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Monthly Archives: April 2012

To Dye For

I enjoy knitting- I have made scarves, hats, and am currently working on the ugliest sweater in the world. It is my first attempt at a sweater, and I knew it was going to be ugly, so I used some free Red Heart yarn that I didn’t know what to do with. I was wondering if there was any biochemistry behind knitting… and what do you know there is! I decided to research the biochemistry behind dying yarn.

The first thing I realized was that dying natural yarn-for example, wool- is WAAAY different than dying acrylic yarn such as Red Heart. In fact, a lot of knitters hate Red Heart with a passion because they say it is scratchy and squeaks when you knit. I was hoping to do half of the post on natural yarn and the other half on acyrlic, but quickly realized that it would turn into the longest post in the world. So this week we are looking just at the biochemistry behind dying acrylic yarn.

The first thing to know about acrylic fiber is that it is made a polymer, which is composed mostly of monomers of polyacetonitrile, or PAN.

Acrylic fiber also contains monomers of vinyl acetate or methyl acrylate.

Acrylic is composed of copolymers; that is, the monomers that create the chain are not all the same. For example, an acrylic copolymer may be composed of 5 monomers of PAN, followed by 1 monomer of methyl acrylate and one monomer of vinyl acetate. Or maybe 3 monomers of PAN, followed by 2 monomers of vinyl acetate. I couldn’t find out exactly what the pattern/arrangement is in Red Heart yarn–it is probably top secret haha. But we do know that most of it is PAN.

Acrylic yarn starts out as a liquid and ends up as a soft string. How does that work? I found a great website that explains how this transformation occurs. Basically, the liquid is squirted through a nozzle that looks like a shower head. Once dried, those strands are combined and twisted into strands of yarn.

Interestingly, the yarn made at Red Heart is dyed while it is still liquid, so the fiber is already colored as it is stretched out and wound. This is of course different from natural fibers, which are typically a white color which is dyed, then stretched out and wound. However, you CAN dye acrylic yarn after it has been made. Since acrylic fiber is very different from natural fiber, different dyes must be used.

Acrylic polymers typically have an overall negative charge. It was really difficult to find out exactly why this is, because most websites just repeated the same explanation using the same wording. When I tried to find some primary sources, I found out that my university does not have access to any of the articles I found interesting 😦 The little information I found explained that the acrylic polymers had anionic (negative) groups attached to them, mostly sulphonate and carboxylate. It seems that persulfate is used to initiate the polymerization of the acrylic in its liquid form. No idea where the carboxylate groups come from.

Whether or not we know where these groups come from, they are present, and they are making the polymers have a negative charge. This property is taken advantage of in order to dye acrylic. Basic, or cationic, dyes have a positive charge and work great to dye acrylic fibers. The positive dye and the negative polymer undergo an ionic interaction-kind of like a magnet.

Before you run out and start dying all your Red Heart yarn, I should tell you that these basic dyes are very toxic. And they PERMANENTLY stain ANYTHING they touch. AND they might be carcinogenic. So I don’t think I will be dying my Red Heart yarn anytime soon!

Here are some links to more information about the creation and dying of acrylic fibers:

And here is an adorable baby walrus that I found while writing this post:

This week’s post has turned out to be a bit more chemistry than biology, but come back next time for the scoop on dyeing natural fibers!

The Business of Running a Lab

This week’s post is a bit off-topic for everydaybiochemistry. Normally we talk about the biochemistry behind common activities, processes, foods, etc. We are still going to learn how something works, but not in a biochemical sense. This week we are learning how to run a lab. Ok, we are not learning EVERYTHING about running a lab, but we are learning about the business side. Many Ph.D. students go to grad school in hopes to one day run their own lab. They want to be the one calling the shots, not the underling. So you would think that grad school would teach you how to call the shots, right?


Grad school teaches you how to DO science. Hopefully how to plan experiments well. But how about managing people? Finances? Not so much. Some (not all, sadly) departments at my institution require graduate students to write a grant proposal for their comprehensive exams, and some have courses dedicated to grant writing. Which is great! But I think we could learn a whole lot more. One side comment: grad schools should provide a foundation for Ph.D. students to pursue a variety of science careers- not just academic tenure. But that’s a whole other post.

I believe that running a lab is a lot like owning a business, and that many of the skills needed to succeed in business can be applied to science. Mr. Braaains has been toying with the idea of running his own business, and recently shared with me a few reasons why he would like to own a business: He wants to be his own boss. He has some ideas of his own that he would like to try out. He thinks it would be fun.

Those reasons sound a bit familiar… They are practically the same reasons why I want to get my Ph.D. I want to run my own lab. I have some personal research ideas that I would like to explore. And I think it sounds like a lot of fun (nerd, I know). So I decided to search the interwebz to see how other scientists are applying business skills to their own science.

And I found some awesome resources! For example, Lab Manager Magazine and Morgan on Science. I also found the results of a survey which showed that 80-90 % of scientists receive little or no formal training on people or money management. About 50% of scientists surveyed said they received informal training on managing people, but only 30% received any informal money management training. So sad. I like what Dr. Morgan Giddings from Morgan on Science has to say about the topic:

People like me who have climbed up the science career ladder have had to learn these things, usually by trial-and-error, and sometimes by getting lucky and having a really good mentor.  But career success in science shouldn’t be a matter of luck. What is lacking is a systematized approach, e.g. a “blueprint” for success.

Why are things this way? I have found a few explanations that seem to make sense.

1. You are expected to learn lab management from your PI, not in class.

Currently, there are no classes in grad school on lab management. My best theory is that people assume you will learn how to manage a lab by watching your PI. Working in a lab is a lot like an apprenticeship. Or like following a rabbi. If you follow your boss around enough you will learn how to manage a lab. Note that I did not say you will learn how to manage a lab well. If any of you have worked in a lab, you know what I am talking about.

2. PI’s don’t get credit for teaching lab management skills.

If your PI is anything like mine, he is always running around putting out fires (not literal ones hopefully!) in the lab, writing grants, editing papers, teaching classes, writing grants, at faculty meetings, writing grants, advising students, oh, and did I say writing grants? Money is really tight now days, so researchers must make more time for writing grant proposals and publishing papers in order to keep the lab going. Lab management training is bound to fall to the wayside.

3. The teachers don’t have training.

Just because you publish a lot of papers does not mean you are a good manager. This reminds me of the pre-grad school advice I received: don’t pick a lab to work in just because the scientist is “famous” or well-published. Rather, try to find an PI who will be a good advisor to you. In fact, I have even heard people say that it doesn’t even matter what the PI is researching as long as he is a good advisor and advocate for grad students. I find it sad that this is true. Maybe I am wishing for too much, but I think students should be able to find a PI who is a good advisor AND studies a topic in which they are interested.

I would like to comment here that lab management skills are not the only thing required for research success. You still need creativity, perseverance, intelligence, etc. But I think that good lab management skills will enhance the success that you already have, and make life easier. And I am all about that.

So, what some business skills that can be applied to research? From my reading, the following four business skills are the most important for running a lab: budgeting, leadership, intellectual property management, and marketing. For each skill set, I have listed a few sites that I found very informative and plan on reading myself.


Budgeting skills are important for getting grants and maintaining them. When writing a grant proposal, you must be able to accurately estimate the amount of money that you will need. Too much, and the reviewers will get suspicious. Too little, and you run out of money before your project is done. The three main components of a budget include personnel, major equipment, and supplies. From my reading, personnel take up the most of your budget. Major equipment can often be shared with other labs in order to reduce expenses. One common tip I have seen for maintaining a lab budget is to set a monthly spending limit, and then monitor how often you spend above or below that limit.


There are different leadership styles, and I recommend that you find out what yours is. That way you can enhance your leadership abilities (or switch to a better leadership style!). One interesting comment I found in my reading is that there is a difference between a leader and a manager. Understanding if you are better at being a leader or a manager will allow you to improve in the area you are lacking.

Intellectual property management

There are increasingly greater connections between academia and business, which I think is great! Our university is making an effort to connect researchers with businesses and vice versa. One of the greatest things I learned about intellectual property management is that you can publish information that you have patented. You do not have to choose academic or industry for success. HOWEVER, you must register your intellectual property BEFORE you publish it. If you publish a paper describing your new scientific technique before letting your patent office know, it is now public information and you cannot patent it.

Marketing your research

The most important lesson I learned from my college speech class was this: Understand your viewers. This has changed not only my oral presentations, but how I write as well. It also applies to grant writing. I have not written any grants yet, but the most common advice I hear are related to the grant reviewer’s experience. The teacher of my grant writing class would always tell us to imagine that our grant reviewer is reading our proposal while riding a cramped airplane on his way to the review session. So plan accordingly when you write.

I think that the ability to market your science will only become more important as funding gets tighter and tighter. If you have to equally interesting proposals before you written by equally qualified investigators, you are going to pick the one that has more significance and impact. If your research is important but you cannot communicate that, your grant will be the one left behind.

Last, if scientists could better market their research, I think that the American public would find science to be more important. The lack of communication between scientists and the public is, in my opinion, the main reason why kids are not going for science careers. I also think that more government funding for science could happen in the future if scientists were better at marketing their research.

Also here is an interesting paper titled, “Research efficiency: Perverse Incentives” that discusses the correct way to use monetary incentives in science.

I know that this is a very cursory review of business and management skills, but I hope it is a starting point for anyone who wants to learn more how to successfully run a lab. I do not claim to know how to succeed in science since I am still a grad student, but I think that it is better to start early than get left behind. So email me in about 10 years when I have my own lab up and running, and we will see if my post is still relevant 🙂