A Whole New Lab (Dealings of a New Professor #1)

I just turned in my first external grant and I am HYPE (C’mon Cystic Fibrosis Foundation). So… I can’t sleep. I wanted to write on what it’s been like a new PI, but that will have to wait because when I sat down, I had kid’s music stuck in my head. When that happens, I have to write new lyrics to get it out of my head. So without further ado, here is that Disney classic from Aladdin, A Whole New Lab.


I can show you the lab

Equipment borrowed and brand new

Tell me, students, now won’t you give this young PI a try


I still work at the bench

Hope to not micromanage

I’m just into the data that I hope you might provide


A whole new lab

A new fantastic project for you

New toys are coming in

Not hard to spend (yet)

I want to do some science


A whole new lab

A dazzling place for you to do

Projects to change the field

Bad bugs will yield

Let me share this whole new lab with you


A whole new lab

Rotate with me

At U of A

Room 221



More on what it’s like to be a PI later. Also, there was a new podcast from the new crew. Check it out at cure4kids.org/ums/sites/teachers/plugins/page.php?id=19





Answering the “what do you do as a scientist” question

When we are asked a question, we must answer two things. We must answer the question of course, but we must also answer the person asking the question. As a parent, I grapple with this all the time.

“Daddy, what are the colors of the rainbow?” my daughter asks me as a little test.

“Well, that would be red, orange, yellow, green, blue, indigo, and violet too” I respond to her in the singsong voice from the show Sid the Science kid. I answered both her and her question.

I could mention that it used to be 5 or 6, we only have 7 because Sir Issac Newton was obsessed with the number 7. (The reason for 7 may not be true but he did coin the 7 colors)

But the real answer is actually infinity. The rainbow is a spectrum of colors meaning you are seeing every just about every color in the visible spectrum, and all the shades in-between them.

The manner in which I answer depends on the person. With my daughter, I answer both the question and the person. There is a way she needs to hear the answer in order for it to make sense (she doesn’t get infinity yet or spectrums). It is (and always will be) a judgement call on how to answer these questions.

“Daddy, how are babies made?”

“Uh…go ask your mom…”

What the asker should know about the scientist is to a certain extent, we are trained to answer just the question itself. In the end, it doesn’t matter how we figure out that A does something to B (at least to most people), it only matters that we figure out how A indeed does something with B (ethically of course). We don’t have to worry about if B or A will understand our answer as to what they do. A and B are what they do. They are defined in this way, before and independent of how we define them. The functions of A and B will never change, we as scientists may only find a new or novel function for them. Their function is static.

You the asker however is dynamic and we should treat you as such. We are dynamic in how we do science as well, but that is another post altogether. You are from different backgrounds, you are from different cultures, you are even different now than you were 5 minutes ago (most likely, 5 minutes ago you would have said the rainbow has 7 colors). We must be dynamic in our responses, not static. But how?

Well, back to the question at hand, how to answer the “what do you do as a scientists” from the scientist point of view. This question can also asked as “what science do you work on?” It takes good judgement to answer because you must answer the question and person. I have previously given a funnel analogy to help here, but now I offer another bit of advice. This may be simple or well known, but it is often omitted.

Come up with a question that might demonstrate that they have unwittingly had experience in your area. Then, try to involve them in your answer. My example is I work with how bacteria process metals in the host, so my first questions are what do you pack in your suitcase (you bring things with you but bacteria can’t bring things with them when they infect you, so where to the get the nutrients they need to survive) and do you take vitamins (they contain the nutrients including metals I study). Find these questions, whatever your field may be. It has been my experience that when people are involved in the answer, they understand it better. There are of course more ways to answer the person and I encourage you to find out a way that suits you best. Maybe try talking to a non-scientist once they know what your project is about. Ask them what finally made the light bulb go off in their head in understanding your work.

Think of your best teachers growing up, what what their style? Did they teach just the subject material, standing up spewing fact after fact, or did they also teach and connect to you?

Talk TO the person to connect to them, not down, not up. TO the person, TO the asker. This is the best way to answer the question and the person, and they will understand what you say and do a whole lot more.



Scientific Distrust: To trust, or not to trust: that is the question.

A friend of mine recently had some TV problems. Issues dealing with good quality sound on some channels and bad sound on other channels. Was it the cords? The cable box? Are the cords plugged into the right place? Something wrong with the speakers? Call a friend for advice? Search online for answers from people that might have had this problem before? Ask a tech expert?

Here is one made up review on the issue “have you tried licking the cord, and then plugging it in?”

Um, no thanks, I’m good. Why? Because you want the information that you are going to try to be vetted well.

Now if 10 independent (and also made up) people said, try licking the cord, then plugging it in…well maybe you might think about it. Maybe. But they would need a YouTube how to video to go along with it!!! Or maybe if one person said it, and the comment was held in high regard by a well-respected tech website, then maybe the method will carry more weight.

So you try all these things and finally something works. You might not even be sure which of the 10 things you changed or tried worked. You might go back to see, but you are just happy that it works.

People do this all the time. Identify the problem and make it better. Well that sounds familiar doesn’t it? Congratulations, you are a scientist, or at the very least you used the scientific method to figure something out. Oh let it be your new phone or computer that is acting up, you will go to the ends of the earth to find out how to fix it. You will become almost obsessed. You have become obsessed.

Here’s the point.

Information is thrown at you constantly, all day every day. Make sure you vet your source. If the article says “Scientist say…” and doesn’t say which scientist, beware. If an article doesn’t cite a source, Beware. If the article only cites themselves as proof, BEWARE!!!

There is a lot of misinformation out there. And much of what “scientist say” gets distorted to make the story better while also getting lost in translation. But please, I beg you, at least make sure you find out the actual person who made the quote or the finding. If the article doesn’t mention who said it, maybe that source isn’t as trustworthy as you thought.

If you are going to go though all that research for a phone, all that experimentation to troubleshoot a phone, using collective opinions of experts from vetted websites for a phone, then why not do that with matters of science research. I’m not asking you to look up the primary source (which can be found here most of the time btw), but I am asking you to know who said it, at least before you quote it as fact. How can you trust someone and you don’t even know who they are?





What exactly does a scientist do all day anyway???



So we have Bill Nye, Dr. Horrible, Crazy mad scientist cartoon person, BeakerEinstein, and the question of the day. Most of this is meant to be humorous, however, sometimes that top right panel does creep into the public sentiment. Now later I will get in to who we are, why we do what we do, how we do what we do, and where (which places/settings) we do it, but for now, lets focus on the what.

I have made an oversimplification below, but there is a lot of truth to it. As scientists, we want to find out how something works, then we want to break it, or make it work better. That’s it. No really, that’s the essence of what we do. What does this gene do? What does this protein do? What does that pathway do? How can break this pathway if it occurs in something that causes harm (tumor, bacteria, virus)? How can me make it better if it is something we need for survival (a drug to lower cholesterol, a pain reliever, a surgical procedure to repair someone’s heart)? (Forgive my bio-medical bias)


Health Related Science 101


With me so far???

OK, now if you will, picture a funnel. This funnel represents our focus for science topic.  At the top of the funnel you have broad focus, the names of the ailments/diseases such as pneumonia, cancer, and cystic fibrosis. As we go deeper into the funnel we start to narrow our focus on a specific aspect of that ailment or disease. The further we get, the more specific our area (and the smaller number of people that understand/work in that area). For instance here is the path down of the “funnel” I work on…

Pneumonia –> Streptococcus pneumoniae (a bacteria that can cause pneumonia) –> bacterial survival (inside and outside the host) –> nutrients (because bacteria have to eat) –> metal (metals can be nutrients, check the back of your vitamins) –> metal regulation (must maintain the proper amount of metal inside) –> metal export (get the excess and bad metals out) –> copper.

How in the world did I get to copper?!?!?! Now I’m so deep into the narrow part of funnel that I’m almost stuck (I really need to lay off the cookies). With this example, don’t worry so much about the science topic itself, but know that each scientist has a funnel just like it. Actually, not just one. That is our process, it can get complex VERY quickly.

One of the major problems is as scientist, we start explaining what we do from the bottom of the funnel. I work on copper export in Streptococcus pneumoniae. oookkkkkkk…um…why???? Whats the point???? I work on Tyrosine-protein kinase zap-70. What in the world does that do? Because we start so low in the funnel to explain things we let down the public. We as scientist cannot in good faith expect you to meet us as where we are. Quite honestly, there are scientist in our own field that cannot meet us where we are in our respective funnels. Our focus sometimes gets so narrow that we  lose perspective on the big picture during our explanation to loved ones, friends, and random strangers. Please understand that our not stating the big picture does not make what we are doing unimportant nor does it mean we don’t know what the end goal is of what we are doing. We just need to come further up in the funnel to tell you whats going on and we need to practice that skill, because it is a skill that is lacking in our scientific community. So again I say, we want to figure out how something works, then break it or make it better. Now come on down the funnel with us, I guarantee you will learn something new. We do just about every day.



P.S. Einstein lost the rap battle on that TI-82 line

P.P.S Comments are welcome