18 November 2009

Leafy Green Scientist: Environmentally-Friendly Pipet Tips

I figure there is a bit of overlap between vegans and environmental-types (myself being one with a foot in both camps), so I am going to post an occasional series on green issues in the lab. I don't think I'm stepping on anyone's toes here, plus all the blogs and teevee shows all are emphasizing green stuff, maybe this is all I need to be cool.

For the first installment of the Leafy Green Scientist (like it?), I shall review the edek™ Enviro-Ergo-Friendly Pipet Tips from ISC BioExpress. I will say at this point that I have received no compensation for this review in any way. I have only received a few sample tips from ISC, but only from my regular job as a lab rat and not for purpose of review.

When I first heard about these tips, I was excited. You don't see environmental issues being given much consideration with many of the products you order in the lab. But as I said, people are thinking green, and these pipette tips are an example of that. I saw them in another lab, and decided to check them out.

The edek™ boxes are paperboard, unlike most tip boxes which are high-density polyethylene (HDPE) or a similar plastic. And that is the extent of the green-ness of this product.

How is that green? Well, paperboard is recyclable. Which is good, but so is the plastic in regular tip boxes. Plus many scientists love to reuse the plastic boxes, either use with new racks of tips, or for other various lab uses. I've used them for everything from disposing of waste tips to blocking western blots. I suppose one could also reuse the paperboard boxes, but since they are not as strong or waterproof, their uses are more limited.

Paperboard is also biodegradable. Plastic is not, but then again I don't see many compost bins in labs. Nor recycle bins for that matter. If you don't have both in your lab let that be a big fat hint for what to do when you're waiting for that agarose gel to run.

So what's up with these tips anyways? Well, the real innovation is the addition of a rubbery TPE (thermoplastic elastomer) section to the top of the top, near where it grabs onto the pipettor. This makes it easier to seal onto the pipettor, in my testing. Since less force is needed to make a seal, a strong plastic box is not needed, and a cheaper paper box can be used. This can also be low-impact on your wrist when you put the tips on, but in my testing I still tended to jam it on there. Maybe that would change with continued use.

The implementation of the paper box in this case is one rack per box: There is no refill system. I'd think if they really wanted to be green they'd have refills.

Another caveat I saw in these pipet tips is that while TPE is conceivably recyclable, I have yet to hear of a commercial or residential recycling program that accepts it, especially an item that is part TPE and part polypropylene. Sure, most of us couldn't recycle any tips we use, even if we wanted, because they'd be contaminated with one thing or another. But I have recycled some of my tips in the past (especially if I'm just pipetting water or something). If I used these tips I definitely could not.

About the only concessions I'll give to the edek™ for green cred is that the box is not made from petroleum, and that some of the inks on the box are soy-based. Everything else I think is a bit of greenwashing, unfortunately. I may be being a hater, and shooting down someone for atleast trying to be greenish, but I want to call it how it is. I hope that ISC doesn't give up, but instead tries harder. You can do it! You'd already doing better than Fischer, as far as I can tell. Just don't stop there.

If any of you readers know of any other products I should review, either environmentally- or animal-friendly, just comment below.

10 November 2009

Poorly Designed Experiments: Shiv a Pig or the Terrorists Win

I have decided to highlight some of the bad as well as the good, in a new segment called Poorly Designed Experiments. I want to shame some of the bad practices out there, and point out some alternatives that would have avoided any animal suffering.

Our first inelegant experiment comes via NCBI ROFL, showing that I'm not the only one finding this paper to be laughable. Though I don't think the pigs involved were smiling:

Byard RW, Cains GE, Gilbert JD. (March 2007) Use of a pig model to demonstrate vulnerability of major neck vessels to inflicted trauma from common household items. The American Journal of Forensic Medicine and Pathology. 28(1):31-4.

Basically they stabbed "previously euthanized" pigs with pens and other objects to show that no matter what we ban from planes, we will never be 100% safe. Ignoring for the moment the whole charade that these pigs were wallowing happy under rainbows before they passed on painlessly before being used in this study, I have to say I agree with the basic purpose of this study: That security theater is not security.

But the fact that you can stab someone to death with innocuous objects has been proven time and time again, and no place with stricter security than the prison system. One only has to go to the San Quentin Prison Museum to see any number of weapons improvised from the scant items allowed to inmates. Need I mention that that list is a lot more restrictive than what is allowed on commercial planes (and yet they are allowed liquids), and even involves strip-searching. But there are still more than 50 homicides in prisons in the U.S. each year, and a greater number of injuries caused by improvised weapons. Sure, it's a small percentage of the population, but probably a lot larger than the amount of pilots and flight attendants who have been injured similarly. You may argue that those human deaths in out abyssmal prison system outweigh the culling of a few pigs, but then I was able to pull up that website without killing anything. I bet the researchers could have easily obtained photos and castings of wounds from these homicides, and had just as good, if not better, data for their study.

Basically it's the laziness of this study that bugs me. They drove to the hog farm and stabbed some pigs as opposed to contacting hundreds of prison hospitals and collating all the data.

Returning to the pig sourcing issue: I spent some time digging to find swine dead of natural causes. I can't find any information. I hear of this practice a lot in the literature, and on shows like Mythbusters, but it seems be be a black box. Whether this is some informal process where one can just call any old factory farm and they will just happen to have any number of offed pigs for you, or of there are some organized distributors out there I don't know. Either way, it supports the meat industry, either by saving a farm the disposal costs or by purchasing an otherwise unprofitable carcass.

Here are some studies that show similar information without killing pigs:

And here is something to make you laugh after reading about horrible eye trauma. It's more relevant than a unicorn chaser.

30 October 2009

Vegan Witchcraft (and Traditional Medicine)

I saw this conveniently-timed article today on a "Witches' Market" in La Paz. So I thought I could make my own seasonally appropriate post.

On the article itself: They mention surreptitiously putting powdered dog's tongue in a person's meal to make them fall in love with you. I'd think for many of us any effect would not last longer than finding out what we just ate, vegan or no.

Also, I liked this quote:
Garcia Fernandez says that most of the fetuses are the results of miscarriages, and the larger ones of still births. Some are obtained if slaughtered llamas happen to be pregnant.

Sure, It's still not vegan, but you could say it's vegetarian, depending on if you think life begins at birth or conception. I mean, some people think eggs are meat and not vegetarian.

What does this all have to do with science? Well, there is a short trip from love potions to traditional medicines for sexual dysfunction. Many traditional medicines have 'gone mainstream' to Western medicine (like aspirin, or even vaccines it could be argued), and in some places like China and India, there is less of a distinction between traditional and modern medicine.

There is a lot of work being done to give rigor and validation to these traditional methods. I tried a search for "traditional Chinese medicine" on PubMed and got so many results I couldn't pick just one.

Sure, many of these medicines are herbs like ginseng and ginko, but in China you can get a prescription for meat if you qi is low. Fortunately in this case, there are alternatives. Likewise, in the case above, the animal impact can be reduced. There is already pressure for alternatives to things like tiger penis and rhinoceros horn because of endangered species legislation and enforcement.

Now while I have spent this post showing how this related to veganism and science, what this whole mess needs is a booster shot of both. We need more science to prove that dog tongue does not induce love and rhinoceros horn does nothing more than accelerate the extinction of pachyderms (they are, look it up). This will reduce the number of animals killed for ingredients and the amount of humans killed by quackery. We need more veganism because there should be more pressure for animal-free versions of these medicinals. Whether it's of Western derivation, like a vaccine made with eggs, or of traditional origin, like herbs substituting for bear bile.

27 October 2009

Future of Vaccine Production

Heard this NPR story while getting my vehicle emissions test today. They don't have a transcript yet, but it basically shows how slow and inefficient current vaccine production with embryonated chicken eggs is. One tidbit I got is that one opts for the nasal vaccine and not the shot, you use only 1/100th of an egg as oppose to a full chicken abortion.

The hope is that they are starting to use animal cell lines, which while they may have originally come from an animal have long since stopped harming that particular animal. They mentioned a canine kidney cell line, as opposed to Vero cells (mentioned often on this site) as being a much better system for viral production.

Then they went a step further, and bring up a new caterpillar-derived system for making viral proteins for a vaccine. This was new to me. I was worried at first, because cell-free protein synthesis using wheat germ or rabbit reticulocytes ends up killing the heat or rabbit.

After some digging, I found that the system uses a cell line (and not fresh animals for each batch) from a moth, the fall armyworm (Spodoptera frugiperda) with help from Baculovirus. Exciting stuff.

Further reading:
1) Maiorella, B., Inlow, D., Shauger, A., & Harano, D. (1988). Large-Scale Insect Cell-Culture for Recombinant Protein Production. Nature Biotechnology. 6:1406-1410.

2) Ikonomoi, L., Schneider, Y.-J., Agathos, S. N. (July 2003). Insect cell culture for industrial production of recombinant proteins. Applied Microbiology and Biotechnology. 62(1):1-20.

Post Scriptum:
This post has been mentioned here. Thanks Mr. Dandelion!

23 September 2009

Eggless Swine Flu Vaccines coming to Europe

This is an update on a story being followed here. I was perusing the Baxter website for news, and found this out-of-date update. Deciding to do some minor journalism, I emailed them, and just got a reply from Karoline Traschler, Project Marketing Manager for Global Marketing Vaccines:

We thank you for your interest in our H1N1 vaccine. We expect European licensure by end of September. We have to inform you that it will not be available on the US market.

The last sentence is of concern, being stateside and all. I replied asking for clarification, but I'd imagine it'd have to do with the stricter drug safety regulations here (thanks a lot, thalidamide!). I'll keep you posted.

16 September 2009

Vaccines from Plants

I was browsing PubMed and stumbled upon a summary of the Third International Conference on Plant-Based Vaccines and Antibodies which just took place in June. I didn't manage to get access to the full article, but the fact that this has been around since 2005 piqued my interest. Sure, I'd expect that people are experimenting with vaccines in bacterial hosts, the same way any other protein is cranked out in E. coli. This was a little unexpected to me, so I dug deeper.

  1. Santi, L. (September 2009). Plant derived veterinary vaccines. Veterinary Research Communcations. 33 Suppl 1:61-6.

    This article is pretty accessible to non-biologists, and gives a good introduction to this research area. While it's focus is on vaccines for non-human animals, the techniques can clearly be used for human pathogens. I think the concentration on veterinary diseases is mainly due to the amount of testing (read: cost) required to get FDA approval. Edible vaccines also have the benefit of reducing the reliance on antibiotics in non-human animals, and thus slowing the evolution of antibiotic resistance. Conceivably this approach could increase mutation in antigens targets by the vaccines, but I still think that it's a net benefit.

  2. Tacket, C.O. (2009). Plant-Based Oral Vaccines: Results of Human Trials. Current Topics in Microbiology and Immunology. 332:103-17.

    This shows that for both bacterial and viral pathogens, this approach can work in humans. It also has the advantage of not having to involve needles nor chemical (or animal-derived) additives, and is much more stable. Seems to indicate to me that this economical approach will soon be the more common one.

  3. Chebolu, S., and Daniell, H. (2009). Chloroplast-Derived Vaccine Antigens and Biopharmaceuticals: Expression, Folding, Assembly and Functionality. Current Topics in Microbiology and Immunology. 332:33-54.

    I think I'm just a sucker for an exotic host for protein expression. The authors tout the smaller genome and other features that make it a good expression host, But I can see how this could even further reduce problems with allergies and so forth: If you have the vaccine grown up in wheat, and someone has Celiac's disease, you can theoretically transplant the chloroplasts into corn without having to retransfect with a whole new mosaic virus. That and I also like how they say right in the abstract how this can be done "an environmentally friendly manner."
So by no means exhaustive, but it sounds promising to me. It may be a decade before we're chowing down on quinoa for our booster 'shot,' but by that time one plant could literally be a panacea of vaccines.

30 June 2009

Scientific Vegan

Just read a post that was the converse of my site. Being more of a vegan heading towards science than the other way around. A Mr. Meaner at QuarryGirl.com undertakes some rigorous testing on food served at all-vegan restaurants in the Los Angeles area. They determined that a number of places had food contaminated with animal products, and in one case suspect foul play. Mostly though, as the trail is taken all the way to the Taiwanese goverment, they blame poor labelling at the manufacturer. And kudos to them for being so persistent. It is noted that new legislation in Taiwan on such matters goes into effect tomorrow and should help straighten things out. Expect a some changes at your local restaurants, especially the Asian veg ones.

I do see a few issues with the experiment. First, I'd like to know which tests specifically they used. As Schmod on BoingBoing points out:
For starters, are there any legitimately vegan ingredients that could register a false-positive on these tests? What is the effectiveness of the testing kits that they used? Why were they afraid to disclose the manufacturer of said kits?
Ideally the manufacturer's protocol and so forth could be published to eliminate these questions.

Also, I think they should have a better negative control than just the lab bench. That information is good, but ideally you want something in the ballpark of the other things being tested, perhaps a home-cooked vegan dish with known ingredients. Similarly, I think they should have found menu items that were the as close to similar as possible at each restaurant. I note that quesadillas were common, but I think they should have done only quesadillas (or close analogs like a taco or something). At the very least, only doing veg-chicken dishes or something with a single unifying common ingredient (or supposed common ingredient). I can't really compare a quesadilla to tiramisu.

All in all though, they did a good job, and i'd like to see more of this thing. Perhaps Mr. Meaner can repeat the experiment in a year or so after the labelling laws in Taiwan go into effect? One can hope.


17 June 2009

Human Lungs are Better for Testing than Rat Lungs

A good step in getting rid of animal testing recently, according to The New Scientist. Kelly BéruBé at the University of Cardiff has developed a way to scaffold human lung cells in 3d. This will allow for more accurate data over 2d cultures because it accounts for air flow and so forth, but also it will be more accurate over non-human animal models because it is using human cell lines. Remember, if we tested chocolate on dogs it'd be banned and if we tested strychnine on hamsters it would be counted as nontoxic.

Eventually the technique could be applied to chips, and theoretically be used as a substritute for the canary in the coal mine. Perhaps literally.


02 May 2009

Sucrose and Animal Bone Char

Sucrose (refined table sugar) is a common chemical used in the lab. It can be used in media for growing cells, but more commonly it is used to make solutions denser. I have used it instead of glycerol in Laemmli sample buffer for SDS-PAGE gels.

As many of you may know, the reason why most table sugar at the grocery store is white is because it is filtered through burned cattle bones. You may think that this could possibly be different in the lab. While you probably will not see turbinado sucrose in the supply cabinet anytime soon (if ever), there could always be the possibility that some chemical can be used for lab-grade sucrose that would not be acceptable for food-grade sucrose.. According to my cursory research this is not the case.

Bone char is not only a concern for vegans, but also for many protein biologists. A previous lab I worked in did a lot of sucrose step-gradients, and the primary investigators there were very concerned about protein contamination, and the bone char issue was something they discovered and had to deal with. Some of them had been working on prions, and because of the difficulties of prion decontamination they had also been looking into mammal-free supplies.

A message to Sigma-Aldrich garnered this reply from Harry Dapron, Technical Service Senior Scientist:

Sigma-Aldrich does not make this product and so I contacted our supplier of this product. They did confirm that it is bleached/filtered using bone char. I cannot speak of any other product because other sugars that you have referred to in general may come from several different suppliers.
A question to Fisher got a similar response. I did learn that product 4005 from J.T. Baker is NOT filtered with bone char. It seems like the higher purity versions may be more likely to be animal-free. If anyone finds out any more brands that are animal-free or not, let me know. I'm working on a database or chart that has all the info.

I wonder though if other chemicals are refined this way. I don't think any salts would be, as grocery-store salt is not. But would dextrose? Further research is clearly needed.

28 April 2009

Vaccines without Chickens

You may not know that 'vaccine' originally meant something like 'bovine.' They don't involve cows anymore, but they do usually use chickens. Or atleast eggs in development with a nascent and pliable immune system that can be manipulated to make antibodies. Like many crude methods, this takes time, is imprecise, and causes problems for people with allergies and ethical concerns.

So to work in another animal into this post, I heard a report this morning regarding swine flu. It mentioned a company that has found a way to make vaccines faster, and more importantly, egg free. According to Baxter's site, they use Vero cell cultures instead of the eggs. While originally derived from the kidney of a grivet, I feel it is so far removed from that long-dead monkey to consider that aspect to be ethically OK. Sure, people with monkey allergies and concern over hereto unknown prion diseases can object, but atleast it's not aborting factory-farmed chickens. One step at a time folks!

One concern with this methodology (and also with in vitro meat) is that Vero cells are typically grown with the use of fetal bovine serum (FBS). Thus exchanging chicken fetuses for cattle fetuses. Net gain of zero, unless you think the unhatched chicken eggs are vegetarian, but that's a slippery slope. I looked into it a little more, and according to a document on the Baxter site:

"Also, Baxter’s Vero cell system is capable of producing very high yields of influenza virus without the addition of any animal-derived serum."
That's possibly great news. I sent them an email to confirm. I'll post if there is a reply.

Swine Flu May Test Baxter
Baxter Vaccines
Vero Cell Backgrounder

26 April 2009

You're not alone, or alternately titled, There are More of us Than You Think

So I thought I'd start out with a show of solidarity. I often feel like I'm the only one making lunches complicated at work, but I prefer to think that we're just evenly distributed across the workforce.

According to a handy list on The Wikipedia, there are atleast two notable vegan scientists: String theorist Brian Greene, and molecular geneticist George Church. Clearly a list that needs some additions.

And while a slight tangent, there are a number of vegan M.D.s. To name a few there's Dr. Michael Greger (A former classmate of mine, actually, not to name drop), Dr. Neal D. Barnard, and T. Colin Campbell (of the China Study). There's even a whole organization for vegan physicians. Maybe soon there will be one for us too. Baby steps.

Like I said, needs some fleshing out (pun not intended). Anyone have additions? Signal-to-noise ration on my web searches is kind of low.

23 April 2009

Epic First Post!

Hello all. Or maybe just hello me at this point. In any event, I have started this blogarooni.

Basically I hope this site will fill a need I see out there. I'm vegan, and a scientist, and I don't want to leave my ethics behind when I'm in the lab. I always loved animals and most living things, and that's why I went into biology. I never really understood the "I like animals, let's kill one and study it." mindset that some biologists have. But I guess to draw parallels to eating, I'm sure people just don't think about it too much. Which is odd for a scientist, I suppose: To not be thinking.

But beyond the visceral avoidance of vivisection, as a vegan I am always looking at ingredient labels and trying to figure out what is what and where it comes from. I do it at the market and I reflexively do it the the chemical supply cabinet. But unlike food, for which there are endless guides and resources out there, there isn't much information on what lab chemicals are made from. I'm hoping to start remedying that.

So I hope to gather information on animal use and animal products, and share what I find out with the interwebs. I also hope to have some discussions about various questions that arise. I know when people think about vegan issues and discussion they think trollbait, but I am going to try real hard to keep things civil here. I don't want any fights people, so be nice!

So there you go. Not too much ramble was it? Let me know what you think. And feel free to drop a line with topic ideas or suggestions. This won't just be about Biology, but that's what I know best, but if you know that theres some animal issue with particle physics or something, let's hear it!