Category: ideas

Creature matching game

Here’s an idea for a game. It would be like the kid’s game Memory, where cards are turned over and matches are taken off the playing area. Instead of using identical pictures, images of different animals or plants would be used. Any pair could be matched by a player. The play would be quite similar to standard Memory.

The idea would be to match organisms by evolutionary similarity. So scoring would give maximum points for animals of the same species, next most for same genus, fewer points for animals in the same order, and no points for creatures in different phyla. The easiest implementation would be as a computer game with the computer dealing with scoring. Alternatively cards could be made the lineage described on the back. Each classification category could be displayed a different color or with a different symbol and the first/highest point matching lineage symbol give the points for the match.

This would make the play interesting as any pair could be matched but the player would have to decide if a pair was good enough to pick up or to wait for a better and higher scoring pair next turn.

The design aspect of picking a card set could make an easy set or a hard set, and two aspect of the choice would affect this. First, if animals fall into close pair groups that are distantly related (two parrots, two foxes) then the set would be easier. Having graduated and overlapping groups of cards make the set harder (dog, fox, skunk, weasel, otter, raccoon). Also, how much the player knows of these animals and their relationships can make a card set easier or harder. Some groups are obvious–birds, whales, bats–while other animals are either not as well known (i.e., coatis) or don’t have an obvious lineage (i.e., wolverine). And all these examples are mammals. Invertebrates would make a ridiculously hard game! So sets for kids could be easy and moderate to hard sets can be created.

Here are three game sets:
Mammals, butterflies, and marine invertebrates.

Preventing wisdom teeth

I have thought for years that it should be possible to regrow teeth. Teeth should be one of the easiest body parts to regrow. It seemed likely that the tooth bud, once formed, would receive signals from its local environment and grow into the correct type of tooth and emerge into place. That’s what happens during normal adult tooth development. So generating a tooth bud looks to be the key step. And indeed, in the past few years there have been reports of progress from research in this area. See this news article and this paper from the Yelick lab in São Paulo, Brazil.

But much easier than growing teeth should be killing tooth buds. Specifically, if the buds of wisdom teeth were killed then the painful, expensive surgery to remove wisdom teeth could be avoided.

Tooth buds form during fetal development. Wikipedia has a detailed overview. Wisdom teeth don’t begin to calcify until a person is 7 to 10 years of age. It should be fairly easy to kill the tooth bud at early stages. An injection into the tooth bud of a localized cytotoxin, either a general one or perhaps one specific to dividing cells would kill the stem cells that form of the core of the tooth bud. A toxin dose that kills cells within a 1-2 mm radius of the injection site should be effective. The gums will heal up and then the tooth bud will be gone. The dentist should be able to pick the injection location based on the expected eruption site. Inspection of x-rays may help pinpoint the bud location. A jig could be used to precisely position the needle tip.

Googling briefly I don’t see any other mention of this idea. It would be easy to test experimentally in animals if one can be found with late enough tooth development.

Hobby molecular biology

What would be required to set up an inexpensive system for hobbyists to experiment with biology? Consider PCR for example. PCR requires heat stable polymerase, primers, nucleotides, buffer.

The DNA polymerase is easy to purify from E. coli carrying the plasmid. Grow bacteria containing plasmid expressing Taq DNA polymerase, boil, spin down denatured proteins, and you are left with the DNA polymerase.

Primers can be bought inexpensively–$0.35 per base, a pair of 18-mers cost less than the shipping. Though they are inexpensive only if one set gets used repeatedly.

The cost of buffer (NaCl, MgCl2, Tris) is negligible.

Nucleotides are expensive up front, $150 for a set of dNTPs (dATP, dCTP, dGTP, dTTP), but this works out to about $0.06 per 50 ul PCR reaction.

Can nucleotides be prepared by a hobbyist? Nucleotides are easy to obtain-DNA is a major constituent of cells and is easy to purify. DNA + DNAase = dAMP, dCMP, dGMP, and dTMP. How can the trinucleotides be regenerated?

One route is to do it enzymatically using
polyphosphate:AMP phosphotransferase (PPT) and adenylate kinase (AdK) with polyphosphate (polyP) as the energy source (Resnick and Zehnder, 2000). It is not clear how the trinucleotide product would be separated and purified. Presumably different enzyme pairs could be used to regenerate the other dNTPs from the monophosphates.

These other enzymes could be cloned in E. coli expression vectors and purified either by tagging them with His6 and using a Ni or Co resin. Or by cloning heat-stable isoforms from one of the extremophiles and using a one-step boiling purification like that used for Taq polymerase.

Update: Bochkov et al., 2006 describe a method of preparing dNTPs from digested DNA. DNA is digested with DNAase and Nuclease S1. DNAase chews DNA into show oligonucleotides and the nuclease breaks them down to single dNMPs.

Then a crude extract of E. coli is prepared that contains the kinases to convert dNMPs to dNTPs along with the acetokinase. The kinases use ATP. ATP must be regenerated, and this is done using acetokinase with acetyl phosphate ($30/g) as an energy source. Combined dNMPs were converted to dNTPs with at least 86% regeneration and separated from reactants by chromatography on a Dowex 1×2 anion exchanger. The conversion was followed by thin-layer chromatography.

For PCR it may be possible to use a crude purification of nucleotides, but purification protocols would need to be developed and tested.

Where’s Phil Agre?

Phil Agre ran the Red Rock Eater mailing list for many years, it was active during the 90’s. I think I started reading it in the late 90’s. The emails ran down to a trickle in 2002, in part I think due to Phil getting a permanent position at UCLA. The mailing list archive indicates it ran up to Jan 2005.

Phil Agre’s mailing list in essence was one of the first blogs. The content was mainly links and commentary by Phil with occasional longer essays. He was one of the best people thinking about what the internet could be used for and how it was changing the world.

After 2002, the Red Rock Eater list went into abeyance then seemed to have stopped for good. Phil Agre seems to have dropped off the net. In this comment thread a UCLA student says he was ill. I fear it is very serious to keep him off line so long.

His essays, “Advice for undergraduates considering graduate school” and “How to be a leader in your field” are internet classics.

Here is an essay I found interesting titled What Is Conservatism and What Is Wrong with It?

Update: He’s literally missing. This site is run by friends looking for him.
Update 1/31/09: UCLA police talked with him. He’s alive, though not well.

Idea: clearing pre-cancerous cells

Cells become cancerous through a multi-step process. The cells pick up several mutations, each clearing a natural limit on cell division and usually increasing the rate at which the cells divide. By the time a person gets old their body has many pre-cancerous clumps of cells, and cancer occurs when one of the cells in one of the clumps picks up a final mutation and becomes fully cancerous.

Cancer has proven very difficult to treat, but perhaps it is easier to treat at the pre-cancerous stage. The idea would be to treat healthy people at middle age or later and kill most of their pre-cancerous cells. This would make the pool of cells that can develop into cancer much smaller and reduce the incidence of cancer.

Chemical chemotherapy drugs would be a poor choice for this–I expect they are not effective on slowly dividing pre-cancerous cells and these drugs are also damaging.

Instead, it may be possible to trigger apoptosis (cell suicide) in pre-cancerous cells. These cells are losing their differentiation and activating abnormal signaling pathways. They are likely stressed and may already be primed to undergo apoptosis. One of the organism’s anti-cancer mechanisms is to trigger apoptosis in pre-cancerous cells. The idea here is to supercharge this mechanism.

So the idea would be to treat the person with a cocktail of drugs that induces apoptosis by activating the apoptotic signaling pathways. The treatment should be strong enough to trigger a wave of apoptosis in the most susceptible cells clearing most pre-cancerous cells from the body. There would be some normal cells killed as well but they will be replaced by normal tissue processes.

Report & short

The fracture of the US financial system gives me an idea for a new business model.

1) Raise some capital.

2) Use a tiny fraction to hire a few business/finance reporters, and have them find a company riddled with fraudulent business practices. How hard can it be–this stuff is common and not very well hidden. Look at Enron, Halliburton, the Madoff Ponzi scheme.

3) Then short the company’s stock, send the evidence to the appropriate regulatory and oversight agencies, feed the info to the press, and profit!

Hobbiest scale prototyping?

One of the coolest technologies around are the rapid prototyping technologies: CNCs, Laser scanning, and Stereolithography. I first ran into stereolithography at a UK campus fair soon after I arrived, I forget which one.

In stereolithography a 3D computer model gets formed into a actually plastic part using a process in which heat from a laser polymerizes a liquid. Each pass forms a layer, and layers of under 0.1 mm are added to build the complete part. This technology was developed in the late 1980’s and is now fairly common though very expensive. The machines are $50-150k, and shops will turn out a part for a few hundred dollars. Incredible stuff.

Part made with stereolithography

The University of Kentucky has a Rapid Prototyping shop with a Stereolithography machine on campus.

Two things make this tech expensive, the monomer plastic ($200+ per liter) and the machines. The monomer is magic stuff, 21st century chemistry, and can’t substituted.

Can a machine be made more cheaply? Perhaps. Instead of the UV laser and X/Y scanning optics, how about using a DLP and a UV bulb? The DLP (an array of computer controlled mirrors, the display tech for bright computer projectors) directs the UV light to the correct part of the work area, the monomer polymerizes, the part is lowered, and the cycle repeats.

Could this work? It seems plausible. Best as I can tell, the monomer needs to be heated 20-30°C to polymerize. This is done in ~100μs by the laser, so a UV bulb shining for longer might be able to polymerize the monomer. The UV laser (100mW typically) has an intensity equivalent to 10,000W shining on a small 2cm x 2cm work area, so a 200W or 400W UV bulb (commercially available) shining for 1/10 of a second should in theory work. Losses due to heat dissipation may make a longer light pulse necessary, but it would likely still be under a second if this will work at all. The monomer could be preheated to the highest temperature where polymerization doesn’t occur to help polymerization along.

The result would be a simple and cheap stereolithography device with a small working area (2cmx2cmx15cm)! It could be built for very little ($200 UV bulb, $100 old DLP projector, $200 lenses and misc parts), with the high cost of the plastic monomer the biggest limitation. A DLP chip with 1000×1000 mirrors would have a 0.02 mm resolution. If UV intensity required for polymerization isn’t limiting, at 0.075 mm resolution a standard DLP would give a 7.5cm x 7.5cm working area and allow larger parts to be built.

What is the cost in plastic monomer for the parts? About 15c to 50c for a small Lego size piece, compared to the 5c a block cost for Legos.


Update: I had a look around for cheaper & more accessible plastic monomer. Two turned up–rubber stamp photopolymer resin and screen printing photopolymer emulsion.

The rubber stamp photopolymer is inexpensive and would likely UV cure in under a minute (1s or 60s is hard to gauge). Unfortunately, the resin is quite viscous, 60,000 cps, quite thicker than honey. So likely too thick for adding a thin layer at a time.

Screen printing photopolymer emulsion appears more promising. It polyvinyl alcohol or polyvinyl acetate with diazo or SBQ crosslinking initiators. It forms a plastic that is fairly weak and not water resistant but which can be hardened with secondary UV curing and hardening agents. UV polymerization typically takes a few minutes (with a source of 1-2 W/cm2); a strong UV source should reduce the time to under a minute. These photopolymer emulsions typically have viscosities of 3,500 to 12,000 cps, much more suitable!

Pepper spray antidote

Pepper spray has been around for years now, but there is not commonly available antidote. And we know how the active ingredient, capsaicin acts to active, or hold open, the ion channels that transduce pain signals. In fact, a quick Google shows that capsaicin binds and activates a receptor called the vanilloid receptor subtype 1 (VR1), a member of a group of related receptors called TRP ion channels that are activated by temperature changes.

Capsaicin chemical structure
Capsaicin chemical structure (from Wikipedia)

So an antidote would be an inhibitor of the VR1 receptor, and such a thing should be easy to find, or create, and in fact another Google shows that several have been created. Capsazepine was the first inhibitor discovered, way back in 1994. Activators and inhibitors of this receptor have many potential uses as analgesics and anti-inflammation compounds so there is a lot of research interest.

Capsaicin inhibitor capsazepine (from Wikipedia)

A spray containing one of these inhibitors should be an effective antidote for pepper spray. But surprisingly no such inhibitor is available! The small quantities of purified inhibitors are available in small quantities for research purposes (i.e. capsazepine, 50mg for $455 but I can’t find anyone who has made an antidote preparation. This should be safe and fairly easy. Safe, because it would be applied mainly externally, and because pepper spray is itself fairly safe–aside from the pain and shock it is used to cause. It doesn’t have other, non-specific side effects. And relatively easy to make because the literature describes the synthesis of inhibitors from capsaicin itself. So the starting product used to make an inhibitor can be capsaicin, and capsaicin is readily available in large quantities!

Wikipedia: Discovery and development of TRPV1 antagonists

Idea: car pushie

Have you ever had to push your car around? Very hard when it is possible at all. So let’s make a short distance car mover. Here’s one way to do it:

Put the front wheels on remote control dollies. Have one remote control work both dollies. The remote control would send two sets of signals, one for each dolly. The dollies are basically remote control cars with low speed/high torque motors and gearing.built heavily enough to carry the load.

The down side of this is that jacking each wheel would be required to put the dollies in place. Also, if the carts had roller skate sized wheels it would not be able to climb curbs.