an opportunity for students to produce an engineering product or solution with an entrepreneurial slant - resembling a hackathon but over a much more extended time period. This would allow students to work on a truly broad range of engineering disciplines, fully pursue their passion and encourage initiative for interesting opportunities.

Alumni Relations Building on the initial progress made by the CUEA (Cambridge Uni-

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I discovered

it’s the

little things

thAT

really count

At BP there are no small jobs. So when we shut down our Kwinana refinery for maintenance, I had the big challenge of ensuring that more piping joints than we‘d ever opened up before were inspected and repaired or replaced.

Ben Kwan, Engineering, Kwinana, Australia

What will you discover?

At BP, we offer the most exciting and challenging global opportunities for high performing graduates in engineering, science, business and trading.

CUES MAGAZINE

6 Search for W WBP W . C UCareers ES.ORG.UK

versity Engineering Association) last year, this year CUES will incorporate alumni into the activities of the society. The aim is to hold evening talks from inspirational alumni and community events which can introduce networking and mentor relations in an organic manner.

STEM tutoring for less privileged children. It is hoped this, in a small way could also contribute to tackling some of the root issues in the under representation of women and minorities in STEM subjects at schools.

Community Leadership Speaker Events One of the primary goals of CUES is to support A significant new initiative for 2018-19 is to hold a welfare through increased community and colseries of speaker events on key engineering relat- laboration in the Cambridge engineering envied topics. Given the brand and reputation of Cam- ronment. Community enhances the wellbeing bridge and CUES, the society has been as ambi- of our members. CUES promotes this through tious as possible with the calibre of speaker invited. the majority of its operations (particularly welSenior executives and directors will give talks and fare) however we plan to extend this – an exparticipate in panel events to discuss their personal ample of a further community event proposed experiences and their insights into industry. for this year is a multicultural food function (financially supported by the engineering lanOutreach guage department).

Last year, CUES heavily focussed on welfare and diversity initiatives. The society made a In summary, I believe that this year will bring welfare video, started an ‘engineer’s cafe’ as about an exciting and transformative year for well as a meditation/ prayer room and ran di- CUES. I have the utmost confidence in the versity talks & panel events. Following on from committee and look forward to working with the success of these, it is planned to contin- our sponsors to deliver the best value that we ue this focus and to extend the operations to can. For any feedback, suggestions or comalso include outreach. This will entail coordi- ments are welcomed to president@cues.org. nating with the departmental outreach officer uk! and creating links with schools to organise Vere Whittome President 2018-19

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UNDERSTANDING MORE ABOUT AVIATION

Understanding more about aviation Three Cambridge University engineering students recently applied for a summer internship at Marshall Aerospace and Defence Group here in Cambridge. For 10 weeks they have been given experience in different areas of the business working alongside highly skilled engineers and mentors that have given them hands on experience as an engineer in the real world.

Alex Johnson, Chris Barrott and Yana Lishkova had this to say about their 10-wek internship‌

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W

hat have been your best experiences during your summer internship at Marshall Aerospace and Defence Group?

Alex: “Having the opportunity to walk around the Marshall aircraft hangars and to see the work going on with the C-130’s as well as other aircraft is not something you get to do every day! I have particularly enjoyed seeing the work that is being done inside and outside the aircraft as it has inspired me to be part of this engineering set up”.

Chris: “As part of my rotation in the Hercules Technical Support Group, I have assisted with surveys of the aircraft and gained invaluable knowledge. It was great fun being on the flight deck during an enginew test, which was both fascinating and unlike anything I’ve ever done before”.

What have you benefitted from the most?

Chris: “The most beneficial thing has been gaining real work experience at a highly respected and well-known aerospace engineering company and seeing how we can

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apply what has been learned at university to real projects. I feel that I can return to university now with a much clearer idea of what I want to specialise in”.

Yana: “I have observed how a project is started, carried out, tested and certified in the aeronautical industry which is subject to different military standards and procedures.

I have also obtained invaluable CAD training which was not something I had expected to get prior to starting.

Would you consider a career in the aerospace industry?

Alex: “I have been interested in engineering and more specifically aerospace since a young age, however, since working at Marshall ADG they have given me an experience of aerospace engineering applied in an industrial setting and I understand more clearly how the industry works and what sort of skills I would need to succeed. I will definitely be working towards a career in aerospace in the future”.

Chris: “Now that I have worked in different

departments I can see which area best suits me. I feel much more confident in making a future career decision and aerospace is exactly where I want to be”.

Would you recommend the Marshall internship to others?

Chris: “If anyone wants to get a variety of experience in different engineering disciplines and also get up close with some of the aircraft here, this internship is perfectly suited”.

Yana: “Getting work experience at Marshall before completing your degree is incredibly valuable and I would strongly recommend getting this experience in order to have a better chance of getting a job post-graduation. The internship role is a paid position too which is ideal”.

How much does this internship help with your university course?

Alex: “At University, my course usually focusses on the theoretical side of engineering and the internship has allowed me to use that knowledge in the context of an industrial set-

Does this sound like something you would want to do in 2019?

To apply, go to: www.marshalladg.com/careers Deadline for applications – 31st December 2018

ting and to gain some practical understanding of my course”.

Yana: “This internship has enabled me to make a more educated decision for my master’s course at University as well as for my future career path. My mentor has not only provided guidance within the company, but has also taken time to discuss with me the future academic and career options”.

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CAMBRIDGE ENGINEERS IN DYSON

Cambridge Engineers in Dyson F

in is a recent graduate from Christ’s College, opting to study MET in third and fourth year. He undertook a 3-month summer internship with Dyson as well as a six-week industrial placement as part of the Manufacturing course. Fin starts as a Graduate Manufacturing Engineer in September 2018.

With an ever-increasing array of products, from vacuum cleaners to electric vehicles, Dyson employs a full range of engineers from many different engineering disciplines. The broad range of skills developed in my first two years at CUED has proved vital in understanding the principles of Dyson’s core technologies. During my time so far with Dyson I have utilised my knowledge in design, sustainability, materials, electronics and software engineering in addition to manufacturing.

“My proudest moment to date has been developing a solution to a long-term problem that I was tasked with during my six-week placement. I was trusted with a project that had real impact and was given the perfect balance of autonomy and support.

Dyson is fantastic place to work. With great facilities, societies and events all on-site, it’s not only an exciting place to be during working hours, but also outside of them too.

Much like CUED, Dyson is fastpaced, challenging and rewarding.

You’ll be tackling tough problems, making a few mistakes along the way but learning from them every day.

I’m looking forward to starting in September alongside many other like-minded graduates. “ Sam graduated from St Catharine’s College in 2017, also having studied MET. He started as a graduate in September 2017 and has spent a year as a Graduate Engineer in the Manufacturing team at Dyson.

“My first year at Dyson has flown by and I’m already preparing for the next set of graduates starting in September – which includes Fin. I’ve been given responsibility and real project work right from the start, and never felt like I’m being treated any differently because of my graduate status. As part of the manufacturing team I’ve been able to get involved in a broad range of projects across many of Dyson’s existing and new categories, as well as helping improve our internal team processes.

I have been able to use the unique combination of broad and in-depth knowledge gained at CUED to settle in and prove myself a valuable addition to my team. In particular the MET course of my final 2 years has helped immeasurably – modules on operations and business aiding me to understand how and why a large company works the way it does, as well as how different Dyson is to many other large companies. Also, the exceptional experience gained though both the series of factory visits in 3rd year and longer industrial placements in 4th year have been a constant reference and point of comparison during my time at Dyson. Whilst I may not have as many years of employment as CUES MAGAZINE W W W. C U E S . O R G . U K

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some of my team, I am lucky to be able to relate issues to a wide variety of industries.

There are roles within Engineering at Dyson to suit any of the possible 3rd and 4th year choices at CUED. I work alongside design engineers, mechanical engineers, fluid dynamicists, materials engineers as well as researchers and many other disciplines.

I’m looking forward to what’s next after my graduate year comes to an end. There’s so much happening at Dyson that I’ve still got a lot to learn and every day brings something new.

We have both had the opportunity to spend time abroad and had first-hand experience working with other teams across the Dyson.

The Malmesbury headquarters offers great

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spaces to work, as well as a sports centre hall, and two cafés which I’ve used a lot!

There has been constant development and improvement to the site in our time here, so it’s only going to get better by the time you arrive.

There are countless opportunities to get involved in activities outside of work, such as the Challenge Dyson events, volunteering with the James Dyson Foundation, mentoring new starters, and of course the Christmas Party, where fancy dress is taken to the extreme! There are also many clubs where you can meet people who share a hobby, or the opportunity to try something new.”

We would highly recommend all CUES members applying for an internship or a graduate role at Dyson,

[Figure] CUES 2018 ARM Hackathon Selection

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P&G: DO SOMETHING THAT MATTERS FROM DAY ONE

From Day

Do A SomeThing That Matters

s this is the Freshers’ edition of the CUES magazine, some of those reading this will be just about to, or will just have experienced their “Day 1” moment at University. Day 1 of moving into college, pitching up at the gates with a car full of unnecessary items and over-emotional parents. Day 1 of university itself, matriculating, listening to some Latin that no-one prepared you for. And finally, Day 1 of lectures, trooping into an airless lecture theatre to start on a trying, testing yet rewarding degree in Engineering. University takes a lot time, ener-

Edward Holt (Sidney Sussex, 2013), now Process Engineer at Procter and Gamble’s Manchester Manufacturing Plant, writes about how both at university, and at P&G, Day 1, and doing something which matters are incredibly important.

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y One gy and dedication, and so it’s important that you feel you’re doing something which matters.

At P&G, Day 1 is incredibly important too. As a new graduate at P&G, I went directly into a job rather than onto a rotational placement graduate scheme, I therefore felt that I started to make a real impact from the very start. Before I started I thought “Day 1” was just corporate speak and I didn’t understand how I could make an impact in one of the biggest consumer goods companies in the world, on one of the business’ billion-dollar brands, Pampers. But as soon as I started I realised it really would be big responsibility from the start, and I could see how what I was doing would directly impact the output of the plant.

Within my first month, I conducted an effort study, examining every aspect of the department operation. I got the opportunity to present my study to the plant leadership team, and it was then used to set department priorities and budgets for the next fiscal year. I was incredibly proud I could make an im-

pact so quickly. Within the first few months, I was given projects to lead by myself, such as the new product qualification effort on our production lines. It was so interesting to be involved so closely in making the perfect, high quality products which thousands of consumers will see on the shelf and use. I had to work with Research & Development to ensure we could reliably produce all new packaging, I had to coordinate a team of people across the manufacturing lines, making key decisions on stability and quality criteria. I have also been given the opportunity to get stuck in with all of the innovation in automation in the plant. I have worked with Autonomous Guided Vehicle in the palletising department which will deliver a step change in safety and productivity. I have also been involved from the initial project definition stages, liaising with external vendors, delivering the project and ensuring the new innovation we are bringing in will work with our current needs and operations.

Reflecting on the last 12 months of working to deliver these results, I can see they were challenging, but I had the support and confidence of being given real responsibility and accountability to achieve them. I was

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SCHLUMBERGER Q&A

Schlumberger Q&A

(last page continued) also given amazing training, mentoring and leadership from the beginning. So what seemed daunting at the beginning, dissolved into the desire to instead get stuck in and make a real impact, in a company that gave me the confidence and the skills to do so.

So, as you start your own “Day 1” journey, whether it be the beginning of University, or a new course, or a new venture outside of studies. I would encourage you not to be daunted but instead to think about the potential it gives you. Day 1 is a blank slate, a new opportunity to prove yourself and to make a real impact, so take the challenge by the horns and go for it – you might just surprise yourself.

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hy did you choose Schlumberger?

Great downhole technology, interesting field opportunities and Schlumberger’s unwavering commitment to HSE What does a field engineer do in your segment?

I work in the wireline segment, this involves deploying sensors or tools into an oil well on a wire to log (graph) of it’s properties vs depth in the ground What sort of training did you undertake?

There was a 2-3 month intensive training course just after I started in 2015, the rest of the training has mainly been on the job.

This does vary from segment to segment though What is the best part of being a field engineer?

Variety, whether it be working with new equipment, working with different people from around the world or working on a range of rigs over Norway, no offshore trip has ever been quite the same.

What is the hardest aspect of life as a field engineer?

I find managing the offshore work – life balance situation very challenging What are the conditions like in the field?

The conditions offshore in Norway vary slightly from rig to rig, it can be comfortable on a fixed platform with a single cabin, but less so in a shared cabin on a boat in 10m waves What are your future plans/what kind of role are you aiming for next?

After completing the graduate program there are lots of different career paths you can take, right now I’m still undecided.

What advice would you give to Cambridge students thinking of applying?

There’s quite a lot of hands-on work in the field so don’t forget to focus on the practical elements of your course as well as the theory.

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TTP: THE TECHNOLOGY PARTNERSHIP

TTP : The Technology Partnership

I

knew tech consultancies worked on a range solve themselves. Their work is in the vanof engineering problems, I knew consultants guard of global technological progress. But worked in technical and commercial areas, what I hadn’t anticipated is how varied and and from what I had heard it sounded like exciting my own days would be. Work varies a pretty fun job. From websites and careers day on day, week on week, month on month. fairs I pieced together The learning curve is steep “What is technology conmore info – consultan– making the job even more cies applied science and rewarding. sulting?

What does a techtechnology to real world As a sample, let’s take a look problems, projects could at a week in the life. My life, nology consultant really do? span everything from specifically – I’ve lifted this market research to proschedule straight from my In my final years at univertotype building to setting diary a couple weeks ago. up manufacture. This was The only changes I’ve made sity I wasn’t quite sure.” useful to know, but to me have been to withhold comas a student, a lot of this got lost in the sea of mercially sensitive information. info from other recruiters. I wanted something Monday more concrete. I wanted to know what I’d ac10:30am-12am: Teleconference with [COMPAtually be doing as a technology consultant.

NY] for printed electronics A couple years on, I have a pretty good idea.

A great opportunity for the company. These Consultancies do really exciting work. They guys were interested in using our proprietary work with companies that want to solve technology to build wearable electronics – I difficult problems – often the ones they can’t met them at a conference a few weeks ago CUES MAGAZINE W W W. C U E S . O R G . U K

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and they were very keen to chat again. I talked to them about ideas I had, and the scope of a potential project with TTP. 2pm-3pm: Meeting regarding [PATENT] international phase I filed a UK patent for 3D printing a year ago, and we reviewed the search results to prepare for international filing. Generating IP in this new area for us has been very important.

Tuesday All day: Meeting with [COMPANY] in Frankfurt A long but productive day. A colleague and I went to visit a materials company to discuss a new project. We also got a factory tour, and I agreed to prepare a proposal for them.

I had previously done some technical feasibility work for them in our labs which they were excited to hear about.

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10am-2pm: [COMPANY] visit to TTP Another lead from a recent conference. Some contacts I made in [COMPANY] came to TTP to see our facilities and discuss the licensing of one of our proprietary technologies.

2pm-5pm: Booked time on superc o m puter f o r n u merical m o d e lling I was optimizing the design for a fluid feed in

one of our ultrasonic devices. It’s a complex problem involving fluid flow, electrostatics, acoustics, and mechanical vibration – my laptop couldn’t quite hack it.

Thursday 9:30am-10:30am: Call with colleague overseas One of my colleagues was overseas with several life science companies wanting to meet with him. We discussed how to best approach the companies, and what TTP could offer them.

2pm-3pm: Update call with [COMPANY] Our weekly update for our project with [COMPANY]. With two colleagues also on the project, we discussed the weekly prog-

ress and upcoming work.

Friday 1pm-2pm: [MEMS device] brainstorm We do a lot of work in microelectromechanical systems. This brainstorm was for an internal project – something we think is worth keeping inside the company for initial development. Getting four or five consultants into a room can generate ideas very quickly.

2pm-3pm: [MEMS device] numerical modelling The brainstorm produced some excellent ideas – now time to see if they’re going to work.

5pm-5:30pm: Friday evening talk about [SATELLITE COMMUNICATIONS] Every Friday we have a talk about something exciting in the business. It’s a great way to find out more about what else the company is doing, and relax with food and drinks after a week of work.

how deep is the first cut?

You are a surgeon, scalpel in hand.

But skin is tough, flesh is compliant.

Deep cuts are easy. How shallow a cut could a top surgeon make by hand? And how?

There is no answer at the back of the book.

Discuss your approach to this and the real problems you could be solving at TTP every day. explore@ttp.com

Apply yourself.

Explore TTP. www.ttp.com

Another week would look completely different. And you’ve likely noted that this schedule doesn’t fill the whole working day. There was plenty of other work to fill this time. Some of it was project work: market research (for our clients), design work, laboratory testing, prototype construction, reporting, project planning; and some of it was commercial work: market research (for TTP), reviewing contracts, and preparing proposals.

I encourage you to think critically about what motivates you, and think about how certain careers align with this motivation. Think about what kind of work you want to do. I have been lucky to find an employer and a job that offers me freedom – I can do this range of activities in a range of sectors because I want to. If I think something is interesting and worth pursuing, I have the freedom to pursue it. Whatever drives you, and whatever flavour of work you’re looking for, put in the effort to find somewhere that lets you grow as an engineer.

Consultants Tristan Downing CUES MAGAZINE W W W. C U E S . O R G . U K

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What Will You Be? Engineering Careers with Real Responsibility We’re hiring Want a challenging and rewarding career with borderless leadership and development opportunities? Join our team.

Who are we?

We’re a pore-to-pipeline technology company with intern and trainee opportunities for engineering graduates.

Why join us? n Continuously learn and develop new skills n Work with industry-leading technologies n Drive your career in our culture of meritocracy n Enjoy a challenging career in a global, diverse

community where your contribution is valued n Work in a dynamic and creative team environment n Achieve more: we promote from within

careers.slb.com

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CUMIN

A

s the reader of this article, there are three possibilities for your current relationship with machine learning. I’m going to try and convince you that independently of which category you belong to, you should be excited about CUMIN and look forward to engaging with our projects and events.

So what are the three options? First: somehow, you have not heard of machine learning before (or machine intelligence as our department and literally no other department on earth likes to call it).

If that is your stance, welcome - you are the first engineering student admitted to Cambridge from a secluded internet-free island.

The sheer amount of over-sensationalised articles about the rise of AI on makes it impossible to avoid the topic. If the concept is, however, new to you, we are planning on hosting talks that describe the recent developments and the plethora of ways machine learning is being applied in the industry But CUMIN is more than just a spicy name.

If you have heard of machine learning and you are excited by the current developments, applications and the prospect of the field, Cambridge University Machine Intelligence Network is a great place for you to learn more about what’s going on at the forefront of this discipline and get hands-on with ML by collaborating on student projects. We are going to host weekly hack nights (closer to hack late-evenings in reality) together with hackbridge.io where you can work with other students on CUMIN projects, kaggle competitions, or suggest a project of your own.

Some more advanced projects have industry and academia ties with potential to leading to a publication. We will provide access to cloud GPU instances for the heavier of tasks, and host talks by machine learning researchers and engineers about the most recent ad-

vances within both the academia and the industry.

Lastly: even if you have heard of machine learning, but it is not something you want to necessarily pursue in your career, we believe CUMIN still has something of value to offer.

After all, we still haven’t seen the full impact of the breakthroughs in artificial intelligence on all the engineering industries and fields. We are slowly seeing more and more applications, including machine learning methods for generative prototype chassis design [source], or segmenting petabytes of data of images of the human brain [source].

Independently of your future field of choice, machine learning is a tool that is worth being aware of. After all, you might encounter a problem in your career that would be best solved with machine intelligence.

Identifying such problems is a universal skill, and having general knowledge of AI together with domain specific specialisation could allow you to make insights no pure machine intelligence engineer would be able to make.

I hope this persuades you of the fact that CUMIN is not just a spicy name, but a student society that will allow you to learn skills and gain knowledge to ultimately make you a better engineer, no matter your goals.

If you would like to stay up to date with our talks and events, follow us on facebook: Cambridge University Machine Intelligence Network facebook.com/CUMachineIntelligence.

- Bruno K. Mlodozeniec CUES MAGAZINE

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THE GENETIC ENGINEER’S TOOLBOX

by the Cambridge University Synthetic Biology Society

T

he building blocks of life In the past four billion years, nature has sculpted and shaped a plethora of living beings. Every one of those life forms has been equipped with its own unique set of blueprints – how it should survive, adapt to its environment, and reproduce. In almost every organism, these instructions are carried out by just a few types of molecules.

In the 1940’s, deoxyribonucleic acid (DNA) was shown to be the genetic material of most life - the molecule whose sequence “If you’re interested of four different bases is responsible for the storage and passage of information from generation to generation. Since then, in joining the Camdiscovery after discovery has further clarified the workings of bridge University life’s machinery. We now know that DNA is transcribed into Synthetic Biology ribonucleic acid (RNA) messages, which are translated into Society, look out for the protein machinery that drives cellular form and function.

Some proteins have demonstrated the ability to copy, information on our cut, and paste DNA and RNA. Surprisingly, many of these can Facebook page, @ be safely extracted from the complexity of a cell and perform cusbs, or subscribe their functions in an environment with known and controlled to our mailing list at inputs. As a result, a piece of DNA can be subjected to multiple editing operations and returned to the cell, where it will https://lists.srcf.net/ be faithfully transcribed into RNA like any other unadulteratmailman/listinfo/ ed segment. cusbs-interest.”

This ability to alter the information flow within a cell holds enormous promise for fields as wide-ranging as medicine, agriculture, and energy. Humanity can now leverage nature’s inventions to tackle problems previously too small, delicate, or complex.

Just as metalworking and thermodynamics gave rise to the steam engine, molecular tools and an increased systems-level understanding of biology have created a new engineering discipline known as synthetic biology.

Sensors, actuators, and control A cell is analogous to a human-made robot - it senses its environment and turns inputs such as nutrients into desired outputs, which in nature would be more cells. It should be no surprise then that nature has developed a variety of parts akin to those available to an elec-

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[Figure 1] (above)

[Figure2] (bottom)

Bacterial edge detection

Visualization and

system.

purification of

A petri dish smeared

with bacteria is illuminated

bacterial edge detector

through a patterned mask. Cells

DNA parts uwwwwsing

in darkness express a messenger

gel electrophoresis.

molecule X (in purple), as well

Here DNA components

as a gene repressor Y (in red).

were compared by

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Volume 137, Issue 7,2009, Pages 1272-1281, ISSN 0092-8674, https://doi.org/10.1016/j.

tronics hobbyist. Therefore, a genetic engineer who wants to build a system will often start by checking whether the required parts exist in any known organism’s DNA. Natural biological sensors exist for light, heat, voltage, and a variety of other stimuli.

Proteins known as enzymes, that build and degrade other molecules, act as actuators that allow the cell to modify itself or its environment. Other proteins can interact with DNA or RNA to change the levels of protein production, acting as analogue control valves, or in the right configuration, digital switches.

Biological sensors and actuators can be chained such that multiple inputs may regulate multiple outputs, producing complex behaviours.

One recent engineering feat was the construction of a bacterial strain that is not only able to act as a photographic film when spread over a surface, but can detect and highlight only the edges in an image (Fig 1.A). Such an operation in computers requires passing a filter over blocks of the image to determine rapid changes in light intensity, and takes longer the larger the image is. In contrast, the bacterial edge detector finishes the job in the same time because each cell acts as an individual computer that works in parallel and communicates with its neighbours.

Each cell in the circuit has a light sensor that controls the production of two other signals, X, and Y. The sensor triggers a protein binding to a specific regulatory DNA sequence near the genes encoding the signals, altering transcription. When a cell is exposed to light, the switch is off and neither X nor Y may be produced, while it may produce both signals in the darkness. In other words, the sensor acts as a NOT gate for light. The protein Z, responsible for creating a black colour in the bacteria, is under the control of both X and Y. X activates production of Z, while Y suppresses it, so X needs to be present and Y needs to be absent for the cells to turn black.

But since both X and Y are produced in darkness, and neither are produced in light, neither light nor darkness will cause a colour change. So how are

cell.2009.04.048.

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edges found?

The trick is that X may pass freely out of a cell and into a nearby one, whereas Y cannot. This means that cells exposed to light will produce neither X nor Y, but can detect the X produced by nearby cells in darkness (green circles in Fig. 1B). This difference in light level allows cells on the bright side of an edge to satisfy the conditions for production of Z, and thus turn black. In further analogy to electronic components, the decisions made by a single cell can be described by the logic gates in Fig. 1C. Building the genetic machine To put the circuit into practice, pieces of DNA originating from different organisms must be assembled together so that all the genes and control sequences are in the right order to be read by the cell. Most DNA-cutting enzymes recognize a specific sequence, and most DNA-joining enzymes work provided there is a long-enough overlap between the sequences of the two ends to be joined.

Synthetic biologists have developed numerous procedures using these enzymes and/or unique sequence patterns, to systematically join disparate DNA fragments in a specified order. The bacterial edge detector was made up of BioBricks, which exploit one of these systems. Nevertheless, DNA editing is still an exciting area, with emerging technologies such as CRISPR/Cas9 constantly pushing the boundaries for what is possible.

Get involved Here DNA components were compared by their mass-to-charge ratio by passing them through an agarose gel, and marked using a fluorescent dye (photo taken with a smartphone camera!).

The Cambridge University Synthetic Biology Society offers the opportunity to design and implement your own genetic circuits in [Figure volved and edge

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of

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entirely student-led projects. In the past year, we’ve worked on re-implementing the bacterial edge detector described above and trying to expand its response (Figure 2). We’ve created the genetic circuits using Gibson Assembly, a clever method for DNA construction that aims to address some of the problems with the BioBrick system. We’ve also written a computational model that predicts the behaviour of the circuit in time and space using known information about the chemical reactions involved (Figure 3).

If you’re interested in learning more about synthetic biology and gaining practical experience, come to our Fresher’s squash and/or our lab introduction, where we will be demoing the bacterial edge detector. We will be moving to a new project this year, so now’s the perfect time to join our dynamic, resourceful team of engineers, biologists, and mathematicians. Keep posted on our Facebook page, @cusbs, or subscribe to our mailing list at https://lists.srcf.net/ mailman/listinfo/cusbs-interest, for more details and news!

Bill Zong Jia

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CAMBRIDGE DEVELOPMENT INITIATIVE

Cambridge Development Initiative

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Who are we?

Cambridge Development Initiative (CDI) is a student-run non-profit organisation that improves the well-being of community members in the schools, informal settlements, and wider communities of Dar es Salaam, Tanzania.

Each year, approximately 30 volunteers from the University of Cambridge, and 30 volunteers from Dar es Salaam’s universities, are recruited to work full time on our four projects: WaSH, Entrepreneurship, Health and Education. They undergo a comprehensive training programme and meet weekly to plan collaboratively for the implementation of the projects.

Then, at the end of the university year, CDI runs a 2-month programme in Dar es Salaam, from mid-July to mid-September. During this period, the CDI project teams carry out an immersive mixture of project implementation, key partner meetings, government engagement and impact evaluation.

Since 2013, CDI has mobilized over 100 student volunteers to launch sustainable, community-oriented solutions to Dar es Salaam’s most significant challenges.

The four projects are detailed below: Water, Sanitation and Hygiene (WaSH) “Piloting the world’s first simplified sewerage and biogas system – a community-centred sanitation and clean energy solution” The CDI WaSH project aims to offer biogas as a renewable alternative to charcoal for local urban communities, by producing it from human waste. A biodigester turns the waste collected by the sewerage network into biogas in an anaerobic digestion process, which occurs naturally in waterlogged conditions.

“Piloting the world’s first simplified sewerage and biogas system – a community-centred sanitation and clean energy solution”

In the past, the WaSH project has facilitated the construction of three simplified sewerage networks, providing sustainable sanitation to over 450 community members of the informal settle-

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ment of Mjimpya Ward as well as developing an effective method to empower the local community, organising local Sanitation Associations for each network to ensure their sustainable operation - thanks to their commitment and enthusiasm all three networks continue to function effectively.​​​ This year, CDI and Kite directors held consultations with the Vingunguti community, especially the technicians and SUA chairpersons. They met with partners to discuss expansion and collaboration plans with DAWASA, Bridge For Change and Scan Tanzania Ltd. They plan to install a new biodigestor on the site and expand the sewage network. ​

Entrepreneurship “Fostering a spirit of entrepreneurship among young Tanzanian professionals, whose innovative business ideas seek to address salient, community-based development challenges” In the past, the CDI Entrepreneurship team has established an eight-week course, DAREnterprisers, for 22 students at the University of Dar es Salaam, one of the top universities in Tanzania.

The course’s aim was to equip students with the relevant business, social and personal skills to succeed as entrepreneurs. It ended with a sold-out conference, bringing our students together with industry experts and other innovators, who all shared the vision of using ‘impactful

“Fostering a spirit of entrepreneurship among young Tanzanian professionals, whose innovative business ideas seek to address salient, community-based development challenges”

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innovation’ to improve Dar. Businesses formed during the programme had the opportunity to pitch to audiences of several hundred people, with a chance to receive seed capital for their ventures as well.

The DARE to Change Dar Conference, held after the 2016 and 2017 programme cycles, offered a range of events including expert panel discussions, guest speakers and opportunities for networking, amongst other things.

After proving successful, the DAREnterprisers and DARE to Change Dar Conference have been handed over to local government and organisations with the aim to upscale the project in future years.

For the 2017/18 cycle, the Entrepreneurship team is piloting a new “Into Business” project involving a series of stand-alone seminars aiming to teach students the key skills needed to succeed in business. These range from practical skills seminars, such as CV writing and computer skills, to seminars on business ideation and investment. In particular, the project aims to empower local young women in ways that DAREnterprisers did not by employing a structure that is more sensitive to their needs (for example, in terms of content, time commitments, location, etc).

local communities and empowering local leaders to reach a sustainable solution” In the past, the health team has run multiple interactive workshops in the local community.

Last year, three workshops were conducted

by Childbirth Survival International (CSI), using a curriculum devised by community engagement. The curriculum covered the topics of maternal health, UTIs, cervical and b r e a s t cancer and sexual health.

Two sanitation workshops were also conducted, using the Waterscope microscopes to help children understand how microscopes can be used to observe plants, animals and bacteria, and to understand how disease is spread through bacterial transmission (hands, water, flies). It also aimed to help children understand methods for preventing the spread of disease (washing hands with antibacterial soap; boiling water).

Improving access to healthcare products and advice by engaging local communities and empowering local leaders to reach a sustainable solution”

Health “Improving access to healthcare p ro d u c t s and advice by engaging

Observations taken last summer confirm the need for workshops on women’s health and child sanitation. The

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Health team are working towards designing future health workshops in a way that would allow for more rigorous impact evaluations, while also working to engage community health workers so that workshops can be continued after our departure. Lastly, the team will be looking to originate new ideas for creative solutions to other pressing health issues within the community.

Education “Empowering secondary school students to design and implement creative solutions to local problems and become innovative, informed and driven agents for change in their communities” The CDI Education team has worked with students at 13 schools from different districts of Dar es Salaam. In self-evaluation surveys, students reported they felt they had improved in 11 out of 12 skill areas, including evaluation, teamwork and confidence.​​​​ The successfully implemented initiatives ranged from setting up a silent study area in a disused classroom, to informing the community about the importance of education for women.

“Empowering secondary school students to design and implement creative solutions to local problems and become innovative, informed and driven agents for change in their communities”

For the 2017/18 cycle, the plan for the Education Team involves further pilots of an initiative developed last year called KompyutHer, which aims to improve the computer skills of out-ofschool girls in order to improve their confidence and chances of employability. These further pilots will allow the team to determine whether KompyutHer can be developed into a sustainable programme.

Also, the plan is to expand and handover the Career Network Support further in collaboration with Bridge for Change, a local Tanzanian NGO. Why join us?

I’m a WaSH project volunteer working on Biogas. Throughout this process, I have had a lot of fun getting to know both members of the WaSH team and also of the wider CDI team. Furthermore, I’ve picked up many valuable transferable skills, such as grant-writing, organisation of informal fundraising and teamwork skills and have enjoyed the opportunity to apply technical knowledge to the real world.

For more information, visit our: Website: http://www.cambridgedevelopment.org/ Facebook: https://www.facebook.com/CambridgeDevelopment/ Instagram: https://www.instagram.com/cambridgedevelopment/ 32

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PRODUCT SUPPLY AT P&G DO SOMETHING THAT MATTERS #PGDAY 1 Nearly five billion times a day, P&G brands such as Ariel®, Fairy®, Gillette®, Head & Shoulders®, Oral-B® and Pampers® touch people’s lives globally. We are one of the world’s largest consumer goods companies and aspire to build a better world for all of us We hire based on the potential we see in people, so here, you’ll be trusted to dive right in, take the lead, use your initiative, and build billion-dollar brands. We recruit the finest people and develop talent almost exclusively from within

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TTP FULL BLUE RACING

TTP fULL bLUE rACING

S [Figure 1] Full suspenstion assembly including brake disk, upright, coilover shock absorber

“As exams and May Week drew to a close, and most students returned home for the summer, a small core of FBR members remained in the Dyson Centre, and the Oatley Garages.�

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ilverstone: UK. A historic racing track, and yearly, the venue for one of the craziest, friendliest, most innovative motor racing events, Formula Student. The University of Cambridge team is Full Blue Racing: team members have worked hard for nearly two years on the FBR18, and were all keen finally to put it down on its wheels, and take it to the track.

As exams and May Week drew to a close, and most students returned home for the summer, a small core of FBR members remained in the Dyson Centre, and the Oatley Garages. The FBR18 design ethos was simplicity, with a tightly-packaged steel spaceframe, screaming 600cc motorbike engine and simple bodywork. Almost every part of the car is designed by the students in the team, and almost every part is manufactured in-house.

With late nights and early morning a norm for the build-team members, the more advanced parts of the car took shape. A glassfibre-coated, 3D-printed inlet allowed for amazing freedom of form, whilst fixing the strength issues the team has encountered in the past. 3D printing was also vital in the construction of our custom steering wheel, with built-in dashboard and datalogging.

As the deadline of the UK competition, the only one FBR is participating in this year, drew closer,

[ w D

[Figure 2] Test fitting new electronicsshock absorber

more and more milestones were met. The Yamaha R6 engine, something of an heirloom of the team, was heard roaring through its all-new exhaust and inlet system, driven by bespoke electronics. The car sat on its wheels for the first time, and rolled around on precision-machined suspension uprights, sprung by bespoke coilover shock absorbers.

Hand laid-up glassfibre and sheet aluminium bodywork brought spirits to a new high, and the car was packed, like an odd game of Tetris, into a VW Transporter van for the journey to Silverstone.

The work, sadly, didn’t end there. The team was grilled on the design, business plan and costing in the static events. The hard work put in over the two previous years paid off, with results of 30th, 46th and 30th respectively out of over 80 universities.

In amongst these was the ever-difficult scruti-

neering. Formula Student has very stringent rules and regulations, and no car is allowed to compete without this rigorous inspection process, which makes sure every single rule is followed. FBR was sadly held up by a few niggling issues in technical scrutineering, such as a leaking sump and seatbelt mount positions. Despite having no drastic problems, this meant it was impossible for the FBR18 to make it through to the tilt, noise and brakes tests until Saturday, when the dynamic (racing) events began.

Come Saturday morning, the FBR18 flew through technical, chassis and safety scrutineering, before heading over to the tilt table, where the car is tilted to 45 degrees, simulating a 1G cornering load, and checked for leaks. With concerns over the sump, the team was relieved, and overjoyed, to pass first time.

Next step was the noise test, where the engine is run at idle and over 10,000 RPM, to check that it doesn’t breach the maximum noise limit. This should have been an easy pass for FBR, though sadly issues with some chafed fuel pump wiring lost valuable hours.

With these fixed, and the noise test passed, it was time for the FBR18 to take its first tentative steps: the brakes test.

The brakes test is the first time any car actually drives at a Formula Student competition.

It has to accelerate up to speed, and then lock all four wheels under braking power, to prove the system is effective. Technical director Oli Albert fired

[Figure 3] CAD work in the Dyson Centre

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[Figure 4] The FBR18 undergoing the tilt test

up the engine, and drove the car out for its first baby steps.

Although locking one wheel immediately, a promising sign that only bias adjustments would be needed to pass, further issues with differential

mounting and chain tension halted proceedings, with the team retiring to the pits for the evening to fix the issues, for a final attempt on Sunday.

Bleary-eyed, the team rose on Sunday and rolled over to

[Figure 5] All scrutineering stickers achieved, except for brakes test

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the brakes test area. Despite high hopes, and being able to lock two wheels, the best efforts of Oli Albert and Stuart Naylor couldn’t quite push the team through, when chain tension issues re-appeared, along with struggles with the driveability of the engine, and finally put paid to the chances of passing scrutineering.

Even with the disappointment of not getting on track, the team has thoroughly enjoyed the entire process, learned a huge amount and all are ready and raring to keep going, with plans and design for the FBR19 to compete at Silverstone next year already under way.

Fraser McKay

A

A NEW VIDEO GAME

New Video Game

A new video game, designed by researchers at the University of Cambridge, gives teenagers an understanding of electricity by solving a series of puzzles in a bid to encourage more of them to study engineering at university.

The game, called Wired, is available to download and play for free from today, and teaches the key mathematical concepts underpinning electricity.

Electricity affects all of us every day, but is difficult to teach as it is abstract, difficult to visualise and requires lots of practice to master.

“A video game is an ideal way to teach students about electricity as it allows players to visualise the underlying concepts and the relationships between them,” said Diarmid Campbell from Cambridge’s Department of Engineering, and the game’s designer. “It provides a structure for incremental challenges,

each one building on previous ones, and there is a set of tried and tested motivational techniques that can encourage people to push through tricky areas.”

Campbell spent close to two decades in the gaming industry, developing titles for PlayStation, Xbox and PC. He is now a senior teaching associate at Cambridge, and develops video games to inspire more teenagers to study engineering.

Players of Wired will get an intuitive understanding of circuits, the logic of switches, voltage, current and resistance. They do this not by analysing circuits, as in textbooks, but by wiring up circuits to solve problems.

“Most educational games are delivered through the class-

room and only need to be more fun than the lesson they are replacing,” said Campbell. “Wired will be delivered through gaming websites, so it needs to be at least as fun as other video games that people play. We are not gamifying education; we are edu-fying, and perhaps even edifying, a game.”

In many areas of physics, people already have an intuitive understanding of how things behave before they learn about them more formally. For instance, people have been throwing balls around since they were toddlers so when they learn about projectiles and Newton’s

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“A game what I´ll never forget, it teach me, all i learned in my enteire university, with other point of view, the final of the game was very emotional, it was so hard, but really fun, I hope you can launch another game like this, maybe another topics or the same as well, bunch thank you and congratulations, it´s a great game.”

--Steam Review

“A video game is an ideal way to teach students about electricity as it allows players to visualise the underlying concepts and the relationships between them.”

Diarmid Campbell

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laws of motion they have an intuition to guide them in how to apply the equations.

Since electricity is invisible and isn’t something we encourage kids to play with, this intuition isn’t there in the same way. Students can learn the mathematics, but may not have the intuition to know how to apply it. “Students are often told that electricity behaves like water flowing through pipes – which gets you some of the way there, but actually, people don’t really understand how water behaves either,” said Campbell. “How many people can tell you why the shower changes temperature when you flush the toilet?”

According to Campbell, Wired bridges this gap, giving players an intuitive understanding of how electricity behaves and gets players solving problems that are not usually encountered until A-level physics.

The project was supported by The Underwood Trust.

The game is currently available on Mac and Windows.

An installable version can be downloaded at: https://store.steampowered.com/app/885470/Wired/ A browser version of the game can be played at: https://wiredthegame.com/

[Figure] CUES 2018 Garden party selection

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BIOMIMICRY: A SHORT INTRODUCTION

Biomimicry: A Short Introduction

by Chisom Ifeobu

C

atering to the needs of a rapidly growing human population, human-induced climate change, depletion and degradation of natural resources are some of the pressing problems that today’s engineers aim to solve with innovation and technology. The established approach to innovation has been to extract from nature. Another approach now gaining increasing prominence would be to learn from the solutions adopted by nature in solving analogous problems. The conscious practice of imitating nature’s form, processes, and systems to provide innovative solutions to human problems in a sustainable manner is known as Biomimicry.

The importance of emulating nature has been recognized because organisms in nature face similar challenges to humans meet them sustainably.

Humanity can learn how to create handheld displays from the Morpho butterfly, more efficient wind turbines from the humpback whale, faster trains from the kingfisher and carbon-negative building mate40

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rials from the shells of marine organisms.

Nature has arguably adopted a much more energy efficient way of satisfying its needs than humans have. Some of the principles guiding nature’s “manufacturing process” are employing life-friendly materials, water-based chemistry, benign manufacturing, optimization rather than maximization, cyclic processes, shape rather than material and resilience. Biomimicry has become another key tool in the engineer’s toolkit for providing sustainable solutions.

As with all engineering designs, Biomimetic design begins with the problem definition, see Figure 1 – identify

the function and define the context. “What must the design do and under what conditions?”. This human challenge should then be expressed as a biological challenge. Asking for example, “How does na-

Figure1: Biomimicry design spiral [Online Image]. 2018. Retrieved from https://asknature. org/resource/biomimicry-design-spiral/#.

W4kGJOhKhPY

ture prevent the loss of fluid?” rather than “How can we plug a leak?”. This “biologization” is what differentiates biomimetic design from conventional engineering design. The next step is to discover an organism that exhibits a strategy relevant to the challenge and use it as a biological model.

Then, the underlying prin-

ciples behind the biological strategy are abstracted in design terms and emulated to develop a final design that is evaluated.

There are three levels of biomimicry emulation: natural form, process, and system.

Figure 2: The Lily impeller [Online Image].

2018. Retrieved from http://www.paxwater. com/biomimicry

Natural form emulation involves applying the shape or surface texture of organisms found in nature to generate a solution. This is especially apparent in the design of the Lily Impeller named so due to its resemblance to the Calla Lily, see Figure 2. Designed by the founder of Pax Scientific, Jay Harman, who was inspired by spiral flows ever evident in nature from the motion of kelp, to whirlpools, to tornadoes.

This spiral form is a more efficient means of mixing and distributing fluids than the conventional planar designs as evidenced by 15-30% reduction in energy requirements, a 75% drop in noise levels and considerably reduced vibrations. It is currently being implemented in water treatment plants to mix drinking water in storage tanks to prevent stratification. A 6-inch impeller can

mix as much as 10 million gallons of water.

Process emulation involves using the operation or behaviour of organisms with strategies relevant to the challenge being addressed. The Eastgate building in Harare, Zimbabwe is a key example of this, see Figure 3. Its design was adapted from the design of African termite mounds.

The main aim is to maintain a constant interior temperature of 30oC for their food in an environment where the temperature can range from about 2oC to 40oC. To achieve this, they control the convection currents allowing cool air to flow in from the bottom and warmer stale air to flow out from the top. This principle of thermoregulation was applied to the ventilation system of the Eastgate building. Outside air drawn in is either cooled or heated by the concrete in the building depending on which

is hotter, vented to each floor and finally exits through the chimneys at the top of the building. This results in an energy consumption of less than 10% of that of a similarly-sized building with air-conditioning savings of over $3.5million.

Finally, system emulation implies imitating the interactions of many forms and processes in nature. This has led to the development of a few industrial ecosystems which are based on the ecological principle that one organism’s waste is another organism’s feedstock. This development is fostered by establishing trade of by-products between industries and the production

Figure 3: The Eastgate Building compared to a termite mound retrieved from https://video.nationalgeographic.com/video/magazine/ decoder/180511-ngm-decoder-biomimicry-eastgate-centre-zimbabwe

of environmentally and financially sustainable products.

The most well-known example of this is the industrial town of Kalundborg in DenCUES MAGAZINE W W W. C U E S . O R G . U K

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mark comprising of five main entities: the municipality, a 1500MW coal-fired power plant, an oil refinery, a pharmaceutical company and a plasterboard manufacturer that exchange waste materials and energy to increase efficiencies.

Another key example of this which is becoming increasingly popular is the application of biomimicry in repairs of corrosion leaks in pipelines and piping using Platelet Technology. Adapted from the body’s own leak sealant, the platelets. This innovative technology involves the remote injection of particles known as “Platelets” into the pipeline. The pipe flow transports

“It is time to look to nature, not as a stock of materials but a stock of knowledge.”

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the Platelets downstream to the leak site.

Some are entrained into the leak and held against the wall thereby providing a seal and a locator due to the sensors in the Platelets.

It is attuned to the specific needs of the customer. Therefore, it is capable of sealing leaks in small bore, high-pressure piping as well as large piping operating at just above ambient pressure. It is increasingly being applied in oil and gas production systems as sealing a leak can be achieved without any interruption in the fluid transmission and removes the need for an extensive intervention process.

Biomimicry is an emerging discipline necessary for ensuring a sustainable future and is becoming more widespread. It is time to look to nature, not as a stock of materials but a stock of knowledge. It enables remarkable improvements in the quality of existing solutions and fosters sustainable technological innovation.

MY INTRODUCTION TO MACHINE LEARNING THROUGH THE WORLD OF BIOTECH

My introduction to machine learning through the world of biotech

Last summer I had the fortune of interning at an ambitious young start-up called Cambridge Bio-Augmentation Systems, or CBAS for short (pronounced ‘Seabass’). It’s one of the first neural engineering companies in the world and they’re building the connection between the human nervous system and computers. That means they are building a ‘USB port to the body’, a next generation connector for prosthetics that connect to the nervous system and can be controlled with a patient’s brain.

What has this got to do with machine learning? The connector picks up on neural signals travelling from the brain to the limb — these signals are simply voltages. CBAS is developing a neural net (machine learning model) which can understand the signals from the brain. If we can understand messages of the brain, we can feed these as inputs into software.

The idea is to create a new platform technology for interacting with the human nervous system.

My goal in the summer project was to refine this model by testing it on accelerometer and gyroscope data recorded from motion — a simpler dataset than neural signals. The net would classify the motion into a category such as walking, turning or sitting down. My first, and perhaps most important, task was to acquire the data. In our case, the data had to be generated ourselves!

Walking, Walking, Walking…

Neural nets need data; lots of it. In my case, this meant walking for hours up and down the office balcony with a sensor strapped to my leg, much to the amusement of engineers at the other start-ups.

By Raphael Schmetterling

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Fortunately, with the help of Spotify, the odd TED talk and the contribution of my fellow interns, this tedious but necessary task soon produced sufficient data.

If the data fed into a neural net is not collected in the right way, getting useful results can become impossible. Several years ago, a neural net successfully managed to identify cars from images of the streets of LA. The Cambridge PhD students then fed in pictures from their more overcast hometown to find that the model was failing completely. It turned out that the net had not learned to identify cars, but the shadows these cars projected onto the ground in the California sun.

Every detail of even my seemingly simple task had to be thought about in advance, such as the exact positioning of the sensor on the body. Factors such as the route taken around the balcony and the size of our turning circle were also considered, as although the model would ideally be able to process any motion, the range of motion was restricted for my proof-of-concept to increase the chance of success. One factor I initially forgot to include — and which my fellow intern picked up on — was the orientation of the sensor. Some of the time, it was upside down, adding an extra variable to the dataset which was reducing performance. Thankfully the data could be fixed with a script and no rerecording was necessary.

Learning on the Job Before starting this placement, all I knew about was the simple

feed-forw a r d n e u ral net.

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These are essentially functions which take an input such as an image, and produce an output such as a label (‘cat’ or ‘dog’). These models train/learn by looking at tens of thousands of images where the correct answer is known, and tweaking the function algorithmically so that it outputs the right answer more often.

They can then look at a new image without knowing the answer, and tell whether it is of a cat or a dog. These nets can be powerful, but they assume that the inputs are all independent of one another. This is not the case with most data which varies with time, including my own motion recordings. No accelerometer reading is independent of the one before. This is where recurrent neural nets (RNNs) come into play.

An RNN is essentially a series of feed-forwards nets, each one with two inputs: the current data point, and the output of the previous net.

That net was fed the previous data point and the output the net before that. RNNs are very popular and also used in applications such as translation and predictive text, as languages

are great examples of dependent inputs (one word being one input).

Once I’d caught up on the theory, and the particulars of the company’s model, I was ready to start optimising it. This meant tweaking the hyperparameters, a big part of developing neural nets. Hyperparameters are the ‘settings’ on the model which are manually decided before training begins. Take my motion classifier. How many seconds of motion data should be fed into the model as a single input? 1? 5? There is no clear right answer to this and in fact this is one of about 12 hyperparameters on this particular model. Finding the optimum point in twelve-dimensional space is non-trivial, and requires a mixture of intuition and trial and error. Taking the same example, a single input could be taken as half a second of data — the rough duration of a single step.

This will likely perform better than a millisecond, but what about 0.4 seconds? The only way to know is to try it.

Final Thoughts My goal in this placement was to get my first

experience of machine learning in the workplace. Learning about bioengineering was fun, but the principles I picked up would apply in any industry. The end result of my work

“The end result of my work was a classifier which could categorise motion live.” was a classifier which could categorise motion live. The accuracy wasn’t perfect, particularly when transitioning between actions (eg standing up), but good enough to prove the concept. Building this was very satisfying, and has encouraged me to take machine learning courses on my degree. This will combine my new-found intuition with a theoretical grounding. All in all, an experience I really enjoyed.

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APPROACHING THE BRAIN FROM AN ENGINEERING PERSPECTIVE AT HARVARD

Approaching the Brain from an Engineering Perspective at Harvard By Bruno Mlodozeniec

[Figure 1] A picture of the segmented slice of rodent cortex.

This summer I was lucky enough to venture to New England for a New engineering experience; in Boston MA I got to work alongside the brilliant researchers at the Visual Computing Group (VCG) at Harvard on some of the most prospective research in neuroscience.

The researchers in the group, as part of the collaboration with Harvard’s Centre for Brain Science, are part of the overarching effort towards completely mapping the brain’s “connectome” - the complete connectivity diagram of the neuronal circuits within the brain.

If successful, their work could transform much of neuroscience and lead to creation of new bio-inspired machine learning algorithms. It is also the essential step towards even attempting to reverse-engineer the brain.

The task is highly non-trivial. The cerebral cortex of the human brain contains more than 160 trillion synapses, and each neuron receives synaptic inputs from hundreds or even thousands of different neurons, spread out over a large distance. Deciphering the connectome

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of even one type of neuron in the cortex poses enormous challenges.

One of the, if not the most, challenging aspects of the process, however, is what happens once the images have been taken. In the software, the researchers at the Visual Computing Group have to recreate a 3D reconstruction of the brain, automatically segment the 3D model into different classes of neurons and synapses (doing it manually for 100 million synapses is not very feasible, even in an as intern-rich environment as Harvard), and then produce tools for analysis and interpretation of the connectome. The latter is the part of the project I have been working on.

Throughout my time with the group, I was focusing on finding ways to improve the current de-facto method for biological network analysis: network motif discovery. Network motifs can be thought of as recurrent patterns of connections within a network such as that of synapses within the brain. They are particularly interesting within the context of connectomics, because brain motifs can often perform

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f

[Figure 2] Brain Network Motifs

d

[Figure 3] One of the diamond blades used for cutting the brain tissue into slices just a

certain “computational” functions; for instance, the two motifs shown **insert where the picture is in the article, e.g. below, above** are examples of a max() operator and a regulator().

The problem is, this algorithm completely overlooks any information other than what other neurons each of the neurons is connected to. In reality, there is a wide range of additional parameters that determine the function a neuron performs within the neuronal circuit; for instance, a neuron can be excitatory or inhibitory, or its axons could be myelinated resulting in much stronger signals being transmitted.

To alleviate these issues, I, together with my supervisor, had to look for an exploratory method that finds frequent patterns within the network while allowing for a small variation within them, and that can easily take additional parameters into account. One of the key aspects of arriving at such a solution are methods for graph comparison; in particular, how to efficiently evaluate whether two patterns are similar. This might not sound particularly difficult at first, however, these algorithms would need to be run efficiently on networks with billions of connections.

Due to recent developments in artificial neural networks that operate on network data, I investigated whether these models could be applied for “sub-graph” or pattern similarity estimation. These methods have seen high success in for instance social network analysis scenarios, but needed to be heavily adapted to this fundamentally different task.

few nanometres thick.

Overall, the internship has been a great learning opportunity that has personally made me realise the allure of doing a PhD upon completion of the Engineering degree; experiencing the contrast between working in the industry and the more hectic academy was invaluable, and I would recommend it to anyone wondering where the best application of their engineering talents might be.

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ONE SMALL STEP INTO THE DEPARTMENT, ONE GIANT LEAP FOR YOUR CAREER

One small step into the department, one giant leap for your career. By Akhil Sonthi

I

I

undating me very soon. That was the start to my first lecture.

’m sure by now, you have been given advice after advice on how to make a good start to your university career, how to organise your work and how to get involved in university sports and societies.

Maybe you have read articles online. Or maybe you have consulted Cambridge’s finest YouTubers. Regardless, I will give you my advice on how to make the best start to your Engineering experience.

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But first, a word of warning (even though it’s too late): the course is going to be tough. Tougher than an elephant’s skin.

Tougher than Kevlar. Tougher than…okay maybe I should stop there (apologies to the aspiring material scientists out there).

BUT it’s going to be, dare I say it, a fantastic experience.

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The door creaked as I pushed it with all my might. The path led to a large, warm room filled with over 300 homo-sapiens hungry for knowledge. Sweat poured down my face as I took 25kg worth of notepads and Staedtler Triplus Colour pens out of my bag and got ready for the tsunami of information that would be in-

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Okay it’s not that bad. But I definitely went to my first lecture with so much stationery that I could have been Ryman’s supplier. 1st Tip: Do not immediately buy all the pens and folders you can find in Cambridge. Go to a couple of lectures and get a feel for what you actually require. Maybe you need coloured pens/ highlighters, plastic wallets or even a Pritt Stick but the sheer number of people who have unused stationery lying in their bottom drawer is staggering.

T

Try to familiarise yourself with the different areas of the department, most importantly the lecture/lab locations such as lecture theatres, EIETL, Hydraulics Laboratory & DPO and if you ever get lost just ask someone (everyone is super friendly) or download the map off the internet (has saved me for labs in some awkward locations so many times!).

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Cambridge University Engineering Society. Cambridge University Eco Racing.

Cambridge University Spaceflight. These

are some of the fantastic societies you could get involved in and I recommend you sign up to a couple of them and attend the intro sessions just to get a feel for whether it is right for you. 2nd Tip: Do not sign up to absolutely everything at CUED and Fresher’s Fair because you will be bombarded with spam. Instead focus on two or three societies that you can balance with your studies.

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‘Standard credit’. This phrase will become your best friend before you know it as it saves so much time. This is a concept that only exists in the first two years of your degree and allows students to submit work to an ‘acceptable quality’ but still gain full marks. The point of this is so that students (particularly the perfectionists amongst us) don’t spend days perfecting a lab report or coursework when it is more important that the content is understood. However, try to produce work that you are proud where you can without affecting your ‘chill’ time and extra-curricular activities.

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During your four years, you will meet a huge number of people all with their own skill-set and interests so try to keep in touch with as many people as possible because you never know when they can help you out and vice versa. University societies are a good way to interact with a range of people through socials and committee activities.

Y

progress and schedule your supervisions (for the first two years). On the other hand, the Tutor addresses any personal issues relating to mental health and general Cambridge experience. Of course, the roles can overlap sometimes but are reasonably distinguished. Now onto supervisions. These wonderful one-to-two sessions can be rather helpful to understand the lecture content a bit better (especially when the lectures flash by so quickly!).

I would suggest being well prepared for these because they allow you to ask any questions to knowledgeable professors.

It is not uncommon that there is a huge variation in the quality of supervisors but on the whole, you can make the most out of them if you are on top of the lectures and don’t start the supervision work two hours before.

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Finally, I know you have just entered your first year but I would highly recommend keeping your eyes peeled for any internships from October onwards. Most internship applications open at the start of the year so it is good to begin drafting your CV and Cover Letters in advance because they can take so long!

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Very best of luck with your Engineering degree and please do take care of your physical and mental health as it can get quite intense from time to time. Most of all, enjoy the course which you have rightfully earnt a place on through hardwork and passion (hopefully).

You will have probably received countless emails regarding your Director of Studies (DOS), Tutor and Supervisors. The DOS is there to review your academic

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DESIGNING AND BUILDING A WINNIG CARD BOARD BOAT

Designing & Building aWinning

Card board Boat Soaked in stinky river water, we pulled the soggy mess of cardboard and duct tape out of the Cam and onto Jesus Green. It was Suicide Sunday 2017, and my team had just competed in the Cardboard Boat Race. Sadly, our boat’s mediocre voyage didn’t justify our investment of cardboard, tape, and assembly time. It bent and buckled under the uneven load of four rowers, its waterproofing slowly leaked, and it finally sank about halfway through the race course. As we hauled the mess out of the river, I promised my team that we would have a sturdier boat for the 2018 race.

Our old boat’s main problem was its bending strength. Having learned about beam design in IA Structures, I resolved to 50

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by Roy Navid

incorporate ribs spanning the length of the boat in the 2018 design. I made a rough calculation to determine a suitable rib depth with a generous safety factor. Working in CAD, I created a design which could be laser cut and slotted together. I fine-tuned my design so that each part could fit in a Dyson Centre laser cutter. Having struggled to find enough suitable material in the CUED cardboard skip in 2017, I found a website which sold large, cheap sheets of strong cardboard.

I wanted to make sure that my design would work before buying all of the necessary cardboard, so I ordered a few sheets and built a critical section of the boat to see if it could withstand abuse. I was delighted when I could sit, stand, and even jump on the section without it failing! Because the design appeared excessively strong, I sim-

plified it and removed a few of the ribs to save cost. I was confident that I finally had an economical design which would prove its worth on the Cam in June 2018. I bought all of the cardboard and duct tape necessary for the full boat and stored the supplies in my room. It was finally June, and second year exams were over! My team was excited to start construction. We carried our cardboard to the Dyson Centre and began laser cutting parts. It was incredibly satisfying to see the parts drawn on a laptop come to fruition in full size. Our team of four was cutting, taping, and fitting parts together for around 6 hours. I felt as if I was simultaneously running a factory and assembling an immense 3D jigsaw puzzle.

When the boat was finally complete, it looked like a long steel bar attached to a pink nose (we ran out of silver duct tape and used pink instead).

On race day, we carried the boat from CUED out to Jesus Green, lowering it into the Cam with the discipline of an elite rowing crew. However, as we started getting into the boat one by one, I felt it bend slightly at the middle. Fearing a catastrophic failure, I was relieved when the boat straightened itself out once all of us were in and the weight was evenly distributed. With our paddles alternating left and right sides, we made our way to the start line. The boat’s high center of gravity made it very wobbly.

Thankfully, we were able to stabilize the boat by actively shifting our centers of mass.

Ready, set, go! We paddled hard and fast, and I was delighted when we reached an im-

pressive speed without capsizing. Soon were at the front of the group of boats. Not letting up on speed and stability, we managed to complete the course in first place. As is the tradition, the boats that finish the course try to sink each other. After ramming our pink boat nose into a few competitors, our carefully designed engineering marvel reached its inevitable fate. We cleaned up the remains with no doubt in our minds as to the boat’s resounding success.

As engineers, we never tire of improving or tweaking our design to make it PERFECT. Our planned 2019 cardboard boat is no exception. The loading sequence has been adjusted to stress the boat less, the excessive boat length has been pared down to save cost, the base has been widened to increase stability, some ribs have been adjusted to use less cardboard without compromising strength, and I’m hoping to have a décor team so that the boat

looks much more stylish.

Good luck to all 2019 boats!

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Crossword

Down 1. Device used to measure change in velocity (pl.)

3. Band between RF and BB 4. Be behind in phase 6. One component of a complex number (abbr.)

8. Ringed doughnut shape of many inductor cores 9. Containing interfering information 10. Eight bits 11. Output following input in a linear manner 12. Type of screwdriver head (2 wds.)

13. Commercial Off-the-Shelf 14. Common average used for sinewaves (abbr.)

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Across 2. First name of a British scientist of falling apple fame 3. Changed from a “0” to a “1” 5. Which branch of Mathematics studies spatial relations which are unaffected by the continuous change of shape or size of geometric figures 7. Electrical circuit diagram 12. Test equipment that provides a frequency-domain signal display (2 wds.)

15. Constellation : The little bear (2 wds.)

16. Light ray 17. Summers 18. Measure a waveform at regular intervals