Sunday, March 24, 2013

Intelligence and Creativity and Memory

What defines intelligence? or creativity or memory? Is there a way that we can increase our own? How much effort should one invest in bettering their intelligence and creativity as opposed to just using it?

I think about these things often. Having an interesting idea and implementing it is really fun and exciting. Both can be difficult. Ideas are only as good as ones ability to implement them and if you cannot have ideas it doesn't matter how great you are at implementing them.

I have been trying to track when I have my most interesting ideas. It seems that they occur when I am dramatically exposed to a large amount of new stimuli or when I have time to think. I have been having trouble with exposing myself to new stimuli. This is a hard task. Where does one look? I try and read science journals that are out of my field but I am having trouble with this. As for the time to think I have a reminder on my Google Calendar to take 5 minutes a day and try and think of something new. I take 5 minutes and relax and close my eyes and listen to Zoe. It works ok but I think I definitely need the fresh stimuli.

Is there a better way to think? Is the way I think in general about things inferior to a possible different way of thinking? This is really hard to quantify. I often try to modify my thought patterns to be more productive. I have tried to teach myself(very little effort) to be able to hold two things in my mind at one time(There should be an old blog post on that here) . I probably should put more effort into that. Thinking is a very abstract idea. Sometimes my brain is so good at processing complex thoughts and my memory works very well, other times it does not. How do I make things function optimally all the time? Difficult to figure out. I have started drinking alcohol much less. Hmmm but I don't really have many more ideas?

One thing that I can quantify that is related to intelligence and creativity is memory. I have been listening to the audiobook Moonwalking with Einstein. I do prefer paper books but I recently found out I had an account active for a year so I have lots of credits to use... Anyways, as most things do it has inspired me more to better my memory. For the past year or so I have used Memory Trainer an android app. It has taught me interesting things about my memory and has also improved my memory to where I can non-mnemonically memorize sequences of numbers up to around 10 digits fairly easy by chunking. It is free and probably just as fun as Angry Birds or some such game though I have never played Angry Birds so I might not be the correct person to ask. I think by learning some mnemonic memory techniques I can create an overall better memory for the rest of my life.

I decided I would take 5 minutes or so everyday and practice memorizing strings of numbers. I wrote a small program in Perl to allow me to test myself (

I really want to be able to think the best I possibly can. Nothing makes me more excited than having an interesting idea and executing it as you can probably see by my blog. I think the complexity and originality of the idea are what make me excited. These two things require my best creativity, my best ability to generate new ideas and my best brain function to think about complex things. I wish these came easy to me. I think I need to take more time and just relax and think and calm down and experience. Think. Creative. Execute.

If only I was smarter.

And after just sitting and staring off into space for no reason I just had a fun idea!
Do people make more spelling mistakes when they are happy or when they are sad and can we figure this out using twitter?

Thursday, March 21, 2013

Book Recommendations from Vincent Van Gogh

So I read alot. A real lot. Mostly when I have time to burn and I am sitting around at home. Sometimes only 5 minutes sometimes an hour. Most of the books or authors I enjoy I have read. Also, many of the books of that have been written by similar authors. I have come to place were it has become difficult to find a good book recommendation and I resort to choosing random books. Almost.

I have been reading Dear Theo an abridged version of Vincent Van Gogh's letters to his brother Theo. Here is an unabridged version free to read ! Which is crazy. Now I think I will start reading that instead. Though I do love holding a book. Anyways, through these letters I have felt as if I am in conversation with him. He even mentions the books he enjoys reading including Les Miserables... but also Fritz Reuter's My Time in Prison (
Ut mine Festungstid) but unfortunately I cannot find it in English. The humorous thing is that this is not the first time I have taken book recommendations from someone dead. Maybe this is the best way to go about it?

I tried the GoodReads website but it recommended me some awful books. I think it is because of the seemingly random genre's I read. I like John Steinbeck and Sci-fi and Non-Fiction and I also read a Nicholas Sparks book once. I never read Harry Potter or Twilight though. That is based on moral grounds. Well not really. I just have no interest.

I have been studying alot about prediction lately and using machine learning. What I have found is that the reason that some predictions are not good is the lack of data. For instance. If I say I want to predict how many 20-30 year olds will buy a dress in the next year. The first feature you should want is sex, male or female. Just having that one feature changes my prediction capacity drastically.

Anyways, I will write a post up soon about predictions. I need a book recommendation now.

Also, still no luck on Post Docs. 0-3 at the moment but I hear some of my colleagues are 0-20. YIKES!

Monday, March 18, 2013

How Many Proteins Are Actually In There

Sooo, people simulate proteins using Molecular Dynamics. Basically, you are sticking a single virtual protein molecule in a virtual box of H2O molecules and calculating newtons laws of motion to watch what happens.

When you work with proteins experimentally you can rarely see them unless the concentration is really really high or the protein aggregates. Doing certain Biophyiscal measurements, I know the concentration of the protein because I can calculate it based on light absorbance at specific wavelengths but I never had an intuition for what this meant. Normally experimental concentrations range from 1 micromolar to ~5 millimolar and only 5 millimolar if you have a super stable non-aggregating protein.

So how do I compare a single protein in simulation in a 100nm^3 water box to the proteins I work with in a cuvette or NMR tube?

Ok so let's say that the protein is 4kDa so it's weight in grams would be
 (4000/6.022E23) = ~6.6E-21g
 We just divide it's Mass by Avagadro's number since kiloDalton's are an Atomic Mass Unit.

How big is 100nm^3.

1nm^3 is equal to 1E-24 L. WOW!
An MD simulation is ~100nm^3 so we have 1E-22 L.

How many molecules would 1mM be in 100nm^3?

((4000 g * 1 mM) * 1E-22 L) / 6.6E-21 g per one protein = 0.06 molecules

That is not even one molecule!

16.5mM is ~1 molecule.
100mM is ~6 molecules and 165mM is ~10 molecules

So the effective concentration of a small protein in an MD simulation is much much higher then one could ever measure or use in real life. 

I know this is super lame but I liked it.

Sunday, March 10, 2013

Making money by buying stuff on eBay

Yea, yeah, yeah. I know. This sounds like an infomercial but I swear I am not selling anything. All I am telling about is a way I found to make some extra money on eBay. Yeah, it actually works and in some cases I have made over 100% of the purchase price.

So how does it work? Well eBay is based on people searching for specific items. When you try and buy something on eBay you go and type in "rock climbing shoes" or if you are trying to be more specific "5.10 anasazi" or some such. From looking at eBay it seems that the majority of things being sold on eBay are not from you or I or Joey joe joe, they are from companies that buy up large piles of shit for nothing and then sell it all on eBay. This is great because most of the time they don't know what they are selling. If you do know what they are selling and they are selling it for much below the price that it is worth then you make money.

Ok let's have an example. I am scientist and know alot about equipment in the field of molecular biology, biochemistry, biophysics. I can identify things on sight.

If you are a are a molecular biologist you know what this is. It is not a programmable thermal controller. Well that is the name on the device but it is actually colloquially called a Thermal cycler or a PCR machine. Maybe you got the picture already. When things are mislabeled in the title people can't find them with a search so many times they are not bid on or go for really cheap. What one can then do is look up the colloquial name of the product and see how much they usually sell for. If the price + shipping is less than the price you would sell it for +  seller fees + $20 or so then buy it. When it is resold you can always reuse the box and increase your shipping price a little to make even more money. All you are doing is changing the title of the item.

The hard part is finding the miss-used names. That just takes some grunt work of browsing eBay. Just go into the Healthcare, Lab and Life Sciences category on eBay and just browse. That thermal controller one was a good one. Also, people call stir plates "mixers" or "stirrers". People call variacs,  autotransformers. Lots of things like that.

I ended up making about $1000 over 6 months or so. I sold about 30 items with a mode of about $30 some more, some less. Some I lost a little on. This was all before I wrote the tool below instead I would browse and browse.

I think the problem with this business model is throughput. You need to be able to receive and ship packages. Test stuff. Deal with peoples issues. You only have a certain amount of time each day and these things can take time. It is really easy to make $1-5 on eBay but unless the scale is huge you are just wasting your time. I felt like I needed to make around $30 per purchase or I was just wasting my time.

Here is code I wrote to quickly and easily parse eBay for selling prices and prices of stuff that has already been sold Click here for eBay tool.

Things to remember:
1. Sometimes it takes time to sell stuff, a month or more
2. Don't forget seller fees from eBay and paypal they usually amount to about 10-20%
3. Always pay for delivery confirmation when shipping things it is usually less than $1 or $2 and saves you the headache of a customer saying somethign was lost in the mail.
4. Be wary of items that are being sold "AS-IS" especially if testing the device is as simple as turning it on
5. Find keywords in the titles of sold items that correlate with price
6. Buy bulk if you can, some of the most money I made was by winning an auction is which someone was selling alot of something. Such as 5 stir plates or 30 lasers.
7. Sell things as working but no returns or AS-IS working, guaranteed non-Dead on Arrival. You don't know the long-term survival of the item and giving refunds to everything that breaks is just not reasonable.
8. The investment is not great, starting out with $200 is usually good to buy a few items.

Thursday, March 7, 2013


Is there a way to guess better than random chance? I was thinking about this alot. And wrote a program that simulated this and the results were crazy which sent me on a crazy knowledge spree till I figured out that I rediscovered the Binomial Distribution. HAH.

Here is the dilemma. Say you are playing a game that you guess a number between 1 and 10 and a computer guesses and number between 1 and 10.

These outcomes being either a yes, you win when you both guess the same number, or a no you don't, when you don't.
You are trying to win the most. And you know the probability of these outcomes beforehand. Can I have a better win percentage than guessing 1 every single time (~10%). Our apparent probability for randomly guessing is equal to 1/N . Where N is the number of possible outcomes.

How can I win 10% of the time if I only play a game 9 times. Since winning is an integer. This means my winning percentage for playing 9 Games in a Contest with a 10% win rate is either > 10% or 0.

So the probability that we are above the 10% between 0-9 is much much greater because of the integer rule(I have no idea what this is actually called I just made up a name). The probability increases up to 9 or 19 or 29 &c. Once we hit a number divisible by our probability of success we immediately drop because we can now have an integer higher number of successes.

Let's simulate this.

Trials Probability of > 10% Success
1 0.1
2 0.19
3 0.27
4 0.35
5 0.41
6 0.47
7 0.52
8 0.57
9 0.6
10 0.26

See once we hit 10 our Probability of having greater than 10% success drops because we now need more than 1 success! We can only have an integer number of successes remember! CRAZY!

This is interesting.

Further, we have a binomial distribution.

If we look at a binomial distribution for p=10% and 20 Games/trials which we have from wikipedia!

The x axis is our number of successes and y axis is the probability of x number of successes. Were the blue is 10% chance of success on each attempt, the green is 50% chance and red is 80% chance. Our actual chances of having >= 2 successes in 20 games for a 10% or greater success rate is much greater than 10%! Whoaaaa. Mind blown. Sounds, made-up I know. But let's simulate this and prove it. If we calculate the Binomial Distribution for Chance of success or p = 10%. Here is the Perl code . What what!!! It totally works exactly how the binomial distribution suggests! WHOA!

Here is the calculated Binomial Distribution:

Successes 20 Attempts 30 Attempts
1 0.27017034 0.14130386
2 0.28517981 0.22765622
3 0.19011987 0.23608793
4 0.08977883 0.17706595
5 0.03192136 0.10230477
6 0.00886704 0.04736332
7 0.00197045 0.01804317
8 0.00035578 0.00576379

So the code will calculate how often we break the 10% expected barrier. So for 20 attempts that would be the Sum of 3-8 and for 30 it would be the sum of 4-8. Our simulation results are almost exact! MATH! SCIENCE!

For having greater than 10% success (>2 for 20) the sum for 20 is 32% and with 10000 simulations we have an astounding 32.37%!!! For 30 trials calculated from the Binomial Distribution is 35% and we have 34.93% from the simulation!!

What this says is that we actually have a > 30% chance to beat the odds in a Binomial Trial that one only has a 1/10 chance of success!

My mind is blown. This is true for all replacement Binomials.

So this is what you do. Play the number guessing game with your friend. You both choose a number between 1 and 10 and if you guess the number they guess, you win. Now bet them that you can guess correct greater than 10% of the time. Now play the game 9 times and you have a greater than ~60% chance of winning the bet.


So if you are playing a Binomial game your best chance of success is by playing (1/Probability of Success) -1 games!