User talk:Kdahlquist
From LMU BioDB 2015
If money was no object and you could pursue any other career what would it be and why? - [[Msaeedi23 (talk) 23:16, 7 September 2015 (PDT)]]
- I love my career and if money was no object, I would give myself a research grant so that I could hire an assistant and a technician to help me do what I love! I would be able to give stipends to more students in the summer and not worry about money for supplies or equipment. If you want to know what I would do for an alternate career, I would love to work in a bookstore (which I did in high school) or become an investigative journalist. I think that my research skills would apply, and I think it is a good thing to keep our elected officials accountable.
- — Kdahlquist (talk) 12:12, 8 September 2015 (PDT)
Hello Dr. Dahlquist! What would you say has been the most significant biological discovery made during your career? Thank you! - Nanguiano (talk) 13:30, 2 September 2015 (PDT)
To clarify: I mean the most significant biological discovery anyone has been made throughout the last decade. Nanguiano (talk) 15:29, 3 September 2015 (PDT)
- Rats, I thought that might be what you meant. That's such a tall order, I'll have to think about it some more...
- --- Kdahlquist (talk) 15:44, 3 September 2015 (PDT)
- Can I cheat and say the completion of the Human Genome Project (a little older than a decade now)? I really think that it marks a paradigm shift in biology that we are still in the middle of. Right now there is a lot of buzz about the crispr/cas system for editing genomes. Some are saying that it opens up the possibility of easily modifying the human genome and will lead very soon to genetically modified humans. I don't think it will be so easily implemented, but there's no doubt that this discovery has made it come faster.
- — Kdahlquist (talk) 13:40, 8 September 2015 (PDT)
If you were to turn back time and choose a different field of study, what would it be and why?
--- Jkuroda (talk) 15:34, 3 September 2015 (PDT)
- I have a hard time imagining myself in a different field because I love what I am doing so much. I have strong interests in philosophy of science and women's studies (and the intersection therof), so I might do that. I am interested in the question of how do we know what we know (epistemology) and how factors like gender, race, and class affect it (feminist epistemology). I am also interested in research ethics and the ethics surrounding various biotechnologies. I am actually an affiliate faculty of the LMU Bioethics Institute and will be teaching a seminar next semester on Issues in Biotechnology.
- — Kdahlquist (talk) 13:45, 8 September 2015 (PDT)
Where do you see the lovechild of Computer Science and Biology in 5 years?
- I think that computer science will continue the trend of becoming more fundamental to biology and it will become much more of a standard technique than it already is.
Since beginning this class, what changes have you noted in viewing each discipline individually and together? --Eyanosch (talk) 13:53, 5 September 2015 (PDT)
- One thing that I've noticed is that when we began teaching together in 2006, the open source software movement was just in its beginning stages, at least in bioinformatics, and best practices for software engineering were not necessarily being followed. Now both of those things have really gone mainstream, especially with resources like GitHub for managing code and project development.
- — Kdahlquist (talk) 13:53, 8 September 2015 (PDT)
Dr. Dahlquist, what has been one of the most challenging aspects of your most recent research project? Emilysimso (talk) 15:47, 6 September 2015 (PDT)
- I have four different research projects ongoing, so I'll answer one for each. In the wet lab there were a lot of challenges getting the microarray technology running in the first place. We were having a lot of problems getting uniform hybridization to the chips. It turned out that the chips themselves were faulty and when I got them from a different vendor the problems disappeared. The GRNmap biomathematical modeling project is very complex where we are estimating parameters from data. It has been a challenge to get the normalization for the data correct and to determine the gene regulatory network involved. For the GRNsight gene regulatory network visualization software, it has been finding the time to keep up with the students! And Dr. Dionisio and I encountered numerous issues this summer with XMLPipeDB, which you will be using in this class. Migrating to Java 8 broke the program and Dr. Dionisio had to rewrite large parts of it. For the bioinformatics projects especially, it is difficult to keep up because they are such moving targets, but I love what we do.
- — Kdahlquist (talk) 12:57, 8 September 2015 (PDT)
What would you was the most rewarding/exciting discovery and/or product you have made as a biologist?
--- Troque (talk) 18:48, 6 September 2015 (PDT)
- In terms of the wet lab, it has been really rewarding to make predictions about which transcription factors are involved in cold shock (like HMO1 or HAP4), do the experiment, and then see it is so.
- — Kdahlquist (talk) 13:58, 8 September 2015 (PDT)
Which science fiction authors do you consider to be your favorites? Is there any work of science fiction that has affected you in a personal way? --- Blitvak (talk) 01:26, 7 September 2015 (PDT)
- See this list for my favorites. Since I made this list, there are some others I would add. The Infoquake trilogy by David Edelman (an elementary school classmate) and the www:wake series by Robert Sawyer (just ordered the third book in the series) come readily to mind. I also love the Harry Potter series, especially books 5, 6, and 7.
- — Kdahlquist (talk) 14:27, 8 September 2015 (PDT)
What's your favorite animal?
Jwoodlee (talk) 11:08, 7 September 2015 (PDT)
- I like cats and lolcats!
- — Kdahlquist (talk) 14:32, 8 September 2015 (PDT)
Where do you see the future of bioinfomatics? -- Anuvarsh (talk) 13:03, 7 September 2015 (PDT)I
- I see bioinformatics becoming "mainstream" in the sense that it becomes regularized as a normal part of being a biologist, as opposed to being a specialization. Biomathematics is also trending in that direction. In the last decade at LMU, there has been a steady increase in students like yourself that are either doing some kind of major/minor combination with biology and computer science or mathematics or a biomathematics degree.
- — Kdahlquist (talk) 23:42, 9 September 2015 (PDT)
In what way do you hope that we grow as students throughout the course of this class? --- Malverso (talk) 13:37, 7 September 2015 (PDT)
- I would love to see you stretch beyond what you think you are capable of currently. I would hope that you take full responsibility of your learning and of your final research project in the course, making it truly your own. My best moments in teaching have always come come when students take it beyond what I have even thought of.
- — Kdahlquist (talk) 22:11, 10 September 2015 (PDT)
What is your favorite experiment in biology and why? (i.e. for its elegance or its significance) --- Kzebrows (talk) 16:50, 7 September 2015 (PDT)
- In 1992, Harry Noller and colleagues reported a simple experiment where they digested away 95% of the protein from the large subunit of the ribosome and demonstrated that it could still catalyze peptide bond formation in a simplified experimental setup. This was strong evidence that the ribosome was indeed a ribozyme where the rRNA performed the catalytic activity instead of the ribosomal proteins. I heard about this experiment during a talk given at an undergraduate research conference I attended and the audience gave an audible gasp when this was announced. This strongly influenced my decision to go to graduate school at UC Santa Cruz and study the ribosome.
- — Kdahlquist (talk) 22:56, 9 September 2015 (PDT)
What biology course did you find most challenging during your time as a student? --- Kwyllie (talk) 17:08, 7 September 2015 (PDT)
- The science courses that I found most challenging as an undergraduate were Organic Chmistry, Biochemistry, and Invertebrate Zoology. For Organic Chemistry, I just didn't have the cognitive structure in my head that showed me the connections between all of the reactions we had to learn. I saw them as disparate. I finally started to "get it" and see the connections in the final weeks of the second semester and have often wished that I had the time to take it over with the insight that finally clicked for me. Ironically, I never learned to interpret NMR structures very well, but ended up in an NMR lab for grad school. For Biochemistry, I understood it better, but I think was overwhelmed by the sheer amount of information. I didn't take my own advice of "slow and steady wins the race." Finally, I struggled with Invertebrate Zoology for the same reason as O-chem, funnily enough. I didn't really have a sense of the purpose and structure of the information that I was learning to "make it my own".
- — Kdahlquist (talk) 23:15, 9 September 2015 (PDT)
What is your favorite way to relax when you are overwhelmed or stressed?---Vpachec3 (talk) 18:35, 7 September 2015 (PDT)
- I like to read. Either something new, or one of my favorite books over again (see my answer to Blitv ak's question for a list of favorite books I turn to. Recently, I've liked to walk to Bristol Farms to get a coffee (decaf) and sit and read in their cafe. Although the last time I was there, it was all torn up with construction and I had to go somewhere else. :)
- — Kdahlquist (talk) 22:16, 10 September 2015 (PDT)
What do you believe will be the greatest achievement produced by genetics research this century? What role will computer science play in enabling this accomplishment?
--- Bklein7 (talk) 18:55, 7 September 2015 (PDT)
- I'm going to stretch your choice of the word "genetics" to include systems biology. I think in this century we will see the triumph of "indirect effects." We already talked a little about how we are currently in the genomics era, marked by a paradigm shift from studying things "one gene at a time" to whole systems. Even with this shift, there is still a tendency to attribute properties to "master" genes instead of networks or pathways. The shift will fully be complete when we banish this way of thinking. For example, we tend to think that drugs have the desired effect and then side effects. However, they are all just effects of a drug and it is just our conception of it that calls certain effects side effects. It is similar to the way that we call certain plants "weeds". We are also in the midst of a paradigm shift between the primacy of the DNA/protein world where RNA is simply thought of as an intermediate, to an RNA world where RNA plays a central role in gene regulation. I admit that my own research is DNA/protein-centric because for yeast, that is a pretty good paradigm. But to understand human gene regulation, we are really going to have to remake our models to take into account all of the effects of non-coding RNA. I think currently, we are trying to shoehorn these new discoveries into our old DNA/protein paradigm, where a new RNA-centric paradigm is warranted. See the work of John Mattick for details.
- — Kdahlquist (talk) 22:34, 10 September 2015 (PDT)
What is your favorite memory or event in your research career thus far? --- Lenaolufson (talk) 20:18, 7 September 2015 (PDT)
- This actually turned out to be a tough question! I'm going to answer it with a very recent memory. This past summer, I invited President Snyder to attend my last lab meeting of SURP to hear my research students present on their research. They nailed the presentation and I couldn't be more proud of them and their work. President Snyder was suitably impressed, which means a lot because his background is in mathematics and computer science. You can view their presentation slides here: http://www.openwetware.org/images/8/8f/DahlquistLab_SURP_20150624.pptx. [| Anu] (in our class) was there, so she can give you a first hand description as well.
- — Kdahlquist (talk) 22:42, 10 September 2015 (PDT)
One of your personal interests/hobbies is dance. What style of dance are you most interested in or find most fun?
---Rlegaspi (talk) 02:42, 8 September 2015 (PDT)
- I love watching any style of dance, watching So You Think You Can Dance is a guilty pleasure of mine. When I dance myself, I like folk styles the best. In grad school in Santa Cruz, I was in a Sacred Circle Dancing group and at various points have done Scottish Country Dancing. The former is very meditative and the latter is very energetic and fun. More recently, I played Dance Dance Revolution 3 on my Wii, but not since my son was born 3 years ago--no time!
- — Kdahlquist (talk) 11:33, 8 September 2015 (PDT)
