The 'Natural' Human Diet

image by yummiec00kies

Oftentimes, I have an idea for a post and I procrastinate. Then something else comes to my attention that dovetails with the original idea.

Such is the case now when I watched the Daily Colbert tonight, where the guest was John Durant. He spoke about his new "caveman" diet/way-of-life that he thinks is our one true diet. We should be eating more meat, and no bread. People in paleolithic societies live to ripe old ages as long as they don't die in early childhood. All our diseases are due to our eating "modern" (read: 'processed') foods. And other such nuggets of folk wisdom.

Now you may think that the whole fAtkins diet rebranding gets my knickers in a twist because it's contrary to the vegan thing you heard I like. But that's only a small reason, if any. Mainly it's this whole nostalgia for the past that never was. The cartoon version of primitive humans taking a bite out of a mammoth simply isn't true. I think Wikipedia has a good summary. The concept is just a continuation of the whole natural-is-automatically-good-for-you mantra that just bugs the heck out of me (arsenic, uranium, strychnine, poliovirus, all natural! they must be good for you!)

Durant's main point seems to be that we should eat the diet we have evolved to eat. He just thinks that in the 10,000 years since the dawn of agriculture humans have not evolved.

This brings me to the original item I was going to post, that shows that we have evolved since then. It points to an event that changed our bodies more than agriculture has, that being that Promethean moment we started cooking. Primatologist Richard Wrangham has many interesting points in the podcast, and I plan on digging in to his book (pun intended) for more.

The point that stuck out for me, especially as someone who has done more polyacrylamide gel electrophoresis (PAGE) than is probably good for them. As anyone who has poured their own gels, or had to dispose of used gels knows (or perhaps, only those of the above who read the MSDS), the acrylamide monomer of the gel is described as a potent neurotoxin (atleast when tested on cats).

Yet our friend C₃H₅NO is found in starchy cooked foods that most of us eat every day. Those very same unnatural breads and pastas and baked potatoes that raw-foodists and paleo-dieters flee from. How can this be? Richard Wrangham and others (including your humble narrator) think this is one of many evolutionary adaptations that modern H. sapiens has gained since cooking and processing food.

And I find it especially funny (if morbidly) that much of the negative health indications derive from animal tests, as in the aforementioned one with the poor kitties. If we tested chocolate on dogs, we'd never be able to eat that either (and that's a processed food too). But if we tested all-natural raw strychnine in guinea pigs we'd be in for a shock when that product hit the shelves.

Im not saying we should all load up on deep-fried vegan twinkies, I just think we should eat healthy, and not eat something because it's natural. And of course, eat without killing animals. But you knew that.

If we Find out What we Eat, Do we Find out What we are?

A few new techniques have popped up that are illuminating the food web a little more clearly.

The first caught my ear through the Science Friday weekly video. Two NYC high schoolers, Brenda Tan and Matt Cost, took samples of a number of food items (as well as some amusing non-food specimens) sequenced thw COI gene in the mitochondrial DNA, and checked the 'barcodes.' This method is fairly robust, because using mitochondria you can type from hair and other non-cellular samples, and "even sequences as short as 20 nucleotides could be used to match to just one of the tens of thousands of species in the database."

The project is billed as this general interest science piece, but it has implications for the target demographic of this blog in a few ways, mainly relating to proper labeling. In this project and in a previous project done by the same mentor, many mislabeled products. A few were engangered species, including Sebastes fasciatus, or the Acadian redfish. Though the main trend was to 'downpour' and sell cheaper, more common species in place of rarer and more expensive ones. Even so there is an impact on the environment. Depending on who is doing the mislabeling, as it could be the original fisherman or harvester, this would be skewing much of the data being collected on sustainable wild harvesting of many foods. As this technology becomes more readily available it will be easier to have more accurate and less obfuscated information at the disposal of conversation groups and so forth.

Another point of interest I saw in this project was that this approach can easily be used by vegans in more focused truth-in-labeling tests, similar to those mentioned previously here. And in fact, would be cheaper and more accurate than the specific tests performed in that instance. I think I shall email those folks and see if they are game for it. They clearly have better funding than I.

The second item in my foodweb amalgam post is concerning a technique used to tell diet of an animal (or person) from samples of bone collagen and hair keratin, using ratios of radioactive carbon and nitrogen isotopes present. The study comes via the recently-moved NCBI-ROFL, and is a test on the extent of the infamous Maneaters of Tsavo horrible diet. The study seems like a proof-of-concept of the technique on a flashy general-interest subject to drum up support (nothing wrong with that). I can also see this technique being used to clear up some things of interest to us folk. Were primitive humans mainly meat-eaters? Was Hitler a vegetarian? And for the vegetarians, it could perhaps verify if the milk and eggs are from animals that were not fed other animals.

French Stop Testing Oysters on Mice

Yes, you read that right. I heard this first on the radio, but there are better text versions here in English and here en français.

The gist is that since oysters are filter-feeders in the big wide ocean, and not raised in a closed system of a farm, and they can pick up pathogens pretty easy. So there are naturally food-safety concerns (ignoring the heavy metals and toxins). So many governments started testing digestive fluid from the oysters by injecting it into mice and seeing if they died (the mouse bioassay, or test de la souris). Very base test. Fast forward a few decades, and most governments find faster, cheaper, more reliable, less cruel ways to test the pathogenicity of oysters. Yet up until recently, France was shelling out money (yuk-yuk) for the old muricidal method. Finally, they have switched to the better-in-almost-every-way chemical test.

Why did this happen? Seems many French oyster farmers were upset that mice oftentimes die even if the oysters were 'clean.' This would mean whole regions of coast would be banned from selling oysters, and many people went bankrupt and so forth. So the oysterfolk complained, and eventually got the change they wanted. I can find no indication that any animal-rights groups were involved (they dropped the ball)

Now I am glad that more mice are living, but upset that perhaps more oysters will die. I am more glad that another unreliable animal test has been ditched in favor of a more reliable cruelty-free test. Though I can not find out precisely which test they are using now, it is a good point to bring up when people tell you that animal testing is 'needed.'

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.

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:

• Turbin R, Maxwell D, Langer P, Frohman L, Hubbi B, Wolansky L, Mori M. (September 2006) Patterns of Transorbital Intracranial Injury: A Review and Comparison of Occult and Non-Occult Cases. Survey of Ophthalmology. Volume 51, Issue 5, Pages 449-460
• Patton N. (5 March 2004) Self-inflicted eye injuries: a review. Eye. 18, 867–872.
• Lunetta P, Ohberg A, Sajantila A. (December 2002) Suicide by intracerebellar ballpoint pen. The American Journal of Forensic Medicine and Pathology. 23(4):334-7.
• Ramaswamy R, Dow G, Bassi S. (2006) Pencil Is Mightier than the Sword! Pediatric Neurosurgery. 42:168-170
• Yamaguchi S, Eguchi K, Takeda M, Hidaka T, Shreshta P, Kurisu K. (2007) Penetrating Injury of the Upper Cervical Spine by a Chopstick. Neurologia medico-chirurgica. Vol. 47, pp.328-330
• Tenenholz T, Baxter A B, McKhann G M. (July 1999) Orbital assault with a pencil: Evaluating vascular injury. American Journal of Roentgenology. 173(1):144.

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

Vegan Witchcraft (and Traditional Medicine)

http://www.flickr.com/photos/10392797@N03/ / CC BY-ND 2.0

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.

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!

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.

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.

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.

http://www.quarrygirl.com/2009/06/28/undercover-investigation-of-la-area-vegan-restaurants/