Let's See How Far We've Come

 I'm waking up at the start of the end of the world-

No, no wait. Wrong reference. Boppin' song, but wrong reference. This is a reflection post!

And what a semester it has been. I've learned so much! I started out describing evolution by analogy of a level-up system, where organisms specialize into specific situations by way of natural selection and other mechanisms. Evolutionary theory, I said, was both a theory and a fact - in that it has lots of support, but it's still a scientific theory. I was also pretty stuck on the idea that evolution must take a long time. 

Oh, but how I've learned! Not that I was entirely wrong. I just had some misconceptions. Evolution is a level-up system of sorts. But it's a well-proven fact, theory only in name. And it doesn't take long at all! Evolution speed depends on generation time, and how drastic the difference between generations is. Which, gotta say, can be pretty damn drastic. 

But more important than the factual information I gleaned was what I learned about myself and my relation to science. For instance, I learned that R coding can really suck. BUT, it can also rock my socks off. I can say with confidence that evolution might be one of the coolest topics in science. I learned that I am too neurotic about getting assignments done early, but I have no qualms about asking for help when stuck. And I learned that I write some fire blog posts. 

Basically, I have a lot to be thankful for. A good sense of humor and a solid work ethic made this class pretty easy. Willingness to ask questions and learn from mistakes are essential in bouncing back from hard weeks. I need to chillax sometimes, and know that my schoolwork doesn't define who I am. But overall, I think this was a good class for me. 

Thanks for a fun time, y'all!

No Man's an Island - So Eat a Goddamn Cucumber

I hate it, you hate it, and yet few of us are truly free from the ripples of its existence. I could be talking about homework, or the flu, or the creepy baby in the store that won't stop staring at you like you're the first time they've seen another human being. But I'm not. 

I am, unfortunately, talking about depression. 

Heavy subject, I know. But bear with me. How many of us have dealt with depression in our lives, either personally or second-hand? If you're not raising your hand, I encourage you to really look at your closest circle of friends. Are you sure? 

See, rates of depression are on the rise - especially among the younger generation. We're 6-8 times more likely to experience it than others our age in 1938 (1). In fact, some studies suggest that there may be a steady increase in rates across age cohorts (2). Why? What's with these suddenly sad generations? Is it something in the water? 

Nope. Turns out it's something in our society. 

When modernization of a country is measured by GDP (Gross Domestic Production), rates of depression have a positive correlation with level of modernity (9). More modern countries have more depressed youth. 

Kessler RC, Angermeyer M, Anthony JC, RDEG, Demyttenaere K, Gasquet I, GDEG, Gluzman S, Gureje O, Haro JM, Kawakami N, Karam A, Levinson D, Medina Mora ME, Oakley Browne MA, Posada-Villa J, Stein DJ, Adley Tsang CH, Aguilar-Gaxiola S, Alonso J, Lee S, Heeringa S, Pennell BE, Berglund P, Gruber MJ, Petukhova M, Chatterji S, Ustun TB. Lifetime prevalence and age-of-onset distributions of mental disorders in the World Health Organization’s World Mental Health Survey Initiative. World Psychiatry. 2007;6:168–176.

This, by all accounts, makes no sense. Life should be easier - and thus less depressing - in more modern places. Think about it! Most of us don't have to worry about dying to a flash flood or starvation, of getting deathly ill or hunting for food. All the most extreme risks are gone from our lives. 

But we were evolved for extreme risk. And that is why, hypothesized Hidaka in their 2012 paper Depression as a disease of modernity: explanation for increasing prevalence, depression rates are on the rise. There is a crippling mismatch between the life our brains were designed for and the lives we lead in modern society. 

What are these reasons? There's a quorum and then some. First, our brains and our bodies are in a disconnect. Our bodies are evolved for long periods of famine and high physical activity. I don't know about you, but I haven't encountered either of those recently. But our brains thrive when our bodies are moving (5), and our bodies - once designed to pack on fat for lean times - now suffer from having too much of a good thing. Not to mention the difference in diets - carbohydrates rather than protein and fruits - which leads to disparities in basic nutrients (6, 7) and energy levels present in the foods consumed. All of this leads to obesity, another disease of civilization - which itself lends to higher rates of depression (4). 

Of course, our physical forms aren't entirely to blame. As bad as our situation is, we've exacerbated the effects with our own society. Humans are communal creatures. We've evolved to live together, help each other, and rely on the feel-good bonds of a group. But modern western society is a machine fed on individualism. Our pursuit of freedom from others is a double-edged sword; social competition, isolation, stress, and inequality all contribute to high rates of depression - especially among youth (3). No man is an island - we aren't evolved to be. That's why modern societies with more focus on collectivism (like Japan) also see lower rates of depression (9). And all this to barely even mention the societal pressure to fit in, act right, but still be unique. What a conflicting message! It's no wonder that our brains, hard-wired to fit into groups, form bonds, and help each other tend to wither in such a competitive and conflicting environment. 

All this to say that depression is an endemic of our own creating. But there's good news in that, too. If we made it, we can unmake it. So reach out to your friends. Go on a long walk. Eat a cucumber, for Pete's sake! Your brain and body will thank you. 

1. Twenge J, Gentile B, DeWall C, Ma D, Lacefield K, Schurtz D. Birth cohort increases in psychopathology among young Americans, 1938–2007: A cross-temporal meta-analysis of the MMPI. Clinical psychology review. 2010;30:145–154. 

2. Murphy JM, Laird NM, Monson RR, Sobol AM, Leighton AH. A 40-year perspective on the prevalence of depression: the Stirling County Study. Arch Gen Psychiatry. 2000;57:209–215.

3. Hidaka, B. H. (2012). Depression as a disease of modernity: explanations for increasing prevalence. Journal of affective disorders, 140(3), 205-214.

4. Nesse R. Natural selection and the elusiveness of happiness. Philosophical Transactions of the Royal Society B: Biological Sciences. 2004;359:1333. 

5. Teychenne M, Ball K, Salmon J. Sedentary Behavior and Depression Among Adults: A Review. Int J Behav Med. 2010;17:246–254.

6. Briefel RR. Secular trends in dietary intake in the United States. Annual review of nutrition. 2004;24:401–431.

7. Hoogendijk WJ, Lips P, Dik MG, Deeg DJ, Beekman AT, Penninx BW. Depression is associated with decreased 25-hydroxyvitamin D and increased parathyroid hormone levels in older adults. Arch Gen Psychiatry. 2008;65:508–512.

8. Baglioni C, Battagliese G, Feige B, Spiegelhalder K, Nissen C, Voderholzer U, Lombardo C, Riemann D. Insomnia as a predictor of depression: A meta-analytic evaluation of longitudinal epidemiological studies. Journal of affective disorders. 2011;135:10–19.

9. Kessler RC, Angermeyer M, Anthony JC, RDEG, Demyttenaere K, Gasquet I, GDEG, Gluzman S, Gureje O, Haro JM, Kawakami N, Karam A, Levinson D, Medina Mora ME, Oakley Browne MA, Posada-Villa J, Stein DJ, Adley Tsang CH, Aguilar-Gaxiola S, Alonso J, Lee S, Heeringa S, Pennell BE, Berglund P, Gruber MJ, Petukhova M, Chatterji S, Ustun TB. Lifetime prevalence and age-of-onset distributions of mental disorders in the World Health Organization’s World Mental Health Survey Initiative. World Psychiatry. 2007;6:168–176.

Speciation Speed Run

 Darwin was wrong. 

There, I said it! Go ahead and get angry! Feel free to boo, hiss, and chuck those rotten tomatoes you're hiding behind your back. But I'm right. 

As much as we hold Darwin up in the spotlight, the Father of Evolution didn't get it all right. He had no idea what DNA was, for starters. But more relevant today is his take on the speed of speciation. Darwin postulated that it takes centuries, if not millennia, of minor changes to fully separate one species into two. 

But he. Was. WRONG! 

Wild, right? Let's back up a bit, and I'll tell you why. 

When does one species become two? Darwin was right when he theorized that the split usually isn't instantaneous. You never had a chicken pop out of a dinosaur egg. Speciation is a process. You have a dinosaur, who has a slightly feathery dinosaur, who has a slightly smaller and feathery dinosaur, on and on until you eventually have the domestic terror known today as Gallus gallus. 

But if minor changes constitute speciation, then where do we draw the species lines? What makes an offspring different enough from its ancestors to constitute a new species? Without answering these questions, we can't determine how long speciation takes - because we don't know when speciation actually happens! 

Big questions, short blog. Let's speed things up. 

Darwin knew speciation is a process. Populations undergoing speciation grow slowly more distant in location, genes, ability to interbreed, and morphology, until eventually they seem like they were never the same population at all. There are no distinct stages; it's a continuum of "barely separate, kind of separate, almost completely separate". But most scientists agree that the "final" stage, when one species becomes two, is complete lack of interbreeding. Total reproductive isolation. 

Figuring this out in the wild can be a pain. But it also gives us something to measure. Speciation happens however quickly reproductive isolation happens. So then the question becomes, how fast can reproductive isolation happen?

Though he didn't articulate reproductive isolation in quite the same way, Darwin had the right idea. He theorized that it would take a long time for changes that affected reproduction to build up. And scientists thought that way for decades. Then they started to actually look at speciation. And they realized they were dead wrong. 

Reproductive isolation can happen dozens of different ways - premating isolation, postzygotic isolation, premating-prezygotic isolation, and all the individual methods within those categories. Some of those isolation mechanisms can take hundreds of years to form, just like Darwin postulated. But some, it turns out, are a helluva lot faster. 

How much faster? Let's try 20 generations. The speed of ecological speciation by Hendry et. al (https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2435.2007.01240.x) provides an interesting overview of speciation times in sympatric situations. They conclude that you could have significant differences in just 20 generations, depending on the scenario and the drivers of reproductive isolation studied. That's way faster than expected, even for allopatric species! I mean, 20 generations of bacteria can happen within days. That's way faster than Darwin's millennia! 

Another study, Extraordinarily rapid speciation in a marine fish by Momigliano et. al explores the speciation of European flounders over just 3,000 years. Generation time is roughly 4.2 years for the European flounder (https://www.fishbase.de/summary/1341#:~:text=Generation%20time%3A%204.2%20(2.9%20%2D%206.1)%20years.), which means it only took about 714 generations for speciation! That's, like, hella fast compared to the thousands and thousands of years that Darwin postulated. 

So maybe Darwin was off by a few centuries. Species still takes years for most complex organisms like eukaryotes, right?? 

NOPE. 

What would you do if I told you that some species encounter total reproductive isolation in just one generation? 

Now now, don't go running away yet! It's true! But it's only true because plants are absolutely wild when it comes to genetics. 

The fastest way to create reproductive isolation is to make an organism that cannot reproduce with any other organisms, but can reproduce with itself. Sounds impossible, but it's not. Because sometimes plants do this crazy thing where they duplicate entire copies of their genome. It's called polyploidy. 

Insane, right?! Polyploid plants exponentially increase the size of their genome, mostly by accident. Since you kinda need the same number of chromosomes to mate with something, this causes instant isolation from other plants of their species. The only organism left for our poor polyploid to mate with is itself. If it doesn't die off, generations of self-fertilization, spreading, and accumulating mutation can lead to an entirely new species of plant. And all that from just one generation of change! Talk about rapid speciation. One study I found, entitled The frequency of polyploid speciation in vascular plants by Wood et. al (2009) estimated that "15% of angiosperm and 31% of fern speciation events are accompanied by ploidy increase". That's no small number! 

So how fast is speciation? Sometimes, like Darwin said, it is a long and arduous process. Other times, speciation happens as quickly as you can reproduce. Because biology is wild, nature never has a clean answer, and plants absolutely refuse to make sense. 

God, I love science!

Syngnathidae's Secret to Sexy Success

 The title says it all, folks! Want to get all the guys? Want to look sexy as hell? We've got just the lady to advise you!

Meet Microphis deocata - the pipefish who has it all! She's got slimness, she's got color, she's got....something that looks like the DNA diagram in my Bio 198 textbook...

And yeah, that's right! I said "she"! Like a lovely woman blessed with bone structure, this stunning Syngnathidae (the family of all pipefish) has been evolutionarily gifted with beautiful stripes that her mate just can't match. 

No, literally. It's sexual dimorphism. The males of Microphis deocata don't have stripes. They look less like DNA diagrams and more like your everyday living pipe-cleaner. 

This is pretty weird in the animal world. While use humans are used to both sexes getting dolled up to hunt for potential mates, that just doesn't hold for most animals. Without opposable thumbs and makeup, animals must instead rely on their genetically-given gifts to attract the opposite sex. But usually it's males who do the attracting, and females doing the choosing. These funky flat fish are just pain strange! 

What's with their strange sexual selection? Well, sexual selection itself ain't straight. In fact, sexual selection is rampant in the animal kingdom. Just one trip to Aggieville on a Friday night and I guarantee you'll see it in action yourself! 

Jokes aside, sexual selection is found pretty much anywhere there is a disparity between amount of effort exerted by each half of a mated pair. This disparity can be small, like how a female frogs have fewer eggs over their lifetime than a male frog has sperm. Or the disparity can be MASSIVE, such as a female deer gestating and then guarding a fawn long after the male has gallivanted away. Generally speaking, the more selective the judging individual, the greater the gap in expended energy is going to be. 

Which brings us to the proposed question of pipefish. What's the deal with the flashy female? 

Well I won't leave you in suspense. Remember that "disparity" talk above? Well turns out not every species regulates the offspring protection to the female. And Microphis deocata just so happens to be in the same family as another creature well-known for it's fatherly prowess: 

The Seahorse!

Turns out male incubation of female eggs is a pretty common trait among all members of Syngnathidae - a family which includes seahorses, seadragons, and pipefish. In fact, it's one of the family's defining characteristics - aside from funky faces and a resemblance to horses, dragons, or pipes of course. Male incubation of eggs shifts the responsibility of offspring protection from the female to the male - effectively swapping which sex puts more energy into reproduction. To keep things fair, the female pipefish became the showy sex - letting the males sit back and choose at their leisure! 

You know, if you find DNA diagrams sexy. 

Why Isn't Everything The Same?

Someone smart once asked me, "If natural selection is often assumed to eliminate genetic variation, why is genetic variation not eroded over time?" 

It was Michi. Michi asked me. He asked all of us. 

Yay, blog post time! 

But really, it's a good question. I hadn't really thought of it before, but it makes a lot of sense that diversity-eliminating selection would homogenize living organisms if not given constant new sources of diversity. My first thought was "Oh! Mutation probably keeps selection from overtaking diversity."

Then I remembered our calculations about the frequency of mutation rates. And then I promptly panicked, wondering if we were just a few generations away from a world-shattering loss of diversity. 

But fear not, citizen. For mutation is not the only source for maintaining genetic variety! Really, when you think about it, it's not even the main source. Selection maintains variety all on its own. 

Selection is often assumed to eliminate diversity, in cases like directional and stabilizing selection. But we know those aren't the only kinds of selection. Remember those fish that eat off different sides? Negative frequency-dependent selection isn't an eliminator of diversity, but a promoter. Not to mention heterozygote advantage, where two different alleles must come together to make the most fit organism. Or even just plain ol' heterozygotes, hiding a bum allele behind a strong dominant allele. Genetic variation is tricky, y'all. 

Hell, even standard directional or stabilizing selection isn't perfect. It's gonna miss a few individuals here and there, allowing alleles to survive from one generation to the next. And if you have a phenotype that is vulnerable to a virus but who never gets infected with a virus, selection isn't going to act to take those genes out of the population! Selection is only as strong as the environment around it. 

Consider if you have an environment that changes a lot. There could be different selective forces working on a population at once, depending on the state of the environment. Some parts of the equator experience both desert and flood conditions, depending on the time of year. Selection is forced to balance lots of different, probably conflicting alleles to handle both situations - and in the process maintains genetic diversity. 

This happens a lot in sexual selection, too! Red individuals get more mates, but green individuals survive better because of camouflage - that means two different kinds of selection are each gunning for different traits. It may be that no selective force will overpower the other, and instead populations retain their diversity.  

Of course, some variation we see can be attributed to phenotypic plasticity and the like. And I'm sure I haven't thought of all the ways genetic variation avoids natural selection. There's, like, a lot of ways that variation sticks around in a population. Like. A lot. 

It's sneaky that way. 

A, T, G, C, M & M

 How is the theory of neutral evolution different from the theory of evolution by natural selection? How are they the same?

What's up, science people?! Who wants to talk about ~neutral evolution~?! 

...Yeah, me neither. But I don't make the assignments. Let's get into it. 

Neutral evolution is a big fancy way to describe a weirdly specific situation. Basically, genes mutate all the time. A lot of those mutations don't actually affect anything beyond the DNA sequence. These harmless or "silent" mutations occasionally become fixed into the genome - and they do or do not become fixed at a relatively constant rate. 

This sounds a lot like evolution by natural selection. But it can't be natural selection, since the mutations are fixating at random (and not because they're more or less advantageous). It's evolution done by drift. 

That's a lot of science jargon. I'm gonna translate it into M&M jargon instead. 

Let's say someone is putting five M&Ms of the same color in your bowl every minute. Sometimes they're all red, or all green, etc. But you're also eating a random assortment of 5 every minute. By chance, you might end up with way more green M&Ms over time. It doesn't matter to you, because they all taste the same; you just happened to not grab a bunch of green ones. That's neutral genetic drift. 

Now if you do this experiment over and over again eventually you'll wind up with a bowl full of every M&M color. That's fixation of neutral mutations by genetic drift. It doesn't matter to you that the colors have changed, that doesn't affect how you eat them, but they've still changed. And you'll get solid-colored bowls at roughly a constant rate, with some inputs (those 5 identical M&Ms) sticking around and others not sticking around. Since who stays and who goes is random, it happens at a constant pace. 

Do this experiment enough times, and you should see fixation for each color of M&M at roughly equal rates. 

Now pretend that there are only 4 types of M&Ms, and they're called A, T, C, and G. 

Boom. Neutral evolution via genetic drift. 

The theory of evolution by natural selection is almost identical to the M&M scenario described above. But this time, instead of eating a random 5, you target M&Ms of a certain color. Maybe you're trying to eat all the green ones, or you're trying to eat ever color but the green ones. Either way, since the change is no longer random, it's going to reach "fixation" (elimination of one or most colors) much faster. 

In the real world, this difference between randomly eating 5 M&Ms and choosing a color to target is analogous to neutral evolution and evolution by natural selection, but it can also be pictured as silent and non-silent genotypic change. Remember, natural selection can only act on phenotype; it needs to see the color of the M&Ms its eat. But neutral evolution works even on mutations that don't cause a phenotypic change; thus, it doesn't need to see the color of M&Ms. So while both cause change, one cares about the phenotype and works towards a fitter organism, while the other doesn't care about the phenotype and fixes alleles at random.  

Strangely, because drift fixes alleles randomly, it actually does so at a predictable rate. We can't tell which mutations will be fixed, but we know that some changes will stick around purely by chance. You can think of it as you doing the M&M experiment with your friend. 

Let's say you and your friend work together for five bowls. Then they get greedy and start doing their own experiment for five more bowls. If this scenario is replicating neutral evolution, you'll both be fixating into solid-color bowls at about the same rate. You could then look back on the number of bowls and their colors to determine how long ago you guys separated. If you have five sets of differently colored bowls, that means you separated five bowl-generations ago - five ticks of the metaphorical "clock". 

That's how we use neutral evolution to determine temporal distance between lineages. 

Of course, we're talking candy here, so the analogy isn't perfect. Real-world analysis doesn't care about the "color" of the mutation so much that it happens at a relatively constant rate. If you already know two lineages are related, you can tally up the number of changes between them to get a pretty good idea of how long ago they separated and started neutrally evolving on their own. Scientists are also super smart and know how long it takes for one mutation to fixate, allowing them to literally estimate the years between two lineages. Which is a lot more applicable than counting in bowl-time, let me tell you. 

So go share some M&Ms! Talk to your friends about neat science concepts! Pavlov train them to associate your science ramblings with candy! 

Now if you'll excuse me, I'm going to go ask my roommate to proofread this and thank her with candy. 

One Fish, Two Fish, Yellow, Green, Blue Fish

When it comes to the concepts of evolution, you could throw big words and long-winded explanations at me all day - and I still wouldn't get beyond the metaphorical 2 + 2 = 4. Sure, I can read words and use brain power to turn those words into understanding. If I want a headache. Or I could just talk about fish. 

...I'm gonna talk about fish. 

The proposed question is this: what's with non-random mating? It's not really an evolutionary force, because it can't change allele frequencies. But it is important to evolution, because it provides a situation on which other evolutionary forces can act. And non-random mating does this by messing with genotype frequencies. 

There I go, chucking around big words. Let's get into the fish. 

Pretend we have two alleles in a population of fish. Two copies of one (say, BB) makes blue fish, and having two copies of the other (bb) makes yellow fish. Having one of each (Bb) makes a green fish (This is called incomplete dominance, yada yada jargon jargon, back to the fish). 

        (o_>_)<    (o_>_)<      (o_>_)< 

                                                                   BB           Bb             bb

Look! Fish!

Now let's say this population starts some serious non-random mating. Interbreeding, specifically. Also known as "getting it on" with your close relatives. 

Maybe you've heard of some human populations doing this before. The European royal family, perhaps? Or the Egyptian line of Pharaohs? Both illustrate the potential negative impacts of long-term interbreeding: a rise in recessive genetic disease. But why? Well. Let's go back to the fish. 

When a population interbreeds, we know one thing for certain: the genotype frequencies are going to change. We expect to see a serious drop in green fish (heterozygotes) and a rise in blue and yellow fish (homozygotes). This is because yellow fish can only give yellow alleles and blue fish can only give blue alleles - so the more they mate amongst their close relatives (who are likely to share the same only-blue or only-yellow allele situation), the more those alleles are going to propagate. 

It's a long stretch to connect fish to royal bloodlines, but consider this: what if the yellow color is really disadvantageous? Maybe it makes fish easy to spot.  Inbreeding will result in a lot more easy-to-eat yellow individuals, where there might've been predominately blue and green individuals in a randomly mating population. In such as case as this, the fish might evolve disassortative mating, where individuals try to mate with others who don't look like themselves to decrease the number of homozygous recessive yellow fish. Disassortative mating is advantageous because it increases genetic diversity and lowers the chance of inheriting recessive genetic diseases or recessive, disadvantageous alleles.

In a similar manner to the yellow fish, a recessive disease known as hemophilia plagues the European royal line. The one-time mutation in Queen Victoria probably wouldn't have been a big deal - but the royals just had to keep marrying their cousins (who were a lot more likely to also carry the trait in its harmless heterozygous form), which upped the chances of their "pure-blooded royal" offspring having a serious genetic disease. 

So. Frequently, inbreeding = wimpy children. Populations evolve to avoid it. 

But like everything in science, there are exceptions. 

Some populations have evolved assortative mating, or the selection of a mate who looks phenotypically similar to yourself. Why risk the chance of shagging your cousin? Well, because the benefits outweigh the risk, of course. 

If the coloration of our yellow and blue fish indicate their health (while green is drab and does not), then non-random mating will reinforce those bright colors. Bright fish will mate with bright fish so that their children also inherit that communicator of "I'm bright healthy, breed with me!". 

Or if our fish are highly territorial, breeding with others who look like them will result in even more territorial offspring - which enhances the chance that those offspring will survive and have their own offspring, thus propagating the genetic line. 

And if you have two really good alleles and a really disadvantageous heterozygote, interbreeding can reinforce the good alleles while getting rid of the heterozygotes. 

Before you go judging these assortative maters, just remember: you're one of them! Humans fall right into this category. I'd hypothesize it is because of our communal nature. We would much rather mate with someone from our own culture (who we can understand easily) than someone who looks and acts differently. It's a survival tactic, designed to promote the genetic line we're a part of. But don't quote me on that. I'm speculating for fun, not fact. 

So are our inbreeding fish in a good situation or bad situation?

        (o_>_)<    (o_>_)<      (o_>_)< 

                                                                   BB           Bb             bb

Well, it depends on who you ask.