Temporary Hiatus

Hey everyone that reads this site, sorry I haven’t been keeping up with things, but I’ve been pretty busy in my own life. I’ll try to update the site more in the near future but for now, just know that I’m working hard. Also, you should register to vote in the Democratic primary in your state (if you live in Iowa, the primary is in 2 weeks!) and as you know, I am 100% behind Bernie Sanders and if you think the middle class needs people fighting for it you should be for him too!

 

80s group that brought you such hits as Down Under and Who Can It Be Now

The Mighty Mitochondria

The Charter School of Wilmington specializing in Math and Science (and odd humans)

The title comes from a reference to Tom Hughes, a kid from Charter that was pretty weird (the quote is actually his from once during homeroom where he was dancing around singing it…) among a high school of pretty weird kids. Anyway, the mitochondria are small units within the cell that take care of producing energy from the sugar we provide. To visualize this, see below, the sugar is glucose. Think of any carbohydrates that you eat being made up of glucose which is what the sugars are converted to in the liver or stored as glycogen. We eat carbs, or proteins (which if there are no carbs get converted into glucose or acetyl coenzyme A) or fats (which get broken down into fatty acids (which can be converted by the mitochondria into acetyl coenzyme A) or glycerol which is converted by the liver into glucose)). Long story short, everything (carb, fat, protein) is converted to glucose or acetyl coenzyme A. The body can use glucose and convert it to ATP directly (see Glycolysis below), but not very efficiently. However, some creatures can survive completely in this way (for example, if yeast have sugar and no oxygen, they survive this way through fermentation, except that instead of making pyruvic acid as a byproduct they make ethanol AKA THE GOOD STUFF). All life forms make use of glycolysis inside of cells, and there’s some evidence that ancient conditions on earth may have allowed cells to perform the process WITHOUT enzymes, meaning that you could have sugars (which can form spontaneously under the right conditions) being broken down into energy spontaneously. Nowadays on earth we and all other organisms use enzymes to break down sugar with glycolysis. But the process described above usually happens when there is no oxygen present, what about the other 3/4 of that diagram?

 

 

You probably learned this in high school

 

Well, to finally get back to the point, the mitochondria is responsible for carrying out energy production using oxygen. There are many species that do not produce energy using oxygen (mainly microorganisms that live in environments without oxygen) and there are many many many species (again mainly microorganisms) that do not have mitochondria but still use oxygen to make energy.

This gets to the second interesting part about mitochondria. There is evidence that mitochondria, although firmly a part of many organisms now, was once a stand-alone species. Billions of years ago, it’s possible that mitochondria formed a symbiotic relationship with another single-celled organism. A relationship that was so successful and so long-lived, that now mitochondria can only be found inside other cells. Indeed, most cells of a human have mitochondria and some have different concentrations of mitochondria depending on their need for energy (metabolically active cells like muscle and nerve cells have higher mitochondria counts per cell). The evidence for mitochondria being a separate species at one time stems from the fact that mitochondria have their own DNA  (mtDNA) and this mtDNA exists in most of its symbiotes (like humans) as a closed, circular DNA ring. Do humans have closed circular DNA? No. What do? Bacteria. Additionally, this mtDNA encodes enzymes and other proteins useful only for the mitochondrial function and A LOT of other DNA inside human chromosomes actually looks a lot like mtDNA that somehow was transferred into the human DNA and got stuck there (this happens so much so that only 37/1500 proteins in the mitochondria come from the mtDNA).

Well, it’s funny that I mentioned circular DNA for bacteria in that this relates to aging. Basically, because their DNA is circular, bacteria are all “immortal” and will replicate their DNA forever. This post is starting to go on forever, so I’ll save the third thing I find interesting about mitochondria (it’s role in aging) for another time. Thanks Zach and Dave for encouraging me to write about mitochondria, a topic about which I’m not an expert on but assumedly should know more than the average person.

Republican debate crasher

At the 2015 Republican debate on December 15, there was someone in the audience that was not satisfied with the political system. The man shouted out “Americans need free and fair elections, not billionaire auctions!” Of course the guy was not responded to and the topic was not even brought up (the topic of getting money out of politics). It turns out the person was Kai Newkirk, part of the “99 rise” movement. I think what he did was disruptive but in a good way since the issues that many Americans agree about and feel strongly about are not even being mentioned at these presidential debates. The video below shows his outburst in its entirety.

 

Also, another note about the debate, John Kasich must have been getting speaking tips from a kung fu master because that guy just went crazy with the hand chops. I even made a video about it (see below).

RNA, the nucleic acid you probably haven’t heard of

So, almost every time I explain my current research to people, it’s something like “I do biology research” and then they ask “What kind of research?” and I then say “DNA repair” and then they say “DNA can repair itself?” That is the typical conversation but one thing that’s pretty amazing is that deoxyribonucleic acid (shown below), DNA, has become nearly ubiquitous in our culture. Everyone seems to know what it is, or at least something about it. The heritable genetic material that was hinted at but not verified as DNA until the famous Hershey-Chase experiment of 1952 has in less than 70 years become such a widespread idea, while the other major nucleic acid of life, ribonucleic acid (RNA), is still unknown to the vast majority of people.

 

The only difference is that DNA is chemically more boring than RNA

 

DNA would be NOTHING without RNA, and DNA is largely inactive in the cell, it’s mainly there as the backup copy for RNA since it’s more stable. RNA can pair with DNA, get what it wants from DNA (use it as a template), and then leave DNA behind and go party with some proteins. This is the “central dogma” of biology (shown below).

What’s even more interesting is that RNA can fold up and do almost ALL the functions of life. That’s right people, RNA doesn’t need to go out to party with the proteins, RNA IS THE PARTY. RNA can replicate itself or cut itself (so emo) or join two pieces of RNA together. In fact, many many scientists believe that life began with a completely RNA world. Life is the random combination of RNA that eventually started “coding” into proteins. RNA may have started life, I wish people gave it the freaking credit it deserves (i.e. just knowing that it exists). DNA is like an old phone book or an SQL database, useful, but it might as well stand for Does Nothing Amazing.

Life and how it started

Robocop henchman

Alright, so this is similar to a post I made about 80s music, because I was listening to it again and there are a lot of videos that come with cool 80s movie compilations along with the music. Anyway, the compilation was pretty violent (as Robocop is a violent movie) but it made sense for the most part. I mean, Robocop’s character in the movie is a new technology, this almost indestructible cop, and the villians of the movie of course will try to deal with him as if he’s human (i.e. SHOOT HER! SHOOOOOOT HER! (go see Jurassic Park if that didn’t make sense to you)). So they are unloading A TON of ammo on this cyborg, to little or no effect, but I imagine as a henchman you could get away with participating in a group activity like that, some dumb herd mentality thing and maybe they each think that they are far enough away or isolated that Robocop will not target them with his super-sensitive robotic targeting system and absolutely destroy them (even though he’s just shot a bunch of others like that).

However, the outlier guy at 4:15 (let’s call him John Snow), the guy with the machine gun, he, after seeing 8-10 of his comrades blown away and Robocop not suffering any visible damage despite being shot 50 times with multiple types of guns, John decides to move close to Robocop and start shooting as if it’s the straw that will break Robocop’s titanium back. Why? Have you learned nothing John Snow? Why not just run away? Henchmen are stubborn, that was the overall message of this post. I guess that’s the downside of undying (until they die) loyalty in a criminal organization.

 

Much as sidekicks or “staff” in groups of good guy organizations are marginalized, so too are henchmen marginalized in bad guy organizations. Minor characters seem to have no value, no part to play, but they are the unsung heroes of fiction and the world. Sure, everyone knows famous people, but it’s very rare for people to know of the support group of said famous person. They will know a comedian, but not the guy that hooks up the sound or the lighting, or the person that is hosting that comedian, or the sitter that watches the comedian’s kids. These minor characters, we don’t even know their last names, and sometimes we don’t even name them at all.

Sam Rockwell in Galaxy Quest

 

The homeless person on the street or ANY person on the street is just another face in the crowd. Unless we know them, it’s very hard to identify with anything that happens to them. As much as we are a social species, I think the flaw of humanity is that unless you are part of our “tribe” or to refer to above, unless you are a central character in the story of our life, then it’s very hard to have true empathy. It’s devastating that right now there are so many people dying in mass shootings, but to the shooters it’s almost as if the people they gun down are all just faces in the crowd, nothing compared to the central characters or themes in their own life story. And in very much the same way the reaction to these events takes a faceless, “Oh it’s another mass shooter” type of mentality, again marginalizing the person/people, not trying to understand why it happened, but just treating it like an inevitable outcome that can’t be changed. We are all minor characters, but all of us can change the world to being a better (in the sense that fewer people are suffering) place just by trying to understand other people and empathize with them. Don’t be like the henchman that blindly follows the others in his tribe to destruction. Understand Robocop.

How much does a bombing cost?

Often on the news we hear about how a country bombed another country. During the Iraq war I remember hearing this on the news A LOT, but one thing was never really talked about, what does this actually cost? Well I found a good estimate that I would like to share with you. I know that this is just an estimate but it gives you a rough idea of how much bombing costs.

TLDR; $3M/strike

The report where I got my information

Now in this report they talk about the different aircraft and refueling costs and I know that these are not the only costs (the cost to train the pilots, the cost on the infrastructure of the country being bombed, the innocent people killed, etc.) but I think it can give us a good estimate. A particularly revealing graphic from the report is below.

Bomb

As you can see, the cheaper aircraft are drones like the MQ-1 Predator and the MQ-9 Reaper. However, in the same report they say that a lot of the bombing is done by F-15s, F-16s, and F-22s. Another interesting thing to note is the cost of the munitions, which vary greatly from a tomahawk missile costing over $1M to a GBU-31 bomb (shown below being loaded on a plane) costing a “mere” $30,000. The report talks about how typically each strike involves around 2 munitions being expended.

GBU-31, I wonder if the GB stands for “Great Big”…

 

And so, even at the cheapest of the cheap airstrikes, it will cost $60,000 for the bombs alone. However, the report also did an estimate of targets attacked per month (100) and cost per month (shown below). Now this is only for the “low intensity” bombing campaign, but as you can see from the table below it will cost about $300M a month (probably less but it’s easier for the math), or $10M a day. Now dividing that by the number of targets attacked per day (about 3.3) we get $3M per target attacked. Now it’s worth noting that a lot of the cost may come from the fact that they have to fly lots of planes (sorties) before they actually attack a target (90 sorties a day but only 3.3 attacks per day), but I think we can treat the sorties where they don’t attack as intelligence gathering or an overhead cost to bombing. So, in essence every time you hear “so and so bombed ISIS” now you know that it’s costing about $3M. Tax money well spent? Feel free to leave a comment.

CostPerMonth

Preston Jacobs – Game of Thrones Theorymaster

 

The original cover art for the first book (I remember because my friend Useff lent it to me and I never gave it back)

Alright, so I know that the book series is A Song of Ice and Fire, but I think more people probably know it by “Game of Thrones” since that’s the name of the HBO show. I remember reading the books and finding them decent but by no means spectacular, and then the show came along and the story spread like dragon fire. Anyway, I just wanted to bring to everyone’s (or no one’s, considering the limited readership of this blog) the very detailed and incredibly well laid-out theories of one YouTube poster known as Preston Jacobs. This guy’s channel (link below) goes into detail with all that is happening in the show, but more importantly the books, and does a great job of analyzing everything from the books being science fiction novels INSTEAD of fantasy novels to the genetics of dragons. There are so many plots and subplots within the books and Preston Jacobs really helps to bring them all into focus since it’s hard to follow all of them when they are spread out over thousands of pages.

https://www.youtube.com/channel/UCXU7XVK_2Wd6tAHYO8g9vAA

Powergrid, a very good board game

 

Thanksgiving is right around the corner and it’s during this time that my mind goes to friends, family, food, and board games. While traditionally my family has only really played games like Scrabble or Monopoly, recently we have introduced a more complex (and in many ways more fun) game called Powergrid. Powergrid is simple to learn, hard to master (I have never won a game yet). It involves 4 phases, where you buy power plants (-$), buy resources for the power plants (-$), build power plant stations in different cities (-$), and then get paid (+$). The strategy comes into play in exactly HOW you do each of these steps. The game punishes you for winning and has many subtle complexities that you might not pick up on at first and don’t really need to in order to play and have a good time.

 

Below is a picture of the game already in progress with 3 players (the red, green, and black pieces represent powering stations in several different cities). The numbers on the pipe-looking things are the connection costs that must be paid before you can build in that city (the powering stations must form a connected network between cities). So building costs money to A) make a powering station and B) the cost to connect to the city you want to build in.

You get 3 powerplants max, that can power a certain number of cities (see bottom right of each powerplant card)

 

In addition to building powering stations (the build phase) you need to buy resources to power the plants (resource phase) as well as buy the power plants (plant auction phase) themselves. These phases (mentioned before) involve auctions between the other players. The power plant market is just a randomly drawn set of power plants that people bid on, whereas the resource market (shown below) is composed of a finite set of resources that get replenished (but only by a set amount, meaning that there can be shortage, which means that prices can skyrocket). So who gets to buy resources or power plants first? The player in last place! So the more you’re winning, the more disadvantaged you are for buying stuff. This aspect of the game and many others are what make it fun, there’s usually a chance for you to come back and win after being down. Looking forward to playing (win or lose) soon!

 

Where the U.S. middle class has gone

There are a couple of graphs which explain the phenomenon of why the middle class has been shrinking and people seem poorer (because relatively THEY ARE). So while Americans are more productive (it’s more than doubled since the 70s), wages have stagnated, meaning that people are producing more but not making more money.

That’s the first graph, but these others are also pretty revealing. Basically, where has the money then gone if productivity is going up but wages aren’t? Who’s getting the extra value? THE RICH. So as can be seen from the graphs below income has risen only modestly for almost all Americans but has increased dramatically for the top 1%.

 

 

 

Lastly, it’s worth mentioning that the power of workers, namely organizing together to form unions, may also have an effect. One thing is certain, unions have been getting absolutely smashed by big business. Feel free to leave a comment or if you want more cool graphs, check out the link to this cool article from Mother Jones.

http://www.motherjones.com/politics/2011/02/income-inequality-in-america-chart-graph

 

 

DJ Patil Twitter Storm

So last Saturday I replied to a retweet of DJ Patil (data science guru). The whole exchange involved me responding to another person “StartupLJackson” who posted “No. More STEM workers creates more companies making $, which creates more STEM jobs in the US. We have massive shortage.” My response to this was “More STEM workers, like PhDs making lower than the median wage as postdocs? Or ones out of work?” I went out that night and didn’t see what happened until the next day, when lots of people had responded to StartupLJackson, including DJ Patil again.

  

Mainly the conversation revolved around StartupLJackson making comments about how welding will be completely replaced by machines in 10 years and that lots of “kids” need to get “skills” for the new economy that is coming. Also the argument against postdocs was that they should just get “tech writer” jobs and make a “decent paycheck” instead of staying in their “shitty postdoc jobs.” The two sides were broadly that 1) we need STEM workers (their side) or 2) we don’t and that we already have enough now (which is roughly my side of the argument). I think there’s more evidence on our side, but feel free to comment on your take. I think if the comment was that we need more developers I might agree (and Microsoft’s Steve Balmer would for sure…see link).