Visited the In Real Life.

is this treatland?

I am in San Fransisco for reasons which are better covered in a later post, but it was a stroke of luck because I needed some parts from treatland, but I couldn’t buy them online.  So I just walked over to 3077 17th street in San Francisco…and proceeded to pace back and forth for a bit.

Not treatland. SRS BZNSS HONDAS

You would think that this was treatland, but it wasn’t.  It is apparently a honda bike shop, and they give you a weird look when you walk by because they are SRS BUSINESS.  They also have a nice sign that says something about not working on mopeds, not lending tools and to stay out of the shop.  I thought to myself, surely this couldn’t be treatland…where are the treats?

Treats is here!  In the building marked SH FRANK AND CO.

As I mustered up the courage to go ask them for moped parts, I saw someone pull into a garage across the street on a Derbi.  Ah, I thought, this must be the treatland.  And so it was!  I got a knarp, a clutch cable, a tail light, and a bunch of jets.  Sweet!

And I even saw this sign…

Treat Street

Inspiring People: Cellfyre, Andreas Sturm, and Chris Templeman

Every now and then I run into or chat with people who are really excited about DIYBIO, and it is really these people who get me excited about what I do at BOSSLAB.  I just wanted to give a shutout to a few people who have recently been awesome:

Cellfyre is from Oregon, and intends to start a DIYBIO group out there!  According to her twitter, “Everybody is handed a coupon for scientific knowledge at birth. Many have forgotten to redeem theirs. To create awareness I advocate #DIYBio, #STEM, and #PLoS“.  She came down to BOSSLAB (last week? hard to tell with finals going on) and we talked about what it is like to run a DIYBIO lab, sourcing equipment, and getting people excited.  You can (and should) check out here twitter here!  If you are in Oregon, tweet at her!

Andreas Sturm is a student who works somewhere in Europe (I am unsure of where), and is very ambitious in the development of hardware.  His do it yourself bio-hardware blog should be up soon- I will definitely share it here once it is up!  Since bio-engineering of any kind is very taboo- to the point of being illegal- he has to work closely with his university to do even transformations!  But he still persists in being curious and hacking up useful tools.

Chris Templeman is an engineer and presumably owns Templeman Automation in Somerville.  It turns out he was the driving force behind the sub $200 (if i recall correctly) PCR machine that was released by cofactor bio a while back.  He is smart, excited about biology, so keep an eye out for him.  He is also behind a pretty sweet multitouch computing table kickstarter, here.

Genomes, Environments and Traits Confrence!

Jason Bobe moderates a discussion with George Church and Geraldine Hamilton about personalized medicine microfluidic devices

Today I attended the Genomes Environments and Traits Conference.  It was awesome!  There were talks on all manner of technical breakthroughs from faster and cheaper sequencing, to single-cell sequencing (WITH 3D protein/DNA localization on the intracellular level!!!), to hackable drug delivery kits for 3rd world countries.

The more exciting part for me personally was running into all kinds of DIYBiologists.  It was awesome to finally meet them in person!  Ellen Jorgensen from GeneSpace was there, as well as Joseph Jackson from BioCurious, and (obviously) Jason Bobe from the Personal Genome Project.  There were also some people from the BOSSLAB group there (woo! not sure if they want to be mentioned by name).  I even found somebody from Olins’ neighbor college, Wellesley, and I spotted at least one Babson Jacket in the crowd.

Anyways, this conference got me more excited about biology and science, and this summer at BOSSLAB.

Baby Sea-Animals, Everywhere.

What happens when you let your saltwater tank evaporate off for a month or so, then do a water change?

The punchline here is BABIES.  It turns out that some sea animals, in this case featherdusters, some kind of worm, and snails all like to reproduce when they are put under stress.  Specifically the salinity dropped from 40+ PPT (S.G. 1.032) to 28-30 PPT (S.G. 1.021), the temperature probably dropped as I added room temperature or colder water.  I also agitated the tank with a turkey baster to help the filter pick up snail waste and to dislodge some stubborn algae.

Anyways, here are some pictures of the creatures I noticed, including some nocturnal bristleworm looking things, and copeopods, which I missed in my last post about the denizens of the tank.

Baby snail!

These guys crop up with some regularity actually.  I suspect some of them dont make it, and others rapidly grow up.  Occasionally I see some that are just 1-2mm long, this one was about twice that size.

Just a blurry view of my aquarium…or is it?

At first glance, this is just a really bad photo of the aquarium where the AF decided to focus on the glass.  But when I looked closer…

Upon closer inspection, there is a baby tube worm/featherduster!




I noticed teeny tiny feelers coming out of this guy.  When I tapped the glass, he snapped back into his coil-thing, just like the featherduster!  I can only assume that they are related.  I can’t wait for these to grow up; there are a whole bunch of them sprinkled around the aquarium.

This appears to be a bifurcated bristleworm

This guy may not be a baby, but it certainly caught my attention with its weirdly bifurcated body.  It seems to be due to trauma and not genetic, because one side is much longer and the bifurcation did not seem to be symmetrical.

Last but not least, a copeopod

This guy (to the right of the pink thing in the middle) is a copeopod.  These are ALL OVER the tank, and they feed on pretty much anything.  They like to pester the featherdusters (the burrow/shell of which can be seen directly below the ‘pod).

Thats all for now.  Tomorrow I may go chiton hunting somewhere on the shore of mass, so there may be forthcoming posts about that!

Deizens of the Saltwater Tank

Despite having added only live rock and snails, the 5 gallon hex tank is showing an amazing amount of macro biodiversity.  This is a short post to document what is growing in there!

A multitude of dwarf cerith snails

These guys are the workhorse of the algae fighting army.  There are many of them, in many shapes and a variety of sizes.  They like to crawl up and down the sides of the tank, and will occasionally congregate there.  Sometimes they hitch a ride on the back of larger snails!

This big guy is a florida cerith!

If I had to pick the coolest looking species of snail in the tank, it would be the Florida cerith.  Between their green coloration and rippled shell, they are hard to beat!  Not to mention these snails can self-right themselves!  These are are the largest snails in the tank.

This is the nassarius snail, in the middle. it looks like he is hitching a ride on a Florida cerith

If you zoom in you can tell this is a nassarius on a florida cerith snail.  The nassarius is easily distinguished by its single long stalk that probes for algae.  These guys are speedy!

Heres a nerite snail

My nerites are identifiable by the deep grooves that run along their round shells.  they have two long feelers, unlike the nassarius.  These guys are also very speedy.  Here, the nerite is harassing a dwarf cerith.

This is a featherduster

This guy was quite the find! It came as a hitchhiker on some live rock I bought.  It seems to have grown some since the rock was introduced, and it certainly is less skittish now.  there is another one on the same rock with a green/purple coloration, but it is hard to get a picture of that one because it is shy and very well hidden.


I thought this stuff was algae, but I was wrong!  It turns out to be purple cyanobacteria.  Its HUGE, and the snails seem to nibble at it from time to time.  I really don’t mind it, although it is considered a pest.

Thats all for now!  Maybe I will notice more stuff as time goes on.



Adventure: Dawn Mine at Dusk

You can’t tell, but there is an underground waterfall behind us.

After the Kelsey mine trek, I expected my adventure to Dawn mine to be a light hike, followed by the exploration of a small mine.  It is in the well hiked Millard Canyon, just outside of the suburbs surrounding LA to the north.  It is not even a long hike- the trip report I found here pegs it at a 5 miles round trip.  This was supposed to be a trip to test the mettle of a new potential adventurer, Chloe, for a canceled adventure to the Allison mine.

View of LA from Millard cyn Trail

The team this time was Chloe, the ever-reliable Hardee, and myself.  We began the adventure by purchasing an ANF adventure parking pass at Turners, and heading up lake street to Millard Canyon.  Upon arrival, at about 3:00 PM, the car had some trouble turning off its engine, but once that was sorted we started our hike by heading out on the East road from the first parking lot.  This led us along the crest of a hill that offered superb views of LA and the surrounding cities.  We followed this path and it wrapped around a hill to our right and descended into the valley floor.  Once we hit the rangers cabin, we descended into the river bed and the adventure began in earnest.  We were careful to take note of and remember warning sign that was posted on a large tree in the river bed near the cabin; this would be a waypoint for us on the way back, in case we did not see the cabin.

The Falls!

We continued up the rocky riverbed until we hit a fork.  A high path that looked like a river bank led off to the left, while the other plunged back down into the bed and continued up a rocky tributary.  We decided to go left here and visit Saucer Canyon Falls, which were nice.  We saw some people who had climbed up pretty high. We will definitely be back to climb up them someday!

Captain Crazypants leads the way

Before we returned to the main path, we met a dog (we assumed it belonged to the folks who were up on the falls), who we nicknamed capt. Crazypants.  Hardee had some jerky on him, and the dog would not leave him alone!  As we left, the captain followed us.  At first, we hoped he would go back to his owners, but it quickly became clear that he was leading us to the mine, and not the other way around.  There were also a lot of spray-painted arrows that went in the direction of the mine.

Hardee gets ready to traverse some rocks. Note arrows

We continued up the rocky streamed, doing our best to follow the instructions on Dans hiking pages.  We were looking, in particular for the point where “If you miss the trail you’ll find yourself climbing over and through the granite maze until the massive rocks forbid you to climb any further”.  Fortunately, we never found it and continued up the trail mostly through the riverbed, trying to skirt around spots of still or flowing water, and trying to stick to the more easily traversable river banks.

The captain going the wrong way.

By the time we got past these rocks, we were pretty tired, and the sun was starting to set.  We increased our pace, but our minds were wearied by the unknown length of the road ahead.  Captain Crazypants helped keep our spirits aloft, and kept leading the way.  The sun started to set as we entered a forested portion of the streambed.

The suns last rays illuminate a faraway peak

We were concerned about the sun going down, but we pressed on and eventually found the lower entrance to the mine.  There were many false-positives along the way, but the remains of some kind of steam engine give away the path to the entrance.

Large beams and steam engine on the way to the entrance.  Crazypants is still doggedly leading the way.

More spraypaint indicates exactly where the entrance is, hidden behind a boulder

Once at the entrance, we did a quick check of our lighting equipment.  I personally regret that we only had one light/person.  It just goes to show you that you always need to be over-prepared, even for hikes that seem like they should be easy.  The entrance was flooded, so Hardee and I switched to fivefingers and flip-flops (respectively) and Chloe decided to brave it in her shoes.  As we scouted out the entrance, Crazypants balked at the idea of even getting close to the entrance, and ran off, never to be seen (by us) again.  We miss you Crazypants.

Flooded entrance. Note the hinge on the frame.

As we made our way in, we noticed a lot of wood in the entrance.  I was originally concerned, as it looked like shoring, which would indicate that the miners thought it was unstable.  I breathed a sigh of relief when I looked a little closer and realized that the tops of the posts were not touching anything, and that there were heavily corroded hinges in the frame.  It looked like a gate that had been installed and removed some time ago, according to the LA goldmines website.

It turns out you can make it past the entryway and into the mine proper by carefully walking on the partially submerged wooden beams in entry; the caveat is that they sometimes move, but we were careful and managed to get over them dryly.

Possible passage to an upper level, from the ceiling of the first level.

The first floor of the mine today consists of two main tunnels branching out from the vaulted ceiling directly after the entry.  There are stories and maps of an upper level, but we did not have the time or equipment to explore that area, although we did see passages leading upwards.

To the left, there is a long, rather echo-y passage with several alcoves along its length.  By the time we reached the end of the winding passage, we were proceeding at a brisk walk.  It may have been the underground waterfall in the distance, but I felt like I heard a low rumble as we walked along, and that scared me.  After turning around, we observed a short moment of darkness where we all turned off our lights.  This did not last long, as the darkness is terrifying, and Chloe decided it was time for lights again.

The PIT.

After reaching the main area again, we set out to explore the other passage.  To do this, we had to navigate a thin ledge on the edge of a huge pool of water,  reputed to be 55-80 feet deep.  Scary, and very full of very cold water.  I hypothesize that it was originally another mineshaft, but later they ran into water and it flooded.  Someday, somebody should build an ROV and see what there is to see down there!  Hmm.  Somebody interested in mines, who is an engineer would be perfect for this project!

The way is not shut, but it is certainly wet!

The source of the water

After not falling into the water, we were rewarded with a sort walk to one of the most amazing things I have seen; an underground waterall.  It is pretty clear here that there was a dam built to prevent flooding of all the tunnels when somebody started tunneling up, and hit some kind of aquifer or spring.  This flooded the rest of the tunnel ahead and up-stream of the dam, which we decided not to explore because the water was VERY COLD.  Instead, we gawked at the waterfall, and took pictures of ourselves.

Chloe managing to not get wet.

With the obligatory MySpace photos out of the way, we continued to be amazing and not fall into the pit of frigid water.  We crept back to the main room and carefully exfiltrated the mine, again being careful not to get wet.  Once outside, we changed back to our normal shoes, had a swig or two of water, and snacked a bit.  It was really dusk in the canyon now, and we began our retreat with our flashlights on, proceeding at a safe, comfortable pace.  I was somewhat unsettled by the prospect of a night hike, but there were really no other options.

Socks! Socks! Socks!  Smartwool socks are the BEST!

Suddenly, it was very dark.  Here Chloe is illuminated in a small pool of light from her flashlight, and Hardee can be recognized by his headlamp.

The rest of the trip was spent in darkness, with the only illumination being that from our headlights, as the dim glow of the moon did not penetrate well into the bottom of the canyon.  It is amazing how big the canyon felt in the darkness.

Watch out for drops!

Chloe Points out some especially treacherous parts of the trail.

After many stream crossings, sort climbs down boulders, and a few instances of tripping and almost falling, we arrived back at the fork.  Here we proceeded to climb about 6 feet back up to the riverbank, and headed back to where we had come from.  Upon finding the marked tree and the steep slope next to the cabin, we ascended out of the canyon floor and back onto the trail.  Feeling that we were almost done, we increased our pace, especially when we noticed a pair of glowing eyes on the cliff above us.

Los Angeles at night.

Just before returning to the car, we cleared the canyon that had been obstructing our view of the glittering lights of the Los Angeles basin.  It was truly a fitting end to the adventure to rise out of the darkness and be reminded that the lights of civilization were still burning strong.  After appreciating this for a moment, we headed in the home-hat direction.