Friday, November 30, 2012

Gene expression - variety is the spice of life

Most genes are the same in all humans (as they are in all hippos, hawks, heathers...), but our individual DNA is always slightly different from everyone else's.

But how, you may ask, can we add variety to DNA?

Variety results from several processes, shown in these images from University of California Museum of Paleontology's Understanding Evolution site, a great resource for learning about the history, patterns, and mechanisms of why and how we are what we are.

Genetic shuffling, or recombination, dictates the combination of genes (i.e. big nose or bushy eyebrows) that join together to produce the offspring.  

Mutation is a random change in the structure of DNA, usually due to errors in repairing or copying DNA molecules. The gene for color may be altered in copying, resulting in a brown offspring.
Migration is just individuals from elsewhere joining the population and adding their genetic differences. Dispersing brown beetles may show up one day in a population of greener beetles.
Natural selection means advantageous traits stay in the population because they help their owners survive and reproduce. Brown color is less appealing to birds, so brown beetles reproduce and become a larger segment of the population.
Genetic drift occurs when certain individuals get lucky due to chance (not natural selection): for example, a massive killing of foxes for their fur would benefit the local mouse population and allow slower, less fit mice to reproduce far more than they might normally do.  Or a bunch of green beetles happen to get squished just before reproducing.

Wanna know more?

Thursday, November 29, 2012

Genes as tough as nails: some basics for fitness

In a previous post, I described how some lovely anole lizards in the Bahamas went to the beach showed scientists a thing or two about natural selection.

Anoles with longer, speedier legs were more likely to survive the introduction of a big new land-based predator (a large lizard) and contribute to the gene pool of the next generation. These anoles with the longer legs thus had greater biological fitness in that environment.

anole with long legs - faster? or awkward climber?
photo: Cowenby
anole with short legs - slower? more agile in trees?
photo: Walker Coufal

But how did that trait get passed to their young? And why were some anole lizards longer-legged to begin with?

It was in their genes. Genes are units of heredity (meaning traits pass from parents to offspring) found in each of our cells that carry information that determine your physical traits (more below).

Yes, fitness is necessarily related to genetics (don’t get scared), in that the characteristics that make us (or a lizard, or an oak tree) more fit for a particular environment are stored in genes. While we can often improve our fitness through certain behaviors, there is no way around discussing genes at least a little bit.

I am no expert either so will describe some fitness genetics basics, without getting too technical!

To start: What do you get when you cross a bridge with a bicycle?
Answer: The other side.

OK, sorry. The rest of this post and the next one do contain some (very) basic genetics and why it matters, with some help from the anole lizards.

Read on, because the movement of genetic information and resulting evolution are really key to understanding the biology not only of lizards but of you and me as well!

Monday, November 19, 2012

Who Wants to Live 1,000,000 Years? (Not everyone)

All species do, I would have thought! (except maybe winners of the Darwin Awards, below.)

"Who Wants to Live 1,000,000 Years?" is actually the name of the natural selection survival game for anyone interested in understanding natural selection and evolution.

Your target is to pick some variations within a species that will allow it to live 1,000,000 years, in the face of climatic change, predators, and other challenges.

natural selection survival game
the natural selection survival game - choose your population!

Play with or without kids, learn more about natural selection or Charles Darwin, and take a quiz to see if you remember any of it!

If you can't, you might enjoy The Darwin Awards, which are documented behaviors that severely decreases fitness in humans. Read on for more!

Trying a longer distance

CONGRATULATIONS to all of you!
A group of my friends in the Bangkok Runners group just finished the Bangkok Marathon (42km), Half Marathon (21km), or mini-Marathon (10.5km)

image edited by MdK
I didn't join them, as I'm currently in the USA, rather than Thailand, plus am still increasing my running distance slowly after a forced running break from plantar fasciatis.

But their achievement reminds me of Christmas Day 2011. I recall the 3:30 am wake-up, 4:00 departure, 5:00 start. Chasing Santa? No, it was the Chiang Mai half-marathon!

Running events in Thailand start really early to beat the heat, and, actually, the full marathon started at 4am, so I really can’t complain.

Doi Sutep temple
glorious Doi Sutep temple, near Chiang Mai
I don’t think the full marathoners saw Santa either, but we did run into a group of Buddhist monks coming down from Doi Sutep temple on the mountain outside of town for their dawn ritual of blessing the faithful who come out to the streets and receiving food offerings from them that will be their single meal of the day.

giving alms, photo:

Read on for more on the race and some Thai running sites:

Sunday, November 18, 2012

Natural selection can happen quickly!

Take an island in the Bahamas with a population of anole lizards (this lovely guy called Anolis sagrei, we’ll call him Andy).

Bahamas location, map:
Andy the anole (Anolis sagrei), photo: Ianare Sevi

Males like Andy attract females by displaying, and those with larger, brighter dewlaps (that flap under his chin) are usually most successful breeders. However, the brighter display may also attract the attention of predators.

The Predator (Leiocephalus carinatus), photo: Ianare Sevi
Now add a predatory terrestrial lizard called Leiocephalus carinatus that loves to eat anoles, and you can see the results of natural selection in a single generation.

Scientists actually did this: they introduced the larger lizard to 6 tiny Bahamian islands (and studied 6 others with no “invasion” by the large lizard).

They found that:
  • On “invaded” islands, about half of the anoles survived the new threat. Survivors had longer (faster-moving) legs relative to non-survivors, so guess which genes made it to the next generation?

  • You got it. In the next generation, longer legs were more common.

  • Initially, anoles with longer legs could run faster and escape the new predator. So Andy and the other anoles with longer, faster-moving legs contributed more genes to the next generation than males with shorter, slower-moving legs and almost immediately made up a larger portion of the anole population.
  • the lovely female brown anole
    photo: Matt Edmonds
    the dewlap in action, photo:

  • Andy and his fellow anoles also started spending more time in trees and shrubs, to avoid the big ground lizard.

  • Shorter limbs are better suited to navigating narrow branches and twigs, so anoles with shorter legs survived and bred more successfully there. This move thus enabled the anoles with shorter legs to contribute more to the subsequent generation, and natural selection switched course, almost equally rapidly.

  • Thus, despite (or maybe because of) the shift in behavior (moving up and away from the ground), the genetic make-up and, subsequently, the physical appearance, of the anoles changed rapidly.

  • These surprising findings demonstrate how natural selection functions even within short time periods and switch direction if the difference in success rates between two versions of a gene is sufficiently great.

  • Andy spots a predator - ready to run?

    Thursday, November 15, 2012

    Natural selection at work: discovery of a new gene unique to humans

    Hot off the press is the discovery of a new gene that is found in humans but not in other species, including other great apes.

    gorillas in deep thought?

    What's the big deal?

    This is the first time that a new gene -- carried only by humans and not by apes -- has been shown to have a specific function within the human body.

    Cartoon by Chris Madden:
    check out his science cartoons
    The gene, called miR-941, is especially active in parts of the brain involved in language and in tool use -- two areas that clearly distinguish humans from our nearest cousins.

    The authors speculate that the emergence of miR-941 helped to maintain stem cell populations within humans, which in turn supported longer human lifespans but left human cells more prone to cancer-related transformation.

    So here is an extraordinary example of superior evolutionary fitness resulting from development of a new gene millions of years ago.

    What does this gene do?

    With the development of this gene, early humans apparently improved their use of both tools and language, both key to our current world domination (read: uber-high level of fitness).

    It also seems to have been associated with longer lives and greater vulnerability to cancer cell development.

    Chimp communication not controlled by the miR-941 gene
    Photo: frogbellyand Animal Photos!
    Previous studies have found genetic differences between us and our ape cousins, but these were linked to changes to existing genes (i.e. in various genes shared by humans and non-human apes, we have different versions of the genes, which have resulted in different effects), rather than development of totally new genes.

    The scientists estimate that this gene emerged between 1 and 6 million years ago, after humans and chimps had split from their last common ancestor. Anyone remember that far back?

    The gene seems to have sprung from nowhere at a time when our species was undergoing other dramatic changes: living longer, walking upright, learning how to use tools and how to communicate.

    Scientists believe this gene is connected to cognitive functioning (mental action or process of acquiring knowledge and understanding through thought, experience, and the senses) and consider it key to understanding what make us human.
    golden monkey surprised at his lack of cognition

    For more information, check out the Science Daily description of the findings, or, for the truly motivated, the original paper, published in the journal Nature Communications.

    Survival of the Fittest

    Our interest in health and fitness is huge, and our interest in sex and family even more so. In biology, fitness combines all three!

    In biological terms, the fittest individuals must survive AND reproduce.

    However, they are not necessarily the strongest, fastest, or biggest --- the fittest individuals are those that consistently leaves more offspring in the next generation.

    • An undersized plant with a large seed pod may leave behind more offspring than a taller, heartier plant.
    • Artists and musicians are often known for less-than-healthy lifestyles (think insomnia, depression, drugs, stress) yet may have more offspring than a superbly trained decathlete or body builder.

    playwright gets the girl:
    Marilyn & Arthur Miller

    Winning army bodybuilders (photo: C.Smith (USAG Wiesbaden), Wikimedia Commons)

    So fitness has a very different meaning in biology and evolution than the one we use in everyday life – it doesn’t necessarily mean healthier, just more able to get its genes into the next generation.

    How does this apply to lions, leopards, bears and beetles?

    Monday, November 5, 2012

    Born to run, part II: form

    Form and running injuries

    As a moderate but avid runner who has experienced injuries, I enjoyed Chris McDougall’s book Born to Run and the ensuing discussions of proper running form.

    Seems out of place:
    early human runners lacked motion-control footware
    Our distant history as humans clearly included frequent running and walking over long distances.

    Although we haven’t changed that much since those early hunters, people (mostly) no longer catch our own food (and the few who do use guns or arrows that enable hunting from a distance), we run and walk less, and we use shoes.

    And when we do run, we injure ourselves.

    If running is so natural, why are so many of us injured?

    For more information on running form and its relationship to injury, read on ---

    Born to run, part I: history

    Here's a test question for you biological fitness buffs out there:

    how did humans, who lack the power, speed, claws, or fangs of other species, manage to bring home the bacon often enough to eventually develop the brainpower to invent spears, darts, and arrows they then used to become the dominant hunters across the globe?

    Hint: it has to do with running, but first, a story:

    Blood_fiend crazy clawed humanoid
    (This wasn't us!)
    A small group of expert hunters in the Kalahari track a kudu.

    Slowly at first, measuring its speed and direction from its tracks, they maintain pursuit of the large antelope for hours at different speeds, until one man takes off running after it.

    He dogs the kudu for another couple of hours until the animal collapses from exhaustion, after an 8-hour hunting effort. Hunters survive another day, with food for the clan and enhanced prestige for themselves.
    African hunters track game on foot
    This example of persistence hunting, documented in BBC’s Life of Mammals, is an anomaly in today’s easy-access world of packaged food and neighborhood supermarkets.

    Devolution from hunter to Facebook addictNevertheless, it was a far more common and (at the time) efficient hunting strategy among our early ancestors, despite the danger and physical effort required.

    Genetic and anthropological research
    in Africa, described in part by blogger Yann Klimentidis, has shown support for the persistence hunting hypothesis.

    Though modern work environments hardly require it, you are, despite your current desk job or Facebook addiction, designed for endurance running.

    For more on persistence hunting and its role in improving (biological) fitness, read on!