evolution is real

Evolution is Real and I Have Seen it!

 

By Brent Wells, PhD

It has recently come to my attention that the biggest argument of opponents of evolution is that it has never been witnessed. While I could go on and on about the merits of this argument (considering it is a favorite of proponents of creation – something I’m pretty sure no one here was around to post on Instagram), I will instead give you seven examples of evolution that have occurred in recent history.

 

1) DOG BREEDS

Any evolutionist will tell you that all modern dog breeds share a common ancestor in the wolf, but even if you don’t want to believe that, consider the Chinook; this breed was developed in New Hampshire in the 1920’s. Dog breeding is an example of human-driven evolution yet relies on the exact same principles that drive it in the wild. Random mutation leads to a trait that then becomes fixed in the population if it provides a reproductive advantage. In the case of dog breeds, the mutation is random and we simply select for the traits WE enjoy (docile, smart, loyal, big ears, small tail) and continue to select and select until we have a completely new breed. That’s evolution.

 

2) AGRICULTURE

Speaking of human-driven evolution, the crop industry is probably the single most impressive example, even before the GMO craze. Corn did not begin its time on this earth producing golden, forearm-sized ears for us to smother in butter and salt. Early maize was actually a grass that held 8-10 hard shelled seeds and which required evolutionary selection to become what it is today. In fact corn, as we know it, can’t even survive in the wild on its own so I think it’s safe to say that it wasn’t part of a diet in the Garden of Eden.

 

3) ELEPHANT TUSKS

Poachers are some spectacular scumbags and despite the dwindling African Elephant populations, continue to kill these great animals just for their ivory tusks. In the wild, most male elephants develop large tusks. I say most because there is a small percentage that don’t, or develop smaller tusks, due to a genetic mutation. That number has gone from about 5% to as high as 35% in some areas in the last 150 years. Why? Because male elephants without tusks are undesirable to poachers, which means they are the ones to live and pass on their genes, including the mutation for no tusks, thereby increasing the percentage of offspring that share that trait.

 

4) TOXIC-LOVING FISH

The Hudson River has always had a pollution stigma surrounding it, and maybe rightfully so. It turns out that it was one of the biggest dumpsites for PCBs, which were introduced in 1929 and outlawed 50 years later, in the country. PCBs are deadly to all animals but it turns out one fish, the Atlantic tomcod, evolved a modified gene that allowed it to regulate the toxic effects of PCBs and related chemicals and continue to thrive. This adaptive evolution occurred in as little as 20-50 generations and all since 1929.

 

5) YEAST

Scientists have been able to take single celled brewers yeast, allow them to grow in colonies, and at the end of 350 generations (about 60 days), see traits of multicellularity. This, in fact, might be similar to how the first multicellular organisms came to be on the earth, only this time, we were watching.

 

6) PEPPERED MOTH

The Peppered Moth was widely distributed in England prior to the Industrial Revolution. This color scheme acted as a camouflage as it blended into similarly patterned trees and therefore helped it to avoid predation. As more and more factories began to clutter the landscape, soot from burning coal eventually darkened the trees making the white moth with dark spots easy for predators to spot and eat up. This is when the moths evolved to an all black color, allowing them to once again blend with the color of the surrounding trees and avoid becoming dinner. This is a case of evolution occurring within the last 200 years.

 

7) THE FLU

If you aren’t convinced yet, consider the virus that puts you out of commission with the common cold or the flu at least once a year. Each year your immune system develops antibodies to fight it off, which will stay in your body and remember that specific virus forever, and every year, a new strain comes and catches your immune system off guard. This is not because there are innumerable viruses; it’s because that virus is evolving from year to year into something your body cannot recognize and which can reproduce using your cells. This is what scientists and doctors are referring to when they talk about the risk of vaccines creating a super virus. The idea is that by doing battle with viruses, we are actually pushing them to evolve into something that we cannot effectively prevent or treat which will then have huge impacts on the population.

 

So there you have it, seven examples of evolution happening under the watchful eye of humans. And I could go on. Regardless of how you imagine life originated, because that is a completely different debate, I think it’s hard to deny that evolution is a very real process. You may have noticed a common thread in the examples above – most modern evolution is a result of gross human negligence and since that is not on track to change, I’m betting we will see even more life in nature that will.


Clones In Space, I Have Placed (Infographic)

 

By Brent Wells, PhD

 

Did Lucasfilm Ltd. direct an explosion in cloning efforts at first rumors of the storyline for Episode II, Attack of the Clones? Or did scientist’s unstoppable desire to achieve the impossible instruct the fate of the Empire? We may never know. But the happy coincidence and a recently christened holiday have brought you science in pictures so don’t think about it too much and enjoy.

 

Credit: Brent Wells, PhD
Credit: Brent Wells, PhD.
Click on the image and then expand to full screen.

 

If I’ve managed to assemble this infographic even half as well as I imagine George Lucas can assemble a sandwich, you probably command a decent understanding of the history of cloning technology by now. Like the special effects technologies developed at Industrial Light and Magic (ILM), cloning has advanced from its humble, yet provocative beginnings, into something awe-inspiring and useful at once. Unlike ILM special effects, each subsequent step in the maturation of cloning tech brings something more impressive than before.

 

A new study published just last week in the journal Nature describes the creation of a human, diploid, embryonic stem cell population using SCNT from an adult with Type 1 Diabetes. This is huge for a number of reasons: 1) They were able to use tissue from an adult, which negates any ethical concerns surrounding use of embryonic or fetal tissue. 2) They created diploid cells that can be used in treating human disease. Similar embryonic stem cells were generated in 2011 but were triploid, which means they contained three sets of chromosomes instead of the normal two found in humans, making them non-compatible and therefore inviable for use in disease treatment. 3) The stem cells, cloned from an individual with Type 1 Diabetes, can give rise to the very cells lost due to Type 1 Diabetes, and since they are clones of the affected individual, his/her body will not reject treatment that introduces new cells into their body to replace those lost to the disease.

 

This advancement in cloning technology is a significant step forward in creating stem cell banks that can actually be used in the study and treatment of disease on a case-by-case basis and will extend well beyond Diabetes. It also furthers efforts in the growth of complete replacement organs for those in need of matching donors – after all, there’s no better match for you than you.

 

If you want to learn more about cloning, *waves hand in front of face, uses weird voice inflection* You want to learn more about cloning. You’re going to look into the following resources. I am not the droid you’ve been looking for.

 

Wikipedia, of course

The Basic Science Partnership at Harvard Medical School

The Animal Biotechnology Resource at UCDavis

The Genetic Science Learning Center at the University of Utah Health Sciences

Or just Google it…

 

May the 4th be with you.


The Evolution of the Cutest Creatures in Star Wars

 

By Chris Spencer and Brent Wells, PhD

Credit:  Mary Harrsch (Flickr).
Credit:
Mary Harrsch
(Flickr).

Being such a staple of science fiction, Star Wars contains creatures whose evolution ought to be explainable scientifically. So strap in, and come with us as we cast Darwin’s eye over four species from the Star Wars galaxy:

 

WOOKIEE

The only wookiee we saw in the original trilogy was the enigmatic Chewbacca, but fortunately enough, we were able to get a glimpse of an entire wookiee community in Revenge of the Sith. These powerfully built furry humanoids are an arboreal race from the planet Kashyyyk. Being tree dwellers, they are well adapted for climbing – having sharp grasping claws, and strong backs and calves. Their characteristic fur has evolved for two purposes: it can be any of a range of earthy brown colours for camouflage whilst hunting terrestrially, and it produces a water repellent oil for swimming. Their sharp teeth and keen sense of smell are hallmarks of a species evolved to be hunters.

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Credit: originalpozer (Flickr).
Credit: originalpozer (Flickr).

RANCOR

According to Wookieepedia, rancors are large, carnivorous reptomammals from the planet Dathomir. Before I move on, a reptomammal, as far as I can tell, is a warm-blooded, oviparous reptile. Rancors grow as tall as 8-10 meters with long, pronounced arms and hands and small, under grown legs, kind of like a reverse T. Rex. This massively unbalanced center of gravity would normally be an evolutionary conundrum, but as a reptomammal, it’s clear the rancor plays by nobody’s rules, including natures, just like Earth’s duck-billed Platypus.

The massive size and top heaviness of rancors can be attributed to the low gravity on Dathomir. Alternatively, their size may be a consequence of the rich, almost unending diet the planet provides or the fact that Rancors, unlike regular mammals, lay eggs; it has been suggested that vivipary could limit the size of land-dwelling mammals. One final factor that could have aided in the evolution of such a large predator is the temperate climate the rancor evolved in. An inverse correlation between temperature and body size has been seen in some warm-blooded mammals, maybe because of overheating issues, maybe as a secondary consequence of higher atmospheric CO2, which would lead to more plant food sources and therefore prey food sources. The rancor’s thick, reptilian skin, large claws and teeth, and powerful jaws are all traits that evolved to aid their predatory abilities and their sense of smell became keen to help them find mates.

Rancors give birth to two young at a time, like polar bears, and following their birth, the young are carried on the body (one clutching to its chest and one to its back) until the young reach maturity. This is no easy feat considering the young are up to three meters tall at birth - this is nearly 50% the size of the adult rancor. As an apex predator, we can assume the rancor hunts and therefore attacks its prey. It would also need to defend its kill from other rancor and top predators roaming Dathomir in search of a free meal. Therefore, we can hypothesize that the evolution of its unnaturally long arms came as a way to do battle while the equivalent of a five-year-old child is strapped to its chest. Without extra-long arms with which to work around the front child, the young would surely perish during the battle, preventing the inheritance of genetic information and fixation of traits in the wild population. By carrying double their own bodyweight around in children, rancors have also found a way to lower infant mortality in the species.

 

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Credit: Brendan (Flickr).
Credit: Brendan (Flickr).

TAUNTAUN

These furry bipeds were used on Hoth by the rebellion in the opening scenes of Empire. Living on an enormous snowball such as Hoth will necessitate adaptations not dissimilar to those displayed by polar bears, including being warm blooded (they are reptomammals not unlike the rancor) - as referenced by Han’s innovative use of the interior of a tauntaun. Their tridactyl feet are furry and with splayed toes to act like snowshoes, with claws to help gain purchase on icier terrain. They also have four nostrils serving to warm air before entering the lungs. The larger pair of nostrils can seal to keep snow out during periods of rest. One key aspect of tauntaun physiology is one shared by many arctic fish: anti-freeze in the bloodstream.

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YODA

Credit: Angelo Su (Flickr).
Credit: Angelo Su (Flickr).

Yoda belongs to a species of small, long-lived creatures with green skin. His longevity is a consequence of a calorically restricted diet and an incredibly slow metabolism, something his species evolved in conjunction with their short stature and slow movement. They live in the wet, dark swamps of an unnamed planet similar to Dagobah, where Yoda was later exiled. Their diet is composed primarily of swamp plants and small insects. Yoda’s species has evolved tough claws on their fingers for prying bark from trees in search of beetles and other insects. Their unusually large ears have evolved as a means to avoid capture by larger, carnivorous animals that would gladly have them for dinner. Hearing predators from a distance is particularly necessary given their slow speed. Their green skin was also evolved as a defensive mechanism to help avoid predation through camouflage; green is the perfect colour for blending in with the large ferns and aquatic plants of their home planet and the creatures of this species are all but invisible among the green swamp gases that persistently hang in the air. Do not confuse Yoda’s bursts of speed during battle with a common trait of all members of his species. He was a Jedi Master, which provided him with special skills. A skill he did not possess, however, was a mastery of the English language.

 

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Making Science with The Lights Off

 

By Brent Wells, PhD

Good science has always depended upon the proper equipment and experimental conditions, and as techniques and equipment advance, so do the requirements for accurate temperature control, computer-automated micromanipulation and laser-based imaging equipment. So what do you do when the power grid serving all of those high-tech necessities suddenly ceases to be that thing you take for granted?

You certainly don’t panic. There will be plenty of people taking care of that for you.

 

Having worked in New York City labs during both the 2003 and 2012 (Hurricane Sandy) blackouts, I’ve become a bit of an expert on science in the dark. Here’s some advice to consider should you find yourself in a similar situation.

 

First thing’s first, they will evacuate you from the building whether you are finished with your experiment or not. Your best bet, in the instance of sudden power loss, is to scramble to finish whatever you can (assuming it requires no electricity) before they have time to assess the situation and make a decision to evacuate. And for God’s sake, if you’re rearranging shelves in the -80°C freezer, cram them anywhere you can and shut the damn door immediately. If you know you will not be able to finish something critical before being dragged from the building, a well-scouted, temporary hiding spot can have its benefits. Just practice stealth when sneaking out of the building an hour later.

 

When your pipette is finally pried from your white-knuckled grip, you’re probably looking at a 10 to 17-story walk down to the street. Ease yourself down the stairs. There’s no hurry. You will be seeing plenty of stairs in the immediate future. With any luck, you have a few hours of daylight left; you’re going to want to use them wisely.

 

Now, this is important; before you’ve parted ways with your lab mates, plan your evening. In a few hours, your cell phone will be nothing more than a sick tease in your pocket and I wouldn’t recommend subjecting yourself to the kind of insanity brought on by a night alone staring into the darkness. I would, however, recommend immediately agreeing on a place to BBQ. Not even Edison can prevent you from lighting a fire underneath anything edible, and besides, you’ll want to clean the perishables out of your refrigerator now. This would also be a good time to grab your beer and booze. Where would be the best place to BBQ, you ask? Well, on a rooftop of course. The stairs will be an added hazard, especially later in the night, but you’ll want to get as close to the moon as possible – for the extra light, the diminished gravity, and the right amount of howling.

 

Money saving tip: this is the perfect opportunity to try out your bargaining skills before that trip abroad while becoming a BBQ hero at the same time. Rush to your local grocer and convince them that $5/lb for all of their New York Strip now will seem pretty good in a few hours when they are filling trash bags with unsold chicken thighs.

 

To be certain, all of this is not going to be easy. You’re going to have to make a lot of difficult decisions. For example, when you realize the emergency lights are out in your apartment building stairwell, do you use the flashlight on your cell phone to light the 10 flights or save the battery? Do you reevaluate this decision on the way back down when you are carrying five bags of meat and glass beer bottles? Do you take your new jar of Mayonnaise? You will not see your Mayonnaise again if you do.

 

When I had to make these decisions in 2003, I had just had pins inserted into the second toe of each of my feet and I was supposed to be on crutches. If you, likewise, have limited mobility in this situation, I urge you to convince someone else to grab supplies from your apartment; you will still have to get to that rooftop, remember?

 

I can guarantee, with some certainty, two things about that night the power goes out and two things about the day following. On that night you will 1.) Go too hard and too long, realizing there is nothing better to do and that work will be canceled the next day and 2.) You will be lucky to get from rooftop to street level without incident. On the day following, you will 1.) Feel like hell, especially considering the fact that your AC will have deserted you, and 2.) A friend will come knocking on your door to beg for your assistance in moving precious, temperature-sensitive lab strains to a distant building that happens to be served by a generator.

 

With the subway system crippled, biking will be the only logical means of getting to lab to help your friend. Please, use caution. While your head may be pounding and the morning will seem unusually bright, the intersections will be hazardously dark. You will be quite amazed at how fast morning commuters can degenerate into lawless maniacs when you take away traffic lights, and I wouldn’t recommend testing the new hierarchy of the road on your 30lb Specialized. Ride slow and give way.

 

The move will be tedious and painful. You will not believe how much this person deems ‘critically necessary’. They will offer to buy you lunch and beer for helping, but it will be an empty gesture considering every restaurant and bar are closed. They will forget to make it up to you later.

 

What started as fun and games, as something novel, will get old pretty fast. If it were just lab that were out of power, this might be a decent predicament, but the fun of carrying fresh water up countless flights of stairs daily will begin to wear thin. You will realize that you have, in fact, developed quite a taste for television, climate control and high-speed Internet. You will spend the rest of your week, in the very generator-powered building you were cursing your friend for making you visit, microwaving burritos, watching Netflix and playing board games, wondering if this is some sick approximation of what life will eventually bring. Purchase your checkerboards and dominos now. And I hear army ration packs have a decent shelf life.

 

In the end, you will welcome the power like an old friend when it returns and you might even welcome the idea of getting back to lab. But when the harsh reality of dealing with work that has been suddenly abandoned, as opposed to wisely suspended, is realized, you will look at the Amish with a newfound envy.

 

And don’t forget, you promised your friend you’d help get those precious strains back where they belong.

 


Building yeast chromosome from scratch

Building Better Beer, One Nucleotide at a Time

 

By Brent Wells, PhD

An international team of scientists headed by a group at the New York University Medical Center has created the world’s first eukaryotic synthetic chromosome, meaning they have literally engineered life from its smallest units. Intrigued? You should be.

 

This work, recently published in the journal, Science, was achieved in the common budding yeast, Saccharomyces cerevisiae; the very same little fellow that makes your bread rise and your beer ferment.

 

A chromosome, in case you were wondering, is a continuous grouping of a subset of your genes. All 20,000+ human genes are spread across 23 distinct chromosomes while yeast genes, about 6,000 of them, are spread across 16. The goal of this study was to choose one of those naturally occurring yeast chromosomes and replace it with one synthesized, from scratch, in the lab.

 

How do you synthesize a chromosome? The answer is bit-by-bit-by-bit and with plenty of cheap help.

 

The group started with small, overlapping oligonucleotides, which are very short pieces of DNA - about 70 base pairs in this case. Next, you need an army of undergrads trying to earn an A grade in their Building-A-Genome class, and whose parents are unknowingly paying for your research, to stitch all of these small pieces together into increasingly larger fragments. This is what I imagine building a weave for Rapunzel would be like. Final assembly is completed in the yeast cell where the natural chromosome is replaced, one chunk at a time, with corresponding pieces of synthetic chromosome via a process called homologous recombination.

 

This was not, however, a Gus Van Sant-Psycho-shot-for-shot remake of the original. The chromosome lost a little weight in the process, trimming down to 272,817 base pairs from 316,617. Remarkably, the synthetic yeast were just as viable as the naturally occurring strain, suggesting that there’s a lot of useless DNA floating around in our cells. Among the discarded bits were regions of non-coding DNA called introns as well as transposons. Transposons are DNA sequences that can actually jump around the genome carrying other pieces of DNA with them and which are thought to be a major driving force in evolution.

 

Speaking of evolution, the group also engineered in sequences that would allow them to randomly alter the genome by taking out non-essential genes in a process they call SCRaMbLE-ing. The removal of these genes allows the team to look at the effects of variable-scale genome size reduction on viability. In other words, they can induce a genome ‘scramble’ in millions of yeast cells at once, which will remove different subsets of genes in each, and look at which genes are gone in the ones that survive. This mimics genetic deletion events that can happen naturally during evolution and will help us understand how evolution may occur and the pressures that can lead to the traits it eventually fixes. You can also really speed up a notoriously slow process.

 

This is not the first time a synthetic genome has been attempted, or completed. Groups have had success with viral and bacterial genomes in the past, but this is the first instance of something on this scale. Other groups are currently working on more of the 16 yeast chromosomes with the goal of eventually creating a completely synthetic yeast cell.

 

Beyond the potential to understand mechanisms of evolution and just see if we can actually do it, generation of synthetic organisms have far-reaching commercial potential. Synthetic yeast could be used to generate more efficient bio-fuels, rare medicines for Malaria and Hepatitis and more. And it would be cheap – at least in principle; did I mention they are calling these ‘designer’ chromosomes? I can only assume the synthetic strain was code-named Fendi or Prada.

 

So, should you be worried about ingesting some synthetic yeast during your next trip to Dunkin’ Donuts or Subway? Hardly. Scientists have engineered fail-safes into the synthetic chromosomes that make it impossible for the yeast to live outside of special conditions provided only in the lab. Of course, they did the same thing on Isla Nublar in Jurassic Park and anyone that’s seen Jurassic Park II knows that Jeff Goldblum nailed it when he demanded ‘Nature always finds a way’. But to those alarmist naysayers saying ‘What about the potential for environmental catastrophe?’ Let me offer this recompense: ‘What about the potential for better beer!’