Nov
28
2008
0

Fun things at Mizzou

Just visiting my brother at the University of Missouri, Columbia for thanksgiving and having the American half of the family get together. In addition to watching a truly outstanding Mexican wrestling movie and enjoying deep-fried turkey (without burning down his house), we had a chance to do a little exploring. To the south of the town is the Rock Bridge state park. This is worth a visit – it’s just a small park, but with a large cave. There’s a natural bridge and the cave entrance (the Devil’s icebox). We did a short (2.42 mile) walk around the park, found several (locked) cave entrances in the sinkholes around the area, and enjoyed some of the old roads. Anyway it helped to work off some of the turkey.

Since one of my sisters’ in law and her husband are rangers at a park near Fresno CA, I had a chance to talk about the differences between eastern and western techniques. They don’t think very highly of the Ursack – having witnessed several failures and a fair amount of mashed food. Apparently the bears in that area are well habituated to people. Still not sure how they will work on the east, where the black bears aren’t quite so well trained.

Written by Rob in: outdoors |
Nov
21
2008
1

How to Change Your Grade at Georgia State in Two Easy Steps

A recent change in the mechanism used at Georgia State University for professors to request grade changes is going to make it even easier for students to get the grade they want versus the grade they deserve. Previously, the only security for the grade change process was the existence of a somewhat secret form that was required to change a grade. (a classic example of “security by obscurity”) The professor filled in the form and e-mailed it from his university e-mail address. Then the grade change went in. However, as should be well-known, e-mail addresses provide no real security since e-mail is readily spoofed. It really is an insecure protocol.

Well, even this level of security has gone by the wayside. There is now a spreadsheet to automate the process of generating the secret form and while for the moment it is in secure area on a University web site, it is only a matter of time before it leaks to an insecure area. So here are the two steps needed for a reasonably clever student to change anybody’s grade.

  1. get a copy of the Excel spreadsheet: this is actually not very hard. Since the spreadsheet has to be downloaded from the secure site to a professor’s PC all it is necessary is to enter the office when the professor has left and look for a copy. One could look for backup media and recover a copy there. Or one could be slightly clever and catch an email en-route. With a bit of luck, the professor might even have been using public PC and you could catch it from that by looking at temporary files. By the way it doesn’t have to be the professor of course you’re interested in — so you don’t have to get it from a security conscious professor which might be difficult– instead you could go and find an overworked faculty member handling one of the large introductory classes and you’d be more likely to find the form there. Anyway, once you have the form filling it out is self-explanatory.
  2. spoof e-mail the spreadsheet to the appropriate University Authority:this is now little more difficult than it used to be, because they want an attachment, but it is not beyond the realm of a moderately skilled python or Java programmer. I strongly recommend the latest python email handling libraries. For some reason the University registrar seems to believe that the authentication of logging into the University e-mail server is transitive with the authentication of the e-mail.

Actually, the University has it almost right. The secret form is available only to professors after they have logged in to the reasonably secure web site used to set grades. (although we still use the same username and password for all university-related accounts – which is another poor design) The problem is that the professor has to remove the form from the web site in order to submit it. It wouldn’t be very hard, and I know this from personal experience, to write a form handling procedure in language like PHP that would remove this loophole.

postscript: on further reflection, since the solution to this is sooo easy, some one could be making money from it.

further postscript:  I was just reminded of the number of carefully tailored GSU-specific password phishing attempts we professors get – so someone is trying to corrupt the system – which I hope they fail at.

Written by Rob in: pedagogy,security |
Nov
16
2008
0

O Deer!, O Neanderthal!

There’s a fun wildlife biology teaching game called “Oh Deer”. In it a group of people divide into two sets where one is the deer and one is the environment. Typically you start with 1/4 deer and 3/4 environment. Each set turns their back on the other and decides whether they are shelter, food or water and places their hands over their head (like a house) if shelter, over their stomach if food and over their mouth if water. Then on a command they turn around and the deer try to find someone in the environment who wants what they want. If they do, then both people are deer, and if they don’t then the “deer” becomes part of the environment.

Not surprisingly the deer population rises and crashes with this simulation. If one adds a small amount of predation, either with “wolves” or “hunters” then the population tends to stabilize. (you can make this quite complex)

There’s been a bit of a mystery about why there aren’t Neanderthals around now. Maybe our ancestors hunted them, but maybe not – it’s been the stuff of romantic speculation. In a recent article in the National Geographic, it was pointed out that based on body size and muscle mass the Neanderthals needed about 4000 calories/day to survive. We wiseacres (bad translation of homo sapiens) only need about 2000 calories/day.

It would be fun to try “oh Neanderthal”, where now two species have to get food, shelter and water. The only difference is those Neanderthals who look for food have to get two people to have one stay as a Neanderthal and the rest only have to find one to stay as a homo sapiens. My strong suspicion is that the Neanderthals would quickly disappear. (Actually – to simplify the rules – up to two homo sapiens can share a “food” but could take one each if there were enough)

Metabolic efficiency might be all it takes. (I wonder if the american car companies are aware of this – probably not ;-< )

Written by Rob in: outdoors,science,scouting,Wildlife |
Nov
15
2008
1

What Would Darwin Do?

Second in a series of posts about evolution and the “laws” of biology.

It is sort of amusing to see what kinds of issues helped the chaplain and captain’s companion of the Beagle towards the theory of natural selection. Today we can measure things with such high precision – count individual molecules, read the genetic code of almost any organism, measure distances to 10^-11 meters, time things with errors in seconds per thousands of years while timing intervals that are billionths of a second, that it is hard to image what it was like in, say, 1820 where the very idea of an atom or molecule was controversial, let alone having no real understanding of how biological systems work.

Putting on our 19th century hats, and maybe holding a flower to our noses to mask the 19th century smells (they weren’t overly careful about hygiene) we can identify several related problems that needed to be addressed:

  1. The earth was old. Measurements in the late 1700′s and early 1800′s by Lyell were suggesting that the erosion of stones to form canyons and gorges would have taken 100,000′s if not millions of years. A very simple experiment – go to Hadrian’s wall and find a piece of stone (like a Roman column) that is half buried. We know when it was buried so we can measure the difference in size between the exposed part and the buried part. Dividing that by, say 1700 years, gives us a mean rate of erosion. If we look at an erosion feature, like Cheddar gorge, then we see can estimate the length of time it took to make it. While the number won’t be very accurate – it will be much larger than the 6000 years or so we get from biblical histories.
  2. Fossils. When we look at some rocks, the sedimentary ones that are deposited by erosion we see traces of extinct animals. We find sea and land animals so they can’t have all perished in the flood. We find traces of extinct plants in the Devon coal beds. The deeper, and presumably older, layers have animals and plants that are more different from those that exist today than the higher and more recent layers. But it is clear that they are related to organisms that live today. The vertebrate animals follow the same basic building plans that modern animals follow. There are shellfish and odd shrimp-like creatures and ferns and starfish. They seem to form sets of organisms that are comparable to modern sets.
  3. Why are things the same? There are patterns in animals and plants. Grouping life by physical similarities yields a simple, yet compelling, indexing of every species we know about (thank you Linneaus). Even more amazing – as our navies go on voyages of discovery – rather than conquest – they find new species which (mostly) fit into the same index. Those new groups, which contain things like kangaroos and platypuses, fit into well defined sets that easily fit into our indexing.
  4. Why are things different? This one took a while for the European (mostly English and American) scientists to notice because for some reason the animals and plants of eastern north America are similar to those of northern Europe (in 2008 we know why). We Americans have Oaks, Pines, and Maples – and so do the Brits. We have crows, eagles, deer, foxes, wolves, bears, bison and elk, and so do they. It isn’t until the plants and animals of other parts of the world are described (by devout Church of England scientists who are “describing the glory of God’s creation”) that these differences are noticed. Even though there are different animals and plants in different parts of the world they fit together into a functioning system with different animals performing similar roles. Indeed, the results from small islands in the pacific (does the Galapagos spring to mind?) and isolated continents (Australia, Tasmania and New Zealand) show that the animals and plants are quite different from European ones and yet have similar ecological roles.

There are somethings that we don’t (as of 1820) understand. We do not understand inheritance at all. Can a trait or property be passed from a parent to a child? How? We have anecdotal evidence that there must be some mechanism because our children look like us and we look a bit like our siblings, but how this happens is a mystery. It doesn’t appear to be a simple blending of mom and dad. Further anecdotal evidence can be seen with some of the domestic animals where we have selected for some traits – it is the dawn of “scientific” agriculture – but we don’t have a clear picture of what is going on. Some traits seem to be passed on simply – like blue eyes in people – blue eyed parents have blue eyed children – but then not always – sometimes brown eyed people have blue eyed children (and no the milkman isn’t to blame). But then there are weird effects like differences in calf size that depend on the size of the mother (Maternal effect) – and some people believe that there is a “paternal effect” as well. We have no idea why different species can’t interbreed, nor why common interbreeds like mules are not fertile. (again remember this is 1820 – in 2008 we have a pretty good idea of what is going on). Sometimes animals can be very different physically – say bulldogs and greyhounds – but still the same species, but sometimes they can be very similar -say blue tits and great tits (real English birds) and not interbreed.

Darwin’s brilliance was to realize that problems of time, fossils, similarities and existence of difference required the existence of some sort of selection mechanism and inheritance mechanism. His hypothesis of natural selection – namely that those organisms that are better fitted to produce children that survive will tend to dominate and that those variations will accumulate over time to produce new species forms the basis of modern (2008) biology where we call it a theory. Had he formulated it a few years earlier we’d call it a law – but that is so 18th century. The time delay between his forming this hypothesis and publication was spent trying to understand the mechanisms of selection and inheritance – which he didn’t quite get and would take another 60-80 years for the beginnings of a solid theory.

There are some very simple predictions of the 1820 -type theory that have been borne out over time. The idea that there is a biochemistry of life is truly central – this wasn’t explicitly formulated because chemistry itself wasn’t well understood – has been confirmed by repeated experiments. The way bacteria handle glucose is (mostly) the way we handle glucose. We use the same amino acids, and the same genetic code as bacteria. The mechanism of inheritance – via nucleic acids -seems to be universal on our planet.

One of Darwin’s explicit predictions was that the oldest fossils of humans would be found in Africa because the most similar animals to us are native to there. I think his theories would have had an easier time had he said we evolved in Europe – but that would have been dishonest.

Another surprising thing is that we need to have pre-existing variation to have selection and life goes to a great deal of difficulty to produce variation. One of my favorite examples is in retroviruses such as the human immunodeficiency virus (HIV). Viruses are barely life, because while they reproduce – they use the mechanisms from other creatures to do it. Unlike snakes and wasps HIV can’t run, hunt or flee, yet it is subject to the same selective pressures that any other life is. However, when your progeny is measured in moles, there is another alternative – just make lots of errors when reproducing and some of them will be better than others. So HIV when challenged with effective drugs, evolves by selection to produce viruses that can reproduce in the presence of those drugs. For that matter so do bacteria when challenged with antibiotics (they actually have a split genetic system where essential functions vary slowly but non-essential functions are on small “plasmids” which can have lots of variations quickly) and mosquitoes when challenged with pesticides.

Written by Rob in: pedagogy,science |
Nov
15
2008
1

Being the Best Worm You Can Be

First in a series of posts about evolution, natural selection and the “laws” of biology.

One of the things one often hears from people who don’t understand natural selection and evolution is a statement like “if people descended from apes, why are there still apes?”

The trite answer is that there still are apes, just some of them write blogs, some post silly questions to the newspapers, while others eat termites in the African forests (Homo sapiens is a tail-less large primate after all).  But this masks a deeper confusion.

Like most complicated animals (arthropods, fish, reptiles, mammals etc) we are based on a segmented body plan.  The “six pack” that body builders adore is just a reflection of three of the segments in our abdomen.  In a very real sense we’re worms with legs.

So if we’ve evolved from worms, why are there still worms?

The answer is that worms are just as evolved as we are – only they’ve evolved to be the best worms that they can be.  The things you need to do to be a successful earthworm or annelid sea worm are very different from the things you need to do to be a successful human or dog  or fruit fly.

Earthworms, for example, can be described as a “primitive” animal and physically they are not very different from earthworms of the Jurassic.  “primitive” is not a pejorative term in biology.  It doesn’t mean bad – it means having features that are seen in many species and therefore derived earlier the history of the organism.  We share many “primitive” features with earthworms – we have a head, segments, a central digestive tube, muscles and nerves.  So do fruit flies – both the common ones and the olive fruit flies that so recently featured in our (USA) elections.   (If you ever get the chance to watch the ultrasound inspection of a developing baby, in utereo, keep an eye out because the segmental nature of our body is really clear in a 3-4 month embryo.)

Obviously, though, we’re not earthworms, and we’re not fruit flies.  The derived or “advanced” characteristics that let us type words into a computer and an olive fruit fly devastate the Mediterranean olive crop by laying eggs in the olives are different.  Yet we share many of the developmental control proteins and pathways that we inherited from our annelid ancestors.

Written by Rob in: pedagogy,science,Wildlife |
Nov
14
2008
0

Disgression is (sometimes) the better part of valor

Part of my ritual for being the adult scout herder leader on a trip is to check the weather.  The NOAA site ifs phenominal for giving detailed and usually accurate predictions. Where we are planning to go tonight has a 100% chance of 3/4-1 inch of rain followed by the next night of clear but freezing temperatures.  I’d be ok as would most of the experienced youth, but it wouldn’t be that fun.  So we’ll just have a shorter trip tomorrow.

Written by Rob in: backpacking,outdoors,scouting |
Nov
12
2008
0

More Water fun

Just a quick review of a couple of things for fun on the water.

One of my sons wanted a Kayak for his birthday and after checking on line – and then visiting the helpful folks at go with the flow, we settled on a perception 10. It is a rather nice, relatively inexpensive and indestructible, boat. It is fast – in a choppy lake he was much faster than my wife and me in a small canoe. It is fun – you can go through high (but not ocean high) waves and surf back down wind. It is light – 30 lbs or so – my son can easily move it and I can heft it to a shoulder carry one handed. It has a large cockpit and needs a skirt in cool and choppy weather. Indeed the only complaint is that we haven’t figured out how to put the skirt on the cockpit single handed. (It should be possible).

The other thing we’ve tried recently is a bent-shaft paddle. It really pushes the canoe, both by having a bigger blade than my traditional paddle, and by having and angle that puts the blade straight into the water during most of the draw. Your arms will feel the difference, and the old-style paddle will feel like you are using the handle rather than the blade afterwards. On the other hand the boat really moves with it.

Written by Rob in: outdoors |
Nov
11
2008
4

Persimmons

The native persimmon, Diospyros virginiana, is one of my favorite trees.  It was difficult to find back in the northeast, but is realtively common in northeast Alabama.persimmon fruit that is almost ripe The bright orange fruit isn’t ripe (and indeed edible as it has enough tannin in it when unripe to tan your mouth) until it is very soft – almost rotten feeling. It takes nearly freezing weather to ripen, so now is the time to harvest. I tend to take the pulp and add it (with sugar, cinnamon and ginger) to muffin and bread mixes where it adds a subtle but distinct flavor. Just remember to do your part of the bargain and plant the seeds so there are more trees.

The deer, raccoons and turkeys love it so it doesn’t last long once ripe!

Written by Rob in: outdoors,Wildlife |
Nov
05
2008
0

politics

Well the US election is over, and I must admit I’m not disappointed (too much).  Elections are always tricky when you have students.  It is critical to make it clear that political beliefs will not influence grades.  This may sound trivial – but it is fraught with the occasional trap.  For example, I had a class on election day.  I wanted the students to be aware that voting is, in my opinion, an excellent reason to miss class.  More accurately, I didn’t want a student who was in a long wait at the polling place to feel that they had to trade their voting place for a class session.    So I sent an email to the class to make this clear.  Here’s the trap – I could have been seen as endorsing one candidate – so the email included an explicit statement that it was not endorsing a specific candidate or party.  In fact, I would not and did not discuss politics with the students because I don’t want a student to say “well because the prof. likes “X” and I like “Y” I got a bad grade” or “because ‘joe’ likes “X” and the prof. likes “X” he got a good grade”.

It also gives me a little protection in the rough and tumble world of faculty politics (which I try to avoid).

Written by Rob in: laboratory practice,pedagogy |
Nov
02
2008
1

Always have a “plan b” (or c or d …)

Just a short post. I’m helping (or at least trying to not get in the way of) one of the scouts from my younger son’s troop plan the next backpacking trip. He’d used the wonderful georgiahikes web site to find a few trails, and we went trough them. We initially settled on the Blood Mountain Cove trail, and as a diligent adult leader I called the district forest ranger to see if there was anything we needed to be aware of.

There was. Deer season starts October 19th in Georgia and this is a popular hunting area. It is managed with open areas for deer food – so I’m not surprised.

But we’d picked a plan b (near the Vallhala fish hatchery) and so we’ll just use that.

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