Nov
30
2009
0

The importance of Trilobites

Over thanksgiving, I had a chance to search our favorite fossil site again and found more and better trilobites.   My family and I found better more complete fossils than before including a couple of casts (~35mm long & ~13mm long).

Outside of this being sort of fun, why should anyone care about trilobites?

They are small, aquatic, extinct little shrimp-like critters.  Much of their niche is filled today by other arthropods.   They were widespread and fossils can be found all over the world in sedimentary rocks of the right ages.   Being aquatic means they couldn’t have died by not getting on Noah’s ark.  Being widespread means that they weren’t some sort of freak.  Since anyone can find them, they can’t all be fakes.   So they are direct evidence of evolution you can hold in your hands.

Written by Rob in: outdoors,science |
Nov
24
2009
0

Gearing up for CASP-9

The silly season of casp will soon be upon us and once again we’ll compete.

As usual a few changes will be tested:

  1. Ligands and Heteroatoms.  We have long held that these are important in structure.  They typically have not been evaluated in casp, so the server doesn’t handle them automatically.  This is being fixed and the latest version of AMMP will actually have a casp dump pdb option that will make the filterable.  (dump pdb_tether)
  2. Disulfides It has always been a bit of a pain to handle disulfides.  Code is being written to recognize them and automatically apply the patches.  (removing them from the results is easy)
  3. Compressing Potential We grabbed the competitions hydrogen bonding potential that tends to compress structures.   (if you can’t beat them – join ‘em)
  4. Enhanced fold stability We’ve played with many ways of describing folds to the program in a way that compact, efficient and accurate.  None of them really worked, but it turns out that an approach based on Fred Richards’ ideas about Voronoi polyhedra works very well.  Basically, the Delauney triangulation of the protein is an optimally compact encoding of protein protein contacts.  In tests, using DeLauney vectors as distance restraints improves the model quality dramatically.  I expect that we can use this to merge fragments in a way that is much better than our current geometric technique.  The Delauney vectors combine with our dictionary of common protein sub-structures in a native way to improve loop and insert predictions.
  5. Machine Learning The work my group has done on using fuzzy decision trees should be apply to the evaluation of model quality and be useful as a post hoc scoring function, if not as a potential in its own right.
Written by Rob in: engineering,science |
Nov
22
2009
1

A beneficial side effect of AMD-64 chips

The machines I’ve been building have used the AMD 64 bit chips.  Mostly because they are fast and cheap.  It turns out there is a security benefit – they have a feature that makes them very resistant to garden variety stack overflow attacks.  The  instruction pointer is not writeable from the stack.  (well at least not directly)  So the generic x86 overflow attack simply results in a segment violation or a base error.

Cool, because it means that even with older software (windows XP anyone), the ability of an adversary to muck up your machine is much reduced.  Social engineering attacks will still work, though.

Written by Rob in: engineering,security |
Nov
17
2009
0

Silver Comet Bike Ride

My son’s troop just went on it’s semi-annual bike trip on the silver comet. Between these trips and what we did as a cub den, I think I’ve “section-biked” the whole thing. Anyway we started from Esom station, near, the Alabama state line, and went to “the Rock”, just past Rockmart. We had a nice detour into Rockmart to find the dairy queen. The scouts, ranging from a Webelos 2 who was tagging along to those working on their Eagles had a great time.

trail map of the western part of the trail

Written by Rob in: scouting,trail map |
Nov
17
2009
0

How Not to teach science

Just at the open house for a high school that one of my sons would like to attend. We wandered into the science area to see the demonstrations (after a very nice chat with what looks to be an excellent mathematics teacher) and see members of the current 9th grade class doing something that resembles chromatography on leaves. Except, it sort of was and it sort of wasn’t. The front’s were awful. So since I’ve used a lot of TLC in my murky past, I thought I’d ask a few questions. “what is the solvent? ammonicial ethanol?” – “it’s chromatography solvent”, and that’s what was on the label. So I asked the instructor what were they using. “It has ether in it, I think”.
ARRGH!
ARRGH!
ARRGH!
What they were doing was to put a leaf on a piece of filter paper and use a hard implement like a pencil to crush the leaf along the origin (or start). This damages the paper and means that it is impossible to get a clean chromatogram, and for that matter a reproducible one. Useless bloody useless.

It is just “cargo cult” magic. They don’t know what they are doing or why and they can’t get good results with the method they are using by rote.

If they wanted to do it right, they needed to know what the solvent was, and maybe try a few variations or at least understand why it might work. They should crush the leaves with a little bit of sand in a separate vessel and extract it with a solvent to produce a clean dot on the origin. As a control, they should do the same with a couple of solvents, and as a final control extract just the sand. That would be an experiment.

Written by Rob in: pedagogy,science |
Nov
05
2009
1

Scouts & Facebook

The scouts in my son’s troop have set up their own facebook group. We adults can be fans (and are), but don’t run it. There is also a troop google group that we adults run and use for “serious” business.

It seems to work very well. The scouts are taking ownership of their troop. As fans the adults can respond to questions the scouts raise, but can’t initiate topics. Sometimes the teenage humor is a bit odd, but it’s generally restrained – which is good – because this is a public site.

Written by Rob in: scouting |
Nov
03
2009
3

Birth of a New(ish) Machine

Having teenagers, who like to play computer games – including online ones, we have two desktop machines at home (not counting the museum pieces like a windows 95 machine that doesn’t say “with internet explorer” from back when the internet was “just a fad” (Gates W. 1995)). The “adult” machine was getting to feel a little pokey (windoze 2000, EPIA board that I want to use as an embedded machine, no free disk space), so it was time to build a new one. I also wanted to play with the Nvidia CUDA language extensions and it is a little bit silly to try to put a high end graphics board into an antique machine.

So off to Fry’s we go. (one of the perks of living in a “high tech” area are computer parts supermarkets).

Ended up with an MSI 770-C45 board, a quad AMD 64 bit machine, CPU fan, a PNY 1024M CUDA enabled graphics board, a terabyte SATA drive, 4GB DDR3 memory, a new wireless card and a new power supply. The case, floppy drive, DVD reader, and CD burner are left from the old machine.

The hardware snapped together pretty quickly and then the fun began. Windows XP doesn’t recognize SATA drives, and while the floppy is there, getting the drivers off the MSI DVD is fraught with peril. In fact, two burnt disks latter, I say the heck with it and try to load Ubuntu 8. (the other machine also has a 64bit AMD chip so we had the disks). It well past the “sell by date” and isn’t compatible with the new hardware. So out of frustration, I go back to XP and ignore all the warnings about unrecognized hardware. Miraculously it loads, and even more miraculously it runs! Turn’s out, in an undocumented feature of the mother board, there is an IDE emulation for SATA. Slower than pure SATA, but still fast.

Cool, now just to configure the wireless card, reboot a few dozen times then download the latest Ubuntu for the rest of the machine. Opps. While the new AMD chipset and fan is very quiet in terms of sound. they emit enough radio waves to make the wireless non-functional. Open the case, put in the old card, and its a little better. At least it’s now a registered copy and I can download the antivirus software (by the way these are all legal university staff license copies of software) and firefox, I think moving the antenna away from the machine will solve this, and we’ll see when the coax cable arrives.

In the meantime, I downloaded and burnt a cd of the newest (9.10) Ubuntu on an old Mac. Which did something to the ISO so that it was a bad image. Oh well. do it again, but this time at work (the download) and burn the CD at home (USB disks are really great for this). Now we have Ubuntu up.

So how is it working? Internet connections are ghastly (average about 1-10% of maximum speed) due to RF-noise. CPU speed is amazing, especially with Ubuntu. We see all 4 CPU’s and things that are slow to load like open office scream. I have some more tuning to perform, but it is impressive.

Update: Using a 10ft (3M) cable to move the WIFI antenna works as expected. In fact I’m using the machine to make this edit.

Written by Rob in: engineering,science |

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