18 December 2012

Nonvegan Fossils

Petrified Forest National Park fossil Cynepteris lasiophora, fern
Plant-based fossil of Cynepteris lasiophora
I believed I heard all of those thought-experiment vegan questions.  You know the ones, often asked by nonvegans and start "what if...."  But after about eighteen years of vegan life I heard a new one.  Are fossils vegan?

Well duh, of course fossils are vegan.  Now excuse me while I hot my head against the desk.

Unless time travel were involved.  Can't have the folks of Terra Nova making you fossils.

However, there are some realistic caveats.  Not all fossils are actually fossils in the way most people think.  Some are fakes.  Typically this is not an issue with the sedimentary rock ones, but with amber and ivory.  There is a whole industry in making amber-like jewelry and bric-à-brac by tossing insects into pine sap.  So it is important to know what you are buying.

There's a similar situation with ivory, which many nonvegans have ethical issues about as well.  Mammoth ivory is legal, most elephant ivory is not.  Less scrupulous vendors will mislabel the illegal elephant tusks as coming from extinct mammoths.  If you must buy ivory, do your homework.  But really, you don't have to buy ivory.  To me this treads into territory with fur coats and the like, where the appearance of a poor ethical choice can make it not worth the bother.  Plus many think the legal ivory trade fuels illegal poaching.

And to leave you on a head-hitting-desk note, what if the mammoth ivory is from a resurrected mammoth?

02 July 2012

Yummy Vegan GMO Tomatoes

Happy Tomato
Like many other rationally-minded vegans, I approve of GMOs.  After all, I have personally genetically engineered bacteria, so I have a broader understanding than many J. Q. Publics out there.  I understand that traditional breeding practices are genetic manipulation, just primitive, imprecise, and unpredictable.  This is often hard to explain to people, especially when they are defensive and reactionary.

However a recent news story came to my attention that highlighted how GMOs can be a good thing, and in a way that any random dude can understand.  To summarize, traditional genetic manipulation has given us crappy supermarket tomatoes which pale to fresh summer tomatoes from the garden.  Personally I'm not a tomato lover, unless it's made into marinara or ketchup, but I know I am in a minority on that.

You may say that the problem with tomatoes these days is an issue of goals and not methods.  Tomato breeders have wanted fruit that is primarily durable and disease resistant, and taste is a low priority.  If breeders focused on taste we'd be OK.  However, some of the genes for desired traits, such as uniform ripening, are the same genes that cause poor flavor.  It's almost impossible to breed your way out of that situation.  With engineering many, many versions of the gene quickly can be tried until one allows for both flavor and uniform ripening.  To do that with traditional breeding you'd have to sift through mutations of all of the ~35,000 genes in the tomato's genome.

This brings to the next point, which is if we can identify the desired genes for disease resistance, color, flavor, and all that, we can easily engineer it all into one tomato.  We could have that perfect yummy tomato within years.  However, if we have to breed it 'by hand' it will take decades or longer.  Sure, nothing will replace picking a tomato from the plant in your windowbox at the peak of ripeness on a summer day, but when you're desperate for a splash of red on your sandwich in November, shouldn't that tomato be good-tasting too?

24 May 2012

Animal-free Antibodies

I just found this unpublished post in my list.  I wrote it three years ago, but I hope it tides you over for my next post.
Antibody IgG2
Structure of an IgG2 antibody
Working in biology, especially biochemistry, one invariably has to run Western blots and/or immunoprecipitation. If these pan out, you might do an ELISA (or Enzyme-Linked Immunosorbent Assay if you never wrote it out). What all these depend on are antibodies. Something that still takes injecting a rabbit (or goat, or mouse) with something acting as the antigen, bleeding the rabbit a few times, and then eventually killing it. Not a very happy method for our mammalian buddies.

And it's often not a very effective method. You have to have many different rabbits to get one somewhat decent antibody. And even if you do eventually end up with a monoclonal antibody, it still isn't that reliable, as the existence of a antibody validation site like AntibodypediA shows.

Work is being undertaken to change both the unreliability and the animal welfare impact of antibodies. An article I read recently shows that while this research is still in early stages, it is getting results. The researchers vary a protein sequence using a computer database, and then select for binding efficiency with a column. The proteins are presented on a phage, which being a biological system can add to genetic variation on its own and thus improve selection.

It also reminded me of work being done with antivenoms (or antivenins depending on which flavor of English you speak). Currently antivenoms are obtained by raising poisonous animals, be they snakes, anthropods, or whatever. A dangerous occupation, as I saw first (severely scarred) hand on a recent trip to the สถานเสาวภา Queen Saovabha Memorial Institute snake farm. The venom is diluted and injected into large animals. In Thailand they mentioned using elephants, but outside of the tropics horses are often used, and more recently, sheep. The antivenom is basically an antibody to the venom.

Besides the above-mentioned issues with antibodies in general, antivenoms also have the trouble of causing immune responses in the afflicted individuals: Both to the antivenoms and to unrelated serum proteins in the antivenom dose.

The positive aspect of antivenoms-as-antibodies is that they generally do not change over time, as selective pressure is very low. That means that once one has a good antivenom, it will work for a long time before having to be re-engineered. Once you have a good binding site, you can make a synthetic antibody containing just the ends of the short and long chains, and replace the rest if the antivenom with something that doesn't produce anaphylaxis.

The Importance of Being Tyrosine: Lessons in Molecular Recognition from Minimalist Synthetic Binding Proteins. ACS Chem. Biol., 2009, 4 (5), pp 325–334; Publication Date (Web): March 19, 2009

02 April 2012

Vegan Kids and Omnivorous Kids

All Aboard!
I am the kind of vegan who does not like to stick out and be outspoken, but blend in and win people over with a softer approach.  I don't get offended if someone eats meat in front of me, unless they are making a big deal out of it.  I don't push my views on others, and wait for other people to initiate discussions.  I kind of like it when people come up to me and say they had no idea I was vegan. 

However, like every parent keeps telling me, everything changes when you have wee ones to raise.  I was not raised vegan, but turned when I went to college and had control over my diet.  I like when people can make their own choices:  I think people make stronger commitments when they see the merits in a change and do so willingly.  But with children, there is a lag time between when they can shovel food in their mouths on their own and when they can make an informed choice on what to eat.

As I mentioned, I have no personal experience with vegan kids.  I have been restlessly ruminating over how to handle my kid wanting to eat something that isn't vegan when he's too young to really get the concepts.  There's only so long that an authoritarian because-I-say-so will work without justification.  After all, why does Gwenessa get to eat the cheesy bacon and I don't?

I figured it out when watching Dinosaur Train.  This is a great science show, and despite the animation being less than what I expect from Henson, I can manage to sit through it pretty easily.  It doesn't drive me mental like Ni Hao Kai-Lan.  Though it is intended for an older audience than my little one.  But it has a paleontologist in every episode, so how can I not like?

Anyway, the characters on Dinosaur Train often "compare features" and also note what a newly introduced mesozoic creature eats.  The main characters are not vegetarian, but as the Humane Hominid at the Paleoveganology blog notes, some are happy herbivores.  No one tries to push their diet on another.  They just note and accept it.  It's a good model for children to understand different diets in a nonjudgmental way.  A quick search shows I am not the first to think of this approach, and that it works in vivo

Note that this is a good approach for teaching omnivores about vegans as well.  I imagine using the dinosaur analogy to explain to my kids' friends at some point as well, as long as the show it still on for the next few years (which I imagine it will be).

Though when my toddler starts asking about who Buddy's real father is, I know it's time to "Get outside, get into nature and make your own discoveries!"

21 February 2012

Vegan Black Scientist History Month

February is Black History month, and what better way to celebrate than to shoehorn my blog in there somehow.  While I was not able to find many Black vegan scientists (the best I did with my half-assed web searching was Nduka Okoh, so let me know of others), here are a couple of African-American scientists who made life better for vegans.
Percy Lavon Julian
Percy Julian was an American biochemist who synthesized drugs from plants such as our old friend, Glycine max. Julian capitalized on soybean's flexibility and push the boundaries of it as a chemical factory.  He also opened the first factory for isolated soy protein (though for industrial and not food use).  This is all despite losing jobs because they thought he was white.  Though the job was in a sundown town, so Julian dodged a bullet there, metaphorically and likely literally.

George Washington Carver-crop
George W. Carver
No discussion of African-American History Month is complete without mentioning George Washington Carver.  I know, we all love peanuts and peanut butter and are glad for a man born into slavery elevating this humble African staple, but have you actually looked at his recipes?  Most are easily veganizable, and many others such as peanut sausage (number 42 of 105), are already vegan.  So a good source of ideas for February potlucks.  Carver also applied his steampunk molecular gastronimic wizardry to cow peas (Vigna unguiculata, as in #36 cow pea loaf No. 2), tomatoes (Solanum lycopersicum, #30 fried green), and sweet potatoes (Ipomoea batatas, sweet potato biscuits).  Now I want to have a George Washington Carver potluck.

I'm sure this is just dipping a toe into the pool here.  Let me know who I missed.

16 February 2012

Vegan Stem Cells and Neurons

Induction of iPS cells
The generation of induced pluripotent stem (iPS) cells
Just a quick post today:  You can now make/use vegan neurons and stem cells from skin cells.  Well, the process is vegan, atleast.  This was not the work (as far as I can tell) by an elite cabal of underground vegan scientists, but just researchers trying to make cells that meet standards for safe use in humans.  This doesn't mean that it's free of all those mysterious unnamed 'toxins' from animal flesh as much as free from allergens and crude variable (and unpredictable) animal extracts. 

06 February 2012

A Scientist up in Arm(chair)s

A pig in a poke for only $42!
I have a confession.  I am not a professional scientist at the moment.  I am, as they say, between jobs.  But all the world's a lab and all the people are scientists, or so it says in my Shakespeare fan fiction.  We all do experiments in our lives, some with more rigor than others, and part of my regimen to keep my mind sharp is to maintain this blog.

However, one major problem with a move from a lab stool to an armchair is journal access.  Perennially a problem, even for scientists at major universities, it is exceedingly so once one looses affiliation.  I feel it is one of the biggest problems with the field today.

For those lay-folk who are not familiar, journal access is online access to articles in scientific journals.  Besides a few scattered open-source titles, the majority of publications are behind huge paywalls. As in, you have to pay US $35.00 or so to see one article, if you're not fortunate enough to have access through your university's or institution's subscription.

Typically the most one can get for free is the abstract, which is like the movie description on your DVR, and about as useful.  Also, each article is only published in a single journal, so even if you have some journal access there are usually articles out there you can't access.  Just like all those movies you want to stream but you can't.

Also the obvious refuges one would think would have access have poor to no access:  Public libraries have superficial access if any, and alumni have little or no access (or atleast my Ivy League diploma doesn't get me anywhere).

And before you ask why I don't bother my old coworkers, it's because they're either too busy working 14 hour days, or they will run into the same nonsense as I do.

So this is a problem, but is it really that big of a deal?  I think so, because we need the public to know what we do.  We must have our results and methods be transparent and accessible to all.  We can complain all we want about how a newspaper article exaggerated, misrepresented, or otherwise misinformed the public.  Yet if the public has no other source of information and cannot go to the source, should we be surprised?  This is but an extension of the ivory tower, and although it may not be entirely to blame for distrust and ignorance of evolution or global climate change, it certainly cannot be helping.