I’m doing the damn thing and finally embarking on a PhD journey! Ever since I transitioned from working in industry to working in academia a little over 3 years ago now, I’ve been slowly cracking away at a master’s degree in chemistry and I finished this December. So now I’m working on a PhD for the foreseeable future.  

Won’t it be a lot of extra work? Yes, it will.

Don’t I already have a full-time job?  Yes, I do.

Why am I doing this?!

Because:

a.)  I want the freedom to do whatever I want for my entire career, and I believe having a PhD will help to enable that kind of freedom.

b.)  Learning is a spiritual journey for me. This is how I make the world a better place. I believe learning raises the vibration of the oneness, ie: it makes God happy. It feels like this is my mission on this planet: to collect as much knowledge and experience as possible and dissolve it back into the source. I think the universe loves to be examined and explored. She’s beautiful and sexy and she loves to be checked out. She wants us to find out every little thing about her. The universe loves to be loved and appreciated. Haven’t you ever noticed that when you intentionally shift your mindset to one of gratitude, your life starts going better? When you love and appreciate the universe, she will love and appreciate you right back. Every human, animal, mineral, plant, piece of technology…we’re all just little fractions of the God holograph lovingly gazing at each other, trying to take it all in. Learning is a spiritual act of love for me and it’s what I’m here on this planet to do.

c.)   The research area of the lab I joined is renewable energy, which feels like a noble cause. What could be a more important pursuit in the face of impending planetary doom?

d.)  The principal investigator in this group is ambitious as hell. He’s a big ideas kind of guy and he gets shit done. I think watching how he works will be inspirational.  

So here I am to write about what it is that this lab does because explaining things to “other people” in writing is the best way that I learn (and when I refer to “other people”, I mean mostly myself but also the bots that leave comments on my blog posts with sketchy links that probably gave me a million viruses when I clicked on them.) And, to be honest…so far, I don’t actually know much about what they do in that lab other than they all seem really smart, and it has something to do with renewable energy. But there are all kinds of topics that fall under the category of renewable energy. What does this group do in particular? I don’t really know, let’s take a look at the content they have online and do a little copy/paste, shall we?

“The Boettcher electrochemistry and solar materials laboratory is focused on designing, synthesizing, and understanding materials for applications in solar energy conversion and electrochemical energy storage/conversion. Specific interests include the synthesis and study of heterogeneous electrocatalysts for water oxidation with defined molecular and nanoscale structures, the use of computer simulation and direct electrical measurements to understand semiconductor-electrocatalyst interfaces, and the development of high-performance III-V semiconductor solar conversion architectures using scalable and inexpensive deposition processes. Recent new projects include the development of alkaline membrane electrolyzers for low-cost scalable hydrogen production as well as fundamental aspects of bipolar membranes and electrolyzers.”

Lots of big scary words in there. I need to break this paragraph down word-by-word to absorb it. Let’s start with heterogeneous electrocatalyst.

A catalyst is a chemical that increases the rate of reaction without itself undergoing any significant physical change.

An electrocatalyst is a specific type of catalyst that functions at an electrode surface. So, on the surface of some conductor that can be hooked up to a power supply and charged up.

A heterogeneous catalyst means the phase of the reacting chemical at the beginning of the process is different from the phase at the end.

Changing phase…does that mean we are going from a solid to a liquid? Or a liquid to a gas? Yes, that’s exactly what it means! In fact, here, we are talking about water oxidation, which is the process of splitting water into oxygen and hydrogen. This is a liquid turning into a gas.

Note, hydrogen is a proton. I’m going to use those two words interchangeably throughout this piece. Don’t get confused!

So, to sum up the first half of that big, wordy paragraph: this lab is trying to create and test materials that use electrical and chemical reactions to turn water into hydrogen gas and oxygen gas. This process is called water electrolysis.

Why would we want to turn water into hydrogen gas?

Because, when used in a fuel cell, hydrogen gas generates electrical power and emits only drinkable water and warm air. It’s just about as efficient as gasoline and has near zero greenhouse emissions.

How does a fuel cell work?

There are a bunch of different technologies for fuel cells, I'm going to explain how PEM fuel cells work.

This video gives a pretty good introduction. I grabbed some screenshots from that YouTube to explain what’s going on.

A fuel cell is essentially a sandwich with two metal plates (an anode and cathode) as the bread, and this thing called a Proton Exchange Membrane (PEM) in between.

The PEM is a material made from a special type of polymer designed to let through protons and block electrons. I am not clear on how it does that, exactly! It looks like I’ll need to teach myself some serious chemistry to begin understanding what’s going on here.

Let’s start with understanding what a polymer is. Well, it’s just a material that’s made from large molecules consisting of a bunch of repeating subunits. I remember my biology 101 professor holding up a stack of Legos as an analogy to polymers; Little repetitive building blocks that link together to make a larger structure.

 DNA is a polymer! It’s just a long, twisted ladder with the same 4 components repeating themselves in different combinations over and over. There are also ton of synthetic polymers: polyesther, polystyrene, nylon, Teflon…the list goes on and on.

Proton Exchange Membranes are made of a special type of polymer called an ionomer, which means that some of the subunits sprinkled throughout the matrix have an electric charge to them. Often, a product called Nafion is used.

The chemical structure of Nafion looks like this:

So…what’s going on here with this big jumble of sticks and letters? I’ve never taken organic chemistry, so this is a lot for me… but what I’m gathering is that when you take this big ugly ionomer structure and soak it in water, the part that I circled in pink (the sulfonic acid group) loses protons and those protons start hopping around from one acid site to another. If you apply an electrical bias, you can get all the protons to move in one direction. This is an electrical current!

Pressurized hydrogen from the fuel is forced through the anode while pressurized oxygen from the atmosphere is forced through the cathode.

An acid is used as a catalyst to split the H2 molecules into protons and electrons.

I had to go into a Wikipedia worm hole to remind/teach myself what it means to be acidic. Remember how the pH scale works? I didn’t. Here’s what I found out: pH is an acronym! It stands for potential of hydrogen. Acids have high concentrations of free hydrogen ions floating around, which means they are hungry for electrons. An acid will slurp up the electrons from the hydrogen, leaving only positively charged protons, which can move across the Nafion membrane.

Ok, so now the protons have made their way across the membrane to hang out with the oxygen molecules on the right side of the fuel cell and they leave their electrons behind on the left side.

That means the right side has a positive charge and the left side has a negative charge. This is a battery! This is exactly what a battery does, it’s just a separation of charge that creates a potential difference. If we connect a circuit between the two charged plates, we can force electrons through the circuit. This will power whatever we’ve got going on in the circuit.

To sum it all up, a hydrogen fuel cell is just a battery that’s charged up by hydrogen and oxygen gas. Acid is used as a catalyst to steal electrons from the hydrogen molecules, making them positively-charged protons which are then encouraged to move across an ionomer membrane. This creates a separation of charge that behaves like a battery.

As an aside, I’d like it to be known that this technology is yet another one of the many gifts given to us by the space industry! Tons of resources were devoted to the study of these Proton Exchange Membranes (PEMs) during NASA’s Gemini project in the 1960’s.

I get on my soap box about this all the time. Space exploration truly is the gift that keeps on giving. Space travel presents us with novel problems that require creative solutions. This forces the development of innovative new technology that we end up using for all kinds of other applications. The list of technology that came from the space industry goes on and on. I don’t know why so many people get all up in arms about how we shouldn’t be devoting resources to space exploration, but those people annoy me.

Anyway…space rant over. Back to fuel cells!

Why are fuel cell vehicles way better than battery powered vehicles?

It takes hours to fully charge a battery powered vehicle and even with a full charge you can’t go that far. Most electric cars can barely get half as far as a car with a full tank of gas. And then when the battery runs out, you have to wait around for a long time to recharge it. Hydrogen cars can go just as far as gasoline-powered cars, and you can refill the tank with hydrogen in the same amount of time that it takes to refill a car with gasoline. There are already hydrogen powered cars cruising the streets in California.

But we aren’t just talking about cars for fuel cell applications; Trains, planes, spacecraft, power for big industrial settings…all of this could be powered by hydrogen fuel cells to create a completely green economy.

Sounds great, right? A battery that works better and takes less time than the current Lithium-ion batteries and is also completely carbon neutral?

Wrong! Hydrogen fuel only counts as renewable energy if the process of making the hydrogen is renewable.

Currently, hydrogen is primarily made through steam-methane reforming. This is a process where high-temperature and high-pressure steam is combined with natural gas to create hydrogen gas. Natural gas is not all that green…

So, this lab’s goal is to develop green technology for creating hydrogen fuel using a process called water electrolysis. We want to mimic the process of photosynthesis, using solar energy to split water into oxygen and hydrogen and store the hydrogen molecules as fuel to power fuel cells.

As far as I can tell, the biggest rock star in the group is this woman named Grace. She takes responsibility for getting stuff done and moving the group forward. She’s graduating in spring which is going to be a big loss to the group, but an enormous gain to the organization she goes on to work for. She spent a couple hours with me explaining how water electrolysis works. Here's what I learned:   

Currently there are three different technologies out there for water electrolysis and they each have some big problems.

We’ve got:

1.) Liquid alkaline

2.)  Proton Exchange Membrane (PEM’s…yay we already learned about those above!)

3.) Anion Exchange Membranes (AEM)

So, how do each of these technologies work? Or I suppose I should say…how don’t they work?

Let’s start with liquid alkaline. I learned a lot from this cute Spanish lady. I included a screen shot of her talk below with a cartoon of the liquid alkaline electrolyzer. It's helpful to refer to the cartoon while I explain how it works. 

In this type of device, you have two metal plates separated by a porous foil that won’t let electrons through; only OH^- ions (these are called hydroxyls). I’m not going to do a deep dive on how that foil transports ions, but I suspect it’s some kind of polymer that forces the OH^- to hop from molecule to molecule, kind of like I described above with the acid group in the PEM. It also isn’t supposed to let gas through; only liquid. I guess this is achieved mechanically with design of the porous foil. The whole thing is submerged in a highly concentrated solution of potassium hydroxide, which is strongly alkaline.

Alkaline is on the opposite end of the pH scale from acids, instead of a bunch of free hydrogen floating around, it has free hydroxyl ions. Instead of wanting to steal electrons, it wants to steal protons.

So anyway, this device is submerged in a liquid that has a strong concentration of hydroxyl ions floating around, and its functionality leans heavily on those hydroxyls flowing through the membrane to react with stuff on the other side. In this case, we have water flowing in on the right side of the cell. Two water molecules react with two electrons to form hydrogen gas and two hydroxyls.

Why does the water react with two electrons and break down into its components? Does water just do this on its own? No, thankfully! Water doesn’t just spontaneously fall apart else we’d be in trouble considering how much water our bodies use to keep us alive. We need to force this reaction to take place by introducing electricity into our system. When you apply a huge voltage to water and add a little bit of electrolyte (the potassium hydroxide), you can force a current through the water which pulls electrons away from the solution at the cathode while forcing electrons into the solution at the anode.

Great, so now on the right side we have water flowing in and reacting with electrons from the electrode to create hydrogen gas and hydroxyls. Hydrogen gas is our product! It bubbles out and gets stored.  The hydroxyls are a liquid and flow over to the left side through the membrane where they become water, oxygen, and electrons. The oxygen gas bubbles out, this is a secondary product! The electrons make their way over to the positive side via a circuit and this supplies the electrons to continue the process on the right side.

Liquid alkaline electrolyzers are great because they are low cost and reliable. They are already used all over the place in big industrial settings for hydrogen production and ammonia synthesis for fertilizer. Unlike the other two technologies we will highlight below, they can be made of materials that are abundant on earth and cheap, like nickel! 

They suck because they suffer from this problem called “shunt current”. This is when current starts going through the tubing instead of the electrode. This becomes more of a problem as you increase the current: more of it goes through the wrong pathway. This is a problem is exacerbated because liquid alkaline electrolyzers have to be constructed as a huge stack containing multiple electrodes in series.

Another huge problem that can occur when you vary the current is that instead of bubbling out, the gas tends to cross over the microporous diaphragm and hydrogen and oxygen gas will mix. You know what happens when you mix hydrogen and oxygen?

This is a picture of an industrial hydrogen plant in China that went boom.

So, because of shunt currents and gas cross-over, you must have a steady current and therefore a non-variable power supply.

Well, you can’t really ask the sun to shine or the wind to blow in a non-variable way, therefore this technology can’t be paired with renewable energy. So, if we stick with liquid alkaline electrolyzers, water electrolysis is never going to be renewable.

X Liquid alkaline electrolyzers are out! They can't be paired with renewables! 

What’s next?

Next up, we have Proton Exchange Membranes (PEM’s), which I described in depth above when I was talking about fuel cells. When we were talking about it above, it was hydrogen in, electron current and water out. But now it’s electron current and water in, hydrogen out.

Look at this cute cartoon I found on Wikipedia! Staring at this for a while helps a lot!

So, as a reminder, the membrane in the middle moves protons across. Water is fed in and electrons are pulled out at the anode side, causing the water to break up into oxygen and protons. The protons move across the Nafion membrane because they are attracted to the abundance of negatively charged electrons that are being forced in at the cathode side. The protons gather up those free electrons and bubble out as hydrogen gas that gets stored. This is our product!

The fact that the thing in the middle is a membrane rather than a porous thing means we don’t have the gas cross-over problem that acid alkaline electrolyzers have. AND, we don’t have to have a bunch of electrodes in a stack so we don’t have the shunt current problem either. Great, so this technology is both safer and able to be paired with renewable energy!

So, what’s the downside with PEM’s? Well, instead of using an alkaline as a catalyst, we are using an acid. This is a problem because acid will chew away most metals. The only metals that are stable in an acidic environment are precious metals like iridium. Since iridium is one of the scarcest metals on earth, this is the bottle neck in PEM electrolyzer production.

X PEM’s won’t work either. They require metals that are too scarce and expensive!

Finally, onto Anion Exchange Membranes. Instead of exchanging protons through the membrane, we exchange hydroxyls...just like with the liquid alkaline electrolyzers! Hydroxyls are ions with a negative charge, the word for that is anions, this is where we get the name Anion Exchange Membrane. These devices get rid of the problems created by PEM’s because they can be used in an alkaline environment rather than an acidic environment. That means we can construct these with earth-abundant metals. 

The biggest problem for AEM’s is poor durability.

Many different polymers have been tried out as the anion-conducting membrane and they are all trash! AEM’s just fall apart faster than PEM’s and no one is totally clear on why that is. It sounds like my first project in this lab is supposed to be trying to understand how/why these things break. 

In the AEM community, it had been thought that the problem with these devices is that the membrane is limiting. However, it’s interesting that the rate of degradation is the same no matter what material the membrane is made from. To get a grip on what’s going on, researchers started incorporating a reference electrode in the middle of the stack. From this electrical information, they learned that it’s not the membrane that’s degrading, it’s the anode!

So, what I'll do is use my Focused Ion Beam to cut a bunch of cross-sections of used devices and unused devices. We’ll compare the two and see if there is any obvious physical degradation on the microscale. Hopefully, understanding how these devices are breaking will help us to make them stronger.

And that’s it! That’s what I’ll be working on for the foreseeable future (on the side of my regular full time job, that is)

So far, I've sliced up a healthy AEM and put all the slice images together into a movie. Here's what it looked like. Next up, I'll work on a used AEM to look for differences and make improvements on my observation methods. 

If you read this far, I am impressed and grateful for your mental fortitude! That's enough nerding out for now. See ya next time!

The Beetle I Found

I’ve been given a tool to feed my obsessive nerdyness. This tool happens to be a company that makes microscopes and I totally tricked someone into hiring me there. 

SO ANYWAY. I found this Beetle. I found it on the black top of some airport. It was all dead and dehydrated. I picked it up because I thought I could glue it to a canvas and make a cool painting around it. It looked like this:

Photo Credit to JJ Blackwood

But I happened to be hanging out with a coworker who suggested we take it to work and look at it. 

So then, I cut off it's leg and I cut off it's head and my friend Marc stuck it into his Scanning Electron Microscope (SEM). It looked FREAKY. I'll show you in a sec but first you need to know that it was a pristonychus terricola (I think) based on a picture I found in a library book called The Anatomy of Insects & Spiders by Claire Beverly and David Ponsonby. 

This is a really cool book because not only is it full of historical drawings that are from as far back as 1255 but it also talks a lot about uses for these bugs in ancient cultures. Turns out, Egyptians were really into Beetles and their traditions around it are fascinating and worth their own blog which I might get to someday. 

Ok, so first of all...let's look at it's leg. 

We are about to look at this part.

This is the hook at the end of it's foot. I was playing with the cutest june bug that I found when I was in Tennessee last weekend. It was crawling all over me and I kept thinking about how it's digging it's little micro-hooks into my skin but they can't cause me pain because they are too small.
That scale bar in the bottom right hand corner says 500 microns. To give you a frame of reference, a strand of human hair can be 17-50 microns for people of European descent and 56-181 microns for people of African descent. If you want to measure the diameter of your own hair, it's really easy! All you need is a laser. Follow these steps. If you are using one of those red laser pointers then it's a helium neon laser and the wavelength, λ, is around 633 nanometers. 

This is what I like to call the leg vertebrae! See in the drawing above how beetles have a whole bunch of joints on the leg? You know what I just found out about these joints? They work like screws! Instead of a ball-and-socket joint like humans have, beetles joints have threads that screw into place. They can do a full 360 rotation and are much harder to dislocate than human joints. 

Here is a close-up of one of the leg vertebrae. It's a beetle-knee!  I think the spikes are for defense based on the fact that they kind of look like medieval armor. I don't know what enemies beetles have besides birds and things that could just swallow their little 10-micron-wide knee weapons whole...but it probably makes them look tough to other bugs.
The schmutz all over it is probably dirt or dust specks. 

This is one of the coolest pictures in here, in my opinion. It's looking into the inside of the leg from where we cut it off. That's right...EXOSKELETON. Besides the support structures, it's totally hollow on the inside! If this beetle hadn't been dehydrating in the sun when it found me, it would have been full of goo.
Exoskeletons are made out of chitin, which is a long-chain polysaccharide. According to Wikipedia, "chitin has some unusual properties that accelerate the healing of wounds in humans". The Egyptians totally knew about that, fyi. As I learn more, I'm starting to suspect that beetles are actually magical. 

Ok, next we are going to look at this long antennae here.

Look at all the little hair follicles! Antennas are for sensing, and are insects' primary olfactory senses. In other words, these are the smellers. I tried to figure out how they work but then got really confused by all the jargon. Maybe one of you bio people can explain it to me? Thaddaeus, I'm looking at you. 

OK, compare the texture of the big antennae to the smaller one.

This one.

Super smooth! They must have two entirely different functions. Like, one for sensing and one for collecting particles...or, something like that. I'm not really sure. 

This is the end of one of the long antennas. The antennas are jointed just like the knees and this one was broken off at one of the joints when I found it. This is really cool because you can see those screw threads I was talking about where their joints come together! See them?
I think the stuff on the end of it is a little speck of pollen.

This is that pollen up close. It's also got this thread stuff all over it. Seems too small to be spider web....maybe a bacteria?

This is that same thread stuff that was all over it. I have no idea what this is.  I looked up SEM images of bacteria and spider webs and they don't really look like this. What do you all think? 

Here it is close-up. See how it's kind of braided like rope but then it's got this gooey part like snot? 

Here is part of it's head. It's got a chunk of dirt and also a little crawly thing. 

Here's the crawly thing up close. Maybe a little bacteria? It's got those little leg-looking things. I actually have no idea what this is. It's hard to put "5um long wormy thing with legs" into google and get meaningful results. I wish I knew more about this stuff so I knew what I was looking at!

Ok, I guess that's enough nerding out for now. See ya next time!




UPDATE: My friend Jessyka told me that the crawly thing might be a nematode. Here is a picture I found online of a nematode:

Yep....looks like it. Nematodes are a parasite to beetles and are used as organic pest control. Maybe that's what killed my beetle. Check out nematode pest control

21 cm cosmology

I haven't blogged in a very long time! I've been spending most of my intellectual energy and free time trying to learn spanish and graduate college instead of nerding out. However, for the next two months I plan on: 1.) Being really broke and 2.) Having lots of free time. This means many more blogs are on the way! Suggestions are welcome. In the meantime, I'd like to share a paper I wrote for my cosmology class this quarter.  It used to be full of lots of equations to describe the quantum behavior of hydrogen but I can't figure out how to insert equations in this thing. Does anyone know how to do that?

 It's a little different than the way I usually write in this blog but maybe you'll dig it anyway!

21 Centimeter Astronomy

The Dark Age

Applications of quantum mechanics have proven to be of great utility in the expanding field of radio cosmology. As astronomers begin to piece together answers to the question, “what did the early universe look like?”, the quantum model of hydrogen plays a large role. Understanding the nature of hydrogen’s hyperfine structure and it’s interaction with radiation becomes crucial to this investigation.

Hydrogen has a forking energy structure: each branch separates into a different set of branches. This branching begins with electrons, which exist in quantized energy levels, known as orbitals, around hydrogen nuclei. Within these orbitals the electrons are subject to two types of angular momentum: orbital (associated with motion of the center of mass) and spin (associated with motion about the center of mass).  While it should be noted that electrons are fundamental particles without interior structure, (and therefore cannot literally spin) this analogy is useful in analyzing the splitting behavior of orbiting electrons. Suffice it to say that electrons carry an intrinsic angular momentum which can alter the total energy.  It is spin that creates the hyperfine structure of hydrogen.

According to classical electrodynamics, a rotating electric charge creates a magnetic dipole. This sets up the electron as a magnetic dipole. The proton, like the electron, has an intrinsic spin, which sets up its own dipole moment in the same direction as the proton’s spin. The dipole of the proton is more complex because it is a composite structure, made up of three quarks, which gives a different gyromagnetic ratio. The proton’s dipole moment creates a magnetic field.

            The difference between levels in hydrogen’s hyperfine structure is an artifact of the interaction between the electron’s dipole moment and the proton’s magnetic field. If the dipole moments of the electron and proton point in the same direction (parallel) the energy of this configuration is slightly higher than if the dipoles point in the opposite direction (antiparallel). It is found that the frequency of a photon emitted during the transition from parallel to antiparallel is 1420MHz, which corresponds to a wavelength of c/v=21 cm. This falls within the microwave region of the electromagnetic spectrum.

The probability of this transition taking place is so small that it is classified as forbidden. To be precise, the probability of such an event taking place is 2.9*10^-15 1/s, or once every 10 million years. As a result, it can never be manufactured in a laboratory. However, evidence of this transmission is detected pervasively in all directions as astronomers look into space. Carl Sagan and Frank Drake considered the 21cm line to be so ubiquitous and universal that they utilized it on the Pioneer Plaque of the Voyager Mission as a single unit measurement in defining length and time. The omnipresence of this extremely improbable detection indicates that the universe contains a tremendous amount of neutral hydrogen.

The dumbbell looking thing the the upper left hand corner represents hydrogen undergoing a spin-flip transition. For those of you that don't know about this plaque, it's floating out in space with the hopes that someday aliens will find it. This plaque and the rest of the bizarro messages on board the Voyager definitely deserves it's own blog. Hopefully I'll get to that soon!

Of special importance to big bang cosmologists are the 21cm transmissions detected at redshifts between z=25 and z=10^3. Radiation detected in this range comes from a period between two important epochs of gas phase change in the early universe: recombination and reionization. To give a brief history of the state of hydrogen throughout time, shortly after the big bang, the universe was radiation dominated. During this period, protons and electrons could not combine to form neutral atoms without being quickly ionized by energetic photons. However, the universe cooled as it expanded, eventually allowing for this reaction to take place. This is known as the epoch of recombination and took place around redshift z=1100.  For several hundred million years following recombination there were no radiating sources, only cold, dark hydrogen. For this reason, the period is referred to as the Dark Age. In this epoch the universe was transparent, meaning photons could travel unimpeded through space. This is important to cosmologists as it means there is much information retained in the photons. The second epoch of the universe, known as reionization, occurred after the gravitational interaction between neutral hydrogen atoms allowed for the formation of the first structures large enough to radiate and ionize surrounding atoms. Astronomers interested in probing the structure of the universe between these two phase changes, when the universe was dominated by cold, dark hydrogen, must examine the fingerprints of such an era:  21cm photons.

Photon emission due to the spin-flip transition of hydrogen is temperature dependent. This means as 21 cm photons are released they will catalyze other reactions from neutral hydrogen nearby. By mapping the intensity of this radiation, cosmologists can develop a precise picture of the topography of the universe during the Dark Age. This is predicted to provide crucial constraints on current models for dark matter and dark energy. Furthermore, neutral hydrogen that has been ionized by those first radiating structures will appear as dark spots in the 21cm background. By examining these anisotropies, cosmologists can gain a firmer understanding of how the process of universal reionization occurred.

Research involving the 21cm line places cosmology on the verge of a new era. However, this field has a long way to go as observation of this transmission is extremely difficult. After redshift, this line is observed on Earth deep into the radio spectrum. This presents many challenges in collecting data as photons in the 21cm spectrum are drowned out by background noise from television transmission and the ionosphere. In the last few years, progression has been made both theoretically and observationally: theoretically, computer simulations of reionization have achieved larger dynamic range and can make more reliable predictions; observationally, plans have been made for four machines to start sensitive 21cm detection in the near future. Precise observations of the 21cm line from distant redshifts promise to revolutionize our understanding of the early universe.   

Sources

Griffiths, David. Quantum Mechanics. 2nd. Upper Saddle River: Pearson Education, 2005. Print.

Pritchard, Jonathan, and Loeb Abraham. "Evolution of the 21 cm Signal Throughout Cosmic History."

Miguel, Morales, and Wyithe Stuart. "Reionization and Cosmology with 21-cm Fluctuations." Annual Rev. Astron. Astrophys.. (2010)

Perception, LSD, and Synesthesia

PERCEPTION. It's crazy, right? The way you view the world around you depends so much on your current state of mind. Whether your perception is altered by your mood, illness, or drugs, it’s plasticity is almost frightening.

Of course, one of the easiest and most marked alterations you can make to your perception is via hallucinogenic drugs. I’ve never tried them myself just because the thought of letting my imagination become my reality kind of terrifies me, to be honest. I don’t think I am emotionally mature enough to deal with the monsters that my personal psyche would create for me. Not yet, anyway. At some point in my future, however, I would love to hallucinate. I think it would be a fascinating experience. I’ve heard that some people are forever changed after taking LSD. You can talk to God. You can come to life-shattering realizations about the universe. Your spirituality and worldview might be forever altered. Like this guy. On the darker side, however, some people come out of LSD trips with permanent psychosis.

It’s hard to find accurate accounts of what people actually experience while on LSD. Google will bring up government websites with obvious bias toward scaring people away from drugs or hippy forums that seem pretty sketchy and not very reputable. Since the experiences of those who take acid are so personal and individualized, I think the best resources available to me are personal anecdotes.

I spent a little time watching people take LSD and talk about their trips on YouTube. Apparently to some people it sounds like a good idea to take video of them selves doing illegal things and post it on the internet. It’s amazing how many people will willfully and enthusiastically incriminate them selves. I did find some interesting stories though. This one is good.

He brings up the monumental question, “what is reality?”. Questioning what is real seems to be common among LSD users. Some people, like the hippy I linked above, might challenge the idea of reality for the rest of their lives. You can see, hear, smell, taste and feel “unreal” things while you are on acid. To the tripper, these things are completely tangible. How could that not eff with your perception of reality?

It’s difficult for our minds to grasp the fact that all sensory perceptions are just electrical and chemical signals in our brains. The reason my computer screen looks the way it does is because photons of a certain frequency stimulate my retina and cause it to send signals to my brain. The same goes for all the information that my brain is taking in from my surrounding: sounds, smells, temperature, air pressure, everything. My brain uses electrical and chemical processes to somehow construct my understanding of what is around me. This understanding of my surroundings is projected into my consciousness and it is the only way I can relate to reality. If the mechanism that allows us to interact with reality is altered, then our personal reality is altered. This can be a significant, permanent change.

If people are forever changed by taking LSD, then it must be permanently altering the structure or function of the brain somehow. But how?

Well… I guess first of all I need to figure out what LSD is, exactly.

LSD stands for lysergic acid diethylamide. So it’s made from reacting two chemicals: lysergic acid and diethylamide.

What are those two things?

Looks like lysergic acid is the good part…

Lysergic acid is found in a fungus known as ergot, it commonly infects rye. More specifically, ergot has high concentrations of a chemical called ergoline. It is from ergoline that lysergic acid is extracted.

When ergoline is ingested it does some knarly things to the body including constricting blood vessels, causing convulsions, headaches, nausea, vomiting, and most famously: hallucinations.

People have known about ergot for a long time. Since the middle ages, controlled doses were used by midwives to induce abortions. There is also evidence of its (intentional?) use thousands of years before this as ergot was found in the stomachs of prehistoric human remains preserved in bogs. Perhaps it was used in prehistoric rituals of spirituality.

It has also been ingested accidently on several famous occasions. Turns out ergot is a trifling little fungus that may have had a hand in several historical events. Many historians have suggested that the behavior of the young women who were “bewitched” during the Salem witch trials was due to ergot poisoning. It has even been linked to The Great Fear, wide spread panic among peasants that helped spur on the French Revolution.

As for the D part of LSD, diethylamide, it’s a bunch of carbons, hydrogens, and a nitrogen strung together. You can get it from mixing ethanol and ammonia. I’m not quite sure of its purpose in LSD. It might be a potentiator, a chemical that enhances the hallucinogenic effects of the lysergic acid. With a potentiator like this, you can just take a drop and go on a mental vacation without the unpleasant effects from the ergoline like vomiting, diarreah, gangrene, ect…Diethylamine sounds like a plus.

OK, so what is it doing to your brain?

Well, LSD is structurally very similar to a chemical called serotonin. 

Serotonin is a neurotransmitter, a chemical that transmits signals from neurons.

This is how neurotransmitters work:

Neurons have lots of little packets of chemicals inside them (like serotonin). When a neuron receives an electrical impulse from the nervous system it converts this electrical signal into a chemical signal by releasing the little packets of neurotransmitters.

Here is a really cool animation.

This one is not as cool but it explains what is happening.

The neurotransmitters swim around in your brain and bond with receiver cells and this causes many varied responses in your body. In the case of serotonin, it might affect your mood, anxiety levels, appetite…the list goes on and on.

I didn’t know much about serotonin so I did a few google searches and I found this great blog by neuroscientist Sheril Kesenbaum that gives a fantastic run down on serotonin. 

Man, I tried really hard to understand what serotonin was all about. One thing Dr. Kesenbaum said that made me feel much better is that no one really understands serotonin because the serotonin system is insanely complicated. Serotonin has LOTS of different functions in our bodies and it fulfils these functions in many different ways.  

When the LSD molecule enters our brain, since it looks a lot like serotonin, it binds to serotonin receptors. This is where LSD gets unpredictable: sometimes it will excite the receptor and sometimes it will inhibit it. The effect is a flood of serotonin or no serotonin at all. This is happening at several serotonin receptors throughout the brain.  When a person takes LSD they are messing with their natural ecosystem of serotonin on a grand scale. For reasons no one understands entirely, this causes a marked change in your sensory perceptions.

LSD distorts sensory perceptions in several ways. My favorite is called synesthesia. This is where sensory perceptions tend to blend together. IE: A person may see music or hear/feel color. This word comes from a real medical condition. Ok, after reading up on it a little, synesthesia is actually my new favorite thing. Synesthesia is a real, documented psychological condition in which the stimulation of one sensory pathway leads to the immediate stimulation of another, unrelated pathway. So, for some people the sound of middle C on a piano might smell like roses or maybe every time they see a humming bird they will taste chocolate or if they have a toothache it will have a color, smell, and taste.

The most common manifestation of synesthesia is that letters and numbers will have a certain intrinsic color. IE: G is orange. 8 is purple. They just are. And yes, they are actually SEEING these colors along with the numbers or letters, not just imagining them. The most compelling evidence is that brain scans reveal the visual color processing sections of a synesthete’s brain lighting up when they are shown a certain number or letter. Furthermore, the colors they report seeing are consistent. If they see J as pink at age 9 it will still be pink when they are 32, and the same goes for all other letters and numbers that have a color. If this were just an artifact of imagination it’s hard to imagine that such remarkable consistency would be maintained throughout a person’s lifetime.

Since you don’t question what you are experiencing until you realize that everyone else is not experiencing the same thing, many people don’t even realize that they have this condition. I found this book on synesthesia called The Frog Croaked Blue and there is this cool quote from a woman who describes the moment when she realized that she perceives the world differently than everyone else,

 “I did not 'discover' my synesthesia until I made a comment to my parents in my mid-twenties about a number. They were disputing some number that I had given them as a statistic and I said, by way of proof, that it could not have been seventy and had to be forty because it was a red number with a warm feel, and it was only halfway up the line to 100. It is extremely strange when the two people who know you better than anyone else regard you as though you were a complete alien. I then went on to describe how my numbers are not only colored, but also have very distinct patterns, as does time - the time of day, days of the week, months within the year, and the years themselves.”

Most synethetes view this as a gift that helps them excel at certain tasks such as spelling, arithmetic, memorization, composing... the list goes on. Two famous composers, Franz Liszt and Nikolai Rimsky Korsakov once had a public disagreement about what color certain keys were! I have no idea of the circumstances of the argument but I really like to imagine these two heartily debating the color of a sound in a room full of uncomfortable people who have no idea what they are talking about because to everyone else, sounds are not colors.

Many brilliant people have been known to be synethetes. As a child, Vladimir Nabokov insisted that the colors of the letters on his blocks were all wrong.  Physicist Richard Feynman describes his colored equations,

"When I see equations, I see the letters in colors – I don't know why. As I'm talking, I see vague pictures of Bessel functions from Jahnke and Emde's book, with light-tan j's, slightly violet-bluish n's, and dark brown x's flying around. And I wonder what the hell it must look like to the students."

One of the things I find the most interesting about synesthesia is that certain perceptions seem to be consistent among different synesthetes. For example, for those who have color/letter synesthesia: S will tend to be yellow, A tends to be red, O tends to be white or black. Different people tend to agree on the intrinsic color of certain letters!

Ok, come with me into the weeds for a sec…

If one person can observe something that is completely tangible to them, it doesn’t necessarily constitute reality. BUT if several people see the same thing isn’t THAT reality? I mean…if you see something unbelievable the first thing you will probably do is ask someone else, “Do you see that too?” and if they do then you know it’s real and not just in your head. If more than one person can agree on seeing the same thing then …What IS this? Is this a different reality?

Synesthetes’ brains must be different from the brains of regular/boring people like me some how. But how? It seems that no one is really sure.

If LSD is temporarily inducing these effects in people who don’t have synesthesia and LSD is known to affect the serotonin system…perhaps it has something to do with serotonin?

Do you have synesthesia? I would love to talk to you about the awesome way you see the world around you!


Obviously, much more research should be done on perception, LSD, and synesthesia, but alas, this subject seems to have widely been abandoned by psychologists and neuroscientists. Perhaps it's a reputation ruiner these days. I did find this 2010 project from the Multidisciplinary Association For Psychadelic Study, though. They used a mysticism scale to quantify spiritual experiences! Imagine that. The mysticism scale was developed by this guy named Ralph W. Hood in 1975. It's 32 questions that are thought to measure mystic experience scientifically. Check it out.  


LSD seems to be a powerful gateway toward an understanding of oneself and our role in the surrounding universe and should perhaps be used in that context. However, while breaking down psychological barriers of the mind can be an enlightening learning experience, it should be noted that these barriers exist for a reason. Sounds like with enough LSD use, it's possible to lose your ability to relate to others, to reality, and effectively, to yourself.  

I think a good way to end this post is with this interview from Saul Williams on LSD and how to use it. Smart dude. He's got some good things to say. Have a watch.

Was Clay the First Life on Earth?

I just finished this book called Seven Clues to the Origin of Life by a biochemist named A.G. Cairns-Smith from the University of Glasgow. He’s got this theory that the first life on Earth was clay. It’s pretty intriguing. I’ll try to explain…

Cairns-Smith is looking to answer the question: how did life spring up on Earth? It’s an elusive puzzle that even the most well respected biologists don’t know how to begin solving.

 Life is highly complicated and organized. Perhaps this could be chalked up to evolution if it weren’t for the fact that the complexity seems to be vital to the whole way that life works. The crucial elements of life (DNA, proteins, lipids, and carbohydrates) depend on each other completely. They are interlocked. You can’t have proteins without DNA, proteins can’t do anything without the energy from lipids and carbohydrates, lipids and carbohydrates are constructed by proteins, and proteins construct DNA which brings you back to the beginning of this sentence.

An analogy that I really like is a stone arch.

You can’t take out one stone without the entire structure collapsing. You also can’t build this kind of arch stone by stone. Similarly, all fundamental pieces of life are necessary to the whole so life could not have evolved piece by piece.

The popular example amongst proponents of intelligent design is a mousetrap, it won’t work unless all the pieces are there simultaneously. They call it irreducible complexity. It’s a pretty valid argument, in my opinion. It’s difficult to imagine how even the simplest life form on earth, a single cell, sprung up out of nothing but the oceans. Why would a bunch of atoms spontaneously and simultaneously organize themselves into a complex system in which every piece depends on the other pieces?

You almost can’t blame people for giving up on this question by just throwing their hands up and saying, “God did it!”. The circumstances that would have been necessary to make the first cells are so unlikely that it’s pretty much preposterous to assume that cells assembled themselves by chance.

Let’s take DNA, for example. DNA is made from nucleic acids. In order to synthesize it in a lab you are going to need a primer, which is a strand of nucleic acid that is used as the starter. In order to make primed nucleic acids there are hundreds of steps that need to be performed in a very precise order. Pouring, stirring, heating, concentrating, agitating…ect.

Sure, you could imagine all of these steps happening on their own in nature. We could imagine a pool evaporating in the sun to create a concentrated solution, lightning striking the pool to agitate it, rainfall to dilute, filtration through rocks… and so on. It’s not that the occurrence of each individual step is too unlikely, it’s that the sequence of hundreds of these events successfully happening one after another is too unlikely. It’s analogous to flipping a coin and throwing heads 10,000 times in a row… if you can make this happen I want to be on your team.

And this is just DNA! We also have lipids, carbohydrates, and proteins to worry about; Each requiring their own long series of steps for synthesis. Not only that but ready-to-go proteins, lipids, carbohydrates, and nucleic acids would have to all be in the same place at the same time in order to assemble themselves into an interlocked cell.

Of course, even extremely improbable events can happen given enough time and all the resources on Earth. However, there wasn’t enough time and there isn’t enough Earth.

What do I mean by this?

Cairns-Smith gives a pretty neat run down of this immense improbability: Let’s say that there are 140 steps to perform in order to synthesize DNA. Let’s also say that the chances of the appropriate event happening naturally at each step is one out of six. Both of these are very optimistic estimates. The chances of, say, lightning striking a certain puddle of chemicals at a certain time, are probably much smaller than one in six. However, if we use one in six we can pretend we are rolling dice, which makes this analogy cuter.

Ok so now we are rolling a dice 140 times in a row and we need the same number to come up every time. This number represents success at each step in the life-making process.

What are the odds of this kind of miraculous rolling actually happening? Since you can roll a 1, 2, 3, 4, 5, or 6, there are 6 possible outcomes for one throw. There are 6*6 possible outcomes for two throws, 6*6*6 possible outcomes for three throws and so on. For 140 throws there are 6 multiplied by itself 140 times possible outcomes.

Put this into google: 6^140. You will get, approximately, 10^109. This is a one followed by 109 zeroes. Try writing that number down just to get a feel for how enormous it is. You will get bored and give up after 10 zeroes, max. Five, if your attention span is slightly longer than mine. The chances of you rolling a dice and getting the same number 140 times in a row are 1 out of this huge freakin number. So, you would need a number of trials that is something like 10^109 in order to hit on the ONE successful trial. 

Well that doesn’t seem like such a big deal…just roll the thing for 10^109 trials. You’ll get the successful one eventually. We have all the time in the world and the whole earth. Sounds feasible…right?

Well, if you were to roll one dice every second since the beginning of earth’s history you can only get through about 10^15 trails. No problem…get more dice. In order to squeeze in 10^109 trails we need to be rolling 10^94 different dice every second.

Turns out 10^94 is a ridiculous number. That’s more than the number of electrons in the observable universe, which means it’s WAY more than the number of atoms that have ever been present on Earth. Earth just doesn’t have enough stuff on it and it hasn’t been around long enough for these kinds of odds.

So, you see what I mean when I say this is a pretty valid argument for intelligent design?

Personally, however, I think it’s quite lazy to assume that cells were prepackaged and handed over to the earth as a finished product. If there is a god I don’t she is as boring as that. As crazy and unlikely as it seems, life has to have started up via natural processes on this planet and I’d like to learn about the ways this could be possible.

Perhaps the very first life was not so interlocked; the pieces not completely dependent on each other. Maybe the stone arch was originally scaffolded, like a wall, and then pieces were gradually subtracted leaving us with the mutually dependent, arch-like system we have now.

Enter this bizarre-o clay theory. I really like it. Maybe you will too!

Let’s start here:

Organisms reproduce by copying the messages that define the organisms. This is what we call passing on genes.  Passing on genetic material that is capable of mutating is all natural selection really requires. Of course, the mutations that are beneficial to an organism’s survival are the ones that get passed on and the ones that are detrimental to survival do not get passed on. This is evolution.

In order to pass on genes, or messages, all we really need are the messages themselves. If the messages can be replicated using readily available materials, then we don’t need all the manufacturing machinery of the cell.

Cairns-Smith proposes that the very first organisms were “naked genes”, genetic material without a cell. He suggests that the atomic structure of crystals served as the very first genes.

I’ll explain. Crystals “reproduce” by making layers. The layers are simply repeating patterns of atoms and ions.

A single layer of kaolinite crystal looks like this:

Due to the sizes and charges of each of these particles, only certain atoms and ions can stack up on top of this layer and become the next layer. Think of it like legos…not just any lego can go on top, it has to have the right hole size. Take it one step further…think of it as legos with positive and negative charge. You can’t stack two like-charges right on top of each other. Therefore, the next layer of legos (atoms) is pretty much determined by the first. Starting to sound like DNA yet?

If your family wasn’t as dorky as mine and you didn’t get a grow-your-own-crystal kit as a kid here are some cool videos of crystals growing:

http://www.youtube.com/watch?v=DKJmBuh-5eg&feature=related

http://www.youtube.com/watch?v=zwqst0aR8D0&feature=fvw

http://www.youtube.com/watch?v=jrKThzpJ5hQ&feature=related

http://www.youtube.com/watch?v=D9OLLrMLdAU&feature=related

http://www.youtube.com/watch?v=QwiPplYoH7Q

Don’t they even kind of look like they are alive??

For a crystal to grow like this it’s necessary for the environment it’s in to be in a state of super saturation. Super saturation is just when there is more stuff dissolved in a solvent than can usually be dissolved… sugar in water, for example. If you add sugar to water while stirring it will dissolve, of course. But if you keep adding sugar the water will get to a point of saturation where nothing else will dissolve. However, if you heat the solution, then EVEN MORE sugar will dissolve and the water will stay more sugary than it ought to be even after cooling… It’s become super saturated! 

All we need now is a seed- a small crystal from which a large crystal can be grown. Put a little crystal fleck in the solution and in no time you will have grown a dazzling crystal! In a super saturated solution, crystals can be added on faster than they are dissolved away. If your saturation level is high enough you don’t even need a seed crystal. Spontaneous seeding can happen on little flecks of dust or on the surface of its container.

Sometimes, especially if the saturation level is very high and crystals are forming fast, the units will add together in the wrong way. When this happens the resulting crystal bit becomes destabilized and it will dissolve faster, not allowing more crystals to grow on top of it. Or maybe the crystals will add together in a way that strengthens the crystal and allows it to last longer. This “mutation” will then repeat itself because, remember, the next layer is determined by the one that came before it. Ahem…evolution by natural selection much?

But even with perfectly constructed crystals, when the stacks of crystals get too heavy they will break off, exposing both ends for continued growth. The crystals “breed” by breaking up as they grow and providing new seeds for more crystals to grow on. So now we have a mechanisms for crystal birth and mortality!

Ok, but eventually the solution is going to run out of stuff to give, right? The crystals can’t keep growing and reproducing forever because sooner or later everything that was dissolved in the solution will be deposited on the crystal. There will be nothing left to make more crystals from.

This is why we need a continuous crystallizer! A continuous crystallizer is a vessel system that allows for inflows and outflows. It just so happens that the whole earth is a continuous crystallizer for clay materials. The earth makes clay all the time…and lots of it!

I know we probably aren’t used to thinking of clay as a crystal but that’s just because the crystals are so small we can’t see them. Here are some pictures of clay way close up:

This is Smectite

Kaolinite

Dickite...haha. God. What am I, 12?

See how there are tiny uniform units that get repeated and stacked up? That’s the signature of a crystal.

Ok, well this whole analogy is cute and all but it doesn’t change the fact that CLAY ISN’T ALIVE. Our genes aren’t made of crystals…they are made of organic molecules. What gives?

Is it possible that modern organic genes could have evolved from crystal genes?

Cairns-Smith thinks so!

It just so happens that certain organic molecules could be very useful to an evolving crystal organism. Not only that, but clay is very good at holding onto organic molecules. Let’s look at some of the important life molecules and how they could be of use to clay crystals. Amino acids and formic acids could be used to control acidity and promote crystallization in clay. Sugars, like polysaccharides will soften and harden under certain circumstances and could serve to control the sliminess of the clay, which is useful if the survival of the clay crystals depend on not being dried out. Nucleotides could be used to bind clay crystals together in certain ways. Perhaps the very first DNA molecules were constructed to interact with clay and lock the pieces of the crystals together.

Now that we have a mechanisms for all these organic molecules to interact, it’s not so difficult to imagine the organic molecules starting to use each other as templates for reproduction instead of the crystals. DNA-like molecules could have come along to help amino acids join up into chains, all the while being protected and promoted inside the “membrane” of a clay crystal. Sooner or later, cell membranes would have had to evolve to replace the clay cradle and proteins would evolve to aid in the assembly process. All this could have been accomplished with more and more sophisticated crystal growth. Remember, the more well-constructed the crystal, the more likely it is that there will be lots of them.

As organic organisms become the more high-tech and efficient organism, one that can construct itself from air and sunshine, they eventually replaced crystal organisms. This would have happened via genetic takeover.

I found this diagram here. It represents a secondary gene type taking over the original gene type.

Is this what really happened? Was our very first ancestor really clay? Hell if I know. Aren’t there some religious stories about humans being created from clay? That might add a whole layer of beauty and humanity to this theory.

There are certainly criticisms of the clay theory but it seems that most of them have to do with the lack of evidence. Unfortunately, we can’t go back in time and watch as the very first life began to evolve. Life springing from clay has also never been demonstrated in a lab setting. Of course, this whole process of evolution from clay to cells would have taken a VERY long time so perhaps it’s not feasible to recreate it in a lab.

Maybe we’ll never know how life began on this planet. And isn’t that great? In a way? Maybe?

Well that’s enough nerding out for now!

But before I go….

I doubt that anyone really reads my blog this closely but I have a few updates and follow-ups. From my alternate biochemistry blog: I got that book, Extraterrestrials, A Field Guide for Earthlings and it’s AWESOME! Tons of cool pictures and hypothetical aliens! It was definitely worth the one penny I paid for it on Amazon, even worth the $4 of shipping. I recommend it.

From my brain waves blog: my eccentric (in the best way) mother bought herself a Mindflex…remember? That maze toy that you control with your brainwaves? It seems to work! I tested it out by doing math problems while the probe was on my head and I made the ball levitate pretty high. Then while I was zoning out and watching TV the ball would fall down. Maybe it has a delay of a few seconds…but overall, I’m a believer! How cool will it be when we develop technology that is even better at measuring and responding to brain activity so that we can begin to control things exterior to our bodies with nothing but thought? YAY! THE FUTURE! Well, someone’s gotta be jazzed about it, right?

OK see ya next time!