Molecular Monday: Meet Glycine

Friends, I’ve told you before: chemistry is hard. But I think I’ve learned enough to be able to introduce you to our first amino acid. This is glycine, the simplest amino acid.

Mr09 Glycine

By my count, amino acids have four key components. They are (in no particular order):

  • An amino group: the part that gives amino acids their name.
  • A carboxyl group: the part that includes a loosely attached hydrogen atom, which makes an amino acid an acid.
  • An alpha carbon: provides structural stability by separating the amino and carboxyl groups. In the highly technical diagram above, the atom with the smiley face is the alpha carbon.
  • The side chain: a group of atoms that attaches to one of the alpha carbon’s two extra bonding sites. An additional hydrogen atom caps whichever bonding site isn’t used for the side chain.

It’s these side chains which really distinguish one amino acid from another. Depending on which side the side chain attaches to, we’ll either have a right-handed or left-handed amino acid.

It’s important to be aware of the “handedness” of amino acids (of the “chirality” of amino acids, to use the technical term). Human DNA and the DNA of all life on Earth only codes for left-handed amino acids. In theory, there could be life forms on other planets that rely on the right-handed kind.

But glycine is a special case. Glycine’s side chain, if we can justifiably call it a side chain, is one single hydrogen atom. This is why glycine is considered the simplest amino acid: you can’t get much simpler than one hydrogen.

Also, this single hydrogen “chain” is indistinguishable from the single hydrogen used to cap the alpha carbon’s other free bonding site. This means glycine is non-chiral. It can be either right-handed or left-handed. I supposed you could say glycine is ambidextrous.

Because glycine is non-chiral and because it is the simplest amino acid, I have a feeling glycine could play a special role in astrobiology. Maybe… just maybe… glycine is universal to all life in the cosmos.

Or maybe not. This is just a pet theory I came up with based on what I’ve learned so far.  I’m sure I’ll have more to say about this as we get to know some of the other amino acids.

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Today’s post is part of a special series here on Planet Pailly called Molecular Mondays. Every other Monday, I struggle valiantly to understand and explain some concept in the field of chemistry. Please note: I suck at chemistry, but I’m trying to learn. If I made a mistake, please, please, please let me know so I can get better.

Sciency Words: Chirality

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Today’s post is part of a special series here on Planet Pailly called Sciency Words. Each week, we take a closer look at an interesting science or science-related term to help us all expand our scientific vocabularies together. Today’s term is:

CHIRALITY

Imagine that we’ve finally placed a lander on the surface of Europa. The lander takes samples and detects amino acids, an essential ingredient for life. That raises a few eyebrows, but amino acids are not exactly uncommon in space. Then scientists realize that Europa’s amino acids all share the same chirality.

That’s the part where everybody freaks out.

Chirality, which is a noun, and chiral, which is an adjective, come from a Greek word meaning hand. You’ll see why in a moment.

Amino acids are made of several parts. By definition, they must include an amino group (one nitrogen atom and two hydrogens).

Mr08 Amino Group

By definition, they must also include a carboxyl group (two oxygens, a carbon, and a hydrogen).

Mr08 Carboxyl Group

They also need to have at least one carbon atom positioned between them, for structural purposes.

Mr08 Alpha Carbon

An amino acid with only one carbon separating the amino and carboxyl groups is called an alpha amino acid. If there were two carbons, it would be a beta amino acid, and so on.

But notice: that central carbon atom still has two available bonding sites.

Mr08 Missing Side Chain 1

So amino acids have one more crucial component called a side chain. It’s these side chains that give each type of amino acid its unique flavor (literally—amino acids taste different from one another, or so I’m told).

But which side do we attach the side chain to?

Mr08 Missing Side Chain 2

Left side it is! And we’ll attach a single hydrogen atom to the right.

Very early in the development of life on Earth, organisms started manufacturing amino acids out of simpler chemicals, and they always made the “left-handed” kind. Why? Coin toss. It could just have easily gone the other way, as far as we know.

To this day, our DNA continues to code for left-handed amino-acids only. As a result, there are more left-handed than right-handed amino acids present on Earth. If we ever find a similar disparity elsewhere in the universe—whether left or right-handed—that would be compelling evidence for the existence of alien life.

By the way: there’s a common misconception about chirality that you sometimes find in science fiction. Supposedly, humans cannot eat foods made from right-handed amino acids, and aliens with right-handed biochemistries cannot eat our left-handed foods. This is not necessarily true. In fact, humans do consume right-handed amino acids. Some of them are useful to our bodies, just not in the construction of proteins, and they’re not coded for by our DNA.

Of course, there are plenty of other reasons humans and aliens probably shouldn’t share food.

Mr08 Alien Food

So the chirality of amino acids might not be your top concern.

Europa: My Favorite Moon

Fun fact about me: Europa is my favorite moon.

Mr07 Moon 1

Oh, sorry Moon. You’re cool too. It’s just… you don’t have an ocean. Or chaos terrain. Or possible alien life. It’s nothing personal.

Mr07 Moon 2

Anyway, on Monday I told you that Congress wants NASA to put a robotic lander on the surface of Europa. But the really interesting bit is deep beneath the surface, where the ice turns to liquid water. Is anything alive down there? Any microbes? Maybe fish? What about alien mermaids?

A lander can’t investigate that sort of stuff. At least not directly. But if you’ve ever seen a picture of Europa…

Mr07 Europa

… you’ll notice the surface is covered in dark reddish-colored lines. These lines appear to be cracks. It’s believed that warm water sometimes forces its way to the surface, carrying with it a mix of minerals and possibly other materials from the oceans below. It’s these minerals which cause the reddish discoloration.

So while a lander can’t sample the ocean water directly, it could examine the materials that have been deposited on the surface. Now, if you’ll allow me to switch my science blogger hat for my science fiction writer hat, I’ll tell you exactly what the Europa lander will find.

Salt. Lots of salt. That won’t surprise anyone. It’s been long assumed that Europa’s ocean is much saltier than the oceans here on Earth. It must be; otherwise the ocean would freeze.

The lander will also detect other minerals as well. And amino acids. That’ll raise some eyebrows, but amino acids aren’t that uncommon. We’ve found them on other planets and we’ve found spectrographic evidence of them all across space. As I reported in last week’s Molecular Monday post, there are literally hundreds or perhaps thousands of different kinds of amino acids in our universe.

Mr07 Surface of Europa

That will make headlines. No, it’s not the same 21 amino acids coded for by human DNA, but this cannot be a coincidence. What natural phenomenon, other than life, could produce such a select few amino acids in such large quantities?

But wait, there’s more. These 21 amino acids have something in common. They have the same chirality. And that’s the part where the entire scientific community freaks out.

Tune in for Friday’s edition of Sciency Words to find out what the heck chirality is and why it’s so important in the search for alien life.

P.S.: My second favorite moon is Titan, followed by Io, Miranda, and Triton. Oh, and Naiad! I love Naiad. But Earth’s Moon totally makes in my top ten. Probably.

Europa: To Land or Not to Land?

NASA has big plans for Europa. It is, after all, Jupiter’s most interesting moon.

Ag04 Europa Blush

But the details of these big plans have been in a state of flux for a while. The mission would undoubtedly include an orbiter, but should it orbit Europa or Jupiter? What about also sending a lander or rover? Or maybe a submarine? Europa does have an ocean somewhere beneath its icy shell.

Okay, there’s no way Congress would pay for all that, so NASA decided to scale down its ambitions. In other words, the mission was descoped. No landers, no rovers, and definitely no submarines. Also, the orbiter would orbit Jupiter. Entering orbit of Jupiter requires less delta-v, and therefore less fuel, than trying to enter orbit of any specific Jovian moon.

But even after scaling everything down, this Europa mission would still come with a hefty price tag. Congress held hearings. This couldn’t go well. So what happened?

Congress told NASA to put the lander back in the mission plan and put up money to pay for it.

Mr06 Europa 1

That’s right. Congress suggested—no, commanded—that NASA include a lander as part of its Europa Clipper mission and provided money to pay for it. I guess you could say this mission was de-descoped. Or maybe it was rescoped.

Now I’m not naïve enough to think that Congress has suddenly developed a deep appreciation for planetary science. It’s more likely this lander will be built by some company that donated generously to someone’s campaign, or maybe it will be built within some influential congress-person’s district.

I’m not a political blogger, so I don’t want to get into that. What I do want to say is this: we’re going to Europa, baby!

Mr06 Europa 2

Links

We’re Going to Europa from SciShow Space.

A Lander for NASA’s Europa Mission from The Planetary Society.

Congress: NASA Must Not Only Go to Europa, It Must Land from Ars Technica. This last link is particular interesting because it suggests that NASA doesn’t really want to go to Europa at all, but Congress is forcing them to do it.

Sciency Words: Agentic State

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Today’s post is part of a special series here on Planet Pailly called Sciency Words. Each week, we take a closer look at an interesting science or science-related term to help us all expand our scientific vocabularies together. Today’s term is:

AGENTIC STATE

Hey, do you want to write a Sci-Fi/Fantasy story about mind control powers?

Mr05 Autonomous Writer

Yes, you do.

Mr05 Agentic Writer

Well, here’s a term—a real life psychology term—that you might want to incorporate into your story. Though I must warn you: this term has a disturbing history.

The agentic state is a state of mind. A person in the agentic state essentially surrenders their free will and acts as an “agent” of another person who is perceived to be in a position of authority.

A series of experiments in the 1960’s demonstrated how easily we humans will do as we’re told. I won’t describe these experiments in full (you can click here to find out more, if you want). The basic idea can be summed up with these questions:

  • Would you inflict pain on another human being because someone in a position of authority told you to?
  • Would you continue inflicting pain, even as your victim screams for you to stop, because an authority figure insisted it was necessary?
  • Would you torture a person to death because you believed that this authority figure would take responsibility if anything went wrong?

According to the experimental results, the answer to all three questions—for the majority of us, at least—is yes.

Why were these experiments conducted? Because of some very famous words. Words that come to us from a dark period in modern history. Words that I’m sure you’ve heard before: “I was just following orders.” It seems that those words and the mode of thinking they represent are deeply engrained in us all. Telepathic mind control powers hardly seem necessary.

Fortunately, this is not all there is to say concerning this line of psychological research. To quote Frank Herbert, “One cannot have a single thing without its opposite.” The opposite of the agentic state is called the autonomous state. Without delving too deeply into philosophical questions concerning free will, I think we can define the autonomous state as a state of mind where you are making your own decisions rather than allowing authority figures to make them for you. At the very least, you’re not blindly following orders that violate your own conscience.

I don’t know about you, but I find it somewhat reassuring to think that while we may be capable of entering one of these mental states, we are also capable of entering the other—provided we’re aware of what is happening to us.

Earth Germs on Mars: What Might Happen?

Warning: the word “might” will appear a lot in today’s post.

When the Curiosity rover left Earth, it might have been contaminated with several different strains of Earthly bacteria. This was a big oops for NASA, especially for NASA’s Office of Planetary Protection, which is supposed to make sure we don’t spread our germs to other planets.

But how bad could the damage really be? Curiosity was headed for Mars. It’s not like Mars has water.

Then we found out Mars does have water. Droplets and trickles of water. Modestly sized puddles of the stuff. Now, even though Curiosity is currently located near actively trickling water, the rover is not allowed to go investigate. It might contaminate the water. It might endanger any ecosystem that might exist in the slightly damp Martian soil.

I wrote previously that we should take the risk anyway. Let Curiosity approach the water. Let Curiosity take a sample. Let Curiosity be curious. What are the odds that microorganisms from cushy, life-friendly Earth could survive on Mars? What are the odds that they could outcompete native life forms that are perfectly adapted to the harsh Martian environment?

That’s how I felt, until last week when I learned about bacterial conjugation.

Mr04 Bacteria of Mars

According to the panspermia hypothesis, life on Earth and Mars might (there’s that word again) share a common ancestor. If so, Martian microbes might be genetically compatible with bacteria from Earth. Through bacterial conjugation, they might be able to share DNA.

They might.

Mr04 Martian Earthling Hybrid

Or they might not.

Finding out that bacteria on Earth and Mars are genetically compatible would be a huge discovery, assuming we knew it was happening. But Curiosity is not equipped to test for that sort of thing. Curiosity isn’t equipped to study biological activity of any kind. So the rover’s presence in and around Martian water flows might trigger changes to the local ecosystem without our knowledge.

So grudgingly, I’ll agree. Let’s keep Curiosity away from the Martian wetlands. It might not worth the risk.

Molecular Monday: How Many Amino Acids Are There?

How many amino acids are there? As I continue my mission to understand the amino acids, this has become an incredibly frustrating question. Everywhere I go, I get a different answer, in part because many sources fail to specify which category of amino acids they’re talking about.

There are 9 amino acids

I got this from a nutrition website. In terms of your diet, there are nine essential amino acids. What’s essential about them? It’s essential that you, as a human being, get them in your diet because the human body cannot make them on its own.

There are 20 amino acids

This seems to be the most common answer. There are twenty standard amino acids. Why are they standard? Because your DNA (and the DNA of all organisms on Earth) directly codes for these specific amino acids, and so these twenty amino acids are incorporated into all the proteins found in your body (and the bodies of every other living thing on Earth).

There are 21 amino acids

The amino acid selenocysteine is also found in some of the proteins in our bodies. It’s just not directly coded by our DNA, so it’s considered non-standard.

There are 23 amino acids

There are two more non-standard amino acids that are only found in prokaryotic organisms (bacteria and archaea). So in total, across all life forms on Earth, there are 23 proteinogenic amino acids, meaning there are 23 amino acids incorporated into proteins.

There are hundreds of amino acids

As important as the 23 proteinogenic amino acids are, there are literally hundreds—maybe thousands—more. The rest are sometimes called non-coding because they’re not coded for by DNA. They’re also called non-proteinogenic because they’re not incorporated into proteins (at least not here on Earth). Sometimes they’re called unnatural, which seems rather unfair. Many of these “unnatural” amino acids serve vital biochemical purposes. Life is made of more than proteins, you know!

Anyway, next Molecular Monday (two weeks from today) we’re finally going to meet an actual amino acid.

Mr03 Glycine

Today’s post is part of a special series here on Planet Pailly called Molecular Mondays. Every other Monday, I struggle valiantly to understand and explain some concept in the field of chemistry. Please note: I suck at chemistry, but I’m trying to learn. If I made a mistake, please, please, please let me know so I can get better.

Sciency Words: Bacterial Conjugation

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Today’s post is part of a special series here on Planet Pailly called Sciency Words. Each week, we take a closer look at an interesting science or science-related term to help us all expand our scientific vocabularies together. Today’s term is:

BACTERIAL CONJUGATION

Bacteria aren’t like us. They’re not stuck with the DNA they’re born with.

Mr02 Bacterial Conjugation

Through a process called bacterial conjugation, one bacterium can donate some of its genes to another. In some cases, this even works between bacteria of different species.

The process begins with something called an “F plasmoid” or “F factor.” Bacterial conjugation has a few things in common with sexual reproduction, so I’m sure you can guess what the F stands for. It stands for fertility. Obviously.

This F plasmoid is actually a strand of DNA looped into a circle. A bacterium that has an F plasmoid is called an F+ cell. A bacterium that doesn’t have it is an F- cell. And when an F+ cell and an F- cell meet, the real fun begins.

  • Step One: The F+ cell grows a hair-like protrusion called a pilus (plural pili).
  • Step Two: The pilus attaches to the F- cell, and a connection is formed. You could think of the pilus as a tiny straw linking one bacterial cell to the other.
  • Step Three: Within the F+ cell, the F plasmoid splits apart right down the center of its double helix structure, like a zipper unzipping. One half is fed through the pilus, and the other half stays put.
  • Step Four: Using the half-strand of DNA as a guide, the F- cell creates a complimentary strand of DNA and zips the two back together. The F+ cell does the same thing with the half-strand that it kept. Now both bacteria have a full copy of the F plasmoid, meaning both are F+ cells, and both can go spread the F plasmoid to other bacteria.

This ability has proven to be really useful for bacteria. It is, for example, one of the mechanisms that spreads immunity to our anti-bacterial drugs.

It’s too bad humans can’t do this, but transferring DNA between multicellular organisms would be a far more complicated matter (though come to think of it, sperm and egg cells do an okay job). But perhaps on some distant alien world, multicellular conjugation is possible. Perhaps it is common even between different species. Maybe some day we’ll meet these conjugating life forms, and awkward conversations will ensue.

Mr02 Multicellular Conjugation

IWSG What’s the Opposite of Writer’s Block?

InsecureWritersSupportGroup

Today’s post is part of the Insecure Writer’s Support Group, a bloghop hosted by Alex J. Cavanaugh. Click here to find out more about this amazing group and see a full list of participating blogs.

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Is there such a thing as a reverse writer’s block? Is there a term for that? I feel like there should be.

This was my crisis this past month. I had too many ideas jockeying for my attention. Granted, my ideas all had some things in common. Space. Spaceships. Space battles. Strong female protagonists, specifically strong female protagonists in space.

But I couldn’t focus on just one idea. Basically, it felt like this:

Mr01 When Story Ideas Attack
If only my love life looked more like my writing life….

I can almost pinpoint the moment when things officially got out of hand. On Friday, February 19th, at approximately 2 p.m., I threw down my pen in frustration and took the rest of the day off.

The next morning, after a generously large and delicious breakfast, I grabbed a notepad and started writing descriptions/plot summaries for all the projects I wanted to work on, starting with Tomorrow News Network (represented by the blonde woman above) and my blog (represented by the planet Venus wearing lipstick).

I ended up with seven projects (including my blog). Seven! It would have been eight, but one story idea turned out to be less interesting than I expected once it was on paper. Also, one of these projects is actually part of my personal diary, so it’s really six. Still, six projects seems like way too many. I need to pick and choose.

Or do I? When I had ideas coming at me from all directions, it was overwhelming. But now, all these ideas are organized. They’re manageable. I think—I don’t know, maybe this is crazy talk—but I think I can do this. And ever since the February 19th reverse writer’s block catastrophe, my confidence has only grown stronger.

So are six (or seven) writing projects too many? How many projects are you working on, and how do you keep multiple projects separate and organized?

Sciency Words: Descope

Sciency Words MATH

Today’s post is part of a special series here on Planet Pailly called Sciency Words. Each week, we take a closer look at an interesting science or science-related term to help us all expand our scientific vocabularies together. Today’s term is:

DESCOPE

What do you call it when a space mission that’s supposed to look like this…

Fb10 Epic Huge Space Probe

… turns out looking more like this?

Fb10 Teeny Tiny Space Probe

It’s called descoping.

Descoping is a term, apparently used at NASA and other space agencies, for when the “scope” of a mission is reduced, usually due to budgetary concerns. At least being descoped is better than being canceled outright, although I can easily imagine missions being descoped to the point that they may as well be canceled.

It seems the term can also apply to military hardware that, once again for budgetary reasons, had to be scaled down. So the verb “to descope” could be doubly useful for science fiction writers.

P.S.: I’d planned to write more for today, but due to budgetary concerns, this blog post has been descoped.