This summer I decided to give into the desire to practice art more often and to learn more about design. One step towards it was to sign up for Creative Bug online courses.
I have been following Lisa Congdon before, I love her patterns and illustrations and of course feel like I can relate to her passion for swimming. Lisa has recently published an illustrated book about swimming. Look how stunning it is!
If you are like me coming to computational biology from a Computer Science background, chances are the last time you heard about covalent bonds is in high school. It is quite useful to understand the basics of biochemistry when studying molecular biology, even if you are just using computational tools.
Thanks to countless MOOCs and other online resources, as well as giant text books on the subject it is only your own time and effort that can limit you. Here I gather the very essentials you need to know if you are starting out as a computational biologist, with a slight tilt towards studying protein evolution, as this is my thing;)
Hope it helps other aspiring bioinformaticians to better understand the bio- part of their subject and will be a good first steps guide. And in the case of studying proteins, chemistry is for sure is an essential part of your knowledge base.
Step 1. Khan academy crash courses on biology and chemistry.
These are simply awesome! Presenting science with practical examples, funny attitude and stunning visualizations.
From molecular building blocks of life to ecology of all the living organisms, I think it’s a great way to dive into life science.
Step 2 From DNA to protein
What is DNA and how proteins are actually synthesized in the cell.
Both of these courses are great, but I think I prefer the Khan academy style of presenting material and quizzes. EdX feels much more academic, which is not a great thing if you want to keep things interesting 🙂 Although authors did a pretty good job anyway.
No real need to do both of them, since there is a lot of overlap in the content. Same authors as in step 2!
Worth mentioning that EdX courses in both step 2 and step 3 have also information on experimental techniques used to study biomolecules, which is useful if you do research. Khan academy is aimed more for the general public.
There are immense benefits of volunteering. You get to experience the country in ways that are pretty much impossible for tourists. You get valuable experience and sometimes training in the area you are interested in. You give back to the community. You get an exciting break from your main career or studies. BUT, if you do a quick google search for “volunteering opportunities in South Africa” or any other warm country with spectacular nature, you’ll quickly realize that you can’t really afford it.
How can donating your time, skills and travelling costs not be enough? Why should one pay thousands of dollars to come and work in often quite challenging conditions away from home? The only answer I have is that demand creates it’s own supply. It can at times be challenging to arrange your own accommodation, transportation and itinerary, so people prefer to just pay the fee and have it all taken care of. The fees that a lot of non-profits have are often much higher than what you’ll spend if you’ll arrange your own accommodation and rent a car/use public transportation. High costs of volunteer programs are usually motivated by the lack of funds and your money will most likely be used for the project in one way or another, so if you have the money, it might be worth it to spare yourself a headache of arranging your travels.
There are many reasons and situations when one can’t and shouldn’t really pay for a volunteering programme though. If you are just a student or a fresh graduate, in the middle of career change or just for whatever reason would really like to keep your costs low, I have good news for you. There are plenty of non-profits out there that will be happy to have you with no additional costs. They will often help you with travel advice, accommodation and sometimes even food in return for your time and skills.
Here are the three steps you need to take to make your free(or at least cheap) volunteering adventure happen:
1. Decide what it is you want to do.
Do you want to work with animals? Do you want to try yourself as a nature guide? Are you interested in nature conservation and ecology? Perhaps you are a native English speaker or would like to teach computer skills or be a sport instructor. Or maybe you are considering a career in social services and would like to get experience in an organisation supporting human rights or working against domestic violence.
2. Decide where you want to go.
Narrow down you geo-search as much as possible and keep in mind the practicalities. Will you handle staying for a few months in a Nature Reserve in the middle of nowhere or living in a rural community far away from a big city? Plan what you want to do and experience when you are not involved with your volunteering project.
3. Search for small and medium sized NGOs…
in the picked area and field and go crazy sending your resume and cover letter to them or looking for an official volunteering programme form. If you are motivated and have necessary skills and qualifications, the NGO will be happy to have you. If there is no information on the organization’s website regarding volunteering/internship opportunities, don’t be put off and contact them anyway. Non-profits are always under-staffed and screaming for people. They might not have time and resources to put together a full blown volunteering programme, but if you are self-reliant and motivated, you’ll be more than welcome to join in and help out.
Here is a list of organizations in South Africa, mostly in the Cape Town areathat I put together when I was looking for opportunities to get more teaching experience and/or get some exposure to field biology and nature conservation. All of these NGOs provide free (or almost free) volunteering opportunities. The minimum stay is usually 6-8 weeks.
Nature conservation and ecology.
1. At SANCCOB you get to become a sea bird rehabilitator for a minimum of 6 weeks, you do have to pay a donation of $140, but you get pretty valuable training for it as well. Besides, penguins are just too cute.
2. Greenpop plants trees all around Cape Town and in Zambia. They offer a variety of skill-based volunteering roles that can help to kick-start your career in the environmental industry.
3. Conservation at work educates farmers and private land owners on conservation issues and sustainability in the Western Cape. Contact the manager directly to find out about the current volunteer opportunities.
4. The Cape Leopard Trust has many interesting projects in the Western Cape, including of course leopard conservation, black eagle research and environmental education. They don’t have any official volunteering program, but with some relevant skills and a lot of motivation you can totally come on board and experience some of the greatest Nature South Africa has to offer.
5. Cape Town Environmental Education Trust(CTEET) is the organisation I’m involved with right now during my stay in South Africa. Their main focus is on youth development through exposure to nature and environmental education, but there are possibilities to participate in sea bird and plant conservation as well. I will definitely be telling you more about them too.
6. River Lodge backpackers seem to have a really nice thing going with different volunteering opportunities ranging from conservation projects and farm stays, to working in the travel industry and social development. It didn’t really work out for me, but it does not hurt to try for you though. I suggest arranging things with them in advance though, because the staff seems to be really busy.
7. Wilderness foundation is supporting several projects within nature conservation, education, social development in Southern Africa. I haven’t contacted them myself, but they seem to be doing a lot of exciting and useful things in Southern Africa.
There are of course many other possibilities in nature conservation, that are often not as easy to find, but the general strategy is to explore different nature parks and conservation projects in the area you are interested in and find an associated non-profit and establish a connection with them. Check out other nature reserves in the Cape Town area here for example. A good strategy is to also check private game lodges and contact them for a combination of work/volunteering opportunities.
Education and social development.
For most of the projects in education the minimum stay goes up to 3-6 months, you will probably need a lot more time to get started and involved in a program. So I would recommend it only if you do want to get teaching experience and training for your career. Quite often you will also need a relevant undergraduate degree(not necessarily completed) to participate.
1. Scalabrini center in Cape Town provides English courses and job search help to adult refugees and immigrants. You can get involved in all aspects of the project.
2. Help kids offers internship opportunities to international Social Work students. You’ll get to work with intervention services, abuse prevention and outreach.
3. SAEP‘s focus is early childhood and youth development and they always need volunteers, especially with teaching qualifications.
There are of course many other projects in South Africa, it just so happen to be that I’m drawn mostly to Cape Town. But I hope this little guide will help you discover your own dream opportunity.
Contributing to a good cause isn’t really as difficult as it seems and certainly is one of the cheapest ways to see the world. So get started on your search and good luck!
I have started my PhD 3 years ago with naive hopes of using Computer Science of solving global healthcare issues, curing cancer…well, you know the drill 🙂 After a year in I wrote a blog post summarising my experience so far, but I actually have never tried to summarise what my research is about to a broader audience. Now that I’m pushing the 2nd year anniversary of being a PhD student ( I’ve taken a gap year after the first 1,5 years), I thought is a good time.
When friends outside of academia (yes, I still have those, but very few) ask me what I do, I usually say something about “studying the mechanisms of generating novel protein structures and functions”. They either look puzzled or nod with understanding. Then the conversation goes back to whatever we were talking about before. I don’t want to give up though!
Let’s do it step by step!
From secondary school biology, you probably remember, that all living organisms consist of cells. In fact, cell itself is the smallest living thing. It uses energy to maintain itself and can reproduce! That is about all that we actually know regarding “what is life”. So as we said, the single cell can reproduce: it contains all the necessary information and machinery that defines the organism. This information is stored in the form of double-stranded DNAs – long molecular chains, formed always of the same subunits, nucleic acids (nucleotides).
With me so far? I’m sure you heard of DNA!
What is this information needed for the cell to function properly? What does it contain? What do we get from DNA? Well, the cell has mechanisms of reading information stored in DNA. It does it in 2 steps: first, it “transcribes” it to a different molecule type called RNAs. To simplify, to read the DNA information, the cell needs to copy it first. It’s like it was encoded for easy storing, but to read it we need to transcode it back and put on a different piece of storage. There are specific “coding rules” used for this step and they are the same across all living organisms! Once the cell has RNA, it can use it to build protein molecules. And no, proteins that cell builds, are not pieces of chicken breasts!
What are proteins anyway?
See those “ribbons” in the featured image, that is schematic representation of a protein!:D
Proteins are big and complicated molecules that perform many different functions in the cell. The cell builds protein molecules from RNA chains it got from the DNA. How does it do it? Well, there are special proteins that can do this job. Welcome to the molecular biology inception!
The diversity of proteins is amazing: some help maintain the cell shape and inner organisation, some manufacture different chemical compounds, others take care of waste by transporting it outside of the cell or make sure that certain elements get through into the cell.
Now, only a small portion of DNA actually stores information needed to make proteins. Only 2% of human genes (areas of DNA) code for proteins. But, that is another story, folks! 🙂
Back to where I come in.
My research is focused on the mechanisms of evolution of proteins. How do new proteins appear? Some proteins exist only in certain species, how did they evolve? So what scientists do is that they gather large amounts of data: DNA and protein sequences from many different species.
Computational tools are used to figure out how these different species and their respective proteins relate to each other. Which protein appeared first? How changes in sequence of the DNA lead to a completely different function of the protein it codes for? What is special about proteins that are specific to certain species?
These are just some of the questions we help answer with the research in our lab.
Got it? Have more questions? Don’t hesitate to ask in the comments!
To be honest, I was a bit sceptical when I first tried plot.ly a couple of years ago. The functionality was limited, company focus seemed to be on enterprise data science, besides, the inability to keep my plots private was the last turn off. It is, sadly, still the reality of academia: you need to keep quiet until you publish.
Plot.ly have come a long way since then though!
academics can get a private account, just contact plot.ly describing your project
If you’ve created graphs in Matlab, R, Julie, Node.js or Python, then you can import them into plotly and share online, so your colleagues can further modify and play with the data. Yes, please!
Plot.ly central mission now is supporting open science, according to their co-founder Matt Sundquist
Effortless integrations with the tools you are already using thanks to their APIs
For all these reasons, I’ve decided it’s worth the time to really tell people about it and how to use it to plot the typical figures that computational biologists usually need. Have a look at this IPython notebook I put together showcasing how to make interactive heatmaps of gene expression, scatter plots and histograms as well as interaction network visualizations using plot.ly.
You can contribute to the showcase of beautiful plots too, just check out their github repo for IPython notebooks.
What is nature conservation all about? Sometimes it is about waking up at a ridiculously early hour (4 am) to make sure there is enough diversity in a population of Southern Grysbok at one of the nature reserves. That is what I’ve done on one of the April mornings as part of my nature conservation experience at CTEET.
Grysbok is a small and shy antelope. It is fairly common in the Western Cape, but yet it is very difficult to spot. Hiding is their expertise. Speed might be another one. This small creature, reaching only around 50-60cm in shoulder height, is very vulnerable to predators, like leopard, jackals, eagles and, of course, humans. So to survive it figured out that the best strategy is to hide in the thick bush vegetation or in a hole left from a seasonal wetland. “Maybe if I don’t move and sit still no one will notice me? I will only move when danger is really close by”.
Given this behaviour, capturing grysbok without hurting them is not an easy task, but the staff of the Milnerton Race Course Conservation area knew what to do. This area of just about 18ha in the middle of the horse race course can only support a population of 6-12 bokkies and animals are basically cut off from other potential habitats due to urban development. So nature conservators have to help them every now and then. If population grows too much, they capture some animals to move them to other nature reserves or game farms, and to introduce more genetic diversity they regularly bring a breeding pair from another area.
The later is what our goal was: to capture a one male and one female grysbok and safely transport them to another nature reserve. The morning was cold and foggy and it took a while to assemble everybody. We were separated in two groups. Around 15 people were holding a huge net up on one side of the area and the rest of us would be the chasers on the other side. I was in the chasers group and our task was to move in a tight half-circle shape trying to eventually narrow down the bokkies’ area by making a lot of noise. We were singing, clapping hangs and shaking the bush. Already in the first few minutes we spotted a female grysbok sleeping in the bushes, I did not even have enough time to turn my camera on, she jumped of the bush and was gone within milliseconds. This tiny creature looks more like a dog with really big ears, I thought. OK, a dog that jumps really high and really fast.
The lady bokkie ran straight to the net and was captured by the skilful nature conservators. To calm her down we all stopped making the noise and were standing very still, while she was blindfolded and carefully carried to the transportation crate.
The male made us work a bit harder, but a couple of hours later we found one as well. By then I was soaking wet and dirty from walking through the wet bush, but the feeling was strangely satisfying. I have seen the master of hiding, the Cape Grysbok!
Truth is, you don’t really have to (in fact, in normal circumstance you shouldn’t) walk around shouting and shaking the bush to know where grysbokkies are. Try to go for walks at your closest nature reserve in the Western Cape and take a closer look at the bush, they like to pick a favourite spot to spend the day in. It can be quite an adventure!
A couple of weeks ago all people talked about in and around Cape Town was the monumental fire, raging through 5,500 hectares of the Cape Peninsula. Thanks to all the hard work that firefighters and hundreds of volunteers put into it, fighting extreme temperatures and wind, the fire has been stopped. Fires always cause a public outcry, concern of people’s safety and a lot of misinformation, especially about the role it plays in the fynbos ecosystem.
Not everyone knows that fynbos are well adapted to burn and for many species fire is essential for their reproduction. Some seeds have been waiting for years buried in the soil for the unique combination of nutrients that comes from the fire they need to grow. Many fynbos species need fire to release their seeds from tightly packed cones.
Each fire is a random process, a lottery, where it’s hard to predict how the ecosystem will look like, some plants will resprout and flourish, some will perish forever. The interplay of temperature, wind and rain will decide the faith of each seed and root.
Kenilworth Conservation Area is a small nature reserve that is located in the middle of the horse race course. Due to its location this 50 ha patch of land has been undisturbed for more than 100 years and naturally became the best preserved Sand Fynbos Area in the Western Cape. The area consists of permanent and seasonal wetlands and lowland fynbos. It’s home to several endangered plant species and the cute microfrog.
The fire at Kenilworth was happening a bit earlier (18th of Feb) than the big fire raging in Muizenberg and was a controlled ecological fire to stimulate the fynbos ecosystem before the rain season.
From afar the area just looks like a warzone, destroyed and sad. But if you get closer you’ll see proteas’ and leucodendrons’ seeds released into the soil, just waiting for the April rains, grasses and restios growing in full power again and wonderful bulbs emerging from the ashes. And the tough alien invasive plants resprouting too, only to create more work for the field rangers removing them to give space to the fynbos.
Kenilworth Racecourse is a privately owned land, so you can only visit the reserve by prior arrangement and with educational or research purpose. You can also join the “Friends of Kenilworth Conservation area” group and join one of many events they arrange at the reserve. Contact them to arrange a visit or for more info, it should be really nice there in the spring when many plants are in bloom or go in the winter, when the frogs are out!
What is so special about dry and dull bush vegetation that clothes the mountain slopes in the Western Cape? You probably have never even heard of it. Even the locals often consider it just an annoying spiky obstacle on their way and a fire hazard to their homes. We do appreciate the occasional rooibos tea, geraniums in our gardens and proteas in our flower arrangements, however.
But there is a special beauty in fynbos, and to experience it you have to be a true adventurer and get close to discover the rich variety of delicate flowers and a truly fascinating toolkit of adaptations that allows these plants to thrive in harsh conditions through wind, droughts and fires.
With more than 7000 species the potential of discovery is endless. It is little wonder that even experts are often puzzled when trying to identify fynbos species.
If you are like me and just starting your botanical journey into the Cape Floral Kingdom, I think, a good place to start is to learn to distinguish between the main fynbos families: Ericas, Proeas, Restios and Geopythes(this last one is actually a group of families).
1. Ericas (Ericaceae) or heather.
Found in moist acid soils, on the seaward facing slopes. These are the brightest flowering shrubs. You can identify them by small, often folded, hard and dryish leaves.
2. Proteas (Proteaceae).
Usually taller than 1.5 meters and can have colourful flowers in the winter when in bloom. They occur at lower altitudes, deep and well drained soils, but require a more fertile soil than most fynbos. Identify them by larger, greener leaves and special shape of flowers.
3. Restios(Restionaceae) or Cape Reeds.
Shallow-rooted group of species related to grass plants. Can be found in the drier parts of the fynbos region. Distinguishing restios from grasses and sedges is quite easy: they have no leaves, just scalelike bracts.
4. Geophytes (bulbous plants).
These are mine and, perhaps, every girl’s favorite. You are probably the most familiar with this group of plants since it includes gladioluses, irises and orchids. The pretty geophytes usually flower during the cool wet months, but I have seen some already in March. Often flowers appear after the leaves have died, to give all the nutrition to the flower. The most spectacular sights is the mass flowering of bulbs after the fire.
I hope this mini guide in fynbos would be useful for you. Now it’s just time to pack water and snacks and head out for your fynbos identification hike. Some of the nature reserves close to Cape Town where you can explore fynbos biodiversity and start identifying plants like a pro-adventurer:
The number #1 rule of the internet should be “DO NOT READ THE COMMENTS”. Especially to the articles discussing the issues of diversity in the tech industry, like this or this one (Swedish). Yet I did, because I care what people think. Maybe that’s because I am a woman. A woman in tech. And here is my personal take on why, in fact, there are so few women in our industry.
Personal truth number one: I never really wanted to go into programming.
It just happened because of [reasons]. Certainly, not because that’s what women do.
Despite growing up in the 2000’s, I didn’t have a personal computer until I was 16 and started studying for a CS degree ( no, I wasn’t a genius, many people in Russia in the 00’s finished school young). My parents just didn’t want me to become “one of these crazy games addicts” and advised me to read books and do sports instead.
When it was time to pick a major in high school, I wanted to go into arts and humanities, but my parents thought I should study economics and be a financially independent woman eventually. So I(we) picked ‘technology and economics’ major. I couldn’t say I particularly enjoyed it or if it was really hard. It was OK. I had really good math and physics teachers. I still remember them with warmth and gratitude. They made science interesting and fun. Besides, TheLoveofMyLife (back then) picked the technology major as well and he got interested in me after I helped him with his math homework. He said I’m smart. That was enough to start loving the class.
Personal truth number two: I never even imagined myself a programmer.
I struggled through “introduction to programming” class in high school. It was impossibly boring. We even had a female instructor for a part of it! She was also pretty and young ( so I can’t blame the lack of role models). But she was impossibly boring for me then as well. She didn’t say much, was quiet and got annoyed with me because I didn’t get it. I probably didn’t try that hard.
Is that programming also? Creating beautiful and fun things like this on the computer. Then sign me up!
This game changing moment along with the complete confusion on picking a career path was followed by the advice of my Physics teacher to study Software Engineering. “You’ll do well”, he said.
You see, there might be a pattern here for me following what other people say. Is that because I’m a woman? 🙂
Long story short, I did study Software Engineering. Through highs and lows. I heard my Electrical Engineering professor in Russia tell me that “women’s place is in the kitchen”, I saw people drop out of the program. I struggled to think in variables and processes and wrote poems during the Quantum Physics lectures. But I’m no quitter. (Well, actually I am, but at some point I realised that I do need to make money and coding pays well )
It got better and better every year, until I was one of the best students in class. I did it!
Personal truth number three: deep down it never felt natural.
Maybe, because I’m a woman. I was always feeling like “well, I’m just getting an education here, don’t mind me”
I coded on the side during studies as well and, to my surprise, enjoyed it. Html kitten turned into test automation systems built in Python&Django, countless websites, machine learning algorithms, mathematical modelling and God knows what else.
There were very few women in our class and even fewer in the workplace*.
* To be completely honest, my first real programming job in Moscow was very special. Out of around 10 developers, two seniors were women. They were amazing. My boss was also extremely supportive and probably is one of the main inspirations I had to actually become a better software engineer.
The situation in Sweden turned out to be worse. The first class I took was “Models of computation”. 99 % of the class were men. And needless to say I was the only woman in every tech team I worked ever since.
Everyone here in Sweden supported and cheered on women in tech though. Geek girl groups, job positions encouraging the female candidates to apply, amazing support for the PyLadies Stockholm I’m leading.
No one ever again told me that my place is in the kitchen (after certain culinary experiments my partner actually tells me the opposite ). Some people even would say that the PyLadies community is not needed, that it is sexist and alienating men.
“Well, what would you do, we are so inclusive, but women are just not interested in programming or technology. What is the point to force them or “artificially” attract females? We should just welcome everyone and the ladies will show up. And if they don’t, then they are not passionate enough”
Am I truly passionate? Am I enough? Well, I don’t know if I’m truly passionate about technology or software. I don’t know if I want to dedicate my whole life to it. Life is too short and the world is too big. I’m still in the exploration phase, getting excited about a new programming language just as much as about genome architecture or political debates. And it’s ok.
Personal truth number four: I still feel like I don’t fit in.
What I do know and what will eventually influence my decision on where to take my life further is the fact that I still feel like I don’t fit in. Probably, because I’m a woman. I don’t drink beer and I don’t enjoy playing Star Craft (ok, maybe only a little bit). I don’t think being “geeky” or “nerdy” is cool (more like embarrassing). I’m completely indifferent to SciFi. I think communication skills are more vital for creating great products than being able to code merge sort on a white board. In my free time, I do anything but sitting in front of my computer. I do very little for open source projects outside of my payed job. I often miss people interaction in my job and realize the only things I said today to my coworkers was “Hello” and “Bye, have a nice evening”. And I often feel like an idiot when I can’t solve something. Maybe, it’s because I’m a woman. I don’t even mention the Bro-culture , the drinkups, the “so, how is it being a woman in tech”?
So, do women really like being helpless and don’t enjoy demanding tech careers? Does your biological gender determine if you’re good at support or development roles? Analytical or creative jobs? Caring for others or being competitive?
Maybe there are fewer women in business and STEM because we are just wired differently?
-> Or maybe it is possible to portray a different image of what technology really is to our kids. What amazing opportunities we have to impact people’s lives, to solve real world problems with code.
-> Maybe it is possible to teach coding and engineering in more than one way, engaging a diverse crowd of people.
-> Maybe it is possible to foster company cultures that aren’t based on over-consuming alcohol, jerk-behaviour and violent video games.
-> Maybe we should think how to make the workplace more family friendly both for mothers and fathers.
-> Maybe we should stop judging people on their looks, hobbies and the way they choose to balance their family life and career and just look at the actual work they produce and unique value they can bring into your business.