Archive for the ‘Animals’ Category

Teleost fish are unique in that they are able to regenerate many different types of tissues throughout their lives, including cardiac, retinal, and renal (kidney) tissues.  Many of these regenerative abilities occur through the action of stem-cell like populations.  Identifying stem cells in fish may help researchers identify analogous cells in human tissues. 

The ability of some fish to regenerate renal tissues is particularly interesting because there is currently no known kidney or nephron (the functional unit of kidneys) “stem cell” in humans.  A recent paper looked at using zebrafish to try to identify nephron stem cells. 

To find out more, check out my latest post for the Stem Cell Network.

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The ongoing debate over shark fin soup continues in California with proposed legislation which aims to curtail the import of fins and prevent the brutal practice of “finning”. Currently, it is illegal to bring in sharks without the fins, but a loophole exists which allows for the import of fins from countries such as China and Mexico, where animal protection legislation is lax or non-existent. If passed, California would join Hawaii in the efforts to prevent shark fins from making it into the soup bowl.  The New York Times recently reported on the issue from California, bringing to light many different viewpoints from the Asian community.

I admire many of the opinions expressed by many of the first generation Americans quoted in this article. It is hard to go against family tradition, especially notoriously traditional Asian families. The concerns they express – environmental and ethical – are backed by science and fact. Finning is cruel and wasteful. Finning not only causes the pain of amputation but also condemns the animal to die slowly, either from suffocation or from being defenselessly picked apart by opportunistic scavengers. Ecologically, the removal of the top ocean predator would be devastating in terms of balance.

In contrast, many of the arguments put forth by their elders seem petty if not downright foolish – the notion that we should be free to eat whatever we want, whatever the cost; the idea that tips for waiters would decrease without shark fins for soup; and so on. Pitted against damning evidence that the shark populations is on the brink of disaster, it is hard to find any respect for this viewpoint.

Many groups have used “culture” as reasons for continuing destructive practices – usually in relation to hunting and eating. The whale hunt is another example. Though perhaps less vicious and less wasteful, it ignores the fact that we are still willfully eating species into extinction. We forget that our technological advances and our incredible ability to kill and destroy efficiently has far outstripped that of our long ago ancestors. And for what? A small bowl of soup, gained at the expense of an animal left to die for lack of appendages?

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I love Carl Zimmer.  I think he’s one of those people who just really get it… and not only does he get it, but he explains things in a way that makes other people get it.

Recently, he published an article on the Loom discussing whales and cancer, based around a recent review published in Trends in Ecology and Evolution.  The basic premise of cancer works like this:

  • Over time, cells make mistakes in DNA replication
  • Mistakes accumulate and eventually, mistakes will affect some vital process
  • This causes cancer

This stands to reason then, that the more cells you have and the longer you live, the more mistakes you will have, and the higher likelihood that you will have cancer.

But if you looked at blue whales, they’re HUGE.  They have a lot of cells and they can live a long time.  Indeed, according to calculations, half of all blue whales should have colorectal cancer.  By the time they reach middle age, ALL of them should be cancer-ridden.  And that’s only one type of cancer!

However, this is not the case.  Indeed, across all studied species, including humans with our often-poor health choices, cancer occurs at a rate of about 30%.  So mice, with their rapid metabolism and short life spans, get cancer at the same rate as whales, with their much slower metabolism and longer life spans.

This suggests that larger animals have evolved mechanisms against cancer that have held it at the approximately 30% mark – regardless of cell number, age or size, which is contradictory to the current paradigms of cancer as a statistical inevitability.  And if that is so, we would be better off studying how larger animals cope with cancer rather than looking at cancer in mice.

That is not to say that we should suddenly be breeding captive whales for laboratory-style research – but so little is known about the health of these animals in the first place, despite the popularity of sea mammals as aquarium entertainment.  A well sequenced genome would be the first informative step – The authors suggest studying the genome to look at differences in cancer defenses among related species with a wide range of sizes, such as whales and dolphins.  Learning more about their health and biology of these animals may yield interesting new avenues in both human health research and animal veterinary medicine.

Zimmer ends his article eloquently:

“But such an undertaking would have to overcome a lot of inertia in the world of cancer research. Cancer biologists don’t look to big animals as models to study–which is one reason there’s not a single fully-sequenced genome of a whale or a dolphin for scientists to look at. For most cancer researchers, mice are the animals of choice.

But if we want to find inspiration for cancer-fighting medicines, mice are the last animal we’d want to consider. It’s like learning how to play baseball from a bench-cooler at a Little League game, when Willie Mays is waiting to dispense his wisdom.”

Again, find the original article at The Loom.

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I’ve been a bad blogger and have not been writing nearly as much as I should. 😦

This week and a bit has probably been one of my most unproductive since the summer, and for that I’m sorry. I’m a bit burned out I think with much writing, both coding and blogging. Hopefully a few days off at Christmas will recharge my batteries!

News the past week and a bit:

  • Shameless self-promotion: My latest blog is up on the Stem Cell Network and recaps the recent annual meeting of the American Society of Hematology.  Please check it out!
  • Earlier this year, Metropolis records released “Electronic Saviors”, a 4 CD collection of industrial music to benefit cancer research and patients.  On December 4, they presented the Foundation for Cancer Research and Wellness with a check for over $22k.  Angry music does solve problems!
  • It received limited coverage, earning only a brief mention in Scientific American, but this past Tuesday, the US Senate finally passed the Shark Conservation Act which bans the practice of taking fins from live sharks.  Shark fins are prized in soups and other delicacies, and unfortunately, many countries which profit from the trade still permit shark finning to occur despite the fragile state of many shark populations.  This is a long overdue step in the right direction.

I’m really going to try to push some posts out in the next few days.  Can’t say much more than that, as I have a crap load of stuff on my to-do list!  Stay tuned…

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My last post on rodent anesthesia looked at the use of chemical anesthesia, in particular, the use of ketamine-xylazine to attain surgical unconsciousness. I identified several issues with the use of this combination, most importantly the lack of dosage control and lack of predictability in response.

So what are the alternatives?

If ketamine-xylazine is not used, most often researchers will turn to an inhalent anesthetic. Inhalents use a vaporizer to deliver a gaseous form of a chemical directly to the rodent via a hose or face mask (or through intubation for larger animals) in combination with oxygen.  The most common inhalant used in rodents is isofluorane gas.

Isoflurane is a halogen-based gas which causes muscle relaxation and unconsciousness.  It used to be used in human medicine, but is now principally used in veterinary medicine and research.

Gaseous anesthetics require more equipment than injectible anesthetics.  In addition to the vaporizer and assorted tubes and hoses, a scavenging system must be used.  Scavengers gather up leftover gases to prevent worker exposure.  Charcoal canisters which absorb residual gases are a common form of passive scavenging, while various types of ventilated hoods can be used for active scavenging.  Never use anesthetics without a proper scavenging system!  Chronic isoflurane exposure has been linked to cognitive decline.

[Aside: I had some bad exposure to isoflurane in the past and it is like being in a fog – you just can’t think.  Little bit terrifying.  Thank God for new careers!  Computers can only ruin my posture and eye sight! … ]

But using all this complicated equipment has it’s advantages!  The vaporizer allows the technician to control precisely how much gas is being delivered to the animal.  If you need to increase or decrease it, you know exactly how much you are raising or decreasing the dosage.  It is much harder to accidentally cause an overdose.  As well, since the gas is being continually delivered, there is no risk that the animal might being to wake up in the middle of a procedure.

For the animals, recovery from isoflurane is much, much quicker than recovery from ketamine-zylazine.  Isoflurane is excreted entirely via the lungs – no residual chemical is left in the system.  So once an animal is removed from the gas flow, it beings to recover immediately.   Full recovery occurs in only a few minutes and aside from regular post-surgical care, rodents do not generally require additional monitoring.

Unfortunately, isoflurane does not provide any analgesic properties aside from unconsciousness during the procedure.  So, analgesic must still be given before and after surgical procedures.

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In my last post, I introduced biogeography as a field which studies how populations and species are distributed.  Distribution is influenced by many factors including biotic factors.  It is a catch-all term which refers to factors relating or due to the biology of the the species, and may include dispersal ability, interspecies interactions, and breeding systems.

Dispersal ability

Dispersal ability is a measure of how well a species can spread from its original home and includes aspects such as fecundity, migratory ability, adaptability and gamete dispersal.  Fecundity describes the reproductive ability of a species.  Migratory ability describes how mobile a species is, and how able it is to move from one habitat to another.  Adaptability measures how well species can adapt to new habitats, such as after a dispersal event.  Gamete dispersal looks at how far a species can disperse its gametes and how well those gametes do after dispersal.

Elephants are not very fecund, for example.  They take many years to mature and when they do mature, they do not produce many young.  Low fecundity combined with slow maturity limits their potential dispersal ability and is a reason why populations are so vulnerable to hunting.

On the other hand, many wind-dispersed plants have a strong dispersal ability – their gametes can go wherever the wind takes them.  Dandelions are an example of a plant which is widely dispersed and distributed.  Thus we can find dandelions in lawns across North America.  But plants do not generally migrate, unless they are able to reproduce from shoots or branches which fall off and are carried by other vectors.

Interspecies Interactions

How does the species interact with other species?  Predator-prey relationships can limit the spread of populations, either through the limitation of food sources for the predator or through prevention of unchecked growth by the prey.  A good example would be the sea otter-urchin-kelp relationship.

Sea otters in the North-East Pacific have historically kept sea urchin populations low through predation.  Urchins feed on kelp as a primary food source.  When sea urchins are few, herbivory levels on kelp are low, allowing kelp populations to expand and diversify over time.  But in the last century or so, local populations of sea otters have become extinct due to hunting pressures.  As a result, the sea urchin populations have expanded and the kelp populations are diminished and diversity is reduced to a few hardy species.

For plants, interspecies interaction can also include the interaction with animal pollinators.  Many plants, especially those endemic to islands such as Hawaii, have very specific pollinators.  Orchids are especially notorious for specifically catering  to certain species of bees or moths for pollination.  Sometimes the shape of the flower may only allow a certain insect inside, or perhaps the scent produced only attracts certain moths.  Dispersal is then limited to areas where these pollinators are present.

Breeding systems

Seed-bearing plants are possessed with a variety of different breeding systems.  The breeding system of a species will often determine how successfully a species will distribute.

Some species are unisexual, that is, male and female plants are separate.  Holly is an example of a unisexual plant.  For unisexual plants, colonizing a new area requires (at least) two “dispersal events” to deliver a male and female plant in order for a sexually reproducing population to establish.

Other plants are bisexual – male and female are present on the same individual.  Rosaceae, the family containing apples and roses, are an example of a bisexual plant.  Within these plants, some are able to fertilize themselves (“self-compatible”) while some are not (“self-incompatible”).  Self-compatible, bisexual plants are the best dispersers.  Only one seed is needed to successfully start a new sexually reproducing population


All these biotic factors, and more, can change the distribution of populations over time.  But it’s not enough to be biologically able or unable to spread to new environments – sometimes it is the environment itself that limits or encourages population growth.  My next post will look at some abiotic factors that affect the distribution of species.

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While in Canada, many universities and institutions remain mum on their animal research activities, researchers in Europe are taking a proactive approach.  There are a few possible reasons for this difference in attitude.  The European research atmosphere is slightly different than that of Canada’s: Certain groups of primates have a legislated right to “inherent value” for example, while no such rights exist in Canada.  Whatever the reason, scientists in Germany and Switzerland have launched an educational initiative called the Basel Declaration which pledges to be more open about research and to engage in public dialogue about research.

As Nature News reports:

“The public tends to have false perceptions about animal research, such as thinking they can always be replaced by alternative methods like cell culture,” says Stefan Treue, director of the German Primate Center in Göttingen. Treue co-chaired the Basel meeting, called ‘Research at a Crossroads’, with molecular biologist Michael Hengartner, dean of science at the University of Zurich, Switzerland. Outreach activities, such as inviting the public into universities to talk to scientists about animal research, “will be helpful to both sides”.

I think that this is a good point that Dr.Treue brings up – the importance of dialogue cannot be understated.  He also makes a good point, that alternatives like cell culture are not always viable or indeed, may not be the “alternative” that activists would hope for.  Growing cells requires a hodgepodge of media to keep the culture alive.  One important constituent of cell culture media is fetal bovine serum, or sometimes fetal calf serum, which as the name suggests, comes from cows.  [Note: FCS and FBS are by-products of the meat industry and would be otherwise wasted if not used by research].  But it is important to note that the absence of research on animals does not mean that animal products will not need to be used in research and is a prime example of how science does a poor job of communicating what it does.

[Note: it is possible to grow cells serum-free, but the cost remains prohibitive at the moment]

And, there is the simple fact that cells grown as tissue culture are just not quite the same as cells in a living body.  Just ask Mark Post, who’s trying to create lab-grown meat.  Using biopsies from donor animals and tissue culture techniques, he’s trying to grow enough meat to create a sausage that looks and tastes like the real thing.  Dr. Post’s long term goal is to create meat without needing to slaughter animals.  While he’s succeeded at growing a strip of pork muscle, the “meat” does not resemble anything from the grocery store.  The tissue is weak and prone to cell death due to lack of stimulation and without the support of a proper vascular system to deliver nutrients uniformly.

A similar case can be made for the use of computer modeling.  I think computer models are great – they drastically reduce the cost of research by allowing researchers to narrow the field of interest.  But at best, computer models only reduce the number of possibilities.  When it comes to testing drugs, for example, a computer model cannot predict all the effects on a substance on a whole body system.  We simply don’t have enough information about all the interactions that occur in the body.  Yet.

That is not to say we should not pursue new tissue culture or modeling techniques.  Quite the opposite – these techniques will improve with time and refinement.  In time, they may even be sophisticated enough that human clinical trials are less reliant on animal data for safety and efficacy testing.

But in the mean time, hopefully initiatives like the Basel  Declaration will foster more openness between the public and the animal research community.

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Wow, what a crazy weekend.  I had a lot of fun at ASH 2010 and I’ll put up a post on that soon.  If any readers are contemplating a trip to Orlando, I have to warn you – the water is absolutely disgusting.  At the convention centre, at the hotel… everywhere…  I do not advocate bottled water, but I kid you not, the tap water smelled and tasted like swamp.  I am eternally grateful to live in Vancouver where the water is decent and good food is the norm rather than the exception!!

  • The world this week has been fixated on the Wikileaks cable releases and the subsequent back lash from the United States government.  I think as writers, we should all be concerned when governments begin to pressure private companies to take action against a publisher of information, be it Wikileaks or your local newspaper.  Where is the backlash against the person who actually stole the information in the first place?
  • Speaking of media – scientists and bloggers  have rallied together to critique and question NASA’s press release and publication on arsenic-based life, and NASA’s subsequent dismissal of the “credibility” of bloggers.
  • The recent shark attacks in Egypt are now being attributed to multiple sharks.  While frightening for tourists and  residents, I can’t shake the dark feeling that some people will again use these attacks to justify hunting sharks, when in fact, illegal feeding and irresponsible “tourism” is most likely to blame.

Not a lot of good news, I’m afraid!  On my end, I will be finishing up part 2 of both the biogeography and rodent anesthesia series this week, stay tuned!  I should also have a new blog coming up on the Stem Cell Network in the next week or two.


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It’s hard to talk about biodiversity without becoming a little bit depressed at the nature of things.  This month’s catch is the particularly gut-wrenching case of bluefin tuna.

Bluefin tuna can by known by many names, including Atlantic bluefin tuna, northern bluefin tuna or giant bluefin tuna.  They are capable of reaching in excess of 1000lbs with lifespans of around 30 years.  Feeding on smaller fish such as sardines or squids, bluefin tuna are also important predators in the marine food chain.  Unfortunately for them, they are considered a prize food fish in many human cultures, and fetch astronomical prices in the Japanese sushi market.

While bluefin tuna have always been fished, the relatively recent popularity of sushi in Western cultures as well as the advent of seine fishing poses an immense threat to this fish.  Indeed, bluefin populations are approaching collapse in many areas of the world and are already extinct in certain regions. Rough estimates put populations at approximately 30% of historic numbers.

Nature News recently commented on the sad state of the bluefin tuna industry, noting that under-reporting and illegal fisheries are common.

The International Commission for the Conservation of Atlantic Tunas (ICCAT)meets this November 17th in Madrid to discuss the bluefin tuna fisheries and set quotas. But as Nature News noted, this commission has largely been ineffective and a recent report released by the International Consortium of Investigative Journalists (ICIJ) highlights the many faults of this lax and under-regulated industry.

As always, the most effective avenue of change still lies with the consumer.  Eating a species into extinction is just a little bit ridiculous and completely unnecessary.  Add bluefin tuna to your list of seafood no-no’s and check out the Vancouver Aquarium’s Oceanwise program for a list of seafoods that should not be ending up on your dinner plate.

[Photo from http://www.oceanriver.org/AtlanticBluefinTuna.php, original by Chris Park]

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There was another flurry articles appearing in student media this past week over UBC’s animal use.

UBC publication The Ubyssey published an article and a well written opinion piece, remarking on the difficult nature of the debate.  Indeed, they echo many of my own sentiments when they remark that “moderate, progressive voices” are needed in this debate.  Mud slinging and fear mongering on both sides does nothing for animal welfare.  Until people are willing to talk rationally about the issues, no real progress can be made for either side.

It’s gotten to the point where being concerned about animal welfare is enough to send people into a frenzy of recrimination and accusations, while being a biomedical researcher arouses suspicion and distrust.  No doubt this blog will get passed around in numerous clandestine emails where I will be alternately skewered or praised by people too afraid to talk about their own opinions.  And why are people afraid?  Part of it is because we have not done a good enough job of educating our researchers and technicians about ethics and educating our public about science.

That’s one of the reasons I found my university ethics classes to be so insightful – it taught you to leave the emotion aside, think critically about an issue, and look at the scientific, ethical and philosophical arguments on both sides of a debate.   This is an important skill that I feel a lot of people are lacking.

Unsurprisingly, I was the only science-oriented researcher present in a 40-person class on biomedical ethics.  😛

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