Thursday, April 20, 2006

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.

Monday, April 17, 2006

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?

Wednesday, April 12, 2006

Airlines -- United vs Delta

I've flown twice in the past month, each time being on different airlines. Usually there is at least a few months between flights, so I don't tend to notice much difference between the airplanes or the airlines. However, I've noticed recently that there are some big differences. All of these comparisons are in coach; I have flown United first-class before and did not have nearly as many problems as I have in coach.

United is the airline I have flown on the most. I always assumed that they were a better airline because they were slightly more expensive and I knew that my father preferred them. However, I found this past weekend that I was not very fond of their airplanes or their service. The flight was very uncomfortable in every aspect: the chairs were not proportioned correctly at all for my body size, giving me a headache; every setup they have for movie screens is horrible, they tend to either be too far away or right above you; the headsets they require you to use are uncomfortable; and they never have room for everyone's carry-on luggage.

I noticed a distinct difference between airplanes while flying United, as well. I flew on a Boeing 757 as well as an Airbus. The Boeing 757 was the most uncomfortable for 2 reasons:

  1. The first reason relates to the seats themselves. It seems that the seats are meant for anyone about 5'6" in height or taller (they can extend up). However, if you are short and do not have a lot of body fat to push you out from the seat in the lower area, the headrest pushes your head forward in an incredibly uncomfortable fashion. Sitting up straight is impossible due to the headrest, and slouching is impossible due to the lack of legroom.
  2. The second reason I disliked the Boeing was the fact that the underseat area for luggage was smaller for the aisle seat than for the other 2! I could not fit my bag easily under the seat, even though the same bag had fit fine on my earlier flights when I was in either the center or the window seats. This problem baffles me, and made my flight even more uncomfortable than it would have been in one of the other seats; ironically, I have always preferred the aisle.

The Airbus was only marginally better. The seat backs were still horribly painful to rest my head on, but slightly less so than on the Boeing. The aisle seat also seems to have the same size area for carry-on luggage as the other 2 seats. But everything else was about the same as the Boeing.

Delta Song was a MUCH better experience. I flew them last month, and was impressed by their planes and service and even more impressed after flying United this past weekend. They incorporate the movie screens into the backs of the seats, so that everyone has their own screen. This setup eliminates the problems of United's screen placement. Also, everyone can watch a different tv program or play a trivia game, making it less likely that you will be bored out of your mind. These screens actually make the provided entertainment entertaining as opposed to something to notice in the background. Their seats are also much more comfortable for those of us that are height-challenged. I was not forced to have my head at an awkward angle if I leaned back in my seat, which in itself makes me want to fly Delta Song from now on.

On a related note, they give you the small earbud headphones which do not pinch on your head as the other ones can, and they will always fit in your ear. I enjoy these much better, although I wonder if they are usable for people with hearing aids? Also, we did not have any trouble fitting our carry-on luggage on the plane. With United, they never had enough bin space for everyone.

The only problem with the Delta/Song acquisition is that Song is being phased out and soon everything will be just Delta. I hope they keep all the great things about Song instead of phasing those out with the name, because right now Song is the only airline I will actually put effort into getting tickets on. Previously I just picked the cheapest ticket, but if I can get a Delta Song ticket for a little more, I'd be willing to pay it (emphasis on "a little"...I'm still a poor grad student).

Too bad I signed up for United frequent flyer miles instead of Delta Song miles...maybe I should buy stock in Delta if they are going to keep the Song amenities.

Women in Computer Science

Visiting Google this past weekend for the Anita Borg Scholarship Retreat I had the chance to meet some great women in my field, as well as learning about some hard truths about being a woman in CS. There was some great discussion on academia vs. industry, that luckily was not overly pro-industry as might be expected.

One problem we see with academia is the path to tenure. As many people know, the path to tenure is arduous and coincides with the child bearing years. This problem of course affects women in all academic fields, not just CS. To succeed in her career, a women tends to need to make more sacrifices than their male counterparts. For instance, having a child is a very touchy subject. Deciding to have a family should be a personal decision, but many women feel that they cannot have a child and stay on top of their profession. As was stated recently in my department, there is no good time to have a child. Our culture expects our women to do the majority of child raising, but yet we do not construct our workplaces to make that possible. Something needs to give for the next generation of working mothers to be able to be successful.

One thing that needs to change is the path to tenure. Although it is extremely hard on women that choose to have a child (or children), it is also extremely hard on the men whose families have made the same decision. Many men seem to have stay-at-home wives to help them out though, but of course the women do not usually have that luxury. Should we sacrifice our careers for our families, or vice versa? Should both men and women have to sacrifice the younger years of their lives to ensure they have a job for the latter years (i.e. spend all their time working towards tenure)? If we truly value life as we claim to, the answer should be "no." Why get a PhD if you will still not have time for your family in the end?

Another problem that affects women disproportionally to men is the question of responsibilities at work. Apparently women tend to be put on more committees in academia (in CS) because the committees need a certain number of women faculty, and the percentage of women faculty tends to be low. However, the time spent on these committees is not considered a valuable use of your time, and does not affect your path towards tenure except for adding on the amount of time per day you need to be on campus and doing work. Also, women are more likely to be given the larger classes to teach. These two facts combine to cause women to be more likely to burn out in academia than their male counterparts. At least in Computer Science where the number of women is low.

Sunday, April 02, 2006

Meeting Famous People

While working on the abstract at my advisor's house, an old friend of hers stopped by. I knew who he was when I heard his name, because he is the author of the textbook I'm using in my independent study! I was also looking through some of his publications earlier in the semester to help with my research. He's an absolutely brilliant guy, but I still got to watch him play hide and seek with my advisor's son while we finished my abstract. Apparently he stops by to discuss papers on his way in and out of the country. But it was very weird to just suddenly be introduced to him, and just sit around and chat about research and related topics! In a way, it's a bit scary because I was constantly afraid of sounding like an idiot.

In a sense, this experience reminds me of the inaugural symposium I went to this past December for the Picower Institute for Learning and Memory at MIT. There were many well known speakers, including five Nobel Laureates (yes, FIVE) in the morning. Seeing that many brilliant people sitting together and discussing the future of neuroscience, philosophy, and related fields was breath taking. One of the most amazing people to be so close to was James Watson, who you should all remember in reference to the double helix of DNA. Even though he's gotten much older, you can see how well his mind still works. Some of the talks were really amazing as well, both academically and overall. If you want to read about this event, you can go to their webpage.

I hope that one day I can accomplish great things and be able to speak intelligently with these people, or at least people of their academic caliber. If I can get through my PhD in a decent amount of time, I have confidence that I will be able to be a success.