Eisen Lab Blog

Viruses as food additives

I find it sad that the world has come to this. The FDA announced that it has approved the use of viruses as a food additive. The particular viruses (known as phage in this case) target and kill common bacterial pathogens found in meat. It is entirely possible that this treatment will lead to reduction in deaths and illnesses. However, it is also possible that there will be unexpected consequences of this treatment and thus anything like this should be done with caution. What saddens me about this whole thing is that it is the wrong way to go about solving the problem. Most of the problem comes from the fact that our meat today in this country does not come to us in reasonable condition. The animals are usually kept in unsanitary conditions where diseases and nasty pathogens are prevalent.

The best way to think about this in my opinion is what I read in The Omnivore’s Dilemma, the new book by Michael Pollan. In this book he talks about how animals now frequently live in what can be considered the equivalent of the slums of the industrial revolution. Cities of animals, frequently wallowing in excrement, is not the best way to prevent bad microbes from getting in our food.

So in recent years all sorts of practices have been developed to kill these microbes in food products. Irradiation, for example. And now, viruses, sprinkled on your meat, to keep the bacteria from growing too much. Give me meat from animals that have not been swimming in their own shit and piss and I will be happy to take my risks without dumping viruses on top.

Deceptive advertising by Amtrak

There is this nice train out here that runs from Sacramento to Oakland called the Capitol Corridor. I really like this train overall since I can take it from dontown Davis to Berkeley and i takes about the same amount of time as driving but is much more relaxing. There are issues with the on time performance of the train but mostly even when it is late it is better than driving if you are going somewhere near a train station.

However, I am pretty pissed off at Amtrak for one of the things they advertise relating to this train. On the Capitol Corridor web site, the highlighted item is frequently a promotion saying “Take the train to Oakland A’s Games this season”. It sounds great since there is now an Amtrak stop right at the Oakland Colliseum where the A’s play. That is, until you look at the train schedule. For night games there is simply no way to take the train to games. This is because the trains stop leaving the stadium at about 8 PM, or just after night games start. Even for day games there is not much offered in the way of getting to and from games on a reasonable schedule. Even when there are technically late trains for Amtrak, most of the trains do not actually stop at the Colliseum. So I am having a hard time figuring out what they mean by “Take the train.”

In other cities in which I have lived they reserve a train to leave just after the game ends. Not here thye don’t (or at least they do not advertise this as an option). It seems lame to promote this idea and then to not have the trains to back it up.

SciFoo Camp Day 3

For Day 3 of FooCamp, I drove over to the Googleplex so missed out on the sociology of the bus. It is always interesting as a meeting progresses through the days to see people who did not know each other previously become more and more comfortable with each other. I supose that happened here too, but Jason and I wanted to be able to scoot on out of there once the festivities ended.

We had another high-quality google meal for breakfast, although it seemed that the nutritionist may have not been given full control since the majority of items at the meal were fried or soaked in sugar or oil (i.e., bacon, french toast, etc). But the food was still good and if one did not like it one could always grab some organic snack inside.

On a side note, I kept cracking up every time I had one of these “Organic FoodBars.” This was funny for two reasons. First, the name of the bar reminds me of something from the movie Repo Man where in the background of scenes, various food items are labelled as “Beer” or “Food.” But the other reason these bars were funny is that everyone kept talking about foobar, which is another one of the O’Reilly folks meetings they are planning and a play on words.

Anyway, this was the day I saw the presentation on HowToons.Com (see earlier posting). I did go to a few other good sessions, but I confess I also spent a decent amount of time in the camping area of the googleplex chatting with other people. I made so many good connections at the meeting it seemed like that was certainly as much in the spirit of the whole thing as going to all the sessions would have been. Eventually had a final scifoo wrap up session where the powers that be asked us for critiques and suggestions for improvement.

In my glee to report on the great aspects of this scifoo, I may have given the impression that all was perfect. This was not the case and there were areas in need of much improvement. I and others brought some such issues up in the discussion here. One thing that was really somewhat unusual and ironic that was less than ideal was how they presented the information from the registration to other scifooers. When we registered on Day 1 we filled out a slip of paper listing five key words or phrases to describe oneself. I figured, this would get converted to electronic format and posted on some web site somewhere or used in some type of RFID tags to meet like minded folks. I mean, we were at Google, for heaven’s sake. But no, instead what they did was simply print out our pictures onto the forms (they were about 4 inches by 8 inches) and then post all the forms on a board. Generally, the whole thing was useless, as people wrote in tiny print and not always very legibly, since they had no idea they would be posted in this way. There were other things in need of work but most of them were minor and unnlike in many other contexts where people point out problems with something at scifoo the audience actually proposed solutions to the problems too. That was a nice touch from my point of view, as it is easy to complain and generally hard to find solutions.

Then, just like that, it was over.

SciFoo Camp Impressions Day2

You know a meeting is good when you simply have no time to check email let alone write in a blog. That was the case at scifoo and is why I am writing now a few days after the fact.

Day 2 was much more epic than the first since of course it was a full day of fooing. I managed to get up pretty early despite the late night (well, I cheated a little compared to others – I was up late but had only half a glass of very bad “single” malt). Many people looked a little rough around the edges in the morning in the hotel lobby… Nothing too surprising there as those who flew in, especially from overseas, met the wrath and illogic of modern airline security. The people from the UK in particular had some pretty good stories about being told they were not even allowed to buy books IN THE AIRPORT to bring on the plane. You might think then they would at least shut down the book sales, but of course no, that would cost them money.

So with TSA delays and jet lag and possibly some drinking I am not sure how they made it out early in the AM. We then all piled into a google provided bus and headed over to googleplex again. The conversations were lively along the way, although some of them had nothing to do with scifoo.

Then we got to googleplex for breakfast. As with food the night before, the food was mostly top notch although never pretentious or wasteful. Although I must say there were some unusual things mixed in (like some pretty heart attack inducing pieces of breakfast cake). I am sure the google nutritionist we met the night before was not overhwlemingly in favor of those items. Yes, google does in fact have some type of nutritionist. I never talked to her in detail to find out what that meant, but I did talk to a few scifoo folks about my theories that she was really a spy (she just seemed to pay way too much attention to all of the actual sessions to simply be the nutritionist; plus she always seemed to be talking on her two way radio). Maybe she had something to do with my theories about the addiction of the word google (see my previous post about this issue). Nutritionist – addiction — seems like there must be a connection there.

Anyway, then the sessions began. Here’s how it was set up. Outside, there was a coutryard with a paved patio section and a giant tent with tables for eating. Inside the main door was a giant room with camping stuff laid out all over the place (in homage to previous foo camps where people really camped). You had to walk through this open air camping section to get to the large grid showing the sessions being offered (people were still filling out session offerings throughout the day). Some sessions were downstairs near the camping room, and others were upstairs and a short 2 minute walk away. In addition, we were near a large cafeteria which including these giant bins with snack food (most of it on the healthy side of snack food which was fine with me) and a large fridge with a diversity of drinks.

I spent much of the day going to sessions relating to “open access” or “citizen science” but triedto force myself out of my box as much as possible. Among the most memorable sessions I went to were one on biology inspired robots (they had a robot gecko that could climb using millions of tiny hairlike projections like geckoes really use). See this Berkeley news release for some examples. Overall, the day was great. I got to catch up with some colleagues, and hang out with my brother who had been unable to come the night before. I also went to some great sessions on exploration (including of the earth’s oceans and of Mars).

Not much was disappointing, although I was still somewhat dismayed to see how scientists support open source software, and open access to data, but then do not always support open access to publications. When asked why, they give the lamest explanations, like, “well, that is just the way it is done.” Perhaps most tellingly, the technology and engineering and physical sciences folks seem to get the Open Access to publications movement more so than the biologists and other life science folks. Maybe that is due to the existence of the physics archives and things like that. Or maybe biologists do not like to speak up when there were multiple folks from Nature there, and they did not want to jeopardize their chances of getting a Nature paper. I think the real explanation is that many of them are, how should I put this politely, afraid of change (note I wanted to say chicken shit there but then decided to be polite).

Anyway, overall the day was great. I even did a presentation jointly with Tom Knight from MIT, where he discussed genome engineering and small genomes and I discussed how one studies mcirobes in their natural environments. I only wish I had thought of this more in advance and had done fewer slides and simply drawn on the board or just talked since we did not leave a ton of time for free discussion. Nevertheless, there were lots of people there and lots of really good questions were asked. Tom even inspired me to consider working on the group of organisms her works on (mycoplasmas, spiroplasmas and their relatives which are these really interested bacteria that do not have cell walls and tend to have really small genomes).

What I noticed happening was that as the day progressed, people spent less time sort of wandering around aimlessly between or during sessions and more time talking to other scifoo folks in the camping area of the main room. In addition, the google herders, in their black shirts, were frequently out in this area also having discussions (in addition to being positioned carefully at all intersections where we might wander off into nofoo land and possibly bump into some magical new google initiative we were not supposed to see). Message to google – you should be careful of the folks with the wandering insect like robots since they did not attract the attention of the intersection guards. In general, the google herders who were there were all very helpful and generally engaging but never obtrusive (they reminded me of stories Ihave heard about the staff on survivor who are always there but try to mostly stay out of the way).

And eventually, the main sessions came to an end and we wandered back outside for dinner in the open air or under the tent. By then everyone seemed to at least have someone they felt comfortable talking to and everything was much less awkward than the night before. Not to say that all was perfect – there were of course the awkward moments and some highly strange people. But unlike many conferences I have been to, since this was a pretty select crowd, even the highly strange people were generally quite interesting once you got past their veneer.

So eventually people piled in to the buses and went back to the hotel. Of course, the night could not end there. But this time, instead of going to the lame bars, we decided to have a party in the hotel lounge. A few of us went out and bought some stuff to drink at a nearby store and we then had a quite pleasant evening talking about Mars, evolution, Nature, and scifoo in the hotel lounge. The only drab moment was when the receptionist came in and said something to the effect of “guests are beginning to complain about the noise” that we shut the doors and talked a little more quietly. I even came up with a good term to use in a new paper I am working on thanks to some of the Mars exploration folks who were there. Eventually, I went to sleep. And thus Day 2 did end.

SciFoo Camp Highlight1 – HowToons and Science Education Reform

I am going to post some blogs on some of the more interesting things I saw at foo camp.

I think by far and away the thing that made the biggest impression on me at scifoo camp was HowToons. From their description:

Howtoons are cartoons showing kids of all ages “How To” build things. Each illustrated episode is a stand-alone fun adventure accessible to all. Our Howtoons are designed to encourage children to be active participants in discovering the world through Play-that-Matters — fun, creative, and inventive — and to rely a lot less on mass-consumable entertainment

In this day and age, science, math and engineering is becoming more and more important for the world. And yet despite much lip service, we seem to be doing a pretty poor job of reaching out to kids and to people not currently interested in these areas. I have been involved in this area for some time and have seen a bunch of different approaches:

  • When I was an undergraduate at Harvard I and another student (Alison Lingane) pushed Harvard to create an undergraduate major in Environmental Studies that covered science, policy, economics, etc but did not take any “pro” or “anti” environment position. The secret goal behind this was to bring science to students who might end up becoming lawyers, congresspeople, senators, etc. Harvard created such a major a few years later called Environmental Science and Public Policy.
  • When I was a graduate student at Stanford, I served on the committee that was charged with redesigning Stanford’s science, math, and engineering requirements for non science majors. (A little aside – although this was over 10 years ago now, the web site I created is still up here – it slipped through the cracks of the Stanford delete mafia). In the end, we came up with a plan to create full year integrated courses that covered a particular are and had science, math, and engineering embedded within the course. None other than Condoleeza Rice was in charge of the committee and I thought the idea for the new courses was so great that I helped design and then teach one of them (a course on heart disease). I was really proud of this course (and won Stanford’s biggest teaching award to boot). But in the end, I think college may be too late to reach students and get them to really appreciate science, math and engineering.

That is why I was so excited about Howtoons. This is one of the most creative and elegant ways to reach out to kids I have ever seen. What they have done is create hands on modules to teach various principles of the world (some engineering, some science, some math). These modules are based on having kids create experiments out of various household goods they have lying around (e.g., 2 liter soda bottles play a big role). The modules are just stunningly cool (I would want to do them as an adult). For example, they have one where the kids make their own safety goggles out of soda bottles, or make ice cream with explanations about why it works. But that is not the best part. The best part is that the instructions for the modules are done in comic books, with beautiful artwork, and entertaining side stories, and are things kids would actually want to read. If you have kids, or do are involved in any way in K-12 science, math or engineering instruction, you really have to check out Howtoons.

They are coming out with a new book soon that enbeds all of their best modules. You can make preorders on Amazon.

Some other cool education related activities were discussed at scifoo. One of the others that stuck with me was a presenation about using the online world SecondLife for education. I will try and write more about that in a later posting.

My 18 month old daughter is in love with google

So I just got back from a 2 day trip to Googleplex for scifoo camp (more on that in other posts). And my wife told me that she mentioned to our 18 month old daughter Analia that I was at Google, as if that would mean anything to her.

And now she cannot stop saying the word. She says it and giggles. If she hears me say it, she starts repeating it over and over again and thinks it is the funniest thing in the world. Here is a video of her saying it.

She loves goofy words, and asks me to repeat them whenever I say them (e.g., I said the word booty the other day and now she says that a lot too – I guess I have to be more careful around her now).

But for some reason google is the best word in her book. Maybe this is part of their secret to success. They have discovered a word that is secretly addictive. I mean, we know that different words can stimulate different parts of the brain. And these guys were at Stanford after all, where there is some pretty good language and neurobiology research. Maybe the key to this whole thing is the word.

Imagine if they had named the system “searchies.” That would give me the heebiejeebies every time I used it. Or how about “smeagol.” Not too appealing either. I may have to enter my daughter in a reeducation camp of some type. Fortunately, I live in Davis, CA, aka the People’s Republic of Davis, so I am sure there are reeducation camps here.

SciFoo Camp impressions Day 1

So here I am back in Davis after an exhausting and pretty exhilarating 2 days.

Friday, I drove from Davis to Sunnyvale the location of the hotel all scifoo camplers were staying at. I stopped on the way in Walnut Creek, to pick up Jason Stajich another one of the scifoo participants (a new Berkeley post doc who works on things related to what I do and thus who I already knew). We saw little traffic in the drive from Walnut Creek to Sunnyvale (it was Friday PM but the traffic was in the other direction most of the way).

We then dumped our stuff (well, I had to change rooms first. My “non smoking room” smelled like someone hung up the sheets in a smoking lounge at the aiport for a month) and hopped on the bus to Googleplex. We had no idea what to expect.

Got to Googleplex and we herded off the bus into a reception area where we picked up some typical conference goodies (name badges, the obligatory logo bag). But already things smelled a little different when they gave us some type of puzzle box for our personal entertainment. Then they proceeded to have use write down some keywords describing our work and they took our pictures (these were later merged together and put up on a bulletin board so you could see if they was anyone else there you just had to talk to). I confess, I never looked at the board. I thought it would be almost against the spirit of the whole thing to seek out people I had some commonality with. I wanted to get to know people I would otherwise probably never encounter.

Then we got the first glimpse of the Google wonderful obsession with decent food. I have been to conferences with really good food and really bad food. This was the first conference/meeting/workshop that I had been to where the food was abundant and potentially healthy (as in, there were always somewhat healthy options) and yet never overbearing. Not only was the official lunch and breakfast and dinner food quite good, but they had these collections of drinks and munchies freely available throughout the day. This included a diverse selection of organic and/or vegan snack items which made me quite happy as I have been drifting more and more towards organic foods and even a litle bit towards vegan foods for some time.

There was a giant tent outside (maybe this was in homage to the foo “camps”, although I think it might have been a permanent fixture there). And we mingled. As at most meetings where I knew very few people, it was a little hard to feel comfortable at first. Do you simply go up and introduce yourself to people “Hi, I’m Jonathan, and I work on evolution” or do you just find the one person you know and stick to them, or do you sit down at a table and mix anonymity with sociality? I chose the latter option and began to get to know some of the scifooers (not sure wat the offical term is for participants in these things).

Eventually, after mingling for a few hours, we were herded inside to a large room and we got the “introduction” to the meeting. The introduction was minimalist but and then we spent about an hour or so, going around the room giving a few words about what we work on. This was not the most useful thing in the world but at least it was not too tedious. This was because we were instructed to say only three words (I was way at the end, after some pretty good humorous lines were used so I just said “intelligently designed evolution”). Some people went over their limit, but it did not drag out too long. There were some pretty good little ditties in this session — only later did I realize that some people knew what to expect in advance and probably had been thinking about this for some time.

That evening we had a few mini presenations but the key to the evening was the unveilling and the signing up on the giant scheduling board. Basically, there were slots for rooms and times. Some rooms were big and some were small. And people signed up for topics in the rooms. It was quite chaoitic op by the board while this was going on – people trying to decide things like “Do I sign up for a big room, or is that too arrogant” or “Should I do more than one presentation”. I did not initially sing up for anything ( I confess, I had not really come prepared to lead a discussion – having not really understood what scifoo camp was going to be about).

The other key to the evening was the adoption of Chatham House rules. This I guess is some British thing whereby nobody is allowed to attribute anything to an individual without their permission. So if someone there said they thought someone you knew was a rube (someone told me this), you could post it in your blog (as I just did) but could not say who said it, without permission. This supposedly would make people speak more freely. I think this was not necessary for this group of people as a did not sense that people were holding back on saying anything negative for fear of attribution (I did see some serious sucking up going on in various venues but when you have the founders of google walking going to sessions, as well as some of the biggest names in various fields it is hard to avoid some fawning).

Eventually, evening number one at Google came to a close. I STILL did not know what to really expect for these open sessions, but I was getting to know people and having a pretty good time (except for the missing reading bedtime stories to my 1.5 year old daughter). We took the bus back to the hotel and it seemed to early to crash so a bunch of us went around the corner from theo hotel to what must be one of the lamest bars in the South Bay (when we walked in one of the patrons complained that we did not have enough women with us like he was going to somehow magically hook up if only there were more women there). But a group of use did hang out there for a couple of hours (the single malt we ordered tasted more like gasoline thant anything else but hey – gas is expesnive these days so maybe they did the switch with good intentions) before wandering back to the hotel (we peeked in the other bar – it was even more suspect than the first).

SciFoo Camp, the prequel

Just got back from a mind and life altering experience. I was a participant in the first scifoo camp, a shindig put together by O’Reilly and Nature and held at the mythological Googleplex campus in Mountain View. I was first invited to this scifoo camp in an email in June from Tim O’Reilly himself and Timo Hannay the director of Web publishing for Nature.


We’d like to invite you to join us the weekend of August 11-13 for
Science Foo* Camp, a free, invitation-only gathering produced by
Nature and O’Reilly Media, and hosted by Google at the Googleplex in
Mountain View, CA. (See the end of this message for more about Nature
and O’Reilly). ……

I confess, I thought this was a mistake or some spoof by a friend since they addresed the email “Dear John” I never use John, always Jonathan. The thing was, the letter seemed so realistic, with details on the hotel and other people who were involved, etc. So I did what any respectible other person would have done. I googled the crap out of all of the people’s names and other details in the letter.

For example I had no frigging idea what this “foo camp” concept was. So I found some old stories about a foo camp last year, where the people actually camped at the O’Reilly headquarters in N. California. This sounded cool to me but also a little wacky since it seemed from reading the few blogs and stories about this that the event had no real schedule and that people sort of showed up and just gave presentations without a detailed plan. Of course, most conferences I go to have detailed schedules and I hate them since the best part about conferences is the talking at the coffee breaks or hanging out in pubs or doing something other than going to canned talks. In particular, the quotes they had at the end of the invitation email made me interested in going:

“The controlled chaos and the random encounters with very interesting people is just what I needed. I learned more than I expected, and got infected with new ideas. Who can ask for more?”

“Big kudos for having the courage to try a self-organizing event and for having succeeded WAY beyond belief!…Foo Camp was truly epic.”

Though I was still not sure if this whole foo camp thing was real or not (more elaborate scams have been pulled on me before) the upside was clearly high – a geek gathering at Google headquarters, just a 1.5 hour drive from Davis where I now live. So I wrote back saying I would come and then waited to learn more …

Human Evolution and Neanderthals

Well, I suppose everyone should have seen this coming. An announcement has been made of plans to sequence the genome of a Neanderthal. The plan is to take DNA extracted from a Neanderthal fossil, and sequence it using a relatively new method from a company known as 454 Life Sciences.

I am torn about this project. Yes, it is cool to read DNA sequence from an extinct species, especially one that has not been around for some time and one of direct relevance to understanding human evolution. On the other hand, I would personally find it much more interesting to try and sequence an ancient Homo sapiens first. This is because the comparison of the Neanderthal to modern humans may not be the right comparison. It would be better to first compare an ancient Homo sapiens sample to modern humans, maybe with both being done with the same methods to be used in the Neanderthal study. This would be for two reasons. First, we do not really know how well the method(s) they are using work. And second, if the methods work well, it is possible that some of the differences they observe would actually be due to degradation or damage to the DNA sample. Therefore, if they simultaneously did work on an ancient Homo sapiens they might better be able to calculate which differences are do to real differences in the Neanderthal DNA and which are due to damage to the sample.

Assuming they do something like this and they are able to detect differences in the Neanderthal genome. What then? In the end, the major area of interest will be population genetic analyses trying to figure out how long Homo sapiens and Neanderthals were separated for and whether there was any interbreeding. To figure this out, they will need more Neanderthal samples and ancient human samples. Nevertheless, it is always good to do something that brings attention to the public for scientific research.