Wednesday, January 6, 2010

Rising from the Seas

The story of how animals arrived on land is one that seems pretty logical and straightforward.

You start with fish, swimming around in the ocean. Some of these fish move to rivers and lakes. But life in a river is very different than life in the ocean. First, fish here have to deal with living in fresh water, and then, importantly, they have to deal with changing water levels. Rivers can flood, and they can also dry up. In theory, a fish that could survive drying would have an advantage over those that have can't, and the best way to do that is to figure out how to breathe air.

Of course, once you're breathing air, then why not go all the way, grow some legs and hit the land. After all, it's going to give you a great advantage if you get to land, there are plants and insects there to eat, and predators can't get to you. Voila! life on land.

The fossil evidence supports this approach to settling the land. Take Tiktaalic roseae a transition fossil found by Dr. Neil Shubin and his team in the Canadian Arctic. This skeleton was initially hailed as the missing link between fish and land animals. As Dr. Shubin has described it, Tiktaalic is a fish that can do pushups. That is, it basically looks like a fish with scales, and gills, but its front fins are elongated, and would be able to push off the ground underneath. Think of the movement of seals and sea lions. Not true walking, but a start. Then, it's just a matter of the fins getting stronger, and the back fins elongating, and you're on your way to becoming a four-legged beast.

The timing works too. Tiktaalic lived about 386 million years ago, then about 8 million years later, we find the first evidence of four-legged (tetrapod) life.

But in this week's edition of Nature, a new wrinkle was added to the story. A group of European researchers have discovered a series of trackways (fossilized footprints), of tetrapods of a variety of sizes, from 50cm up to 2.5 m long. They show a wide diversity, and are well enough preserved to show that these are real limbs, with digits at the end. The only problem is that the trackways were made 10 million years before Tiktaalic was supposed to be alive.

That means 2 things. First, our timing of events is wrong. It's likely that Tiktaalic or a relative was the transitional organism to tetrapods. The fact we haven't found older examples of transitional animals isn't necessarily a problem. Fossils are relatively rare, since they only form under specialized circumstances, and it's possible that the transitional animal lived in an area where fossils wouldn't form. The same is true for the earlier tetrapods. Just because we haven't found any fossils doesn't mean they aren't out there.

The second interesting issue raised by this is that we've built a picture of tetrapods developing in rivers and lakes. But these examples are in salt water. Why did they develop there? What advantage did walking on four legs offer in a marine environment? These are new questions that will take more study, and hopefully discovery of more fossils that will answer them.

Nothing like a fundamental scientific shift to start the new year!

Wednesday, December 23, 2009

Wine Science

Just in time for the holidays, the newspapers seem to be very interested in the health effects of alcohol. The idea that red wine is good for you is nothing new, from the resveratrol to make you live longer (although you'd need to drink vats of wine a day to see a real effect), to the polyphenols that keep your heart strong, red wine seems almost like a miracle food. But what about the whites and sparklings?

Well, white wine doesn't seem to have the same qualities, though that has been debated. But according to the British press, champagne, and its cousins prosecco and cava, may actually be good for your heart. It's because these wines are made from black grapes (pinot noir, and pinot muenier), and according to Dr. Jeremy Spencer from Reading University, the qualities of the grapes do make it through into the finished product. Those qualities? Those would be the polyphenols. Polyphenols are small molecules that block the removal of nitric oxide from the blood stream, and nitric oxide is what keeps the blood vessels nicely dilated, allowing blood to flow through easily, reducing heart strain, and lowering blood pressure. The really good news in this is that unless you're drinking blanc de blanc (champagne made exclusively from chardonnay grapes) any sparkling wine made from a red grape will work (chocolate does too if that's your preference).

And talking of wine, according to the Telegraph, the lighting in a room will change how you perceive a wine. In a test using single bottles of reisling and subtly changing light colours, a group of German researchers found some remarkable results. First, if you use red lighting, then people will perceive a wine as sweeter than under other kinds of lights. And then, red of blue lighting will both increase the perceived price of a bottle of wine. why this would be is still unclear, but the effect seems to be real.

This shouldn't be a big surprise. For almost a decade now there have been studies showing how much our perception of wine is influenced by characteristics other than the taste of the wine itself. In fact, in blind tastings, even sommeliers have been known to be fooled by reds and whites, since the line for taste is frequently blurred. And time and time again, scientists have shown that the bottle a wine is poured from will influence how it gets described.

Even history can play a part, as a recent study showed. This looked at the genes of various varieties, and found that chardonnay (which, particularly in Europe, tends to get very little respect), was the child of gouais, a grape that was banned in parts of Europe for being a 'peasant's grape.' The fact chardonnay is a close cousin of gamay noir, shows how arbitrary some of these decisions can be.

When it comes right down to it, the key to wine is finding something you enjoy. And if it happens to be a red wine, or a champagne, then you're getting a health benefit at the same time!

Happy Holidays!

Wednesday, December 16, 2009

I'm Dreaming of a Green Christmas...

With the Copenhagen conference going on, and the heart of the holiday season, the question keeps coming up of how to keep being environmentally friendly while still enjoying the holidays.

And probably no issue is more highly debated at this time of year than what type of tree to put up, a real one or an artificial one? Assuming of course that you aren't going to forgo trees altogether.

The Victoria, Australia, government is pushing trees in pots, particularly the Wollemi Pine, a rare ancient tree. Not only does it keep your carbon emissions down, but it can help recover a disappearing species at the same time! Of course, here in Canada, Wollemi Pines aren't an option, but there are plenty of pine trees in pots that you could bring in and decorate.

But if you want to stick with tradition, which one should it be? Both sides have their proponents, although it turns out there are strong lobby groups for each option, pointing out the benefits and weaknesses of real versus artificial. The strongest argument I've found was in this article, where the carbon emissions of both are compared. The bottom line? You need to keep an artificial tree for 20 years if you want to compare its carbon emissions from construction with cutting down a local grown tree that was grown specifically for harvesting. And if you know that artificial trees begin to break down after about 9 years, and are mostly made in other countries and then shipped here, real seems to be the best option.

Then, once you've decided on the tree, there's the question of travel. Well, according to this BBC article, if you have to travel, and it's a few hours drive away, you might consider flying. Sure, flying uses a lot of fossil fuels, but a plane is actually more efficient in fuel conversion than a car, so if you fill a plane then your damage per person will be less than if each of you drive. Of course, this doesn't count if you're flying across the continent, or somewhere south, but that's a whole different issue.

In the end though, enjoy the holiday season. It's what we do all year round that really counts. A couple of weeks at this time of year is only a fraction of our carbon footprint. Try and be reasonable, maybe a couple fewer strings of lights, or a slightly smaller portion of meat, and less leftovers, but have a good time!

Wednesday, December 2, 2009

Getting Down and Dirty

OK, so I didn't blog for a couple of weeks, but this one is worth sharing...

Finally, some solid evidence to support the hygiene hypothesis. You've heard this one before, we need to eat dirt when we're small if we're going to be healthy.

It's an idea that has a solid biological underpinning. When we're small, our immune system is yet to properly develop. Exposure to all the 'normal' stuff in our lives (dirt, microbes and the like), trains our immune system to recognize the good from the bad. The problem, according to the hygiene hypothesis, is that if we aren't exposed to all the normal stuff when we're small, our bodies never learn the difference and so over react when we come in contact with those same materials later. That over reaction is the allergy response. The hygiene hypothesis suggests we should expose ourselves to far more dirt as youngsters if we want to be healthy in the long run. The problem with the hypothesis is that it's relied on epidemiological data for its proof. And, as any scientist can tell you, correlation (which is what you find with epidemiology) is not causation.

A couple of new studies are providing that causation. In a European study a group of researchers found that pigs housed outdoors for the first part of life had higher levels of lactobacilli and less immune activity in their guts than pigs kept in an isolation room. What does that mean? Lactobacilli are known to help prevent E. coli and Salmonella from colonizing the gut, which is good news if you want to avoid food poisoning. And as far as the immune activity, again, if the problem we're worried about is hyperactive immune systems, this is a good thing.

The second study is out of the University of California. Here a group of researchers looked at the bacteria naturally found on the skin. They discovered that Staphylococci sp. produce a compound that blocks a key step in the inflammation process. Which means that when you get a cut or scrape, it's the bacteria on your skin that are preventing your immune system from overreacting. That's a good thing: too much immune response and you'll get puffiness, rashes, heat and extra pain.

What all this is telling us is that we have this highly evolved, and tightly intertwined relationship with the bacteria that inhabit our body. These organisms block 'bad' bacteria from colonizing, and it's when they're not there that our immune system gets out of whack, leading to increased levels of immune response, aka allergies.

The irony is that on one level we appreciate that, as we see ads for yogurt containing high levels of lactobacilli. And at the same time, we live in a world that's selling buckets full of hand sanitizers, which are removing the very bacteria we need to protect ourselves.

What should we do? Follow our mother's advice, wash our hands, don't stick your fingers in your eyes, don't chew on your pen, and respect the fact we live in a bacterial world.

If we respect that, we'll only do ourselves good!

Wednesday, October 28, 2009


Hallowe'en this week, and for whatever reason spider science has been making headlines.

For instance, there's a new giant orb-weaver spider from Africa. Orb-weaver spiders are that archetypical spider that most of us think of when we think spiders. They're the ones we see sitting on the webs, that capture insects as they fly by, and are the type we put up as part of our Hallowe'en displays. We have plenty of orb-weaver species here in Canada, but this African one is in a league of its own. First of all, there's the size: the females of this particular species (Nephila komaci) grow to about 10-12 cm across, while the males are 1/5 that size. Can't picture that? It's about the size of the palm of a large man's hand! Then there's the web. Unlike most diaphanous spider webs, this one, over a metre across, is more string like, and is capable of catching small birds. Which the spiders will eat, although they prefer grasshoppers and other insects.

Another spider in the news is the Australian redback. In this case, it's a story of how lazy male spiders can win the mating game. This work comes from the lab of Dr. Maydianne Andrade at the University of Toronto, Scarborough, where they've been studying the mating habits of this relative of the black widow. The interaction of males and females in this species is unique to say the least, it'll be covered in some detail in my book when it comes out in the spring, but for now all you need to know is that the males have to court the females if they want to mate. And it's no short commitment, males have to put in almost 2 hours of attention if they want to mate before they get turned into a meal. Except for this new research, which shows that sometimes males can sneak in and mate without putting in the work, as long as another male has spent the time in courting. The bad news, for the hard worker, is that he doesn't get to mate, he's out-maneuvered by the other male.

And talking of sneaky spiders, earlier this year a spider was discovered making a decoy. By taking refuse and packing it together on the web, it can make a copy of itself to distract predators.

Why so much spider science? Part of it is probably just pure curiosity. But spiders are interesting for another scientific reason. They're a great model for studying evolution and behaviour. Take the male/female size difference. By looking at closely related spiders, we can understand what's driving this evolution in size disparity. The same with behaviour; spiders are a great system for looking at sexual conflict between males and females, and again, sometimes closely related species can behave quite differently, which lets researchers ask interesting questions.

If only they were a little cuter...

Wednesday, October 21, 2009

What's it all about?

Sex anyway.

From a biological perspective, sex is something of a mystery. First of all, it's inefficient. If you want to reproduce sexually, the first thing you need to do is get two individuals, one of each sex, together in the same place. Then, they have to like each other, at least enough to procreate. And, for males, that's the end of the biological role. Sure, humans, and plenty of other species, use males to help protect the offspring, or provide food, or for myriad other reasons. But if those males weren't there using up resources, there could be more females, and potentially twice as many offspring around. More offspring means a greater chance of success for a species.

Which is where researchers have looked for the problems that might be associated with asexuality. By the way, for the purpose of this, I'm going to talk about asexuality in general terms, in fact there are two quite distinct forms, true asexuality, where reproduction is by either fission (like in bacteria) or parthenogensis (where females produce eggs that turn into fully functional organisms), or self-fertilization (where an animal produces both eggs and sperm and is able to fertilize their own gametes).

But back to the problems. The first one is the build up of potentially damaging mutations. This is sometimes referred to as Muller's Ratchet. Basically, the theory is that copying between generations isn't perfect. Each new generation will pick up a few mutations from its parent. That means as time passes, the number of mutations will increase. On its own, each mutation is not a particularly big problem, but if you collect enough, your health is going to suffer, and the species will become less viable. Remember also, that mutations are generally irreversible, so it's not like they are going to fix themselves from one generation to the next. The male then, the theory goes, helps get rid of these mutations by bringing in new genetic information that mixes with the mothers, and hopefully slows the mutation rate.

There's a second theoretical problem that relates to the enviroment. In this problem, you have a species that's wonderfully adapted to where it's living. But then something changes. It might be a new virus that the species hasn't seen before. Or the temperature might start to change. Whatever it is, if you don't have a gene that allows you to adapt, you're in trouble. Males in this case are often the source of the needed genes that either allow resistance or adaptation.

At least those are the theories. What Dr. Patrick Phillips and his team from the University of Oregon wanted to figure out was whether the theories were true or not. In an advanced online publication in Nature Magazine he took C. elegans and manipulated it to turn it into a self-fertilizing hermaphrodite. Sure enough over time, these worms built up mutations, showing the first theory has merit. Then, when challenging the hermaphrodites with a bacterial pathogen, again they were unable to resist infection and disease. In both experiments, controls with hermaphrodites that could outbreed with males did just fine, showing that males do prevent these problems.

So, men can take heart, biologically we do have a function. And of course beyond the basic genetic role, human males, and males of many other species have expanded their role to protection and sharing in the general raising of young. Which is good, we wouldn't want to end up like the Triplewart Seademon. Males of this species are simply a parasitic bag of sperm attached to their female...

Wednesday, October 7, 2009

Nobel Week

My favourite week of the year!

I'm going to do things a little differently in the blog this week. I could describe the winning nobel prizes, but there are plenty of sources for that information. Instead, I'm going to talk about why I think there's still room for the Nobel categories.

There's been some debate this year (as there is every year) about the relevance of the prizes today. There are plenty of fields, important to modern science, that aren't captured in the Nobel's list of possibilities. Environmental research, for instance, is not captured by Medicine, Physics or Chemistry. There's an argument to be made that the categories should be redefined and broadened to recognize fields that didn't exist in the time of Nobel himself.

I'm going to argue against that. Well, not vehemently, because if there were more categories, that would only be a good thing. But when you look at this year's awards, it seems to me that the Nobel committee does pay attention to relevance.

All of these three science awards are for relatively recent work. And in each case, real practical outcomes that affect vast numbers of people, have been achieved. Telomere research has taught us about aging, and cancer and lots of diseases. The CCD and fibre optics have changed communication forever, and we're only scratching the surface of their potential. Ribosomes are a fundamental building block in the cell, and we have a whole class of antibiotics that owe their existence to the understanding of the ribosomal structure. But in all these cases, none of the practicl outcomes would have been possible without the fundamental discoveries of the researchers. In the end, that's what's great about the Nobel prizes. At a time when a lot of research funding is headed to 'applied' research, those who perform basic work can still be gratified to know that their fundamental science will be applauded and recognized by the most famous award of all.

Keep the Nobels, but make more prizes too!