Thriving in a multidisciplinary world: technical & communication skills are key

So fun! We got to learn how to say good morning in Portuguese to start off the talk on Managing Scientific Data in a Multidisciplinary world by Claudia Bauzer Medeiros. Halfway through we also had a Tolkien reference! If 10AM seems early to you, this was a talk you could enjoy despite sleepiness.

As Claudia says, we are drowning in data and need to be able to help scientists in other areas cope with that problem. This includes models and visualization as well, which is right up my area of interest! Of course, all of this also means that you need not only technical skills but great communication skills, which seems to be the theme of the conference thus far.

Some of the points made really relates to a lot of what came up in the Santa Fe Institute Complex Systems summer school this summer: you need to learn how to work with people from other disciplines and learn to speak their scientific language to have success. Of course, she calls this Data-driven science, which is different from what we call it in complex systems, but that's because she is coming from the data analysis side. I love that she had an image combining experiments, archives, literature, and simulations as facts used to help answer questions but that it's not enough: you also need data and information from collaborators not just your own set of it.

What I really love about all of this was the point that we are in an interdisciplinary world, and this should inform how we teach computer science. The implication, at least from my perspective, seems to be that the future is in collaboration between computer science and other fields and we need to prepare new computer scientists to succeed in this environment. One point here was how to get access to data as often people are not willing to give it up. Thus the Tolkien reference: the data is their "precious!"

I was not expecting, however, a section title slide called "Emotion." But the point was still a great one: you need to get people emotionally involved to have cooperation. This all ties back into the point of communication abilities being key for collaboration, as it is very difficult to have a successful conversation with someone if you can't understand their perspective on the subject.

Thesis Proposals

Well, a few weeks ago I passed my thesis proposal. For our proposals we have a 1 hour talk that is open to the public, the audience can ask questions, and then after the audience Q&A only the committee members and the student stay in the room. They then discuss the work, what they think of the proposed work, etc. Then the student is kicked out of the room while the committee discusses the work further, then the student is let back in to be told that they passed and what the committee wants to see for the thesis to be considered complete.

I was actually nervous, even though I essentially knew I'd pass. I think many of my practice talks went much better than the real one, but everyone said it went well and that they were intrigued by my work. Our department chair actually stopped by my cube last week to ask a question, give a suggestion, and say he was really interested in what I was doing. So it seems to have gone well! Also, multiple students have stopped me to talk about it and how it might apply to other fields, so I'm feeling better and better about it!

Now is the crazy part: all I have left to do is finish it! My goal is to be done in May 2011, although I hope to finish most of the main research before next fall so that I'll be ready to start sending out applications. How exciting!

Environment and GHC Occasionally Collided

On Friday Mary Lou Jepsen spoke about her experiences with the One Laptop per Child and her company Pixel Qi that she started to continue that work. Apparently then have shipped approximately 1 million laptops already. In one African country an 11 year old girl created a laptop hospital to fix the broken laptops for other kids, after figuring out how to fix them herself. The laptops come with 6 extra screws, as Mary had envisioned the laptop to be fixable by the children themselves. I think this anecdote is yet another that supports the idea that girls are just as likely to be interested in computers as boys, as long as you don't tell them they shouldn't be (implicitly or explicitly).

I was also impressed to hear how little power these laptops take, and that they can be charged with a bicycle, cows walking on a treadmill-like device, and other non-traditional energy sources. According to her graphs, if a large number of people began to use these laptops instead of their traditional laptops, we could save a significant amount of energy. The laptops have innovative power saving capabilities, as the screen is exceptional in its low power usage, and the hard drive and processors are turned off whenever they aren't being used even if the computer is still on. Any action by the user essentially turns them back on immediately, so the user doesn't really notice that anything was turned off. How cool is that?! These laptops have so many capabilities that it would be great to have on ALL laptops!

Not only do I love that there is such an innovative laptop, I also love how environmentally friendly the use of it is. I wonder, of course, how environmentally friendly the actual development of the device is compared to other laptops. I hope that one day we can make computing have a much lower environmental impact, and maybe this laptop is a step in the right direction. Any guesses on how long that will take?

On a related note, GHC was overall much more environmentally friendly than usual. Every attendee was given a reusable plastic water bottle and encouraged to use that instead of plastic cups throughout the event. ThoughtWorks gave out organic cotton paper that when planted will bloom flowers, NetApp gave away organic chapstick, the free Microsoft t-shirt was made with organic cotton, and overall a lot less "stuff" was given away. Although it's always fun getting stuff, we really don't need it. There were even bins at the conference center for attendees to place any unwanted free stuff, that would then be donated to local schools. I think it's great that the organizers took the time to try to be more responsible toward the environment, and I hope the trend continues for future conferences.

Mary Lou Jepsen's thoughts on being a women in Technology

On Friday Mary Lou Jepsen spoke about her experiences with the One Laptop per Child and her company Pixel Qi, but she also gave suggestions on how to approach being a woman in computing. She quoted Gloria Steinem as saying "Sexism is still confused with nature as racism once was." Although the quote was initially referring to Hillary Clinton vs. Barack Obama, it still applies that often gender is the most limiting factor in equality today. Personally, I hope we can work to change this for the next generation.

She said that you should always negotiate before accepting an offer, because it helps them think of you as a good negotiator and then they'll give you better jobs later on. Getting that extra little bit is important in the beginning (before accepting an offer is your best chance for the next 2 years to make a change like that), but letting them know you'll negotiate is possibly more important.

She reminded us all not to give up too easily as well. She claims that getting your degree (PhD, if relevant) is very important as well. Although we see men who have succeeded very well without finishing their degrees, we don't really see women in that position. Having the degree will give you that extra believability, and make it harder for people to discount your ideas and criticisms. This is important more for women than it is for men, due to that inadvertent/invisible/unacknowledged sexism problem.

The biggest point and my favorite point is that it all boils down to confidence. When she was taking testosterone, her entire world view changed. She suddenly thought of herself as the smartest person in the world, she was always angry, and she was always thinking about sex. Nothing was different in her life but the testosterone. She feels that these feelings came from the same place as the self-doubt without the testosterone came from: being unsure about herself. Although the story is funny, it also points out that quite often the same feelings manifest themselves different ways in the different genders. What she wants everyone to learn from her experience is that when a guy is giving this type of attitude, stand up to him; he's not any more sure that his idea will work than you are that your idea will work. Don't let that type of attitude stop you, know that it means that you have a good chance of winning if you don't give up. I think this is advice that many women in technology really need to hear, as often the biggest barrier to success is dealing with the people who seem to want to put you down no matter what.

Her last piece of advice is to give credit to others, and stand up to take credit of your own work as well. If you give credit, people are more likely to believe you deserve the credit you ask for. Take advantage of the fact that you'll be easier to remember because you look different than the millions of guys in your position, and that companies will be more likely to remember you; so if you do something good, that reputation will last well.

GHC Keynote Fran Allen on Diversity

Both of the keynote speakers at GHC have been very interesting. On Thursday we were honored by hearing Francis Allen, the first woman to win the Turing Award (the highest award in the computing field). I actually had the honor of meeting Fran Allen on the shuttle ride from the Denver Airport to the Keystone resort. She's a great lady, and definitely has strong opinions about where the field of computing is going as well as the state of women in our field. Although she spoke primarily of technical aspects of the field during her talk, she also spoke on her beliefs about the reason the number of women in computing dropped, based on her experiences in the field. Apparently, in the 1960's the field of computing started to become a major at universities and was based out of engineering departments. Well, engineering departments were primarily male, so suddenly women who were entering computing from other fields were blocked from entry as they didn't have the engineering knowledge that was suddenly defined as necessary. So by the 1970's the number of women had dropped in the field, and the glass ceiling started to exist.

This is a view of the problem that I've never heard before, and find very interesting. For everyone who actually thinks that women don't belong in computing or aren't capable of being in computing, this could finally convince them they are wrong. Not only are women now a large number of engineers graduating each year (I believe it's around 50%), which proves that we are capable of being engineers, it also proves that women have always been interested and the reason they left is that they were pushed out by sudden strict requirements. Of course, these are things that most of us believe anyway, but maybe a true history of the changes in computing would help remind everyone that men are not automatically better at it, they just shaped the field in a way that preferred them at the time. We have bigger problems to look at too, like visibility and perception of computing, but if we can work on increasing everyone's knowledge of how our field became defined it may help the rest of our work as well.

My favorite quote from her talk is that she is "both honored and concerned" about being the first woman to win the Turing Award. If you want to read about the technical aspects of her talk & her views on awards, the GHC Wiki page on her keynote has lots of details (written by me!).

JK Rowling Gives Harvard Commencement Speech

Sorry, I'm a little behind on the news it seems! But perhaps not all of you have seen this speech yet.

Both the video and transcript of her speech

Today I ran across a link to the speech that J.K. Rowling gave at Harvard's commencement this spring. Among other things, this speech gives insight into why her characters are the way that they are, and why the evil characters are evil in the ways that they are. It seems that she values empathy and compassion above many things, mostly due to her experiences working at Amnesty International while in college. It was great to see the speech that she gave, both because it echoed many of the thoughts I have had over the past few years and because it helped give insight into who she is besides the author of the Harry Potter books.

Cancer Stem Cells

Event: Robert Weinberg
Date: Tuesday, April 18, 2006
Time: 4:30 PM to 6:00 PM

This talk was on cancer stem cells, a topic very pertinent to my research. The beginning of the talk was on basic cancer information, which made it very obvious that it was occurring at an undergraduate venue (Amherst College). He did reaffirm a few numbers for me though, such that a cell can only split a max of about 50 times and that that probability for mutation is very low (at most 1 in 1x10^6 according to him).

The later part of the talk was actually on stem cells, and was interesting after we got past the description of what the different types were (stem, progenitor, differentiated). Apparently it is possible to separate stem and non-stem cells from a group by the proteins they each have on their surface. The stem cell will have a different type from the other ones. So, you can bind a die to an antigen that will bond with only the stem cell protein, and then bind dies to antigens that bond with the other cells' proteins, and use light refraction to see the different colors and separate them out. That is very interesting for both cancer and regular medical/biological research.

Also interesting was a discussion on whether or not tumors are organized hierarchically like regular cells are. In regular sets of cells, we have stem cells that are a sort of "super parent" in the fact that they can create any type of cell (most people would know this just from the regular news). These cells can create progenitor cells (he called them "transit-amplifying cells" and I like to call them "blast cells") that are capable of differentiating into a specific type of cell. The children of blast cells eventually become differentiated cells, which are basically a mature cell that will not change its function during its lifetime. Blast cells can also create more blast cells, and when stem cells split they create a new copy of themselves (so that there is one blast cells and one stem cell). Originally it was assumed that tumors were only made of mature cells, and that stem cells did not exist in a tumor as stem cells are less likely to mutate. There was speculation that a tumor cell might incur a change that turned it into a tumor stem cell, however.

So, at this talk he described a study showing that tumor stem cells did indeed exist. A group apparently split apart tumor cells the same way that regular cells were split apart, using antigens. Tumor initiating cells appear to be a small minority, which is a property of stem cells. This makes sense, as other cells would be unable to split enough times to form a proper tumor, although personally I'm not sure that limit would still be in place in a tumor cell. When an experiment was done with the separated cells, however, it was found that the cells they thought were stem cells could create a tumor in a mouse if only 200 of them were implanted whereas 20,000 of the others failed to form a tumor when implanted. Usually researchers implant 100,000's of cells to get a tumor growing, so it is interesting that only 200 of a specific type would be necessary. This experiment is why many agree that tumors do have stem cells.

One implication from the existence and ability of tumor stem cells involves metastasis, which is when a tumor migrates to another part of the body or tissue to become cancer. If only tumor stem cells are capable of growing a tumor, would only tumor stem cells be involved in metastasis? If so, could we stop metastasis by killing the stem cells?

There are still many things that are not known though. For instance, no one is sure if regular stem cells are likely to become tumor stem cells. Since stem cells don't replicate often and the majority of mutations are going to occur due to replication (or at least be spread by it), it seems unlikely. Most people currently assume that progenitor cells are the ones that become tumor stem cells, as they are only slightly different from stem cells to begin with.

There are treatments out there (he named "Gleevac") that can kill off all of the tumor except the stem cells. So once you stop with the treatment, the tumor is just replenished from the stem cells. Companies would like to make a treatment to kill the tumor stem cells, but no one can figure out how to do that without killing the healthy stem cells as well (which would probably kill you in the end, as the body is constantly killing and replenishing cells). The reason the current treatment doesn't work is that it ruins a cell's DNA, and cells that split frequently end up dying because they can't fix their genes in time to split. However, stem cells don't replicate frequently, so they are able to repair the damage before splitting.

So if we can research tumors in a similar way to regular cell growths, and figure out how to get rid of those stem cells, we've cured cancer! Which of course is easier said than done.

Global Climate Crisis

I saw Al Gore give a talk at Google on Friday, April 7th, and even got to shake his hand afterwards. It was a great talk about the state of the climate changes and global warming. I was incredibly impressed with the fact that his talk concentrated on the facts, and was not political. There were of course political jokes here and there, and slight pokes at the current administration, but I do not feel that they detracted from the point he was trying to get across. The Q&A session afterwards had more of a political agenda due to the questions that were asked, but overall I think it was very well done.

Below is a summary of what he talked about, including quick facts. All of this information will be in the movie coming out this year entitled An Inconvenient Truth, which I recommend seeing and plan to see myself.

• He calls it the "climate crisis" because "global warming" doesn't truly encompass the issues, and makes it sound less like a local problem
  
• The word "crisis" is written as a combination of 2 characters in Chinese, one for "danger" and one for "opportunity" -- this tidbit of information is a good summary of the talk
  
• There are a lot of global places that are showing signs of global warming: Mt. Kilamanjaro is out of glaciers, and Glacier National Park is out of glaciers, for 2 examples.
  
• You can compare the amount of CO2 in the atmosphere by checking the amount in glaciers (they save the gas in pockets of air) and comparing it to numbers taken over the past 40-some years. The amount of CO2 has never gone over 300 ppmv (parts per million), but is now at 400 ppmv. 45 more years of following the same increase trend as the past 40 (there was a graph) would be catastrophic due to the large amout that would then be in the air. We are talking exponential growth here.
  
• The actual temperature of the ocean is higher than predicted by an actual computer monitor taking only natural causes in to account. A computer model that predicted the increase based on human interference from 30 years ago has accurately predicted the temperature up until now. That model shows it to continue to increase at a rate that will probably kill off most of the sea life in our lifetimes.
  
• In March 2004, Brazil had the first typhoon in South America; a very big sign of changing global climates and ocean temperature.
  
• We are having more flooding and more drought: the heavy rains cause flooding, but due to the rains all coming down at once the aquifers do not have time to refill, causing drought in the non-rain time.
  
• Glaciers:
  
  • We have lost 40% of the thickness of hte arctic glaciers
    
  • There is currently a higher temperature increase at the north pole than at the equator. If these glaciers melt, the ocean will be warmed a great deal because these glaciers currently reflect a majority of sunshine in the winter months. If this warming occurs, the therma-haline pump between Canada and Europe could stop working, which currently helps control the ocean temperature and warms Europe. Europe could be thrust in to an ice age if this happens, with high consequences to the rest of the planet as well.
    
  • Larsen Ice Shelf in Antartica disappeared. It is just completely gone, this huge piece of ice. The small melting areas tunneled to the bottom of the glacier, heating the water and causing the land based ice to fall.
    
  • Land based ice melting causes the ocean height to rise, because that water was not part of the ocean previously. Water based ice melting does not cause the ocean height to rise, because it was part of the ocean to begin with.
    
  • Greenland melting (which it has already begun to do visibly) will raise sea levels worldwide by 20 feet, as all of those glaciers are currently land based. Currently 50 cubed miles are lost a year from the Greenland glacier. If this melting is not stopped, all of the Netherlands (not to mention most of Florida and many other regions) will be entirely under water in our lifetime.
    
• Due to this warming, there is less frost on the ground during winter, and therefore invasive speacies come sooner. This is causing devastation to whole forests and other natural habitats.
  
• Coral has died in the Caribbean because of warming ocean temperatures.
  
• There will be more infectious diseases and mosquitos due to this warming, as they will be able to survive easier.
  

The year to fear is 2050...yes, if things keep going as they are, we will have a flooded and possibly uninhabitable planet by that time.

If you take nothing out of these bullet points, there are 2 things I want you to remember. First, 53% of the news puts global warming in doubt, whereas 0% of actual scientists doubt it. Big oil companies and others are literally paying people to act as specialists and claim that global warming is fake. Two, we are basically the one big country that has not ratified the Kyoto Protocol, and it cannot succeed without us because we output much more CO2 than the other countries, even per person. The rest of the world understands the problem, and wants to fix it but for some reason we are too worried about what it will do to the economy. But by not following the Kyoto Protocol and decreasing our emissions, we are losing some of our economy. For instance, our car makers are suffering right now; if they made more fuel efficient cars they could sell them to other countries, but right now they can't because their cars are not up to the standards required!

There's no reason not to try to fix our mistakes and save the Earth. Otherwise, our children might be the last generation before we plunge back to the dark ages or become extinct. It really is that imminent, and something really does need to be done about it.

If you are unsure of terms or why I think something matters, just ask. I did a semester project on global warming when I was an undergraduate, I took a geology class where we discussed much of this, and I have a full year of college level chemistry behind me. I could write a post on each of those bullet points I think, but I will refrain from doing so for now. However, it really is a very important topic, and we really need to take care of our planet because IT'S THE ONLY ONE WE HAVE!

Please see his movie or research more on this topic (preferably not in the american news, as there are many lies there) if you are not already familiar with the key points. If we do what we are capable of doing with the technology we have now, we actually CAN get our CO2 levels down to that of 1970! It's only a matter of trying and making the government know that it should be a priority! Because really, what's the point of fighting terrorism and finding cures to diseases if we aren't even going to have a planet in 50 years?