Biotechnology and recyclability/circularity through Helsinki fashion week

I had the lovely opportunity to discuss with Olivia Rubens, a positive knitwear women’s wear designer, super interesting topics such as sustainability and fashion. These topics within the realm of biotechnology, synthetic biology, the end-of-life of our clothes, and side-streams are at the core of our beliefs. We also discussed human & climate positive centered garments and microbes,  creating new circular systems and new materials from glucose with fungi, and enzymes that eat plastics.

(c) Olivia Rubens and Marco G. Casteleijn. 2020.





I know it has been a while to vent ideas via the blinking cursor into the white void of blogism. It is so.

I, again, tried to believe I could finish my first draft of my novel by entering NaNoWriMo. I even had time for it, yet I wrote less than I ever did (at least for this novel).

Instead, “Wordexpanding”, a hyperlink novel written together with my dear friend and fellow poet Ville at the Cave (the blog where I hide a lot of my writing) & Chameleon’s stories has flown away and is going fast. I really enjoy these 100 word stories and poems that we are trying to forge, without any discussions, into a larger story. They may take some research and the dense messages of 100 words is reflected in the time it takes to write them. There is no NaNoWriMo robot-high speed traffic of characters spawn via the blinking cursor into the cloud-memory mind.

So that pressure was to restrictive. Now I will write again for “The Death of an Emperor”, I will try week by week, and I will deepen the characters better (thanks to a great on-line course I am taking at the same time). Also for the course I need to write, though its a different kind of writing.

Finally, then soon I will be reading again. The winter is upon us, the cozy warm bus awaits. Humming to bring me 2 hours of reading a day. Neil Stepheson latest book is lurking at me from my bookshelf for far to long.

So I unfurl myself in the dark day today, awakening to the possibilities and so I wrote once again today. NaNoWriNoMore, but #Iamwriting!



The Fridays – Introduction (to the introduction)

Do not start with solutions, but start with the problem...
Do not start with solutions, but start with the problem…

Lets call is appligeddon, the writing of the EU grant application is taking up a lot of time. So that is why I have not written anything for / on Friday. Last time I discussed the purpose and necessity of a good good abstract. Now I would like to address the introduction of a grant application.

Granted, not every grant application starts with an introduction in the classic sense as we know it from a written article or how we write it in a thesis. However, when you start discussing what you want to do (your aim(s)) how you going to do what you want to do you  (your methods) you need to warm up the readers. In regards to many grant applications this means you are explaining why you need the money more than someone else. Typically the review will have a means to score the application given a set of guidelines. If you tick off all the boxes, your application is better than one that does not. Some systems include scoring, and sometimes a few sets of scores need to meet a threshold (like the one we are working on now). However, in general you need to break the ice fast and be clear and precise in explaining what the problem is and why it is so important to solve this problem. Later you will have to convince that you and your methods are the only ones and for sure the best ones in the world to solve this problem, which is so important in the first place.

So this is where you introduction starts. Often I see a long three-four paragraph build-up leading to the problem. This clarifies the problem when you first see it, but it is not a good hook. What do you rather read: a page introduction on the early life of Charles Foster Kane, how he reflects his position in his family when he was a child, or that memorable opening scenes that makes you want to followed his life’s story to the end?

A grant application is not a classic story in that sense, but grab the attention from the beginning. In stead of starting like this:

A  promising new family of more complex protein based therapeutic agents, known as biologics is coming to light. [MORE BACKGROUND]. Resources spent in drug research increase exponentially, while the number of new drugs that come to the market remain constant.

Here we start with providing an answer to a problem that follows later. The reader did not know yet what the problem was, so the solution is not very evident. So lets start like this:

Resources spent in drug research increase exponentially, while the number of new drugs that come to the market remain constant, a phenomenon known as “Eroom’s law” coined as the reverse of Moore’s law in computer technology: the exponential increase in transistor density. To drastically revert this trend a new methodological approach is required. One of the most promising approaches is a new family of more complex protein based therapeutic agents, known as biologics.

Problem, naming the problem so we can refer to is later on without having to fully spell it out again, we need a solution! The answer is: biologics!

Now the reviewer can appreciate from the first paragraph what will come. Surely this is to brief for the full introduction, but now there is room to expand. Next time I will talk about the introduction some more. Maybe about a funnel…

The Fridays – the Abstract

title-too-longHé this guy can’t write, he put a capital in the middle of a title! Yes, I did. On purpose. Last week I hinted at the abstract. Today I want to share some of my thoughts on it.

The abstract of an article is basically just a 250 word or so summary of the article you are about to read. The abstract is a tool for the reader to see if they are interested in reading the whole article. They found your abstract via search, or via referencing of another article. Often they find your abstract via your title. Now I am not skipping the art of writing a title, I will leave it for another day, but Research is indicating* that with a shorter title the reader is more engaged, reads more of the article and that articles with shorter titles are more likely to be cited than articles with longer titles. Why? Clarity in writing and nothing else. If you can express your self in a few words regarding the title, you are inclined to be more clear throughout the article.  I spoke about clarity before, and again we can see the importance of it. I am writing this blog for several reasons; one of them is to ‘stretch my leg’ so to say. To practice my writing, to apply myself to be more clear in my wording. It is important.

Now, lets say you got a great title and a crappy abstract. You will disappoint people right away; they will not read the rest of you awesome message in your article or grant application. This applies to books as well; if you give the reader a most engaging hook in the start of the story you will lose them quickly if you never deliver on that promise. Good introduction, best application ever, super exciting conclusions of your work will not get read if your abstract is bad.

A summary of the contents of a book, article, or formal speech.

Consider the definition of an abstract, presented here as a quote. Yes it needs to be a summary of things to come, but especially in grant writing if you cannot capture the imagination of the reader here, you will lose them forever. In the case of a grant application this is the difference between the application getting read in full or not. I know which application is getting funded in this scenario. So what else does the abstract need?

It needs to activate the reader in wanting to read more. Clarity is one, getting you vision across is another. I will try to give an example:

” The Biopharmaceutical optimization and New Biological Entity facility would be part of [NAME]. The facility would extend the service of the platform to evaluation of engineered libraries of mRNA and proteins.
Currently 1/6 of the total volume of the pharmaceutical industry comprises of bio-therapeutics. The predicted market growth of bio-therapeutics is 7 – 15% per year and it is expected that the pharmaceutical importance of protein therapeutics will increase in the future. Several academic research groups are carry out ground breaking research in finding new endogenous proteins with biological functions. For therapeutic purposes, however, the proteins should be optimized, and for this, protein engineering and screening of protein libraries are needed. This unit would facilitate maturation of the original protein findings towards functional therapy.
Through this application we aim at establish a high throughput facility that focuses on screening pharmaceutically interesting proteins and mRNA species. The proteins and mRNA will be engineered based on the goals and end-points of the customers. For example, we can look for reduced immunogenicity, affinity improvements, or altered intracellular distribution or pharmacokinetics of the proteins. We will develop cell free expression systems, methods to investigate glycosylation patterns, and provide preliminary information about proteins that show promise as potential drug candidates, biochemical tools or as drug delivery vehicles.
Related equipments in the pipeline for protein engineering and expression, or as accessories, will include automated liquid handling, protein purification (for a small selection of altered proteins), characterization, and methods to investigate protein stability and aggregation. These parameters are of utmost importance for early protein drug formulations. The proposed infrastructure would facilitate a high throughput protein optimization platform towards lead molecules and their characterization in terms of stability, solubility, aggregation and delivery.
The total sum applied for is XXX XXX €. This application is not part of any network , but it has obvious links to ‘Translational technologies’, ‘Structural biology’, and ‘Stem cells and biomaterials’.”

I was involved late at the writing this application and I think it summarizes the application well. We did not get the funding though and I feel now thinking about the impact we thought we could have in the long run we may have been too modest. So on the fly** I will try to rewrite this abstract with that in mind:

“In order to transcend ‘Eroom’s’ law and break the barrier of the diminishing returns in drug development despite exponential increase in research and development a radical new approach is needed. Ground breaking research in finding new endogenous proteins with biological functions is not considering the therapeutic purpose. Only optimized proteins have a chance to meet the though quality requirements of clinical testing to find the patient to provide proper treatment. After discovery of a protein with potential, i.e. a lead molecule, several rounds of engineering and screening of protein libraries are needed. A dedicated research unit would facilitate maturation of the original discovery towards functional therapy.

Our aims are to invest the funds to establish a facility that focuses on the screening of lead-molecules, such as proteins and RNA, and to engineer them in high throughput based on the goals and end-points of the customers. The funding will provide us with better and faster methods to reduce immunogenicity, to improve affinity, to alter intracellular distribution or pharmacokinetics of the new biological drugs. Novel tool such as cell free expression systems will be at the core of the technological platform. We envision that the long-term impact of the pre-clinical data we will generate will overcome the stringent quality controls at a much earlier stage.

We propose a structural investment of XXX XXX € to acquire dedicated equipment needed for protein engineering and protein expression. The platform will include an automated liquid handling station, protein purification equipment, and equipment to investigate protein stability and aggregation. The proposed infrastructure and research methods would be unique in [PLACE] and  would facilitate a high throughput protein optimization platform towards lead molecules and their characterization in terms of stability, solubility, aggregation and delivery for the whole of [Country].”

I tried to follow the order proposed from these guidelines. So with clearly stating the problem and motivation at the beginning first, to then be more indicating the impact the money would make, without too much detail about the method I hope I am enticing you to read on. To see the whole application. To get from “Mêh” to “Wow”. Let me know if the comments if I succeeded? I may use it then for a future application!

*) This image in this article is made by the authors of this articles and are under (c) of the article. If just borrowed it. Please contact me via the comments if you it is not allowed in any form.

**) I mean here I did this while writing this blog, not at an earlier stage nor with prior feed-back.

The Fridays – Clarity

clarityThe quality of coherence and intelligibility. Yes, this is very important. First of all, in scientific writing we need to be understood. This is important if your peers read your text, but maybe even more so if others read it. In other words: the reader needs to understand what you mean.

Of course the text needs to be written following the proper grammar rules, spelling should be perfect and writing hooks to draw the reader in and through the article or grant proposal are a given.

However, scientific writing is often taught at school and universities for a reason. Poetic freedom in the phrasing does not convey coherence and intelligibility, or clarity. Side by side the two next sentences are trying to convince the reader about a trend in the data:

  1. We [the authors] feel that deriving from graph 1 we can conclude that no trend is apparent.
  2. Analysis of graph 1 showed no trend [evaluated by method X].

We  can clearly see the difference, the graph should not be open for interpretation if it is used to make a statement or an argument. In science presenting any data for the public eye is definitely an invitation to interpret the data from the reader’s perspective. The text is there to weight it, agree, or counter with scientifically sound arguments. Scientific ‘truths’ change all the time due to better understanding of the underlying phenomena.


the message of any give scientific text is to make a clear what has happened, or in case of a grant application, how things will be done in the future. There should be no room for opinion nor should is be a slideshow of the data produced. The reader should ‘get’ what the author(s) message is.

The fundamental purpose of scientific discourse is not the mere presentation of information and thought, but rather its actual communication – George Gopen, Judith Swan*.

From the quote above we may get a hint in the difference of a novel and a scientific article. A bit more difficult is an article written about a scientific article. Most often this is a statement or opinion about its message. I would argue that most articles about science news are not scientific in nature, but I am open for the discussion.

Now,  a scientific text is typically divided in following sections:

  • (an abstract)
  • The introduction – Background, state of the art, statement of what was done/aims.
  • Methods – How did we do this thingy/how will we do this thingy
  • Results – This is what we have observed and how much the data is worth within the context.
  • Discussion – (Sometimes mixed with the Result section) reflects the quality of the results and how the results compare to the state of the art and beyond.
  • Conclusion – This is what we found and this is what it means.
  • References

Grant applications may follow a similar scheme or more likely are presented in the form of a project plan/project work-flow. Of course you do not have results yet, but you will tell how you expect the future results will impact society/your research field/your aims/teaching/etc… There is also a tiny bit of room for your opinion, but be careful! It should be a logical statement that flows from the presentation, not your personal feeling about the topic: “give me money, because I think it is the most important research ever!” does not work. A discussion of a topic A, described in reference of problem B, which can be solved with a novel method C is a better argument, but I will get back to that another day.

I want to discuss from my point of view each section mentioned in the bullet-list above from a grant proposal point-of-view in the next blog posts. The reason for this is twofold: (a) I am writing a grant right now. It may clear my head and help in the writing, and (b) before you present data that you have done, you need money to do the work. So logically the article comes later. Also I need to get back to the lab…

*) Please find an excellent article by George Gopen and Judith Swan on the The Science of Scientific Writing to find more details on how to write more clearly if you are interested.

The Fridays – the hard 2%

keep-calm-tomorrow-is-friday-Deadlines. A fearful word since it has the word ‘dead’ in it. Lines can be scary too for some. In academia it often means a day most things are sort of done. We can push the deadline away a bit.

However, when I see it in my colleagues’ eyes: the tired, frantic look.

“I have no time right now”

Then I know: an application deadline is coming up. Application deadlines are strict and dangerous. We all had the servers of the grant institution crash on us those last minutes before the deadline, because everybody submits their ‘final_final_v3.1.pdf’ document 2 minutes before the deadline. So everything must be ready and done.

Unlike writing a story or a book, writing an application is (most often) a collaborative effort. Even if the full text is only from your hand you do need feed-back on the budget, feed-back from your boss or ask your students to write some small parts for you. A more likely scenario for larger applications is a chain of events that need to happen: (1) Idea, (2) formulate idea, (3) find research partners, (3) find/know/discover where to get money, (4) write sciency bits (yeah!), (5) find the right template for the application, (6) fill all that is needed, (7) the last 2%.

Yes I know it looks like I cannot count. Truth of the matter is that in order to do the research we need the money, and in order to truly work on your long-term vision you need a certain critical mass. That critical mass comes from obtaining results with a long and deep impact. I know that sounds vague. Lets just say I am not there yet. So for me this means I need to apply where ever I can. I swear I almost talk to strangers on the street to see if they have something in common with me so we can write and application together so I can get some money to do the research I want to do. By applying to “whatever” you do need to bend you previous results and ideas into the scope of the application. I think this is how the term “creative writing” was invented. If you have to bend to far, it gets broken. Reviewers see broken things, and have a magical wand to detect cracks, so be aware of that.

Sometimes you need to find new partners because the grant call requires a certain expertise you do not have and you do not know anybody in your network who does. That is hard, and cold-calling even in Academia is hard. Sometimes it works, sometimes it does not. Sometimes it does not even work after you get the money. Most of the times your collaborators that are sharing a grant and the grant writing with you want the same as you: money for their research.

So back to the writing of a collaborative piece. Now a few sciency bits (yeah!) are stuck together and from the general idea/grant-call come the aims of the project. Oh **** it is a project. Maybe do some project management courses later in the year? Then fill the template(s). Aims funnel into work-packages, which funnel into tasks. It is going great! Gantt chart made! Budget. Mmmm, better have some email/Skype with the others. Meetings with grant writing specialist (often called Research Managers or something similar): ok we have numbers on the page. Done!

Oh wait, tomorrow is Friday (the deadline is often on a Friday) and we need to still write about Societal Impact/Measuring Societal Impact/Management Structure/Project Management/Do we have all the signatures?/Something else not Sciency*. Ofter it is something you cannot decide alone, you have only a paragraph left for it, so you make the figures a bit smaller/outline a bit broader/go to font 11*. It is crunch time (your family hates you now): the last 2% are often the hardest and take the most time.

This is what makes writing applications hard and a skill you need to train. How are you clear to the reviewers? How do you get them to read the full application, because you know their time is limited as well. Reviewers are researchers like you, with deadlines and applications to write. How to get them past the abstract? The writing hook(s) we put in our stories and books apply here as well. Despite the mandatory bits and the hard parts like project management, budgets and other non-sciency bits, the text needs to be clear and well written. That takes practice as well. These almost marketing-like skills to sell your ideas in word and written text I do like, however I fully agree with some of my fellow scientist (most of whom are much better scientists than me) it should not be such a big part of the Science.

Luckily I like to write. For most is as fearful as the word deadline, I just do not like the last 2%…

*) take your pick

The Fridays – Part 1

32005daWriting. For some it is a nightmare. I hear it often from students at the lab. Similarly, a writers block for authors is a nightmare. Writing is the answer to both problems.

I know this sounds strange, but the best way to get out of a writer’s block is to write. Anything. The inspiration for the other thing will come back by itself.

So also goes my advice to students, my first supervisor gave me the same advice when I started my 9 month lab project for my bachelor thesis: “Start writing today”. I was surprised, “But I do not have any data yet!” A smile. “Then write the layout of your thesis, and fill it out along the way.” My PhD supervisor told me the same for the article that needed to be written, but where not all the data was in. “Just fill what we have, and make bullet-points of what you think we still need to do.” Clearly these people were more experienced than I am, so I listened (mostly) to their advice. The thesis and articles got done, with respectable merit, though looking back it could have been a lot better.

Start writing today

For compelling reasons I do not fully understand why I need to write and share my writing effort with others. I like the feed-back; as much as I enjoy stories of others, I like it when other like my stories. About these efforts I share some of my personal struggles and day-to-day insights on Mondays. What I like to do on Fridays is to write about writing I have to do to (indirectly) pay the bills.

Let me explain that briefly: I am a researcher and I am working in Academia. This means I need to write grants so I can do research. Out of these grants also comes my salary. Grants are easier to obtain if you show that you do things and know what you are doing. You are judged on how you write and your track-record. Only then comes the idea for the research into play. A track-record is a list of accomplishments: awards (including grants), conference talks, teaching if relevant, but above all: articles.

So in order to get paid I need to write grants, most often in collaboration with other people who also need money, and in order to get grants I need to write articles. Of course no articles without data. One other great piece of advice from my supervisor during my Master’s thesis work: “Get the data first.” It is one of my weaknesses, I like new challenges and new ideas. It takes discipline to finish a project and move to the next, especially when you know how to finish it.

make bullet-points

I think some of the lesson of during my studies and career as a researcher can be applied to daily writing as well. I am not good at making a frame work for my book, in other words Making the Bullet-Points. Yet in my articles and grant writing it is where I start. I do write to write more, as I explained earlier. Data collection for writing my book and lyrical poems “My Opaque Dreams” I do beforehand and on the fly. New insights and new twists in the story require research into topics on the spot. I do not have an eduction in Greek mythology, nor in Chinese culture. So I have to investigate, filter and write.

So therefore with this introduction I will leave you now this Friday and will next time try to write something about grant writing. I am currently perpetually writing a grant (a though one: for the EU) and at the same time editing a review article we are working on.

Get the data first

(I need to go to the lab now…)

Image is (c) the Upturned microscope under a licence