User talk:Kam D. Dahlquist

Hi Dr. Dahlquist, I was wondering, after reading the Stewart and Janovy reading, whether or not you have ever thought about switching the specimens you currently do research on, for a completely different animal? Nicholas A. Rohacz 20:11, 23 January 2011 (EST)


 * When I was an undergraduate, I worked on an single-celled algae species named Chlorella pyrenoidosa. For two of my rotation projects in graduate school, I worked on the plants Ginkgp biloba and Arabidopsis thaliana.  For my thesis, I studied E. coli.  During my postdoctoral research, the lab was studying mice, but I was not directly involved with working with the mice myself, although I did take the training when I first started.  I've also worked with the fruit fly, Drosophila melanogaster, for a genetics lab I taught at another school.  It's only when I started my first faculty position that I decided to work on yeast.  Now that you have asked and I've thought about it, if I were to switch organisms, I would probably pick another single-celled one.  I'm most interested at what goes on at the cellular level and it seems simplest to me to work on that with an actual single-celled organism.  They are simpler than cells from multicellular organisms.  They are definitely easier to work with and the work is more straightforward because there is less complexity in these cells in general.  In my Biological Databases class that I teach with Dr. Dionisio in the Fall, the students create gene databases for different microorganisms, so if I was really going to switch organisms, I might pick a bacteria that we worked on for Biological Databases.  In that class we've worked on Vibrio cholerae, Plasmodium falciparum, Mycobacterium tuberculosis, Mycobacterium smegmatis, Helicobacter pylori, Salmonella typhimurium, and, of course, yeast.

&mdash; Kam D. Dahlquist 13:23, 24 January 2011 (EST)

Hey Dr. Dahlquist!! Why did you choose to co-teach a math class instead of merely staying in the field of biology? Sarah Carratt 16:56, 16 January 2011 (EST)


 * The short answer is that Dr. Fitzpatrick and I do research together and we were both interested in sharing our common interest with students in a class. As to why I am interested in biomathematics in the first place, the field that I work in has become math-intensive in order to analyze and model the data.  What we are able to do by combining our efforts in biology and mathematics is much greater than what either of us would be able to achieve alone using just biology or mathematics.  Research is becoming more and more interdisciplinary as the problems get larger and larger and require expertise from different areas to solve.

&mdash; Kam D. Dahlquist 18:52, 17 January 2011 (EST)

Hello there Dr. Dahlquist! After reading Janovy, I was wondering if you can recall your earliest memory that might have lead you to the career path you have chosen? Carmen E. Castaneda 08:36, 16 January 2011 (EST)


 * I don't know how old I was (sometime early in elementary school), but my parents bought me a book called something like Charlie Brown's Big Book of Questions. In that book, I learned that all life was made of cells and that a human had trillions of cells in his or her body.  The book also talked about matter being made of atoms and I wondering about the relationship between atoms and cells, like which was bigger or smaller.  My parents were good about fostering my interest in science and in junior high school I participated in a summer CTY program in Biology at a local high school.  Biology was one of my favorite classes in high school, so in college I continued along that track, most interested in how cells work.

&mdash; Kam D. Dahlquist 19:26, 17 January 2011 (EST)

Hi Dr. Dahlquist! I was wondering why you chose to study cell biology other than any other discipline in the Biology field?Alondra Vega 11:57, 16 January 2011 (EST)


 * If you see my answer to Carmen's question above, I was intrigued by cells from when I was very little. I would more properly call myself a Molecular Biologist as opposed to a Cell Biologist because what I am particularly studying is gene regulation which falls more into the area of molecular biology.  I am just really interested in how cells work at the molecular level.  I am interested in other fields of biology as they intersect with cellular mechanisms.  Now that DNA sequencing is so cheap, there are lots of opportunities for field and organismal biologists to ask cellular questions.  &mdash; Kam D. Dahlquist 20:33, 17 January 2011 (EST)

Hello Dr. Dahlquist. Perhaps a simple question for you: What do you think is the role of engineering in the field of bio research? James C. Clements 00:30, 17 January 2011 (EST)


 * Biology is becoming increasingly interdisciplinary and is pulling theories and methods from the mathematics, physical sciences, and engineering in order to understand the very large datasets we are not generating in biology. For example, genomics needs to make sense of the huge amount of information generated when a genome is sequenced, as well as other high-throughput methods that are regularly being used.  Other fields in biology are also generating large data sets such as studies in biodiversity. The fields of mathematical biology and bioinformatics are explicitly pulling from mathematics and computer science and are the ones with which I am most familiar, so I can be more specific about those.  We are going to be learing about gene regulatory networks later in the course; scientists are thinking of them as biological circuits and are applying principles from electrical engineering to understand them and also create them in the lab.  The field of synthetic biology is actively trying to engineer biological circuits.  A lot of the people in this field have pages on this wiki.  Conversely, I think that increasingly, engineers are getting interested in biology as a rich domain of problems to solve.

&mdash; Kam D. Dahlquist 19:58, 17 January 2011 (EST)

<!-- Dr. Dahlquist, I would like to know the work ethic that it takes to become a prominent scientist or member to the scientific community? Bobak Seddighzadeh 03:20, 26 January 2010 (EST)Bobak Seddighzadeh


 * Bobak, scientists work very hard with long hours. One of the difficult things about being a scientist is finding a balance between work and a personal life.  &mdash; Kam D. Dahlquist 21:53, 27 January 2010 (EST)

Hey Dr. Dahlquist, I was wondering what made you decide to become a professor in Biology? --Kristoffer T. Chin 15:48, 20 January 2010 (EST)

Hi Dr. Dahlquist! I was wondering how you decided to become a professor and what drew you to come work at LMU? Amanda N. Wavrin 21:12, 23 January 2010 (EST)


 * Kris and Amanda, your questions are related, so I'll answer them together. I have always loved school since I was a little kid, and I always admired my teachers.  So, I wanted to be a teacher since I was a little kid.  Each year I advanced in school, I wanted to teach that grade, so by the time I got to college, I wanted to be a college professor.  I went to college at Pomona College, which is a liberal arts college smaller than LMU.  I really liked that environment because I'm not just interested in biology, but in other fields such as philosophy, ethics, politics, the arts, etc.  I thought that if I could teach at a liberal arts college, I would have more opportunities to interact with colleagues in those fields in addition to teaching and doing research in biology, which I love.


 * Finding a faculty position involves an element of luck. The colleges and universities that have positions open in your field at the time you are ready to look for a job is a little random.  I was lucky there was a position open for someone in my field when I was looking.  When I interviewed at LMU, I was impressed by the collegiality and community shown by the faculty and students.  I liked how faculty were collaborative in their teaching and research.  I enjoyed the time I spent having pizza with the biology students in particular.  I'm very glad that I made the decision to come here.  &mdash; Kam D. Dahlquist 22:03, 27 January 2010 (EST)

Hi Dr. Dahlquist, My question is how did you become so good at using computers and websites such as this? J&#39;aime C. Moehlman 19:17, 20 January 2010 (EST)


 * J'aime, in a word, practice, practice, practice. I am motivated to learn new things because it helps me with my research and teaching.  I'm willing to try new things even though it can be uncomfortable at first, especially when I am first learning.  I am not afraid of making a mistake or breaking the computer.  I try to work with people who know more than me and I pay attention to what they do and try it myself.  I first learned how to use MediaWiki about two years ago.  Mostly, I just looked at other people's code and used trial and error to figure out how to do stuff.  Because I have so much experience now, even with something new, I generally know how to figure things out.  As you gain experience, you will be able to learn things faster.  So, be willing to learn and don't be afraid to try something new!  &mdash; Kam D. Dahlquist 22:08, 27 January 2010 (EST)

What's up, Dr. Dahlquist? (I had to use a different greeting than the two before me) Anyway, if you could choose one place in the world to live for a year, where would it be and why? --Alex J. George 00:17, 21 January 2010 (EST)


 * Alex, hmmmm. My favorite place that I lived in the past was Santa Cruz, where I went to graduate school.  I was sad to leave there after living there for four years.  It was a beautiful place to live, next to the beach and mountains.  Also, it had a lot of book stores, good restaurants, and whole food stores (the real kind that sells grains in bins, not the Whole Foods chain).  Two years ago, my husband and I traveled in Austria because I went to a conference held in Vienna.  I thought that Vienna would be a great European city to live in--great art, great music, great public transportation, great coffee and chocolate, but what we really liked was the lake district around Salzburg.  It seemed like it would just be a very beautiful place to live.  &mdash; Kam D. Dahlquist 22:15, 27 January 2010 (EST)

Good Afternoon Dr. Dahlquist, My question is if you were given the opportuinty to switch careers would you do so? And if you would what would it be and why? *Salomon Garcia Valencia 18:27, 23 January 2010 (EST):


 * Salomon, It's hard for me to imagine a life in which I wasn't doing science. All the things I could imaging switching to still involve science somehow.  I'm becoming more and more interested in politics and government.  AAAS offers fellowships for scientists to be advisors to the federal government for a year (either working for Congress or the Executive branch) and I might apply to do that sometime.  I'm also interested in investigative journalism, which is going away now that newspapers are dying.  My favorite non-science job I've ever had is working at an independent book store (although those are going away, too).  &mdash; Kam D. Dahlquist 22:20, 27 January 2010 (EST)

Dr. Dahlquist, what is your philosophy of teaching? How has this philosophy changed (if it has) over the course of your career? Janelle N. Ruiz 03:12, 24 January 2010 (EST)


 * Janelle, when you apply for a faculty position, you have to write a teaching philosophy. I add to this statement every year as part of my faculty service report (a yearly report on my teaching/advising, research, and service that I submit to the Chair of the department and Dean), and I updated it quite substantially as part of my application for tenure and promotion to Associate Professor last year.  The take-home message of my teaching philosophy is that science is a process and you learn it by doing it.  When I design a course, I reflect upon what I do as a practicing scientist and how break that down into manageable steps that students can take.  I reflect on what I know (with my head), what skills I have (with my hands), and the personal qualities that I need (with my heart) to do my science.  I try to include authentic research into my courses.  I would say that my philosophy has matured over time so that I have become more student-centered instead of teacher-centered.  I have gained a lot of practical experience that I did not have at the beginning on how to manage the logistics of a course.  I participate in the scholarship of teaching and learning which is a scientific way to approach teaching where I gather data on what and how students learn and use that information to improve my teaching the next time.  This course is very much in keeping with the philosophy that you learn by doing.  &mdash; Kam D. Dahlquist 22:37, 27 January 2010 (EST)

Hello Dr. Dahlquist, I wanted to ask if you hope to center on teach Bioinformatics full time at Loyola if you had a choice. I know that you were a great professor for Cell Function, but i feel as we got into Bioinformatics things got even better and seemed to be a very strong fit. Again, this would be only if it was your choice to fully teach Bioinformatics, or do you prefer teaching both? Kevin A Paiz-Ramirez 9:15 pm, 24 jan 2010 (EST)
 * Kevin, I like teaching courses at all levels of the curriculum, both lower division, like Cell Function, and upper division, like Biological Databases, Bioinformatics Lab, and Molecular Biology of the Genome. I also like to teach courses for non-science majors (even though I only got to do that once) and seminars for seniors (I've only done that once as well).  The one thing that I would like to do with Cell Function is to have the opportunity to take students into the computer lab to do some bioinformatics.  There is a lot we could do that would fit with the course, but because of the class size, there's no computer lab I can use.  I would like it even better if we could actually have a lab section for the course so that we could do some lab experiments that went along with the content of the course.  I really like teaching courses where there is some type of lab or practical aspect where we get down to doing real research.  &mdash; Kam D. Dahlquist 22:44, 27 January 2010 (EST)

Hi Dr. Dahlquist, I was wondering what was your first course that made you so interested in Bioinformatics? Also, what were your strategies in developing your skills? 00:26, 25 January 2010 (EST) Ryan N. Willhite


 * Ryan, I never took a course in bioinformatics (at least in the way that you probably mean) because those courses did not exist when I was in college or graduate school. I started teaching bioinformatics workshops myself when I was a postdoctoral researcher.  I got interested in the field because I was interested in how biological pathways worked in a cell.  But when I was in graduate school, people would take two years to clone and sequence a single gene, let alone all the genes in a pathway.  When the human genome project was completed, we finally had the technology to study all the genes at once and I was excited that we could start answering the questions I had about pathways in the cell.  To make the best use of this technology, we needed computer programs to analyze the data, so bioinformatics was a good fit for me.  &mdash; Kam D. Dahlquist 22:57, 27 January 2010 (EST)

Hello, Dr. D. What are you favorite and least favorite aspects of having a career in academia? Angela A. Garibaldi 23:47, 25 January 2010 (EST):


 * Angela, my favorite aspect of working in academia is that I get paid to do what I love--learn new things. My least favorite aspect is that academia is essentially a feudal system that has not changed much since the 1600's when it was invented.  It is set up so that the people at the bottom have very little power and the people at the top have a lot of power, with lots of step functions where the result is all or none (getting your PhD, getting tenure).  Also, there are still very few women at the top (full professors, administrators).  There is a lot of sexism and misogyny that go on that would not be tolerated in other sectors of society.  But still, I think this is the best career for me.  &mdash; Kam D. Dahlquist 23:05, 27 January 2010 (EST)

Besides the areas of your research (including Bioinformatics, ribosome structure, yeast, etc.) what other aspects of Biology interest you the most? Michael R. Pina 11:19, 26 January 2010 (EST)


 * Michael, that's a tough question, you've named all of my favorite areas of biology! :) I like learning about evolution because it is the foundation of biology.  I subscribe to both Science and Nature and I like to browse the articles to keep abreast of what's current in general in biology, so in some sense, I could say that I like it all.  Things that draw my attention tend to be "big picture" questions that look at things like a system.  That's why biology is so exciting right now because more and more researchers are asking system's level questions.  &mdash; Kam D. Dahlquist 23:08, 27 January 2010 (EST)

Week 4 assignment
Hi Dr. Dahlquist, I have a question on the assignment for this week. I am currently having a difficult time understanding Part 2 Activity 2 in calculating for Min and Max Difference. In the first table, I was able to use the Clustdist tool with one of my alignments with 3 clones. The page that it took me gave me a screen that looks like this

The problem I have is now calculating for the min difference and the max difference. I am not sure how i am supposed to select the highest and lowest pairwise scores. Do it add up all the distance matrix for the x-coordinate of S2V1-3 and then compare that to the other clones and use the smallest sum and highest sum and those would be my min and max difference after multiplication of 285?

I am also having a difficult time understanding how to look at the maximum and minimum difference across subjects. The instructions are a bit unclear --Kristoffer T. Chin 00:19, 13 February 2010 (EST) -->