Naturpodden - Det tidiga livet på jorden

I was invited by Naturpodden to the Uppsala Science Fair SciFest to talk about early life. A great interview by Johanna Sköld and Emil Nilsson.

Rejection letter

You get a lot of rejection letters as a scientist... I'm sad I didn't make it to the Swedish Academy of Young Researchers, but I'm glad they have a good crop of applicants. And there is almost a next year!

Darwin Days at the museum of natural history

Me and Darwin think deeply about evolution.

Thanks guys for a great - very ambitious - outreach project! I think we can conclude that Darwin's birthday has been highly celebrated.

https://darwinatmuseum.wordpress.com/

Existential ponderings

(Translation from Swedish: "Does the university exist in reality?")

A week into my new job, a foray to the library and a sense of existential dread makes itself known. 

First day at work

Look at that - the biotechnologist is back at his old Alma Mater at SLU where it all started - this time as a lecturer. I look forward to new challenges, and especially I look forward to have proper time for my students. I have a good feeling about this.

You guys...

The best thing with Academia is the constant hellos - all the amazing people you meet.

The worst thing with Academia is the constant goodbyes - all the amazing people you leave

I'm one of the fortunate souls who have been at Molecular Evolution twice, so I'm also one of the wretched souls who have to say goodbye twice. Keep on being awesome, MolEvolers. I look forward to lots of cool science from you guys.

Thanks so much, Thijs, for my time in your group and the awesome opportunity to work with korarchaea. And thanks for the XKCD parting gift - how well you know me

New paper

Life goal: Use the word "smorgasbord" in a scientific article.

FINALLY I got my Boston paper out. Thanks so much, colleges and contributors, for teaching me just how weird the world of oceanic microbiology can be.

https://www.ncbi.nlm.nih.gov/pubmed/29225592

Gender equality a quality issue

With discrimination sadly still being an active force behind faculty composition - especially at higher career stages - and with Sweden not being an exception however much we would like it to be, it is good to remind ourselves that gender inequality is not a "women's problem"- it is a quality problem that should concern everyone. When recruitment and quality assessment procedures are clouded by well documented biases (see below for a few links) we do not make a fair judgement of scientific value. If we let mediocre science slip by because the first name author is a man, or let superb science stand by the side because the principle investigator is a women we are not doing are jobs right.

Are we really going to be OK with that?

In academia we proudly defend our right to moderate our own, to assess quality and to determine scientific value. If we are to live up to that trust we have to take an active stand against discrimination, based on gender and based on other factors. We have to do more than notice the problem - we have to take active part, starting with our own biases.

A seminar on gender equality in academia organized by Lynn Kamerlin at Uppsala University lead to an constructive discussion about how to empower women in science with several good suggestions.

Educate everyone involved in application processes in the biases involved

Train yourself to be aware of your own biases

Form mentorship programs

Provide career support

Work actively to include women in panels and conferences, but avoid getting them boggled in busywork.

Critically evaluate who does what works at the department, big and small

Highlight outstanding women

Speak up about problems you encounter

Discuss discrimination as a science quality issue

We were also reminded not to lose hope. Even if the statistics can be incredibly depressing things are getting better. And we can make a HUGE difference for ourselves and those around us.

Test your own biases

Nepotism and sexism in peer-review

The different worlds of academia: a horizontal analysis of gender equality in Swedish higher education

Science faculty’s subtle gender biases favor male students

Women’s equality in the Scandinavian academy: a distant dream?

Motivating the motivators

"Just tell me what will come on the exam... Just tell me the pedagogic tools I should use..."

A seminar discussing THIS paper led to an interesting discussion on teaching pedagogics. Many familiar classroom situations are recognizable also among the teachers themselves when they are taught pedagogics. There will be the highly motivated squad that uses every new trick and pedagogic tool, there will be those that are stuck in their rut and there will be the ones that only do minimal effort and would most of all like to get back to their lab. And just as we can use our fancy activation techniques to catch help students forward, you should be able to do the same with their teachers.

The thing is, teachers WANT to be good at what they do. That is part of our academic self image and, as Jerome K. Jerome reminds us, every kid wants to be the one with the pointer, telling the others what to do. And just as students, teachers want to take the easy road and just learn a few tricks when what they really need is to get into a new way of thinking.

What teachers need is again the same as what students need - supervision, help to build a culture and fora to foster communication. To what extent do course supervisors create meetings between their TAs? To what extent to heads of programs have teachers exchange pedagogic expectations with each other? To what extent do the university offer pedagogic courses and seminars?

There is a persistant idea that teaching is less valued than research. I feel the university fairly easy could take the edge of. To put it bluntly - if we are to feel that time and effort spent on education is valued we actually have to value it. At Uppsala University formal education in pedagogics is a requirement to teaching positions and it is part of the evaluation criteria for new hires. That is excellent, but more can be done. How about a fund for research money with educational professioncey as the highest prioritized selection criteria? That way researchers can put in the extra hours in education and still be able to send a PhD to a conference.

The mystery of the pink lake

Listen to me explain (in Swedish) in Aftonbladet's Morning TV why a lake in California is turning pink.
Spoiler alert: Purple Sulfur Bacteria

(https://tv.aftonbladet.se/abtv/articles/91487)

From hells heart I stab at theeee, thaumarchaea

After a career in the lab, where sampling meant walking to the -80 upstairs I was VERY exited to finally be on a real research vessel. Watch me pipett in the sun on M/S Fyrbyggaren, hunting for archaea in the Baltic Sea.

The day I met the king of Sweden

Photo: Markus Marcetic, Royal Swedish Academy of Science

What does it feel like to - as a young researcher, unsure of yourself and your ability to make it in your chosen field - get validation in the most bombastic way possible?

Pretty neat, let me tell you.

I didn't quite realize what I signed up for when I applied to the Crafoord stipend. I merely wanted to test out my idea and maybe get some sequencing money. I didn't realize I would be invited to the Royal Swedish Academy of Science for dinner, or that I would shake hands with the king, or that I would meet Tomoko Ohta!!!!!

The proud receivers of the Crafoord stipend

Photo: Markus Marcetic, Royal Swedish Academy of Science

I'm very happy for the honor, but more importantly for the validation. I have been told as clear as can be that, yes, my ideas are worth listening to.

Dark Microbial Matter

Crafoord prize winner Tomoko Ohta - Progress of the near-neutrality concept in evolution

My favorite Crafoord lecturer Lindell Bromham - From mutation to macroevolution: Connecting genetic variation to the generation of biodiversity

All Crafoord seminar holders

What is growing in the water bath? Master student wanted to find out!

Archaea is the least studied of the three domains of life. Known to live in the most extreme habitats they are nevertheless common in all parts of the biosphere. Varied, understudied and immune to most forms of antibiotics they pose unique challenges to study, and that is where you enter the picture.

The Archaea lab at the Limnology department studies population structure of archaea in their natural habitat, and we want to correlate those studies with the properties of cells in cultivation.

In this project you will cultivate two strains of archaea - a halophile that is adapted to extreme levels of salt, and a thaumarchaeon that is adapted to the harsh life in the oxygen limited ocean. You will start the cultivations, explore different techniques to monitor and manipulate growth and characterize growth parameters.

You will be in the startup phase of the project, so your ability to learn, adapt and communicate methods is very important. At the end of the project you will not only report your result - you will teach the rest of the lab how to do it.

For contact and further information, please email Erik.Pelve@ebc.uu.se

Archaea Online Journal Club

So many new articles, so little time. Let us help each other. Welcome to Archaea Online - a digital journal club about everything archaeal. We discuss new articles using the PeerWise platform.

The goal of the journal club is to gather grad students and researchers of all fields that study archaea - be it metabolism, cell biology, ecology, evolution or anything else. We will discuss a broad selection of articles to reflect the wide range of our field.

PeerWise is a system originally developed as an educational tool for classrooms that allows the users to help each other dissect the material by writing and answering questions. That way we build up a question bank together and can focus on the most relevant aspects of the article.

We will read one paper per month. What is next in your todo-pile?

To join , please subscribe to the google group and you will get a PeerWise ID within a few days. https://groups.google.com/forum/#!forum/archaea-online

How it works:

You read the paper, you write questions, you answer questions and evaluate the quality of other people’s questions - that’s really all there is to it :-)

As any teacher know, there are no better way to learn something than to teach it, and by writing questions we have to put ourselves in that position. Not only will we decide what from the article is worth asking about, we also have to think of suitable answers and - because of the multiple choice format - possible ways of misunderstanding the material.

We refine the questions continuously during the month, so you can work through them whenever it suits you best. If you have a busy months and just want to skim through other people’s question that is fine too - as long as a few people contribute questions each month we will have enough to get by. There is also nothing stopping you from going back to old papers. In time we will have built up a question bank that can be useful for new people in the field, e.g. as introduction for new students.

PeerWise Introduction: https://peerwise.cs.auckland.ac.nz/docs/students/

The group is run by Erik Pelve, postdoc at Uppsala University who dabbles both in cell biology, evolution and ecology of the most interesting organisms in the world. I also run the twitter archaea outreach account ThirdDomain. For any question, don’t hesitate to get in touch: erik.pelve@ebc.uu.se

Join: https://groups.google.com/forum/#!forum/archaea-online

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Oktober 2016: Back to the classics - the paper who gave us one of the most known phylogenetic trees and the phylum korarchaeota
Tag: Barns_etal_1996
Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences.
https://www.ncbi.nlm.nih.gov/pubmed/8799176

September 2016: Methane production in hydrothermal vents
Tag: Topcuoglu_etal_2016
Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents.
http://www.ncbi.nlm.nih.gov/pubmed/27547206

August  2016: The untapped potential of archaeal pili
Tag: Makarova_etal_2016
Diversity and Evolution of Type IV pili Systems in Archaea
www.ncbi.nlm.nih.gov/pubmed/27199977

September 2015: Let's start off the journal club with some ecology/metabolism. In a recent Nature paper Palatinszky et. al. finds a new way to feed into the nitrifyng process, with a little (a lot of) help from our friends the thaumarchaea.
http://www.ncbi.nlm.nih.gov/pubmed/26222031

August 2015: The first paper is THE first paper - Woese and Fox 1977, the first conceptual description of archaea as something other than bacteria.
http://www.ncbi.nlm.nih.gov/pubmed/270744

Lokiarchaeota - The shapeshifter bug in the mud

This is the story about a bug - a very special bug and how it was found. It is named Lokiarchaeota after the trixter god from ancient Nordic mythology (you might know him from the Marvel comics and movies where he is Thor's evil brother) and it is special because no one knew anything like that existed before. As all good stories it starts with mud.

Do you like to play in the mud? There is a team of scientists from Uppsala University (that's in Sweden) who sure does. And they found some really cool mud to play with. It comes from the bottom of the ocean, not that far from Iceland. When scientists play with mud they do it just like you do - they poke it with a stick, or they sift it and look for interesting things. But since they only had a few grams of the mud (they had to use a submarine to get it) and the interesting things they looked for was so small, they had to use a really, really good stick. The stick they used is called metagenomics.

Imagine that you were looking for insects in the mud, but all you found were bits and pieces. An antenna or a facet eye, a wing and lots and lots of legs. Then you would have to sit down and piece it all together, like a jigsaw puzzle. Connect the eyes to the head to the thorax to the legs and you get an ant. Other pieces become a ladybug or a fly. And you would have to be really good at puzzles to find where all the legs go. That's what the scientists from Uppsala did, only instead of legs and wings they used DNA, which is molecule inside the cells of all life - big and small (that's what metagenomics means - looking at DNA from all bugs at the same time, not one by one). And the scientists were really good at puzzles, so using only the DNA they could piece together almost the entire little bug - and it was the strangest bug they had ever seen.

But before I tell you about Lokiarchaea I want to tell you about bugs in general. Not "bug" as in insect but "bug" as in microbe, the tiny little things that you have to use a microscope to see. Do you know how small the bugs they were looking for are? Think of the smallest thing you can see without a magnifying glass. A little speck of dust, or the tip of the antenna of an ant or the dot in the end of this sentence. On that little speck, thousands or millions of microbes can fit quite cosily. They are about one micrometer long - that's a millionth of a meter. Each bug is a single cell - instead of being made from millions and millions of cells like you are, each cell is on their own. These kind of bugs are everywhere. Some like to swim in the ocean, some like to live in the soil. Some lives in your stomach and help you eat, and a few likes to get in your stomach and make you sick. Some are round and some are oblong, some stick to each other, some have little hairs that they use for swimming and some just float around.

There are three kinds of microbes. There are bacteria, who are almost everywhere. There are eukaryotes, who are bigger and like to eat the other two (Actually, not all eukaryotes are microbes - plants and mushrooms and dinosaurs and dogs and you are all eukaryotes too). And there are archaea, who not many people know about. They look a bit like bacteria but once you poke with them they are different - it's a bit like how birds and bats both have wings and can fly, but look really different when you look close. Archaea and bacteria have been around for almost as long as Earth - more than three billion years - but eukaryotes showed up "just" two billion years ago.

One thing that is interesting with eukaryotes is that they look a bit like archaea and a bit like bacteria (and a lot like none of them). And here is what's really interesting with Lokiarchaea. They have DNA that is shared with many other archaea, but they also have DNA normally found only in eukaryotes. In fact, they are more closely related to eukaryotes than any other archaea that we have ever seen before.

The Lokiarchaea have pieces of DNA - genes - that codes for actin. That is a protein that was previously only known from eukaryotes and is used for all sort of things that relates to the cell shape. It can be used to bend and form the cell. It can be used to send signal from one part to the other - and it can be used to pick up things from outside the cell. That last thing is exciting because one idea of how eukaryotes came to be is that an archaeal cell picked up a bacterial cell and that they stuck together after that. Maybe it was something much like the Lokiarchaeota that used the actin genes to pick up a bacteria. There are also other genes that are important for eukaryotes, including something that is called the ESCRT-system which is used to move things around in the cell and lots of genes for proteins called GTPases that are used as switches that control when things happens in the cell. We are not used to other things than eukaryotes having these genes, so that's why we think that the Lokiarchaea are actually more closely related to us than other archaea - a bit like how dinosaurs with feathers are more closely related to birds than other dinosaurs.

So that's the reason why this new bug is so exiting. It is a new kind of archaea we didn't know existed. It may very well be our closest relative among the archaea and bacteria, and it has taught us a lot about something really strange that happened two billion years ago. It has many genes that we didn't know existed outside eukaryotes that give us a rough idea of what genes the first eukaryotes had, and that's something we have wanted to know for a long time.

The thing is, bacteria and archaea are pretty easy compared to eukaryotes. They have small cells and not that much DNA, but the eukaryotic cells are huge and there are multiple compartments and lots and lots of DNA we don't know what it does, and we don't really now how a simple cell like an archaeon can evolve into a complex cell like an eukaryote. Well, thanks to Lokiarchaeota we now have a clue. Despite being rather simple, the Lokiarchaeota contains lots of the same genes as eukaryotes, and many of them are involved in changing how the cell is organized. That's why it is named after a shape shifting god. That, and because there is a place in the ocean floor not far away from where it was found that is called 'Loki's castle' (which is an incredible cool place - check it out).

The thing that I find most interesting with Lociarchaea is actually not what we know but what we don't know about them - because that is lots. Everything we know comes from the DNA, kinda like how most things we know about dinosaurs comes from their skeletons. We have never seen the cells of Lokiarchaea in a microscope or grown them in an aquarium, so we don't know if they are round or oblong, small or large. We don't know how they grow or what they like to eat, although we can make a few guesses. The mud they live in is cold and dark and doesn't contain much food of any kind, so they probably grow very slowly. We don't know how different they are from each other, we don't know how many there are (although there are probably lots, because there is so much mud in the sea floor). We don't know how they interact with bacteria, if they actually eat them or if they just ignore them, and we don't know what they use all these unusual genes for.

Still, it is pretty good for a little piece of mud and a really good stick. A lot of scientists have become existed about this - you can read more about what they are saying here and here, and read the original article here. If there is one thing this discovery tells us it is that there are lots of cool things out there to discover. So next time you play with mud - keep an eye out for any unusual bugs - who knows, maybe you will be the one to find the next one.

Living Sunlight

Penny Chisholm is one of my favorite researchers, not only because she is world-leading in studies of the arguable most important organisms in the world (if you disagree - hold your breath while doing it), but because she has done what every scientist in the world should do. She has written a children's book explaining her field and why it's awesome. Thanks for the future scientists you inspire, Penny.

Here is her acceptance speech for her (very well deserved) Killian's Award Lecture. A lifetime's worth of Prochlorococcus in one hour.

Playing with Science

The MIT Science Communication Society, ComMIT hosted a preschool science demonstration. I had the opportunity to talk about the microbes in their gut, in their food and in the ocean. The demonstration of how sneezing spreads viruses was especially popular.

It was fun event that was good for inspiring kids and parents and really good for getting students and postdocs from different departments to talk to each other about what we do. And it reminded us all that science is fun.

Devotion Science Fair

I had the privilege to judge at Devotion Science Fair in Boston and I was impressed by the creativity I saw. Both social and natural sciences were represented and the projects ranged from the familiar ("which paper airplane flies best") to the speculative ("How is this exoplanet heated?") to the wonderfully creative ("What color is DNA of different fruits?"). The winner in the group I judged studied perception of gender norms in different age groups with a project that would be worthy of publication if they had a larger population size.

Student activation in large classes

I have learned so many wonderful techniques for student activation that would work like a charm if I had ten students for a week - but what do you do with 100 students when you have them one hour? Luc Bussière from Stirling University in UK led a discussion at Uppsala University about activation techniques in large classes.

Vital for any teacher-student interaction is the ability to ask and answer questions. A question box is an easy technique to get student feedback and to set up a channel for questions and answers. While the technique is as basic as can be - a cardboard box and a bunt of paper - it is immediately accessible for everyone. However, the transcription of questions is time consuming and the format does not readily allow for follow up questions. I would never completely dispense of it because however quaint it may seen in a world overflowing of digital communication the simple box on your desk signals your availability as a teacher.

GoSoapBox and Socrative create fora for Q&A sessions, quizzes and polls. They both have similar functions. The polls are pretty good and provide an alternative to clickers or plickers. The quiz function is more flexible in Socrative than GoSoapBox, with the ability to phrase the answer in multiple ways but the students gets less immediate feedback since summaries of answers are reserved for the teacher's screen. The free version of GoSoapBox only allows 30 students. A drawback with these methods is that they require the students to have their own hardware (or for it to be provided from the course), and opens the pandoras box of the endless distracting potential of startup and login problems, sound effects and social media. But then again - that is how researchers typically experience meetings nowadays, with laptops and tablets open to take notes, check mail, look up references, work on manuscripts and hold twitter conversations on dedicated hashtags. If we believe us to be capable of it, why not the students? I may give it a try, but I will probably wait for a situation that require the students to sit by a computer anyway.

A really neat tool is PeerWise that allows students to create multiple choice questions for each other, with tools for evaluation and discussion and even bragging right badges as incentive for participation. This tool requires very little teacher activity and has been well received by students who see the potential to create a good revision tool for themselves. My first thought is to use it as an flipped classroom technique and ask students to create a question related to the material a day or two before the session. PeerWise is in use in Uppsala and has good recommendations. I will try it.

To have the students give each other peer review on essays and reports by working from a scoring rubric can be used to give students feedback as well as train them in thinking like a teacher rather than a learner - which in my opinion is the best way to learn anything. While I think the feedback and sense of validation can be valuable the real gain for me is the change of perspective. The students are not only providing an answer - they are evaluating it.

The tool Screencastomatic for oral student feedback on written work is not meant to activate students but to be a time saver for the teacher (which is also a vital task for EdTech). It allows for a short audio comment given by the teacher together with a video screencap of the document so text can be highlighted and edited as you speak. A webcam video can be included. I may try it next time I have lots of report to grade.

EdTech is a jungle where everyone tries to find a tool that suits their teaching style. The tools reviewed here have the advantage that they are easy to set up and can complement other materials without the lectures having to be tailor made for them. As always the techniques have to complement the content rather than the other way around.

My privileged postdoc: A story about a cis, heterosexual, white man in STEM

Drawing to the end of my two years at MIT it is time to look back and regard my postdoc through the lens of structure. As a researcher I am used to think in terms of individual achievements - I made this study, I taught this class, I got this grant - and forget that I work in a larger context. It's a sad fact that people are treated differently. My time as a postdoc - indeed, my entire career - has been made possible not only because my academic merits or personal capability, but by the unfair advantages I get just by being me. The least I can do is to acknowledge that. Let's count the ways.

Gender
I'm a man. This has given me an advantage in how I'm perceived and the behavior I meet. The committee that granted me my postdoc grant, the editors and reviewers that accepted my papers, students and collaborators, all have tended to see me as more credible and competent than if I had had any other gender. The only reason I could go abroad at all and leave the support network back home was that my wife agreed to stay at home with children for two years and take a break in her own career, a decision heavily influence by the gender roles both of us has grown up with. I never had to hesitate to go on a field trip, join the conference bar or otherwise limit the scope of my social interactions for fear of sexual harassment.

I'm cis. My gender is in sync with what people assume when they look at me. I didn't have to worry about getting correct medical care or if my gender would complicate my medical insurance or official documents. I have not hesitated to travel during my time her for fear of complications at the passport control. I haven't had to worry about peers and colleges "finding out" my gender status and react negatively. I have never been worried about being the victim of hate crime.

Sexuality
I'm heterosexual. My spouse and children were automatically included in my VISA and insurance. Our marriage has never been challenged, no one questioned the parentage of the child who was born in the US. I have never been worried about negative reactions to my sexuality. I have never been worried about being the victim of hate crime.

Skin color
I'm white and doesn't belong to a culture or nationality commonly discriminated against. I lived in USA during the Ferguson shooting. My very first month in Boston was during the marathon bombings and the massive manhunt that followed, yet I never feared for my safety or that of my children. My postdoc grant was awarded to me by a committee who was well aware that my name coded me as a Swede and I never had reason to debate whether I should include my picture in my CV or not. I have never been suspected of not belonging in my own department, regardless of the time of the day. I have never been worried about being the victim of hate crime.

Whenever I was overlooked or dismissed I didn't have to worry about underlying structures and could focus directly at the matter at hand. My imposter syndrom was never fueled by real discriminatory structures. The fact that I don't have had to worry about any of these factors is in itself an advantage that has saved me lots of time and energy.

There is more of course. All these factors have given me more advantages than the ones listed, many that I'm not aware of, and there are other factors as well. My age for example, which put me in the expected bracket for my career stage and doesn't exclude me from applying from grants, or my nationality that made the VISA procedure easy and made it possible for friends and family to visit, or my socioeconomic class that made my PhD possible in the first case. In fact, just about the only structures I can think of that have hindered me rather than being of benefit are the facts that I'm not a native English speaker and that I have a family to lure me away from the lab at night. But I think I have made my point.

"Privilege" is a loaded term, surrounded by controversy, but at its core there is nothing mysterious about it. It's all those little differences in how people are treated and perceived, every day, every week, every year, every stage of your career that accumulate and make a real difference. It's tangible, it's unfair and it's real.

So where do I go from here? Acknowledging my privileges is a good start but it will be of little help those who don't share them. Keeping an eye on my own behavior and biases is a good way to continue. How much time and space do I take in meetings, and on who's expense? How do I treat peers and students of different backgrounds? What structures exist at my university that reduce the opportunities for people without my background and how can I use my privileged position to change them? What do I do to challenge my own assumptions?

My postdoc has been many things. It has been a fantastic opportunity, it has been an adventure, it's been hard work and challenges - and it has been a privilege.

Some further reading.

http://conditionallyaccepted.com/2013/09/02/racism-sexism-academia/

https://www.cfa.harvard.edu/~srugheimer/Women_in_STEM_Resources.html

https://tenureshewrote.wordpress.com/2014/11/13/im-not-taking-career-advice-from-old-white-dudes-anymore/

https://tenureshewrote.wordpress.com/2013/09/26/dont-be-that-dude-handy-tips-for-the-male-academic/

http://blogs.plos.org/absolutely-maybe/7-tips-for-women-at-science-conferences/

http://diversity.mit.edu/intuitively-obvious-videos/

http://harvardmagazine.com/2014/08/sexual-harassment-academic-fieldwork

http://www.reducingstereotypethreat.org/definition.html

http://smallpondscience.com/2015/02/02/a-conversation-that-can-help-protect-your-students/

http://www.nytimes.com/2014/09/20/opinion/science-has-a-sexual-assault-problem.html?_r=0