The Birds and the Bacteria

A double dose of science goodness for you, my galleons. Aren’t you lucky?

Scientists in Savannah, GA (can anyone read this city’s name in anything other than a lazy, rolling Southern drawl?) have spent the last 30 years studying the songs of sparrows. Which probably does not involve them sitting out on their large porches, sipping mint juleps and listening to the local wildlife, but dammit all, that’s how I want to imagine it went down.

Anyway, the Savannah scientists have discovered that the songs of their sparrows have changed over the course of 30 years. Which might not be too surprising (one would think they’d have to vary their songs every so often, to keep the ladies interested), but considering sparrows actually only learn one type of song in their lives, it is very interesting. The scientists liken it to human speech patterns, making the comparison that the way people spoke in the 80s is quite different than how we speak today. After all, slang terms rise and fall, becoming a central feature of the language of a certain time period. The same holds true for birds- their songs are full of little bits of “slang”, clicks and trills that change over time.

It’s a fascinating look at cultural evolution. Male sparrows learn their song from the males around them, meaning the changes in song are learned changes being passed to new generations. It’s likely the changes came about thanks to the fickle nature of females- their preference for males with shorter trills, for example, means those males will reproduce with them and will teach youngsters the same trilling technique. And all this happened in a mere 30 years, allowing us to study the evolutionary patterns. Awesomesauce.

***

Even astronauts have to worry about splattered bugs on their windshields, even if those bugs are microscopic little bacteria. A recent study by NASA of the middle and upper troposhpere has revealed that a host of microorganisms hang out in the trophosphere, a region of the atmosphere 4-6 miles above the Earth’s surface. This raised some sciencey eyebrows, seeing as the trophosphere is a difficult environment for life to flourish in.

The microorganisms consisted of a variety of bacteria types, as well as a few fungi. The types of bacteria varied depending on where the air samples were taken- marine bacteria were found in air samples from above the ocean, while terrestrial bacteria were abundant in the above-ground air samples.

Of course, whether the microorganisms actually make their home in the troposphere is not yet known. While the troposphere does contain carbons than many of the varieties of found bacteria could thrive on, it’s also likely the microorganisms get kicked up there from the planet’s surface. Frankly, based on the concentrations of marine bacteria over water and terrestrial bacteria over land, I’d wager the latter. Still, it was surprising for the NASA group to find so many of the little buggers kickin’ it way up there.

Atmospheric scientists are keenly interested in this discovery for a few reasons. The first is that these microorganisms might play a role in the formation of ice, impacting weather patterns. And second, it could represent a new form of long-distance bacteria transport that would be of note for disease transmission models.

Who knows, maybe there are whole bacterial colonies hanging out in the clouds… An odd ecosystem (unless you are a Care Bear), but hey, whatever works for you, little bacteria.

Beat-Bots

A few months ago, dear galleons, we talked about artificial jellyfish created using rat heart muscle tissue. Some real Frankstein-y cyborg shit.

But of course, those jellies were just the beginning. Behold the latest in rat heart robotics:

 

That odd little guy is a little biological robot that walks. Well, okay, he doesn’t so much walk as he inches along as the rat heart muscle powering him causes his little body to flex.

Bio-bots like this guy were created at the University of Illinois. The 7mm long bots were printed on 3D printers using hydrogel (a biological substance frequently used in tissue engineering). After the bot was created, the underside of it was coated with a layer of living cardiac tissue. Rat heart tissue, to be precise.

As the heart tissue “‘beats”, the board-like protrusion on the bot contracts and curls under, pushing the little bot just the teeniest bit forward. Slowly, it can inch its way across a surface.

And I do mean slowly. The top speed one of these little bots has been clocked at is 1mm every 4 seconds (1.5cm per minute).

So… why make them?

The Illinois researchers hope the bots could (with many modifications) eventually work as toxin sensors, going into various environments and ferreting out toxins, then (possibly) neutralizing them.

Until then, they plan on trying to create bots in different shapes, as well as seeding the bots with different types of cells (like nerve cells or light-sensitive cells) to give them new capabilities.

The future is coming for us, galleons.

…It’s just inching along really, really slowly.

SQUIDMAN, ASSIST ME!

Galleons, meet Acropora nasuta, a colorful stony coral:

Besides being quite pretty, Acropora nasuta is interesting for another reason-

It’s motherfucking Aquaman.

Which, granted, might not seem very impressive (he is, after all, a bit of a ponce). But the coral is pretty neat. See, it’s not just people that go in and fuck with reefs. There are actually toxic species of seaweed that can destroy our pretty coral friend.

But fear not, my anthozoaphilic galleons, for the little coral is not defenseless. For it can CALL UPON THE CREATURES OF THE SEA TO SAVE IT.

Well, not sharks, which would be rather useless against seaweed, but rather gobies!

There are many species of gobies, and these little fish are among a multitude of aquatic life that make their home in coral reefs. But what makes these little guys unique in their neighborhoods is that they are the only ones who respond to distress signals from the seaweed-infested coral. Other fish, like damselfish, flee the coral when it’s in distress. “The neighbourhood is going to hell, we’re out of here,” Mark Hay, of the Georgia Institute of Technology, explained. “But the gobies both come out and trim the algae.”

The experiment was actually pretty fascinating. The research team exposed gobies to various selections of water. Sometimes, they took water from directly around the seaweed. Other times, they took it from where the seaweed and coral were in contact. They then exposed the gobies to these water samples. The gobies did not react to the seaweed only water, but moved toward the source of the seaweed/coral samples. But it only worked for their home coral- when the tests were run with a related coral species, the goby didn’t react at all.

Coral with goby residents have it made- they see a 30% reduction in the invading seaweed within three days. Some goby just straight up eat the seaweed, while other species just work to trim it away from the coral. Either way, the coral wins. And some gobies gain more than just a safe home- the seaweed also makes the little fish more toxic to predators.

Nature is way cooler than comic books.

A Panoply of Protozoan Persuasions

Sometimes, it can seem as if men and women are completely different species (at least, that’s what the trashy magazines and multitude of shitty books on relationships would have you believe). Indeed, the behavioral and hormonal differences between the two can often feel like an insurmountable gap for some.

But imagine how much tougher those whinging tits would have it if they had to contend with seven sexes, not just two.

Sound crazy? Well, it’s not crazy if you’re a protozoa. Namely, not if you are Tetrahymena thermophila, which are fairly common fresh water ciliates who just so happen to have seven different genders (conveniently named I – VII). Not only that, but our little unicellular friend also has two nuclei: a macronucleus for all its basic cellular functions, and a micronucleus dedicated to getting it on.

That’s right- their sex life is too complicated for their regular nucleus. An individual sex cannot reproduce with another of the same type (Type I can’t have little protist babies with another Type I, for example), but those 7 sexes can combined in 21 different combinations.

So yeah, it’s a little more complicated than man + woman = baby.

But what’s really interesting about these little guys is that those 7 sexes are not evenly distributed through the population. See, their sex is not determined solely by genetics (like a human’s is). Instead, their genes give them a probability of being born a certain sex- the environment is actually the determining factor (this is not a unique trait- there are many other species, including the three-lined skink lizard, that incorporate temperature and environment into sexual determination).

The sex-influencing mat gene and 13 other alleles are the influencing genetic bits. And the mat gene comes in multiple varieties, so when you really think about it, it’s no wonder the little guys need a completely separate nucleus to handle procreation.

Anyway, the alleles that allow for the possibility of multiple different gender outcomes perform better than those that only allow for one, which eventually skews the population a bit.

Seven sexes may seem like overkill, but it appears to be working for these little guys. They’re like a tiny, Earth-based version of Star Trek Species 8472 (which had 5 sexes, I believe)… only not as ugly:

I’m not sure how you determine this thing’s sex, but sure, go over there and check between its legs… I fucking dare you.

The Flies Don’t Lie… Or Do They?

Galleons, the primary reason I value science over religion is that science pursues the truth, whereas religion does not. And the search for truth is a constantly shifting thing. We build on it, tear it apart, start again. As our technology advances, our insights into the mysteries of the universe deepen. As we grow as a society, it is our science that is slowly unveiling the truth around us.

There is nothing more beautiful than that. Nothing more important.

But even scientists are human, prone to stumbling, mistakes, oversights. There are rules and methods in place to minimize subjectivity in experiments and to make sure all studies and experiments are held to rigorous standards. And yet, the human element slips through.

This becomes particularly problematic when that human element causes a flawed test/experiment that is not caught for years because scientists get lax and don’t follow the rules. If they let the one study stand as fact, without replicating it to test the validity of its assertions, then we have a problem. A big one.

As my hero/idol/personal god Richard Feynman once said:

When I was at Cornell, I often talked to the people in the psychology department. One of the students told me she wanted to do an experiment that went something like this–it had been found by others that under certain circumstances, X, rats did something, A. She was curious as to whether, if she changed the circumstances to Y, they would still do A. So her proposal was to do the experiment under circumstances Y and see if they still did A.

I explained to her that it was necessary first to repeat in her laboratory the experiment of the other person–to do it under condition X to see if she could also get result A, and then change to Y and see if A changed. Then she would know the the real difference was the thing she thought she had under control.

She was very delighted with this new idea, and went to her professor. And his reply was, no, you cannot do that, because the experiment has already been done and you would be wasting time. This was in about 1947 or so, and it seems to have been the general policy then to not try to repeat psychological experiments, but only to change the conditions and see what happened.

Nowadays, there’s a certain danger of the same thing happening, even in the famous field of physics. I was shocked to hear of an experiment being done at the big accelerator at the National Accelerator Laboratory, where a person used deuterium. In order to compare his heavy hydrogen results to what might happen with light hydrogen, he had to use data from someone else’s experiment on light hydrogen, which was done on different apparatus. When asked why, he said it was because he couldn’t get time on the program (because there’s so little time and it’s such expensive apparatus) to do the experiment with light hydrogen on this apparatus because there wouldn’t be any new result. And so the men in charge of programs at NAL are so anxious for new results, in order to get more money to keep the thing going for public relations purposes, they are destroying–possibly–the value of the experiments themselves, which is the whole purpose of the thing. It is often hard for the experimenters there to complete their work as their scientific integrity demands.

What is true of psychology and physics is true across the board. Sometimes, scientific integrity slips. And this is a major concern.

I bring this up because there is evidence that an extremely well-known study involving fruit flies (people always think about lab rats, but I think we discuss experiments involving fruit flies with much greater frequency) has recently come under fire as being “fatally flawed.” It’s Angus John Bateman’s 1948 study regarding the evolutionary advantage male fruit flies gain from being promiscuous.

It’s kind of a big deal.

See, this study was huge. It has informed and influenced an entire sub-field of evolutionary biology. As Patricia Adair Gowaty, a professor of ecology and evolutionary biology at UCLA, said, “Bateman’s 1948 study is the most-cited experimental paper in sexual selection today because of its conclusions about how the number of mates influences fitness in males and females.”

However, in all the intervening decades, the experiment has never been repeated using the exact methods Bateman used. Until now. And the results are shaking the foundation of this section of evolutionary biology.

So, in case you are unfamiliar with the experiment (or just need a refresher), here’s what it’s all about:

Bateman created isolated little populations of fruit flies in jars, either 5 males and 5 females or 3 males and 3 females. Within their isolation, the fruit flies were free to mate at will. Bateman then studied the progeny that survived to adulthood. However, even within these isolated populations, Bateman needed a reliable way to determine the parents of the grown children.

Enter the defects.

Bateman selected first generation fruit flies with very specific genetic mutations. Squinty eyes. Curled wings. Thick bristles. Without the technology of today that allows us to determine the genetic parentage of the flies, Bateman needed strong, visible, transferable mutations.

So, by placing 6 or 10 flies in these communities with 6 or 10 different, extreme mutations, Bateman could work backward to determine the parentage of the fly children.

Well, some of them, that is. And that’s where the problem lies. See, if you know your genetics, you know those fly babies could display the mutations of both parents, the mutation of only one parent, or no mutations at all. So Bateman could only study the fly children that demonstrated two mutations because they were the only ones that could have both parents reliably identified.

Maybe you see the problem now. The sample was skewed.

Gowaty and her team were the ones who replicated Bateman’s famous experiment, and they found that those double mutation children were the least likely to survive to adulthood (as you are probably aware, mutations often represent a disadvantage to the carrier). So the roughly 25% of the fly progeny exhibiting the double mutations were the most likely to die, shrinking the sample even further. With a sample that small, there’s no way Bateman could accurately equate the number of mates for each adult subject.

But that’s not the only problem with Bateman’s study. Turns out, according to his methodology, more offspring were assigned to fathers than to mothers (leading to the conclusion that male flies were more promiscuous). But all of those fly babies need both a father and a mother.

So, Bateman’s study has some glaring issues. But were the conclusions sound?

Uh… the results are inconclusive, as it turns out.

The markers used to determine parentage (those pesky mutations) actually influence the parameters being measured. Because when the mutated children die off before reaching adulthood (as they are more likely to do), the results become biased. The children are no longer an accurate measurement of the number of mates each adult fly had, because not all of them survived.

“Here was a classic paper that has been read by legions of graduate students, any one of whom is competent enough to see this error,” Gowaty said. “Bateman’s results were believed so wholeheartedly that the paper characterized what is and isn’t worth investigating in the biology of female behavior.”

Let this serve as a lesson to the scientific community. This is a study that should have been retried immediately. Certainly at some point in the last 60+ years, right? We can’t be constrained by strong theories and paradigms. In the world of science, all it takes is one person with a new perspective to come along and shatter these existing limitations, stretching our knowledge and pushing us ever closer to the truth. That is the purpose driving every scientist, that rigorous pursuit of truth.

Here’s hoping that we take away from this revelation a renewed understanding of the need for strong scientific integrity. And here’s also hoping that shattering this foundation allows scientists like Gowaty (who studies female mating habits in various species) a chance to find the truth, unhampered by the constrictions of paradigms set by a flawed study.

Brand New ‘TAG’: Scientists Rewrite Genome

I love making German puns (especially when nestled within a Doctor Horrible reference)…

Anyway, a recent bit of news out of Harvard, Yale, and MIT (yes, we’re playing with the big boys today) is an interesting piece of tech that could revolutionize genetic manipulation.

Galleons, I assume you are all familiar with the find-and-replace function common in word processors. The Massachusetts Bay Transportation Authority is all too familiar with it, as they recently made a hilarious mistake on their commuter rail tickets in the month of June. Apparently, they did a find-and-replace on their tickets, replacing “MAY” with “JUN”, which led to:

Good times.

On the whole, however, find-and-replace works quite well. And scientists have found a way to harness this common function and apply the basic concept to changing pieces of a cell’s genome.

Skeptical? You aren’t the only ones.

“We did get some skepticism from biologists early on,” says Peter Carr, senior research staff at MIT’s Lincoln Laboratory. “When you’re making so many intentional changes to the genome, you might think something’s got to go wrong with that.”

However, the researchers have managed to do hundreds of targeted edits of E. coli gene stuffs in living cells, with the altered bacteria behaving normally.

So, how do they do it?

There are four nucleotides involved in the genetic code of most DNA (and you’ll probably recognize, if not their names, then the letters themselves): Adenine, Thymine, Guanine, and Cytosine. When you take three of these nucleotides and put them together in sequence, you get a codon. There are 64 unique codons in the genetic code. On the most basic level, most codons add an amino acid to a growing polypeptide chain, which eventually becomes a protein in the capable hands of our friends, ribosomes. However, some codons (known oh-so-cleverly as stop codons) stop the addition of an amino acid to that chain.

Within E. coli, the TAG stop codon in the rarest (like Mew). Which makes it a prime target for our find-and-replace endeavor. An endeavor that requires some much more specialized tech than your average word processor. After all, it’s not like we can just open up a text file and type in our terms, replacing all with the click of a button:

The first bit of tech is multiplex automated genome engineering (MAGE), which locates specific DNA sequences and replaces them with a new sequence as the cell copies its DNA. Using this, scientists assume direct control of the changes happening within a cell.

The second is conjugative assembly genome engineering (CAGE), which gives them precise control over a process that bacteria use to exchange genetic material, wherein one bacterium builds a little extension/bridge to its neighbor and passes a piece of its genetic material to its new bridgemate.

Specifically, scientists used MAGE to manufacture 32 strains of E. coli in which they replaced 10 of the TAG stop codons with TAA stop codons. But there are 314 total edits required to completely replace all of the TAG codons, so scientists decided to use CAGE to make things a bit simpler.

Basically, they built a playoff bracket for their little bacteria strains, with each one sharing a bit of genetic goodness with one other strain. So, after Round 1 of CAGE, 16 strains were standing, each now containing 20 edits. Then they were put back into CAGE for Round 2, which yielded 8 strains with 40 edits each.

They’ve managed to get their strains down to 4 (with 80 edits in each, roughly a quarter of the total 314 needed), and they believe they’re on track to create that single strain with all of the needed substitutions.

After they’ve managed to substitute all of the TAG codons, they are going to go in and delete the machinery that reads that particular codon. After all, if it doesn’t exist anymore, why should the cell be able to read it? That will free up this slot for a whole new purpose, which scientists can use to encode new amino acids.

***

But… why? That’s always the question, galleons. While it just sounds cool to muck around in a cell’s genome like that, we all know scientists have to have some ulterior motives when bothering to create such sophisticated technology in an attempt to fine-tune this kind of genetic tampering.

And this is where shit gets scary.

See, with this technology, scientists could engineer bacteria that are resistant to viruses. Because viruses can only infect a cell if the bacterial and viral genetic codes are the same. Change the genetic code and the bacteria suddenly becomes safe from those pesky viruses.

While scientists claim they could also create little genetic firewalls that prevent their engineered bacteria from spreading their genes to natural bacteria (or just prevent them from being able to survive in the wild in general), I’m just saying…

It sounds like we’ve taken our first steps toward the accidental creation of a zombie virus and the subsequent apocalypse.

Galleons, get your shotguns.

Yes, I Spent My Saturday Night Reading About Kin Selection and Mucking About With Game Theory… So What?

There are a lot of words that can be used to describe me.

Altruistic is not one of them.

That being said, I’ve always found the concept of the altruistic individual a fascinating (if mostly unbelievable) concept. I’m cynical and tend to think, realistically, that little to no true altruism can occur- everyone is out for something, even if it’s simply the endorphin rush that accompanies helping someone else out. And yet, I still enjoy entertaining the notion of what real altruism would be like, both for the individual and en masse.

It’s not really something I’m good at- imagining another person’s emotional reaction to events. I lack a lot of the empathy that seems inherently built into other members of my gender. Still, as a mental exercise, it can be diverting to at least make the attempt.

The question of how altruism could evolve within a species, however, was never something I thought much about. I’ll grant you that this is largely because I dismiss altruism as utterly useless- it serves no real survival purpose.

Or does it?

***

Biology is not my strong point (insert some crude joke about biology and sex here, hur hur), scientifically speaking, though that doesn’t mean I don’t find it interesting. It just tends to take a backseat to physics and chemistry for me.

Usually.

Therefore, the concept of social evolution was not one I was wholly familiar with (and, frankly, given the sheer scope of biology and evolution, I can’t say with any real conviction that I’m familiar with it now). We all know about Charles Darwin, the HMS Beagle, and evolution by natural selection. If you are not radical Christians and/or batcrap crazy, you probably accept this scientific theory as fact. The overwhelming amount of evidence supporting natural selection and evolution is quite impressive, after all.

Social evolution is another facet of evolutionary biology. One that was not covered in my public school education, though I’m almost positive I’ve run across a mention of it somewhere before… Anyway, social evolution is concerned with social behaviors that have fitness consequences for others. There are four ways to categorize these social behaviors, depending upon their fitness consequences for the donor and recipient:

I know you love it when I include a diagram for your viewing pleasure, dear galleons.

So, to get back to our original issue- altruism is one of the possible categories of social behaviors. Seems about right.

But, I have to ask: Why would any organism pursue an altruistic course when it would lead to absolutely zero benefit to them? I mean, as Darwin himself said, “he who was ready to sacrifice his life, as many a savage has been, rather than betray his comrades, would often leave no offspring to inherit his noble nature.”

***

Kin selection is the current prevailing theory for the prevalence of altruistic behavior among organisms, having ousted the weak group selection theory that went before. Group selection suffered from the notion that, while a tribe of altruistic individuals would indeed triumph over others, due to their cohesion and the help they provide one another, this idyll would be shattered by just one selfish mutant in their ranks. This mutant, due to the fitness advantages its selfishness would gain it, would out-produce the altruists and the village altruism would quickly become swamped by selfishness. The ease with which altruism would be banished from a tribe served as a major stumbling block for group selection, as it really didn’t help explain the evolution and prevalence of altruism.

In the late 60s/early 70s, a new theory emerged to topple group selection. This theory was kin selection.

To understand how kin selection works, let’s imagine that altruistic behavior is genetic. This altruism gene makes its bearer share food with others. Which is nice, but (as mentioned above) this puts the altruistic individual at a fitness disadvantage. While they share their food with those around them, the selfish individuals hoard theirs. The altruistic individual will have less food than everyone else, thus their fitness disadvantage. As with group selection above, this disadvantage will quickly cause the altruism gene to die out as the species evolves.

However, let us now imagine that these altruistic types, instead of just sharing with anyone, only share with those that are related to them. Suddenly, a new pattern emerges. Because relatives are genetically similar, there is a possibility that, when the altruistic individual shares food with a family member, that family member also carries the altruistic gene (but does not express it). While this behavior still lowers the altruistic individual’s fitness, it increases the fitness of relatives- relatives who have a higher-than-average chance of carrying copies of that same altruism gene. Which means there will be a high chance that the altruism gene will carry into the next generation (via the relative of the altruistic individual) and spread. Which means that altruism can, in principle, be spread through natural selection.

Because of the strange nature of altruism’s evolution, it cannot be measured through relative fitness (the amount of progeny of an individual) but by inclusive fitness (the degree to which a trait is passed from generation-to-generation, including both direct and indirect methods). There’s some math that goes along with inclusive fitness, but I really don’t feel like getting into it- not that it’s not interesting, just that I think it will send me spiraling off topic. If you are curious, look up Hamilton’s rule.

***

The key to the evolution of altruism is that correlation between donor and recipient. We can illustrate this with one of my favorite aspects of game theory (we might have to do a series of posts on game theory, just because I love it good)- the Prisoner’s Dilemma.

I was inordinately excited when I realized I could work this in tonight, I hope you all know…

Anyway, here’s an example of the Prisoner’s Dilemma:

Two suspects are arrested by the police. The police have insufficient evidence for a conviction, and, having separated the prisoners, visit each of them to offer the same deal. If one confesses and the other remains silent, the confessor goes free and the silent accomplice receives the full 20-year sentence. If both remain silent, both prisoners are sentenced to only one-year in jail for a minor charge. If they both confess, each receives a five-year sentence. Each prisoner must choose to confess or to remain silent. Each one is told that the other would not know about their decision before the end of the investigation. How should the prisoners act?

Because we all love diagrams, we’ll now arrange this problem in a familiar fashion:

What makes the Prisoner’s Dilemma so goddamn fascinating is how it tends to pan out. The goal of this game (as with most in game theory) is for the player to maximize their own payoff, with no concern for the other individual’s. The end result is a Pareto-suboptimal solution (in which it is impossible to make one person better off without necessarily making someone else worse off). Rational choice leads both players to confess, even though both players would reap a greater reward (only 1 year in jail) if they cooperated. For, even though both players would get a bigger payout if they remain silent, they have no way of knowing what the other player will do. Since in any individual situation confessing is more beneficial than remaining silent, all rational players will confess.

Anyway, I’m sure you are all fascinated (you should be) by this, and if you are curious, you should delve a little deeper, as the Prisoner’s Dilemma gets particularly interesting when the same players play the game multiple times.

But what does this have to do with the evolution of altruism?

Let’s substitute our altruistic/selfish individuals into our Prisoner’s Dilemma. In place of confessing, we place selfish actions. In place of remaining silent, we place altruistic ones.

We can easily see that, if the game is played rationally, selection seems to favor the selfish. This is true. The only way the altruistic benefit is if they are paired with another altruist. The only way selection can favor altruism is if there is a greater-than-random chance of altruists being paired with one another in the game.

And how can we guarantee a greater-than-random chance of pairing altruists (or those recessively carrying the altruism gene)?

You guessed it: kin selection! That is how it all works. The reason altruism can survive.

Interesting, no?

***

So, what have we learned today?

Being selfish is easier, has higher payouts for the individual, and doesn’t involve this messy “kin selection” bullshit.

Also, the evolution of altruism tends to hint heavily at inbreeding…

Don't make Jesus make this face, galleons.

Inbreeding is wrong.

Don’t be an altruist.